+ 28 0.0 0.0 0.0 Crub_svsplocus 819 845 (649155) + (ATAA)n Simple_repeat 1 27 (0) 1
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 Crub_svsplocus 819 845 649155 + (ATAA)n Simple_repeat 1 27 0
28 0.00 0.00 0.00 Crub_svsplocus 819 845 (649155) (ATAA)n#Simple_repeat 1 27 (0) c_b1s251i0
Crub_svsplocu 819 ATAAATAAATAAATAAATAAATAAATA 845
(ATAA)n#Simpl 1 ATAAATAAATAAATAAATAAATAAATA 27
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0)
+ 398 31.3 7.0 2.4 Crub_svsplocus 1862 2103 (647897) + L3 LINE/CR1 3824 4076 (23) 2
ANNOTATION EVIDENCE:
398 31.32 7.02 2.37 Crub_svsplocus 1862 2103 647897 + L3 LINE/CR1 3824 4076 23
398 31.32 7.02 2.37 Crub_svsplocus 1862 2103 (647897) L3#LINE/CR1 3824 4076 (23) m_b1s001i0
Crub_svsplocu 1862 GTTGTTCTAGGATATAAGACAAGGAACAATGG-TGGATATTA--GAAAGC 1908
v i i iivii ii v v - vi -- ii -
L3#LINE/CR1 3824 GTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTACAGGGAG- 3872
Crub_svsplocu 1909 ACAGATTTCACCTGGACATCAGAAAAACTTCCCCAAGAGTAAGAGAAGGT 1958
i iv vi i v i i vi ii i v i v v-v
L3#LINE/CR1 3873 GCAGATTTCGGCTCAATATAAGGAAGAACTTTCTAACAATCAGAGC-TGT 3921
Crub_svsplocu 1959 TCAGCAATGG----GGTTG------GAGGTGGGAAATAATTCTTCACTGG 1998
i iv ---- i ------ i vi iivvii v
L3#LINE/CR1 3922 CCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGG 3971
Crub_svsplocu 1999 AGGCCATTCAA-CACAAACTAAGTGGCCATTTATCAGGGATGCTGGAATA 2047
-ii - v ii iii i i i i v i-
L3#LINE/CR1 3972 AGG-TGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAG-A 4019
Crub_svsplocu 2048 ATGGATTTTTGC-TCTGGGAAGGGAAA-TGTGCTAGATGAGCTC-AAGGT 2094
v ii - -- v ii- vi v -
L3#LINE/CR1 4020 AGGGATTCCTGCATC--GGATGGGAGGTTGGACTAGATGACCTCTAAGGT 4067
Crub_svsplocu 2095 TCGTTCCAA 2103
i v
L3#LINE/CR1 4068 CCCTTCCAA 4076
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.98
Transitions / transversions = 1.96 (49/25)
Gap_init rate = 0.06 (14 / 241), avg. gap size = 1.64 (23 / 14)
+ 359 16.4 0.0 0.0 Crub_svsplocus 2407 2467 (647533) + Chaplin1B_DR DNA/hAT-Charlie 5 65 (845) 3
ANNOTATION EVIDENCE:
359 16.39 0.00 0.00 Crub_svsplocus 2407 2467 647533 + Chaplin1B_DR DNA/hAT-Charlie 5 65 845
359 16.39 0.00 0.00 Crub_svsplocus 2407 2467 (647533) Chaplin1B_DR#DNA/hAT-Charlie 5 65 (845) m_b1s001i1
Crub_svsplocu 2407 GGTCAGCAACCTGCGGCTCCAGAGCCACATGCGACTCTTTGAACCTTCCC 2456
i i i i iivv v
Chaplin1B_DR# 5 GGTCAGCAACCCGCGGCTCTAGAGCCGCATGCGGCTCTTTAGCGCTGCCC 54
Crub_svsplocu 2457 CTGTGGCTCCC 2467
i
Chaplin1B_DR# 55 TTGTGGCTCCC 65
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.99
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 235 14.8 4.8 1.6 Crub_svsplocus 2486 2535 (647465) + EnSpm-9_DR DNA/CMC-EnSpm 683 734 (7886) 4
ANNOTATION EVIDENCE:
235 14.75 4.84 1.56 Crub_svsplocus 2486 2535 647465 + EnSpm-9_DR DNA/CMC-EnSpm 683 734 7886
235 14.75 4.84 1.56 Crub_svsplocus 2486 2535 (647465) EnSpm-9_DR#DNA/CMC-EnSpm 683 734 (7886) m_b1s001i2
Crub_svsplocu 2486 GAGAGAGAGACAGAGACAGAGAGAG-GCAATCGCGCTTCCC-TGCT-TCT 2532
v v - vi v i iv - - v
EnSpm-9_DR#DN 683 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCGCGTTCGCCGTGCTGTGT 732
Crub_svsplocu 2533 GCT 2535
-
EnSpm-9_DR#DN 733 G-T 734
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.90
Transitions / transversions = 0.50 (3/6)
Gap_init rate = 0.08 (4 / 49), avg. gap size = 1.00 (4 / 4)
+ 33 5.3 0.0 0.0 Crub_svsplocus 2536 2575 (647425) + (TCTCCC)n Simple_repeat 1 40 (0) 5
ANNOTATION EVIDENCE:
33 5.27 0.00 0.00 Crub_svsplocus 2536 2575 647425 + (TCTCCC)n Simple_repeat 1 40 0
33 5.27 0.00 0.00 Crub_svsplocus 2536 2575 (647425) (TCTCCC)n#Simple_repeat 1 40 (0) c_b1s251i1
Crub_svsplocu 2536 TCTCCCTCTCCCTCTCCCTCTCCCTCTCTCTCTCTCTCTC 2575
i i
(TCTCCC)n#Sim 1 TCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTC 40
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 235 14.8 4.8 1.6 Crub_svsplocus 2576 2586 (647414) + EnSpm-9_DR DNA/CMC-EnSpm 735 745 (7875) 4
ANNOTATION EVIDENCE:
235 14.75 4.84 1.56 Crub_svsplocus 2576 2586 647414 + EnSpm-9_DR DNA/CMC-EnSpm 735 745 7875
235 14.75 4.84 1.56 Crub_svsplocus 2576 2586 (647414) EnSpm-9_DR#DNA/CMC-EnSpm 735 745 (7875) m_b1s001i2
Crub_svsplocu 2576 TGTGTGTGTGT 2586
EnSpm-9_DR#DN 735 TGTGTGTGTGT 745
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.90
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 10), avg. gap size = 0.0 (0 / 0)
+ 234 16.8 2.8 3.9 Crub_svsplocus 2782 2961 (647039) C IMPB_01 Satellite (2125) 423 246 6
ANNOTATION EVIDENCE:
234 16.77 2.78 3.93 Crub_svsplocus 2782 2961 647039 C IMPB_01 Satellite 246 423 2125
234 16.77 2.78 3.93 Crub_svsplocus 2782 2961 (647039) C IMPB_01#Satellite (2125) 423 246 m_b1s001i3
Crub_svsplocu 2782 TGGAGAACAGCTTGAAGCCAACTTTCCAG-GTGAGCAGCAGATAG-GAGA 2829
i - - v vi?-- - v - - v -
C IMPB_01#Satel 423 TGGAAAACA-CTTGA-GCAAAACN--CAGAGAGAG-AG-AGAGAGAGAGA 380
Crub_svsplocu 2830 GAGGGAGAGGGGGGAAGAGAAAGAGAGAGAGAGAAAGAGAGAGGGGGAGA 2879
i i i ii i i i i
C IMPB_01#Satel 379 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 330
Crub_svsplocu 2880 GA-AGAGAGAGAGAGAAAGAGAGTGGGGGA-AGAG-GACTGGCAGACCAA 2926
- i v i i - - vv iv vvi
C IMPB_01#Satel 329 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 280
Crub_svsplocu 2927 GGGCAGATAGAGAGAGAGGGAGAGAGAGAGAGAGA 2961
i - v i
C IMPB_01#Satel 279 GAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 246
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.38
Transitions / transversions = 1.64 (18/11)
Gap_init rate = 0.07 (12 / 179), avg. gap size = 1.00 (12 / 12)
+ 248 17.2 1.2 6.5 Crub_svsplocus 2999 3010 (646990) C DNA8-25_DR DNA (3100) 867 796 7
ANNOTATION EVIDENCE:
248 17.16 1.23 6.49 Crub_svsplocus 2999 3073 646927 C DNA8-25_DR DNA 796 867 3100
248 17.16 1.23 6.49 Crub_svsplocus 2999 3073 (646927) C DNA8-25_DR#DNA (3100) 867 796 m_b1s001i4
Crub_svsplocu 2999 ATCCTT-TTTACCTGTGTGTGTATGTGTATATATATATATACATACCTCA 3047
v - ivv i iv --
C DNA8-25_DR#DN 867 ATACTTATTTACCCCAGTGTGTATGTGTATATATATATATATATATAT-- 820
Crub_svsplocu 3048 GAAAACAAATATATACATACATACAT 3073
-- v i v i i i
C DNA8-25_DR#DN 819 --ATATATATATATATATATATATAT 796
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.87
Transitions / transversions = 1.17 (7/6)
Gap_init rate = 0.07 (5 / 74), avg. gap size = 1.00 (5 / 5)
+ 259 23.4 4.3 0.0 Crub_svsplocus 3011 3073 (646927) + Harbinger-2_DR DNA/PIF-Harbinger 2339 2403 (1924) 8
ANNOTATION EVIDENCE:
259 23.40 4.26 0.00 Crub_svsplocus 3011 3073 646927 + Harbinger-2_DR DNA/PIF-Harbinger 2339 2403 1924
259 23.40 4.26 0.00 Crub_svsplocus 3011 3073 (646927) Harbinger-2_DR#DNA/PIF-Harbinger 2339 2403 (1924) m_b1s001i5
Crub_svsplocu 3011 TGTGTGTGTATGTGTATATATATATATACATACCT-CAGA-AAACAAATA 3058
i i iv -i v - v i v
Harbinger-2_D 2339 TGTGTGTGTGTGTGTATATATATATATATATATATATATATATATATATA 2388
Crub_svsplocu 3059 TATACATACATACAT 3073
i i i
Harbinger-2_D 2389 TATATATATATATAT 2403
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.72
Transitions / transversions = 2.00 (8/4)
Gap_init rate = 0.03 (2 / 62), avg. gap size = 1.00 (2 / 2)
+ 44 0.0 0.0 0.0 Crub_svsplocus 3074 3111 (646889) + (AC)n Simple_repeat 1 38 (0) 9
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 Crub_svsplocus 3074 3111 646889 + (AC)n Simple_repeat 1 38 0
44 0.00 0.00 0.00 Crub_svsplocus 3074 3111 (646889) (AC)n#Simple_repeat 1 38 (0) c_b1s251i2
Crub_svsplocu 3074 ACACACACACACACACACACACACACACACACACACAC 3111
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACAC 38
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 259 23.4 4.3 0.0 Crub_svsplocus 3117 3141 (646859) + Harbinger-2_DR DNA/PIF-Harbinger 2404 2435 (1892) 8
ANNOTATION EVIDENCE:
259 23.40 4.26 0.00 Crub_svsplocus 3112 3141 646859 + Harbinger-2_DR DNA/PIF-Harbinger 2404 2435 1892
259 23.40 4.26 0.00 Crub_svsplocus 3112 3141 (646859) Harbinger-2_DR#DNA/PIF-Harbinger 2404 2435 (1892) m_b1s001i5
Crub_svsplocu 3112 C-TATA-ATGAAGGTAAAAAAGGATATATGCA 3141
i- - iv vi i i ii i
Harbinger-2_D 2404 TATATATATATATATAGAGAGAGATATGTGCA 2435
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.72
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2)
+ 102 3.4 5.6 1.8 Crub_svsplocus 9178 9337 (640663) + (TTTTC)n Simple_repeat 1 166 (0) 10
ANNOTATION EVIDENCE:
102 3.35 5.62 1.81 Crub_svsplocus 9178 9337 640663 + (TTTTC)n Simple_repeat 1 166 0
102 3.35 5.62 1.81 Crub_svsplocus 9178 9337 (640663) (TTTTC)n#Simple_repeat 1 166 (0) m_b1s252i0
Crub_svsplocu 9178 TTTTC-TTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC 9226
-
(TTTTC)n#Simp 1 TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC 50
Crub_svsplocu 9227 TTTTCTTTTCTTTTCTTTTCTTTTCTTTCTCCCTCCCTCTTTC-TTTC-T 9274
- - i ii - - -
(TTTTC)n#Simp 51 TTTTCTTTTCTTTTCTTTTCTTTTCTTT-T-CTTTTCT-TTTCTTTTCTT 97
Crub_svsplocu 9275 TTC-TTTC-TTTC-TTTC-TTTC-TTTC-TTTCTTTTCTTTTCTTTTCTT 9318
- - - - - -
(TTTTC)n#Simp 98 TTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTT 147
Crub_svsplocu 9319 TTCTTTTCTTTTTCTTTCT 9337
ii
(TTTTC)n#Simp 148 TTCTTTTCTTTTCTTTTCT 166
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.08 (12 / 159), avg. gap size = 1.00 (12 / 12)
+ 11 24.8 0.0 2.6 Crub_svsplocus 9486 9525 (640475) + A-rich Low_complexity 1 39 (0) 11
ANNOTATION EVIDENCE:
11 24.76 0.00 2.56 Crub_svsplocus 9486 9525 640475 + (AAGAAAA)n Simple_repeat 1 39 0
11 24.76 0.00 2.56 Crub_svsplocus 9486 9525 (640475) (AAGAAAA)n#Simple_repeat 1 39 (0) m_b1s252i1
Crub_svsplocu 9486 AAGAAAAAAGAAAATCAAAAAGAAATAAAAGTGTAAAAGA 9525
vvi i i v -iv
(AAGAAAA)n#Si 1 AAGAAAAAAGAAAAAAGAAAAAAGAAAAAAG-AAAAAAGA 39
Matrix = Unknown
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1)
+ 298 3.9 1.7 0.8 Crub_svsplocus 9787 10134 (639866) + (TCTT)n Simple_repeat 1 351 (0) 12
ANNOTATION EVIDENCE:
298 3.94 1.72 0.85 Crub_svsplocus 9787 10134 639866 + (TCTT)n Simple_repeat 1 351 0
298 3.94 1.72 0.85 Crub_svsplocus 9787 10134 (639866) (TCTT)n#Simple_repeat 1 351 (0) c_b1s251i3
Crub_svsplocu 9787 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 9836
(TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 50
Crub_svsplocu 9837 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC-CTCTCTCTC 9885
-i i i
(TCTT)n#Simpl 51 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 100
Crub_svsplocu 9886 TCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTTTCTTTCTTTCTTTCTT 9935
i i - - i i i
(TCTT)n#Simpl 101 TCTTTCTTTCTTTCT-T-TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 148
Crub_svsplocu 9936 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC--TC 9983
--
(TCTT)n#Simpl 149 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 198
Crub_svsplocu 9984 TTTCTCTC-TTCCTTCCTTCTCTT-TTTCTTTGTTTC-TCCTTTCTTTCT 10030
i - i i - - v - i
(TCTT)n#Simpl 199 TTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCTTTCTTTCT 247
Crub_svsplocu 10031 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 10080
(TCTT)n#Simpl 248 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 297
Crub_svsplocu 10081 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 10130
(TCTT)n#Simpl 298 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 347
Crub_svsplocu 10131 TTCT 10134
(TCTT)n#Simpl 348 TTCT 351
Matrix = Unknown
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.02 (8 / 347), avg. gap size = 1.12 (9 / 8)
+ 12 16.7 5.9 0.0 Crub_svsplocus 11471 11504 (638496) + (GTTG)n Simple_repeat 1 36 (0) 13
ANNOTATION EVIDENCE:
12 16.66 5.88 0.00 Crub_svsplocus 11471 11504 638496 + (GTTG)n Simple_repeat 1 36 0
12 16.66 5.88 0.00 Crub_svsplocus 11471 11504 (638496) (GTTG)n#Simple_repeat 1 36 (0) m_b1s252i2
Crub_svsplocu 11471 GTTGCTT-GTGGGTTGCTT-GTGGGTTGGTAGGTTG 11504
v - v v - v v
(GTTG)n#Simpl 1 GTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTG 36
Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2)
+ 15 4.1 4.0 0.0 Crub_svsplocus 11974 11998 (638002) + (TTGT)n Simple_repeat 1 26 (0) 14
ANNOTATION EVIDENCE:
15 4.13 4.00 0.00 Crub_svsplocus 11974 11998 638002 + (TTGT)n Simple_repeat 1 26 0
15 4.13 4.00 0.00 Crub_svsplocus 11974 11998 (638002) (TTGT)n#Simple_repeat 1 26 (0) m_b1s252i3
Crub_svsplocu 11974 TTGTTT-TTTTTTTGTTTGTTTGTTT 11998
- v
(TTGT)n#Simpl 1 TTGTTTGTTTGTTTGTTTGTTTGTTT 26
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1)
+ 275 27.6 1.9 2.8 Crub_svsplocus 13939 14046 (635954) C MIRc SINE/MIR (161) 107 1 15
ANNOTATION EVIDENCE:
275 27.62 1.85 2.80 Crub_svsplocus 13939 14046 635954 C MIRc SINE/MIR 1 107 161
275 27.62 1.85 2.80 Crub_svsplocus 13939 14046 (635954) C MIRc#SINE/MIR (161) 107 1 m_b1s001i6
Crub_svsplocu 13939 GTGATTAGCCCAAAGTCACTCAACCACTTTCAGTG-CTGAGGCAGGACTA 13987
i v i v i i v --v - v v i v
C MIRc#SINE/MIR 107 GTGACTTGCCCAAGGTCACACAGCTAGT--AAGTGGCAGAGCCGGGACTC 60
Crub_svsplocu 13988 GAACTCACCATCTCCTGGTTTTTAGGTCAG-GATCTTCACCACTGCACCA 14036
i vvvii ii iiv vi - v i-
C MIRc#SINE/MIR 59 GAACCCAGGTCTTCCTGACTCCAAGTCCAGTGCTCTTT-CCACTGCACCA 11
Crub_svsplocu 14037 AACTGGCTCG 14046
v v
C MIRc#SINE/MIR 10 CACTGCCTCG 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.32
Transitions / transversions = 0.93 (14/15)
Gap_init rate = 0.05 (5 / 107), avg. gap size = 1.00 (5 / 5)
+ 225 18.9 0.0 0.0 Crub_svsplocus 29991 30043 (619957) C EnSpm-9_DR DNA/CMC-EnSpm (7830) 790 738 16 *
ANNOTATION EVIDENCE:
225 18.87 0.00 0.00 Crub_svsplocus 29991 30043 619957 C EnSpm-9_DR DNA/CMC-EnSpm 738 790 7830
225 18.87 0.00 0.00 Crub_svsplocus 29991 30043 (619957) C EnSpm-9_DR#DNA/CMC-EnSpm (7830) 790 738 m_b1s001i7
Crub_svsplocu 29991 TCTCTTTCTCTCCCTCACAAACTGAGAGAGATACACACACACACACACAA 30040
i i v vv v v v i v
C EnSpm-9_DR#DN 790 TCTCTCTCTCTCTCTCACACACACACACACACACACACACACACACACAC 741
Crub_svsplocu 30041 ACA 30043
C EnSpm-9_DR#DN 740 ACA 738
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.74
Transitions / transversions = 0.43 (3/7)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 241 15.0 0.0 13.2 Crub_svsplocus 30019 30095 (619905) + IS3EU-1_DR DNA/IS3EU 6611 6678 (2026) 17
ANNOTATION EVIDENCE:
241 14.97 0.00 13.24 Crub_svsplocus 30019 30095 619905 + IS3EU-1_DR DNA/IS3EU 6611 6678 2026
241 14.97 0.00 13.24 Crub_svsplocus 30019 30095 (619905) IS3EU-1_DR#DNA/IS3EU 6611 6678 (2026) m_b1s001i8
Crub_svsplocu 30019 AGATACACACACACACACACAAACAAAACCAGGTGTGTATATCTGATATA 30068
i ? v? ---- iv i i ---
IS3EU-1_DR#DN 6611 AAATACANACACACACACACACNCA----CGCGTATATATAT---ATATA 6653
Crub_svsplocu 30069 TAGATATAATTCTGAATATATATAGTG 30095
v -- v iv
IS3EU-1_DR#DN 6654 TATATATA--TATATATATATATAGTG 6678
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.26
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.12 (9 / 76), avg. gap size = 1.00 (9 / 9)
+ 340 18.2 5.1 1.2 Crub_svsplocus 30997 31074 (618926) + REX1-2_DR LINE/Rex-Babar 3282 3362 (0) 18
ANNOTATION EVIDENCE:
340 18.17 5.13 1.23 Crub_svsplocus 30997 31074 618926 + REX1-2_DR LINE/Rex-Babar 3282 3362 0
340 18.17 5.13 1.23 Crub_svsplocus 30997 31074 (618926) REX1-2_DR#LINE/Rex-Babar 3282 3362 (0) m_b1s001i9
Crub_svsplocu 30997 ATGTACACTGAGAGCTTATGCACCGGAGACAAATTCCTTGTGTGCCT--A 31044
ii v i v vi i iv --
REX1-2_DR#LIN 3282 ATGTACACTGGAAGCTTCTGTAGCCAAAACAAATTCCTTGTGTGTGTGAA 3331
Crub_svsplocu 31045 TCACACTTGGCCAATAAAAT--ATTGTAATTT 31074
v - i-- v i
REX1-2_DR#LIN 3332 GCACACTTGG-CAATAAAACTGATTCTGATTT 3362
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.06
Transitions / transversions = 1.33 (8/6)
Gap_init rate = 0.04 (3 / 77), avg. gap size = 1.67 (5 / 3)
+ 17 4.0 0.0 3.7 Crub_svsplocus 31075 31102 (618898) + (ACCT)n Simple_repeat 1 27 (0) 19
ANNOTATION EVIDENCE:
17 4.00 0.00 3.70 Crub_svsplocus 31075 31102 618898 + (ACCT)n Simple_repeat 1 27 0
17 4.00 0.00 3.70 Crub_svsplocus 31075 31102 (618898) (ACCT)n#Simple_repeat 1 27 (0) m_b1s252i4
Crub_svsplocu 31075 ACCTACCTATCTAACCTACCTACCTACC 31102
i -
(ACCT)n#Simpl 1 ACCTACCTACCT-ACCTACCTACCTACC 27
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1)
+ 1038 31.7 4.3 0.5 Crub_svsplocus 31902 32322 (617678) C L3 LINE/CR1 (22) 4077 3641 20
ANNOTATION EVIDENCE:
1038 31.74 4.28 0.46 Crub_svsplocus 31902 32322 617678 C L3 LINE/CR1 3641 4077 22
1038 31.74 4.28 0.46 Crub_svsplocus 31902 32322 (617678) C L3#LINE/CR1 (22) 4077 3641 m_b1s001i10
Crub_svsplocu 31902 GTTGGAAGGGACCTTGGAGGTCATCTAGTCCAAACCCCTGCTC-AGGCAG 31950
i v i iiii - v
C L3#LINE/CR1 4077 GTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCATCCGATGCAG 4028
Crub_svsplocu 31951 GAAACCAT---ATGCCATTTCAGACAAATGGCTTTC-----TCTTCTTAA 31992
v v --- iiv ii v i iiv ----- v i
C L3#LINE/CR1 4027 GAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGA 3978
Crub_svsplocu 31993 AAACTTCCAGCGTTGGAGCATTCACCGCTTCTGGAGGCAGGTTGTTCCAC 32042
v i i vi i vii ii i ?v viii i
C L3#LINE/CR1 3977 ACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTCCAT 3928
Crub_svsplocu 32043 TGGTTAATTGTTCTAACTGTCACGAAGTTTCTCCTTA-GTT----CTAGG 32087
vv vi iv i i i i vi ii -i ---- v ii
C L3#LINE/CR1 3927 TTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAA 3878
Crub_svsplocu 32088 TTT-CTTCTCTGTTTAGTTTCCATCCCTTG---CTTGTCCTGCCTTCAGG 32133
i - i i -- ii i v --- v i i v
C L3#LINE/CR1 3877 TCTGCCTCCCTGT--AACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGG 3830
Crub_svsplocu 32134 CACTTTGGAGAATAGCTTGGCTCCCTCTTCTTTGGGGCAGCCCCTAAGAT 32183
vi iviiv iv iviv iviiv i i v i
C L3#LINE/CR1 3829 AGCCACACAGAATAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAAT 3780
Crub_svsplocu 32184 ATTGGAATGCTGTTATCATGTCACCCCTCGTCCTTCTCTTCATTAAACCA 32233
v vi v i v i vivi vii ii i
C L3#LINE/CR1 3779 ATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCCAGGCTA 3730
Crub_svsplocu 32234 GACATACCCAATTCCAGCAACCGTTCCTTATATGTTTTAGCCTCCAGTCC 32283
i v i vv i viv i ii v
C L3#LINE/CR1 3729 AACATCCCCAGTTCCTTCAACCGTTCCTCATATGACATGGTTTCCAGACC 3680
Crub_svsplocu 32284 CCTGATCATCTTTGTTGCTCTTCTCTGTACTCTTTCTAG 32322
i v i i v i i v v vi i
C L3#LINE/CR1 3679 CTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAG 3641
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.40
Transitions / transversions = 1.71 (84/49)
Gap_init rate = 0.02 (9 / 420), avg. gap size = 2.22 (20 / 9)
+ 635 26.6 1.1 1.1 Crub_svsplocus 32442 32616 (617384) C L3b LINE/CR1 (459) 4773 4599 21
ANNOTATION EVIDENCE:
635 26.59 1.14 1.14 Crub_svsplocus 32442 32616 617384 C L3b_3end LINE/CR1 573 747 459
635 26.59 1.14 1.14 Crub_svsplocus 32442 32616 (617384) C L3b_3end#LINE/CR1 (459) 747 573 m_b1s001i11
Crub_svsplocu 32442 TCTAAAGTCTCAACATCTTTTTTACATCATGGTGACCAAAACTGGATGCA 32491
i ?v v i ii v ?ii ? v i i i
C L3b_3end#LINE 747 TCCAANTTCTCCACGTCCCTTTTAAANTGTGGNGCCCAGAACTGAACGCA 698
Crub_svsplocu 32492 GTACTCCAAGTGTAGCCTTACCAAGGCATTGTAAAGTGGTATTAATACTT 32541
i? ?i v iv vv i i v ?? vi i
C L3b_3end#LINE 697 GTACTCCAGNTGNGGCCTGACCAGCGCAGAGTAGAGCGGGANNATCACCT 648
Crub_svsplocu 32542 CACGTGATTT--TGATTCTATCCCTCTGTTAATGCAGCCCAGCACTGTGT 32589
v v ? i --i i-- v ? i iv ii ii
C L3b_3end#LINE 647 CCCTTGNTCTGTCGG--CGATNCTTCTGTTAATGCAGCCCAAGATCGCAT 600
Crub_svsplocu 32590 TGGCCTTTATGGCAGCTGCAGCACACT 32616
i i v i iv i
C L3b_3end#LINE 599 TAGCTTTTTTGGCAGCCGCGTCGCACT 573
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.98
Transitions / transversions = 1.88 (30/16)
Gap_init rate = 0.02 (3 / 174), avg. gap size = 1.33 (4 / 3)
+ 13 0.0 0.0 0.0 Crub_svsplocus 40429 40445 (609555) + (ATG)n Simple_repeat 1 17 (0) 22
ANNOTATION EVIDENCE:
13 0.00 0.00 0.00 Crub_svsplocus 40429 40445 609555 + (ATG)n Simple_repeat 1 17 0
13 0.00 0.00 0.00 Crub_svsplocus 40429 40445 (609555) (ATG)n#Simple_repeat 1 17 (0) m_b1s252i5
Crub_svsplocu 40429 ATGATGATGATGATGAT 40445
(ATG)n#Simple 1 ATGATGATGATGATGAT 17
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0)
+ 13 24.8 0.0 0.0 Crub_svsplocus 40763 40800 (609200) + A-rich Low_complexity 1 38 (0) 23
ANNOTATION EVIDENCE:
13 24.76 0.00 0.00 Crub_svsplocus 40763 40800 609200 + (AAAAAGG)n Simple_repeat 1 38 0
13 24.76 0.00 0.00 Crub_svsplocus 40763 40800 (609200) (AAAAAGG)n#Simple_repeat 1 38 (0) m_b1s252i6
Crub_svsplocu 40763 AAAAAGGTCAAAAGATAAATTACAAAGAAAAAAGGAAA 40800
vv i v vv v i
(AAAAAGG)n#Si 1 AAAAAGGAAAAAGGAAAAAGGAAAAAGGAAAAAGGAAA 38
Matrix = Unknown
Transitions / transversions = 0.33 (2/6)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 15 7.4 3.2 3.2 Crub_svsplocus 43578 43608 (606392) + (CCTC)n Simple_repeat 1 31 (0) 24
ANNOTATION EVIDENCE:
15 7.40 3.23 3.23 Crub_svsplocus 43578 43608 606392 + (CCTC)n Simple_repeat 1 31 0
15 7.40 3.23 3.23 Crub_svsplocus 43578 43608 (606392) (CCTC)n#Simple_repeat 1 31 (0) m_b1s252i7
Crub_svsplocu 43578 CCT-CCTCCACCCCCTTCCTCCCTCCCTCCCT 43608
- - i i
(CCTC)n#Simpl 1 CCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCT 31
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2)
+ 333 29.5 1.8 2.0 Crub_svsplocus 47653 47816 (602184) + L3 LINE/CR1 1338 1455 (2644) 25
ANNOTATION EVIDENCE:
246 36.20 0.00 0.61 Crub_svsplocus 47653 47816 602184 + CR1-L3B_Croc LINE/CR1 467 629 2648
246 36.20 0.00 0.61 Crub_svsplocus 47653 47816 (602184) CR1-L3B_Croc#LINE/CR1 467 629 (2648) m_b1s001i12
Crub_svsplocu 47653 AAAGAATATGATATAGTTGTCATTATAGAAACATGGTGGGATAAAACCCA 47702
ii v i v iv v ii vv v
CR1-L3B_Croc# 467 AAGAAATTTGATATAATTGGCATTACTGAAACCTGGTGGGACGATTCGCA 516
Crub_svsplocu 47703 CAAATGGAACACTCAGCTAGAGGGATTTCAATTGTTTAAAAGAAACAGAC 47752
ii v iii v iv v?vv v v v vi ii iii v
CR1-L3B_Croc# 517 TGACTGGAATGTTAAAATCNCTGGTTATAACCTGTTTAGGAAGGACAGAG 566
Crub_svsplocu 47753 CAAATAAAAGAGGAGGCAGAGTTTCTTTCTCTATATAAGAAATAACTACA 47802
iii v vi vv vi vi vv v iv i v
CR1-L3B_Croc# 567 CGGGTAAAAGAGGCGGGGGAGTGGCGCTCTACATTAAAGACACCATTACC 616
Crub_svsplocu 47803 TATCTACAGAATTA 47816
i i -i i
CR1-L3B_Croc# 617 TGTTT-TAGAGTTA 629
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 48.40
Transitions / transversions = 1.03 (30/29)
Gap_init rate = 0.01 (1 / 163), avg. gap size = 1.00 (1 / 1)
333 26.95 2.54 2.54 Crub_svsplocus 47657 47774 602226 + L3 LINE/CR1 1338 1455 2644
333 26.95 2.54 2.54 Crub_svsplocus 47657 47774 (602226) L3#LINE/CR1 1338 1455 (2644) m_b1s001i13
Crub_svsplocu 47657 AATATGAT---ATAGTTGTCATTATAGAAACATGGTGGGATAAAACCCAC 47703
i --- v i ii--- i v iii i i
L3#LINE/CR1 1338 AATACGATCTCATAGGTATCACC---GAGACTTGGTGGGATGGGACTCAT 1384
Crub_svsplocu 47704 AAATGGAACACTCAGCTAGAGGGATTTCAATTGTTTAAAAGAAACAGACC 47753
i v i vvv v i i i v?vvv i i
L3#LINE/CR1 1385 GACTGGAATACGGCGATGGAAGGGTANACCTTGTTCAAAAGAAACAGATC 1434
Crub_svsplocu 47754 AAATAAAAGAGGAGGCAGAGT 47774
v ? i i ?
L3#LINE/CR1 1435 TANTAGAAGGGGAGGNAGAGT 1455
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.78
Transitions / transversions = 1.58 (19/12)
Gap_init rate = 0.03 (4 / 117), avg. gap size = 1.50 (6 / 4)
+ 416 30.5 2.1 2.1 Crub_svsplocus 49445 49686 (600314) C BEL11-I_DR LTR/Pao (1767) 4232 3782 26
ANNOTATION EVIDENCE:
416 33.76 0.00 0.00 Crub_svsplocus 49445 49601 600399 C BEL11-I_DR LTR/Pao 4076 4232 1767
416 33.76 0.00 0.00 Crub_svsplocus 49445 49601 (600399) C BEL11-I_DR#LTR/Pao (1767) 4232 4076 m_b1s001i14
Crub_svsplocu 49445 CTTGGTTAACAAAGTTCTTATTTGTTGGCACATATTGCCATTGTTGCGGG 49494
i i ii i v iv v i v i i vv
C BEL11-I_DR#LT 4232 CTTGGTCAGCAGGGTTTTGATCGGTTGGGACGTATTTCCACTGCTCAGGG 4183
Crub_svsplocu 49495 CAAGAAGATGTTCCAATTCCTTTCTCTCTGTTGCTTACATGGACGTAGAA 49544
iiv vi iv iiv i i v v ivi iv ii
C BEL11-I_DR#LT 4182 TGCGTGGACCTCTGAATCCTTTGCACTCTGTTGTGCACATACACGTGAAA 4133
Crub_svsplocu 49545 GTGTCTGTTTTGTTTGCAGATGTAGCTTAATATCACCTTGCTGTCTGCGT 49594
v vi vv ivv i i i v iv vi
C BEL11-I_DR#LT 4132 CTTCCTGGATCTATTACAGATGTAACCTAAGACAACCTTGCTGTCTGAAT 4083
Crub_svsplocu 49595 AGAAGGT 49601
v
C BEL11-I_DR#LT 4082 AGAATGT 4076
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.72
Transitions / transversions = 1.21 (29/24)
Gap_init rate = 0.00 (0 / 156), avg. gap size = 0.0 (0 / 0)
377 29.01 2.99 2.99 Crub_svsplocus 49520 49686 600314 C BEL-45_DRe-I LTR/Pao 3782 3948 1852
377 29.01 2.99 2.99 Crub_svsplocus 49520 49686 (600314) C BEL-45_DRe-I#LTR/Pao (1852) 3948 3782 m_b1s001i15
Crub_svsplocu 49520 CTCTGTTGCTTACATGGACGTAGAAGTGTCTGTTTTGTTTGCAGATGTAG 49569
v i v i i i vi v i v iiiv i i
C BEL-45_DRe-I# 3948 CTCGGTTGTTGACATAGACATAAAATCGTCTGGTCTGATTATGTATATAA 3899
Crub_svsplocu 49570 CTTAATATCACCTTGCTGTCTGCGTAGAAGGTGGTGGACTGTAGTTCAAG 49619
i i i v i i ivv v v v v
C BEL-45_DRe-I# 3898 CCTAACACCACCTTGCTGTCAGTGTAGAAGGTGATGACGTCTAGATCCAT 3849
Crub_svsplocu 49620 GCACAACGTCTTTGGTATCAAGTT-GGTCAGCT--TTACA--GCCAAAGT 49664
iv --- iv -- v i v- -- v -- ? iii
C BEL-45_DRe-I# 3848 GTCCA---TCTCAG--ATGAAATGAGGTCAGCTACTTCCACTGNCAAGAC 3804
Crub_svsplocu 49665 GGTGCCACATAGTTCTAGCCTT 49686
v iiv v i
C BEL-45_DRe-I# 3803 TGCAGCACAGAGTTCTAACCTT 3782
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 36.75
Transitions / transversions = 1.24 (26/21)
Gap_init rate = 0.05 (8 / 166), avg. gap size = 1.25 (10 / 8)
+ 16 24.3 0.0 5.4 Crub_svsplocus 52703 52761 (597239) + (TCCGCT)n Simple_repeat 1 56 (0) 27
ANNOTATION EVIDENCE:
16 24.31 0.00 5.36 Crub_svsplocus 52703 52761 597239 + (TCCGCT)n Simple_repeat 1 56 0
16 24.31 0.00 5.36 Crub_svsplocus 52703 52761 (597239) (TCCGCT)n#Simple_repeat 1 56 (0) m_b1s252i8
Crub_svsplocu 52703 TCTGCTTTGGCTTCCGCGTCAGCCTCTGCTTCAGCTTCTCTTTTGGCTGC 52752
i iv v v i i v - vi -- i
(TCCGCT)n#Sim 1 TCCGCTTCCGCTTCCGCTTCCGCTTCCGCTTCCGCTTC-CGCTT--CCGC 47
Crub_svsplocu 52753 TTCCGCTTC 52761
(TCCGCT)n#Sim 48 TTCCGCTTC 56
Matrix = Unknown
Transitions / transversions = 1.20 (6/5)
Gap_init rate = 0.05 (3 / 58), avg. gap size = 1.00 (3 / 3)
+ 292 15.1 5.4 1.3 Crub_svsplocus 56074 56147 (593853) + Chaplin1B_DR DNA/hAT-Charlie 1 77 (833) 28
ANNOTATION EVIDENCE:
292 15.06 5.41 1.30 Crub_svsplocus 56074 56147 593853 + Chaplin1B_DR DNA/hAT-Charlie 1 77 833
292 15.06 5.41 1.30 Crub_svsplocus 56074 56147 (593853) Chaplin1B_DR#DNA/hAT-Charlie 1 77 (833) m_b2s001i0
Crub_svsplocu 56074 CACAGGTCGGCAACCTGCGGCTCCGGAGCCGCATGCGGCTCTTTGAGC-C 56122
vi i i ii - -
Chaplin1B_DR# 1 CAGGGGTCAGCAACCCGCGGCTCTAGAGCCGCATGCGGCTCTTT-AGCGC 49
Crub_svsplocu 56123 TTCCCCTGCGGCTCCC---AGCCTTCTC 56147
v i i --- i i
Chaplin1B_DR# 50 TGCCCTTGTGGCTCCCTGGAGCTTTTTC 77
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 15.75
Transitions / transversions = 4.50 (9/2)
Gap_init rate = 0.04 (3 / 73), avg. gap size = 1.67 (5 / 3)
+ 366 18.3 5.3 1.0 Crub_svsplocus 56157 56198 (593802) + EnSpm-9_DR DNA/CMC-EnSpm 686 728 (7892) 29
ANNOTATION EVIDENCE:
366 18.28 5.32 1.02 Crub_svsplocus 56157 56198 593802 + EnSpm-9_DR DNA/CMC-EnSpm 686 728 7892
366 18.28 5.32 1.02 Crub_svsplocus 56157 56198 (593802) EnSpm-9_DR#DNA/CMC-EnSpm 686 728 (7892) m_b2s001i1
Crub_svsplocu 56157 AGAGAGAGACAGAGACAGAGAGAGGAATTGCGCTTCCC-TGCT 56198
v v ii vi i iv -
EnSpm-9_DR#DN 686 AGAGAGAGAGAGAGAGAGAGAGAGAGAGCGCGTTCGCCGTGCT 728
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 18.45
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.02 (1 / 41), avg. gap size = 1.00 (1 / 1)
+ 41 0.0 0.0 0.0 Crub_svsplocus 56199 56233 (593767) + (TC)n Simple_repeat 1 35 (0) 30
ANNOTATION EVIDENCE:
41 0.00 0.00 0.00 Crub_svsplocus 56199 56233 593767 + (TC)n Simple_repeat 1 35 0
41 0.00 0.00 0.00 Crub_svsplocus 56199 56233 (593767) (TC)n#Simple_repeat 1 35 (0) c_b2s251i0
Crub_svsplocu 56199 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 56233
(TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 35
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0)
+ 366 18.3 5.3 1.0 Crub_svsplocus 56234 56284 (593716) + EnSpm-9_DR DNA/CMC-EnSpm 729 783 (7837) 29
ANNOTATION EVIDENCE:
366 18.28 5.32 1.02 Crub_svsplocus 56234 56284 593716 + EnSpm-9_DR DNA/CMC-EnSpm 729 783 7837
366 18.28 5.32 1.02 Crub_svsplocus 56234 56284 (593716) EnSpm-9_DR#DNA/CMC-EnSpm 729 783 (7837) m_b2s001i1
Crub_svsplocu 56234 GTGTGTGTGTTTGTGTTTTTTTTTGTGTGTGT----GTGTGTATGTAAAA 56279
v v v v v ---- i i i
EnSpm-9_DR#DN 729 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGA 778
Crub_svsplocu 56280 GAGAG 56284
EnSpm-9_DR#DN 779 GAGAG 783
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 18.45
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 4.00 (4 / 1)
+ 49 14.4 4.3 0.0 Crub_svsplocus 56505 56598 (593402) + GA-rich Low_complexity 1 98 (0) 31
ANNOTATION EVIDENCE:
49 14.42 4.26 0.00 Crub_svsplocus 56505 56598 593402 + (AG)n Simple_repeat 1 98 0
49 14.42 4.26 0.00 Crub_svsplocus 56505 56598 (593402) (AG)n#Simple_repeat 1 98 (0) m_b2s252i0
Crub_svsplocu 56505 AGATAG-GAGAGGGGGGGAGAAAGAGAGAGAGGGAGAGAGAGAGAGAGAG 56553
v - i i i i i
(AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 50
Crub_svsplocu 56554 AG-GAAAGAGAGAGAGAGAGAAAGAAAGAGAGCGGGGGA-AGAG-GAG 56598
- i i i v i i - -
(AG)n#Simple_ 51 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 98
Matrix = Unknown
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.04 (4 / 93), avg. gap size = 1.00 (4 / 4)
+ 248 24.8 0.0 18.8 Crub_svsplocus 56625 56738 (593262) + EnSpm-9_DR DNA/CMC-EnSpm 675 770 (7850) 32
ANNOTATION EVIDENCE:
248 24.84 0.00 18.75 Crub_svsplocus 56625 56738 593262 + EnSpm-9_DR DNA/CMC-EnSpm 675 770 7850
248 24.84 0.00 18.75 Crub_svsplocus 56625 56738 (593262) EnSpm-9_DR#DNA/CMC-EnSpm 675 770 (7850) m_b2s001i2
Crub_svsplocu 56625 GAGGGAGGGAGGGAGAGAGACAGAGAGAGAGAGAGAGAGACCCTTTTGAC 56674
i i i v - v v i v
EnSpm-9_DR#DN 675 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-CGCGTTCGCC 723
Crub_svsplocu 56675 ATCTAAAATGAAGATAACACTGCATATATCCTTTTTTTACCTGTGTGTGT 56724
i ----------------i ii i i -v v v v iiv
EnSpm-9_DR#DN 724 GT----------------GCTGTGTGTGT-GTGTGTGTGTGTGTGTGTGT 756
Crub_svsplocu 56725 ATGTGTGTGTGTAT 56738
i i
EnSpm-9_DR#DN 757 GTGTGTGTGTGTGT 770
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 26.57
Transitions / transversions = 1.56 (14/9)
Gap_init rate = 0.16 (18 / 113), avg. gap size = 1.00 (18 / 18)
+ 226 25.9 0.0 0.0 Crub_svsplocus 56701 56754 (593246) + L1-53_DR LINE/L1 1467 1520 (4926) 33 *
ANNOTATION EVIDENCE:
226 25.93 0.00 0.00 Crub_svsplocus 56701 56754 593246 + L1-53_DR LINE/L1 1467 1520 4926
226 25.93 0.00 0.00 Crub_svsplocus 56701 56754 (593246) L1-53_DR#LINE/L1 1467 1520 (4926) m_b2s001i3
Crub_svsplocu 56701 TATCCTTTTTTTACCTGTGTGTGTATGTGTGTGTGTATACATACATACAT 56750
iv iiv i ii ii ii i
L1-53_DR#LINE 1467 TATTATTTTTTTGTATGTGTGTGTATGTATGCATGTATGTATGTATATAT 1516
Crub_svsplocu 56751 ATGT 56754
i
L1-53_DR#LINE 1517 GTGT 1520
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 34.76
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)
+ 267 15.0 0.0 0.0 Crub_svsplocus 56716 56755 (593245) C hAT-N53_DR DNA/hAT-Ac (3021) 2798 2759 34
ANNOTATION EVIDENCE:
267 15.00 0.00 0.00 Crub_svsplocus 56716 56755 593245 C hAT-N53_DR DNA/hAT-Ac 2759 2798 3021
267 15.00 0.00 0.00 Crub_svsplocus 56716 56755 (593245) C hAT-N53_DR#DNA/hAT-Ac (3021) 2798 2759 m_b2s001i5
Crub_svsplocu 56716 TGTGTGTGTATGTGTGTGTGTATACATACATACATATGTA 56755
i i i i i i
C hAT-N53_DR#DN 2798 TGTGTGTGTGTGTGTGTGTGTATACACACACACACACGCA 2759
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 14.72
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 55 3.7 0.0 0.0 Crub_svsplocus 56858 56913 (593087) + (AC)n Simple_repeat 1 56 (0) 35
ANNOTATION EVIDENCE:
55 3.66 0.00 0.00 Crub_svsplocus 56858 56913 593087 + (AC)n Simple_repeat 1 56 0
55 3.66 0.00 0.00 Crub_svsplocus 56858 56913 (593087) (AC)n#Simple_repeat 1 56 (0) c_b2s251i1
Crub_svsplocu 56858 ACACACACACACACACACACACACACACACACATACACACACAAACACAC 56907
i v
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50
Crub_svsplocu 56908 ACACAC 56913
(AC)n#Simple_ 51 ACACAC 56
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)
+ 19 7.2 0.0 0.0 Crub_svsplocus 57814 57842 (592158) + (AACAA)n Simple_repeat 1 29 (0) 36
ANNOTATION EVIDENCE:
19 7.25 0.00 0.00 Crub_svsplocus 57814 57842 592158 + (AACAA)n Simple_repeat 1 29 0
19 7.25 0.00 0.00 Crub_svsplocus 57814 57842 (592158) (AACAA)n#Simple_repeat 1 29 (0) m_b2s252i2
Crub_svsplocu 57814 AACAAAACAAAACAAAGCAAAACATAACA 57842
i v
(AACAA)n#Simp 1 AACAAAACAAAACAAAACAAAACAAAACA 29
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 13 12.4 0.0 12.5 Crub_svsplocus 57843 57854 (592146) + (AACA)n Simple_repeat 5 40 (0) 37
ANNOTATION EVIDENCE:
13 12.40 0.00 12.50 Crub_svsplocus 57810 57854 592146 + (AACA)n Simple_repeat 1 40 0
13 12.40 0.00 12.50 Crub_svsplocus 57810 57854 (592146) (AACA)n#Simple_repeat 1 40 (0) m_b2s252i1
Crub_svsplocu 57810 AACCAACAAAACAAAACAAAGCAAAACATAACACACATACACACA 57854
v - - - - - v v v
(AACA)n#Simpl 1 AACAAAC-AAAC-AAACAAA-C-AAACA-AACAAACAAACAAACA 40
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.11 (5 / 44), avg. gap size = 1.00 (5 / 5)
+ 18 12.8 0.0 2.9 Crub_svsplocus 58009 58044 (591956) + (ATT)n Simple_repeat 1 35 (0) 38
ANNOTATION EVIDENCE:
18 12.78 0.00 2.86 Crub_svsplocus 58009 58044 591956 + (ATT)n Simple_repeat 1 35 0
18 12.78 0.00 2.86 Crub_svsplocus 58009 58044 (591956) (ATT)n#Simple_repeat 1 35 (0) m_b2s252i3
Crub_svsplocu 58009 ATAATTCATATTATTATTATTATTATACATTATTAT 58044
v vv -i
(ATT)n#Simple 1 ATTATTATTATTATTATTATTATTAT-TATTATTAT 35
Matrix = Unknown
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1)
+ 4502 32.5 3.2 3.2 Crub_svsplocus 58784 61930 (588070) + RTE1_ChrAsi LINE/RTE-BovB 83 3230 (6) 39
ANNOTATION EVIDENCE:
4502 32.49 3.21 3.18 Crub_svsplocus 58784 61930 588070 + RTE1_ChrAsi LINE/RTE-BovB 83 3230 6
4502 32.49 3.21 3.18 Crub_svsplocus 58784 61930 (588070) RTE1_ChrAsi#LINE/RTE-BovB 83 3230 (6) m_b2s001i6
Crub_svsplocu 58784 ATGCCATGCAGGGCCACCCAAGACGGACAGGTTATAGCAGAGAGTTCTGA 58833
i - i v ii vi vv vv i v
RTE1_ChrAsi#L 83 ATACCA-GCAGGGTCACCCATGGTGGACAGGTTTCAGATGAGCTTCCAGA 131
Crub_svsplocu 58834 CAAAATGTGATCCACT-GGAGAAGGAAATGGCAAACCACTCCAGTATCTT 58882
i ---- ivv - ii i i i i i i i v v v
RTE1_ChrAsi#L 132 CGAA----GACAGACTAGGAAGAAGGAGTGACGAACTACTTCCGAATATT 177
Crub_svsplocu 58883 T-GCCA-TGAAAATCCCATGGACAGTACTAAAAGGAAGAAAGATATGACG 58930
- i - i ii i i i vvi vivv vv iii
RTE1_ChrAsi#L 178 TAGTCACTGAAAACCTTATGAATAGCAGAGAAACACTGTCAGATATAGTG 227
Crub_svsplocu 58931 CTGGAAGATGAGCCCCTCAGGTCGGAAGGTGTCCAATATGCTATTGGGGA 58980
i i i iiii v v i
RTE1_ChrAsi#L 228 CCGGAAAATGAGCCCCTCAGGTTGGAAGGCACTCAAAATGCGACTGGGGA 277
Crub_svsplocu 58981 AGAGCAGAGGGCTAGTACTAGTAGCGCCAGAAAGAATGAAGCGACTGGGC 59030
---v v vv vvv v iiiivvivi v v iv
RTE1_ChrAsi#L 278 AGAGC---TGCCTCCTCAAAGTAGAGTTGACCGTGATGACGCGAATGGAG 324
Crub_svsplocu 59031 CAAAGCCGAAAGGACGCTCA---GCTG--TGGATATATCTGGTGGTGAAA 59075
i vivi vi --- --v ii i v vivii i
RTE1_ChrAsi#L 325 TAAAGCCCGCGGGACCTTCATTTGCTGATGGGGCACAACTCAAAATGAAG 374
Crub_svsplocu 59076 GGAAAGTCCAATGCTGTAAAGATTTTTTCTCCATAGGAACCTGGAATGTA 59125
i --- -- v iiv vv?v v v
RTE1_ChrAsi#L 375 AGAAA---CA--GCTGTAAACATCCATTGANAATCGGAACATGGAATGTA 419
Crub_svsplocu 59126 AGATCCATGAATCAAGGCAAGCTAGACGTAGTCAAAAAAGAGATGACAAG 59175
v vvi vi v ii i v v v i iv v
RTE1_ChrAsi#L 420 CGAAGTATGAATCTGGGAAAATTGGAAGTTGTCAAAAATGAAATGGAACG 469
Crub_svsplocu 59176 ACTGAACATCGACATCTTAGGAATCAGCGAACTAAAATGGACAGGAATGG 59225
vv i i v i i i i v v v
RTE1_ChrAsi#L 470 CATAAACATCGATATCTTAGGCATTAGTGAGCTGAAATGGACTGGTATTG 519
Crub_svsplocu 59226 GTGAATTTAACTCAGATGACCATCAGGTATACTACTGTGGGCAA----GA 59271
iv v i v v i ivv v - iv v ----i
RTE1_ChrAsi#L 520 GCCATTTTGAATCTGACGACCACATGGTTTACTA-TGCCGGGAATGACAA 568
Crub_svsplocu 59272 ATCCCTCAGAAGAAATGGAGTAGCCTTCATAGTCAATAAAAGAATAGGAA 59321
--- v ii i v v v v v i iv vvv
RTE1_ChrAsi#L 569 AT---TGAAGAGGAATGGTGTTGCATTCATCGTCAAAAAGAACATATCCA 615
Crub_svsplocu 59322 AAGCAATACTGGGATACAATCCTCAAAATGACAGAATGATCTCTATTCGA 59371
i v i vv i i iv vvvvi i i i v i v v
RTE1_ChrAsi#L 616 GATCAGTCATGAGGTACAACGCTGTCTGTGATAGGATAATATCCATGCGC 665
Crub_svsplocu 59372 ATCCAAGGCAAACCATTCAGTATCACAGTAGTCCAAATCTATGCCCCAAC 59421
v v i v i? v i i i vi vi i i i v
RTE1_ChrAsi#L 666 CTACAGGGAAGNCCAGTTAATACCACTATTATTCAAATTTACGCACCAAC 715
Crub_svsplocu 59422 CACTGCTGCTGAAGAGGATGAAATTGACCAGTTCTATGAAGCCCTACAGC 59471
ivv iiiv v vv i iv vii v --
RTE1_ChrAsi#L 716 CACTAAAGCCAGTGAGGATGAAATAGAAGAATTCTACCAACTTCTTCA-- 763
Crub_svsplocu 59472 ACCTTATAGAATT-----AACAC-CAAAAAATGATGTCCTTATCATCATG 59515
i v --- ----- i- vv - vi v i iv
RTE1_ChrAsi#L 764 ATCTGA---AATTGATCAAACATGCAATCAA-GATGTATTGATCATTACT 809
Crub_svsplocu 59516 GGGGATTGGAATGCTAAGGTAGGAAGCCAAAAGGTA--ACCGGAATAACA 59563
v v v i v i v -- i -- i iiv
RTE1_ChrAsi#L 810 GGTGATTGGAATGCAAAGGTTGGGAGCAAAGAGGAAGGATC--AGTAGTT 857
Crub_svsplocu 59564 GGCAAGTTTGGCCTTGGAG-TACAAAATGAAGCAGGGCACAGGCTAATAG 59612
v i v v - -i v v iv ?v vv i
RTE1_ChrAsi#L 858 GGAAAATATGGCCTTGGTGATA-GAAATGATGCTGGAGANCGCATGATAG 906
Crub_svsplocu 59613 AATTTTGTCAAGAGAATACGATGGTCATAACAAACACTCTTTTCCAACAA 59662
i iv ivv ivvv v vv i ii i ivi i
RTE1_ChrAsi#L 907 AATTCTGCAAAACCAATGATTTGTTCATTTCAAATACCTTCTTTAGACAG 956
Crub_svsplocu 59663 CCCAAGAGACGGCTCTACACATGGACATCACCAGACGGTCAACATAGAAA 59712
vi i v v i vvv i
RTE1_ChrAsi#L 957 CATAAGAGACGACTATACACATGGACCTCACCAGATGGAATACACAGAAA 1006
Crub_svsplocu 59713 TCAGATTGACTATGTGCTCTGCAGCCAAAGA---TGGAGAAGCTCTATAC 59759
i ii --- i vv i --- i i i
RTE1_ChrAsi#L 1007 TCAAATTGACTACAT---CTGCGGAAAGAGACGATGGAAAAGCTCCATAT 1053
Crub_svsplocu 59760 AGTCAGTAAAAACAAGACCAGGAGCTGACTGTGGCTCAGATCATGAGCTT 59809
vi v i i v vv i v ii v
RTE1_ChrAsi#L 1054 CATCAGTCAAAACAAGGCCAGGGGCAGACTGTGGAACAGACCATCAATTG 1103
Crub_svsplocu 59810 CTCGT-TGCAAAATTTAGGCTTAAATTGAAAAAAGTAGGGAAAAG--CAC 59856
i - - i ii v ii i i iiii v --
RTE1_ChrAsi#L 1104 CTCATATGCAAA-TTCAAACTGAAGCTGAAGAAAATGAAAACAAGTCCAC 1152
Crub_svsplocu 59857 TAG-GCCACTCAGGTATGAACTAAATCATATTCCTGATGAATATACAGTA 59905
v - --- ii v vi vi i vvv v v vv
RTE1_ChrAsi#L 1153 GAGAGCCA---AAATATGACCTTGAATATATCCCACCTGAATTTAGAGAT 1199
Crub_svsplocu 59906 GAGGTGACAAATAGATTTAAGGAACTGGAT-CTGATAGACAGAATGCCTG 59954
v vv vi i i viv i ii i- i - v vi v
RTE1_ChrAsi#L 1200 CATCTGAAGAACAGATTTGATACATTAAACACTAA-AGACCGAAGACCAG 1248
Crub_svsplocu 59955 AAGAACTATGGATGGAAGTTCGCAACATTGTACAAGAGGTA-GCAACTAA 60003
ii i ivv vi iviv ii v i v - --
RTE1_ChrAsi#L 1249 AAGAGTTGTGGGATGACATCAAGAACATCATACATGAAGAAAGCAA--AA 1296
Crub_svsplocu 60004 AACCATCCCAAAGAAAATGAAATGCAAGAAAG---CAAAATGGCTGTCTG 60050
ii ivvi v - - v i i--- v v
RTE1_ChrAsi#L 1297 AGTCATTAAGAAGACAA-GAAA-GAAGGAAAAGGTCAAAATGGATGTCAG 1344
Crub_svsplocu 60051 AGGAAGCTTTGCAAATAGCTGAGGAAAGAAGGGAAGCGAAAGGCAAA--G 60098
i ii vi v v v vvvv iv v i v v - --
RTE1_ChrAsi#L 1345 AAGAGACACTGAAACTTGCTCTCCAGCGTAGAGATGCTAAAG-CAAATGG 1393
Crub_svsplocu 60099 GAGAAA------GATACACCCAATTGAATGCAGAATTCCAGAGAGTAGCT 60142
i ------ i vv- ii iiv i i i ivi
RTE1_ChrAsi#L 1394 AAGAAATGAGGAGGTACAAG-AGCTGAACAGAAAATTTCAAAGGTCAGCT 1442
Crub_svsplocu 60143 AGAAGAGATAAGAATGCCT--TCTTA-AATGAACAGTGCAAAGAAATAGA 60189
v ii i i--- v-- v - i vv vv i
RTE1_ChrAsi#L 1443 CGAGAAGACAAA---GCCAAATATTACAACGAAATGTGCAAAGATCTGGA 1489
Crub_svsplocu 60190 ---AGAAAACAACAGAATAGGGAGGAC-----CAGAGATCTCTTCAAGAA 60231
--- -- i - i i ----- -v i - --
RTE1_ChrAsi#L 1490 GTCAGAAAAC--CAAAA-AGGAAGAACACGCTCAG-CATTTCT-CAAG-- 1532
Crub_svsplocu 60232 AATTGGAGATA-TGAAGGGAATGTTTCATGCAAAGATGGGCATGAT-AAA 60279
--i i iv - ii vi - v vvv ivvv i v -i
RTE1_ChrAsi#L 1533 --CTGGGGGAACTGAAGAAAAAATT-CAAGCCTCGACTTTCGTTATTGAA 1579
Crub_svsplocu 60280 GGACCAAAATGGCAGAGACCTAACAGAGGCAGAAGAGATTAAGAAGAGAT 60329
iivvvvv i vvvi i vv v iiv i i ii
RTE1_ChrAsi#L 1580 GGATTCTCTGGGCAAATTATTGAATGATGCAGAAAGCATCAAAAGAAGAT 1629
Crub_svsplocu 60330 GGCAAAACTACACAGAAGAACTATACAAGAATGA---GCTTAACATCCCA 60376
v ii v ivv i v i v --- v i ii i --
RTE1_ChrAsi#L 1630 GGAAGGAATACACAGAGTCACTGTACCAAAAGGAAATGGTTGATGTTC-- 1677
Crub_svsplocu 60377 GATAACCA---CAATGAGATGGTCAT-TGACCTCGAACCAGACATCCTAG 60422
--- i--- - i i - - i vv i ivv v ii
RTE1_ChrAsi#L 1678 ---AACCGTTTCAA-GAGGTAG-CATATGATCAAGAGCCAATGATACTGA 1722
Crub_svsplocu 60423 AATGTGAAGTGAAATGGGCCTTAGAAAATCTGAGCAACAACAAAGCTAGT 60472
iviv vv v v v ii ii vi ivv v i vvvv
RTE1_ChrAsi#L 1723 AGGAGGAAGTCCAAGGTGCATTGAAGGAATTGGCAAAGAACAAGGCACCA 1772
Crub_svsplocu 60473 GGAGGTGACAGTATTCCAGCTGAG--CTATTCAAAATCTTAAAAGACGAT 60520
iv ii v vvv ii i-- - i ---- iv v vv
RTE1_ChrAsi#L 1773 GGAATTGATGGAATAAAAATTGAAATCT-TTCAAGA----AAGTGAGGCG 1817
Crub_svsplocu 60521 GCAGTAAAAGTGCTACATTCA-ATTTGCCAGCAAATTTGGAAAAC--TTA 60567
v?ii i ii - i -v ? iv i --i
RTE1_ChrAsi#L 1818 GCACNGGAGGCACT-CACTCATCTNTGCCAAGAAATTTGGAAGACAACTA 1866
Crub_svsplocu 60568 ACAGTGGCCACAGGATTGGAAAAGGTCAGTTTACATTCCAATTCCAAAGA 60617
v -- ivvv i i v v vii v v
RTE1_ChrAsi#L 1867 TC--TGGCCGACTGATTGGAAGAGATCCGTATTTGTGCCCATTCCAAAGA 1914
Crub_svsplocu 60618 AAGGCAATGCCAA-AGAATGTTCAAACTATCGCACCATTGCACTCATTTC 60666
i ii i- -i ivv ii v v ?v vi v v
RTE1_ChrAsi#L 1915 GAGGTGAC-CCAACGGAATGCGGAAATCATCGGACAATNTCTTTGATATC 1963
Crub_svsplocu 60667 ACATGCTAGTAAAGTTATGCTTAAAATCCTATAAGCTAGACTCCA-GCAG 60715
v v v i v ii vv i iivvv i v - -
RTE1_ChrAsi#L 1964 CCATGCGAGTAAAGTTTTACTAAAGGTAATACAGAAACGGCTGCAAGCA- 2012
Crub_svsplocu 60716 TATGTGGATCGAGAACTACCAGAAGTACAGGCAGGATTTCGAAGAGGCAG 60765
ii v iv v i v i v iv v
RTE1_ChrAsi#L 2013 TACATTGACAGAGAACTTCCAGAGGTTCAAGCCGGATTCAGAAGAGGCCG 2062
Crub_svsplocu 60766 AGGAACTAGAGATCAAATTGCCAACATACGCTGGATCATGGA-GAAAGCT 60814
v v i vvv ii ii v v v v- -
RTE1_ChrAsi#L 2063 TGGAACGAGGGATATCATTGCTGATGTCCGATGGATCTTGGCTGAAAGC- 2111
Crub_svsplocu 60815 AGGGAGTTCCAGAAAAACATCTACTTCTGCTTCATTGACTATGCAAAAGC 60864
i i v i ii i i v i i i
RTE1_ChrAsi#L 2112 AGAGAATACCAGAAAGATGTTTACCTGTGCTTTATTGACTACGCAAAGGC 2161
Crub_svsplocu 60865 CTTTGATTGTGTGGATCACAACAAATTGTGG-CAAGTCCTTAAAGAG-AT 60912
i i ii ii i - -- v ivii -
RTE1_ChrAsi#L 2162 TTTCGATTGTGTGGATCATGACAAGCTATGGACAA--CATTGCGAAGTAT 2209
Crub_svsplocu 60913 GGGAGTACCAGACCATCTCATTTGT-CTCTTGAGAAACCTATATGTGGGT 60961
i vi v i v - i v - v i i i ii ii
RTE1_ChrAsi#L 2210 GAGTATTCCGGAACA-CTTAATTGTGCTCATGAGGAATCTGTACATGGAC 2258
Crub_svsplocu 60962 CAAGAAGCAACAGTGAGAACCGAACACGGAACCACTGATTGGTTCAAAAT 61011
i iiv vv v i i v v i
RTE1_ChrAsi#L 2259 CAAGAGGCAGTTGTTCGAACAGAACATGGGAACACTGAATGGTTTAAAAT 2308
Crub_svsplocu 61012 TGGAAAAGGAGTCCGGCAAGGCTGTATACTGTCACCCTGCCTATTTAACT 61061
iii v v i i i v v v i i i i
RTE1_ChrAsi#L 2309 TAAGAAAGGTGTGCGACAGGGTTGTATTCTTTCACCATACTTATTCAACC 2358
Crub_svsplocu 61062 TATATGCAGAGCACATCATGAGAAAGGCAGGGCTAGATGAATCAAAAGTT 61111
i v v v vv i i v i v vv vv
RTE1_ChrAsi#L 2359 TGTATGCTGAGCAAATAATCCGAGAAGCTGGGTTATATGAAGAAAAACGT 2408
Crub_svsplocu 61112 GGAATTAAGATTGCCGGGAGAAATATCAACAACCTAAGATGTGCAGATGA 61161
v i i vv i vvi i iv i
RTE1_ChrAsi#L 2409 GGCATCAGGATTGGAGGAAGACTCATTAACAACCTGCGATATGCAGATGA 2458
Crub_svsplocu 61162 TACCACTCTGATGGCAGAAAGTGAAGAGGAACTAAAGAGCCTCTTGATGC 61211
v ii v v v vi iviii vi v
RTE1_ChrAsi#L 2459 TACAACCTTGCTTGCTGAAAGTGAAGAGGACTTAAAATATTTACTGATGA 2508
Crub_svsplocu 61212 GGGTGAAGAAGGAGAG--TGCAAAAGTTGGCTTGAAACTCAACATTAAGA 61259
i i v ii v v -- v iiv -- v v v ii v
RTE1_ChrAsi#L 2509 AGATCAAAGAGCACAGCCTTCGGTA--TGGATTGCATCTCAATGTAAAGA 2556
Crub_svsplocu 61260 AAACCAAAATCATGGCATCCGGTCCTCT---CA--ATTCCTGGCAAATAG 61304
v v vi vv i v vv --- -- i iv -----
RTE1_ChrAsi#L 2557 AAACAAAAATCCTCACCACTGGACCAATAAACAACATTCTTATCA----- 2601
Crub_svsplocu 61305 ATGGGGAAGAAATGGAGGTAGTGACAGATTTTATTTTTCTGGGCTCCAAG 61354
i i i i v i v v vi i i i v v v vv
RTE1_ChrAsi#L 2602 ACGGAGAAAAGATTGAAGTTGTCAAGGACTTCATTCTTCTTGGATCAACT 2651
Crub_svsplocu 61355 ATCACCTCAGATGGGGACTGCAGCCAAGAAATTAAAAGACGC-TTGCTCC 61403
v v vv i iii v i i v i- -vi
RTE1_ChrAsi#L 2652 ATCAACACTCACGGAAGCAGCAGTCAAGAAATCAAACGACGTATTGC-AT 2700
Crub_svsplocu 61404 TGGGGAGGAAAGCTATGGC---AAATCTAGGCAGCATTCTAAAAAGCAGA 61450
i --- v v iiv --- i i vvvi ivi vi i i i
RTE1_ChrAsi#L 2701 TAG---GCAAATCTGCTGCACAAGACCTTTTTAAAGTGTTGAAGAGCAAA 2747
Crub_svsplocu 61451 GACATCACCCTGCCAACAAAAGTGCGTATAGTCCAGGCCATGGTTTTCCC 61500
ii v i vvi v i iv iii i v ii
RTE1_ChrAsi#L 2748 GATGTCAGCTTGAGGACTAAGGTGCGCCTGACCCAAGCCATGGTATTTTC 2797
Crub_svsplocu 61501 AGTTGCAATGTATGGCTGTGAAAGTTGGACCATAAGAAAGGCTGAGCGCA 61550
i vi vvii vv i i vi i iv vv v i
RTE1_ChrAsi#L 2798 AATAACCTCATATGCATGCGAAAGCTGGACAGTGAATAAGGAAGACCGTA 2847
Crub_svsplocu 61551 AAAGAATTGAGGCCTTTGAACTATGGTGCTGGAGAAGACTCCTGCGAGTC 61600
i v ? ii i i v vi vi v
RTE1_ChrAsi#L 2848 GAAGAATTGATGCNTTTGAGTTATGGTGTTGGAGGAGAATATTGAAAGTG 2897
Crub_svsplocu 61601 CCCTGGACTGCAAGGCGCTCAAACTGGTCAGTCCTAGAAGAGATCAACCC 61650
v i v iiv vv v v i v vi i ii vv v
RTE1_ChrAsi#L 2898 CCATGGGCTGCCAAAAGAACCAACAGATCTGTGTTGGAAGAAGTGCAGCC 2947
Crub_svsplocu 61651 CGACTGTTCTTTAGAAGGCCA-GAT-CCTGAAGTT-GAAACTCAAGTACT 61697
v v i i - i - -v ii v - vvv --
RTE1_ChrAsi#L 2948 AGAGTGCTCCTT-GGAGGCCAGGATGGCCAAACTTCGTCTCTCA--TACT 2994
Crub_svsplocu 61698 TTGGCCACCTAATGAGAAGGAAGGATTCACTGGAGAAGAGCCTAATGCTG 61747
i v iv vi v i i vv v i iiiv v i v
RTE1_ChrAsi#L 2995 TCGGACATATTGTCAGGAGGGACCAGTCGCTGGAGAAGGATATCATGTTT 3044
Crub_svsplocu 61748 GGAAAGATTGAGGGCAATAGAAGAAGGGGACGACAGAGAATGAGGTGGCT 61797
v i v iv v i i v vvvv ii i v
RTE1_ChrAsi#L 3045 GGTAAGGTGGAGGGTCAGAGAAAAAGAGGAAGACCCCCAGCGAGATGGAT 3094
Crub_svsplocu 61798 GGATGGAGTCACTGAAGCAGTAGGTGTGAATTTAAATG-GACTCCAGAAG 61846
v iiii ------i i vvvi iii i ii - i vv ---
RTE1_ChrAsi#L 3095 TGGCAAAGT------GGCAGCATCGATGGGCTCAAGCGTGGCAACAG--- 3135
Crub_svsplocu 61847 ATGGTAGAGGACAG--GAAGACCTGGAGGAA---CGT-----TGTCCATG 61886
- ? - vii --v i i v vi vi--- ----- v i
RTE1_ChrAsi#L 3136 -TNGT-GAGGTTGGCCCAGGATCGGGCAGTGTTTCGTTCTGCTGTGCATA 3183
Crub_svsplocu 61887 GGGTCGCGATGGGTCGG-ACACGACT---TCGCAATTAACAACAACAA 61930
v i - - --- v vi
RTE1_ChrAsi#L 3184 GGGTCGCTATGAGTCGGTAC-CGACTCGATGGCACCTAACAACAACAA 3230
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 41.88
Transitions / transversions = 1.05 (508/482)
Gap_init rate = 0.05 (151 / 3146), avg. gap size = 1.33 (201 / 151)
+ 266 17.5 0.0 0.0 Crub_svsplocus 66664 66703 (583297) + AmnSINE2 SINE/tRNA-Deu 80 119 (239) 40
ANNOTATION EVIDENCE:
266 17.50 0.00 0.00 Crub_svsplocus 66664 66703 583297 + AmnSINE2 SINE/tRNA-Deu 80 119 239
266 17.50 0.00 0.00 Crub_svsplocus 66664 66703 (583297) AmnSINE2#SINE/tRNA-Deu 80 119 (239) m_b2s001i7
Crub_svsplocu 66664 CAAGGTTGACTCAGCCTTCCATCCTTTTGAGGTTGATAAA 66703
i i i i ii v
AmnSINE2#SINE 80 CAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAGATAAA 119
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 14.68
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 17 12.9 2.1 6.5 Crub_svsplocus 69315 69362 (580638) + A-rich Low_complexity 1 46 (0) 41
ANNOTATION EVIDENCE:
17 12.95 2.08 6.52 Crub_svsplocus 69315 69362 580638 + (AAATCTA)n Simple_repeat 1 46 0
17 12.95 2.08 6.52 Crub_svsplocus 69315 69362 (580638) (AAATCTA)n#Simple_repeat 1 46 (0) m_b2s252i4
Crub_svsplocu 69315 AAATATAAAACCTGAAATTTAAAA-CTCAAATCTGAATAAATCTAAAAT 69362
v i i i - v -- -
(AAATCTA)n#Si 1 AAATCTAAAATCTAAAATCTAAAATCTAAAATCT--A-AAATCTAAAAT 46
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4)
+ 14 11.6 2.2 9.5 Crub_svsplocus 69983 70027 (579973) + A-rich Low_complexity 1 42 (0) 42
ANNOTATION EVIDENCE:
14 11.58 2.22 9.52 Crub_svsplocus 69983 70027 579973 + (GAAA)n Simple_repeat 1 42 0
14 11.58 2.22 9.52 Crub_svsplocus 69983 70027 (579973) (GAAA)n#Simple_repeat 1 42 (0) m_b2s252i5
Crub_svsplocu 69983 GAGAGAAAGGAAATGATAAGAGAAG-CAGAGAGAAAGAAATAAAGA 70027
i - - - - -v i v
(GAAA)n#Simpl 1 GAAAGAAA-GAAA-GA-AAGA-AAGAAAGAAAGAAAGAAAGAAAGA 42
Matrix = Unknown
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.11 (5 / 44), avg. gap size = 1.00 (5 / 5)
+ 225 19.5 1.2 3.6 Crub_svsplocus 70604 70688 (579312) + Tx1-11_DR LINE/L1-Tx1 5637 5719 (81) 43
ANNOTATION EVIDENCE:
225 19.52 1.18 3.61 Crub_svsplocus 70604 70688 579312 + Tx1-11_DR LINE/L1-Tx1 5637 5719 81
225 19.52 1.18 3.61 Crub_svsplocus 70604 70688 (579312) Tx1-11_DR#LINE/L1-Tx1 5637 5719 (81) m_b2s001i8
Crub_svsplocu 70604 CTATGTTATTTTTTATGTTTTTTTACTCTTGCTCTCCTTTCTTTTTTTCA 70653
v v v v i vi i v i v
Tx1-11_DR#LIN 5637 CTCTGTTTTTTTTTCTTTTTTTCTTTTTTTTCTCTTCTTTGTTTTTTTCA 5686
Crub_svsplocu 70654 C-TATTTTATCTATTCCTTAAGAAATGTAAATGTGA 70688
- i i--i iv -
Tx1-11_DR#LIN 5687 CTTATTTCATT--CTTGTTAAGAAATGTAAA-GTGA 5719
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 22.74
Transitions / transversions = 1.00 (8/8)
Gap_init rate = 0.05 (4 / 84), avg. gap size = 1.00 (4 / 4)
+ 454 23.0 5.3 0.0 Crub_svsplocus 71792 71904 (578096) + Plat_L3 LINE/CR1 3442 3560 (13) 44
ANNOTATION EVIDENCE:
454 23.01 5.31 0.00 Crub_svsplocus 71792 71904 578096 + Plat_L3 LINE/CR1 3442 3560 13
454 23.01 5.31 0.00 Crub_svsplocus 71792 71904 (578096) Plat_L3#LINE/CR1 3442 3560 (13) m_b2s001i9
Crub_svsplocu 71792 TGGAAAATTTTAAGAAGAGACTGGACAGCCATTTGTCTGAAATGGTATAG 71841
i vi i v i ? i ivii v
Plat_L3#LINE/ 3442 TGGAGATCTTTAAGAAAAGAATAGACANCCATCTGTCCTGGATGGTTTAG 3491
Crub_svsplocu 71842 --GTTT-CCTTCCTGA--GCAGGTGGTTGGTCTAGATGACCCC-CAAGAT 71885
--i i- v i-- v i v i i - i i
Plat_L3#LINE/ 3492 TCATTCACCTGCCTGGAGGCAGGGGGCTGGACCAGATGACCTCTCGAGGT 3541
Crub_svsplocu 71886 CCCTTCCAACTTTATTATT 71904
i i ?v
Plat_L3#LINE/ 3542 CCCTTCCAGCTCTANGATT 3560
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 27.81
Transitions / transversions = 2.25 (18/8)
Gap_init rate = 0.04 (4 / 112), avg. gap size = 1.50 (6 / 4)
+ 2893 29.4 0.9 0.5 Crub_svsplocus 72181 73042 (576958) + L3 LINE/CR1 3215 4080 (19) 45
ANNOTATION EVIDENCE:
2893 29.37 0.93 0.46 Crub_svsplocus 72181 73042 576958 + L3 LINE/CR1 3215 4080 19
2893 29.37 0.93 0.46 Crub_svsplocus 72181 73042 (576958) L3#LINE/CR1 3215 4080 (19) m_b2s001i10
Crub_svsplocu 72181 TTTGCAGACGACACCAAGCTGGCAGGAATAGCCAACACTCCAGAAGACAG 72230
i v v i i i v?ii v
L3#LINE/CR1 3215 TTTGCAGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGATGACAG 3264
Crub_svsplocu 72231 GCTTAAGATACAGAAGGATCTGGACAGACTTGAACACTGGGCACTAACTA 72280
iv i v i ? v i v iv vvv i
L3#LINE/CR1 3265 AATCAAGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAAACCA 3314
Crub_svsplocu 72281 ACAAAATGAAATTCAATGGTGAAAAAAGCAAGGTTCTACATTTAGGCAAG 72330
i i ii v v v i i i i ivvi
L3#LINE/CR1 3315 ACAAGATGAAATTTAACAGGGATAAATGTAAAGTCCTGCATTTAGGTTCA 3364
Crub_svsplocu 72331 AAAAACCAAATGCACAAGTACAGTATAGGTGGCACCATGCTCAATAGTAG 72380
i v v i ivi v i vv i ii i
L3#LINE/CR1 3365 AAAAATCAACTGCACAAGTACAGGATGGAGAGGATCTGGCTTAGCAGCAG 3414
Crub_svsplocu 72381 TAACTGTGAGAGGGACCTCGGAGTCCTAATAGACAATCACTTAAATATGA 72430
vvvi i ii v i ii i v viiv vi v
L3#LINE/CR1 3415 TTCACGTGAAAAAGACCTAGGGGTTTTAGTTGACCGCAAGCTCAATATGA 3464
Crub_svsplocu 72431 GCCAGCAGTGTGCTGCAGCTGCCAAAAAGGCCAACACAGTGCTAGGCTGC 72480
i v ii i i ii i vi
L3#LINE/CR1 3465 GCCAACAGTGTGATGTGGCTGCCAAAAAAGCTAATGCAATCTTAGGCTGC 3514
Crub_svsplocu 72481 ATTAACAGAGGGATAGAATCAAGATCACGTGAAGTATTAATACCACTCTT 72530
i i v vi v ? v v i v i v i v v
L3#LINE/CR1 3515 ATTAATAGAAGTATAGTGTCCAGANCAAGGGAGGTAATAGTCCCGCTGTA 3564
Crub_svsplocu 72531 CAATGCCTTGGTAAGGCCACACTTGGAATACTGCATCCAGTTTTGGTCAC 72580
vv vi v i ii i i i i i v i
L3#LINE/CR1 3565 CTCTGCGCTGGTCAGACCACATCTGGAGTATTGCGTTCAGTTCTGGGCGC 3614
Crub_svsplocu 72581 CACGATGTAAAAAAGATGTTGAGACTCTAGAAAGAGTACAGAGAAGAGCA 72630
iv v i ii ii v vv i iv v v i i
L3#LINE/CR1 3615 CACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCG 3664
Crub_svsplocu 72631 ACAAAGATGATTAGGGGACTGGAGGCTAAAACATATAAGGAACGGTTGCT 72680
v i i v i v ii i viv i vv
L3#LINE/CR1 3665 ACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAA 3714
Crub_svsplocu 72681 AGAATTGGGTATGTCTAGTTTAACGAAGAGAAGGACAAGGGGGGACATGA 72730
i i v i ii iiv iviv i i
L3#LINE/CR1 3715 GGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACATGA 3764
Crub_svsplocu 72731 TAGCAGTATTCCAATATCTCAGGGGCTGCCATAAAGAAGAGGGAATTAAG 72780
v v v i v i i ivi - ii
L3#LINE/CR1 3765 TAGCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGG-ATTAGA 3813
Crub_svsplocu 72781 C-TATTTTCCAAAGTACCTGAAGGCAGGACAAGAAGCAACGGGTGGAAAC 72829
- i viivi iv v i i v i v i ii
L3#LINE/CR1 3814 CTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGT 3863
Crub_svsplocu 72830 TAATCAAGGAGAGAAG---CAACCTAGAACTAAGGAGAAACTTCCTGACA 72876
-- i iv ii--- ii ii iv - ii i i
L3#LINE/CR1 3864 TA--CAGGGAGGCAGATTTCGGCTCAATA-TAAGGAAGAACTTTCTAACA 3910
Crub_svsplocu 72877 GTGAGAACAATTAACCAGTGGAACAACCTGCCTCCAGAAGCAGTAAATGC 72926
i v i vi iv vv i iiiv v? i i i iiv
L3#LINE/CR1 3911 ATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTC 3960
Crub_svsplocu 72927 TCCAACACTGGAAGTTTTTAAGAAGAGACTGGACAACCATTTGTCCGAAA 72976
i iv i v i v i ii i v ii
L3#LINE/CR1 3961 CCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGA 4010
Crub_svsplocu 72977 TGGTGT---AGGGTTTCCTGC-CCGAGCAGGGGGTTGGACTAGATGACCT 73022
v --- v -i iiii i
L3#LINE/CR1 4011 TGTTGTAGAAGGGATTCCTGCATCGGATGGGAGGTTGGACTAGATGACCT 4060
Crub_svsplocu 73023 CCAAGGTCCCTTCCAACTTT 73042
i i
L3#LINE/CR1 4061 CTAAGGTCCCTTCCAACTCT 4080
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 37.13
Transitions / transversions = 1.68 (158/94)
Gap_init rate = 0.01 (8 / 861), avg. gap size = 1.50 (12 / 8)
+ 338 11.7 3.3 1.6 Crub_svsplocus 73001 73061 (576939) + MIR3 SINE/MIR 144 205 (3) 46 *
ANNOTATION EVIDENCE:
338 11.67 3.28 1.61 Crub_svsplocus 73001 73061 576939 + MIR3 SINE/MIR 144 205 3
338 11.67 3.28 1.61 Crub_svsplocus 73001 73061 (576939) MIR3#SINE/MIR 144 205 (3) m_b2s001i11
Crub_svsplocu 73001 AGGGGGTTGGACTAGATGACCTCCAAGGTCCCTTCCAACTTT-AC-TACT 73048
i i i i - - v
MIR3#SINE/MIR 144 AGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCT 193
Crub_svsplocu 73049 ATTATTAATATGA 73061
v -v
MIR3#SINE/MIR 194 ATGATT-CTATGA 205
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 12.76
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3)
+ 14 4.9 0.0 0.0 Crub_svsplocus 75399 75419 (574581) + (AAC)n Simple_repeat 1 21 (0) 47
ANNOTATION EVIDENCE:
14 4.94 0.00 0.00 Crub_svsplocus 75399 75419 574581 + (AAC)n Simple_repeat 1 21 0
14 4.94 0.00 0.00 Crub_svsplocus 75399 75419 (574581) (AAC)n#Simple_repeat 1 21 (0) m_b2s252i6
Crub_svsplocu 75399 AAAAACAACAACAACAACAAC 75419
v
(AAC)n#Simple 1 AACAACAACAACAACAACAAC 21
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
+ 13 18.3 2.6 2.6 Crub_svsplocus 76130 76168 (573832) + (GATTTAA)n Simple_repeat 1 39 (0) 48
ANNOTATION EVIDENCE:
13 18.28 2.56 2.56 Crub_svsplocus 76130 76168 573832 + (GATTTAA)n Simple_repeat 1 39 0
13 18.28 2.56 2.56 Crub_svsplocus 76130 76168 (573832) (GATTTAA)n#Simple_repeat 1 39 (0) m_b2s252i7
Crub_svsplocu 76130 GATTTAAGGATTAAGATTT-AGAGTTGAAAATTTGTGATT 76168
iv - - v i iv
(GATTTAA)n#Si 1 GATTTAAGATTTAAGATTTAAGA-TTTAAGATTTAAGATT 39
Matrix = Unknown
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2)
+ 15 26.7 1.8 1.8 Crub_svsplocus 76219 76274 (573726) + (AATATG)n Simple_repeat 1 56 (0) 49
ANNOTATION EVIDENCE:
15 26.73 1.79 1.79 Crub_svsplocus 76219 76274 573726 + (AATATG)n Simple_repeat 1 56 0
15 26.73 1.79 1.79 Crub_svsplocus 76219 76274 (573726) (AATATG)n#Simple_repeat 1 56 (0) m_b2s252i8
Crub_svsplocu 76219 AATATGTTTATTTATATGAAAATTATTTTGTA-ATGAAATGAGAATAAGA 76267
vv vv v v v v v - - iv v
(AATATG)n#Sim 1 AATATGAATATGAATATGAATATGAATATGAATATG-AATATGAATATGA 49
Crub_svsplocu 76268 ATATGAA 76274
(AATATG)n#Sim 50 ATATGAA 56
Matrix = Unknown
Transitions / transversions = 0.09 (1/11)
Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.00 (2 / 2)
+ 18 4.0 0.0 0.0 Crub_svsplocus 77075 77100 (572900) + (AACA)n Simple_repeat 1 26 (0) 50
ANNOTATION EVIDENCE:
18 3.96 0.00 0.00 Crub_svsplocus 77075 77100 572900 + (AACA)n Simple_repeat 1 26 0
18 3.96 0.00 0.00 Crub_svsplocus 77075 77100 (572900) (AACA)n#Simple_repeat 1 26 (0) m_b2s252i9
Crub_svsplocu 77075 AAGAAACAAACAAACAAACAAACAAA 77100
v
(AACA)n#Simpl 1 AACAAACAAACAAACAAACAAACAAA 26
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
+ 281 25.6 6.1 1.7 Crub_svsplocus 77108 77222 (572778) + L1-97_DR LINE/L1 2924 3043 (2537) 51
ANNOTATION EVIDENCE:
281 25.65 6.09 1.67 Crub_svsplocus 77108 77222 572778 + L1-97_DR LINE/L1 2924 3043 2537
281 25.65 6.09 1.67 Crub_svsplocus 77108 77222 (572778) L1-97_DR#LINE/L1 2924 3043 (2537) m_b2s001i12
Crub_svsplocu 77108 AAAGCACCTGGGCCAGATGGTATACCTGTAGAA--ATGCATAAAATTG-- 77153
i v v --v i v --
L1-97_DR#LINE 2924 AAGGCTCCTGGGCCCGATGGTATACCTGTAGAATTTTACAAAAAATTGCA 2973
Crub_svsplocu 77154 ---AATCTTTAAGCCCAATGTTGTTGGATCTATTCAATGAGGTCCTAACC 77200
--- v - v v i- ii v vv i viv iivv
L1-97_DR#LINE 2974 GGTAAAC-TTATGCCCCAC-TTACTTGAAGTATTTAATGAGTCGCTGGAA 3021
Crub_svsplocu 77201 AAAGCTAAAATACCAGCCTCAT 77222
v vvv v i
L1-97_DR#LINE 3022 AAAGGTATTCTACCACCCTCGT 3043
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 29.04
Transitions / transversions = 0.53 (10/19)
Gap_init rate = 0.04 (5 / 114), avg. gap size = 1.80 (9 / 5)
+ 259 29.2 2.6 3.5 Crub_svsplocus 77211 77327 (572673) + Tx1-43_DR LINE/L1-Tx1 3007 3122 (2372) 52 *
ANNOTATION EVIDENCE:
259 29.22 2.56 3.45 Crub_svsplocus 77211 77327 572673 + Tx1-43_DR LINE/L1-Tx1 3007 3122 2372
259 29.22 2.56 3.45 Crub_svsplocus 77211 77327 (572673) Tx1-43_DR#LINE/L1-Tx1 3007 3122 (2372) m_b2s001i13
Crub_svsplocu 77211 TACCAGCCTCATGGGAAGAAGCCCTTCTCACTTTGATTCCTAAGAAAAAT 77260
vv vii i iv i v v v v i ii-
Tx1-43_DR#LIN 3007 TACCTTCCTCATGCAGAAAAGCTGTTTTGACATTGTTGCCTAAAAAAGG- 3055
Crub_svsplocu 77261 TCAGACTTGGCGCATATTAAG-AACTATAGACCTATTTCTCTATTAAATT 77309
-- ii ii vv - - i iv i v i vi v
Tx1-43_DR#LIN 3056 --AGATCTAACTGA-ATTAAGGAATTGGAGACCTGTTGCTCTACTATGTA 3102
Crub_svsplocu 77310 CAGATTATAAGAT--TTTCA 77327
ii --
Tx1-43_DR#LIN 3103 CAGATTATAAAGTGCTTTCA 3122
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 37.94
Transitions / transversions = 1.36 (19/14)
Gap_init rate = 0.05 (6 / 116), avg. gap size = 1.17 (7 / 6)
+ 228 37.8 0.0 0.0 Crub_svsplocus 77285 77427 (572573) + L1-67_DR LINE/L1 2811 2953 (2415) 53 *
ANNOTATION EVIDENCE:
228 37.76 0.00 0.00 Crub_svsplocus 77285 77427 572573 + L1-67_DR LINE/L1 2811 2953 2415
228 37.76 0.00 0.00 Crub_svsplocus 77285 77427 (572573) L1-67_DR#LINE/L1 2811 2953 (2415) m_b2s001i14
Crub_svsplocu 77285 TATAGACCTATTTCTCTATTAAATTCAGATTATAAGATTTTCATGGCTAT 77334
i v vv i vi i iv i i ivv vi
L1-67_DR#LINE 2811 TACAGACCTATATCGGTACTAAATATAGACTATAAACTCTTTACCTCAGT 2860
Crub_svsplocu 77335 AATGGTGCAAAGGCTTGAAAGATTCCTAGCAGATTTTATTCATTCTGATC 77384
vv i ivv i vv i vv iv i v v v
L1-67_DR#LINE 2861 CCTAGCTAAAAGACTTGAACTACTAATGCCGGAATTAATTAATTCTGATC 2910
Crub_svsplocu 77385 AAAATGGCTTTCTATCCAAAAGATACATAAGAAATAATGTCAG 77427
vi v v v v iiv ii v i viii i i
L1-67_DR#LINE 2911 AAACCGGATTTATTTGCGGCAGGCAAACACAGGACAATGTTAG 2953
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 49.30
Transitions / transversions = 0.93 (26/28)
Gap_init rate = 0.00 (0 / 142), avg. gap size = 0.0 (0 / 0)
+ 232 24.6 1.6 0.0 Crub_svsplocus 77469 77529 (572471) + L1MdTf_I LINE/L1 3126 3187 (4137) 54
ANNOTATION EVIDENCE:
232 24.59 1.64 0.00 Crub_svsplocus 77469 77529 572471 + L1-11_DR LINE/L1 3126 3187 4137
232 24.59 1.64 0.00 Crub_svsplocus 77469 77529 (572471) L1-11_DR#LINE/L1 3126 3187 (4137) m_b2s001i15
Crub_svsplocu 77469 AAAAGCAAATGGGTT-TAATTTTCCTCGACGCACAAAAAGCATTCGACAA 77517
i vvi i- i ivi v v
L1-11_DR#LINE 3126 AAAAACAAATCTATCATAGTCACCCTCGACGCAGAAAAAGCCTTCGACAA 3175
Crub_svsplocu 77518 TGTGAAATGGGA 77529
v i v i
L1-11_DR#LINE 3176 AGTAAACTGGAA 3187
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 30.18
Transitions / transversions = 1.14 (8/7)
Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1)
+ 259 31.2 6.5 5.2 Crub_svsplocus 77576 77822 (572178) + L1MdTf_I LINE/L1 3960 4209 (2370) 54
ANNOTATION EVIDENCE:
259 31.17 6.48 5.20 Crub_svsplocus 77576 77822 572178 + L1MdTf_I_orf2 LINE/L1 2758 3007 1674
259 31.17 6.48 5.20 Crub_svsplocus 77576 77822 (572178) L1MdTf_I_orf2#LINE/L1 2758 3007 (1674) m_b2s001i16
Crub_svsplocu 77576 TAAATATGTTCAAATCAGTTTATTCTAAACAGGCAGCAAAAGT---AGTA 77622
i v v v i i ivvi vi i v vi ---
L1MdTf_I_orf2 2758 TAAACATGATAAAAGCAATCTACAGCAAACCAGTAGCCAACATCAAAGTA 2807
Crub_svsplocu 77623 ATTCATGGAGAAATGATCGACAGC--TTCCAAATTCAAAA--AGGTATGA 77668
--- i v v v - -- i ---ii -- v iv
L1MdTf_I_orf2 2808 A---ATGGAGAGAAGCTGGA-AGCAATCCCA---CTAAAATCAGGGACTA 2850
Crub_svsplocu 77669 GGCAAGGTTGTTCGTTATCGCCACTGTTGTT----CATATTATCTCCCGA 77714
i i ii ii v v - iiiv ---- v ii ---
L1MdTf_I_orf2 2851 GACAAGGCTGCCCACTTTCTCC-CTACCTTTTCAACATAGTACTT---GA 2896
Crub_svsplocu 77715 GGTATTAATTAGAGTAATTCGGCAAGATGAACAGATTAAAGGTTTAGAGA 77764
i iii i i v vi iv i i vv v i
L1MdTf_I_orf2 2897 AGTATTAGCCAGAGCAATTCGACAACAAAAGGAGATCAAGGGGATACAAA 2946
Crub_svsplocu 77765 TC--AAGAGAGAAACGTTTAAAACACAAGCTTTTGCAGACAAT-T--TAG 77809
i-- i i v-- i i iv vi ii - --
L1MdTf_I_orf2 2947 TTGGAAAAGAGGAAG--TCAAAATATCACTTTTTGCAGATGATATGATAG 2994
Crub_svsplocu 77810 TTTTTATAATTGA 77822
v v v
L1MdTf_I_orf2 2995 TATATATAAGTGA 3007
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 41.78
Transitions / transversions = 1.52 (44/29)
Gap_init rate = 0.08 (20 / 246), avg. gap size = 1.45 (29 / 20)
+ 333 29.9 4.7 4.3 Crub_svsplocus 78034 78354 (571646) + L1-23_DR LINE/L1 3972 4371 (1343) 55
ANNOTATION EVIDENCE:
316 32.01 5.61 4.63 Crub_svsplocus 78034 78354 571646 + L1-18_DR LINE/L1 4048 4371 1343
316 32.01 5.61 4.63 Crub_svsplocus 78034 78354 (571646) L1-18_DR#LINE/L1 4048 4371 (1343) m_b2s001i17
Crub_svsplocu 78034 AACTATGATAAGTTAATTGA-----TTAAAAAGGATTTAGATATTTGGAC 78078
i iv i ----- iv v vv iv
L1-18_DR#LINE 4048 AATTATGATAAAATAATTAACACAGTTAAAAAGGATTTGCAGAGGTGGGA 4097
Crub_svsplocu 78079 CAACCTATAGCTCTCCTTCATGGGCAGAATCGCTATAATCAAAATGAATG 78128
vivv ivi v v vv v i i i vv i v i i
L1-18_DR#LINE 4098 GGTGCTACCACTATCATTGTTTGGTAGGATTGAAACAATAAGAATGAATA 4147
Crub_svsplocu 78129 TGCTACTGAAAATTTTATTTTTGTTCCAATGTATACCCATAAAACTGGAT 78178
vi iv i v i v i i i viv ----
L1-18_DR#LINE 4148 TTTTACCTAGATTTCTTTTTTTATTTCAGTCCCTACCCATA----TGGAT 4193
Crub_svsplocu 78179 --AAGAATTT-TTTTCAAAACCTTA-ATAAAATTATACTCAAATTCATCT 78224
--vv v ii-iv i v iv - v iii i
L1-18_DR#LINE 4194 TCCTGTATCCACATTTAACATGTTAGATAAACTTATATCTAGATTCATCT 4243
Crub_svsplocu 78225 TGCGAGGA-AAAAGAGCAAGGATCAAATTAAAA---TT-ACTGCAGGATT 78269
v - i - i v v v i v i --- - i vi --
L1-18_DR#LINE 4244 GGC-AGAACAGACGACCCAGAATAAGATTAAAAACGTTAATTTTAGGA-- 4290
Crub_svsplocu 78270 CAAAGGAAAGGGGGGGAGACTTGGCCTCCCTGACCTGGAAAAATATTATC 78319
- iv i vv --- i vi ii iii v v i
L1-18_DR#LINE 4291 -AAAGATAAGGGAGGGCTAC---GTCTCCCAAATTTAAGATATTATTATT 4336
Crub_svsplocu 78320 AGGC--CACAG--TACTATTATGGGTAGGGGATTGGATA 78354
i -- v --i vii ---- v i
L1-18_DR#LINE 4337 GGGCTGCTCAGCTCACAGCTA----TAGTGGACTGGATA 4371
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 42.63
Transitions / transversions = 1.13 (52/46)
Gap_init rate = 0.07 (24 / 320), avg. gap size = 1.38 (33 / 24)
333 28.57 4.06 4.06 Crub_svsplocus 78090 78286 571714 + L1-23_DR LINE/L1 3972 4168 1411
333 28.57 4.06 4.06 Crub_svsplocus 78090 78286 (571714) L1-23_DR#LINE/L1 3972 4168 (1411) m_b2s001i18
Crub_svsplocu 78090 TCTCCTTCATGGGCAGAATCGCTATAATCAAAATGAATGTGCTACTGAAA 78139
v iv i v viv i v i v iv
L1-23_DR#LINE 3972 TCTCATTTCTAGGAAGAATAAATGTAATAAAAATGAATGTACTTCCTAAA 4021
Crub_svsplocu 78140 ATTTTATTTTTGTTCCAATGTATACCCATAAAACTGGATAA-GAATT--T 78186
v i v i i vi i---- i ivv i-i --
L1-23_DR#LINE 4022 TTCTTATATTTATTCCAGTCCATACCT----AGCTACTTAGCAAATTCAT 4067
Crub_svsplocu 78187 TTTTCAAA-ACCTTAATAAAATTATACTCAAA-TTCATCTTGCGAGGAAA 78234
- i vvi - - i v viviiv
L1-23_DR#LINE 4068 TTTTCAAAGATCTTAATAAACACAT-CTCAAAGTTTATCTGGAACAATAA 4116
Crub_svsplocu 78235 AAGAGCAAGGATCAAA---TTAAAATTACTGCAGGATTCAAAGGAAAGGG 78281
v iv v i --- iv v v ---i v i v
L1-23_DR#LINE 4117 AAGACCGCGTATTAAAATTTCTAAATTAATGAAG---CCTAAAGACAGGG 4163
Crub_svsplocu 78282 GGGGA 78286
v
L1-23_DR#LINE 4164 GTGGA 4168
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 35.49
Transitions / transversions = 0.93 (26/28)
Gap_init rate = 0.07 (13 / 196), avg. gap size = 1.23 (16 / 13)
+ 1860 27.8 1.6 1.1 Crub_svsplocus 79320 79847 (570153) + L3 LINE/CR1 3507 4077 (19) 56
ANNOTATION EVIDENCE:
1860 29.86 1.40 0.70 Crub_svsplocus 79320 79889 570111 + L3 LINE/CR1 3507 4080 19
1860 29.86 1.40 0.70 Crub_svsplocus 79320 79889 (570111) L3#LINE/CR1 3507 4080 (19) m_b2s001i19
Crub_svsplocu 79320 TAGGCTGCATTAACAGAGGGATAGAATCAAGATCACGTGAAGTATTAATA 79369
i i v vi v ? v v i v i v
L3#LINE/CR1 3507 TAGGCTGCATTAATAGAAGTATAGTGTCCAGANCAAGGGAGGTAATAGTC 3556
Crub_svsplocu 79370 CCACTCTTCAATGCCTTGGTAAGGTCACACTTGGAATACTGCATCCAGTT 79419
i v v vv vi v ii ii i i i i
L3#LINE/CR1 3557 CCGCTGTACTCTGCGCTGGTCAGACCACATCTGGAGTATTGCGTTCAGTT 3606
Crub_svsplocu 79420 TTGGTCACCACGATGTAAAAAAGATGTTGAGACTCTAGAAAGAGTACAGA 79469
i v i iv v i ii ii v vv i iv v v
L3#LINE/CR1 3607 CTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGA 3656
Crub_svsplocu 79470 GAAGAGCAACAAAGATGATTAGGGGACTGGAGGCTAAAACATATAAGAAA 79519
i i v i i v i v ii i viv i i
L3#LINE/CR1 3657 GGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAA 3706
Crub_svsplocu 79520 CGGTTGCTAGAATTGGGTATGTCTAGTTTAACGAAGAGAAGGACAAGGGG 79569
vvi i v i ii iiv iviv i
L3#LINE/CR1 3707 CGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGG 3756
Crub_svsplocu 79570 GGACATGATAGCAGTATTCCAATATCTCAGGGGCTGCCATAAAGAAGAGG 79619
i v v v i v i i ivi
L3#LINE/CR1 3757 AGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGG 3806
Crub_svsplocu 79620 GAATTAAGC-TATTTTCCAAAGCACCTGAAGGCAGGACAAGAAGCAACAG 79668
- ii - i viivi v v i i v i v ii
L3#LINE/CR1 3807 G-ATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGG 3855
Crub_svsplocu 79669 GTGGAAACTAATCAAGGAGAGAAG---CAACCTAGAACTAAGGAGAAACT 79715
ii -- i iv ii--- ii ii iv - ii
L3#LINE/CR1 3856 GTGGAAGTTA--CAGGGAGGCAGATTTCGGCTCAATA-TAAGGAAGAACT 3902
Crub_svsplocu 79716 TCCTGACAGTGAGAACAATTAATCAGTGGAATAGCTTGCCTCCAGAAGCA 79765
i i i v i vi iv vv i i vi v? i i
L3#LINE/CR1 3903 TTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTA 3952
Crub_svsplocu 79766 GTAAATGCTCCAACACTGGAAGTTTTTAAGAAGAGACTGGACAGCCATTT 79815
i iiv i iv i v i v i iii i
L3#LINE/CR1 3953 GTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTT 4002
Crub_svsplocu 79816 GTCCGAAATGGTGT---AGGGTTTCCTGC-CCGAGCAGGGGGTTGGACTA 79861
v ii v --- v -i iiii i
L3#LINE/CR1 4003 GTCAGGGATGTTGTAGAAGGGATTCCTGCATCGGATGGGAGGTTGGACTA 4052
Crub_svsplocu 79862 GATGACCTCCAAGGTCCCTTCCAACTTT 79889
i i
L3#LINE/CR1 4053 GATGACCTCTAAGGTCCCTTCCAACTCT 4080
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 38.08
Transitions / transversions = 1.82 (109/60)
Gap_init rate = 0.01 (8 / 569), avg. gap size = 1.50 (12 / 8)
318 10.18 3.23 4.92 Crub_svsplocus 79837 79898 570102 + CR1L_fAlb LINE/CR1 33 93 6
318 10.18 3.23 4.92 Crub_svsplocus 79837 79898 (570102) CR1L_fAlb#LINE/CR1 33 93 (6) m_b2s001i20
Crub_svsplocu 79837 CCTGCCC-GAGCAGGGGGTTGGACTAGATGACCTCC-AAGGTCCCTTCCA 79884
ii- i - -i
CR1L_fAlb#LIN 33 CCTGCTTTGAGCAGGAGGTTGGACTAGA-GACCTCCTGAGGTCCCTTCCA 81
Crub_svsplocu 79885 ACTTTACTATTATT 79898
i v --
CR1L_fAlb#LIN 82 ACCTGA--ATTATT 93
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 11.18
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5)
+ 337 14.6 0.0 0.0 Crub_svsplocus 79848 79895 (570105) + MIR3 SINE/MIR 144 191 (17) 57
ANNOTATION EVIDENCE:
337 14.58 0.00 0.00 Crub_svsplocus 79848 79895 570105 + MIR3 SINE/MIR 144 191 17
337 14.58 0.00 0.00 Crub_svsplocus 79848 79895 (570105) MIR3#SINE/MIR 144 191 (17) m_b2s001i21
Crub_svsplocu 79848 AGGGGGTTGGACTAGATGACCTCCAAGGTCCCTTCCAACTTTACTATT 79895
i i i i ivi
MIR3#SINE/MIR 144 AGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATT 191
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 16.86
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 342 30.2 3.1 3.1 Crub_svsplocus 80338 80610 (569390) C L1M5 LINE/L1 (1480) 4231 3919 58
ANNOTATION EVIDENCE:
312 32.96 3.30 3.30 Crub_svsplocus 80338 80610 569390 C L1-25_DR LINE/L1 3959 4231 1480
312 32.96 3.30 3.30 Crub_svsplocus 80338 80610 (569390) C L1-25_DR#LINE/L1 (1480) 4231 3959 m_b2s001i22
Crub_svsplocu 80338 ATCTGGGAAACCTAAACCTCCCCTTTCTTTGGCATCCT-GTAATGCCTTT 80386
i v i ii v v - vvv- i ii v
C L1-25_DR#LINE 4231 ATTTGGTAAGCCTAAACCTCCTTTATCTTTTG-ATAAAAGCAATGTTTTA 4183
Crub_svsplocu 80387 CATTTTATTCTTGCCTTCTTACTGGACCACACAAATTCTATGGTTAATTT 80436
i i v i vi vvi i ii i viiiv v
C L1-25_DR#LINE 4182 TATTTTATCCTAGCTTTCTTTTTCTGCCATATGAATTTTCCAAATATTTT 4133
Crub_svsplocu 80437 ATTCAGCTCCTTAAAAAATTTCTT------GTCTAGTTGAATTGGGATAT 80480
ii i vvv ---- v------ ivi v -- i v v
C L1-25_DR#LINE 4132 ATCTAACGAATTAAA----TTCTGAGACAGGCACATTT--ACTGGGAGAG 4089
Crub_svsplocu 80481 TCTGAAACAGGAATATCATTTTAGGTAAGATGTTCATTTTCACTGCAGCA 80530
v i ii v vv v i i iv i i i i vv
C L1-25_DR#LINE 4088 ACTGGAACAAAAAAAGAAATCTGGGTAGTATGTTCATTCTTATTACCTCA 4039
Crub_svsplocu 80531 ATTCTCCCAAGTAATGAAAGATGCAAATTTTTCCAACAGTCCAAATCTAC 80580
v v i v v i vvi i v vv ii - i
C L1-25_DR#LINE 4038 ATTCTACCCAGTAATGAGAGAGGAAGAAGCTCCCATCTTTTTAAATC-AT 3990
Crub_svsplocu 80581 TTTTATATT-CTTTACCA-ATTTGCCATAATT 80610
vv -i ii - -i
C L1-25_DR#LINE 3989 TTTTAACTTGTTTTATTAGATTTG-TATAATT 3959
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 44.34
Transitions / transversions = 1.12 (46/41)
Gap_init rate = 0.05 (13 / 272), avg. gap size = 1.38 (18 / 13)
342 26.16 2.73 2.73 Crub_svsplocus 80483 80592 569408 C L1-19_DR LINE/L1 3919 4028 1571
342 26.16 2.73 2.73 Crub_svsplocus 80483 80592 (569408) C L1-19_DR#LINE/L1 (1571) 4028 3919 m_b2s001i23
Crub_svsplocu 80483 TGAAACAGGAATATCATTTTAGGTAAGATGTTCATTTTCACTGCAGCAAT 80532
i ii vv v i v v i i i i ivi
C L1-19_DR#LINE 4028 TGAAATAAAAAATTAATTCTTGGTAATATATTCATTTTTATTACGTTAAT 3979
Crub_svsplocu 80533 TCTCCCAAGTAATGAAA---GATGCAAATTTTTCCAACAGTCCAAATCTA 80579
i i i --- iv --- iv v
C L1-19_DR#LINE 3978 TCTTCCAAGCAGTGAAATGGGGAGCAAATT---CCAACGTTCCAAATCTT 3932
Crub_svsplocu 80580 CTTTTATATTCTT 80592
i v v i
C L1-19_DR#LINE 3931 CCTTAATCTTTTT 3919
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 30.22
Transitions / transversions = 1.55 (17/11)
Gap_init rate = 0.04 (4 / 109), avg. gap size = 1.50 (6 / 4)
+ 395 27.9 5.6 6.5 Crub_svsplocus 80739 80879 (569121) C L1M5 LINE/L1 (1881) 4265 3712 58
ANNOTATION EVIDENCE:
300 31.05 3.54 3.54 Crub_svsplocus 80739 81162 568838 C L1-31_DR LINE/L1 3452 3875 1977
300 31.05 3.54 3.54 Crub_svsplocus 80739 81162 (568838) C L1-31_DR#LINE/L1 (1977) 3875 3452 m_b2s001i24
Crub_svsplocu 80739 TCTTTGTTTTGTTTCTATTTATTTTCAAACTTGC-CAGATCCCCATACTC 80787
v v v v v vv i -i ivv v - i i
C L1-31_DR#LINE 3875 TCTGTGTTTTTTGTATATTTAATTTATAACCTGCATAGGAACCAA-ATTT 3827
Crub_svsplocu 80788 TTCCAATATGTTGAATAGTTTCTGCCCTGATTGTTCTGGGTCTTCTAATA 80837
i i viv v v ivv vvv v- v v v v v
C L1-31_DR#LINE 3826 CTCCAGTAAAGTCATTAGTTCAGGAAGTGAG-GTTGTGGGTGTGCTTAAA 3778
Crub_svsplocu 80838 TAAATGCTAAGT--TGTCTGCATAAGCTTGGAGTTTGTATGTTTCTTTCT 80885
- v i --ii viv vvv i ivi v iiv
C L1-31_DR#LINE 3777 TAAAT-CAAAATATCATCTGCATACAATGCCAGCTTGTGAATATCTCCAT 3729
Crub_svsplocu 80886 TAATCTTAAGTCCTTTAATCTGTTCTTCTTGTCTTA-CTACTCTAGCAAG 80934
v v v vv v v ivvi - i i v iv -
C L1-31_DR#LINE 3728 TTATGTTTATACCTTTAATATTTTTAGTTTGTCTTATCCATTGTGCCAA- 3680
Crub_svsplocu 80935 AATTTCTAATATATATA-TAAATAACAATGGCGCAAGAGGACATCCTTGT 80983
iv - v -i i vi vv i
C L1-31_DR#LINE 3679 AGGTTCTA-TATATAGAGCAAATAACAATGGTGAGATTGGGCATCCTTGT 3631
Crub_svsplocu 80984 CTTGTATCTTTCTGT-ATGTTGAAT-TTATCAGTGGCCTCTCCATTTATT 81031
vi vivi - -- -v i v ivv v
C L1-31_DR#LINE 3630 CTTGTCCCACGTTGTAATGTT--ATGGTGTCTGTGAGGTATCCATTTATT 3583
Crub_svsplocu 81032 ATGATCTGGAC--CT--TTTATTCAGAATATATAGCGGTTATCACGTTTA 81077
v v i i -- -- vvi - i - iv ii viv v
C L1-31_DR#LINE 3582 TTTATCCGGGCTACTGGTTTATTGTAAAT-TGTA-CGAATGCCTTTTATA 3535
Crub_svsplocu 81078 AAATTTTT-TCT---CCAACATCCATTAATTTTAGCTATTGGATCATAAA 81123
i i- v --- - iv i ---v - iv v -
C L1-31_DR#LINE 3534 AAGTTTTCATGTATGCCAA-ATCTTTCAA---GAGCT-TTATATAA-AAA 3491
Crub_svsplocu 81124 TTGCCAATTGACATTATCAAAAGCCTTCTGTGCATCAAG 81162
vvi v vvi vi i
C L1-31_DR#LINE 3490 AGACCAATTTACAGAGTCAAAAGCCTTCTCCGCGTCAAG 3452
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 38.63
Transitions / transversions = 0.65 (50/77)
Gap_init rate = 0.06 (25 / 423), avg. gap size = 1.20 (30 / 25)
395 25.14 4.79 4.79 Crub_svsplocus 80801 80988 569012 C L1M5_orf2 LINE/L1 1969 2156 1138
395 25.14 4.79 4.79 Crub_svsplocus 80801 80988 (569012) C L1M5_orf2#LINE/L1 (1138) 2156 1969 m_b2s001i25
Crub_svsplocu 80801 AATAGTTTCTGCCCTGATTGTTCTGGGTCTTCTA-ATATA-AATGCTAAG 80848
i ? viviv v i? i i -i ? - --i v
C L1M5_orf2#LIN 2156 AGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAAT--CATG 2109
Crub_svsplocu 80849 TTGTCTGC--ATAAGCTTGG-AGTTTGTATGTTTCTTTCTT---AATCTT 80892
ii -- ?--- i- --- i i ---
C L1M5_orf2#LIN 2108 TCATCTGCGAATAAN---GACAGTTT---TATTTCTTCCTTTCCAATCTT 2065
Crub_svsplocu 80893 AAGTCCTTTAATCTGTTCTTCTTGTCTTACTACTCTAGCAAGAATTTCTA 80942
v vv v i v i i i i v i v i ii i
C L1M5_orf2#LIN 2064 TATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCA 2015
Crub_svsplocu 80943 ATATATATAT-AAATAACAATGGCGCAAGAGGACATCCTTGTCTTGT 80988
i i - i -i iv i i v? v
C L1M5_orf2#LIN 2014 GTACA-ATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGT 1969
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 32.03
Transitions / transversions = 2.00 (30/15)
Gap_init rate = 0.08 (15 / 187), avg. gap size = 1.20 (18 / 15)
346 29.43 5.67 5.67 Crub_svsplocus 80825 81159 568841 C L1PREC2_orf2 LINE/L1 1798 2132 1162
346 29.43 5.67 5.67 Crub_svsplocus 80825 81159 (568841) C L1PREC2_orf2#LINE/L1 (1162) 2132 1798 m_b2s001i26
Crub_svsplocu 80825 GGGTCTTCTA-ATATA-AATGCTAAGTTGTCTGCATAAGCTTGGA--GTT 80870
i - - --i v i -- i vv --
C L1PREC2_orf2# 2132 GGGTTTTCTAGATATAGAAT--CATGTCGTCTGCA--AACAGGGATAGTT 2087
Crub_svsplocu 80871 TGTATGTTTCTTTCTTAATCTT---AAGTCCTTTAATCTGTTCTTCTTGT 80917
- i- i i vv v --- v i - i v ii i
C L1PREC2_orf2# 2086 TG-AC-TTCCTCTCTTCCTATTTGGATGCCCTTTA-TTTCTTTCTCTTGC 2040
Crub_svsplocu 80918 CTTACTACTCTAGCAAGAATTTCTAATA-TATATATAAATAACAATGGCG 80966
v i i i v i i i - i - i iv i i
C L1PREC2_orf2# 2039 CTGATTGCTCTGGCCAGGACTTCCAATACTATGT-TGAATAGGAGTGGTG 1991
Crub_svsplocu 80967 CAAGAGGACATCCTTGTCTTGTATCTTTCTGTATGTTGAATTTATCAGTG 81016
vi i ii vv i vi v vv viv --ii
C L1PREC2_orf2# 1990 AGAGAGGGCATCCTTGTCTTGTGCCGGTTTTCAAGGGGAATGCTTC--CA 1943
Crub_svsplocu 81017 GCCTCT--CCATTTATTATGATCTGGACCTTTTATTCAGAATATATAGCG 81064
i i -- i v v v i iv vvi iivv v i v
C L1PREC2_orf2# 1942 GCTTTTGCCCATTCAGTATGATGTTGGCTGTGGGTTTGTCATAGATGGCT 1893
Crub_svsplocu 81065 GTTATCACGTTTAAAAT-TTTTTCTCCAACATCCA-TTAATTT-TAGCTA 81111
v i i- i ii - v i i i i i - v v-v i v
C L1PREC2_orf2# 1892 CTTATTAT-TTTGAGGTATGTTCCTTCAATACCTAGTTTATTGAGAGTTT 1844
Crub_svsplocu 81112 TTGGATCATAAA------TTGCCAATTGACATTATCAAAAGCCTTCTGTG 81155
-- v i ------ -- ---- i i v
C L1PREC2_orf2# 1843 TT--AACATGAAGGGATGTTG--AATT----TTATCGAAAGCCTTTTCTG 1802
Crub_svsplocu 81156 CATC 81159
C L1PREC2_orf2# 1801 CATC 1798
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 37.41
Transitions / transversions = 1.45 (55/38)
Gap_init rate = 0.09 (29 / 334), avg. gap size = 1.31 (38 / 29)
362 31.12 2.00 2.00 Crub_svsplocus 80878 81077 568923 C L1_Mur1_orf2 LINE/L1 2761 2960 1724
362 31.12 2.00 2.00 Crub_svsplocus 80878 81077 (568923) C L1_Mur1_orf2#LINE/L1 (1724) 2960 2761 m_b2s001i27
Crub_svsplocu 80878 TTCTTTCTTAATCTTAAGTCCTTTAATCTGTTCTTCTTGTCTTACTACTC 80927
vii i vv vi i i v i v i ii
C L1_Mur1_orf2# 2960 TTCTTTGCCAATTTGTATCCCCTTGATCTCTTTTTGTTGTCTTATTGTTC 2911
Crub_svsplocu 80928 TAGCAAGAATTTCTAATA-TATATATAAATAACAATGGCGCAAGAGGACA 80976
v v i v i - - i ivv v vi v i
C L1_Mur1_orf2# 2910 TAGCTAGCACTTCGAGTACTATAT-TGAATAGATATGGGGAGAGTGGGCA 2862
Crub_svsplocu 80977 TCCTTGTCTTGTATC---TTTCTGTATGTTGAATTTATCAGTGGCCTCTC 81023
vi --- v iv v viv i -- -ii?
C L1_Mur1_orf2# 2861 TCCTTGTCTTGTCCCCGATTTCAGTGGGATTGCTTCA--AGT-ATNTCTC 2815
Crub_svsplocu 81024 CATTTATTATGATCTGGACCTTTTATTCAGAATATATAGCGGTTATCACG 81073
v v v v i iv vi iiv i v v vv i i
C L1_Mur1_orf2# 2814 CATTTAATTTGATATTGGCTGTTGGTTTGCAGTAAATTGCTTTTATTATG 2765
Crub_svsplocu 81074 TTTA 81077
C L1_Mur1_orf2# 2764 TTTA 2761
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 41.00
Transitions / transversions = 0.97 (30/31)
Gap_init rate = 0.03 (6 / 199), avg. gap size = 1.33 (8 / 6)
303 26.58 6.83 8.31 Crub_svsplocus 81004 81442 568558 C L1-25_DR LINE/L1 3130 3562 2149
303 26.58 6.83 8.31 Crub_svsplocus 81004 81442 (568558) C L1-25_DR#LINE/L1 (2149) 3562 3130 m_b2s001i29
Crub_svsplocu 81004 GAATTT--ATCAGTGGCCTCTC-CATTTATTAT-GATCTGGACCTTTTAT 81049
-- v v i vi - vi v - i v ii
C L1-25_DR#LINE 3562 GAATTTGGAACACTGACCGTTCACCCTTATTCTTGATTTTGACTCTTTAT 3513
Crub_svsplocu 81050 TCAGAATATATAGCGGTTATCACGTTTAAAATTTTTTCTCCAACATCCAT 81099
-- v i v v---- i i- ii v v v i
C L1-25_DR#LINE 3512 --ATAATATGTTGA----ACCAT-TCCACAAATTTTTCTCCAAAACCCAT 3470
Crub_svsplocu 81100 TAATTTTAGCTATTGGATC-ATAAATTGCCAATTGACATTATCAAAAGCC 81148
vv v i - i v v - v v ii vi i i
C L1-25_DR#LINE 3469 TTCTATCAG-TGTTTGCTCTAAAAATAGCCAATCAACTCTATCGAAAGCT 3421
Crub_svsplocu 81149 TTCTGTGCATCAAG---GAACAGAAGTGC---CACTTGAC----GATCAC 81188
vv --- iv v v --- vi v ----v i i
C L1-25_DR#LINE 3420 TTCTCAGCATCAAGACTGAGAAGCATTGCATTCTTTTTACTTTTTACCGC 3371
Crub_svsplocu 81189 TATGCGATTCATAAAATTCAAAAATGCCTAAGATTGTTCTTATATTCCGC 81238
- -i v ---- i ------- i ---v
C L1-25_DR#LINE 3370 TATG-GATT-GTAAATTT----AATGTCT-------TTCTTACATT---A 3337
Crub_svsplocu 81239 TTAGTC---TGTC--TTTTGGTAAAAACCCATTTTGATCCGAATGTATGA 81283
i i--- -- i- v i v i iv v v
C L1-25_DR#LINE 3336 TTGGTTCCATGTCGGTTTTGA-ATAAATCCAGTTTGATCTGGTTTTATTA 3288
Crub_svsplocu 81284 AATCAATTAGGTAC-TTTTTGAATCTA-TCCGCCATTATTGAGGCAAAAA 81331
v vv -- -v iii- i v v v iv v
C L1-25_DR#LINE 3287 CATCTTTTA--TACAATTTTGAATTCGTTTCGCCAATATAGATGTTAATA 3240
Crub_svsplocu 81332 TTTTATAGTCAGAATTCAATAATGAT--ATAGGTCTATAATT-TTGTATC 81378
i viv iv - - i-- v v i - i i
C L1-25_DR#LINE 3239 TTTTGTAGTCTACACACAA-AA-GACTGATAGGACGATAACTATTGCATT 3192
Crub_svsplocu 81379 -CAT--GTTTTTTTCCGCTTCTTCTTTTGGAAT--CAATATTATATTTGC 81423
- i -- v i v -- -- v iv --ii v ---
C L1-25_DR#LINE 3191 GCGTAGGATCTTTAC--CTTC--CTTATACAATACTGAAATTATA---GC 3149
Crub_svsplocu 81424 CTCTGACCAGGACTTAGGT 81442
v v i v
C L1-25_DR#LINE 3148 ATCTGACCATGATTTTGGT 3130
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 31.51
Transitions / transversions = 0.88 (50/57)
Gap_init rate = 0.12 (52 / 438), avg. gap size = 1.27 (66 / 52)
338 29.80 6.03 7.17 Crub_svsplocus 81127 81408 568592 C L1-67_DR LINE/L1 2772 3050 2318
338 29.80 6.03 7.17 Crub_svsplocus 81127 81408 (568592) C L1-67_DR#LINE/L1 (2318) 3050 2772 m_b2s001i30
Crub_svsplocu 81127 CCAATTGACATTATCAAAAGCCTTCTGTGCATCAAGGAACAGAAG----- 81171
vvv i i i v ivvi -----
C L1-67_DR#LINE 3050 CCAATTGACTGAATCAAAGGCTTTTTCTGCATCAAGACTTAGAAGAACAG 3001
Crub_svsplocu 81172 -TGCCACTTGACGATCACTA-TGCGATTCATAAAATTCAAAAAT--GCCT 81217
- v i v vii iiv - ii i v i v- v i i -- i
C L1-67_DR#LINE 3000 CTGGCACCTTAGAGTCGTGAATATGACTGATGAT-TTGAAGAGTTCGTCT 2952
Crub_svsplocu 81218 AAGATTGTTCTTATATTCCGCTTAGTCTGTCTTTTGGTAAA--AACCCAT 81265
v i -i i i------ i i ----- i -- i iv
C L1-67_DR#LINE 2951 AACATTGTCCT-GTGTTT------GCCTGCC-----GCAAATAAATCCGG 2914
Crub_svsplocu 81266 TTTGATCCGAATGTATGAAATCA---ATTAGGTACTTTTTGAATCTATCC 81312
v vv v v v--- - v i--i i v iv
C L1-67_DR#LINE 2913 TTTGATCAGAATTAATTAATTCCGGCATTAG-TAGTTC--AAGTCTTTTA 2867
Crub_svsplocu 81313 GCCATTATTGAGGCAAAAATTTTATAGTCAGAATTCAATAATGATATAGG 81362
i vv i i i v viv i i vi
C L1-67_DR#LINE 2866 GCTAGGACTGAGGTAAAGAGTTTATAGTCTATATTTAGTACCGATATAGG 2817
Crub_svsplocu 81363 TCTATAAT-TTTGTATCCATGTT--TTTTTCCGCTTCTTCTTTTGGAAT 81408
i v- v ii ii v v -- ---- i
C L1-67_DR#LINE 2816 TCTGTAAGATGTACACTCTTCTTTATTTTTCC----CTTCTTTTGGGAT 2772
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 36.95
Transitions / transversions = 1.29 (44/34)
Gap_init rate = 0.10 (28 / 281), avg. gap size = 1.32 (37 / 28)
232 31.03 4.56 5.46 Crub_svsplocus 81225 81575 568425 C L1-35_DR LINE/L1 2879 3226 2255
232 31.03 4.56 5.46 Crub_svsplocus 81225 81575 (568425) C L1-35_DR#LINE/L1 (2255) 3226 2879 m_b2s001i31
Crub_svsplocu 81225 TTCTTATATTCCGCTTAGTCTGTCTTT-TGGTAAAAACCCATTTTGATCC 81273
vi vv viv i- v v i i i
C L1-35_DR#LINE 3226 TTCTTATATTATGGATAGTGCTTCTTCCTGGAATAAATCCATTCTGATCT 3177
Crub_svsplocu 81274 GAATGTATGAAATCAATT-A--GGTACTTTTT--GAATCTATCCGCCATT 81318
-- i - -- i - -- i vv v-- ii iv v v
C L1-35_DR#LINE 3176 --ACGT-T--AACCAATTTATTGATAAATTTACAGAGCCTATTAGCGAGT 3132
Crub_svsplocu 81319 ATTG-AGGCAAAAATTTTATAGTCAGAATTCAATAATGATATAGGTCTAT 81367
i v- i v v - ii iv v iv iv v
C L1-35_DR#LINE 3131 GTTTTAGACAATATTTTT-TGATCAACATTGAGGAGAGAGATAGGTCTAT 3083
Crub_svsplocu 81368 AATTTTGTATCCATGTTTTTTTCCGCTTCT-TCTTTT---GGAATCAATA 81413
----i iv v i- i i vvii i - --- i v i
C L1-35_DR#LINE 3082 A----CGCCTCAAC-TTCTTCTGGATTTTTATCTTTTTTAGGAATTACTG 3038
Crub_svsplocu 81414 TTATATTTGCCTCTGACCAGGACTT--AGGTATTTTAGCATCGGTTAATA 81461
v v v v vv i -- -- v ii iv --- i
C L1-35_DR#LINE 3037 TAATAATAGCCTCAGAGAAAG--TTGGAGGTAGTCCAGTTT---TTAATG 2993
Crub_svsplocu 81462 CGGCATTGAAAACTTCTA-GTAGGTATTGATTGAGTACATGTTGTTG--T 81508
v-ii iv i - i ii v v i -- v ii --
C L1-35_DR#LINE 2992 CC-TGTTGAAAGGTTTTAAGCAAATATGGAGTAAGTA--TGTGGCCGAAT 2946
Crub_svsplocu 81509 TCTTTATATAGTTCCACTGGTATTCCATCTGGGCCAGTCGCCTTATTGAT 81558
i vi v i vi i vv ii iv v
C L1-35_DR#LINE 2945 TTTTTATATAGTTCAGCAGGCAGCCCATCTGGACCAGGAGTTTTACAGTT 2896
Crub_svsplocu 81559 CTTTTGTTTATTTATAG 81575
i vivv
C L1-35_DR#LINE 2895 TTTTAAAGTATTTATAG 2879
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 39.24
Transitions / transversions = 1.10 (54/49)
Gap_init rate = 0.08 (29 / 350), avg. gap size = 1.21 (35 / 29)
+ 348 34.8 3.1 3.7 Crub_svsplocus 80880 81366 (568634) C Nimb-4_DR LINE/I (3905) 5756 5273 59
ANNOTATION EVIDENCE:
348 34.76 3.08 3.72 Crub_svsplocus 80880 81366 568634 C Nimb-4_DR LINE/I 5273 5756 3905
348 34.76 3.08 3.72 Crub_svsplocus 80880 81366 (568634) C Nimb-4_DR#LINE/I (3905) 5756 5273 m_b2s001i28
Crub_svsplocu 80880 CTTTCTTAATCTTAAGTCCTTTAATCTGTTCTTCTTGTCTTACTACTCTA 80929
i v v vi iii ivi i v v i i iivi
C Nimb-4_DR#LIN 5756 CCTTATTAATGTTAATCCCCCCAATTGATTTTTCTTCTCTAATTGCCTGG 5707
Crub_svsplocu 80930 GCAAGAATTTCTAATATATATA-TAAATAACAATGGCGCAAGAGGACATC 80978
v iv - i i i-i i v iv v vi i v
C Nimb-4_DR#LIN 5706 GCTAGAGGTTC-AATGTACATGGCAAACATCAGGGGAGAGAGGGGACAAC 5658
Crub_svsplocu 80979 CTTGTCTTGTATCTTTCTGTATGTTGAAT---TTATCAGTGGCCTCTCCA 81025
i i v vi i v - vv --- v v iv i vv -- i
C Nimb-4_DR#LIN 5657 CCTGCCTAGTTCCTTTTTCTA-GTTTTATCTTTTTTGAAAGACAAC--CG 5611
Crub_svsplocu 81026 TTTATTATGATCTGGACCTTTTATTCAGAATATATAGCGGTTATCACGTT 81075
v v ivii i viv iv - i iv v vvi v i
C Nimb-4_DR#LIN 5610 TTTATTTTTATCCTAGCCTCTGGGTTTGAATATA-AACATTGAAAGCTTC 5562
Crub_svsplocu 81076 TAAA-ATTTTTTCTCCAACATCCA--TTAATTTTAGCTATTGGATCATAA 81122
v-i v vi - -- iv v ivi ii v - v
C Nimb-4_DR#LIN 5561 TAACTGTATTTTCTGTAA-ATCCAAATCTATATTAAACATTAAATAA-AT 5514
Crub_svsplocu 81123 ATTGCCAATTGACATTATCAAAAGCCTTCTGTGCATCAAGG--AAC-AGA 81169
v v ivi i v v -- - i
C Nimb-4_DR#LIN 5513 ATTCCCAATTTACACAGTCAAAAGCTTTCTCTGCATCTAGGCTAACTAAA 5464
Crub_svsplocu 81170 AGTGCCACTTGACG--ATCACTATGCGATTCATAAAATTCAAAAATGCCT 81217
v i-- i i -- vi - vii ii viv ------- v
C Nimb-4_DR#LIN 5463 ATTGCT--TTAATGTGATCTTT-TTTAATTTGTCGTATT-------GCAT 5424
Crub_svsplocu 81218 AAGATTGTTCTT--ATATTCCGCTTAGTCTGTCTTTTGGTAA-AAACCCA 81264
i - v i -- vivi v i v iivv - v
C Nimb-4_DR#LIN 5423 GA-AGTGTCCTTCTATATTATCTTGAGTCTGCCGTCCTCTAATAAACCCT 5375
Crub_svsplocu 81265 TTTTGATCCGAATGTATGAAATCAATTAGGTACTTTTTGAATCTATCCGC 81314
v iivi v v iv iiv iv ii i v iv
C Nimb-4_DR#LIN 5374 GTTTGATCTATGTCTATCAAATCAGGTAAAAATGTTTCAAGTCTCTTGGC 5325
Crub_svsplocu 81315 CATTATTGAGGCAAAAATTTTATAGTCAGAATTCAATAATGATATAGGTC 81364
i vv v v v viv i v vv i i
C Nimb-4_DR#LIN 5324 TAAAATAGAGGCAAATAATTTATAGTCTACATTTAAAACAGACACAGGTC 5275
Crub_svsplocu 81365 TA 81366
C Nimb-4_DR#LIN 5274 TA 5273
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 46.74
Transitions / transversions = 1.01 (82/81)
Gap_init rate = 0.06 (27 / 486), avg. gap size = 1.22 (33 / 27)
+ 395 27.9 5.6 6.5 Crub_svsplocus 81367 81575 (568425) C L1M5 LINE/L1 (1881) 3711 2879 58
ANNOTATION EVIDENCE:
300 31.05 3.54 3.54 Crub_svsplocus 80739 81162 568838 C L1-31_DR LINE/L1 3452 3875 1977
300 31.05 3.54 3.54 Crub_svsplocus 80739 81162 (568838) C L1-31_DR#LINE/L1 (1977) 3875 3452 m_b2s001i24
Crub_svsplocu 80739 TCTTTGTTTTGTTTCTATTTATTTTCAAACTTGC-CAGATCCCCATACTC 80787
v v v v v vv i -i ivv v - i i
C L1-31_DR#LINE 3875 TCTGTGTTTTTTGTATATTTAATTTATAACCTGCATAGGAACCAA-ATTT 3827
Crub_svsplocu 80788 TTCCAATATGTTGAATAGTTTCTGCCCTGATTGTTCTGGGTCTTCTAATA 80837
i i viv v v ivv vvv v- v v v v v
C L1-31_DR#LINE 3826 CTCCAGTAAAGTCATTAGTTCAGGAAGTGAG-GTTGTGGGTGTGCTTAAA 3778
Crub_svsplocu 80838 TAAATGCTAAGT--TGTCTGCATAAGCTTGGAGTTTGTATGTTTCTTTCT 80885
- v i --ii viv vvv i ivi v iiv
C L1-31_DR#LINE 3777 TAAAT-CAAAATATCATCTGCATACAATGCCAGCTTGTGAATATCTCCAT 3729
Crub_svsplocu 80886 TAATCTTAAGTCCTTTAATCTGTTCTTCTTGTCTTA-CTACTCTAGCAAG 80934
v v v vv v v ivvi - i i v iv -
C L1-31_DR#LINE 3728 TTATGTTTATACCTTTAATATTTTTAGTTTGTCTTATCCATTGTGCCAA- 3680
Crub_svsplocu 80935 AATTTCTAATATATATA-TAAATAACAATGGCGCAAGAGGACATCCTTGT 80983
iv - v -i i vi vv i
C L1-31_DR#LINE 3679 AGGTTCTA-TATATAGAGCAAATAACAATGGTGAGATTGGGCATCCTTGT 3631
Crub_svsplocu 80984 CTTGTATCTTTCTGT-ATGTTGAAT-TTATCAGTGGCCTCTCCATTTATT 81031
vi vivi - -- -v i v ivv v
C L1-31_DR#LINE 3630 CTTGTCCCACGTTGTAATGTT--ATGGTGTCTGTGAGGTATCCATTTATT 3583
Crub_svsplocu 81032 ATGATCTGGAC--CT--TTTATTCAGAATATATAGCGGTTATCACGTTTA 81077
v v i i -- -- vvi - i - iv ii viv v
C L1-31_DR#LINE 3582 TTTATCCGGGCTACTGGTTTATTGTAAAT-TGTA-CGAATGCCTTTTATA 3535
Crub_svsplocu 81078 AAATTTTT-TCT---CCAACATCCATTAATTTTAGCTATTGGATCATAAA 81123
i i- v --- - iv i ---v - iv v -
C L1-31_DR#LINE 3534 AAGTTTTCATGTATGCCAA-ATCTTTCAA---GAGCT-TTATATAA-AAA 3491
Crub_svsplocu 81124 TTGCCAATTGACATTATCAAAAGCCTTCTGTGCATCAAG 81162
vvi v vvi vi i
C L1-31_DR#LINE 3490 AGACCAATTTACAGAGTCAAAAGCCTTCTCCGCGTCAAG 3452
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 38.63
Transitions / transversions = 0.65 (50/77)
Gap_init rate = 0.06 (25 / 423), avg. gap size = 1.20 (30 / 25)
395 25.14 4.79 4.79 Crub_svsplocus 80801 80988 569012 C L1M5_orf2 LINE/L1 1969 2156 1138
395 25.14 4.79 4.79 Crub_svsplocus 80801 80988 (569012) C L1M5_orf2#LINE/L1 (1138) 2156 1969 m_b2s001i25
Crub_svsplocu 80801 AATAGTTTCTGCCCTGATTGTTCTGGGTCTTCTA-ATATA-AATGCTAAG 80848
i ? viviv v i? i i -i ? - --i v
C L1M5_orf2#LIN 2156 AGTAGTTTNTTTGTAGATTCTTTNGGATTTTCTACGTANACAAT--CATG 2109
Crub_svsplocu 80849 TTGTCTGC--ATAAGCTTGG-AGTTTGTATGTTTCTTTCTT---AATCTT 80892
ii -- ?--- i- --- i i ---
C L1M5_orf2#LIN 2108 TCATCTGCGAATAAN---GACAGTTT---TATTTCTTCCTTTCCAATCTT 2065
Crub_svsplocu 80893 AAGTCCTTTAATCTGTTCTTCTTGTCTTACTACTCTAGCAAGAATTTCTA 80942
v vv v i v i i i i v i v i ii i
C L1M5_orf2#LIN 2064 TATGCCTTTTATTTCTTTTTCTTGCCTTATTGCACTGGCTAGGACCTCCA 2015
Crub_svsplocu 80943 ATATATATAT-AAATAACAATGGCGCAAGAGGACATCCTTGTCTTGT 80988
i i - i -i iv i i v? v
C L1M5_orf2#LIN 2014 GTACA-ATGTTGAATAGAAGTGGTGANAGCGGACATCCTTGTCTTGT 1969
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 32.03
Transitions / transversions = 2.00 (30/15)
Gap_init rate = 0.08 (15 / 187), avg. gap size = 1.20 (18 / 15)
346 29.43 5.67 5.67 Crub_svsplocus 80825 81159 568841 C L1PREC2_orf2 LINE/L1 1798 2132 1162
346 29.43 5.67 5.67 Crub_svsplocus 80825 81159 (568841) C L1PREC2_orf2#LINE/L1 (1162) 2132 1798 m_b2s001i26
Crub_svsplocu 80825 GGGTCTTCTA-ATATA-AATGCTAAGTTGTCTGCATAAGCTTGGA--GTT 80870
i - - --i v i -- i vv --
C L1PREC2_orf2# 2132 GGGTTTTCTAGATATAGAAT--CATGTCGTCTGCA--AACAGGGATAGTT 2087
Crub_svsplocu 80871 TGTATGTTTCTTTCTTAATCTT---AAGTCCTTTAATCTGTTCTTCTTGT 80917
- i- i i vv v --- v i - i v ii i
C L1PREC2_orf2# 2086 TG-AC-TTCCTCTCTTCCTATTTGGATGCCCTTTA-TTTCTTTCTCTTGC 2040
Crub_svsplocu 80918 CTTACTACTCTAGCAAGAATTTCTAATA-TATATATAAATAACAATGGCG 80966
v i i i v i i i - i - i iv i i
C L1PREC2_orf2# 2039 CTGATTGCTCTGGCCAGGACTTCCAATACTATGT-TGAATAGGAGTGGTG 1991
Crub_svsplocu 80967 CAAGAGGACATCCTTGTCTTGTATCTTTCTGTATGTTGAATTTATCAGTG 81016
vi i ii vv i vi v vv viv --ii
C L1PREC2_orf2# 1990 AGAGAGGGCATCCTTGTCTTGTGCCGGTTTTCAAGGGGAATGCTTC--CA 1943
Crub_svsplocu 81017 GCCTCT--CCATTTATTATGATCTGGACCTTTTATTCAGAATATATAGCG 81064
i i -- i v v v i iv vvi iivv v i v
C L1PREC2_orf2# 1942 GCTTTTGCCCATTCAGTATGATGTTGGCTGTGGGTTTGTCATAGATGGCT 1893
Crub_svsplocu 81065 GTTATCACGTTTAAAAT-TTTTTCTCCAACATCCA-TTAATTT-TAGCTA 81111
v i i- i ii - v i i i i i - v v-v i v
C L1PREC2_orf2# 1892 CTTATTAT-TTTGAGGTATGTTCCTTCAATACCTAGTTTATTGAGAGTTT 1844
Crub_svsplocu 81112 TTGGATCATAAA------TTGCCAATTGACATTATCAAAAGCCTTCTGTG 81155
-- v i ------ -- ---- i i v
C L1PREC2_orf2# 1843 TT--AACATGAAGGGATGTTG--AATT----TTATCGAAAGCCTTTTCTG 1802
Crub_svsplocu 81156 CATC 81159
C L1PREC2_orf2# 1801 CATC 1798
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 37.41
Transitions / transversions = 1.45 (55/38)
Gap_init rate = 0.09 (29 / 334), avg. gap size = 1.31 (38 / 29)
362 31.12 2.00 2.00 Crub_svsplocus 80878 81077 568923 C L1_Mur1_orf2 LINE/L1 2761 2960 1724
362 31.12 2.00 2.00 Crub_svsplocus 80878 81077 (568923) C L1_Mur1_orf2#LINE/L1 (1724) 2960 2761 m_b2s001i27
Crub_svsplocu 80878 TTCTTTCTTAATCTTAAGTCCTTTAATCTGTTCTTCTTGTCTTACTACTC 80927
vii i vv vi i i v i v i ii
C L1_Mur1_orf2# 2960 TTCTTTGCCAATTTGTATCCCCTTGATCTCTTTTTGTTGTCTTATTGTTC 2911
Crub_svsplocu 80928 TAGCAAGAATTTCTAATA-TATATATAAATAACAATGGCGCAAGAGGACA 80976
v v i v i - - i ivv v vi v i
C L1_Mur1_orf2# 2910 TAGCTAGCACTTCGAGTACTATAT-TGAATAGATATGGGGAGAGTGGGCA 2862
Crub_svsplocu 80977 TCCTTGTCTTGTATC---TTTCTGTATGTTGAATTTATCAGTGGCCTCTC 81023
vi --- v iv v viv i -- -ii?
C L1_Mur1_orf2# 2861 TCCTTGTCTTGTCCCCGATTTCAGTGGGATTGCTTCA--AGT-ATNTCTC 2815
Crub_svsplocu 81024 CATTTATTATGATCTGGACCTTTTATTCAGAATATATAGCGGTTATCACG 81073
v v v v i iv vi iiv i v v vv i i
C L1_Mur1_orf2# 2814 CATTTAATTTGATATTGGCTGTTGGTTTGCAGTAAATTGCTTTTATTATG 2765
Crub_svsplocu 81074 TTTA 81077
C L1_Mur1_orf2# 2764 TTTA 2761
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 41.00
Transitions / transversions = 0.97 (30/31)
Gap_init rate = 0.03 (6 / 199), avg. gap size = 1.33 (8 / 6)
303 26.58 6.83 8.31 Crub_svsplocus 81004 81442 568558 C L1-25_DR LINE/L1 3130 3562 2149
303 26.58 6.83 8.31 Crub_svsplocus 81004 81442 (568558) C L1-25_DR#LINE/L1 (2149) 3562 3130 m_b2s001i29
Crub_svsplocu 81004 GAATTT--ATCAGTGGCCTCTC-CATTTATTAT-GATCTGGACCTTTTAT 81049
-- v v i vi - vi v - i v ii
C L1-25_DR#LINE 3562 GAATTTGGAACACTGACCGTTCACCCTTATTCTTGATTTTGACTCTTTAT 3513
Crub_svsplocu 81050 TCAGAATATATAGCGGTTATCACGTTTAAAATTTTTTCTCCAACATCCAT 81099
-- v i v v---- i i- ii v v v i
C L1-25_DR#LINE 3512 --ATAATATGTTGA----ACCAT-TCCACAAATTTTTCTCCAAAACCCAT 3470
Crub_svsplocu 81100 TAATTTTAGCTATTGGATC-ATAAATTGCCAATTGACATTATCAAAAGCC 81148
vv v i - i v v - v v ii vi i i
C L1-25_DR#LINE 3469 TTCTATCAG-TGTTTGCTCTAAAAATAGCCAATCAACTCTATCGAAAGCT 3421
Crub_svsplocu 81149 TTCTGTGCATCAAG---GAACAGAAGTGC---CACTTGAC----GATCAC 81188
vv --- iv v v --- vi v ----v i i
C L1-25_DR#LINE 3420 TTCTCAGCATCAAGACTGAGAAGCATTGCATTCTTTTTACTTTTTACCGC 3371
Crub_svsplocu 81189 TATGCGATTCATAAAATTCAAAAATGCCTAAGATTGTTCTTATATTCCGC 81238
- -i v ---- i ------- i ---v
C L1-25_DR#LINE 3370 TATG-GATT-GTAAATTT----AATGTCT-------TTCTTACATT---A 3337
Crub_svsplocu 81239 TTAGTC---TGTC--TTTTGGTAAAAACCCATTTTGATCCGAATGTATGA 81283
i i--- -- i- v i v i iv v v
C L1-25_DR#LINE 3336 TTGGTTCCATGTCGGTTTTGA-ATAAATCCAGTTTGATCTGGTTTTATTA 3288
Crub_svsplocu 81284 AATCAATTAGGTAC-TTTTTGAATCTA-TCCGCCATTATTGAGGCAAAAA 81331
v vv -- -v iii- i v v v iv v
C L1-25_DR#LINE 3287 CATCTTTTA--TACAATTTTGAATTCGTTTCGCCAATATAGATGTTAATA 3240
Crub_svsplocu 81332 TTTTATAGTCAGAATTCAATAATGAT--ATAGGTCTATAATT-TTGTATC 81378
i viv iv - - i-- v v i - i i
C L1-25_DR#LINE 3239 TTTTGTAGTCTACACACAA-AA-GACTGATAGGACGATAACTATTGCATT 3192
Crub_svsplocu 81379 -CAT--GTTTTTTTCCGCTTCTTCTTTTGGAAT--CAATATTATATTTGC 81423
- i -- v i v -- -- v iv --ii v ---
C L1-25_DR#LINE 3191 GCGTAGGATCTTTAC--CTTC--CTTATACAATACTGAAATTATA---GC 3149
Crub_svsplocu 81424 CTCTGACCAGGACTTAGGT 81442
v v i v
C L1-25_DR#LINE 3148 ATCTGACCATGATTTTGGT 3130
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 31.51
Transitions / transversions = 0.88 (50/57)
Gap_init rate = 0.12 (52 / 438), avg. gap size = 1.27 (66 / 52)
338 29.80 6.03 7.17 Crub_svsplocus 81127 81408 568592 C L1-67_DR LINE/L1 2772 3050 2318
338 29.80 6.03 7.17 Crub_svsplocus 81127 81408 (568592) C L1-67_DR#LINE/L1 (2318) 3050 2772 m_b2s001i30
Crub_svsplocu 81127 CCAATTGACATTATCAAAAGCCTTCTGTGCATCAAGGAACAGAAG----- 81171
vvv i i i v ivvi -----
C L1-67_DR#LINE 3050 CCAATTGACTGAATCAAAGGCTTTTTCTGCATCAAGACTTAGAAGAACAG 3001
Crub_svsplocu 81172 -TGCCACTTGACGATCACTA-TGCGATTCATAAAATTCAAAAAT--GCCT 81217
- v i v vii iiv - ii i v i v- v i i -- i
C L1-67_DR#LINE 3000 CTGGCACCTTAGAGTCGTGAATATGACTGATGAT-TTGAAGAGTTCGTCT 2952
Crub_svsplocu 81218 AAGATTGTTCTTATATTCCGCTTAGTCTGTCTTTTGGTAAA--AACCCAT 81265
v i -i i i------ i i ----- i -- i iv
C L1-67_DR#LINE 2951 AACATTGTCCT-GTGTTT------GCCTGCC-----GCAAATAAATCCGG 2914
Crub_svsplocu 81266 TTTGATCCGAATGTATGAAATCA---ATTAGGTACTTTTTGAATCTATCC 81312
v vv v v v--- - v i--i i v iv
C L1-67_DR#LINE 2913 TTTGATCAGAATTAATTAATTCCGGCATTAG-TAGTTC--AAGTCTTTTA 2867
Crub_svsplocu 81313 GCCATTATTGAGGCAAAAATTTTATAGTCAGAATTCAATAATGATATAGG 81362
i vv i i i v viv i i vi
C L1-67_DR#LINE 2866 GCTAGGACTGAGGTAAAGAGTTTATAGTCTATATTTAGTACCGATATAGG 2817
Crub_svsplocu 81363 TCTATAAT-TTTGTATCCATGTT--TTTTTCCGCTTCTTCTTTTGGAAT 81408
i v- v ii ii v v -- ---- i
C L1-67_DR#LINE 2816 TCTGTAAGATGTACACTCTTCTTTATTTTTCC----CTTCTTTTGGGAT 2772
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 36.95
Transitions / transversions = 1.29 (44/34)
Gap_init rate = 0.10 (28 / 281), avg. gap size = 1.32 (37 / 28)
232 31.03 4.56 5.46 Crub_svsplocus 81225 81575 568425 C L1-35_DR LINE/L1 2879 3226 2255
232 31.03 4.56 5.46 Crub_svsplocus 81225 81575 (568425) C L1-35_DR#LINE/L1 (2255) 3226 2879 m_b2s001i31
Crub_svsplocu 81225 TTCTTATATTCCGCTTAGTCTGTCTTT-TGGTAAAAACCCATTTTGATCC 81273
vi vv viv i- v v i i i
C L1-35_DR#LINE 3226 TTCTTATATTATGGATAGTGCTTCTTCCTGGAATAAATCCATTCTGATCT 3177
Crub_svsplocu 81274 GAATGTATGAAATCAATT-A--GGTACTTTTT--GAATCTATCCGCCATT 81318
-- i - -- i - -- i vv v-- ii iv v v
C L1-35_DR#LINE 3176 --ACGT-T--AACCAATTTATTGATAAATTTACAGAGCCTATTAGCGAGT 3132
Crub_svsplocu 81319 ATTG-AGGCAAAAATTTTATAGTCAGAATTCAATAATGATATAGGTCTAT 81367
i v- i v v - ii iv v iv iv v
C L1-35_DR#LINE 3131 GTTTTAGACAATATTTTT-TGATCAACATTGAGGAGAGAGATAGGTCTAT 3083
Crub_svsplocu 81368 AATTTTGTATCCATGTTTTTTTCCGCTTCT-TCTTTT---GGAATCAATA 81413
----i iv v i- i i vvii i - --- i v i
C L1-35_DR#LINE 3082 A----CGCCTCAAC-TTCTTCTGGATTTTTATCTTTTTTAGGAATTACTG 3038
Crub_svsplocu 81414 TTATATTTGCCTCTGACCAGGACTT--AGGTATTTTAGCATCGGTTAATA 81461
v v v v vv i -- -- v ii iv --- i
C L1-35_DR#LINE 3037 TAATAATAGCCTCAGAGAAAG--TTGGAGGTAGTCCAGTTT---TTAATG 2993
Crub_svsplocu 81462 CGGCATTGAAAACTTCTA-GTAGGTATTGATTGAGTACATGTTGTTG--T 81508
v-ii iv i - i ii v v i -- v ii --
C L1-35_DR#LINE 2992 CC-TGTTGAAAGGTTTTAAGCAAATATGGAGTAAGTA--TGTGGCCGAAT 2946
Crub_svsplocu 81509 TCTTTATATAGTTCCACTGGTATTCCATCTGGGCCAGTCGCCTTATTGAT 81558
i vi v i vi i vv ii iv v
C L1-35_DR#LINE 2945 TTTTTATATAGTTCAGCAGGCAGCCCATCTGGACCAGGAGTTTTACAGTT 2896
Crub_svsplocu 81559 CTTTTGTTTATTTATAG 81575
i vivv
C L1-35_DR#LINE 2895 TTTTAAAGTATTTATAG 2879
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 39.24
Transitions / transversions = 1.10 (54/49)
Gap_init rate = 0.08 (29 / 350), avg. gap size = 1.21 (35 / 29)
+ 240 23.5 1.8 11.9 Crub_svsplocus 82075 82185 (567815) C L1M1 LINE/L1 (3146) 3000 2900 60
ANNOTATION EVIDENCE:
240 23.51 1.80 11.88 Crub_svsplocus 82075 82185 567815 C L1M1_orf2 LINE/L1 791 891 2403
240 23.51 1.80 11.88 Crub_svsplocus 82075 82185 (567815) C L1M1_orf2#LINE/L1 (2403) 891 791 m_b2s001i32
Crub_svsplocu 82075 CCCTCAT-GTA-TGCTTTTGCCGTATCCCAAATGTTCTGCAAGGATGTAT 82122
v - - i v v i vv v v i
C L1M1_orf2#LIN 891 CCCTCTTAGTACTGCTTTTGCTGTATCCCATAGGTTTTGGTATGTTGTGT 842
Crub_svsplocu 82123 CCTCATTGTCATTTGCTTGAAAGAAAAGGTGCATCTCTTTCTCCATTCTT 82172
iii i i v- ----------- i v iii
C L1M1_orf2#LIN 841 TTCCATTATCATTTGTTTC-AAGAAA-----------TTTTTCAATTTCC 804
Crub_svsplocu 82173 TCCTTAAATTCTT 82185
i v
C L1M1_orf2#LIN 803 TTCTTAATTTCTT 791
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 28.24
Transitions / transversions = 1.30 (13/10)
Gap_init rate = 0.13 (14 / 110), avg. gap size = 1.00 (14 / 14)
+ 260 25.2 5.6 5.6 Crub_svsplocus 82259 82384 (567616) C L1M3 LINE/L1 (3338) 2802 2677 61
ANNOTATION EVIDENCE:
260 25.21 5.56 5.56 Crub_svsplocus 82259 82384 567616 C L1M3_orf2 LINE/L1 568 693 2595
260 25.21 5.56 5.56 Crub_svsplocus 82259 82384 (567616) C L1M3_orf2#LINE/L1 (2595) 693 568 m_b2s001i33
Crub_svsplocu 82259 ATTATGGTCTGCCCAAATGCTAGGTTCAATATCAAT-TTCTTGAATTTCC 82307
i v vvv i i v vii v - i --
C L1M3_orf2#LIN 693 ATTGTGGTCGGAAAAGATACTTGGTATGATTTCAATCTTCTTAAATTT-- 646
Crub_svsplocu 82308 GAGGCTAA---TTCTTTTGTAAACCATAGCATGT---CTATCCTGGTCCA 82351
--- i --- v ii- - i --- vvv
C L1M3_orf2#LIN 645 ---GTTAAGACTTGTTTTGTGG-CC-TAACATGTGATCTATCCTGGAGAA 601
Crub_svsplocu 82352 TGATCTGTGTCTATTAGAAAAGTATGTGTATTC 82384
v i viii v i v
C L1M3_orf2#LIN 600 TGTTCCGTGTGCGCTTGAGAAGAATGTGTATTC 568
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 28.51
Transitions / transversions = 1.00 (15/15)
Gap_init rate = 0.08 (10 / 125), avg. gap size = 1.40 (14 / 10)
+ 282 31.5 7.4 2.7 Crub_svsplocus 89188 89363 (560637) + BEL11-I_DR LTR/Pao 1547 1730 (4269) 62
ANNOTATION EVIDENCE:
282 31.54 7.39 2.72 Crub_svsplocus 89188 89363 560637 + BEL11-I_DR LTR/Pao 1547 1730 4269
282 31.54 7.39 2.72 Crub_svsplocus 89188 89363 (560637) BEL11-I_DR#LTR/Pao 1547 1730 (4269) m_b2s001i34
Crub_svsplocu 89188 TGTCCAATTCATAAATCTTCACATTCTCTAAACAACTGCAAAGAATTTGG 89237
v vvvi i i v iv v i i iv ii
BEL11-I_DR#LT 1547 TGTCCTATTCATAAAAAGCCACATCCCCTCAGAAAGTGTAGAGGTTTCAG 1596
Crub_svsplocu 89238 AAGAAAGTCCTTGGATGATCGAAAGGCCCTGCTCAAAGAGCATAGGATAT 89287
iiii v vvv iv i i ii v i v ivvv v
BEL11-I_DR#LT 1597 GGAGAAGACCTTGCTGGACAGGAAAGCTTTCCTCAGAGAGAACTCCATTT 1646
Crub_svsplocu 89288 GCTTCAAGTACTAT-----GACT---CACATGGCCAAAGATTGC---GCA 89326
i i i i ----- --- vv v i i---
BEL11-I_DR#LT 1647 GCTTTAAATGCTGTTCCTCGACTACCCACCAGGCAAAGGATTGTAAGGCA 1696
Crub_svsplocu 89327 GTTAAGGTGAAATGCCACCTG--TATAACAGTGACAAGC 89363
- -- vv i --i -- ii
BEL11-I_DR#LT 1697 G-TAA--TCCAGTGC--TCTGAATGCAACAGTGACAAGC 1730
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 42.02
Transitions / transversions = 1.25 (30/24)
Gap_init rate = 0.05 (9 / 175), avg. gap size = 2.00 (18 / 9)
+ 278 34.1 3.4 3.4 Crub_svsplocus 94339 94599 (555401) C Gypsy72-I_DR LTR/Gypsy (779) 3542 3286 63
ANNOTATION EVIDENCE:
232 33.66 3.76 3.76 Crub_svsplocus 94339 94551 555449 C Gypsy3-I_DR LTR/Gypsy 3330 3542 779
232 33.66 3.76 3.76 Crub_svsplocus 94339 94551 (555449) C Gypsy3-I_DR#LTR/Gypsy (779) 3542 3330 m_b2s001i35
Crub_svsplocu 94339 TTCCATTTGTCCATCTG--TCTGAGGGTGATGGCTAGATG-TCAGTCCCT 94385
i i -- -- ivii ii v - v -- i
C Gypsy3-I_DR#L 3542 TTCCGTTTGTCCATTTGATTCTG--GGTGGAAACCGGAGGATAAG--CTT 3497
Crub_svsplocu 94386 G-AGTGGTCCCTAAGAGGGAT---AAAAATTCTTTCCAAAATGCAGATGT 94431
- --- ---v i iv v i vvi v v
C Gypsy3-I_DR#L 3496 GTAGTGGTCCCT---AGGGATTGACAGAACGCTTGCCAGAATCGGGAGGA 3450
Crub_svsplocu 94432 AAATTGCACCCCCCTGCCAGAGATGATGCGTTGGAGTGCCCCATGCAATC 94481
i vivi vii v i ivi i viiv viv v
C Gypsy3-I_DR#L 3449 AAACTGAGGTCCCCGATCTGAGACGATGTCCTGGGGAATGCCAAAGACTC 3400
Crub_svsplocu 94482 TATAAATGTGCTGGATGAAAAGTTTTGCTAAGGCCTTTGCAGTGGGAATC 94531
iv v ii v vv vv iv iivvv i v v -v
C Gypsy3-I_DR#L 3399 TGAACACATGGTTCATGACTAGTTCGGCCGTCTCTTTGGCCGTGGGAA-G 3351
Crub_svsplocu 94532 TTTTGGCAAGGG-ATGAAGTG 94551
v i i - i
C Gypsy3-I_DR#L 3350 TTTAGACAGGGGAATGAAGCG 3330
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 39.35
Transitions / transversions = 0.97 (34/35)
Gap_init rate = 0.06 (13 / 212), avg. gap size = 1.23 (16 / 13)
278 36.06 1.89 1.89 Crub_svsplocus 94388 94599 555401 C Gypsy-129_DR-I LTR/Gypsy 3286 3497 828
278 36.06 1.89 1.89 Crub_svsplocus 94388 94599 (555401) C Gypsy-129_DR-I#LTR/Gypsy (828) 3497 3286 m_b2s001i36
Crub_svsplocu 94388 GTGGTCCCTA-AGAGGGATAAAAATTCTTTCCAAAATGCAGATGTAAATT 94436
i i -i vv ii v- v i vvi v v
C Gypsy-129_DR- 3497 GTAGCCCCTATGGACTGGCAAAAAG-CTTGCCAGAATCGGGAGGAAAATT 3449
Crub_svsplocu 94437 GCACCCCCCTGCCAGAGATGATGCGTTGGAGTGCCCCATGCAATCTATAA 94486
vivi i v i v ii iv i viiv viv v viv v
C Gypsy-129_DR- 3448 GAGGTCCTCGGTCTGAGACAATGTCTTGGGGAATGCCAAAGACTCGGAAC 3399
Crub_svsplocu 94487 ATGTGCTGGATGAAAAGTTTTGCTAAGGCCTTTGCAGTGGGAATCTTTTG 94536
i v vv iv i iv ivvv i v -v v
C Gypsy-129_DR- 3398 ACGTGATTTATGGTAAGCTCGGCTGTCTCTTTGGCAGTGGGAA-GTTTGG 3350
Crub_svsplocu 94537 GCAAGGG-ATGAA--GTGCACCTGTTTGGAAAACAAGTCTGTGACTGTCC 94583
- -- v -- ivi iiii i ii v
C Gypsy-129_DR- 3349 GCAAGGGAATGAATCGTGCAGC--TTTGGAAAATCGGTCCACAATTACCA 3302
Crub_svsplocu 94584 AGACAACAGTATGCCC 94599
i i iii v
C Gypsy-129_DR- 3301 AAATAGTGGTATTCCC 3286
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 47.54
Transitions / transversions = 1.08 (39/36)
Gap_init rate = 0.03 (7 / 211), avg. gap size = 1.14 (8 / 7)
+ 842 32.7 4.1 5.2 Crub_svsplocus 95111 96468 (553532) C Gypsy72-I_DR LTR/Gypsy (7010) 4400 1693 63
ANNOTATION EVIDENCE:
327 34.59 0.00 0.00 Crub_svsplocus 95111 95243 554757 C Gypsy64-I_DR LTR/Gypsy 2637 2769 1499
327 34.59 0.00 0.00 Crub_svsplocus 95111 95243 (554757) C Gypsy64-I_DR#LTR/Gypsy (1499) 2769 2637 m_b2s001i37
Crub_svsplocu 95111 GATGTTCTTTCTCCCTGGTAAATGTTTGAGTTTAAATTGGAACTGGTGAA 95160
i vv ivvi iivv v v v ii iiv
C Gypsy64-I_DR# 2769 GGTGTTCTTTGACCCTGGCCTGTACGAGAGTGTAAAGTTGAATCGACTAA 2720
Crub_svsplocu 95161 AATGCTGGGACCAGCGGGCTTGTTTGGGATTGAGTTTCCTGGGCATTTTC 95210
ivv i i i i i v ii ii v i vi v
C Gypsy64-I_DR# 2719 AATAAAGGGACCAGCGGGCCTGTCTAGAACTCAGCCTTTTGGCCGTGCTA 2670
Crub_svsplocu 95211 AGGGCTTCCAAATTTTTGTGATCAGTCCACACC 95243
vivv i i i v v
C Gypsy64-I_DR# 2669 ATATATTCTAAATTCTTGTGGTCTGTCCAGACC 2637
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 43.47
Transitions / transversions = 1.19 (25/21)
Gap_init rate = 0.00 (0 / 132), avg. gap size = 0.0 (0 / 0)
304 31.46 6.68 10.36 Crub_svsplocus 95145 95683 554317 C Gypsy-173_DR-I LTR/Gypsy 2155 2675 1572
304 31.46 6.68 10.36 Crub_svsplocus 95145 95683 (554317) C Gypsy-173_DR-I#LTR/Gypsy (1572) 2675 2155 m_b2s001i38
Crub_svsplocu 95145 AATTGGAA-CTGGTGAAAATGCTGGGACCAGCGGGCTTGTTTGGGATTGA 95193
v - ? i -i viv i viv i?
C Gypsy-173_DR- 2675 AAATGGAATCTGGNGAAGA-ACAATGACCAGCGGGCCTGGCGGGGACNGA 2627
Crub_svsplocu 95194 GTTTCCTGGGCAT-TTTCAGGGCTTCCAAATTTTTGTGATCAGTCCACAC 95242
ivii -i - v ivv v ii i v vvvi
C Gypsy-173_DR- 2626 GTCGTTT-AGCATCTTTGAGATATTGCAGGTTTTTATGATCTGTGATTAC 2578
Crub_svsplocu 95243 CTGGAAGGGGATTTTGTTGCCTTCCAGGAACTGTTGCCAC---------G 95283
i ivv ivi? i vv v i ---------
C Gypsy-173_DR- 2577 CTGGAAAGGATGTTTAGCNCCCTCCAGCCAATGTCGCCACTCCTCCAGGG 2528
Crub_svsplocu 95284 TGAG--TAATGCCCAACGTATCCCATAAGCCTCCTTCTCCCATACGGGCC 95331
i -- i v i i?ivv i ---- vi ivv vi ------
C Gypsy-173_DR- 2527 CGAGCTTGATGGCTAGNAGTTCTC----GATTCCCGATGTCATA------ 2488
Crub_svsplocu 95332 AGCGCTGTTCTGCTT--CCG---TGAGTTTCTTGGATGTATATGCACAGG 95376
------i ? i-- --- i i viv v v
C Gypsy-173_DR- 2487 ------ATTCTNCTCCGCCGGACTAAGTTTCCTGGAGAAATAGGCACATG 2444
Crub_svsplocu 95377 GTTGCAATACCCCTT-----CATTGTTTTCTTGTAATAGAACAGCCCCCA 95421
v v i --v -----i ii vvvvi vi i i i
C Gypsy-173_DR- 2443 GATGGAGTA--ACTTGGGAGTACCGTGGAACTGAGATAGGACGGCTCCCA 2396
Crub_svsplocu 95422 CTGCCACATCACTTGCATCTGCCTGTATTATGAAGGGCTTATTCATGTCT 95471
v viiiviivvv i i v i i vv iiiv v
C Gypsy-173_DR- 2395 CTCCGGTGGTGGAGGCATCTACTTCTACTATGAAAGGCAAATCTGGGTCA 2346
Crub_svsplocu 95472 GGGTGCCTTAGGACTGGTTCGGC-AGAA-AAAAGTCTCTTT-AGTCTCTC 95518
vv i v --- -v i- i ii - ?i iiv
C Gypsy-173_DR- 2345 GGGTGAGTCAGGAGTGG---GGCTCGAGTAAAGGCTTCTTTGAGNTTTCG 2299
Crub_svsplocu 95519 AAACGCTGCTTGGC-ACTCCATTGTCCATGTTAGTGGCTGGATAGGTTTT 95567
i v -- -i i -- -------- iv v v iv i
C Gypsy-173_DR- 2298 GAAGGCTGC--GGCGGCTTCA--G--------AAGGCCAGGATAATTTCT 2261
Crub_svsplocu 95568 ACTGAGGATGCTCCCTTCGTTTTT-AGTAAGTTAGTGAG-GGG------- 95608
-- i --------- ii - v i i - -------
C Gypsy-173_DR- 2260 --TGGG---------TTTATTTTTGAGAAGGTTGGTGAGTGGGGCGGTGA 2222
Crub_svsplocu 95609 CAAGGCTATCTGGGCAAATGAGGGATGAATTGGCGGTAAAAGTTTGCAAA 95658
i i i ------- i v v i i i v i i
C Gypsy-173_DR- 2221 CGAGACTGT-------AGTTATGAATAAATCGTCGATAGAAGTTTGCAAA 2179
Crub_svsplocu 95659 GCCTAGGAAACTTTGTAGTTGCTTT 95683
v v v v -
C Gypsy-173_DR- 2178 GCCGAGGAATCGTTGGAGTT-CTTT 2155
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 38.71
Transitions / transversions = 1.24 (84/68)
Gap_init rate = 0.12 (67 / 538), avg. gap size = 1.34 (90 / 67)
373 28.39 1.90 1.90 Crub_svsplocus 95388 95545 554455 C Gypsy39-I_DR LTR/Gypsy 4471 4628 421
373 28.39 1.90 1.90 Crub_svsplocus 95388 95545 (554455) C Gypsy39-I_DR#LTR/Gypsy (421) 4628 4471 m_b2s001i39
Crub_svsplocu 95388 CCTTCATTGTTTTCTTGTAATAGAACAGCCCCCACTGCCACATCACTTGC 95437
v i i i i ii i v vi v i v
C Gypsy39-I_DR# 4628 CCTTCCTTATCTTCCTGCAGCAGGACAGCGCCAGCTCCTACAGCACTTGC 4579
Crub_svsplocu 95438 ATCTGCCTGTATTATGAAGGGCTTATTCATGTCTGGGTGCC-TTAGGACT 95486
i vi v i i v iv vi i i- - iv
C Gypsy39-I_DR# 4578 ATCTACCTCCATTTTAAAAGGCTTTTCGAAATTTGGA-GCCATTAACACT 4530
Crub_svsplocu 95487 GGTTCGGCAGAAAAAAGTCTCTTTAGT-CTCTCAAACGC-TGCTTGGCAC 95534
vv vv v v i v- i - i v - - i
C Gypsy39-I_DR# 4529 GGAGCTTCACACAGAAGTG-CTTTAATACTTTCAAAGGCATGC-TGGCAT 4482
Crub_svsplocu 95535 TCCATTGTCCA 95545
?iv v
C Gypsy39-I_DR# 4481 TCNGATGACCA 4471
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 35.49
Transitions / transversions = 1.10 (23/21)
Gap_init rate = 0.04 (6 / 157), avg. gap size = 1.00 (6 / 6)
842 33.84 3.32 3.32 Crub_svsplocus 95632 96233 553767 C Gypsy72-I_DR LTR/Gypsy 1693 2294 2003
842 33.84 3.32 3.32 Crub_svsplocus 95632 96233 (553767) C Gypsy72-I_DR#LTR/Gypsy (2003) 2294 1693 m_b2s001i40
Crub_svsplocu 95632 GATGAATTGGCGGTAAAAGTTTGCAAAGCCTAGGAAACTTTGTAGTTGCT 95681
i v i v i i v vi iivv
C Gypsy72-I_DR# 2294 GATGAATCGCCGGTAAAAATTGGCGAAGCCCAGGAACCGCTGTAACGCCT 2245
Crub_svsplocu 95682 TTCTTGTGCGGGGTGGTGCCCAATCTAATACTGCTCTGACCTTTTCTGGG 95731
vv v iv i v i vi v v i i iv v
C Gypsy72-I_DR# 2244 TTCGGGAGTCGGGTGGCGGCCAGTCGGAGACAGCCCTAACCTTCGCAGGG 2195
Crub_svsplocu 95732 TCCATTTCAATGCCCTGGGGGGA---TATGCGATAACCTAGGTAGTCTAT 95778
viv vv viivv --- --- iv i i v vvv i
C Gypsy72-I_DR# 2194 TCCATGCGAAGTCCCTCAACTGAAATTATG---TGTCCCAAGAAGGAAAC 2148
Crub_svsplocu 95779 CCTTTCCTGG---TGGAATTCGCATTTTGAGAGTTTGGCATATAGGTGGG 95825
--- vv --- i ivvvivi vi i v iv
C Gypsy72-I_DR# 2147 ---TGACTGGACATGGAATTCGCACTTCTCCGCCTTTACATACAGCTGAT 2101
Crub_svsplocu 95826 CGGCATGCAGCTTCTTTAAAACTGCTCTGACAACGTTG-ACGTGTTCCTC 95874
ivv vv ivi v iv - v i vvii - i v
C Gypsy72-I_DR# 2100 TCTCCAGCAGCCGTTGTAGCACT-CGCCGAACGTGTTGGACATGTTCCTG 2052
Crub_svsplocu 95875 TTTTGTTTCGGTGAAGATAAGAATGTCATCCAAGTAAACAAGGAC---CC 95921
iv v ivvvi vi i i ii ---ii
C Gypsy72-I_DR# 2051 CATGGCGGAAGAAAAAATAAGAATGTCATCCAAATAAACAAAAACAAATT 2002
Crub_svsplocu 95922 CCTTAAACAGGTGCTCCCTTAGAACGTCATTGATTAATTGCAT-AAAGAC 95970
vv v v --- i vv v i i iv i - v -
C Gypsy72-I_DR# 2001 GATTAATCATGT---CTCGGAGTACATCGTTGACGAGT-GCCTGAAAGAC 1956
Crub_svsplocu 95971 TGCAGG-GCCCCCTTGTAATCCAAATGGCAAGACTTTGAATTGATAGCAC 96019
v - viivv - ii i vvviv v v iii
C Gypsy72-I_DR# 1955 TGCTGGAGCATTGGTG-AGCCCAAATGGCAGGACAAGATATTCAAAATGC 1907
Crub_svsplocu 96020 TCCATGGGGCAGTTAAATGCAGTCTTCCATTCGTCCCCTTCCTTAATTCT 96069
i vi vvv i i v i i v v v
C Gypsy72-I_DR# 1906 CCAGTGGGCGTGTTGAATGCGGTCTTCCATTCGTCACCCTCCCTCATACG 1857
Crub_svsplocu 96070 CACGCGATAGTAAGCTTCCCTTAGGTCTAG-TTTA-GAAAAATTTT-TCC 96116
v v i v iv v i i- i- i -i
C Gypsy72-I_DR# 1856 GACGAGATGGTAAGCATTGCGTAGGTCCAACTTTGTGAAAAATCTTGCCC 1807
Crub_svsplocu 96117 CTTTCGATAGGTGTGACAGC--ATGTCTTTCATGAGGGGCAGAGGGTATA 96164
i v i v i -i vi -- v ----v i v i i iv
C Gypsy72-I_DR# 1806 CCTGCAAGAGAT-CGAAGGCCGAAG----ACATAAGCGGTAGGGGGTACC 1762
Crub_svsplocu 96165 GGTTGCTTTCACTGATTGT---ATTCAGGGCCCTATAATCCACGCATAAA 96211
i --- i v i i --- iiv i v i i i viii
C Gypsy72-I_DR# 1761 GAT---TTTTAATGGTTATGTCATTCAAACCTCGATAGTCTATGCAGGGG 1715
Crub_svsplocu 96212 CATAAAGAGCCATCCTTCTTCT 96233
ii i i i
C Gypsy72-I_DR# 1714 CGCAGAGAACCATCCTTTTTCT 1693
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 41.02
Transitions / transversions = 1.03 (100/97)
Gap_init rate = 0.05 (31 / 601), avg. gap size = 1.29 (40 / 31)
688 34.61 3.83 3.58 Crub_svsplocus 95633 96468 553532 C Gypsy138-I_DR LTR/Gypsy 3563 4400 7010
688 34.61 3.83 3.58 Crub_svsplocus 95633 96468 (553532) C Gypsy138-I_DR#LTR/Gypsy (7010) 4400 3563 m_b2s001i41
Crub_svsplocu 95633 ATGAATTGGCGGTAAAAGTTTGCAAAGCCTAGGAAACTTTGTAGTTGCTT 95682
i ivv i i v v i ii v v vi vi
C Gypsy138-I_DR 4400 ATAAATCTCCGATAAAAATTGGCAAACCCCAAAAATCGTTGTACCTCTTT 4351
Crub_svsplocu 95683 TCTTGTGCGGGGTGGTGCCCAATCTAATACTGCTCTGACCTTTTCTGGGT 95732
vvi vi iv v v i i ii i i vi v i
C Gypsy138-I_DR 4350 AACTGAACATGGTTGTGGCCAATCCAGTACTGCCTTAATCTTGCCAGGAT 4301
Crub_svsplocu 95733 CCATTTCAATGCCCTGGGGGGATATGCGAT-AACCTAGGTAGTCTATCCT 95781
i v v iviivvv -- v - i i v i- v iv
C Gypsy138-I_DR 4300 CCATCTGAAGGCTACATTTGGATA--CTATGAACCCAAGAAA-CGACACT 4254
Crub_svsplocu 95782 TTCCTGG-----TGGAATTCGCATTTTGAGAGTTTGGCATATAG-GTGGG 95825
--- ----- vi ivvv i ii iv i -v v
C Gypsy138-I_DR 4253 TT---GGAGACATGGAATTCGCTCTTCTCCAGCTTAACGAACAGTCTGTG 4207
Crub_svsplocu 95826 CGGCATGCAGCTTCTTTAAAAC-TGCTCTGACAACGTTG-ACGTGTTCCT 95873
ivv -i i vvvvv i - - v -i - i i i
C Gypsy138-I_DR 4206 TCTCA-ACAACTGGGAGAGAACCTGC-CGGACA-TGTTGTACATGCTCTT 4160
Crub_svsplocu 95874 CTT--TTGTTTCGGTGAAGATAAGAATGTCATCCAAGTAAACAAGGAC-- 95919
v --i ii -- vi i v i ii --
C Gypsy138-I_DR 4159 CATAGCTACTT--GAAAAAATAAGTATGTCATCCAAGTAAACGAAAACAA 4112
Crub_svsplocu 95920 -CCCCTTAAACAGGTGCTCCCTTAGAACGTCATTGATTAATTGCAT-AAA 95967
-i iv v ---v v i i i v - v -i
C Gypsy138-I_DR 4111 ATCTGTTCAACA---TCTCCCTGAGGACATCATTAATGAA-TGCCTGGAA 4066
Crub_svsplocu 95968 GACTGCAGGGCCCCCTTGTAA-TCCAAATGGCAAGACTTTGAATTGATAG 96016
v v -v vi ii -v v vv i viv v
C Gypsy138-I_DR 4065 GACGGCTGGG-GCATTTACAAGGCCAAAGGGCATTACCTGATATTCATAG 4017
Crub_svsplocu 96017 CACTCCATGGGGCAGTTAAATGCAGTCTTCCATTCGTCCCCTTCCTTAAT 96066
iivi ii ? vv v i i i i i
C Gypsy138-I_DR 4016 TGGCCTGTNGGGGTGTTAAAAGCGGTCTTCCACTCATCTCCTTCCTTGAT 3967
Crub_svsplocu 96067 TCTCACGCGATAGTAAGCTTCCCTTAGGTCTAGTTTAG-AAAAAT--TTT 96113
i v vv i v ii v i ii v - i -- vv
C Gypsy138-I_DR 3966 CCTGACCAGATGGTAAGCATTTCTGAGGTCCAACTTCGTAAAGATAGTGG 3917
Crub_svsplocu 96114 TCCCTTTCGATAGGTGTGACAGCA-TGTCTTTCATGAGGGGCAGAGGGTA 96162
iv i v ii vv -ii v - --- v i iv
C Gypsy138-I_DR 3916 CGCCCTGCAGTATCT-CAAAAGCAGTG---TTCATTAGGGGTAATGGGTA 3871
Crub_svsplocu 96163 TAGGTTGCTTTCACTGAT--TGT-ATTCAGGGCCCTATAATCCACGCATA 96209
vv i - -- v i -- - iiv i v ii vi
C Gypsy138-I_DR 3870 ACGATT-CTT--AATGGTGATGTGATTCAAACCTCTATAATCAATACAGG 3824
Crub_svsplocu 96210 AACATAAAGAGCCATCCTTCTTCTCTCTTAAAAGGACCGGGCAGCCACTT 96259
iv iv i vvv vvvvviv i --i v v iv v
C Gypsy138-I_DR 3823 GTCGAAGACTCCCATCCTTCTTGGAAACAAAAAAGA--AGCCTGCTCCTG 3776
Crub_svsplocu 96260 TAGGCTTGGCT---GGCTCAATGAAACCTCTCTCTAGGGTTTTTTTTATG 96306
i ivv i --- viv v v v i ii iv i v
C Gypsy138-I_DR 3775 CAGGTGAGGTTGAAGGGCGAATGAATCCACTGTCTAGAGCCTCGTTCAAG 3726
Crub_svsplocu 96307 AATCTTTCCATTTC--CTCCTTCTCCTTTGGGCTCATGGAGTATAATCTG 96354
v i i vv --i i vvvvv i--v v i -
C Gypsy138-I_DR 3725 TATTTCTCCATGGCAGTTCTTTCAGGAATGGA--GAGGGAGTACAATCT- 3679
Crub_svsplocu 96355 GGCTTCGGG--AGATTTGCCCCAGGCTTGAATTCAATGGTACAGTC-TGT 96401
-i i i --i ii i ivii i i v i - i
C Gypsy138-I_DR 3678 -ACCTCGAGGTGGGCTTGCTCCAGGTACAAGTTCAATAGAACAATCATAT 3630
Crub_svsplocu 96402 GGGTCGGTGGGGGGG-AGCTCATCCGCCCTCTCCTCACTGAAAACTTCAG 96450
i- i v - iivv viv ivvvv i i i v
C Gypsy138-I_DR 3629 GGA-CGATGCGGGGGTAATGAAGTAGCCTGAGACTTACTAAAGACTTCAC 3581
Crub_svsplocu 96451 CAAGGTCTCTGTATTCCT 96468
ii i iv i
C Gypsy138-I_DR 3580 TGAGATCCATGTATTCTT 3563
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 45.93
Transitions / transversions = 1.10 (146/133)
Gap_init rate = 0.06 (50 / 835), avg. gap size = 1.24 (62 / 50)
+ 15 19.6 0.0 0.0 Crub_svsplocus 97434 97462 (552538) + (C)n Simple_repeat 1 29 (0) 64
ANNOTATION EVIDENCE:
15 19.61 0.00 0.00 Crub_svsplocus 97434 97462 552538 + (C)n Simple_repeat 1 29 0
15 19.61 0.00 0.00 Crub_svsplocus 97434 97462 (552538) (C)n#Simple_repeat 1 29 (0) m_b2s252i10
Crub_svsplocu 97434 CCCCCCTCCCAACCCCCCACCCTCCCCCC 97462
i vv v i
(C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 29
Matrix = Unknown
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 19 10.3 2.1 6.5 Crub_svsplocus 100311 100358 (549642) + A-rich Low_complexity 1 46 (0) 65
ANNOTATION EVIDENCE:
19 10.26 2.08 6.52 Crub_svsplocus 100311 100358 549642 + (AAATCTA)n Simple_repeat 1 46 0
19 10.26 2.08 6.52 Crub_svsplocus 100311 100358 (549642) (AAATCTA)n#Simple_repeat 1 46 (0) m_b2s252i11
Crub_svsplocu 100311 AAATATAAAACCTGAAATTTAAAA-CTAAAATCTGAATAAATCTAAAAT 100358
v i i i - -- -
(AAATCTA)n#Si 1 AAATCTAAAATCTAAAATCTAAAATCTAAAATCT--A-AAATCTAAAAT 46
Matrix = Unknown
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4)
+ 812 24.9 3.5 1.2 Crub_svsplocus 100753 101014 (548986) C L3 LINE/CR1 (19) 4080 3830 66
ANNOTATION EVIDENCE:
379 14.66 5.26 1.27 Crub_svsplocus 100753 100828 549172 C CR1-3_Croc LINE/CR1 3522 3600 5
379 14.66 5.26 1.27 Crub_svsplocus 100753 100828 (549172) C CR1-3_Croc#LINE/CR1 (5) 3600 3522 m_b2s001i42
Crub_svsplocu 100753 AATAATAATAGTAGTAAAGTTGGAAGGGACCTT-GGAGGTCATCTAGTCC 100801
v i- v ii i i-i
C CR1-3_Croc#LI 3600 AATCATAG-AGAAGTAGGGCTGGAAGGGACCTCCAGAGGTCATCTAGTCC 3552
Crub_svsplocu 100802 AACCCCCTG-CTAGGGCAGGA--AACCCTA 100828
- ii -- v
C CR1-3_Croc#LI 3551 AACCCCCTGCCTGAGGCAGGATCATCCCTA 3522
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 16.69
Transitions / transversions = 2.67 (8/3)
Gap_init rate = 0.05 (4 / 75), avg. gap size = 1.25 (5 / 4)
812 29.09 2.83 1.20 Crub_svsplocus 100768 101014 548986 C L3 LINE/CR1 3830 4080 19
812 29.09 2.83 1.20 Crub_svsplocus 100768 101014 (548986) C L3#LINE/CR1 (19) 4080 3830 m_b2s001i43
Crub_svsplocu 100768 AAAGTTGGAAGGGACCTTGGAGGTCATCTAGTCCAACCCCCTG-CTAGGG 100816
i i i ii- iiiv
C L3#LINE/CR1 4080 AGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCATCCGATG 4031
Crub_svsplocu 100817 CAGGAAACC---CTACACCTTTTCAGACAAATGGCTATCCAGTCTCTTCT 100863
v --- v v ii v i ii i v
C L3#LINE/CR1 4030 CAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCT 3981
Crub_svsplocu 100864 TAAAAACTTCCAGTGTTGGAGCATTTACTGCTTCTGGAGGCAAGCTGTTC 100913
i v i vi i vii i i i ?v iv ii
C L3#LINE/CR1 3980 TGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTC 3931
Crub_svsplocu 100914 CACTGATTAATTATTCTCACTGTCAGGAAGTTTCTCCTTAGTTCTAGGTT 100963
i vv vi ivii v i i i ii - vi ii ii
C L3#LINE/CR1 3930 CATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTA-TATTGAGCC 3882
Crub_svsplocu 100964 G---TTTCTCTCCTTGATTAGTTTCCACCCGTTGCTTCTTGTCCTGCCTT 101010
--- i vi i -- ii i v i v i i
C L3#LINE/CR1 3881 GAAATCTGCCTCCCTG--TAACTTCCACCCATTGGTCCTAGTTCTGCCCT 3834
Crub_svsplocu 101011 CAGG 101014
v
C L3#LINE/CR1 3833 CTGG 3830
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 36.95
Transitions / transversions = 2.38 (50/21)
Gap_init rate = 0.02 (6 / 246), avg. gap size = 1.67 (10 / 6)
+ 13 20.8 2.1 4.3 Crub_svsplocus 101638 101685 (548315) + (TTTTTC)n Simple_repeat 1 47 (0) 67
ANNOTATION EVIDENCE:
13 20.78 2.08 4.26 Crub_svsplocus 101638 101685 548315 + (TTTTTC)n Simple_repeat 1 47 0
13 20.78 2.08 4.26 Crub_svsplocus 101638 101685 (548315) (TTTTTC)n#Simple_repeat 1 47 (0) m_b2s252i12
Crub_svsplocu 101638 TTTTTATTTTTCTTTACTCTTGCTCTCCTTTCTTTTT-TTTCACTGTTT 101685
v -i vi -i - iv v
(TTTTTC)n#Sim 1 TTTTTCTTTTTCTTT-TTCTTTTTCT-TTTTCTTTTTCTTTTTCTTTTT 47
Matrix = Unknown
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3)
+ 17 19.6 0.0 6.1 Crub_svsplocus 103756 103807 (546193) + (TAA)n Simple_repeat 1 49 (0) 68
ANNOTATION EVIDENCE:
17 19.64 0.00 6.12 Crub_svsplocus 103756 103807 546193 + (TAA)n Simple_repeat 1 49 0
17 19.64 0.00 6.12 Crub_svsplocus 103756 103807 (546193) (TAA)n#Simple_repeat 1 49 (0) m_b2s252i13
Crub_svsplocu 103756 TATTAATATTGCACAATAATAATAATAATAATGAAAAATCACTAAAAATG 103805
v v -v i - v - v v i
(TAA)n#Simple 1 TAATAATAAT-AATAATAATAATAATAATAAT-AATAAT-AATAATAATA 47
Crub_svsplocu 103806 AT 103807
(TAA)n#Simple 48 AT 49
Matrix = Unknown
Transitions / transversions = 0.33 (2/6)
Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.00 (3 / 3)
+ 16 0.0 0.0 0.0 Crub_svsplocus 104139 104155 (545845) + (A)n Simple_repeat 1 17 (0) 69
ANNOTATION EVIDENCE:
16 0.00 0.00 0.00 Crub_svsplocus 104139 104155 545845 + (A)n Simple_repeat 1 17 0
16 0.00 0.00 0.00 Crub_svsplocus 104139 104155 (545845) (A)n#Simple_repeat 1 17 (0) m_b2s252i14
Crub_svsplocu 104139 AAAAAAAAAAAAAAAAA 104155
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0)
+ 2146 35.5 1.5 1.5 Crub_svsplocus 106324 107694 (542306) + MamGypsy2-I LTR/Gypsy 1375 2746 (1420) 70
ANNOTATION EVIDENCE:
2146 35.53 1.53 1.46 Crub_svsplocus 106324 107694 542306 + MamGypsy2-I LTR/Gypsy 1375 2746 1420
2146 35.53 1.53 1.46 Crub_svsplocus 106324 107694 (542306) MamGypsy2-I#LTR/Gypsy 1375 2746 (1420) m_b2s001i44
Crub_svsplocu 106324 CTACAAGAAGTCTGCAAAGAATTTGC--AGATGTTTTC--AGCCCCCAGC 106369
i ivv vii v -- i i i -- v---- i
MamGypsy2-I#L 1375 CTACAGGAAGTTGTCAACAGATTTCCCAAGGTATTCTCCGAGG----AAC 1420
Crub_svsplocu 106370 TGGGCACGTACAAAGGACTCCCTGTGTCACTAAAGTTAGACCCCACTGTC 106419
vi v ii ivvv v i vv vi i i vi ii i
MamGypsy2-I#L 1421 TGGGAGCTTACAAGAGGGAGCCAGTGTCATTCCATCTGGATCCAGCCATT 1470
Crub_svsplocu 106420 ACCCCTATTAGAATCAAAGCAAGAAGGGTCCCTTTTGCTTTAAAGGGTAA 106469
i v v vivv v v iv v i i iiv
MamGypsy2-I#L 1471 GCACCAATTCACTTGAAAGCTAGAAATGTACCTTTTGCTCTAAGGAAAAA 1520
Crub_svsplocu 106470 AATTGACACTGAATTAGACAAATTGATTCAGCAAGGAGTCTTAGAACCTG 106519
? vivv ii v vv vi i iv i v i i v v
MamGypsy2-I#L 1521 AANTGAAGAAGAGCTTGAGCATCTAATCAAACAAGGTGCCCTCGAACCAG 1570
Crub_svsplocu 106520 TCGACTC-CAGTCCTTGGGAGACCCCCATTGTCACGCCTCTTAAGGCAAA 106568
i- v -i vi vv vv iv v ivv viv v v v
MamGypsy2-I#L 1571 TT-ACACATACCCGGTGGGCTATACCAATTGCGCCGGTACTAAAGCCTAA 1619
Crub_svsplocu 106569 TGGGGACATTCGCATCTGTGCAGATTACAAATGCACTCTAAATAAGGCAT 106618
vi vi vv vv i v i i v i i
MamGypsy2-I#L 1620 TGGTAAGGTGAGACTTTGTGGAGACTACAAGTGCACTGTGAATAAGGCAC 1669
Crub_svsplocu 106619 TGCAGCAACATGCCTATCCTGTTCCTGTGGTCAGTCATATCCTGGCCTCC 106668
vv i iv v v v ii i vv v ivii
MamGypsy2-I#L 1670 TTAAGCAGCACCCATATCCAGTGCCTGCAGTCAATCAACTCCTTGCTGTT 1719
Crub_svsplocu 106669 CTCAAGGGGGGGCGCGTTTTTGCAAAGCTTGACCTAGCTCAGACGTATCA 106718
iivv iiviv i i v i ii v
MamGypsy2-I#L 1720 CTTGCTGGGGAAAAGGTCTTTGCAAAACTTGACCTTGCCCAAGCTTATCA 1769
Crub_svsplocu 106719 ACAGCTGCCTGTTGATGATGCTGCTGCTGTAGCTCAGACCATTGTGACCC 106768
vii i i i v vv i i v ii v i
MamGypsy2-I#L 1770 ACAGCTGATCGTCGGTGATGCTACTGCAGACGCCCAAACAATCATCACTC 1819
Crub_svsplocu 106769 ATAGGGGGGCATTCAAGGTAAAGAGGTTACAATTTGGAGTAAATGTCGCT 106818
v i vii v v vi v i i i vvv i i
MamGypsy2-I#L 1820 ATCGAGGGGCATTCCGAGTTAAGCGCCTTCAGTTCGGAATTTCTGTTGCC 1869
Crub_svsplocu 106819 CCTGGAATTTTCCAAAGCGTAATGGAAAACACACTACGGGGTATACAAGG 106868
iv v v i v vii vivvi v v v
MamGypsy2-I#L 1870 CCTGGAATTTTCCAGTGCTTCATGGAGACCCTGCTTTCTAGGATTCCAGG 1919
Crub_svsplocu 106869 GGTTTGCCCCTATTTTGATGATGTCTTAATTGCAGGGGATCTACACAC-- 106916
v vvvv v i i i -- v v v v--
MamGypsy2-I#L 1920 TGTGGTACCATATTTCGATGATGTCCTGAT--CATGGGATCAACAGAGGA 1967
Crub_svsplocu 106917 --AACTTAGCTGAGAGATTAAGGGCTGTTCTGCTAAGGTTCAGGAAAACG 106964
-- i- v i i vvi vv i i vvv v iiv v v i
MamGypsy2-I#L 1968 TGAACTC-GCGGAAAGACTTCAGGAAGTCCTACATCGTTTCGATACATCA 2016
Crub_svsplocu 106965 GGCCTCAAACTTAAGAAGGACAAATGTAAAATTGGGGTGCCTTTTACAG- 107013
iv vi v v i v i i ii--- ii vv -
MamGypsy2-I#L 2017 GGTATCCGAGTGAAAAAGGAGAAATGTGAAATCGGAA---CTTCCAGTGT 2063
Crub_svsplocu 107014 -ATTTTCT-GGGATTCAAAATCGATGCTACCGGAATTCACCCTGCTGAAT 107061
- ii -i v v viv i i i v ii v v
MamGypsy2-I#L 2064 CACCTTCTTAGGCTACCGCATCAATGCTGCTGGTATTCACCCCACTCAAG 2113
Crub_svsplocu 107062 CCAA---AC-TGAAAGCCATTATGCATGCCCCTAGGCCGAAGTCCAAGGC 107107
vi --- - v v v i i---- vv i i-v i
MamGypsy2-I#L 2114 ATAAGGTACGTGCAATCCATGACGCG----CCTACTCCAAAA-ACAAAGC 2158
Crub_svsplocu 107108 CAAA-CTACAGGCTTTTCTGGGCCTTCTGAATTTCTATAACTCCTTCCTC 107156
v i - v i i i v v v iv ivii i i
MamGypsy2-I#L 2159 AAGAGCTTCAAGCCTTCCTGGGGCTACTCAATTTCTACCATGTTTTTCTT 2208
Crub_svsplocu 107157 CCAAACAAAGCTAGTGTAGCCGAGCCTCTTCACAGGCTCTTGGAAAAACA 107206
v v i v vii v i v iv v vi i --
MamGypsy2-I#L 2209 CCACAAAAGGCAACCATTGCTGAGCCACTTCATCGCCTACTGGGAAAA-- 2256
Crub_svsplocu 107207 GGCAGT--GTGGCAGTGGTCACAAAAACACGAAGCAAGTTTCAATGAGGT 107254
iv -- iv v v ivv i i i vviv vivi v
MamGypsy2-I#L 2257 GGCGTTCCGTGGCGTTGGACTCGCCAGCATGAGGACGCTTTCCGGAATGT 2306
Crub_svsplocu 107255 CAAGGCCTTACTCACTTCTAACAGTGTGCTTGCACATTTCAATGAATCCC 107304
vvv i v ii vvv v i v i iviv
MamGypsy2-I#L 2307 CAAGCAGTTATTGACTTCCGAGTCTGTGCTAGTACATTACGATGAACATA 2356
Crub_svsplocu 107305 TTCCTGTGTGCATCGCTTGTGATGCTTCTCCTTATGGGGTGGGAGCCGTA 107354
vv vv viv ii ivv i v i v iv i i
MamGypsy2-I#L 2357 AACCACTGTTTCTTACCACTGACGCTTCACCTTACGGTGCTGGAGCTGTG 2406
Crub_svsplocu 107355 CTAAGCCACCTCAGATCAGACGGAACTCAGGTTCCTGTTGCATATTACTC 107404
v vvv vii i v v iv vi v i
MamGypsy2-I#L 2407 CTTAGCCACAAAATGCCAGATGGCACTGAGGCACCAATTGCTTACTACTC 2456
Crub_svsplocu 107405 CAGAACCTTGTCTTCTGCTGAGCGAAATTATGCTCAAATAGACAGGGAGG 107454
v vv v i v i i i i v v ii i
MamGypsy2-I#L 2457 AAGAACAATGTCATCTACAGAACGGAACTATACACAAATTGACAAAGAAG 2506
Crub_svsplocu 107455 CTTTAGCTGTTGTTTCTGGAATCAAAAAATTCCATGATTTTCTATATGGC 107504
ii v i iv v i i i ii i vi v i
MamGypsy2-I#L 2507 CCCTTGCTGTTATCGCGGGAGTCAAGAAGTTCCACAACTACCTCTACGGC 2556
Crub_svsplocu 107505 AG-GCATTTCACGGTCTTCACTGACCATAAGCCTTTGTTGGGACTGCTTA 107553
v - v - ii i vi i i i v v vi v
MamGypsy2-I#L 2557 CGTGCCTTT-ACAATTTGTACTGATCACAAGCCTCTTTGGGGACTCTTTT 2605
Crub_svsplocu 107554 CCACACATAAACAAACTCCCCAGATCATCTCCCCCAGAATGCTGAGATGG 107603
i viv i vv v ivi i v v vv v v v v
MamGypsy2-I#L 2606 CTAAGGATAAGCCTACGCCCTTAATTATGTCACCACGTATGCAGCGCTGG 2655
Crub_svsplocu 107604 TCTATCTTTCTGTCTGCCTATGATTTCTC-CTTACTTCACAAACCTGGGA 107652
vv v i v vvv i i v v - iii - i i
MamGypsy2-I#L 2656 AGTCTTTTGCTCAGTGCTTATGACTACGCGCTTGTCT-ACAAGCCTGGAA 2704
Crub_svsplocu 107653 AGGAAATGGGCCATGCTGATGGCCTCAGTAGATTACCCCTGC 107694
ii v ivvvv v v iv vi i v
MamGypsy2-I#L 2705 GAGCAATATCGAATGCTGATGCCCTGAGCCGTCTGCCACTGC 2746
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 45.52
Transitions / transversions = 0.88 (224/256)
Gap_init rate = 0.02 (34 / 1370), avg. gap size = 1.21 (41 / 34)
+ 802 31.8 4.5 4.2 Crub_svsplocus 107886 108462 (541538) + Gypsy-175_DR-I LTR/Gypsy 1490 2068 (895) 71
ANNOTATION EVIDENCE:
802 31.82 4.51 4.15 Crub_svsplocus 107886 108462 541538 + Gypsy-175_DR-I LTR/Gypsy 1490 2068 895
802 31.82 4.51 4.15 Crub_svsplocus 107886 108462 (541538) Gypsy-175_DR-I#LTR/Gypsy 1490 2068 (895) m_b2s001i45
Crub_svsplocu 107886 AAAAGGAACGAATTGTCCACCTTCCAGGGTTGTCTGCTTTGGGGAAGCAG 107935
i i i i ii v v i ivv i i vv v v
Gypsy-175_DR- 1490 AGAAAGGATGAGCTGACAATCCAACAAGGCTGTCTTATGTGGGGAAGGAG 1539
Crub_svsplocu 107936 AGTTGTCATTCCTACCTCAATGAGGA-CTAGGGT----CTTAGGTTCCCT 107980
i v i - v viv - i ---- i iii? i v
Gypsy-175_DR- 1540 GGTAGTTATTCCT-CCTAAATTGCGATCCAGGGTGCTGCCTGAANTTCAT 1588
Crub_svsplocu 107981 CCACGAGGGTCATCCTGGCATTGTACGCATGAAGGCGCTTGCATGCAGCC 108030
v v ---- v ii i i v iv ii vv ii
Gypsy-175_DR- 1589 ACAGGA----CATCCAGGTGTCGTGCGAATGAAGGCAGTTGCGCGGCGTT 1634
Crub_svsplocu 108031 ATTTGTGGTGGCCTGGGTTAGATAGAGACATTGAAGCTA----AGGTG-C 108075
v v ------ ii vv i v - ---- v -
Gypsy-175_DR- 1635 ATGTCTGGTGGCC------AGGCATTGACACTCAAG-TAGAACAGTTGTC 1677
Crub_svsplocu 108076 ATGCA--TGCCACCTTTGTCAACGCTCGCACCCTGAAATGCCCCAAG--- 108120
vi -- i viii i iv---- v i - v vi ---
Gypsy-175_DR- 1678 AAACAACTGTCAGTCCTGCCAACAA----ACGCTAAAA-GCACCTGGACC 1722
Crub_svsplocu 108121 --CTCCTGTACATAGATGGGAGGAAACACAGTCTCCATGGTCTAGGGTGC 108168
-- iv ivvv i iviiv v v ivvv vi
Gypsy-175_DR- 1723 TTCTCCCTTACACCCCTGGAAATGGCCAGAGTCTCCTTGGCAACGTATGC 1772
Crub_svsplocu 108169 ACATTGACTATGCTGGGCCCTTTCAGGGTCAATTCTTCTTGGTCCTAGTT 108218
ii v v v v v viv vii v v? v
Gypsy-175_DR- 1773 ATGTAGACTATGCTGGTCCATTTGAGGGACAAACGTGTCTCGTCGNAGTA 1822
Crub_svsplocu 108219 GATAGCCATTCAAAATGACTTGAGGTTGTACCTG-TCTCTTCCACCACCA 108267
ivi i i i ii i - iiv - vvv v i vv
Gypsy-175_DR- 1823 GATGCTCACTCAAAGTGGCCCGAAG-TGTGTGTGATGGATTCAACTACAT 1871
Crub_svsplocu 108268 CTGCAAAGACTATTCAAGTACTGAGGGGGACTTTTGCTGCA-CACGGGCT 108316
i i iviviv iv - - i v
Gypsy-175_DR- 1872 CTGCAAAGACCATTCAAGTGCTGAGGACATTATTTAGT-CATCATGGCCT 1920
Crub_svsplocu 108317 TCCAGACGTCCTCGTGTCTGACAATGGCCCTCAATTCACTTCTTCCGAAT 108366
v v v vvvi i i v i i ivvv i
Gypsy-175_DR- 1921 TCCAGAAGTGCTGGTTAGCGATAATGGTCCTAAGTTCACCTTGGACGAGT 1970
Crub_svsplocu 108367 TCCAAGC-TTTCTTACAGGCCAACATGATTCGTCATGC-CAC---CTCTG 108411
ii - i - i i -- i -- ii - --- ?
Gypsy-175_DR- 1971 TCCAGACATTTCTCA-AAGCTAAC--GGT--GTCACACACACACGCTCTN 2015
Crub_svsplocu 108412 CGCCCTTCCACCCGTCCACCAACGGTATGGTTGAACGCATGGTTC--GCA 108459
i i i iv v i iv iv --i
Gypsy-175_DR- 2016 CACCTTTTCACCCAGCCACGAATGGCTTGGCGGAACGCATGGTTCAGACA 2065
Crub_svsplocu 108460 TCA 108462
Gypsy-175_DR- 2066 TCA 2068
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 40.41
Transitions / transversions = 1.15 (94/82)
Gap_init rate = 0.06 (37 / 576), avg. gap size = 1.35 (50 / 37)
+ 320 18.8 0.0 3.1 Crub_svsplocus 115258 115323 (534677) C MIR3 SINE/MIR (1) 207 144 72 *
ANNOTATION EVIDENCE:
320 18.77 0.00 3.12 Crub_svsplocus 115258 115323 534677 C MIR3 SINE/MIR 144 207 1
320 18.77 0.00 3.12 Crub_svsplocus 115258 115323 (534677) C MIR3#SINE/MIR (1) 207 144 m_b3s001i3
Crub_svsplocu 115258 AATAATAATAATAATAGTAGTAGTAAAGTTGGAAGGGACCTTGGAGGTCA 115307
v i- v - i ivi i i i i
C MIR3#SINE/MIR 207 AATCATAG-AATCATAG-AATGTCAGAGCTGGAAGGGACCTTAGAGATCA 160
Crub_svsplocu 115308 TCTAGCCCAACCCCCT 115323
i
C MIR3#SINE/MIR 159 TCTAGTCCAACCCCCT 144
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.35
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2)
+ 6104 28.9 2.4 2.1 Crub_svsplocus 115267 117414 (532586) C L3 LINE/CR1 (19) 4080 1948 73
ANNOTATION EVIDENCE:
381 17.76 8.79 1.02 Crub_svsplocus 115267 115357 534643 C CR1-3_Croc LINE/CR1 3503 3600 5
381 17.76 8.79 1.02 Crub_svsplocus 115267 115357 (534643) C CR1-3_Croc#LINE/CR1 (5) 3600 3503 m_b3s001i4
Crub_svsplocu 115267 AATAATAGTAGTAGTAAAGTTGGAAGGGACCTT-GGAGGTCATCTAGCCC 115315
v - v ii i i-i i
C CR1-3_Croc#LI 3600 AATCATAG-AGAAGTAGGGCTGGAAGGGACCTCCAGAGGTCATCTAGTCC 3552
Crub_svsplocu 115316 AACCCCCTGCTCG-GGCAGGA--AACCCTAC----ACCATTTCGGACAA 115357
ii - -- v i---- ii iv
C CR1-3_Croc#LI 3551 AACCCCCTGCCTGAGGCAGGATCATCCCTATCCAAACCATCCCATACAA 3503
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.96
Transitions / transversions = 3.00 (12/4)
Gap_init rate = 0.06 (5 / 90), avg. gap size = 1.80 (9 / 5)
6104 29.37 2.16 2.16 Crub_svsplocus 115282 117414 532586 C L3 LINE/CR1 1948 4080 19
6104 29.37 2.16 2.16 Crub_svsplocus 115282 117414 (532586) C L3#LINE/CR1 (19) 4080 1948 m_b3s001i5
Crub_svsplocu 115282 AAAGTTGGAAGGGACCTTGGAGGTCATCTAGCCCAACCCCCTGCTCGG-G 115330
i i i i iiii i-
C L3#LINE/CR1 4080 AGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCATCCGATG 4031
Crub_svsplocu 115331 CAGGAAACCCT---ACACCATTTCGGACAAGTGGCTGTCCAGTCTCTTCT 115377
v --- v ii v iii i v
C L3#LINE/CR1 4030 CAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCT 3981
Crub_svsplocu 115378 TAAAAACTTCCAGTGTTGGAGCATTTACTGCTTCTGGAGGCAAGCTGTTC 115427
i v i vi i vii i i i ?v iv ii
C L3#LINE/CR1 3980 TGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTC 3931
Crub_svsplocu 115428 CACTGATTAAT-TTTCTAACTGTCAGGAAGTTTCTCCTTAGTTCTAGGTT 115476
i vv vi i-vi i i i i ii - vi ii ii
C L3#LINE/CR1 3930 CATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTA-TATTGAGCC 3882
Crub_svsplocu 115477 G---CTTCTCTCCTTGATTAGTTTCCACCCGTTGCTTCTTGTCCTGCCTT 115523
---ii vi i -- ii i v i v i i
C L3#LINE/CR1 3881 GAAATCTGCCTCCCTG--TAACTTCCACCCATTGGTCCTAGTTCTGCCCT 3834
Crub_svsplocu 115524 CAGGTGCTTTGGAGAAT-AGCTTAATTCCCTCTTCTTTATGGCAGCCCCT 115572
v v iviiv - ii - ivi i i
C L3#LINE/CR1 3833 CTGGAGCCACACAGAATAAGTCTAA-TCCCTCTTCCACATGACAGCCCTT 3785
Crub_svsplocu 115573 GAGATATTGGAACACTGCTATCATGTCCCCCCTTGTCCTTCTCTTCGTTA 115622
v i v v v i i vivi vii
C L3#LINE/CR1 3784 CAAATATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCCA 3735
Crub_svsplocu 115623 AACTAGACATACCAAATTCTAGCAACCGTTCCTTATATGTTTTAGCCTCC 115672
ii i v v i ivv i viv i ii
C L3#LINE/CR1 3734 GGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACATGGTTTCC 3685
Crub_svsplocu 115673 AGTCCCCTAATCATCTTTGTTGCTCTTCTCTGTACTCTTTCTAGAGTCTC 115722
v i v i i v i i v v vi i vv v
C L3#LINE/CR1 3684 AGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTGTC 3635
Crub_svsplocu 115723 AACATCTTTTTTACATCGTGGTGACCAAAACTGGATGCAGTATTCCAAGT 115772
ii ii i v vi i v i i i i i ii
C L3#LINE/CR1 3634 AATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAATACTCCAGAT 3585
Crub_svsplocu 115773 GTGGCCTTACCAAGGCATTAAAGAGTGGTATTAATACTTCACGTGATCTT 115822
i v iv vviv v i v i v i v v ? v
C L3#LINE/CR1 3584 GTGGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCTCCCTTGNTCTG 3535
Crub_svsplocu 115823 GATTCTATCCCTCTGTTAATGCAGCCTAGCACTGTGTTGGCCTTTTTGGC 115872
iv v i i iv i ii i i
C L3#LINE/CR1 3534 GACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTTTTTTGGC 3485
Crub_svsplocu 115873 AGCTGCAGCACACTGCTGGCTCATATTTAAGTGATTGTCTACTAGGACTC 115922
ii v i v iv viiv v ii i
C L3#LINE/CR1 3484 AGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAACTAAAACCC 3435
Crub_svsplocu 115923 CGAGGTCCCTCTCACAGTTACTACTATTGAGCATGGTGCCACCTATGCTG 115972
v ii i ivvv i ii i vv i v ivi i v
C L3#LINE/CR1 3434 CTAGGTCTTTTTCACGTGAACTGCTGCTAAGCCAGATCCTCTCCATCCTG 3385
Crub_svsplocu 115973 TACTTGTGCATTTGGTTTTTCTTGCCTAAATGTAGAACCCTGCTTTTTTC 116022
v i ivvi i i ii i v v
C L3#LINE/CR1 3384 TACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGACTTTACATTTATC 3335
Crub_svsplocu 116023 ACCATTGAATTTCATTTTGTTAGTTAGTGCCCAGTGTTCAAGTCTGTCCA 116072
v ii i i i vvv vi v i v
C L3#LINE/CR1 3334 CCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTCCAGCCTGTCGA 3285
Crub_svsplocu 116073 GATCCTTCTGTATCTGAAGCCTGTCTTCTGGAGTGTTGGCTATTCCTGCC 116122
? i v vi vi v ii?v i i i v
C L3#LINE/CR1 3284 GATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATCCCTCCC 3235
Crub_svsplocu 116123 AGCTTGGTGTCGTCTGCAAATTTGATGAGTTCCCCATCTATCCCTTCATC 116172
v i i iviv v vi
C L3#LINE/CR1 3234 AGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCATC 3185
Crub_svsplocu 116173 CAAGTCATTGATGAAGATGTTGAAGAGTACTGGGCCCAGAACAGAGCCCT 116222
i i v v v v i
C L3#LINE/CR1 3184 CAAGTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAGAGCCCT 3135
Crub_svsplocu 116223 GGGGCACCCCACTACACACTTCCCTCCATATAGATGCAGTTCCATTGAGG 116272
v v v v i vi v iiiv v i vv
C L3#LINE/CR1 3134 GTGGCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTAATC 3085
Crub_svsplocu 116273 ACCACTCGCTGAGTACGGCCGGTCAGCCAGCTACGGATCCATCTGGTGGT 116322
v iivi i i v i i i iiiv
C L3#LINE/CR1 3084 AACACCTTTTGGGTACGGTCGTTCAACCAGCTACGAATCCACCTAACTGT 3035
Crub_svsplocu 116323 GGTTCTGTCTACCCCACATTTTTCTATCTTGTCAAGTAGTAGGTTGTGAT 116372
iv viii i v i i i v vv v vi ii v
C L3#LINE/CR1 3034 ACTATCATCCAGCCCATATTTCTCCATCTTGTCCACAAGGATATCATGAG 2985
Crub_svsplocu 116373 CTACTTTATCAAATGCCTTACTGAAGTCCAAGTAAATTATGTCCACAGCA 116422
vv i i i ii v i ? i i
C L3#LINE/CR1 2984 AGACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTGTCTACGGCA 2935
Crub_svsplocu 116423 TTCCTCTGATCCACTAATTTTGTCACTTGGTCAAAGAATGCAATAAGATT 116472
i i i i i v v iivi i v v i i
C L3#LINE/CR1 2934 TTCCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGGAAATGAGGTT 2885
Crub_svsplocu 116473 TGTCTGGCATGATCTATTTTTGACAAACCCATGTTGGCTTTTAGTAATGA 116522
v i ii i i iiii i ii i v
C L3#LINE/CR1 2884 AGTTTGGCATGACTTGTTCTTAGTGAACCCATGCTGGCTCCTAGTGATCA 2835
Crub_svsplocu 116523 ---CTTTGTTTGCCTCTAGGTGTTCGTTGATTCGTTGTTTGATTATCTTT 116569
--- iv --- i i iivi iivvi i v iv
C L3#LINE/CR1 2834 CCGCTTCCTTT---TCTAAGTGCTCACAAACCATCTGTTTAATAATCCGT 2788
Crub_svsplocu 116570 TCCAGGATCTTCCCAGGTATTGAGTTCAGGCTGATAGGTCTGTAATTTCC 116619
i i i v i v i vv i v iv i ?
C L3#LINE/CR1 2787 TCTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTTNC 2738
Crub_svsplocu 116620 TGGATCCATTTTTTTTCCTTTTTTGAGGATGGGAACTACATCAGCTCTTT 116669
v i i i i ii? i ? ? iv i v i
C L3#LINE/CR1 2737 AGAATCCATCTTTTTTCCCTTTTTAAAANTAGGNACNACATTTGCCCGTC 2688
Crub_svsplocu 116670 TCCAGTCCTCTGGTAGTTCCCCTGTGTTCCAGGATCTTTGAAAAATATAG 116719
i i vi ii i vi iv i i v i - v
C L3#LINE/CR1 2687 TCCAGTCTTCTGGCACCTCTTCCGTTCTCCGTGATTTCTCAAAGAT-TAC 2639
Crub_svsplocu 116720 TT-CAGTGGCTCCGATATCACATCTGCCAGTTCCTTGAGAACTCTGGGGT 116768
iv- i i vv v i v v i i
C L3#LINE/CR1 2638 CGACAGCGGTTCCGCGATCACATCTGCAAGTTCTTTCAGTACCCTGGGAT 2589
Crub_svsplocu 116769 GTAATCCATCTGGTCCTGGCGATTTGAACTCATCTAGGCTGGACAGGTGC 116818
i i v v i i iivi vi
C L3#LINE/CR1 2588 GTAATTCGTCTGGGCCTGGAGACTTGAACTCATTTAAAGCGGCTAGGTGC 2539
Crub_svsplocu 116819 TCCCTAACCATTTTCTTGCCTATCTT-AACTTGTGTTTCTGTTT-----T 116862
i v i i i ii -ii vvi i ivi -----
C L3#LINE/CR1 2538 TCTCTTACTATCTCCTCACCTATCTTGGGCTTCAATTCCCTCTTAACGAT 2489
Crub_svsplocu 116863 GTTTTTTATGGCACTATTTTTAATAGGTTGGTCTG----TTTTTTCCCTT 116908
v v --- iv ii -------- ---- iv ii
C L3#LINE/CR1 2488 GTTTGTTCT---ACCCTTTCCA--------GTCTGAAGATCATTCTCCTT 2450
Crub_svsplocu 116909 TGT-GTAAAGACAGATGCAAAACACGAGTTAAATAGTTCTGCTTTCTCCC 116957
vi - vi i v i v i i i
C L3#LINE/CR1 2449 GATAGAGAAGACGGAAGCAAAATAGGAGTTGAGTAGTTCTGCTTTCTCTC 2400
Crub_svsplocu 116958 TGTTGTTTGTCACCTTCTTGCCACTTCCACCCACTAATGGACCAATCGTT 117007
ii i i v v ivi ii v v v vi ii i vi ?i
C L3#LINE/CR1 2399 TGTCATCTGTTAACATTACGCCATCTGCCCCAAGCAGCGGGCCTGTCNCT 2350
Crub_svsplocu 117008 TCCTTCACTTTTTTCTTGTTTTTTACATG---TTGAAAGAAGC--TTTTT 117052
i --- ii ii i iivv i--- -- -- ?
C L3#LINE/CR1 2349 TTCTT---TTTCCTTCTGCTCCGAACATAGCTTTGAA--AAGCCTTNTTT 2305
Crub_svsplocu 117053 TTGTTATTTTTGAC---TTTGGTCGCAAGCCTTAGTTCATTTTGAGCCTT 117099
i ii ii --- vv i i i i i
C L3#LINE/CR1 2304 TTGTTGTCCTTAGCATTTTTTTTCGCAAGCCTCAGCTCATTCTGGGCTTT 2255
Crub_svsplocu 117100 GGCTTTCTTCACTTCATGTTTGCAGGCTCGGGCTATTTGCTGATATTCTG 117149
i i i v vii vi i i v ? i iv ----i i
C L3#LINE/CR1 2254 AGCCTTCCTGACACTATTCTTACAGGCTTGTGNTACTCTCT----CTTTG 2209
Crub_svsplocu 117150 -ACTTAGTTATGTTCCCCTCTTTCCACTTTCT-ATACTTGTCCTTTTTAT 117197
-v i i- vi ii - v v -
C L3#LINE/CR1 2208 TCCTTGGTTATA-TGTCCTCTTTCCATCTTCTGATACATGTCCTTTTAA- 2161
Crub_svsplocu 117198 CTTTCAATTTG---TCAGAGAGTTCTTTATGCAGCCATGCTGGTTTCTTT 117244
----- i --- i ? i ? i i v
C L3#LINE/CR1 2160 -----AATCTGACATCAGAGAATNCTCTATGNAGCCACGTTGGTTTCTTA 2116
Crub_svsplocu 117245 TGAGAGCTGTTGTTTTTCCTCTTTGTTGGTATTGTGCTAGACTGTGCTTT 117294
viv vv viivi i i ii - ii ------i iv v
C L3#LINE/CR1 2115 AATGCCCTCCCTCTTTTCTTCCTCATTGG-ATCAT------TTGTAATTG 2073
Crub_svsplocu 117295 TATT----ATCTCATTTTTCAAAATTTCCCAAGCTTCTTGAGTTGT-TTT 117339
v ---- i v i ii ?v i iii -
C L3#LINE/CR1 2072 TAGTCAGAATTTCATTTTTAAGAGCTTCCCANCCCTCTTGAGCCATCTTT 2023
Crub_svsplocu 117340 CCCCTTGAGGATTCTTATCCATGGAATCCTTCCCAAGCCCTCTCTAAGTT 117389
iii -- iii?iv v v i--viii i i
C L3#LINE/CR1 2022 CTTTTTGAG--TCTCNGGCCATGGAATCATACCT--CTTTTCTCTGAATT 1977
Crub_svsplocu 117390 TATTGAAATTAGCT----CTCTTGAAGTC 117414
v iv ---- v i
C L3#LINE/CR1 1976 TTTTGAAATCTGCTTTTCCTCGTAAAGTC 1948
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.26
Transitions / transversions = 1.81 (395/218)
Gap_init rate = 0.03 (66 / 2132), avg. gap size = 1.39 (92 / 66)
+ 68 0.0 0.0 0.0 Crub_svsplocus 120770 120827 (529173) + (CA)n Simple_repeat 1 58 (0) 74
ANNOTATION EVIDENCE:
68 0.00 0.00 0.00 Crub_svsplocus 120770 120827 529173 + (CA)n Simple_repeat 1 58 0
68 0.00 0.00 0.00 Crub_svsplocus 120770 120827 (529173) (CA)n#Simple_repeat 1 58 (0) c_b3s251i0
Crub_svsplocu 120770 CACACACACACACACACACACACACACACACACACACACACACACACACA 120819
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50
Crub_svsplocu 120820 CACACACA 120827
(CA)n#Simple_ 51 CACACACA 58
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
+ 17 0.0 0.0 4.0 Crub_svsplocus 120857 120882 (529118) + (TAAA)n Simple_repeat 1 25 (0) 75
ANNOTATION EVIDENCE:
17 0.00 0.00 4.00 Crub_svsplocus 120857 120882 529118 + (TAAA)n Simple_repeat 1 25 0
17 0.00 0.00 4.00 Crub_svsplocus 120857 120882 (529118) (TAAA)n#Simple_repeat 1 25 (0) m_b3s252i0
Crub_svsplocu 120857 TAAATAAATAAAATAAATAAATAAAT 120882
-
(TAAA)n#Simpl 1 TAAATAAAT-AAATAAATAAATAAAT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1)
+ 17 12.6 4.3 4.3 Crub_svsplocus 121719 121765 (528235) + A-rich Low_complexity 1 47 (0) 76
ANNOTATION EVIDENCE:
17 12.59 4.26 4.26 Crub_svsplocus 121719 121765 528235 + (TAAAACA)n Simple_repeat 1 47 0
17 12.59 4.26 4.26 Crub_svsplocus 121719 121765 (528235) (TAAAACA)n#Simple_repeat 1 47 (0) m_b3s252i1
Crub_svsplocu 121719 TAAGAAAATAAATTTTAAAA-A-AAATCAGTAAAACATAAAACATAAAA 121765
- v viv - - v -
(TAAAACA)n#Si 1 TAA-AACATAAAACATAAAACATAAAACA-TAAAACATAAAACATAAAA 47
Matrix = Unknown
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.09 (4 / 46), avg. gap size = 1.00 (4 / 4)
+ 13 4.3 3.9 3.9 Crub_svsplocus 128171 128196 (521804) + (CCTC)n Simple_repeat 1 26 (0) 77
ANNOTATION EVIDENCE:
13 4.34 3.85 3.85 Crub_svsplocus 128171 128196 521804 + (CCTC)n Simple_repeat 1 26 0
13 4.34 3.85 3.85 Crub_svsplocus 128171 128196 (521804) (CCTC)n#Simple_repeat 1 26 (0) m_b3s252i2
Crub_svsplocu 128171 CCT-CCTCCACCCCCTCCCTCCCTCCC 128196
- - i
(CCTC)n#Simpl 1 CCTCCCTCC-CTCCCTCCCTCCCTCCC 26
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2)
+ 16 0.0 0.0 0.0 Crub_svsplocus 133581 133598 (516402) + (CA)n Simple_repeat 1 18 (0) 78
ANNOTATION EVIDENCE:
16 0.00 0.00 0.00 Crub_svsplocus 133581 133598 516402 + (CA)n Simple_repeat 1 18 0
16 0.00 0.00 0.00 Crub_svsplocus 133581 133598 (516402) (CA)n#Simple_repeat 1 18 (0) m_b3s252i3
Crub_svsplocu 133581 CACACACACACACACACA 133598
(CA)n#Simple_ 1 CACACACACACACACACA 18
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0)
+ 12 20.9 4.3 2.1 Crub_svsplocus 134468 134513 (515487) + A-rich Low_complexity 1 47 (0) 79
ANNOTATION EVIDENCE:
12 20.92 4.35 2.13 Crub_svsplocus 134468 134513 515487 + (TAAAAGA)n Simple_repeat 1 47 0
12 20.92 4.35 2.13 Crub_svsplocus 134468 134513 (515487) (TAAAAGA)n#Simple_repeat 1 47 (0) m_b3s252i4
Crub_svsplocu 134468 TAAGAAAATAAATTTTAAAA-AAATCAG-TAAAACATAAAAGATAAAA 134513
- i vvv - v vv - v
(TAAAAGA)n#Si 1 TAA-AAGATAAAAGATAAAAGATAAAAGATAAAAGATAAAAGATAAAA 47
Matrix = Unknown
Transitions / transversions = 0.14 (1/7)
Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3)
+ 267 17.5 0.0 0.0 Crub_svsplocus 135920 135959 (514041) + AmnSINE2 SINE/tRNA-Deu 80 119 (239) 80
ANNOTATION EVIDENCE:
267 17.50 0.00 0.00 Crub_svsplocus 135920 135959 514041 + AmnSINE2 SINE/tRNA-Deu 80 119 239
267 17.50 0.00 0.00 Crub_svsplocus 135920 135959 (514041) AmnSINE2#SINE/tRNA-Deu 80 119 (239) m_b3s001i6
Crub_svsplocu 135920 CAAGGTTGACTCAGCCTTCCATCCTTTTGAGGTTGATAAA 135959
i i i i ii v
AmnSINE2#SINE 80 CAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAGATAAA 119
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.68
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 410 26.4 0.0 0.0 Crub_svsplocus 138857 138962 (511038) + X24_LINE LINE/L2 104 209 (105) 81
ANNOTATION EVIDENCE:
410 26.42 0.00 0.00 Crub_svsplocus 138857 138962 511038 + X24_LINE LINE/L2 104 209 105
410 26.42 0.00 0.00 Crub_svsplocus 138857 138962 (511038) X24_LINE#LINE/L2 104 209 (105) m_b3s001i7
Crub_svsplocu 138857 CACCTATCCTCCGCGAGCTGCACTGGCTTCCTGTGGGTCTCCGGACGCAA 138906
i v iiv v ?i vv ii iii
X24_LINE#LINE 104 CACCTGTGCTCCGCAGTCTGCACTGGCTACCNATTTGCTTCCGAGTGCAA 153
Crub_svsplocu 138907 TTCAAGGTGTTGGTTATCACCTTTAAAGCCCTTCATGGCATAGGGCCAGG 138956
ii v v i v vi iv i v v
X24_LINE#LINE 154 TTCAAGGTGTTGACTTTAATCTATAAAGCCCTATATGGTTTGGGCCCTGG 203
Crub_svsplocu 138957 TTACTT 138962
i
X24_LINE#LINE 204 TTACCT 209
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.64
Transitions / transversions = 1.33 (16/12)
Gap_init rate = 0.00 (0 / 105), avg. gap size = 0.0 (0 / 0)
+ 29 0.0 0.0 3.2 Crub_svsplocus 139334 139365 (510635) + (TAAA)n Simple_repeat 1 31 (0) 82
ANNOTATION EVIDENCE:
29 0.00 0.00 3.23 Crub_svsplocus 139334 139365 510635 + (TAAA)n Simple_repeat 1 31 0
29 0.00 0.00 3.23 Crub_svsplocus 139334 139365 (510635) (TAAA)n#Simple_repeat 1 31 (0) c_b3s251i1
Crub_svsplocu 139334 TAAATAAATAAATAAATAAATAAATAATATAA 139365
-
(TAAA)n#Simpl 1 TAAATAAATAAATAAATAAATAAATAA-ATAA 31
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1)
+ 332 28.2 1.9 1.9 Crub_svsplocus 141118 141283 (508717) C Gypsy64-I_DR LTR/Gypsy (291) 4044 3833 83
ANNOTATION EVIDENCE:
319 31.20 2.48 2.48 Crub_svsplocus 141118 141278 508722 C Gypsy164B-I_DR LTR/Gypsy 3884 4044 291
319 31.20 2.48 2.48 Crub_svsplocus 141118 141278 (508722) C Gypsy164B-I_DR#LTR/Gypsy (291) 4044 3884 m_b3s001i8
Crub_svsplocu 141118 ATGGAAAACTGGGTGAATTTTCCCTAAAAGTCTAGGG---AGTTTTAGTT 141164
i v ii- --ii? --- i v i
C Gypsy164B-I_D 4044 ATGGAAAACCGGGTGAATGTTTT-TAAA--CTNAGGGCTTAATTTGAGTC 3998
Crub_svsplocu 141165 CTACTGTGACTGAGTTGATGATCCTTACTATGGGGAAAGGCCCCAAGAAT 141214
vv i vv iii vv i i v iv i i v v
C Gypsy164B-I_D 3997 GAACCGACACTGGACTGAGCACCTTGATAATGGGAAAAGGTCCAATGAAT 3948
Crub_svsplocu 141215 TTTGGTCCCAATTT-CTTGCTGGGCAATTTGAGGCATATATATTTAGTTG 141263
v - v v- v i i iviv i vi i vv
C Gypsy164B-I_D 3947 TTGGGTCCCAATTTACGTGA-GGGAAGTCTGAGAGGAATGTCCTTGGAAG 3899
Crub_svsplocu 141264 ACAAATAAACCTTTT 141278
vi i i i
C Gypsy164B-I_D 3898 ACAACCAGACTTTCT 3884
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.41
Transitions / transversions = 1.23 (27/22)
Gap_init rate = 0.04 (6 / 160), avg. gap size = 1.33 (8 / 6)
332 26.96 1.71 1.71 Crub_svsplocus 141167 141283 508717 C Gypsy72-I_DR LTR/Gypsy 3833 3949 348
332 26.96 1.71 1.71 Crub_svsplocus 141167 141283 (508717) C Gypsy72-I_DR#LTR/Gypsy (348) 3949 3833 m_b3s001i9
Crub_svsplocu 141167 ACTGTGACTGAGTTGATGATCCTTACTA-TGGGGAAAGGCCCCAAGAATT 141215
v v i i i v - - v i v vi
C Gypsy72-I_DR# 3949 ACAGTCACCGGGCTCATGATC-TTACTAATGGGGTAGGGCCCAATAAATT 3901
Crub_svsplocu 141216 TTGGTCCCAATTT-CTTGCTGGGCAATTTGAGGCATATATATTTAGTTGA 141264
v v - i ii- vi i ivi v v
C Gypsy72-I_DR# 3900 TAGGTGCCAATTTTCCTGCTGAA-ACCTTAAGAGGTAGATCTTTAGTTGA 3852
Crub_svsplocu 141265 CAAATAAACCTTTTCCCCA 141283
i vi v iv v
C Gypsy72-I_DR# 3851 TAACCACACCCGTTGCCCA 3833
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.15
Transitions / transversions = 0.94 (15/16)
Gap_init rate = 0.03 (4 / 116), avg. gap size = 1.00 (4 / 4)
+ 352 34.5 3.6 3.3 Crub_svsplocus 141621 141958 (508042) C Gypsy64-I_DR LTR/Gypsy (794) 3474 3144 83
ANNOTATION EVIDENCE:
352 34.44 3.51 3.51 Crub_svsplocus 141621 141933 508067 C Gypsy64-I_DR LTR/Gypsy 3162 3474 794
352 34.44 3.51 3.51 Crub_svsplocus 141621 141933 (508067) C Gypsy64-I_DR#LTR/Gypsy (794) 3474 3162 m_b3s001i10
Crub_svsplocu 141621 CCCATTGGT--GGCCGGATGAAAAGCAGATGATGAACCTTGAGATGATCC 141668
i -- -- i vv v v iii iivv v vi
C Gypsy64-I_DR# 3474 CCCGTTGGTCTGG--GGATGGAATCCTGAAGACAGACTCGTAGAGGCCCC 3427
Crub_svsplocu 141669 AATTAATGTAAGGAAACTTC--TCCAAAACTTTGCTGTGAACTGCAACCC 141716
i i-- vi v v -- i v vvii i viiv
C Gypsy64-I_DR# 3426 GATC--TGTCGGCAAAATTCCTTCCAAAACCTGGAGACGAATTGGGGGCC 3379
Crub_svsplocu 141717 CCTGTCCAAAATTATTTGCTTAGTGGCG--CCATGCAGCCGGTAGATACG 141764
i vi i ii iv --i vi vi-- v v --i i
C Gypsy64-I_DR# 3378 CCTATCGGAGACCACAT--CTACCGGAAGACCATGAATCCGG--AACACG 3333
Crub_svsplocu 141765 TT-TCAGGAACAATTTGGTCAGTCGT-TGGGCAGATGGGAGTCCTTTGCA 141812
v- ivv v ii iv vi- v v -- vi
C Gypsy64-I_DR# 3332 TGATCAACCACCACCTGAGCAGTCTCCTTGGCAGAGGGGAGT--TTTGGG 3285
Crub_svsplocu 141813 GGTG--ATGAAATGAGCCTGCTTT-GACAACAGGTCTATTACAGTCCAGA 141859
i v -- - - v vv i ii v vvii
C Gypsy64-I_DR# 3284 AGAGGAATGAAATGAGCC-GCTTTNGAGAAGCGGTCCACCACCGTGAGAA 3236
Crub_svsplocu 141860 TGACAGTATTTCCATTACTTTCAGGTAGGTCTACTATAAAATCCATAGCT 141909
i i v v vvv i viiv i i v vi
C Gypsy64-I_DR# 3235 TGACGGTGTTGCCCTTCGATTCAGGTAGGCCAGTGACAAAGTCAAGGGCT 3186
Crub_svsplocu 141910 ATTTCTTCCCATGGTTGAGAAGGG 141933
vv v vv v vi i
C Gypsy64-I_DR# 3185 AAGTGTGACCAGGGACGGGAAGGG 3162
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.08
Transitions / transversions = 0.93 (50/54)
Gap_init rate = 0.06 (18 / 312), avg. gap size = 1.22 (22 / 18)
234 34.53 4.29 0.69 Crub_svsplocus 141819 141958 508042 C Gypsy-194_DR-I LTR/Gypsy 3144 3288 1032
234 34.53 4.29 0.69 Crub_svsplocus 141819 141958 (508042) C Gypsy-194_DR-I#LTR/Gypsy (1032) 3288 3144 m_b3s001i11
Crub_svsplocu 141819 GAAATGAGCCTGC-----TTTGACAACAGGTCTATTACAGTCCAGATGAC 141863
i i ----- v v ivvi v i ivii ii
C Gypsy-194_DR- 3288 GGAATGAGTCTGCACGCCTTGGAAAATCTATCAATTACGGTTAGAATGGT 3239
Crub_svsplocu 141864 AGTATTTCCATTACTTTCAGGTAGGTCTACTATAAAATCCATAGCTATTT 141913
i v v v vv vii v i iii v v
C Gypsy-194_DR- 3238 GGTATTGCCTTGAGATGTGGGGAGATCCGTTATAAAATCGATAGCTATAT 3189
Crub_svsplocu 141914 CTTCCCATGGT-TGAGAAGGGTCTGCGACAGGTTGCAGTAACCCAG 141958
vvvv ? - v ii vv ii -i i i i i
C Gypsy-194_DR- 3188 GGGACCANGGTCTGCGGGGGGTGGGTAA-GGGTTGTAATAATCCGG 3144
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.82
Transitions / transversions = 1.18 (26/22)
Gap_init rate = 0.02 (3 / 139), avg. gap size = 2.33 (7 / 3)
+ 247 18.6 1.7 1.7 Crub_svsplocus 142489 142548 (507452) C Gypsy64-I_DR LTR/Gypsy (1602) 2261 2202 83
ANNOTATION EVIDENCE:
247 18.64 1.67 1.67 Crub_svsplocus 142489 142548 507452 C Gypsy164-I_DR LTR/Gypsy 2202 2261 1602
247 18.64 1.67 1.67 Crub_svsplocus 142489 142548 (507452) C Gypsy164-I_DR#LTR/Gypsy (1602) 2261 2202 m_b3s001i12
Crub_svsplocu 142489 TTCTAGATTTTTGTGATCTGTCCATACCTCAAATGGCA-CCTTGCTCCCT 142537
i i v v v v v - i v -
C Gypsy164-I_DR 2261 TTCTAGATTTTTATGGTCGGTCCAGACCACAAAAGGAACCCCTGAT-CCT 2213
Crub_svsplocu 142538 TCTAGATAGTG 142548
vi
C Gypsy164-I_DR 2212 TCTAGCCAGTG 2202
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.44
Transitions / transversions = 0.57 (4/7)
Gap_init rate = 0.03 (2 / 59), avg. gap size = 1.00 (2 / 2)
+ 241 35.7 1.4 2.1 Crub_svsplocus 142651 142793 (507207) C Gypsy69-I_DR LTR/Gypsy (1779) 2557 2416 84
ANNOTATION EVIDENCE:
241 35.72 1.40 2.11 Crub_svsplocus 142651 142793 507207 C Gypsy76-I_DR LTR/Gypsy 2416 2557 1779
241 35.72 1.40 2.11 Crub_svsplocus 142651 142793 (507207) C Gypsy76-I_DR#LTR/Gypsy (1779) 2557 2416 m_b3s001i13
Crub_svsplocu 142651 TTTGTTCTTTTGCAGTAACACAGATCCAACTGCCACATCGCTGACGTCGG 142700
vii i i vii i v v v vvv i i ii
C Gypsy76-I_DR# 2557 TTTCCCCCTCTGGGATAGCACAGCTCCCACTCCCACATCTGAGGCATCAA 2508
Crub_svsplocu 142701 CTTGAATCACAAAGGGTTCCCCTGGG-CGGGGGTGCTTAGGACCGGTTCA 142749
vi i vvii i-iv i iv v iv v
C Gypsy76-I_DR# 2507 CTTCGACCACAAAGGGTAATTCTGGATTCGGGATAGTAAGGATGGGTGCA 2458
Crub_svsplocu 142750 GCAGCAAATAGTCTCTTTAAATTCTC-AAAAGCTGTTTGACAGCC 142793
vi i -v viv i i i -i i ii --
C Gypsy76-I_DR# 2457 GAGGTAAAT-CTGCGTTTGAGTTCCCTGAAAGCCGCCT--CAGCC 2416
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 46.47
Transitions / transversions = 1.50 (30/20)
Gap_init rate = 0.04 (5 / 142), avg. gap size = 1.00 (5 / 5)
+ 556 32.6 3.9 3.9 Crub_svsplocus 142864 143466 (506534) C Gypsy69-I_DR LTR/Gypsy (1967) 2354 1720 84
ANNOTATION EVIDENCE:
301 35.89 0.88 2.22 Crub_svsplocus 142864 143091 506909 C Gypsy-115-I_DR LTR/Gypsy 2130 2354 1967
301 35.89 0.88 2.22 Crub_svsplocus 142864 143091 (506909) C Gypsy-115-I_DR#LTR/Gypsy (1967) 2354 2130 m_b3s001i15
Crub_svsplocu 142864 AGAGGAAGGGCAATCTTGGCAAAAGAGG-GGGTGAATTGACAATAAAAGT 142912
viv i v - vi vv - ii vi v ii i
C Gypsy-115-I_D 2354 AGAGGCGCGGCGAGCT-GGCTGAAGTTGCGAATGAAACGCCGGTAAAAAT 2306
Crub_svsplocu 142913 TGGCAAAGCCCAGAAAGCTCTGGAGCTGTTTGCAAGTCTTTGGAGGCTGC 142962
i v v v vvvi ii vv i i viv
C Gypsy-115-I_D 2305 TGGCAAAACCAAGAAACCTCTGCAGGGCCTTGCGGGAGTCTGGGGTTGGC 2256
Crub_svsplocu 142963 CATTCAATTATAGCTTTCACCTTGGCTGGATCCATTTCAATACCCTCATT 143012
v v ii i i vv i vv vivv v ivi
C Gypsy-115-I_D 2255 CAATCTACCACAGCCTGAACTTTCTCTGGATCCATGCGCATCCCCTCGAC 2206
Crub_svsplocu 143013 GGAAATTCTGTAGCCAAGATAGTCTAATCGGGTTTG-ATGAAATTCACAT 143061
v v ivv i iv v - ivvv iv iv v - ?v i
C Gypsy-115-I_D 2205 CGACACGATATGTCCCAGA-AAAGGAACAGACTGTGCATGAAANACGCAT 2157
Crub_svsplocu 143062 TTCGACAATTTGGCATAAAGCTTGGCATTC 143091
vv ivi i i---
C Gypsy-115-I_D 2156 TTCTCCGCCTTGACATAAAGCC---CATTC 2130
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.72
Transitions / transversions = 0.78 (35/45)
Gap_init rate = 0.03 (7 / 227), avg. gap size = 1.00 (7 / 7)
471 28.06 2.49 2.49 Crub_svsplocus 142864 143064 506936 C Gypsy-209_DR-I LTR/Gypsy 2029 2229 1951
471 28.06 2.49 2.49 Crub_svsplocus 142864 143064 (506936) C Gypsy-209_DR-I#LTR/Gypsy (1951) 2229 2029 m_b3s001i14
Crub_svsplocu 142864 AGAGGAAGGGCAATCTTGGCAAAAGAGG-GGGTGAATTGACAATAAAAGT 142912
v ii? - i v vvv- i vi i i i i
C Gypsy-209_DR- 2229 AGCGGGGNGGCAA-CTTGACTAAAGTTTCGGATGAAACGGCGATAGAAAT 2181
Crub_svsplocu 142913 TGGCAAAGCCCAGAAAGCTCTG--GAGCTGTTTGCAAGTCTTTGGAGGCT 142960
i i ? i v -- v i ii ii ? --- i?i v
C Gypsy-209_DR- 2180 TGGCGAAACCNAGGAATCTCTGCAGCGCCGTCCGTGANTC---GGGNACG 2134
Crub_svsplocu 142961 G-CCATTCAATTATAGCTTTCACCTTGGCTGGATCCATTTCAATACCCTC 143009
- ? i iv viv? v ? viii ?
C Gypsy-209_DR- 2133 GGCCANTCGATTACCGCGCGNACCTTCGCNGGATCCATGCTGATNCCCTC 2084
Crub_svsplocu 143010 ATTGGAAATTCTGTAGCCAAGATAGTCTAATCGGGTTTG-ATGAAATTCA 143058
?viv i i?vi ? ? v - i?v i i i? iv -
C Gypsy-209_DR- 2083 NGCCGAGACNACGNANCCTAGA-AANGTGACCGANTCGGCATGAAATTCA 2035
Crub_svsplocu 143059 CATTTC 143064
i
C Gypsy-209_DR- 2034 CACTTC 2029
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.21
Transitions / transversions = 1.75 (35/20)
Gap_init rate = 0.04 (9 / 200), avg. gap size = 1.11 (10 / 9)
546 34.73 4.88 4.70 Crub_svsplocus 142893 143466 506534 C Gypsy72-I_DR LTR/Gypsy 1720 2294 2003
546 34.73 4.88 4.70 Crub_svsplocus 142893 143466 (506534) C Gypsy72-I_DR#LTR/Gypsy (2003) 2294 1720 m_b3s001i16
Crub_svsplocu 142893 GGTGAATTGACAATAAAAGTTGGCAAAGCCCAGAAAGCTCTGGA--GCTG 142940
i i v ii i i i v v v -- iv
C Gypsy72-I_DR# 2294 GATGAATCGCCGGTAAAAATTGGCGAAGCCCAGGAACCGCTGTAACGCCT 2245
Crub_svsplocu 142941 TTTGCAAGTCTTTGGAGGCTGCCATTCAATTATAGCTTTCACCTTGGCTG 142990
i vi v-- v v v iivv i ii v v v
C Gypsy72-I_DR# 2244 TTCGGGAGTCG--GGTGGCGGCCAGTCGGAGACAGCCCTAACCTTCGCAG 2197
Crub_svsplocu 142991 GATCCATTTCAATACCCTCATTGGAAATTCTGTAGCC-AAGATAGT--CT 143037
i viv vv viv v iv - vi v--
C Gypsy72-I_DR# 2196 GGTCCATGCGAAGTCCCTCAACTGAAATTATGTGTCCCAAGAAGGAAACT 2147
Crub_svsplocu 143038 AATCGGGTTTGATGAAATTCACATTTCGACAATTTGGCATAAAGCTTGGC 143087
i ii ii--- i i i vv ivi vi v vivi
C Gypsy72-I_DR# 2146 GACTGGAC---ATGGAATTCGCACTTCTCCGCCTTTACATACAGCTGATT 2100
Crub_svsplocu 143088 ATTCAATAGTTTCTTTAACATTTCTCTCACCAGCTTTATGTGATCAGTCA 143137
v i ii iivi v i ----- i ii---- i - ii v
C Gypsy72-I_DR# 2099 CTCCAGCAGCCGTTGTAGCA-----CTCGCCGA----ACGTG-TTGGACA 2060
Crub_svsplocu 143138 TATTCGTGC-TGT---------ATATCAGGATTTCATCAAGATACACCAA 143177
i v - v--------- v v i v v i v v
C Gypsy72-I_DR# 2059 TGTTCCTGCATGGCGGAAGAAAAAATAAGAATGTCATCCAAATAAACAAA 2010
Crub_svsplocu 143178 AACCCCTTTGTACAAGTGATCATGT-----AGGACCTCATTAATCAACTG 143222
vvv -----i v i ----- v v i i - i v
C Gypsy72-I_DR# 2009 AACAAATT-----GATTAATCATGTCTCGGAGTACATCGTTGA-CGAGTG 1966
Crub_svsplocu 143223 CAT-AAATACATCTGGGGCCCCCTGT-AGTCCAAATGGCATGACTTTGAA 143270
v - v vv i viiv- - i v ---i i
C Gypsy72-I_DR# 1965 CCTGAAAGACTGCTGGAGCATTG-GTGAGCCCAAATGGCAGGAC---AAG 1920
Crub_svsplocu 143271 CTAAT--AGCTCCCCATAGGACA-GTTGAAGGCAGTTTTCCACTCGTCTC 143317
v v -- iv v vv i i- v i i i v
C Gypsy72-I_DR# 1919 ATATTCAAAATGCCCAGTGGGCGTGTTGAATGCGGTCTTCCATTCGTCAC 1870
Crub_svsplocu 143318 CCTCTTTTATTCTCACTCAGTAATATGCTTCTCTTAGGTCTAATTTAGTG 143367
ii i v vv vvii ii v v iv v i i v
C Gypsy72-I_DR# 1869 CCTCCCTCATACGGACGAGATGGTAAGCATTGCGTAGGTCCAACTTTGTG 1820
Crub_svsplocu 143368 AAGAAACT---CCCCTTAACCAGATGGGTTAATAAATCCTTTAGGAGTGG 143414
i v --- vv vv v ivvivii vv v v vi i
C Gypsy72-I_DR# 1819 AAAAATCTTGCCCCCTGCAAGAGATCGAAGGCCGAAGACATAAGCGGTAG 1770
Crub_svsplocu 143415 GAAGGGTATTCATTTTCCACACTCACAGCATTGAGACCCTTATAGTCTAT 143464
-- iiv iv iiv i iiv v i iiv
C Gypsy72-I_DR# 1769 G--GGGTACCGATTTTTAATGGTTATGTCATTCAAACCTCGATAGTCTAT 1722
Crub_svsplocu 143465 GC 143466
C Gypsy72-I_DR# 1721 GC 1720
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.98
Transitions / transversions = 0.98 (94/96)
Gap_init rate = 0.07 (38 / 573), avg. gap size = 1.45 (55 / 38)
556 32.69 3.12 3.12 Crub_svsplocus 142895 143374 506626 C Gypsy69-I_DR LTR/Gypsy 1734 2213 2032
556 32.69 3.12 3.12 Crub_svsplocus 142895 143374 (506626) C Gypsy69-I_DR#LTR/Gypsy (2032) 2213 1734 m_b3s001i17
Crub_svsplocu 142895 TGAATTGACAATAAAAGTTGGCAAAGCCCAGAAAGCTCTGGAGCTGTTTG 142944
ii i i i v i v i v i vi -
C Gypsy69-I_DR# 2213 TGAACCGGCGATAAAAGTTGGCGAACCCTAGAAATCTTTGTAGTTCCTT- 2165
Crub_svsplocu 142945 CAA-GTCTTTGGAGGCTGCCATTCAATTATAGCTTTCACCTTGGCTGGAT 142993
v- i v ii vv ?i i v iv i vv ?vvvi
C Gypsy69-I_DR# 2164 CACTGTTTTGGGGAGAGGCCANCCAGTGACTGCCTGAACCTTGGNGTCGT 2115
Crub_svsplocu 142994 CCATTTCAATACCCTCATTGGAAATTCTGTAGCCAAGATAGTCTAATCGG 143043
v iv v v v vvi vv v v i------ ivi
C Gypsy69-I_DR# 2114 CCATTTCCACTCCGTGATGGCTGATAATGTATCCCAGG------AACGAG 2071
Crub_svsplocu 143044 GTTT--GA----TGAAATTCACATTTCGACAATTTGGCATAAAGCTTGGC 143087
i -- ---- i i vv iii i i - i
C Gypsy69-I_DR# 2070 GTCTTGGACACGTGGAATTCACACTTCTCCGGCTTGGCGTAGAG-TTGGT 2022
Crub_svsplocu 143088 ATTC----AATAGTTTCTTTAACATTTCTCTCACCAGCTTTATGTGATCA 143133
v ---- ?v v vv- v i vv ii -- v v --
C Gypsy69-I_DR# 2021 TTTCTTGTAANCGTGTCAA-AACAGTCCTGACGTC--CTTGATGTGTT-- 1977
Crub_svsplocu 143134 GTCATA--TTCGTGCTGTATATCAGGATTTCATCAAGATACACCAAAACC 143181
iv -- v v vvi v v ? v vi v vi v
C Gypsy69-I_DR# 1976 GTTCTAGGTTGGGGGAATAGATCAGGATGTCATCNATATAGGCGATGACA 1927
Crub_svsplocu 143182 CCTTTGTACAAGTGATCATGTAGGACCTCATTAATCAACTGCATAAATAC 143231
v v ivvi vivv ii ii ? v ivi vvi v
C Gypsy69-I_DR# 1926 CATTTGTTCAGCAAATCTCTGAAAATTTCATTNATGAATGACTGGAAGAC 1877
Crub_svsplocu 143232 ATCTGGGGCCCCCTGTAGTCCAAATGGCATGACTTTGAACTAATAGCTCC 143281
?v ? vvii?vv? ? v v i ?vv v i v iv
C Gypsy69-I_DR# 1876 NGCTGGNGAGTTNGCNAGNCCATAGGGCATAACNAGGTATTCATAGTGCC 1827
Crub_svsplocu 143282 CCATAG--GACAGTTGAAGGCAGTTTTCCACTCGTCTCCCTCTTTTATTC 143329
v -- v -- v i iivv ?
C Gypsy69-I_DR# 1826 CCCTAGTGGTCAG--GAACGCGGTTTTCCACTCGTCTCCCTCCCGGATNC 1779
Crub_svsplocu 143330 TCACTCAGTAATATGCTTCTCTTAGGTCTAATTTAGTGAAGAAAC 143374
vv i?vi v v vii v v i i v v
C Gypsy69-I_DR# 1778 GAATNAGGTTATAAGCACTTCTGAGGTCAAGTTTGGTGTAGATAC 1734
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.12
Transitions / transversions = 0.69 (62/90)
Gap_init rate = 0.04 (21 / 479), avg. gap size = 1.43 (30 / 21)
+ 472 13.0 0.0 0.0 Crub_svsplocus 143467 143535 (506465) + URR1B DNA/hAT-Charlie 1 69 (156) 85
ANNOTATION EVIDENCE:
472 13.04 0.00 0.00 Crub_svsplocus 143467 143535 506465 + URR1B DNA/hAT-Charlie 1 69 156
472 13.04 0.00 0.00 Crub_svsplocus 143467 143535 (506465) URR1B#DNA/hAT-Charlie 1 69 (156) m_b3s001i18
Crub_svsplocu 143467 CAGTGGTTCTCAACCTGTGGGTCGCAACCCCATTTGGGGTCGAACAACCA 143516
i i v v i v
URR1B#DNA/hAT 1 CAGCGGTTCTCAACCTGTGGGTCGCGACCCCTTTGGGGGTCGAACGACCC 50
Crub_svsplocu 143517 TTTCACGGGGGTCACCAAA 143535
i i v
URR1B#DNA/hAT 51 TTTCACAGGGGTCGCCTAA 69
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.27
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
+ 245 12.1 0.0 0.0 Crub_svsplocus 144121 144153 (505847) + URR1B DNA/hAT-Charlie 193 225 (0) 86
ANNOTATION EVIDENCE:
245 12.12 0.00 0.00 Crub_svsplocus 144121 144153 505847 + URR1B DNA/hAT-Charlie 193 225 0
245 12.12 0.00 0.00 Crub_svsplocus 144121 144153 (505847) URR1B#DNA/hAT-Charlie 193 225 (0) m_b3s001i19
Crub_svsplocu 144121 GGGTCACGGCATTAAAAAGGTTGAGAACCACTG 144153
i i ii
URR1B#DNA/hAT 193 GGGTCGCAGCATTAGGAAGGTTGAGAACCACTG 225
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.41
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 13 22.8 6.2 3.0 Crub_svsplocus 146872 146936 (503064) + (TTTC)n Simple_repeat 1 67 (0) 87
ANNOTATION EVIDENCE:
13 22.79 6.15 2.99 Crub_svsplocus 146872 146936 503064 + (TTTC)n Simple_repeat 1 67 0
13 22.79 6.15 2.99 Crub_svsplocus 146872 146936 (503064) (TTTC)n#Simple_repeat 1 67 (0) m_b3s252i5
Crub_svsplocu 146872 TTTTTTTGTTTCTTT-ACTCTTGCTCTCCTTTCTTCCTTT-TTT-TTTCA 146918
i v -vi v - i i - - v
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCTTTCT 49
Crub_svsplocu 146919 CTATTT-TATCTATTCCTT 146936
i v - v - i
(TTTC)n#Simpl 50 TTCTTTCTTTCT-TTCTTT 67
Matrix = Unknown
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.09 (6 / 64), avg. gap size = 1.00 (6 / 6)
+ 273 29.4 4.0 4.0 Crub_svsplocus 148988 149139 (500861) C Gypsy138-I_DR LTR/Gypsy (6125) 5285 5134 88
ANNOTATION EVIDENCE:
273 29.45 3.95 3.95 Crub_svsplocus 148988 149139 500861 C Gypsy138-I_DR LTR/Gypsy 5134 5285 6125
273 29.45 3.95 3.95 Crub_svsplocus 148988 149139 (500861) C Gypsy138-I_DR#LTR/Gypsy (6125) 5285 5134 m_b3s001i20
Crub_svsplocu 148988 GGTTGCAGTAGCCCAGGAGTTT---TTCCCGGGATTCTTTTCGTTGTGGC 149034
v i v vv v i--- ii -- i viv -
C Gypsy138-I_DR 5285 GGGTGCAGCAGGCCTTGAGGTCGGGTTCTTGG--TTCCTTGTTTTGTG-C 5239
Crub_svsplocu 149035 ACATACAGTACAACTTTTTACAAAGTTTTCCACATCCTTTTTCAGCCCCG 149084
v vi vivviv vivv i v i ii
C Gypsy138-I_DR 5238 ACAAACAGAGCAAGCAGCAACAAAGTTGCGGACATCCTTCTGCAGTCTTG 5189
Crub_svsplocu 149085 GCCACCAAAATTGCCGGCGGGTGAG-GTGTAGGGTTTTCAAATA--TCCA 149131
v vvi i -v - i -- i --i
C Gypsy138-I_DR 5188 GCCACCAAAATTTCCTCTGGATGAGCTTGT-GGGTTCT--AGTAGTCCCA 5142
Crub_svsplocu 149132 AAGTGTCC 149139
ii i
C Gypsy138-I_DR 5141 GGGTGCCC 5134
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 35.76
Transitions / transversions = 1.05 (22/21)
Gap_init rate = 0.06 (9 / 151), avg. gap size = 1.33 (12 / 9)
+ 441 31.7 2.9 2.9 Crub_svsplocus 149414 149855 (500145) C Gypsy72-I_DR LTR/Gypsy (1399) 2889 2481 89
ANNOTATION EVIDENCE:
316 29.12 5.50 5.50 Crub_svsplocus 149414 149631 500369 C Gypsy103-I_Dr LTR/Gypsy 2593 2810 1476
316 29.12 5.50 5.50 Crub_svsplocus 149414 149631 (500369) C Gypsy103-I_Dr#LTR/Gypsy (1476) 2810 2593 m_b3s001i21
Crub_svsplocu 149414 CGGGATAGCGCATCAG-CTAGAAAGTTCTTTCCTCCTGGTATGTACTTTA 149462
v v i - v v - vvi v v v ivv
C Gypsy103-I_Dr 2810 CGGGAGAGGGCATCGGGCTTGACA-TTCTTGGTTCCAGGTCTGAATGATA 2762
Crub_svsplocu 149463 GAGTGAAGTTGAAGCGGTTAAAGTACTGTGCCCACCGTACTTGCTTTGGG 149512
i i v i i v vv v v vi i iivv
C Gypsy103-I_Dr 2761 GGGTAAATTTAAAGCGGTCAAAGAAGAGGGCCCAGCGAGCCTGTCGAGGG 2712
Crub_svsplocu 149513 GACAATTT----GC-GA--GGAGTTTTCAGTGCCTCTAGGTTCTTGTGAT 149555
v iii ---- - -- vv v ------- v i
C Gypsy103-I_Dr 2711 GTCAGCCTCCTGGCCGAACGGATATAT-------TCGAGATTCTTGTGAT 2669
Crub_svsplocu 149556 CTGTCCATACCTCAAATGGCACCTT--GCT--CCCTTCTAGATAGTGTCG 149601
i v vvi v ---- -- -- vi v
C Gypsy103-I_Dr 2668 CCGTCCAGACCAGGAAAGG----TTGGGCTGCCCCTTCTAGCCAGTGACG 2623
Crub_svsplocu 149602 CCAGTTCAATAGCGCCCACCTAATTGCGAA 149631
v i vvi v vi i i v
C Gypsy103-I_Dr 2622 CCACTCCCCCAGAGCCAGCCTGACTGCCAA 2593
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.76
Transitions / transversions = 0.62 (23/37)
Gap_init rate = 0.08 (18 / 217), avg. gap size = 1.33 (24 / 18)
441 25.67 2.09 2.09 Crub_svsplocus 149414 149604 500396 C Gypsy172-I_Dr LTR/Gypsy 2505 2695 1521
441 25.67 2.09 2.09 Crub_svsplocus 149414 149604 (500396) C Gypsy172-I_Dr#LTR/Gypsy (1521) 2695 2505 m_b3s001i22
Crub_svsplocu 149414 CGGGATAGCGCATCAGCTAGAAAGTTCTTTCCTCCTGGTATGTACTTTAG 149463
v v v vv? vi vv? ? v?i vv v v
C Gypsy172-I_Dr 2695 CGGGAGAGGGCATCCGCTTTNATATTCTTTGANCCNGGANCGTAGGTGAC 2646
Crub_svsplocu 149464 AGTGAAGTTGAAGCGGTTAAAGTACTGTGCCCACCGTACTTGCTTTGGG- 149512
v?? i ?v v v ? i v i i v -
C Gypsy172-I_Dr 2645 TNNGAAGTCGAAGCGNGTAAAGAACAGNGCCCATCTTGCTTGCCTGGGGT 2596
Crub_svsplocu 149513 ---GACAATTTGCGAGGAGTTTTCAGTGCCTCTAGGTTCTTGTGATCTGT 149559
--- ? ?v v ---- ? i? vvv i i
C Gypsy172-I_Dr 2595 TNAGNCNCTTGGC----AGNTCNCAGATACTCTAGATTCTTATGATCTGT 2550
Crub_svsplocu 149560 CCATACCTCAAATGGCACCTTGCTCCCTTCTAGATAGTGTCGCCA 149604
?v?v vvii vvvi v? i i vi ?
C Gypsy172-I_Dr 2549 NANGACGGTGAATGGGTGTTTGGNCCCCTCCAGCCAGTGTCNCCA 2505
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.53
Transitions / transversions = 0.45 (15/33)
Gap_init rate = 0.03 (6 / 190), avg. gap size = 1.33 (8 / 6)
307 37.12 3.18 3.18 Crub_svsplocus 149447 149855 500145 C Gypsy-195_DR-I LTR/Gypsy 2481 2889 1399
307 37.12 3.18 3.18 Crub_svsplocus 149447 149855 (500145) C Gypsy-195_DR-I#LTR/Gypsy (1399) 2889 2481 m_b3s001i23
Crub_svsplocu 149447 CCTGGTATGTACTTTAGAGTGAAGTTGAAGCGGTTAAAGTACTGTGCCCA 149496
vv vv v i ? i v iv v v
C Gypsy-195_DR- 2889 CCTGGTCGGTAAGTGAGAGTGAAATNGAAGCGGTTGAAGAATAGAGACCA 2840
Crub_svsplocu 149497 CCGTACTTGCTTTGGGGACAATTTGCGAGGAGTTTTCAGTGC-CTCTAGG 149545
v i i -viv vii v i vvv vv v vii i- v i
C Gypsy-195_DR- 2839 ACGTGCCTG-GCGGGGGTTGAGTCGCTTTGCCTGTTGGATGTACTCGAGA 2791
Crub_svsplocu 149546 TTCTTGTGATCTGTCCATACCTCAAATGGCACCTTGCTCCCTTCTAGATA 149595
i i vvii i i v vvvi viv i i vi
C Gypsy-195_DR- 2790 TTCTTGTGGTCCGTGAGCACTTCGAAAGGGTGTTTGGCACCCTCCAGCCA 2741
Crub_svsplocu 149596 GTGTCGCCAGTTCAATAGCGCCCACCTAATTGCGAAGGCCTCTTTCTCCC 149645
v v i vvi v iv i iv v iviv i v v
C Gypsy-195_DR- 2740 GTGTCTCCATTCCTCCAGGGCTAACTTAACGGCTAGTAACTCTCTGTCAC 2691
Crub_svsplocu 149646 AGATTGCCCATCTTCGCTCGCTCTCAGTGAATTTCTTAGAGGTGTAGGCA 149695
vv ----- vv v i - iivv ---- i vv v
C Gypsy-195_DR- 2690 CTAT-----ATGATAGTTC-CTCTCAGTGGGAGT----GAGGCGGTGGGA 2651
Crub_svsplocu 149696 CAGGGTTGCA---GGATCCAATTT-TTGT--TCT----TTTGAAGTAACA 149735
v iv --- vi ii - -- ---- i iii i
C Gypsy-195_DR- 2650 GAGGAATGCACACGGATGTAGCTTGTTGTCATCTCCTCTCTGGGATAATA 2601
Crub_svsplocu 149736 CTGCTCCAACCGCCACATC-GCTGGCGTCGGCTTGAATCACAAAGGGTTC 149784
i vv i -i -- vi vv iiiii ii
C Gypsy-195_DR- 2600 CTGCCCCAACGCCTACATCTAC--GCGTCCACTTCCACTGTGAAGGGTCT 2553
Crub_svsplocu 149785 CCCTGGGCAGGGGTGCTTTAGAACCAGTTCAGCGGCAAATAGTCTCTTTA 149834
vi iv iv vv?v i ivi v v ii vv v v
C Gypsy-195_DR- 2552 GTCTGGGTTGGGAAGGANAAGGATAGGTGCAGAGGTGAAGCGACTCTTGA 2503
Crub_svsplocu 149835 AATTCTCAAAAGCT-GTTTGAC 149855
ii v ii i i- i i
C Gypsy-195_DR- 2502 GGTTGTTGAAGGCCAGTTCGGC 2481
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 49.08
Transitions / transversions = 0.96 (72/75)
Gap_init rate = 0.05 (20 / 408), avg. gap size = 1.30 (26 / 20)
+ 622 34.2 5.6 4.4 Crub_svsplocus 149921 150771 (499229) C Gypsy72-I_DR LTR/Gypsy (1969) 2313 1394 89
ANNOTATION EVIDENCE:
340 34.29 0.00 0.00 Crub_svsplocus 149921 150060 499940 C Gypsy105-I_Dr LTR/Gypsy 2174 2313 1969
340 34.29 0.00 0.00 Crub_svsplocus 149921 150060 (499940) C Gypsy105-I_Dr#LTR/Gypsy (1969) 2313 2174 m_b3s001i24
Crub_svsplocu 149921 AGTTCTGCAAGAGGAAGGGCAATCTCGGCAAAAGAAGGGATGAATTGACG 149970
v iv i vivi v v ivvvvv vi v
C Gypsy105-I_Dr 2313 AGTGCTGTTAGGGGTGCAGCAATCTGGCCAAAGTTCCTGATGAAACGCCG 2264
Crub_svsplocu 149971 ATAAAAGTTGGCAAAACCCAGAAAGCTTTGGAGCTGTTTGTGAGTCCTTG 150020
i v i v vi v ivvi i vvii
C Gypsy105-I_Dr 2263 ATAAAAGTTGGCGAATCCCAGGAACCGCTGCAGTGCCTTGCGAGAGTCTG 2214
Crub_svsplocu 150021 GGGGTTGCCATTCGATTATAGTTTTTACCTTGGCCGGATC 150060
i v v i iiv i iii v v
C Gypsy105-I_Dr 2213 GAGTTGGCCACTCGGCAACAGCCCTTACCTTTGCAGGATC 2174
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.55
Transitions / transversions = 0.85 (22/26)
Gap_init rate = 0.00 (0 / 139), avg. gap size = 0.0 (0 / 0)
622 34.72 5.40 3.82 Crub_svsplocus 149959 150551 499449 C Gypsy72-I_DR LTR/Gypsy 1693 2294 2003
622 34.72 5.40 3.82 Crub_svsplocus 149959 150551 (499449) C Gypsy72-I_DR#LTR/Gypsy (2003) 2294 1693 m_b3s001i25
Crub_svsplocu 149959 GATGAATTGACGATAAAAGTTGGCAAAACCCAGAAA--GCTTTGGAGCTG 150006
i v i i i i i -- v iiv iv
C Gypsy72-I_DR# 2294 GATGAATCGCCGGTAAAAATTGGCGAAGCCCAGGAACCGCTGTAACGCCT 2245
Crub_svsplocu 150007 TTTGTGAGTCCTTGGG-GGTTGCCATTCGATTATAGTTTTTACCTTGGCC 150055
i v --- - iv v ivv i iii v v v
C Gypsy72-I_DR# 2244 TTCGGGAGTC---GGGTGGCGGCCAGTCGGAGACAGCCCTAACCTTCGCA 2198
Crub_svsplocu 150056 GGATCTATTTCAATATCCTCATTGGAAATTCGGTAGCC-AAGATAGT--C 150102
i i viv vvi viv vv iv - vi v--
C Gypsy72-I_DR# 2197 GGGTCCATGCGAAGTCCCTCAACTGAAATTATGTGTCCCAAGAAGGAAAC 2148
Crub_svsplocu 150103 TAATTGGGTTCGGTGAAATTCACATTTTGACAATTTGACATAAAGCTTGG 150152
i i ii---i i i i ivv ivi v v viv
C Gypsy72-I_DR# 2147 TGACTGGAC---ATGGAATTCGCACTTCTCCGCCTTTACATACAGCTGAT 2101
Crub_svsplocu 150153 CATTCAATAGTTTCTTTAACACTTCTCTCACTAGCTTTATGTGATCATTC 150202
iv i ii iivi v i ivi vv vv i vv ii v v v
C Gypsy72-I_DR# 2100 TCTCCAGCAGCCGTTGTAGCACTCGCCGAACGTGTTGGACATGTTCCTGC 2051
Crub_svsplocu 150203 ATGTTTGTGCTGTATATCAGGATATCATCAAGATACACCAAAACCCCTTT 150252
viv vivviv v v i i v i v v vvv -
C Gypsy72-I_DR# 2050 ATGGCGGAAGAAAAAATAAGAATGTCATCCAAATAAACAAAAACAAATT- 2002
Crub_svsplocu 150253 GTACAAGTGATCATGT-----AGAACCTCATTAATCAACTGCAT-AAATA 150296
----i v i ----- v v i i - i v v - v
C Gypsy72-I_DR# 2001 ----GATTAATCATGTCTCGGAGTACATCGTTGA-CGAGTGCCTGAAAGA 1957
Crub_svsplocu 150297 CATCTGGGGCCCCCTGT-AGTCCAAATGGCATGACTTTGAACTAAT--AG 150343
vv i viiv- - i v ---i iv v -- i
C Gypsy72-I_DR# 1956 CTGCTGGAGCATTG-GTGAGCCCAAATGGCAGGAC---AAGATATTCAAA 1911
Crub_svsplocu 150344 CTCCCCATAGGACA-GTTGAAGGCAGTTTTCCACTCGTCTCCCTCTTTTA 150392
v v vv i i- v i i i v ii i
C Gypsy72-I_DR# 1910 ATGCCCAGTGGGCGTGTTGAATGCGGTCTTCCATTCGTCACCCTCCCTCA 1861
Crub_svsplocu 150393 TTCTCACCCGGTAGTATGCCTCTCTTAGGTCTAACTTAGTGAAGACACT- 150441
v vv vv i i v v iv v i v i vv -
C Gypsy72-I_DR# 1860 TACGGACGAGATGGTAAGCATTGCGTAGGTCCAACTTTGTGAAAAATCTT 1811
Crub_svsplocu 150442 -CCCCTTAGCCAG-----GTGGGTCAATAAATCCTTTAGGAGGGGGAGGG 150485
- i - v ----- vi i i - i -----i vi v v
C Gypsy72-I_DR# 1810 GCCCCCT-GCAAGAGATCGAAGGCCGA-AGA-----CATAAGCGGTAGGG 1768
Crub_svsplocu 150486 GGTATTTATTTTCCACACTTACAGCATT---------GTAGTCTACACAG 150526
iiv iv iiv iiv ---------i ii
C Gypsy72-I_DR# 1767 GGTACCGATTTTTAATGGTTATGTCATTCAAACCTCGATAGTCTATGCAG 1718
Crub_svsplocu 150527 AGACGAAGAGACCCATCTTTTTTCT 150551
i i v v i
C Gypsy72-I_DR# 1717 GGGCGCAGAGAACCATCCTTTTTCT 1693
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.46
Transitions / transversions = 1.00 (99/99)
Gap_init rate = 0.06 (36 / 592), avg. gap size = 1.53 (55 / 36)
580 34.18 5.67 4.51 Crub_svsplocus 149960 150771 499229 C Gypsy69-I_DR LTR/Gypsy 1394 2214 2031
580 34.18 5.67 4.51 Crub_svsplocus 149960 150771 (499229) C Gypsy69-I_DR#LTR/Gypsy (2031) 2214 1394 m_b3s001i26
Crub_svsplocu 149960 ATGAATTGACGATAAAAGTTGGCAAAACCCAGAAAGCTTTGGAGCTGTTT 150009
ii i i v i v v i vi
C Gypsy69-I_DR# 2214 ATGAACCGGCGATAAAAGTTGGCGAACCCTAGAAATCTTTGTAGTTCCTT 2165
Crub_svsplocu 150010 GTGAGTCCTTGGGGGTTGCCATTCGATTATAGTTTTTACCTTGGCCGGAT 150059
vvvv ii v i vv ?i ii v iv ii vv ?vvvi
C Gypsy69-I_DR# 2164 CACTGTTTTGGGGAGAGGCCANCCAGTGACTGCCTGAACCTTGGNGTCGT 2115
Crub_svsplocu 150060 CTATTTCAATATCCTCAT---TGGAAATTCGGTAGCCAAGATA----GTC 150102
i v ivi v v --- iv --- v v iv ----
C Gypsy69-I_DR# 2114 CCATTTCCACTCCGTGATGGCTGATAAT---GTATCCCAGGAACGAGGTC 2068
Crub_svsplocu 150103 TAATTGGGTTCGGTGAAATTCACATTTTGACAATTTGACATAAAGCTTGG 150152
--- iiv - i i ivv iii i i i -
C Gypsy69-I_DR# 2067 T---TGGACACG-TGGAATTCACACTTCTCCGGCTTGGCGTAGAG-TTGG 2023
Crub_svsplocu 150153 CATTC----AATAGTTTCTTTAACACTTCTCTCACTAGCTTTATGTGATC 150198
iv ---- ?v v --- v vvii v vvv v - i
C Gypsy69-I_DR# 2022 TTTTCTTGTAANCGTGTC---AAAACAGTCCTGACGTCCTTGATGTG-TT 1977
Crub_svsplocu 150199 ATTC-ATGTTTGTGCTGTATATCAGGATATCATCAAGATACACCAAAACC 150247
i - v v v vvi v i ? v vi v vi v
C Gypsy69-I_DR# 1976 GTTCTAGGTTGGGGGAATAGATCAGGATGTCATCNATATAGGCGATGACA 1927
Crub_svsplocu 150248 CCTTTGTACAAGTGATCATGTAGAACCTCATTAATCAACTGCATAAATAC 150297
v v ivvi vivv i ii ? v ivi vvi v
C Gypsy69-I_DR# 1926 CATTTGTTCAGCAAATCTCTGAAAATTTCATTNATGAATGACTGGAAGAC 1877
Crub_svsplocu 150298 ATCTGGGGCCCCCTGTAGTCCAAATGGCATGACTTTGAACTAATAGCTCC 150347
?v ? vvii?vv? ? v v i ?vv v i v iv
C Gypsy69-I_DR# 1876 NGCTGGNGAGTTNGCNAGNCCATAGGGCATAACNAGGTATTCATAGTGCC 1827
Crub_svsplocu 150348 CCATAG--GACAGTTGAAGGCAGTTTTCCACTCGTCTCCCTCTTTTATTC 150395
v -- v -- v i iivv ?
C Gypsy69-I_DR# 1826 CCCTAGTGGTCAG--GAACGCGGTTTTCCACTCGTCTCCCTCCCGGATNC 1779
Crub_svsplocu 150396 TCACCCGGTAGTATGCCTCTCTTAGGTCTAACTTAGTGAAGACA----CT 150441
vv i?v vi v vii v v ii i v i ----
C Gypsy69-I_DR# 1778 GAATNAGGTTATAAGCACTTCTGAGGTCAAGTTTGGTGTAGATACGGGCT 1729
Crub_svsplocu 150442 CCCCTTAGC----------CAGGTGGGTCAATAAATCCTTTAGGAGGGGG 150481
i v v i---------- ? ------- i ------- i i
C Gypsy69-I_DR# 1728 TCACGTAGTTGTTCNAGGGCAGGNGGG-------ACC-------AAGGGA 1693
Crub_svsplocu 150482 AGGGGGTATTTATTTTCCACACTTACAGCATT---------GTAGTCTAC 150522
i viv vi iv v v ivi --------- v i
C Gypsy69-I_DR# 1692 AGAGGGTAACGATACTTGACAGTGACGTTATTCAANCCTCGGTAGTCGAT 1643
Crub_svsplocu 150523 ACAGAGACGAAGAGACCCATCTTTTTTCTCTTTGAACAACACAGGTGCTC 150572
i ?i i vvi i i ivi v v vvvv v
C Gypsy69-I_DR# 1642 GCANGGACGGAGACCTCCATCCTTCTTCTCCACGAAGAAGAATCCTGCTG 1593
Crub_svsplocu 150573 CCACGGAAGATTTGGCCCGTTCAATAAACCCCCTCGCTCGGTTCTTGTTC 150622
?i ? iv ?v i v?v iv iv v vvv? v vi iv iv
C Gypsy69-I_DR# 1592 CNGCNGGTGANGTAGANGGTCGAATGTAACCAGANGCTAGGGCCTCCTCG 1543
Crub_svsplocu 150623 ACATATCGCTGCATCTCCTCCATTTCGAGGGGGGACATAGCATACA---T 150669
ii vvi v vv i vvi i iv i v? vi v ---
C Gypsy69-I_DR# 1542 ATGTATGTTTCCATGGCTTGAGTTTCGGGACGAGACAGNGGGTAAACTTT 1493
Crub_svsplocu 150670 CCTCTGACGTGGGAGTTTGGCTCCGGGCACCAGTTCGATGGAGCAGTCAT 150719
v i v v iiiv i---ii i v i ? vi vi
C Gypsy69-I_DR# 1492 GCTTTTAGGTGGGGACATA---TTGGGTAGCAGTTCAATNGCACAGTCCC 1446
Crub_svsplocu 150720 TGGGTCTGTGAGGGGGTA---GGGCATCACATTCTTT---TTCACTGAAC 150763
vi ? vi ? --- ------ v --- ii i
C Gypsy69-I_DR# 1445 AAGGNCGATGAGGNGGTAGTTGGGC------TGCTTTAGATTTGCTGAAT 1402
Crub_svsplocu 150764 ACCTCCGC 150771
i
C Gypsy69-I_DR# 1401 ACCTCTGC 1394
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 45.29
Transitions / transversions = 0.84 (121/144)
Gap_init rate = 0.06 (48 / 811), avg. gap size = 1.73 (83 / 48)
+ 19 28.7 0.0 4.8 Crub_svsplocus 151433 151541 (498459) + (TTTATTT)n Simple_repeat 1 103 (0) 90
ANNOTATION EVIDENCE:
18 24.40 6.67 2.13 Crub_svsplocus 151433 151522 498478 + (TTTA)n Simple_repeat 1 94 0
18 24.40 6.67 2.13 Crub_svsplocus 151433 151522 (498478) (TTTA)n#Simple_repeat 1 94 (0) m_b3s252i6
Crub_svsplocu 151433 TTTAGTTA-TAGTTTAGTT-TTACTTTATTT-TCT-TTTTTTTAGTTTAT 151478
v - vi v - vv - i - v -
(TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTA-TTTAT 49
Crub_svsplocu 151479 TTAGTTAATTTA-GCATGTGCTGGTTTTTTTATTT-TTTATTTTTT 151522
- v -vi v ii vi v - v
(TTTA)n#Simpl 50 TTA-TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATT 94
Matrix = Unknown
Transitions / transversions = 0.50 (6/12)
Gap_init rate = 0.09 (8 / 89), avg. gap size = 1.00 (8 / 8)
19 28.74 0.00 4.82 Crub_svsplocus 151455 151541 498459 + (TTTATTT)n Simple_repeat 1 83 0
19 28.74 0.00 4.82 Crub_svsplocus 151455 151541 (498459) (TTTATTT)n#Simple_repeat 1 83 (0) m_b3s252i7
Crub_svsplocu 151455 TTTATTTTCTTTTTTTTAGTTTATTTAGTTAATTTAGCATGTGCTGGTTT 151504
i v v v v vv v vvi - -i vvv
(TTTATTT)n#Si 1 TTTATTTTTTATTTTTTATTTTTTATTTTTTATTTTTTAT-T-TTTTATT 48
Crub_svsplocu 151505 TTTTATTTTTTATTTTTTGAGCTTTCTCTTTTTTCTT 151541
- -i i v v
(TTTATTT)n#Si 49 TTTTATTTTTTATTTTTT-A-TTTTTTATTTTTTATT 83
Matrix = Unknown
Transitions / transversions = 0.36 (5/14)
Gap_init rate = 0.05 (4 / 86), avg. gap size = 1.00 (4 / 4)
+ 12 24.1 0.0 0.0 Crub_svsplocus 152015 152048 (497952) + GA-rich Low_complexity 1 34 (0) 91
ANNOTATION EVIDENCE:
12 24.12 0.00 0.00 Crub_svsplocus 152015 152048 497952 + (AAGG)n Simple_repeat 1 34 0
12 24.12 0.00 0.00 Crub_svsplocus 152015 152048 (497952) (AAGG)n#Simple_repeat 1 34 (0) m_b3s252i8
Crub_svsplocu 152015 AAGCAAGGAAGAAATGAAGCAAGAGATGAAGGAA 152048
v i v v ii v
(AAGG)n#Simpl 1 AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA 34
Matrix = Unknown
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0)
+ 18 0.0 0.0 9.7 Crub_svsplocus 152868 152901 (497099) + (AAAGAA)n Simple_repeat 1 31 (0) 92
ANNOTATION EVIDENCE:
18 0.00 0.00 9.68 Crub_svsplocus 152868 152901 497099 + (AAAGAA)n Simple_repeat 1 31 0
18 0.00 0.00 9.68 Crub_svsplocus 152868 152901 (497099) (AAAGAA)n#Simple_repeat 1 31 (0) m_b3s252i9
Crub_svsplocu 152868 AAAGAAAAAGAACAACAGAAAAAAGAAAAAGAAA 152901
- - -
(AAAGAA)n#Sim 1 AAAGAAAAAGAA-AA-AG-AAAAAGAAAAAGAAA 31
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.09 (3 / 33), avg. gap size = 1.00 (3 / 3)
+ 285 24.7 4.3 4.3 Crub_svsplocus 153523 153675 (496325) + L1-8_DR LINE/L1 1764 1879 (3369) 93
ANNOTATION EVIDENCE:
285 24.33 4.31 4.31 Crub_svsplocus 153523 153638 496362 + L1-8_DR LINE/L1 1764 1879 3369
285 24.33 4.31 4.31 Crub_svsplocus 153523 153638 (496362) L1-8_DR#LINE/L1 1764 1879 (3369) m_b3s001i27
Crub_svsplocu 153523 ATGAAAGAAGATTGGGAATTGAGAGAC-TATTG--GCGTG--AATGCAAC 153567
vii v ii ivi - v -- v -- ----
L1-8_DR#LINE/ 1764 ATGATGAAAGATTTGGGGTTGGTGGACATATGGAGGCTTGTCAAT----C 1809
Crub_svsplocu 153568 CAAGAAGAAAGGGACTTTATCTTTTTTTCAGATAGACACCAATCTTTCTC 153617
v - i i v v i i v iv iv v
L1-8_DR#LINE/ 1810 CTAGA-GAGAGAGAGTATACCTTCTTTTCACATAATCATAAATCTTACTC 1858
Crub_svsplocu 153618 AAGAATTGATTTCTTTTTGAT 153638
v v i
L1-8_DR#LINE/ 1859 AAGAATAGATTACTTTTTGGT 1879
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.61
Transitions / transversions = 0.93 (13/14)
Gap_init rate = 0.07 (8 / 115), avg. gap size = 1.25 (10 / 8)
234 25.69 4.39 4.39 Crub_svsplocus 153562 153675 496325 + L1-25_DR LINE/L1 2163 2276 3435
234 25.69 4.39 4.39 Crub_svsplocus 153562 153675 (496325) L1-25_DR#LINE/L1 2163 2276 (3435) m_b3s001i28
Crub_svsplocu 153562 TGCAACCAAGAAGAAAGGGACTTTATCTTTTTTTCAGATAGACACCAATC 153611
v v - i i iv i v ivi vi vv
L1-25_DR#LINE 2163 TGCACCCTA-AGGAAAGAGACTTTACATTCTTTTCACATGTGCACGGAAG 2211
Crub_svsplocu 153612 TTTCTCAAGAATTGATTTCTTTTTG---ATCACAA-CAGATTTATACAAC 153657
i v v -i v --- i v - v i -
L1-25_DR#LINE 2212 CTACTCAAGAATAGA-CTATTTTTGTATACCAAAAGCAGATATATATAA- 2259
Crub_svsplocu 153658 AGGGT-GAAGAATGTAAAA 153675
--i -i i i
L1-25_DR#LINE 2260 --AGTAAAAGAGTGTAGAA 2276
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.90
Transitions / transversions = 1.15 (15/13)
Gap_init rate = 0.07 (8 / 113), avg. gap size = 1.25 (10 / 8)
+ 492 30.7 4.1 4.8 Crub_svsplocus 154270 154837 (495163) + L1-102_DR LINE/L1 678 959 (2043) 94
ANNOTATION EVIDENCE:
402 33.40 4.40 4.59 Crub_svsplocus 154270 154837 495163 + L1-1_Testu LINE/L1 3680 4246 2086
402 33.40 4.40 4.59 Crub_svsplocus 154270 154837 (495163) L1-1_Testu#LINE/L1 3680 4246 (2086) m_b3s001i29
Crub_svsplocu 154270 AATATTCAAATCACAGA---TATAAACAATTATTTAGGTAAAGTAAATTT 154316
i i - v --- i iv ii v iv i vi
L1-1_Testu#LI 3680 AACATCCAAATC-CTGAACTTATAAATAGATATTTGAGAAGTGTGAAACT 3728
Crub_svsplocu 154317 TTCTAAATTAACAGAAGATCAGGAAAAAGAGATTAATGGTTTAATTACTA 154366
vi v ii vv i v v viiv vvv i i viv i i
L1-1_Testu#LI 3729 ACCTCAGCTCTCAGAGGATGATGTGGCAGCTCTTGATAGGCAAATTGCTG 3778
Crub_svsplocu 154367 AGGAAGAAATTG---TTACAGCTATTAAACAATTGAAATTGGGCAAAGCG 154413
vi i i --- ii --- iv v i iviii v
L1-1_Testu#LI 3779 CAGAGGAAGTTGAAGTTGTA---ATTAAGAATTTAAAATCCAATAAAGCT 3825
Crub_svsplocu 154414 CCGGGTACGGATGGGTTGACATCTATT---TATTATAAAACTTTAGTAGA 154460
i v v v--- ivv--- i i i iviv
L1-1_Testu#LI 3826 CCAGGTCCCGATGGGTTT---TCTGGGGAGTATTATAGAGCTCTAAAGCA 3872
Crub_svsplocu 154461 AGAGATGATTCAACCATTGTG--TGAATTGTTTAATAATTTATTACAGGG 154508
v v i i -- i v i-- ii v i
L1-1_Testu#LI 3873 AGTGTTGGTCC--CTATTTTAACTGAATTGTTTAATGGTATATTGCAGGG 3920
Crub_svsplocu 154509 GCTAGAGATCCCTCCA---TCTTGGCGTAATGCATTTATATCATTG--AT 154553
vvv --- --- v vivi v --v v ii v --
L1-1_Testu#LI 3921 GAACGAGAT---TCCAGATTCATGGAAAGAGGCA--AAAATTGTGGTCAT 3965
Crub_svsplocu 154554 TCCAAAAGATAATCAAGATCTTAC--ATTGCCTAAAAATTATAGGCCTAT 154601
v viivv -- ivi vv -- i i
L1-1_Testu#LI 3966 TCCTAAAGAAGGAAAAGATCTTACCAATTGTGCATCA--TACAGACCTAT 4013
Crub_svsplocu 154602 ATCCCTTTTA---AATGTGGATTATAAAATTTTTGCAAAAATTTTAGCCA 154648
v --- --- vv v v ii vi v
L1-1_Testu#LI 4014 TTC---TTTAATTAATGTGGATGCTAAAATTTATGCCAAGGTGCTAGCAA 4060
Crub_svsplocu 154649 ATAGGCTTATGGGGATTTTGCAGCAGCTTATACATAAGGATCAATCGGGA 154698
i ii v vv vv i vvv iiv i v ivvv i v i
L1-1_Testu#LI 4061 ACAGATTGAGTGTCATCTTGCCCAAATATGTTCACCCTGACCAATCTGGG 4110
Crub_svsplocu 154699 TTTATAACTGGAAGGTACATGAAAAATAATGTTAGACAAATCATTAATTT 154748
ii vi v i iv ivvvi i i vi iiv v
L1-1_Testu#LI 4111 TTCGTTGCTGGCAGGCATCTATCTGATAATATCAGAAGAACTCTGAATTT 4160
Crub_svsplocu 154749 -AT-TAGAGTATTTAGAAAAGAATAACCAAGTCTCTGCTG-GC-CTGATA 154794
- - v i i ----- vvv i- v - v - - v v
L1-1_Testu#LI 4161 GATCTATAATGTT-----AATTCTAG-CAATTCT-TCCTGTGCGCTGCTT 4203
Crub_svsplocu 154795 TTTTTGGATGCTGAAAAAGCCTTTGACCAAGTGAATTGGCAGT 154837
i i i iiv i v v
L1-1_Testu#LI 4204 TCTTTGGATGCTGAGAAAGCCTTCGACCGGCTGGAGTGGGAGT 4246
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.82
Transitions / transversions = 0.97 (89/92)
Gap_init rate = 0.07 (38 / 567), avg. gap size = 1.34 (51 / 38)
492 28.06 3.86 4.96 Crub_svsplocus 154537 154821 495179 + L1-102_DR LINE/L1 678 959 2043
492 28.06 3.86 4.96 Crub_svsplocus 154537 154821 (495179) L1-102_DR#LINE/L1 678 959 (2043) m_b3s001i31
Crub_svsplocu 154537 GCATTTATATCATTGATTCCAAAAGATAATCAAGATCTTACATTG--CCT 154584
v v i v v i vi iv - v - i --
L1-102_DR#LIN 678 GCATTGATAACACTGATACCCAAAAAAGACAAAGA-CGTA-ACTGATCCT 725
Crub_svsplocu 154585 AAAAATTATAGGCCTATATCCCTTTTAAATGTGGATTATAAAATTTTTGC 154634
iv i v vv v v v i i ii v v
L1-102_DR#LIN 726 GCAAACTATAGGCCAATAAGCCTTATCAATGTTGACTGTAAGGTGTTGGC 775
Crub_svsplocu 154635 AAAAATTTTAGCCAATAGGCTTATGGGGATTTTGCAGCAGCTTATA---C 154681
vi i vv v viviii i i v- -- ---
L1-102_DR#LIN 776 AAAAATACTGGCCTCTCGGCTGGAAAAGGTTTTACC-CAG--TATAATTC 822
Crub_svsplocu 154682 ATAAGGATCAATCGGGATTTATAACTGGAAGGTACATGAAAAATAATGTT 154731
i i ivi v v vv i v vi iv i v
L1-102_DR#LIN 823 ATAAAGACCAGGTGGGCTTTATTAAGGGGAGGTCCTCGGCAGATAATGTG 872
Crub_svsplocu 154732 AGACAAATCATTAATTTA------TTAGAGTATTTAGAAAAGAATAACCA 154775
v vi vv i------ i v i v v v --
L1-102_DR#LIN 873 AGAAAAATGGTGCATTTGATGCGGTTAAATTATTCAGACAATACT--CCA 920
Crub_svsplocu 154776 AGTCTCTGCTGGCCTGATATTTTTGGATGCTGAAAAAGCCTTTGAC 154821
----i v -- - i i i
L1-102_DR#LIN 921 A----TTGCAG--CT-ATATCTCTGGATGCTGAAAAGGCCTTTGAC 959
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.80
Transitions / transversions = 0.85 (35/41)
Gap_init rate = 0.06 (17 / 284), avg. gap size = 1.47 (25 / 17)
+ 352 33.7 3.6 4.1 Crub_svsplocus 154359 155021 (494979) + Nimb-4_DR LINE/I 5039 5698 (3963) 95 *
ANNOTATION EVIDENCE:
352 33.66 3.62 4.09 Crub_svsplocus 154359 155021 494979 + Nimb-4_DR LINE/I 5039 5698 3963
352 33.66 3.62 4.09 Crub_svsplocus 154359 155021 (494979) Nimb-4_DR#LINE/I 5039 5698 (3963) m_b3s001i30
Crub_svsplocu 154359 AATTACTAAGGAAGAAATTGTTACAGCTATTAAACAAT--TGAAATTGGG 154406
vi i v v v v - i -- i v ii-
Nimb-4_DR#LIN 5039 AATTACAGAGGAGGAATTAGATAAAGCTAT-AAATAATCTTAAAAATAA- 5086
Crub_svsplocu 154407 CAAAGCGCCGGGTACGGATGGGTTGACATCTATTTATTATAAAAC-TTTA 154455
i i i v i vv vi iv v ivv iv vi -
Nimb-4_DR#LIN 5087 TAAAACACCCGGCAATGATGGTCTACCTTCTGAATGGTTCAAAACATTTA 5136
Crub_svsplocu 154456 GTAGAAGAGATGATTCAACCATTGTGTGA--ATTGTTTAATAATTTA-TT 154502
i- i --i v iv v vvv -- ii vivvi -
Nimb-4_DR#LIN 5137 A-AAAAGAGAT--CTCACCTCTTCTTATATCATCATTTAATTGGACACTT 5183
Crub_svsplocu 154503 ACAGGGGCTAGAGATCCCTCCATCTTGGCGTAATGCATTTATATCATTGA 154552
v i - i i i v v vi v v v v v
Nimb-4_DR#LIN 5184 AAAGAGGC-AGAAATTCCCCCTTCTTGGAGGGAAGCAATTATCTCAGTCA 5232
Crub_svsplocu 154553 TTCCAAAAGATAATCAAGATCTTACATTGCCTAAAAATTAT--AGGCCTA 154600
v v viivv i v-- v i vii iv iv i -- i i
Nimb-4_DR#LIN 5233 TACCTAAAGAGGGGAAGGATA--AAACTCTTTGTAGTTCATTTAGACCTG 5280
Crub_svsplocu 154601 TATCCCTTTTAAATGTGGATTATAAAATTTTTGCAAAAATTTTAGCCAAT 154650
i iv i i v v vvvv v
Nimb-4_DR#LIN 5281 TGTCTGTTTTAAATGTAGACTATAAATTATTTGCCTCTATTTTAGCCAAG 5330
Crub_svsplocu 154651 AGGCTTATGGGGATTTTGCAGCAGCTT--ATACATAAGGATCAATCGGGA 154698
i i-iiiv -i v v v -- v i vi v i i
Nimb-4_DR#LIN 5331 AGACTTG-AAACATTTT-TACCTGATTTGATAGACATAGATCAAACAGGG 5378
Crub_svsplocu 154699 TTTATAACTGGAAGGTACATGAAAAATAATGTTAGACAAATCATTAATTT 154748
v vv v i v ivv i i- vii ivv v vi
Nimb-4_DR#LIN 5379 TTTATTAGAGGACGGCAGACTCAAGATAATA-TAGAAGGACACTTCATGC 5427
Crub_svsplocu 154749 ATTA-GAGTATTTAGAAAAGA----AT--AACCAAGTCTCTGCTGGCCTG 154791
v - vv v i ---- -- v - i iv i i --
Nimb-4_DR#LIN 5428 AATACGACAAATTAAAAAAGATCACATTAAAGCAA-TTTTAGTTAGCC-- 5474
Crub_svsplocu 154792 ATATTTTTGGATGCTGAAAAAGCCTTTGACCAAGTGAATTGGCA--GTTT 154839
------- i v i i iiv i v --i
Nimb-4_DR#LIN 5475 -------TAGATGCAGAGAAAGCTTTTGACTGTGTAAATTGGGAATATTT 5517
Crub_svsplocu 154840 ATGTTATGTTTAATTAAGGAGATGAATTTTGGACAAAATATA-TTACAAG 154888
v v - vi vv i - iv v i - v
Nimb-4_DR#LIN 5518 ATTTAATGTTTAA-TATAGATTTGGA-TTTACAGAAAATACAGTTAGAAG 5565
Crub_svsplocu 154889 TATTATCTAATA--TATA-TCAAAAACAGACTGCTCAACTTATTGTAAAT 154935
iv ---i i-- - vv -v viiv v vvi i
Nimb-4_DR#LIN 5566 CTTT---CAATGTTTATATTCAAACCCAGA-GGCTAGGATAAAAATAAAC 5611
Crub_svsplocu 154936 GGGGGTTTGTCAGAGGCTTTTGTAATAGAAAAAGGTACAAGACAGGGATG 154985
vv i v i iivvv viv v v v i v
Nimb-4_DR#LIN 5612 GGTTGTCTTTCAAAAAAGATAAAACTAGAAAAAGGAACTAGGCAGGGTTG 5661
Crub_svsplocu 154986 CTCGTTATCCCCGTTATTGTTTGTTTTA-ACATTGGA 155021
ii vi v i vi iv iiv i- i
Nimb-4_DR#LIN 5662 TCCCCTCTCTCCCCTGATGTTTGCCATGTACATTGAA 5698
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.85
Transitions / transversions = 0.88 (100/114)
Gap_init rate = 0.06 (41 / 662), avg. gap size = 1.24 (51 / 41)
+ 336 30.4 3.7 4.1 Crub_svsplocus 155349 155643 (494357) + L1-88_DR LINE/L1 3787 4080 (1346) 96
ANNOTATION EVIDENCE:
336 30.39 3.73 4.08 Crub_svsplocus 155349 155643 494357 + L1-88_DR LINE/L1 3787 4080 1346
336 30.39 3.73 4.08 Crub_svsplocus 155349 155643 (494357) L1-88_DR#LINE/L1 3787 4080 (1346) m_b3s001i32
Crub_svsplocu 155349 TAATTATGAAAAGTTGTGGACGGAGGTACAGAAGGATTTAAA-AAATTGG 155397
i i vv v ii vv i vv i - i --
L1-88_DR#LINE 3787 TAATCATGAAAAGTTATTTAGGGAAATTAAAACCGATTTGAATAGA--GG 3834
Crub_svsplocu 155398 ACA-ATTTACAGTTATCCCTTATGGGTAGAATTGCAGTTATTAAAATGAA 155446
i - i v v - i iv i v v iv i
L1-88_DR#LINE 3835 ATATACTTCCACTT-TCTCTCCTAGGAAGAATTGAAAGTATTAGAATGAA 3883
Crub_svsplocu 155447 TGTCCTGCCAAAGTTTATTTTTC-TGTTTCAAATGTTACCTATT-CTAAA 155494
i i - v v - v vvi v i -i iv
L1-88_DR#LINE 3884 TGTTCTACC-AAGATTATTGTTCATTTTTCAAAGCCTTCCTGTTGTTGTA 3932
Crub_svsplocu 155495 GAGTGATCGTAATTTAGATGAATGGCAAAAAGGTATTAATAAATTTGTTT 155544
vviii vvv i i -v vi iv i vvv i
L1-88_DR#LINE 3933 CCACAATCTGCATTCAAAT-CATTACAAAAGTGCATTTCAAAATTTATTT 3981
Crub_svsplocu 155545 GGGCAGGG-AAAAAACCAAGGGTGAAACTTAAAA---TAATGCAAGATTT 155590
- ii- ii i viv --- i iv ---
L1-88_DR#LINE 3982 -GGCAGAACAAAAGGCCAAGAGTGCGCCTTAAAATTCTGATGTCAGA--- 4027
Crub_svsplocu 155591 TCGTGAGAG-A--GGTGGACTCAAGGTACCAAATATGAAATTGTATTATG 155637
--- i i - -- v vii v i v i i v v
L1-88_DR#LINE 4028 ---TAAGGGTAATGGTGGTCTGGGGCTGCCTAACATAAAAATGTATTATT 4074
Crub_svsplocu 155638 ATGCTG 155643
iv
L1-88_DR#LINE 4075 GGGCTG 4080
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.04
Transitions / transversions = 1.10 (45/41)
Gap_init rate = 0.07 (20 / 294), avg. gap size = 1.15 (23 / 20)
+ 32 22.3 5.5 3.1 Crub_svsplocus 156781 156907 (493093) + (TTCT)n Simple_repeat 1 130 (0) 97
ANNOTATION EVIDENCE:
32 22.29 5.51 3.08 Crub_svsplocus 156781 156907 493093 + (TTCT)n Simple_repeat 1 130 0
32 22.29 5.51 3.08 Crub_svsplocus 156781 156907 (493093) (TTCT)n#Simple_repeat 1 130 (0) m_b3s252i10
Crub_svsplocu 156781 TTGTTT-TTTTTTTCTTTCTTTCTTT-TTTC-TTCTGTACTATTACTTAT 156827
v - i - - - v - - vi
(TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT-TTCT-TT-CTTTC 47
Crub_svsplocu 156828 ATACTTT-TTTATATATGT-TTTATTTTTCGCCTAC-CTCTTTCTTT-TT 156873
v v - v v v v - v i iv i v -i -
(TTCT)n#Simpl 48 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 97
Crub_svsplocu 156874 TCTTTCTCTCTCTCTTTTCTTTTTTCCTTTTTTT 156907
i i - i i i
(TTCT)n#Simpl 98 TCTTTCTTTCTTTC-TTTCTTTCTTTCTTTCTTT 130
Matrix = Unknown
Transitions / transversions = 0.92 (11/12)
Gap_init rate = 0.09 (11 / 126), avg. gap size = 1.00 (11 / 11)
+ 31 20.7 2.1 4.3 Crub_svsplocus 156901 156996 (493004) + (TTA)n Simple_repeat 1 94 (0) 98 *
ANNOTATION EVIDENCE:
31 20.69 2.08 4.26 Crub_svsplocus 156901 156996 493004 + (TTA)n Simple_repeat 1 94 0
31 20.69 2.08 4.26 Crub_svsplocus 156901 156996 (493004) (TTA)n#Simple_repeat 1 94 (0) m_b3s252i12
Crub_svsplocu 156901 TTTTTTTTAATATATATTATTTATCTTAAAGTTTATGTTATGTA-TATTA 156949
v v v - vv v vvi vv i - -
(TTA)n#Simple 1 TTATTATTATTAT-TATTATTATTATTATTATTATTATTAT-TATTATTA 48
Crub_svsplocu 156950 TTATTA-TATATATTATTATTATGATTTTCACTATTATTATTAATTAT 156996
- - v v i i -
(TTA)n#Simple 49 TTATTATTAT-TATTATTATTATTATTATTATTATTATTATT-ATTAT 94
Matrix = Unknown
Transitions / transversions = 0.33 (4/12)
Gap_init rate = 0.06 (6 / 95), avg. gap size = 1.00 (6 / 6)
+ 13 24.8 0.0 0.0 Crub_svsplocus 157063 157100 (492900) + G-rich Low_complexity 1 38 (0) 99
ANNOTATION EVIDENCE:
13 24.76 0.00 0.00 Crub_svsplocus 157063 157100 492900 + (GGGGG)n Simple_repeat 1 38 0
13 24.76 0.00 0.00 Crub_svsplocus 157063 157100 (492900) (GGGGG)n#Simple_repeat 1 38 (0) m_b3s252i13
Crub_svsplocu 157063 GGGGGGGGGGAGGGTGGGGTGGTTTGGGAGGGGGGTGG 157100
i v v vvv i v
(GGGGG)n#Simp 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 38
Matrix = Unknown
Transitions / transversions = 0.33 (2/6)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 258 30.3 1.5 1.5 Crub_svsplocus 161046 161238 (488762) C Gypsy72-I_DR LTR/Gypsy (1538) 2744 2549 100
ANNOTATION EVIDENCE:
248 32.80 2.07 2.07 Crub_svsplocus 161046 161238 488762 C Gypsy69-I_DR LTR/Gypsy 2549 2741 1504
248 32.80 2.07 2.07 Crub_svsplocus 161046 161238 (488762) C Gypsy69-I_DR#LTR/Gypsy (1504) 2741 2549 m_b3s001i33
Crub_svsplocu 161046 TGCGGGATAGGGCATCTGCCAGGAAATTCCTCCCCCCTGGTAAGTGTTTG 161095
i v vvivii i v?iv vvii ivv
C Gypsy69-I_DR# 2741 TGCGAGAGAGGGCATCTGCCTTACGGTTCTTGNTGCCTGGGCGATAGGTG 2692
Crub_svsplocu 161096 ATTTTGAATGTGAACCGGTGGAAGTGTTGTGACCACTGGGCTTGTTTTGG 161145
i v i vv ? vv vi viv ?i i i i v
C Gypsy69-I_DR# 2691 ACTGTAAAATTGAANCGGGTGAAGAATAAAGACCANCGAGCCTGTCTGGG 2642
Crub_svsplocu 161146 GGTGAGTTTTCTCGGCATTTTTAGGGC-TTCCAAGTTCTTATGGTCTGTC 161194
v v iv -v i iivii-i ? i i i v
C Gypsy69-I_DR# 2641 GTTTAGTCGTC-GGGCACTTTTGATATACTCNAGGTTTTTGTGGTCTGTG 2593
Crub_svsplocu 161195 CAGACCTGGAATG---GGATTTTGTTCCCTTCCAGGAAGTGCTGCCA 161238
vvi i ? --- --iv i - ? vv ?i
C Gypsy69-I_DR# 2592 ATAATCTGGAANGGATGGA--CGGCTCCC-TCNAGCCAGTGNCGCCA 2549
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.55
Transitions / transversions = 1.07 (32/30)
Gap_init rate = 0.03 (6 / 192), avg. gap size = 1.33 (8 / 6)
258 28.00 0.99 0.99 Crub_svsplocus 161100 161200 488800 C Gypsy105-I_Dr LTR/Gypsy 2644 2744 1538
258 28.00 0.99 0.99 Crub_svsplocus 161100 161200 (488800) C Gypsy105-I_Dr#LTR/Gypsy (1538) 2744 2644 m_b3s001i34
Crub_svsplocu 161100 TGAATGTGAACCGGTGGAAGTGTTGTGACCACTGGGCTTGTTTTGGGGTG 161149
vv iv vivv v vi i viv
C Gypsy105-I_Dr 2744 TGAAATTGAACCGGCTGAAGAAGAGAGACCAGCGGGCTTGTCTTGCATTG 2695
Crub_svsplocu 161150 AGTTTTCTCGGCAT-TTTTAGGGCTTCCAAGTTCTTATGGTCTGTCCAGA 161198
ii i - v-v v vv v i ii i
C Gypsy105-I_Dr 2694 AGCCTTTT-GGCAGAGTTTATGTATTCAAGGTTTCTGTGGTCTGTCCAGA 2646
Crub_svsplocu 161199 CC 161200
C Gypsy105-I_Dr 2645 CC 2644
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.70
Transitions / transversions = 0.75 (12/16)
Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.00 (2 / 2)
+ 245 29.1 4.6 6.5 Crub_svsplocus 161249 161421 (488579) C Gypsy35-I_DR LTR/Gypsy (231) 4233 4064 101
ANNOTATION EVIDENCE:
245 29.05 4.62 6.47 Crub_svsplocus 161249 161421 488579 C Gypsy35-I_DR LTR/Gypsy 4064 4233 231
245 29.05 4.62 6.47 Crub_svsplocus 161249 161421 (488579) C Gypsy35-I_DR#LTR/Gypsy (231) 4233 4064 m_b3s001i35
Crub_svsplocu 161249 GCCCACCTCACAGCGTACGC-CTCCTTTTCCCACAGC-----GCCCAATG 161292
ii v -i v - i - i i-----i --i
C Gypsy35-I_DR# 4233 GCCCATTTCACTGC-CAAGCACTCCTTCTCC-ACGGTTGAATACC--GTG 4188
Crub_svsplocu 161293 TTGCTCCATGTCAGAGAGTTTTCTGGACATGTAGGGACAGGGTTGCAGCT 161342
v v v -- ii vvv i v vv v ii
C Gypsy35-I_DR# 4187 TTTCTCGAGG--AAGGAGTTTTCTGCTAATGTAAGCAATGGGATGCAATT 4140
Crub_svsplocu 161343 GCCCCTTGTCGTTTTCCTGTAGCAATACTGCTCCTACTGCTACATCACT- 161391
-i -- i i i v i v i -vi i i i- -
C Gypsy35-I_DR# 4139 -TCCCTTGT--TCTCCTTGTAGAAGTACAGCTCCCA-GACCACGTT-CTG 4095
Crub_svsplocu 161392 -TGCATCAGCTTGGGTTATGAATGGCTTATC 161421
- ii ii i i i i i
C Gypsy35-I_DR# 4094 ATGCATCAGTCTGGACTGTAAACGGTTTACC 4064
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.40
Transitions / transversions = 2.13 (32/15)
Gap_init rate = 0.08 (14 / 172), avg. gap size = 1.36 (19 / 14)
+ 758 34.1 2.8 2.8 Crub_svsplocus 161579 162182 (487818) C Gypsy72-I_DR LTR/Gypsy (2003) 2294 1691 100
ANNOTATION EVIDENCE:
758 34.07 2.81 2.81 Crub_svsplocus 161579 162182 487818 C Gypsy72-I_DR LTR/Gypsy 1691 2294 2003
758 34.07 2.81 2.81 Crub_svsplocus 161579 162182 (487818) C Gypsy72-I_DR#LTR/Gypsy (2003) 2294 1691 m_b3s001i36
Crub_svsplocu 161579 GATGAACTGACGGTAGAAATTAGCGAATCCCAGGAAGCTTTGTAGTTGCT 161628
ii v i i v v vi iivv
C Gypsy72-I_DR# 2294 GATGAATCGCCGGTAAAAATTGGCGAAGCCCAGGAACCGCTGTAACGCCT 2245
Crub_svsplocu 161629 TTCTCGTGCGGAGTGGCGCCCACTCCAGCACCACCCGGACCTTCTCGGGG 161678
vv v iv i v v viiv vi vi v i
C Gypsy72-I_DR# 2244 TTCGGGAGTCGGGTGGCGGCCAGTCGGAGACAGCCCTAACCTTCGCAGGG 2195
Crub_svsplocu 161679 TCCATCTCTATGCCTTCAGTTGA---TATGTGGTAGCCCAAGTAGTCAAT 161725
vivv vv i ii --- v--- v vv i
C Gypsy72-I_DR# 2194 TCCATGCGAAGTCCCTCAACTGAAATTATGTGT---CCCAAGAAGGAAAC 2148
Crub_svsplocu 161726 TCTCTGTTTATGAAAATCGCACTTTGACAATTTTGCATAGAAGTTGGCTG 161775
vv vvi i v ivv ivi i v - i ii -
C Gypsy72-I_DR# 2147 TGACTGGACATGGAATTCGCACTTCTCCGCCTTTACATACA-GCTGATT- 2100
Crub_svsplocu 161776 CTCT--CACTTTTTTCAAAACTGCTCTGACTAATTTTATGTGCTCCTCTT 161823
i-- viiv vi iv vvi vi vvi vv ii i viv
C Gypsy72-I_DR# 2099 CTCCAGCAGCCGTTGTAGCACTCGCCGAACGTGTTGGACATGTTCCTGCA 2050
Crub_svsplocu 161824 TAGTCTCTGTAAATATAAGGATGTCGTCCAGGTAGACGAGGACCCCTTTG 161873
i ivvvv v v i i ii i i ii vvv vi
C Gypsy72-I_DR# 2049 TGGCGGAAGAAAAAATAAGAATGTCATCCAAATAAACAAAAACAAATTGA 2000
Crub_svsplocu 161874 TATAG--GTGCTCCTTCAGTACTTCATTGATCCACTGCATGAA-GACCGC 161920
- i--i - iivv v i - v v v - i
C Gypsy72-I_DR# 1999 T-TAATCATG-TCTCGGAGTACATCGTTGA-CGAGTGCCTGAAAGACTGC 1953
Crub_svsplocu 161921 GGGGGC-TCCCTGCAGCCCAAACGGCAAGACCTTAAATTGGTAGCAT-CC 161968
v i - ivv - i i vvv v --i iv -
C Gypsy72-I_DR# 1952 TGGAGCATTGGTG-AGCCCAAATGGCAGGACAAGATATT--CAAAATGCC 1906
Crub_svsplocu 161969 CATAGGGCA-GTTGAATGCGGTCTTCCACTTGTTCCCCTCCTTAAATCTA 162017
vv i- i i iv i v vv vi
C Gypsy72-I_DR# 1905 CAGTGGGCGTGTTGAATGCGGTCTTCCATTCGTCACCCTCCCTCATACGG 1856
Crub_svsplocu 162018 ATGTGATAATAGGCCTCCCTTAAGTCCAGATTTGTG-AAGATTTTTCCCT 162066
i v ii i v iv v i iv - i i v i
C Gypsy72-I_DR# 1855 ACGAGATGGTAAGCATTGCGTAGGTCCAACTTTGTGAAAAATCTTGCCCC 1806
Crub_svsplocu 162067 TTG--ATAGGTGGGACACC-ATGTCTTTCATGAGGGGGAGAGGGTACAGG 162113
i -- v i v i vi - v ----v i v v i v i
C Gypsy72-I_DR# 1805 CTGCAAGAGATCGAAGGCCGAAG----ACATAAGCGGTAGGGGGTACCGA 1760
Crub_svsplocu 162114 TTGCTTT--TGCTTATGGCGTTCAAGGAGTGATAGTCCATGCACATATGC 162161
-- -- v v i ivvvi i vivii
C Gypsy72-I_DR# 1759 TT--TTTAATGGTTATGTCATTCAAACCTCGATAGTCTATGCAGGGGCGC 1712
Crub_svsplocu 162162 AATGTGCCATCCTTCTTTTCC 162182
iv vi i i i
C Gypsy72-I_DR# 1711 AGAGAACCATCCTTTTTCTTC 1691
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.21
Transitions / transversions = 0.96 (98/102)
Gap_init rate = 0.05 (28 / 603), avg. gap size = 1.21 (34 / 28)
+ 226 15.0 0.0 2.5 Crub_svsplocus 163699 163739 (486261) + Tx1-39_DR LINE/L1-Tx1 3121 3160 (2292) 102
ANNOTATION EVIDENCE:
226 15.01 0.00 2.50 Crub_svsplocus 163699 163739 486261 + Tx1-39_DR LINE/L1-Tx1 3121 3160 2292
226 15.01 0.00 2.50 Crub_svsplocus 163699 163739 (486261) Tx1-39_DR#LINE/L1-Tx1 3121 3160 (2292) m_b4s001i0
Crub_svsplocu 163699 TGTCATCCATCCTGATCAGCAGCTACCATGTGGCAGGGAGA 163739
i - v ii v v
Tx1-39_DR#LIN 3121 TGTCATCCATCCTGACCAG-ACCTACTGTGTGCCAGGCAGA 3160
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.81
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1)
+ 56 0.0 0.0 0.0 Crub_svsplocus 165793 165840 (484160) + (CA)n Simple_repeat 1 48 (0) 103
ANNOTATION EVIDENCE:
56 0.00 0.00 0.00 Crub_svsplocus 165793 165840 484160 + (CA)n Simple_repeat 1 48 0
56 0.00 0.00 0.00 Crub_svsplocus 165793 165840 (484160) (CA)n#Simple_repeat 1 48 (0) c_b4s251i0
Crub_svsplocu 165793 CACACACACACACACACACACACACACACACACACACACACACACACA 165840
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACA 48
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 22 20.9 0.0 0.0 Crub_svsplocus 166453 166496 (483504) + (C)n Simple_repeat 1 44 (0) 104
ANNOTATION EVIDENCE:
22 20.85 0.00 0.00 Crub_svsplocus 166453 166496 483504 + (C)n Simple_repeat 1 44 0
22 20.85 0.00 0.00 Crub_svsplocus 166453 166496 (483504) (C)n#Simple_repeat 1 44 (0) m_b4s252i0
Crub_svsplocu 166453 CCCCCCTACCCCCCCAACCCCCCAACCCCCTACCCCCCCCCCCC 166496
iv vv vv iv
(C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 44
Matrix = Unknown
Transitions / transversions = 0.33 (2/6)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
+ 14 25.7 2.9 4.3 Crub_svsplocus 166662 166731 (483269) + (TAATATT)n Simple_repeat 1 69 (0) 105
ANNOTATION EVIDENCE:
14 25.70 2.86 4.35 Crub_svsplocus 166662 166731 483269 + (TAATATT)n Simple_repeat 1 69 0
14 25.70 2.86 4.35 Crub_svsplocus 166662 166731 (483269) (TAATATT)n#Simple_repeat 1 69 (0) m_b4s252i1
Crub_svsplocu 166662 TAATAATTATTATTTAAAATTTAATCATAAAATAAATGGAAATTT-TTAG 166710
v v v - vv - v vi v -v -
(TAATATT)n#Si 1 TAATATTTAATATTTAATATTTAAT-ATTTAAT-ATTTAATATTTAATA- 47
Crub_svsplocu 166711 TTCCATATTTAAT-CTGAATAT 166731
iv -i v
(TAATATT)n#Si 48 TTTAATATTTAATATTTAATAT 69
Matrix = Unknown
Transitions / transversions = 0.27 (3/11)
Gap_init rate = 0.07 (5 / 69), avg. gap size = 1.00 (5 / 5)
+ 312 37.8 3.0 2.5 Crub_svsplocus 169127 169596 (480404) C Gypsy72-I_DR LTR/Gypsy (861) 3505 3034 106
ANNOTATION EVIDENCE:
312 37.77 2.98 2.54 Crub_svsplocus 169127 169596 480404 C Gypsy-165-I_DR LTR/Gypsy 3034 3505 861
312 37.77 2.98 2.54 Crub_svsplocus 169127 169596 (480404) C Gypsy-165-I_DR#LTR/Gypsy (861) 3505 3034 m_b4s001i1
Crub_svsplocu 169127 CCAGAATTGAGCCATAAATTGTACACCACGGTCTGAAATAAT---TCGAC 169173
ivi v v iv v v i --- i iv
C Gypsy-165-I_D 3505 CCAGAATCTGGACAGAAATTGTGGACCTCGGTCAGAAACAATGTCTTGGG 3456
Crub_svsplocu 169174 GAGGTGCCCCATGCAAA---TGATAAATATGGGTTAAAAACATTTTGGCC 169220
i- ----iv --- - i v vv vv vi ii -
C Gypsy-165-I_D 3455 GAA-TGCC----AAAAACTCTGA-AAACATGGCTTATTATGAGCTCAGC- 3413
Crub_svsplocu 169221 AGTCTTCTT-GCCGACAGCAGTCCCTTA--CAG-GGTATGAAATGGGCTT 169266
ii - ii i--- i-- - v vi vv
C Gypsy-165-I_D 3412 AGTCTCTTTAGCCGATGGCAA---CTTGGGCAGAGGAATGAACCGGGCAG 3366
Crub_svsplocu 169267 GTTTTGAAAACAAGTCAACTACTGTCCATATAATGGTGTAACCCCGTACC 169316
vi v ivi v i vii v i iv vi i vivv
C Gypsy-165-I_D 3365 CCTTGGAAAATCGGTCCACCACAACCAATATGACCGTGTTGCCCTGGGAG 3316
Crub_svsplocu 169317 TCCGGTAGGTCAACTATAAAATCCATTCCAATGTCCTGCCATGGCTGATT 169366
vvi v vi viiv i vvvv v vivi v ivi v
C Gypsy-165-I_D 3315 AGTGGAAGTCCCGTAATGAAATCCAGGGAAAGGTGTGACCAAGGCCTGTG 3266
Crub_svsplocu 169367 TGGGTCAGATACTGGTTGTAACAACCCCATTGGTCTTTTGGGTACTACCT 169416
v iv i vv v v i ii vvv vi v v iv ivi
C Gypsy-165-I_D 3265 GGGAACAGGTAAGGGATGGAGCAGTCCCTGAGGTCGCTGGTGTGATGATT 3216
Crub_svsplocu 169417 TTGATTGTGCACAGATGTGACAACCCTTCACATATGTTTCCACGTCCTTC 169466
vvi vvv v iv i iv i vvi iv i i i
C Gypsy-165-I_D 3215 TTCCCTGACAACATACTTGGCAGGCCTCCACATAACCTTTAACATCTTCC 3166
Crub_svsplocu 169467 CTCATTCCAGGCCACCAAAATTGATGTCTGGCTAGGTGTAACGTCTTCAG 169516
i i vvv vi i v ivv iv v v v-- i
C Gypsy-165-I_D 3165 TTTATGGAAGGCCACCAAAAGCGACGTCGGAGGAATTCTAAAGTA--CGG 3118
Crub_svsplocu 169517 GAA--ACCGAAATGGCCGGCTAATTTAGAATCATGACAACGGTGATATAT 169564
-- viii v ii vi v vv iv vv v i
C Gypsy-165-I_D 3117 GAACTACCTGGGTGGCAGGTCAATACAGACTCATGACCCCACTGCAAGAC 3068
Crub_svsplocu 169565 GCGATCTCGTAATCCCTG-GGGA-ATATAGAGTC 169596
vi v i v v ii - - i
C Gypsy-165-I_D 3067 CTGAGCTCGCACTGCTCGAGGGACATATAGAGCC 3034
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 50.15
Transitions / transversions = 0.82 (78/95)
Gap_init rate = 0.04 (20 / 469), avg. gap size = 1.30 (26 / 20)
+ 335 34.5 1.2 1.4 Crub_svsplocus 169848 170258 (479742) C Gypsy72-I_DR LTR/Gypsy (1666) 2863 2508 106
ANNOTATION EVIDENCE:
335 31.43 1.40 2.11 Crub_svsplocus 169848 169990 480010 C Gypsy72-I_DR LTR/Gypsy 2622 2763 1534
335 31.43 1.40 2.11 Crub_svsplocus 169848 169990 (480010) C Gypsy72-I_DR#LTR/Gypsy (1534) 2763 2622 m_b4s001i2
Crub_svsplocu 169848 AGTTGGAATTGGAAACGTTGGAAATATTGTGCCCAATGCACATGTTTAGG 169897
v i i - i iivi v v v ii vi v ii i v
C Gypsy72-I_DR# 2763 AGGTGAAGTTG-AAGCGCCCAAAAAATAGAGCCCAGCGGGCCTGCCTGGC 2715
Crub_svsplocu 169898 AGACAACCGCCTAGGCGTTTGTA-GAACTGCTAGATTCTGGTGGTCTGTC 169946
vv iv ii i v i - v - i iv i v
C Gypsy72-I_DR# 2714 ATTCAGACGTTTGGCCGTCTGTATGTACTGC-AGGTTCCTGTGATCAGTC 2666
Crub_svsplocu 169947 CACACTTCAAAGGGATGTTGT-GCCCCCTCCAATAAATGGCGCCA 169990
vvv - ii i- iv i
C Gypsy72-I_DR# 2665 CACACAAGAAAGGG-TACTGCCGCCCCCTCCAACCAGTGGCGCCA 2622
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.61
Transitions / transversions = 1.32 (25/19)
Gap_init rate = 0.04 (5 / 142), avg. gap size = 1.00 (5 / 5)
259 37.95 0.78 0.78 Crub_svsplocus 169927 170181 479819 C Gypsy-165-I_DR LTR/Gypsy 2508 2762 1604
259 37.95 0.78 0.78 Crub_svsplocus 169927 170181 (479819) C Gypsy-165-I_DR#LTR/Gypsy (1604) 2762 2508 m_b4s001i3
Crub_svsplocu 169927 CTAGATTCTGGTGGTCTGTCCACACTTCAAAGGGATGTTGTGCCCCCTCC 169976
i vi vvii i vi i i v v v
C Gypsy-165-I_D 2762 CTAGGTTCTTATGGTCTGTAAGTACCTGGAAAGGATGTCGAGCGCCCTCA 2713
Crub_svsplocu 169977 AATAAATGGCGCCAGGTGGATAAGGCCCATTTTACCGCAAATGCCTCCTT 170026
iiv vvivvvi v i v v iiiv iiv
C Gypsy-165-I_D 2712 AGCCAATGGCGCCATTCTTCCAAGGCCAACTTAACAGCAAGCAGCTCTCG 2663
Crub_svsplocu 170027 TTCCCACACAGCCCATCTCCTCTCCGTATCTGTTA-GCTTCTTGGAAGTG 170075
v v ivvvi vi v v v i iv vi - vv v - vi
C Gypsy-165-I_D 2662 GTCCCCCACGTGGTAGTTGCGCTCGGCATTAGACAGGCGACGT-GACATG 2614
Crub_svsplocu 170076 TAGGCACATGGTTGTAAATTGCCCTGGCGGTTTCGTTGGAGCAAAACTGC 170125
v i v v iv v v vvivi i vi viii iv
C Gypsy-165-I_D 2613 AAAGCACAGGGGTGTAGTTTTCCATCCTCATTCCTCTGTGATAAAATGGC 2564
Crub_svsplocu 170126 CCCCACAGCCACGTCGCTAGCATCGGCCTGTACCATGAATGGGTGT-TCC 170174
i i v i vvvi vi v i - i - i
C Gypsy-165-I_D 2563 TCCTACACCCACATCTGAGGCATCCACCTCTACCATAAA-GGGTATGTCT 2515
Crub_svsplocu 170175 GGGTCAG 170181
i i
C Gypsy-165-I_D 2514 GGATTAG 2508
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 51.29
Transitions / transversions = 0.88 (45/51)
Gap_init rate = 0.02 (4 / 254), avg. gap size = 1.00 (4 / 4)
259 33.09 1.45 1.45 Crub_svsplocus 170121 170258 479742 C Gypsy-24-I_DR LTR/Gypsy 2726 2863 1666
259 33.09 1.45 1.45 Crub_svsplocus 170121 170258 (479742) C Gypsy-24-I_DR#LTR/Gypsy (1666) 2863 2726 m_b4s001i4
Crub_svsplocu 170121 ACTGCCCCCACAGCCACGTCGCTAGCATCGGCCTGTACCATGAATGGGTG 170170
v i v v i i v i i i v v iiv
C Gypsy-24-I_DR 2863 ACAGCCCCTAAACCCACATCACTTGCGTCAGTCTGTACCTTGAAGGAAAG 2814
Crub_svsplocu 170171 TTCCGGGTCAGCATATA-ATAGTACAGGTTCTTGTGCGAACAACGTTTTT 170219
v vii i -i i - i ii v ivv i i v- i i
C Gypsy-24-I_DR 2813 GTCAAAGTTAG-GTGTACACAACACAGGTGCTCTAGTGAGCT-CATCTTT 2766
Crub_svsplocu 170220 AAAGAT-TCGAATGCCCGTTGACACTCAGCTGTCCAGTTC 170258
i vi i- i v v v v v i
C Gypsy-24-I_DR 2765 GATAACATCAAAGGCACGTTGACACTCATCAGACCAATTC 2726
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.74
Transitions / transversions = 1.37 (26/19)
Gap_init rate = 0.03 (4 / 137), avg. gap size = 1.00 (4 / 4)
+ 253 17.5 0.0 0.0 Crub_svsplocus 170226 170265 (479735) C Gypsy70-I_DR LTR/Gypsy (2406) 3068 3029 107 *
ANNOTATION EVIDENCE:
253 17.50 0.00 0.00 Crub_svsplocus 170226 170265 479735 C Gypsy52-I_DR LTR/Gypsy 3029 3068 2406
253 17.50 0.00 0.00 Crub_svsplocus 170226 170265 (479735) C Gypsy52-I_DR#LTR/Gypsy (2406) 3068 3029 m_b4s001i5
Crub_svsplocu 170226 TCGAATGCCCGTTGACACTCAGCTGTCCAGTTCAAAGATT 170265
ivii i i i
C Gypsy52-I_DR# 3068 TCGAATGCTAACTGACATTCAGTTGTCCAGTTCAAAGGTT 3029
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.93
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 628 31.1 4.9 4.7 Crub_svsplocus 170324 170947 (479053) C Gypsy70-I_DR LTR/Gypsy (1973) 2352 1660 107
ANNOTATION EVIDENCE:
231 29.41 0.00 0.00 Crub_svsplocus 170324 170391 479609 C Gypsy-129_DR-I LTR/Gypsy 2285 2352 1973
231 29.41 0.00 0.00 Crub_svsplocus 170324 170391 (479609) C Gypsy-129_DR-I#LTR/Gypsy (1973) 2352 2285 m_b4s001i6
Crub_svsplocu 170324 CACCACAGTGGCAAAGGAGGGGATAGATTGCCTGTAGAAATTAGCAAATC 170373
vi ivvvi ii vi i i v
C Gypsy-129_DR- 2352 CACCACAGTGCTAAAATTTAGGATGAATTTTCTATAAAAATTAGCAAAGC 2303
Crub_svsplocu 170374 CCAAGAACCTTTGTAGTT 170391
i v vi i v
C Gypsy-129_DR- 2302 CCAGGAAACGCTGCACTT 2285
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.12
Transitions / transversions = 1.22 (11/9)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
585 31.80 5.04 4.87 Crub_svsplocus 170353 170947 479053 C Gypsy-194_DR-I LTR/Gypsy 1660 2255 2065
585 31.80 5.04 4.87 Crub_svsplocus 170353 170947 (479053) C Gypsy-194_DR-I#LTR/Gypsy (2065) 2255 1660 m_b4s001i8
Crub_svsplocu 170353 GCCTGTAGAAATTAGCAAATCCCAAGAACCTTTGTAGTTGGCGGCGGGTT 170402
i i v i v v ii i v i vvivivv
C Gypsy-194_DR- 2255 GTCTATAGAAATTTGCGAAGCCAAGAAATCTTTGGAGCTCTTTAATGGTT 2206
Crub_svsplocu 170403 CTTGGAGCTTG--CCATTCCAAAACACTCCGTACCTTACCTGG--ATCCA 170448
-- i i -- ii v vviii i -- v--
C Gypsy-194_DR- 2205 CT--GGGTTTGGGCCATTTTAATACTGCTTGCACCTT--CTGCTCATCCA 2160
Crub_svsplocu 170449 TTTCCACACC-----TGCCGCTGAAATCCGGAACCCCAAATAATCGATGC 170493
vv i ----- iv -- --- v i iiv ivv -
C Gypsy-194_DR- 2159 TGGCCACGCCCTCAGTGCCAAT--AAT---GTATCCCAGGAAGGAGATG- 2116
Crub_svsplocu 170494 GCTCCTTG-TGAAATTCACATTTGGATAGTTTACAATACAATTGAGCGTC 170542
v vi - i i vvv vvv i i - i i
C Gypsy-194_DR- 2115 GATGTTTGGTGGAATTCACACTTCTCTAGTTTTGCATATAATCG-GTGTT 2067
Crub_svsplocu 170543 C-AGCAGTTTCGTTAATACACTACG--TAC-TAACTGAATATGTTCCTCC 170588
- vi -- i vi i v-- - i i - i i i
C Gypsy-194_DR- 2066 CGATTAGT--CGTTGAAGCACTGCCCTTACGTGACCGA-TGTGTTCTTCT 2020
Crub_svsplocu 170589 AATGTTTGTGAGTAAATAAGTATATCATCTAGATATAC-CAGTATGCCA- 170636
iv v vv i i v v i -- i v- i ivv -
C Gypsy-194_DR- 2019 AGGGATTCAGAATAGATCAGGATGTCATC--GATGTAGACAATGACCCAG 1972
Crub_svsplocu 170637 CGATATAG-ATGGTCATGCAGAAATTCTTGATAAGCTGCATG-AATACAG 170684
vv - viivv v vi iv i i- v - i
C Gypsy-194_DR- 1971 CGATTAAGCATGTCTCGGAAGACGTCATTAATAAA-TGCTTGGAACACAG 1923
Crub_svsplocu 170685 CTGGGGCTCCTTG-TAACCCGAAAGGCATCACCTTAAAT-----TGGTAA 170728
v- i vi - ii i v -- i ----- i ii
C Gypsy-194_DR- 1922 A-GGGACTGTTTGCTAGTCCGAAGGGCATGACC--AAGTATTCATAGTGG 1876
Crub_svsplocu 170729 CTGC--CTAGTGGACAATTAAACGTCATCTTCCACTCATCCCCCTTCTTT 170776
i -- i -----i i?i i vv
C Gypsy-194_DR- 1875 CCGCTACTAGTAGA-----GAACGCNGTTTTCCACTCATGGCCCTTCTTT 1831
Crub_svsplocu 170777 ACCCTTACCCTATAATATGCTTCACGGAGGTCTAACTTCGTGAAGATCTT 170826
ii v i vv vi v vii i v i v i - v
C Gypsy-194_DR- 1830 ATTCTAATCAAATTGTAAGCACTACGGAGATCGAGCTTAGTAAAG-TATT 1782
Crub_svsplocu 170827 TCCAGCAG--CCAAATGAGTAAGAAGCT-CCTTCATAAGCGGTAAGGGGT 170873
--i -- vv ?iv vvii - vvv iv v i ii
C Gypsy-194_DR- 1781 T--GGCAGTGCGTAATNGTTCTAGAGCTGCCGGGACTAGAGGCAGAGGGT 1734
Crub_svsplocu 170874 ACACCTGCTCTA-TGCACAGGGCGTTGAGGCCCTGGAAGTCTACACATAA 170922
viv i iv - i - vv i v i v v i ii
C Gypsy-194_DR- 1733 ACCTGTACTTGACTGTA-ATTGCATTGAGCCCCCGGTAGTCGATACATGG 1685
Crub_svsplocu 170923 CTGCAGTCCCCCGTCCTTCTTCTCC 170947
vi i i v
C Gypsy-194_DR- 1684 GCGTAATCCACCGTCCTTCTTCTCC 1660
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.05
Transitions / transversions = 1.17 (97/83)
Gap_init rate = 0.08 (46 / 594), avg. gap size = 1.28 (59 / 46)
628 30.97 5.05 4.83 Crub_svsplocus 170353 170827 479173 C Gypsy70-I_DR LTR/Gypsy 1806 2281 2014
628 30.97 5.05 4.83 Crub_svsplocus 170353 170827 (479173) C Gypsy70-I_DR#LTR/Gypsy (2014) 2281 1806 m_b4s001i7
Crub_svsplocu 170353 GCCTGTAGAAATTAGCAAATCCCAAGAACCTTTGTAG---TTGGCGGCGG 170399
i v v iiv --- v -i i
C Gypsy70-I_DR# 2281 GCCTATAGAAATTCGCAAAGCCCAAGAATTGTTGTAGAGCTTTGCG-TGA 2233
Crub_svsplocu 170400 GTTCTTGGAGCTTGCCATTCCAAAACACTCCGTACCTTACCTGGATCCAT 170449
-- iv i iv v vi i vii v vi
C Gypsy70-I_DR# 2232 G--CCAGGAACCGGCCAGTCGGAGACAGCTCTTACCTTTTCTGGATCCAT 2185
Crub_svsplocu 170450 TTCCACACCTGCCGCTGAAATC-CGGAACCCCAAA---TAATCGA-TGCG 170494
ivv ii iv i i i-i v i ---v ii - v
C Gypsy70-I_DR# 2184 TCGAATGCCCTCCACCGAAATTATGGAACCCAAGAACGGAACTGACTGGG 2135
Crub_svsplocu 170495 CTCCTTGTGAAATTCACATTTGGATAGTTT-ACAATACAATTGAGCGTCC 170543
-----i vvvi vvv iv - - i i viv
C Gypsy70-I_DR# 2134 C-----ATGAAAAAGGCATTTCTCTGCTTTGACAA-ATAACTGATTCTCC 2091
Crub_svsplocu 170544 AGCAGTTTCGTTAATACACTACGTACTAA----CTGAATATGTTCCTCCA 170589
ii vvi -- - - i ---- i i iv vv
C Gypsy70-I_DR# 2090 AGCAGCCTCTGCA--ACACT-CGT-CTGACGTGCTGGATGTGCACCTGGA 2045
Crub_svsplocu 170590 ATGTTTGTGAGTAAATAAGTATATCATCTAGATATACCAGTATGCCACGA 170639
iv vvv v iv i i v i i i i v iv --- -i
C Gypsy70-I_DR# 2044 GAGAGGGAGAAAAGATGAGAATGTCATCCAGGTACACAAAAA---CA-AA 1999
Crub_svsplocu 170640 TATAGATGGTCATG-----CAG-AAATTCTTGATAAGCTGCAT-GAATAC 170682
- v v vi ----- - v iv ii - v - v
C Gypsy70-I_DR# 1998 T-TTGTTTATCATGTCTCTCAGCACATCATTGACGAG-TGCCTGGAAGAC 1951
Crub_svsplocu 170683 AGCTGGGGCTCCTTG--TAACCCGAAAGGCATCACCTTAAAT-TGGTAAC 170729
-- v --i i i i v vv -- - vvv v
C Gypsy70-I_DR# 1950 AGCTGGGG--CATTGGACAGCCCAAAGGGAAGAAC--TAAATATTCAAAG 1905
Crub_svsplocu 170730 TGCCTAGTGGACA-ATTAAACGTCATCTTCCACTCATCCCCCTTCTTTAC 170778
i ivi-i v ivi v i i v i
C Gypsy70-I_DR# 1904 TGCCCAGTGGGGGTGTTAAAGGCGGTCTTCCACTCATCGCCCTCCCTAAT 1855
Crub_svsplocu 170779 CCTTACCCTATAATATGCTTCACGGAGGTCTAACTTCGTGAAGATCTTT 170827
vv vv ii i v ii v i i i i i
C Gypsy70-I_DR# 1854 CCGGACCAAATGGTACGCGTTGCGCAGGTCCAACTTTGTGAAAACCCTT 1806
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.45
Transitions / transversions = 1.12 (74/66)
Gap_init rate = 0.07 (35 / 474), avg. gap size = 1.34 (47 / 35)
+ 267 25.8 2.2 2.2 Crub_svsplocus 171087 171177 (478823) C Gypsy70-I_DR LTR/Gypsy (2751) 1577 1487 107
ANNOTATION EVIDENCE:
267 25.84 2.20 2.20 Crub_svsplocus 171087 171177 478823 C Gypsy88-I_DR LTR/Gypsy 1487 1577 2751
267 25.84 2.20 2.20 Crub_svsplocus 171087 171177 (478823) C Gypsy88-I_DR#LTR/Gypsy (2751) 1577 1487 m_b4s001i9
Crub_svsplocu 171087 TCAATCGCACAATCCAT-TGGGCGATGAGGTGGTAAGC-TATCGCAATCT 171134
i v i - - i i i i v-vi v vv
C Gypsy88-I_DR# 1577 TCGATGGCGCAATC-ATATGGACGGTGGGGCGGTAAGGAGGTAGCTCTCT 1529
Crub_svsplocu 171135 TGTTCACTAAATACAGCTTTGAGGTCATTGTACACAGCTGGGA 171177
v -i v vi v vvi i
C Gypsy88-I_DR# 1528 TCTT-GCTAAAGACAGCTTTGAGGTGGTGGTACTGGGCTGGAA 1487
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 27.24
Transitions / transversions = 0.92 (11/12)
Gap_init rate = 0.04 (4 / 90), avg. gap size = 1.00 (4 / 4)
+ 508 30.1 3.5 2.2 Crub_svsplocus 175638 176073 (473927) C MamGypsy2-I LTR/Gypsy (883) 2080 1755 108
ANNOTATION EVIDENCE:
343 33.00 4.81 0.93 Crub_svsplocus 175638 175845 474155 C Gypsy163-I_DR LTR/Gypsy 3445 3660 771
343 33.00 4.81 0.93 Crub_svsplocus 175638 175845 (474155) C Gypsy163-I_DR#LTR/Gypsy (771) 3660 3445 m_b4s001i10
Crub_svsplocu 175638 GTGTGGTGTGGT------GGCAAAGAAGAAAGTCAGCTAACCTGTGATGC 175681
iv ------i v i vv - i v vi
C Gypsy163-I_DR 3660 GTGTGGTGTATTCCTATAAGCCAAGAGGAAAGTGTGC-AATCTTTGATTT 3612
Crub_svsplocu 175682 CAGTTGCCGTGA----GTGATTCTCTTTAAAGCATCTTTGGTAGTACGCA 175727
v vvi v v ---- i v - i i v i viv vi i
C Gypsy163-I_DR 3611 AAGGAACCCTTATCCTGCGATGCT-TTCAGAGCCTTTTTTAGAGTCTGTA 3563
Crub_svsplocu 175728 CCATACGCTCAGCCTGGCCGTTGGAAGCTGGATGGAATGGTGCAGATGTG 175777
v v i v i i v v v v v
C Gypsy163-I_DR 3562 CGAAACGTTCAGCCAGACCATTTGTAGATGGATGGTATGGTGCAGATTTG 3513
Crub_svsplocu 175778 GCATGCCAGATCATGTTGGCTTGAAGAAAAGCCTGAAACTCAGAAGACGT 175827
iii i iv vvii vii v i i v i vvvv ii
C Gypsy163-I_DR 3512 ATGTGTCGTATACCATTCATTTGTAGGAAGGACTGGAACTCTTCTGACAC 3463
Crub_svsplocu 175828 GAATTGGGATCCGTTGTC 175845
i iv i
C Gypsy163-I_DR 3462 GAGTTGGGGGCCATTGTC 3445
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.57
Transitions / transversions = 0.94 (33/35)
Gap_init rate = 0.02 (4 / 207), avg. gap size = 3.00 (12 / 4)
508 32.50 1.84 1.84 Crub_svsplocus 175705 176030 473970 C Gypsy-175_DR-I LTR/Gypsy 1755 2080 883
508 32.50 1.84 1.84 Crub_svsplocus 175705 176030 (473970) C Gypsy-175_DR-I#LTR/Gypsy (883) 2080 1755 m_b4s001i11
Crub_svsplocu 175705 TAAAGCATCTTTGGTAGTACGCACCATACGCTCAGCCTGGCCGTTGGAAG 175754
viv v vv vi v i i v vi i v vi
C Gypsy-175_DR- 2080 TAAAGCCCGTTTTGATGTCTGAACCATGCGTTCCGCCAAGCCATTCGTGG 2031
Crub_svsplocu 175755 CTGGATGGAATGGTGCAGA-TGTG-GCATGCCAGATCATGTTGGCTTGAA 175802
i i v ? -i - ii iv v i -- i vi
C Gypsy-175_DR- 2030 CTGGGTGAAAAGGTGNAGAGCGTGTGTGTGTGACACC--GTTAGCTTTGA 1983
Crub_svsplocu 175803 GAAAAGCCTGAAACTCAGAAGACGTGAA-TTGGGATCCGTTGTCGGAGAC 175851
v i i ivvvi v - i - i i vvi
C Gypsy-175_DR- 1982 GAAATGTCTGGAACTCGTCCAAGGTGAACTTAGGA-CCATTATCGCTAAC 1934
Crub_svsplocu 175852 AAGGACATCTGGAAGACCATG-TGAGGCAAAGATTCCTCTCAGCACCTGG 175900
v v v i - v-i v v vii i i
C Gypsy-175_DR- 1933 CAGCACTTCTGGAAGGCCATGATGAC-TAAATAATGTCCTCAGCACTTGA 1885
Crub_svsplocu 175901 ATGGTCCTAGTAGTAGTAGTGGAGGAGACAGGA-ACA-ACCTCTAGCCAT 175948
i v i vv v -- vv vv - - i vi i
C Gypsy-175_DR- 1884 ATGGTCTTTGCAGATGTAGTTGA--ATCCATCACACACACTTCGGGCCAC 1837
Crub_svsplocu 175949 TTGGAATGGCTGTCCATGAGGAGAAGGAAGAATTGCCCCTGAAAGGGTCC 175998
v i ivii i iv?v vi iv viv i v v v
C Gypsy-175_DR- 1836 TTTGAGTGAGCATCTACTNCGACGAGACACGTTTGTCCCTCAAATGGACC 1787
Crub_svsplocu 175999 AGCATAGTCAATGTGTACCCTTGACCATGGAG 176030
v ii i iv v vi v
C Gypsy-175_DR- 1786 AGCATAGTCTACATGCATACGTTGCCAAGGAG 1755
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.81
Transitions / transversions = 0.93 (50/54)
Gap_init rate = 0.04 (12 / 325), avg. gap size = 1.00 (12 / 12)
467 29.42 3.81 2.31 Crub_svsplocus 175733 176073 473927 C Gypsy158-I_DR LTR/Gypsy 3223 3568 823
467 29.42 3.81 2.31 Crub_svsplocus 175733 176073 (473927) C Gypsy158-I_DR#LTR/Gypsy (823) 3568 3223 m_b4s001i12
Crub_svsplocu 175733 CGCTCAGCCTGGCCGTTGGAAGCTGGATGGAATGGTGCAGATGTGGCATG 175782
i v vi? ? v ? v v? vi i
C Gypsy158-I_DR 3568 CGTTCTGCCAANCCGTTGGAAGNTGGATGGTANGGTGCTGTNGTCACGTG 3519
Crub_svsplocu 175783 CCAGAT--CATGTTGGCTTGAAGAAAAGCCTGAAACTCAGAAGACGTGAA 175830
i? -- v?i ? i-- vi v? ? vv? vv i
C Gypsy158-I_DR 3518 CTNGATGCCATTNCGNCTC--ATGAATNCCTNAAACTCTTNACTCGTAAA 3471
Crub_svsplocu 175831 TTGGGATCCGTTGTCGGAGACAAGGACATCTGGAAGACCATGTGAGGCAA 175880
viii?vv i v v v vv iv v v iv ?v vi
C Gypsy158-I_DR 3470 ACAANTGCCATTGTCCGACACTACCATTTCAGGTAATCCATGTNCGCTAA 3421
Crub_svsplocu 175881 AGATTCCTCTCAGCACCTGGATGGT---CCTAGTAGTAG---TAGTGGAG 175924
iv iiv ?vv v ---? v v? --- ? v
C Gypsy158-I_DR 3420 AACTCTGTCTCAGNTACTCGATGGTAACNCGAGANGTAGAANTANTCGAG 3371
Crub_svsplocu 175925 GAGACAGGAACAACCTCTAGCCATTTGGAATGGCTGTCCATGAGGAGAAG 175974
- ? v ----- ? i v i i ivii iv i vv
C Gypsy158-I_DR 3370 G-GANACG-----CNTCCATCCACTTGGAGTGAGCATCCACCAGAATCAG 3327
Crub_svsplocu 175975 GAAGAATTGCCCCTGAAAGGGTCCAGCATAGTCAATGTGTACCCTTGACC 176024
i v v vi i i ? v ? i v ii vv
C Gypsy158-I_DR 3326 AAACATTTTTCCTTGGAANGGACCNGCATAGTCAATATGGATTCTTCTCC 3277
Crub_svsplocu 176025 ATGGAGTATATGTCTCCTCCTACCTATGTACAGGGGCCT-----GGGGCA 176069
v v vv i v?i? i ?vvi vv ? ?i----- i
C Gypsy158-I_DR 3276 AGGGCGGCTGTGGNCNCTCCCANGGGTGTAATGGNGCNCGAGCAGGGGCG 3227
Crub_svsplocu 176070 TTTC 176073
i
C Gypsy158-I_DR 3226 TTCC 3223
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.48
Transitions / transversions = 0.72 (41/57)
Gap_init rate = 0.04 (12 / 340), avg. gap size = 1.75 (21 / 12)
+ 2017 33.2 3.2 2.8 Crub_svsplocus 176950 178231 (471769) C MamGypsy2-I LTR/Gypsy (1418) 2748 1462 108
ANNOTATION EVIDENCE:
2017 33.22 3.20 2.80 Crub_svsplocus 176950 178231 471769 C MamGypsy2-I LTR/Gypsy 1462 2748 1418
2017 33.22 3.20 2.80 Crub_svsplocus 176950 178231 (471769) C MamGypsy2-I#LTR/Gypsy (1418) 2748 1462 m_b4s001i13
Crub_svsplocu 176950 CTGTAGAGGTAATCTGTTTAGGCCATCTGCATGGCCCATTTCTTTACCTG 176999
i v i iv v i i v v vvvvi v i v v
C MamGypsy2-I#L 2748 CTGCAGTGGCAGACGGCTCAGGGCATCAGCATTCGATATTGCTCTTCCAG 2699
Crub_svsplocu 177000 GTTTGTGGACCAGAGTATAGTCATATGC--TGACAGGAAAATTGACCATC 177047
i i v v ii v -- vvii i i -- v
C MamGypsy2-I#L 2698 GCTTGTAGACAAGCGCGTAGTCATAAGCACTGAGCAAAAGACT--CCAGC 2651
Crub_svsplocu 177048 TCAGCATTCTAGGGGATATTATATGAGGG-GTTTGTTTGTTTGTTGTAAA 177096
v v v vv v i v - i - vv i i iiv v v
C MamGypsy2-I#L 2650 GCTGCATACGTGGTGACATAAT-TAAGGGCGTAGGCTTATCCTTAGAAAA 2602
Crub_svsplocu 177097 CAAACCCAGCAGAGGCTTATGGTCTGTGTAGAT-GTGAA---ATGGCCAT 177142
v iv viv i i v ii i - i --- i i
C MamGypsy2-I#L 2601 GAGTCCCCAAAGAGGCTTGTGATCAGTACAAATTGTAAAGGCACGGCCGT 2552
Crub_svsplocu 177143 GTAAGAAATCATGGAATTTCTTTATGCCAGCCACTATTGCCAAGGCTTCT 177192
iv i v i ii i v iv v v iv iv v i
C MamGypsy2-I#L 2551 AGAGGTAGTTGTGGAACTTCTTGACTCCCGCGATAACAGCAAGGGCTTCT 2502
Crub_svsplocu 177193 CTGTCAATCTGCGCGTAATTACACTCTGCAGATGAGAGAGTTCTGGAGTA 177242
i i i ii i v ii i v vv v
C MamGypsy2-I#L 2501 TTGTCAATTTGTGTATAGTTCCGTTCTGTAGATGACATTGTTCTTGAGTA 2452
Crub_svsplocu 177243 GTAGGCCACAAGGACTTGTGTCCCATCAGCCTTGAGGTGGCTCAGCATAG 177292
i v ivi vi i vv v v v v vvv v i
C MamGypsy2-I#L 2451 GTAAGCAATTGGTGCCTCAGTGCCATCTGGCATTTTGTGGCTAAGCACAG 2402
Crub_svsplocu 177293 CCCCAACCCCATAAGGGGATGCATCACAGCTATGCATACAGGCAATTT-- 177340
i i v i v v i vv v v v - -iii --
C MamGypsy2-I#L 2401 CTCCAGCACCGTAAGGTGAAGCGTCAGTGGTAAGAA-ACAG-TGGTTTAT 2354
Crub_svsplocu 177341 -CTCATTGAAATGAGCTAACACAGCATTTGAGGAAAGCAA-GGC--CTTG 177386
-i i v vi i - i i -- iv -ii --
C MamGypsy2-I#L 2353 GTTCATCGTAATGTACTAGCACAG-ACTCG--GAAGTCAATAACTGCTTG 2307
Crub_svsplocu 177387 AC-CTCTGAAAAACTCTTTTCATGGACTTGTG--TCCACTGCCAAGGAGC 177433
-i i i i v- ii -- v i -- vi v i
C MamGypsy2-I#L 2306 ACATTCCGGAAAGCG-TCCTCATG--CTGGCGAGTCCAACGCCACGGAAC 2260
Crub_svsplocu 177434 CTGTTTATCCAAGAGCCAGTGTAA-----CAGCCACTGTGGCCTTGTGAG 177478
viv vi iv v ii v i----- v iv v v v
C MamGypsy2-I#L 2259 GCCTTTTCCCAGTAGGCGATGAAGTGGCTCAGCAATGGTTGCCTTTTGTG 2210
Crub_svsplocu 177479 GTAGAAATGCATGGTAAAAGTTTAACAGTCCTAGAAAAGCCTGAAGTTC- 177527
v vi i i v ii i i i i i i -
C MamGypsy2-I#L 2209 GAAGAAAAACATGGTAGAAATTGAGTAGCCCCAGGAAGGCTTGAAGCTCT 2160
Crub_svsplocu 177528 -GCTTTTGGACTTGTGACTTGGGGCCTGCTGAATTGC-TTTATGCTTGGA 177575
- - vvi - v v v v vv i -iv i- ivv
C MamGypsy2-I#L 2159 TGCTTT-GTTTTTG-GAGTAGGCGCGTCATGGATTGCACGTAC-CTTATC 2113
Crub_svsplocu 177576 TTCAGCAGGATGGATGCCTTCAGCATCAATACGG-AACCCCAGAAATT-- 177622
v ii i i i vv ii i - i iv iv --
C MamGypsy2-I#L 2112 TTGAGTGGGGTGAATACCAGCAGCATTGATGCGGTAGCCTAAGAAGGTGA 2063
Crub_svsplocu 177623 CAGTGGAGGTAACTTCAATCTTACATTTGTCTTGCTTCAGCTTCAGC--C 177670
v i --- i i i i v i vi --i i v--
C MamGypsy2-I#L 2062 CACTGGAAGT---TCCGATTTCACATTTCTCCTTTTTCA--CTCGGATAC 2018
Crub_svsplocu 177671 CTGCTTGGTAGAAACGCAGCAAGACAGCCCTCAGCCTTTCAGCTAAGTTC 177720
v vvi v vv i i vv ivv i v -i
C MamGypsy2-I#L 2017 CTGATGTATCGAAACGATGTAGGACTTCCTGAAGTCTTTCCGC-GAGTTC 1969
Crub_svsplocu 177721 A----CAGATGACTCCCCAGCAATGAGGACATCATCAAAGTAGGG-ACAG 177765
---- v v i-- -ii v i i v - v-
C MamGypsy2-I#L 1968 ATCCTCTGTTGAT--CCCA-TGATCAGGACATCATCGAAATATGGTACC- 1923
Crub_svsplocu 177766 ATCCCAGGAATACCACGGAGC---GTTCACTCCATCACACTCTGGAATAT 177812
iv v v i vii --- --- v vi v v
C MamGypsy2-I#L 1922 ACACCTGGAATCCTAGAAAGCAGGGT---CTCCATGAAGCACTGGAAAAT 1876
Crub_svsplocu 177813 TCCAGGGGCCACATTAACCCCAAACTGCAGCCTTTTTACCTTAAAGGCTC 177862
v vv ii i v v vi v iivi v i
C MamGypsy2-I#L 1875 TCCAGGGGCAACAGAAATTCCGAACTGAAGGCGCTTAACTCGGAATGCCC 1826
Crub_svsplocu 177863 TCCGGTGCGTCAGAATTGTTTGGGCTTCAGCCGTTGCCTCATCAACAGGT 177912
ii i v v vi v v v v v i i iivi
C MamGypsy2-I#L 1825 CTCGATGAGTGATGATTGTTTGGGCGTCTGCAGTAGCATCACCGACGATC 1776
Crub_svsplocu 177913 AGCTGTTGATAGGCCTAAGCCAAATCAAGCTTTGCAAAGA--TTTGCCCC 177960
i i ii v ii i -- v
C MamGypsy2-I#L 1775 AGCTGTTGATAAGCTTGGGCAAGGTCAAGTTTTGCAAAGACCTTTTCCCC 1726
Crub_svsplocu 177961 ACCCCCCTTTGAGTGAGGCCAGAATGTGGCTCACCACAGGCACCGGGTAG 178010
v -------i vivi v i vv ii v ii i i v
C MamGypsy2-I#L 1725 AGC-------AAGAACAGCAAGGAGTTGATTGACTGCAGGCACTGGATAT 1683
Crub_svsplocu 178011 GCATGCTGCTGCAATGCCTTATTTAGTGTACATTTATAGTCCGCACAAAT 178060
vi vv i i vv i i i iv v
C MamGypsy2-I#L 1682 GGGTGCTGCTTAAGTGCCTTATTCACAGTGCACTTGTAGTCTCCACAAAG 1633
Crub_svsplocu 178061 TCGGACTTCTCCATTGGCCTTCAGTGGTCTGACT--ATAGGGGTTTCCCA 178108
vv i iv i v i i-- i i v-- v vi vv
C MamGypsy2-I#L 1632 TCTCACCTTACCATTAGGCTTTAGTA--CCGGCGCAATTGGTATAGCCCA 1585
Crub_svsplocu 178109 TGGACTAGAGCCCACCGGTTCTAAGATGCCCTGCTGGAGCAGCTTGTCCA 178158
iv iv vivviv i v i iii i i v vi v vv v
C MamGypsy2-I#L 1584 CCGGGTATGTGTAACTGGTTCGAGGGCACCTTGTTTGATTAGATGCTCAA 1535
Crub_svsplocu 178159 GCTCTGCATCTATTTTGTTCTTTAGAGCAAAAGGCACCCTTCGGGGCTTG 178208
v v v? v i i vi vi vi v
C MamGypsy2-I#L 1534 GCTCTTCTTCANTTTTTTTCCTTAGAGCAAAAGGTACATTTCTAGCTTTC 1485
Crub_svsplocu 178209 ATCCTGATGGGTGTGATGGCTGG 178231
vvivi v ii
C MamGypsy2-I#L 1484 AAGTGAATTGGTGCAATGGCTGG 1462
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.60
Transitions / transversions = 1.03 (210/204)
Gap_init rate = 0.05 (58 / 1281), avg. gap size = 1.33 (77 / 58)
+ 302 19.9 0.4 2.3 Crub_svsplocus 179507 179617 (470383) + HERV1_I LTR/ERV1 7509 7563 (1238) 109
ANNOTATION EVIDENCE:
268 27.52 0.91 0.91 Crub_svsplocus 179507 179616 470384 + Harlequin LTR/ERV1 5647 5756 1140
268 27.52 0.91 0.91 Crub_svsplocus 179507 179616 (470384) Harlequin#LTR/ERV1 5647 5756 (1140) m_b4s001i14
Crub_svsplocu 179507 AATTTGTTTATTGAAAT-GGCTGAGGAGGTGGCAAAAACACTCACTGTAA 179555
- v -i i v v i vv iv v v v
Harlequin#LTR 5647 AATTTGTTT-TTGCAATTAGCCGAGCATGTAGCCCAGTCTCTCAATGTCA 5695
Crub_svsplocu 179556 AGAATTGTTTTGTATGTGGTGGTACCAACATGGGGGAGCAATGGCCATGG 179605
vvvvv v v v iivv i v
Harlequin#LTR 5696 CTTCATGTTATGTATGTGGAGGAACTGTAATGGGAGATCAATGGCCATGG 5745
Crub_svsplocu 179606 GAAGCTTTAGA 179616
iiv
Harlequin#LTR 5746 GAAGCCCGAGA 5756
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.80
Transitions / transversions = 0.43 (9/21)
Gap_init rate = 0.02 (2 / 109), avg. gap size = 1.00 (2 / 2)
302 12.74 0.00 3.64 Crub_svsplocus 179561 179617 470383 + HERV1_I LTR/ERV1 7509 7563 1238
302 12.74 0.00 3.64 Crub_svsplocus 179561 179617 (470383) HERV1_I#LTR/ERV1 7509 7563 (1238) m_b4s001i15
Crub_svsplocu 179561 TGTTTTGTATGTGGTGGTACCAACATGGGGGAGCAATGGCCATGGGAAGC 179610
v v i i v v i
HERV1_I#LTR/E 7509 TGTTATGTATGTGGAGGTACCAATATGGGAGACCAATGGCCCTGGGAGGC 7558
Crub_svsplocu 179611 TTTAGAG 179617
--
HERV1_I#LTR/E 7559 --TAGAG 7563
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.96
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2)
+ 304 34.4 5.8 5.5 Crub_svsplocus 179957 180337 (469663) C HERV3-int LTR/ERV1 (2440) 5407 5026 110
ANNOTATION EVIDENCE:
304 34.44 5.77 5.50 Crub_svsplocus 179957 180337 469663 C HERVE_a LTR/ERV1 5026 5407 2440
304 34.44 5.77 5.50 Crub_svsplocus 179957 180337 (469663) C HERVE_a#LTR/ERV1 (2440) 5407 5026 m_b4s001i16
Crub_svsplocu 179957 AGAGCCTGCAGCTGTT-CTG--ATTTAACAGTATCTGCCACTTGTTCAGA 180003
i i i- -- i ivvi i iv v i v--i
C HERVE_a#LTR/E 5407 AAAGCCTGTAGCTGTCGCTGTAATTCAATTTCACCTAACTCTCGG--GGA 5360
Crub_svsplocu 180004 GT-TCTGGACACCTGGTTTGAGTAGGTTGGGGACTCTGCCATACAATAAT 180052
-i vi ivvv v vi vv i v v -- i v
C HERVE_a#LTR/E 5359 GTGCCTGGAAGCCCCCGTAGTATAGGAGGAGGCCTATG--ATACAGTATT 5312
Crub_svsplocu 180053 TCA-AAGGGAGACACGAGCAGCCCCCTTTGT-----GGGGCACACCTTAC 180096
- ------ i v ivi v ----- ii i v i
C HERVE_a#LTR/E 5311 TCATAAGGG------GAGTATCCTGTTTTCTTAGAAGGGGTGCATCTAAT 5268
Crub_svsplocu 180097 CACAACCAGGGCCATATTTAAAGCATCTGGCCACTTAAGCTGAGTCTCCT 180146
ivi v ivi vvv ii v v iv v iiivv i
C HERVE_a#LTR/E 5267 TTTAAACAATACCATAGGAAGGGCCTGTATCCACTTTAATCCTGTTTCCT 5218
Crub_svsplocu 180147 GACATATTTTTGCCAATTTTTCCTTAATGGTCT-ATGTATTCTCTCCACC 180195
i iv i vi v ii i i i- vi v
C HERVE_a#LTR/E 5217 GACATACTTTCCCTAAACTATTTTTGATAGTCCGATTCATTCGCTCCACC 5168
Crub_svsplocu 180196 CTTCCTCCTGA---TTGAGCATGG-AAACTACA-GTCAAGCTTCCATGTT 180240
i --- v ---i vvi - ii vi - -- v v
C HERVE_a#LTR/E 5167 TT---TCCGGAACTCTGAGGTCGGTAGGCGGCATGT--AGCTTCCAAGTG 5123
Crub_svsplocu 180241 ATTCCTAGCATAGCTGCTATCTTTTG------GGTGGCTCTATGGATAAA 180284
iiiivvi i i ------ vii i------ i
C HERVE_a#LTR/E 5122 ATTCCTAATGCCTTTGCTGTCTTCTGTACCAAGTCAGCC------ACAAA 5079
Crub_svsplocu 180285 TTCAGGACCATTATCTTAAGAGATTCTAGATGGCAACCCATACCTGGGAA 180334
iv v v i v ivv vvi v ii v i
C HERVE_a#LTR/E 5078 CGCCGGCCCGTTATCTGAGCCGATTCGTAAGGGCAGTCCAAACCTAGGAA 5029
Crub_svsplocu 180335 TAA 180337
C HERVE_a#LTR/E 5028 TAA 5026
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.31
Transitions / transversions = 1.21 (68/56)
Gap_init rate = 0.08 (31 / 380), avg. gap size = 1.39 (43 / 31)
+ 16 0.0 4.3 0.0 Crub_svsplocus 180371 180393 (469607) + (CTT)n Simple_repeat 1 24 (0) 111
ANNOTATION EVIDENCE:
16 0.00 4.35 0.00 Crub_svsplocus 180371 180393 469607 + (CTT)n Simple_repeat 1 24 0
16 0.00 4.35 0.00 Crub_svsplocus 180371 180393 (469607) (CTT)n#Simple_repeat 1 24 (0) m_b4s252i2
Crub_svsplocu 180371 CTT-TTCTTCTTCTTCTTCTTCTT 180393
-
(CTT)n#Simple 1 CTTCTTCTTCTTCTTCTTCTTCTT 24
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.05 (1 / 22), avg. gap size = 1.00 (1 / 1)
+ 1303 34.6 4.8 2.4 Crub_svsplocus 180896 181948 (468052) C HERV3-int LTR/ERV1 (3659) 4767 3690 110
ANNOTATION EVIDENCE:
1303 34.64 4.84 2.41 Crub_svsplocus 180896 181948 468052 C HERV3 LTR/ERV1 3690 4767 3659
1303 34.64 4.84 2.41 Crub_svsplocus 180896 181948 (468052) C HERV3#LTR/ERV1 (3659) 4767 3690 m_b4s001i17
Crub_svsplocu 180896 GCTTCCCTGTCTGCCTTATTATTTCCTAATTGAATATCTGATGCTCC--- 180942
i vi i -- ivi- ii i ---
C HERV3#LTR/ERV 4767 GCCTCCCTGTCTGCCTTTCTGTTTCCT--TTGGCC-TCTAGTGTTCCTGC 4721
Crub_svsplocu 180943 CTTCTGATGGCCTTTGCAATGCATTACAGCTACTTCCTTAGGCTCCCACA 180992
i i v ii i ? i i i v vv i
C HERV3#LTR/ERV 4720 CTTTTGGTGCCCCCTGCAGTGCATNACAGCCACCTTCTTTGGGGCCCATA 4671
Crub_svsplocu 180993 CACTATTCAGCAGATGCAATATCTGTGGTCC--ATATTTAACATCCATTC 181040
vi ii iv v i iv i v -- --i i v iv iv i
C HERV3#LTR/ERV 4670 CAGCATCTAAGAGCTGTAGAATTTCT--TCCTTGTACTTTATTTCTTTTT 4623
Crub_svsplocu 181041 CCC-CTGAAGTTATAAGTCCTCTTACTTTGTATAAGGCTCCATGGACTTG 181089
- i v vi v vi i i v
C HERV3#LTR/ERV 4622 CCCTCCGCAGTTAAGAGTCCTCTTTCTTTGTATATAGCCCCATGAACATG 4573
Crub_svsplocu 181090 CACTGTTAGGAATGCATACTTAGAGTCTGTGTAAATATTAATGCACTTTC 181139
v? vivi v i i i ? i ivivi vi
C HERV3#LTR/ERV 4572 CAANGTGGCAAAAGCATATTTGGAATCNGTGTAAATATTGACCTTTTTGT 4523
Crub_svsplocu 181140 CTTTTGCCAACTCCAAAGCTCTAGTTAATGC-ATGCAGGTCAGCTAGCTG 181188
i i vvv i v i iv - -i v v ivv
C HERV3#LTR/ERV 4522 CTTTTGCTAGCAAAAGAGCTCTTGTCAGGGCTAT-TAGCTCTGCCTTCTG 4474
Crub_svsplocu 181189 AGCATTTGTAACGGGCGGAAGTTGCTCAGCTTCCCATACTTCCTCCAAAA 181238
i ?vv? vv vv v vv v? i ivvi vvv ?i
C HERV3#LTR/ERV 4473 GGCNGANGTTCCGGTAGGCAGAGGCTGNGCCTCTACCACTGAGTCCAANG 4424
Crub_svsplocu 181239 TCACCACAGCACATCCTGCCTTTCGAATGTCTTCTTGCATAAAACTAGTT 181288
v i i v iivv i ivi v i ii iv
C HERV3#LTR/ERV 4423 TCACCACTGCATACCCGGCTCGGCGGACCCCTTCTAGTACGAAACTGCTT 4374
Crub_svsplocu 181289 CTACCCGTGTA-TATTGTAAAGTCTGGATCAAGCAGGGGGAC--ATCTCT 181335
i i i v - -i v i i --v v i i --i v
C HERV3#LTR/ERV 4373 CCATCTGTGAAGTATT-CAACGTCCGGGTC--CCCGAGGGGCCGGTCTGT 4327
Crub_svsplocu 181336 CATGTCTGAGCGGCTAGCGTAAGTTTCTTCAATAGCTTGTGTGCAACTAT 181385
? vi vvv v v v viii v v iv i? viiii ii?
C HERV3#LTR/ERV 4326 NAGATCTCTCCGGCTTGAGAACACCTCATCTACCGTNTCCACACAGTNAT 4277
Crub_svsplocu 181386 G--TGTGGTTTCCAAGTCTGATTCAGGCAGCAGCGTGGCTGGATTCAGTG 181433
--v v ?i vi ii - i - iv i i i ? v
C HERV3#LTR/ERV 4276 GAAGGGGGNCTCCCGGTTCGA-TCGGG-AGCAAGGTAGCCGGGTTNAGGG 4229
Crub_svsplocu 181434 AGTT---TGAT--TAAATTAATATAACCATTGGATTAT-GTATTATTAGG 181477
v ---? v -- v v iiii----- v - i - vv v
C HERV3#LTR/ERV 4228 TGTTCACNGTTTCTAAAGTTATGCGG-----GGATTTTCGCA-TAGGAGC 4185
Crub_svsplocu 181478 GCTTGATACTTTAGCATGCGTGGGTTGGTCAGCCACAAATGTCCT-TTTG 181526
v i i ivviv v vi i v vi i vvii i - i
C HERV3#LTR/ERV 4184 CCCTGGTACCGAGTCATTCTCGGATTTGATAACCAATGGTGCCCTCTCTG 4135
Crub_svsplocu 181527 CTTC--TAAGACAGCTTTAA--AAGCATGGGGTGTGTAGATATCTAACTT 181572
v i -- --- i v --i iii v iivii ivii ii v
C HERV3#LTR/ERV 4134 GTCCATTAA---AGTTATAACCGAGTGCGGCGTACCCGGATGGTCAGTTG 4088
Crub_svsplocu 181573 TTGTCCAAAAGTCAACTTGTTAGCTTCCTGTGTTAATAACGCTGTTCCAG 181622
i v i ii i ii i iv v vv
C HERV3#LTR/ERV 4087 CTGTCCTAGAGTCAGTTTGTTAGCTTCTTGTGCCAGTAGGGCGGTGGCAG 4038
Crub_svsplocu 181623 CACTTGCTTTAAGGCAAGCCGGCCATCCTCTGGCTACATTGTCAAGCTGT 181672
vvv i vv ?vvv i ivv v ii i
C HERV3#LTR/ERV 4037 CTAGTGCCTTAAGGCAAGGAGGCCATCCNAGCGCCACGGAGTCCAATTGC 3988
Crub_svsplocu 181673 TTAGACAGATAAGTGACCGGGTGATGCCAGGTTCCT---ACT-------- 181711
i i i ii v iv i v v --- --------
C HERV3#LTR/ERV 3987 CTGGATAAGTACGCCACCGGGCGATGCCATGATCCTATGACTTGAGTCAG 3938
Crub_svsplocu 181712 ----------GCCA---CATTTTGCTT-TGTATCTACAAACAGTTGAAAT 181747
---------- --- v i i- v iv i v --- -
C HERV3#LTR/ERV 3937 GACCCCTATAGCCATTCCCTTTCGCTCGTGGACATACAGAAA---GAAA- 3892
Crub_svsplocu 181748 AACTTTTCCAAGTCTAGTAGACCTAAACTAGGGGCACACATTAGAGCCTC 181797
ii vvii ?i i i v iviv viivi ii i
C HERV3#LTR/ERV 3891 GGCTTAGTTANATCTGGCAGTCCTAAGGCTGGGGCCTGAGTTAAGGCTTC 3842
Crub_svsplocu 181798 CTTGAGAGCGGTGAAGCTGTTATTTTCTTGCTG--TTCCTATCGCAATGG 181845
i v-vi v v i-? iiv i i v ii --i i vv v iv
C HERV3#LTR/ERV 3841 TTTGAT-TTGTTTAAA-NGCCTTCTCCTGGTCGGCCTCCCAGAGGAGGGG 3794
Crub_svsplocu 181846 TTCTTTATCTCCCA-CTTTGTGGCCTCATATAGGGATTTTGCTATTAAAC 181894
i i v i v- i iv ii v i ? ivv
C HERV3#LTR/ERV 3793 CTCCTTTTCCCCCCTCTTTGTGGCTTCATATAATGGCTTAGCCATNAGCG 3744
Crub_svsplocu 181895 TAAAGGTAGGGATCCATATTCGGCAGAAGCCAGCAGCAACTAAAAATCCT 181944
vi iv v v v v v v vv i ii
C HERV3#LTR/ERV 3743 AGAAATTTGGGATCCAGATGCGGCAGAACCCTGCTGCCCCTAAGAACTCT 3694
Crub_svsplocu 181945 CTTA 181948
C HERV3#LTR/ERV 3693 CTTA 3690
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 45.41
Transitions / transversions = 1.23 (196/160)
Gap_init rate = 0.04 (46 / 1052), avg. gap size = 1.67 (77 / 46)
+ 372 16.9 0.0 0.0 Crub_svsplocus 182606 182676 (467324) C HERV3-int LTR/ERV1 (6302) 2499 2429 110
ANNOTATION EVIDENCE:
372 16.90 0.00 0.00 Crub_svsplocus 182606 182676 467324 C HERV1_I LTR/ERV1 2429 2499 6302
372 16.90 0.00 0.00 Crub_svsplocus 182606 182676 (467324) C HERV1_I#LTR/ERV1 (6302) 2499 2429 m_b4s001i18
Crub_svsplocu 182606 CTTCATCCTTTTCTCTTTCTGGACATTCACCCTTCCAGTGTCCTTCCTTC 182655
i i i i ?i v
C HERV1_I#LTR/E 2499 CTTTATCCTTTTCTCTCTCTGGACATTCATCCTTCCAGTGCCCTNTCTGC 2450
Crub_svsplocu 182656 TTACATATGGCACACTGGTTT 182676
i v v i i i
C HERV1_I#LTR/E 2449 TTGCATCTCGCACATTGATCT 2429
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.07
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 12 23.3 0.0 0.0 Crub_svsplocus 182757 182791 (467209) + (TTTCTT)n Simple_repeat 1 35 (0) 112
ANNOTATION EVIDENCE:
12 23.31 0.00 0.00 Crub_svsplocus 182757 182791 467209 + (TTTCTT)n Simple_repeat 1 35 0
12 23.31 0.00 0.00 Crub_svsplocus 182757 182791 (467209) (TTTCTT)n#Simple_repeat 1 35 (0) m_b4s252i3
Crub_svsplocu 182757 TTTCCTTTGCATTTTCTGATCCTTTTTCTTTTCCT 182791
i v v vv i i
(TTTCTT)n#Sim 1 TTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCT 35
Matrix = Unknown
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0)
+ 388 30.9 0.0 2.0 Crub_svsplocus 183054 183205 (466795) C HERV3-int LTR/ERV1 (7762) 1039 891 110
ANNOTATION EVIDENCE:
388 30.88 0.00 2.01 Crub_svsplocus 183054 183205 466795 C HERV1_I LTR/ERV1 891 1039 7762
388 30.88 0.00 2.01 Crub_svsplocus 183054 183205 (466795) C HERV1_I#LTR/ERV1 (7762) 1039 891 m_b4s001i19
Crub_svsplocu 183054 TCTAGTGTCCCTGTGCTTGGCCAGCCTATGTTAAAGCTGGGCCAATCTAC 183103
v? ? ivi vii v ii ivv? i i
C HERV1_I#LTR/E 1039 TCTATNGTNCCCTCGGCCGGCCACCCTACATTAAAAGANGGCCAGTCTAT 990
Crub_svsplocu 183104 CTCACAGAAGATCCTCAACTTATGCCTGCTCCACTTAATACCACAATCCT 183153
i i?i i i v ?vviv ivi ? iv i --
C HERV1_I#LTR/E 989 CTCACAAAGNGTTCTCAGCTTCTGNGGAGTTAGCTTNACCCCATAATC-- 942
Crub_svsplocu 183154 GATCCTCATAAGCAGACTTAAAATGCTTTAACATACACCCCAATGGAGTA 183203
- i v i v v vvv i v i i i i ?
C HERV1_I#LTR/E 941 -ACCATTAAAACCTTTCTTAAAGTTCTTCAGCATGCACTCCAATGGAGTN 893
Crub_svsplocu 183204 AG 183205
i
C HERV1_I#LTR/E 892 GG 891
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.33
Transitions / transversions = 1.42 (27/19)
Gap_init rate = 0.02 (3 / 151), avg. gap size = 1.00 (3 / 3)
+ 540 27.0 3.1 0.0 Crub_svsplocus 184909 185071 (464929) + Plat_L3 LINE/CR1 3393 3560 (13) 113
ANNOTATION EVIDENCE:
540 26.99 3.07 0.00 Crub_svsplocus 184909 185071 464929 + Plat_L3 LINE/CR1 3393 3560 13
540 26.99 3.07 0.00 Crub_svsplocus 184909 185071 (464929) Plat_L3#LINE/CR1 3393 3560 (13) m_b4s001i20
Crub_svsplocu 184909 ATTAACCAGTGGAACAATTTGCCTCCAGAAGCTGTGAATGCTCCAACAAT 184958
v v v iivi i vvvi i i i vv v vv
Plat_L3#LINE/ 3393 ATAAAACACTGGAACGGGCTACCGAGGGAGGTTGTGGAGTCTCCATCCCT 3442
Crub_svsplocu 184959 GGAAGTTTTTAAGAAGAGACTAGACAGCCATGTGCCTGAAATGGTATAGG 185008
ii i i v ? v i ivii v v
Plat_L3#LINE/ 3443 GGAGATCTTTAAGAAAAGAATAGACANCCATCTGTCCTGGATGGTTTAGT 3492
Crub_svsplocu 185009 GTTTT--CTTCCTG-AGG-AGGGGGTTGGACTAGATGACCT-TCAAGATC 185053
vv i-- v - - i i - i i
Plat_L3#LINE/ 3493 CATTCACCTGCCTGGAGGCAGGGGGCTGGACCAGATGACCTCTCGAGGTC 3542
Crub_svsplocu 185054 CCTTCCAACTTTATTATT 185071
i i ?v
Plat_L3#LINE/ 3543 CCTTCCAGCTCTANGATT 3560
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.58
Transitions / transversions = 1.10 (23/21)
Gap_init rate = 0.02 (4 / 162), avg. gap size = 1.25 (5 / 4)
+ 2444 29.2 1.9 0.6 Crub_svsplocus 186556 187363 (462637) + L3 LINE/CR1 3287 4080 (19) 114
ANNOTATION EVIDENCE:
2444 30.66 1.01 0.50 Crub_svsplocus 186556 187345 462655 + L3 LINE/CR1 3287 4080 19
2444 30.66 1.01 0.50 Crub_svsplocus 186556 187345 (462655) L3#LINE/CR1 3287 4080 (19) m_b4s001i21
Crub_svsplocu 186556 GACAGACTTGAACACTGGGCACTAACTAACAAAATGAAATTCAATGGTGA 186605
i v iv vvv i i i ii v
L3#LINE/CR1 3287 GACAGGCTGGAACGATGGGCCGAAACCAACAAGATGAAATTTAACAGGGA 3336
Crub_svsplocu 186606 AAAAAGCAAGGTTCTACATTTAGGCAAGAAAAACCAAATGCACAAGTACA 186655
v v i i i i ivvi i v
L3#LINE/CR1 3337 TAAATGTAAAGTCCTGCATTTAGGTTCAAAAAATCAACTGCACAAGTACA 3386
Crub_svsplocu 186656 GTATAGGTGGCACCATGCTCAATAGTAGTAACTGTGAGAGGGACCTCGGA 186705
v i ivi v i vv i ii i vvvi i ii v i
L3#LINE/CR1 3387 GGATGGAGAGGATCTGGCTTAGCAGCAGTTCACGTGAAAAAGACCTAGGG 3436
Crub_svsplocu 186706 TTCCTAGTAGACAATCACCTAAATATGAGCCAGCAGTGTGCTGCAGCTGC 186755
v ii v viiv v v i v ii
L3#LINE/CR1 3437 GTTTTAGTTGACCGCAAGCTCAATATGAGCCAACAGTGTGATGTGGCTGC 3486
Crub_svsplocu 186756 CAAAAAGGCCAACACAGTGCTAGGCTGCATTAACAGAGGGATAGAATCAA 186805
i i ii i vi i i v vi v
L3#LINE/CR1 3487 CAAAAAAGCTAATGCAATCTTAGGCTGCATTAATAGAAGTATAGTGTCCA 3536
Crub_svsplocu 186806 GATCACGTGAAGTATTAATACCACTCTTCAATGCCTTGGTAAGGCCACAC 186855
? v v i v i v i v v vv vi v i i
L3#LINE/CR1 3537 GANCAAGGGAGGTAATAGTCCCGCTGTACTCTGCGCTGGTCAGACCACAT 3586
Crub_svsplocu 186856 TTGGAATACTGCATCCAGTTTTGGTCACCATGATGTAAAAAAGATGTTGA 186905
i i i i i i v i iiv v i ii ii
L3#LINE/CR1 3587 CTGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGA 3636
Crub_svsplocu 186906 GACTCTAGAAAGAGTACAGAGAAGAGCAATAAAGATGATTAGGGGACTGG 186955
v vv i iv v v i i iv i i v i v
L3#LINE/CR1 3637 CAAACTGGAGCGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGG 3686
Crub_svsplocu 186956 AGGCTAAAACATATAAGGAACGGTTGCTAGAATTGGGTAAGTCTAGTTTA 187005
ii i viv i vvi i v v i ii i
L3#LINE/CR1 3687 AAACCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTG 3736
Crub_svsplocu 187006 ACGAAGAGAAGGACGAGGGGGGACATGATAGCAGTATTCCAATATCTCTG 187055
iv iviv i i v v v i vvi
L3#LINE/CR1 3737 GAGAAGAGAAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAA 3786
Crub_svsplocu 187056 TGGCTGCCATAAAGAAGAGGGAATCAAGCTATTTTCCAAAGCACCTGAAG 187105
v i ivi v vi vi i viivi v v i
L3#LINE/CR1 3787 GGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGG 3836
Crub_svsplocu 187106 GCAGGACAAGAAGGAACGGGTGGAAACTAATCAAGGAGAGAAG----CAA 187151
i v i vv i ii -- i - v ---- ii
L3#LINE/CR1 3837 GCAGAACTAGGACCAATGGGTGGAAGTTA--CAGGGAG-GCAGATTTCGG 3883
Crub_svsplocu 187152 CCTAGAACTAAGGAGAAGCTTCCTGACAGTGAGAACAATTAATCAGTGGA 187201
ii iv - ii i i i i v i vi iv vv i
L3#LINE/CR1 3884 CTCAATA-TAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGA 3932
Crub_svsplocu 187202 ACAGCCTGCCTCCAGAAGCAGTAAATGCTCCAACACTGGAAGTTTTTAAG 187251
ii v v? i i i iiv i iv i v i
L3#LINE/CR1 3933 ATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAG 3982
Crub_svsplocu 187252 AAGAGACTGGACAGCCATTTGTCCGAAATGGTGT---AGGGTTTCCTGC- 187297
v i iii i v ii v --- v -
L3#LINE/CR1 3983 CAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCA 4032
Crub_svsplocu 187298 CCGAGCAGGGGGTTGGACTAGATGACCTCCAAGGTCCCTTCCAACTTT 187345
i iiii i i i
L3#LINE/CR1 4033 TCGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCT 4080
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.96
Transitions / transversions = 1.54 (146/95)
Gap_init rate = 0.01 (7 / 789), avg. gap size = 1.71 (12 / 7)
396 18.27 8.51 0.99 Crub_svsplocus 187270 187363 462637 + CR1-3_Croc LINE/CR1 3503 3603 2
396 18.27 8.51 0.99 Crub_svsplocus 187270 187363 (462637) CR1-3_Croc#LINE/CR1 3503 3603 (2) m_b4s001i22
Crub_svsplocu 187270 TTGTCCGAAATGGT----GTAGGGTT--TCCTGCC-CGAGCAGGGGGTTG 187312
vi ii ----i v -- - ii
CR1-3_Croc#LI 3503 TTGTATGGGATGGTTTGGATAGGGATGATCCTGCCTCAGGCAGGGGGTTG 3552
Crub_svsplocu 187313 GACTAGATGACCTCC-AAGGTCCCTTCCAACTTTACTACTATTATTATTA 187361
i-i i ii v -i v v
CR1-3_Croc#LI 3553 GACTAGATGACCTCTGGAGGTCCCTTCCAGCCCTACTTCT-CTATGATTC 3601
Crub_svsplocu 187362 TA 187363
CR1-3_Croc#LI 3602 TA 3603
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.53
Transitions / transversions = 2.40 (12/5)
Gap_init rate = 0.05 (5 / 93), avg. gap size = 1.80 (9 / 5)
+ 398 12.8 2.9 1.0 Crub_svsplocus 187592 187687 (462313) + CR1-3_Croc LINE/CR1 3531 3600 (5) 115
ANNOTATION EVIDENCE:
340 17.95 6.41 0.00 Crub_svsplocus 187592 187669 462331 + CR1-E3_fAlb LINE/CR1 336 418 20
340 17.95 6.41 0.00 Crub_svsplocus 187592 187669 (462331) CR1-E3_fAlb#LINE/CR1 336 418 (20) m_b4s001i23
Crub_svsplocu 187592 CTCCAAGTATCCTGA-ATATT--AAGGGTTTCCTGCCTG-AGCAGGGGGT 187637
vi i v i- v -- vv i ii-i
CR1-E3_fAlb#L 336 CTCGGAGCAACCTGGGATAGTGGAAGGTGTCCCTGCCCATGGCAGGGGGT 385
Crub_svsplocu 187638 TGGA-CTAGATGACCTCCAAGGTCCCTTCCAAC 187669
- ? ii
CR1-E3_fAlb#L 386 TGGAACTAGATGANCTTTAAGGTCCCTTCCAAC 418
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.22
Transitions / transversions = 1.80 (9/5)
Gap_init rate = 0.05 (4 / 77), avg. gap size = 1.25 (5 / 4)
376 14.75 1.64 0.00 Crub_svsplocus 187612 187672 462328 + L3 LINE/CR1 4019 4080 19
376 14.75 1.64 0.00 Crub_svsplocus 187612 187672 (462328) L3#LINE/CR1 4019 4080 (19) m_b4s001i24
Crub_svsplocu 187612 AAGGGTTTCCTGCCT-GAGCAGGGGGTTGGACTAGATGACCTCCAAGGTC 187660
v v - iiii i i
L3#LINE/CR1 4019 AAGGGATTCCTGCATCGGATGGGAGGTTGGACTAGATGACCTCTAAGGTC 4068
Crub_svsplocu 187661 CCTTCCAACTTT 187672
i
L3#LINE/CR1 4069 CCTTCCAACTCT 4080
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.91
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.02 (1 / 60), avg. gap size = 1.00 (1 / 1)
398 11.76 2.90 1.43 Crub_svsplocus 187619 187687 462313 + CR1-3_Croc LINE/CR1 3531 3600 5
398 11.76 2.90 1.43 Crub_svsplocus 187619 187687 (462313) CR1-3_Croc#LINE/CR1 3531 3600 (5) m_b4s001i25
Crub_svsplocu 187619 TCCTGCCTGAG-CAGGGGGTTGGACTAGATGACCTCC-AAGGTCCCTTCC 187666
v - i-i
CR1-3_Croc#LI 3531 TCCTGCCTCAGGCAGGGGGTTGGACTAGATGACCTCTGGAGGTCCCTTCC 3580
Crub_svsplocu 187667 AACTTTACTACTACTATTATT 187687
i ii v - v
CR1-3_Croc#LI 3581 AGCCCTACTTCT-CTATGATT 3600
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 12.92
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3)
+ 54 0.0 0.0 0.0 Crub_svsplocus 188689 188737 (461263) + (TCCA)n Simple_repeat 1 49 (0) 116
ANNOTATION EVIDENCE:
54 0.00 0.00 0.00 Crub_svsplocus 188689 188737 461263 + (TCCA)n Simple_repeat 1 49 0
54 0.00 0.00 0.00 Crub_svsplocus 188689 188737 (461263) (TCCA)n#Simple_repeat 1 49 (0) c_b4s251i1
Crub_svsplocu 188689 TCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 188737
(TCCA)n#Simpl 1 TCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT 49
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 13 11.0 7.0 4.5 Crub_svsplocus 189482 189524 (460476) + GA-rich Low_complexity 1 44 (0) 117
ANNOTATION EVIDENCE:
13 10.98 6.98 4.55 Crub_svsplocus 189482 189524 460476 + (AGAAGA)n Simple_repeat 1 44 0
13 10.98 6.98 4.55 Crub_svsplocus 189482 189524 (460476) (AGAAGA)n#Simple_repeat 1 44 (0) m_b4s252i4
Crub_svsplocu 189482 AGAA-AAGTAAG-AGATGCAGAA-AAGAAAGAAGAAGAAAAAGGAG 189524
- - - v v - - i i
(AGAAGA)n#Sim 1 AGAAGAAG-AAGAAGAAGAAGAAGAAG-AAGAAGAAGAAGAAGAAG 44
Matrix = Unknown
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.12 (5 / 42), avg. gap size = 1.00 (5 / 5)
+ 26 0.0 0.0 0.0 Crub_svsplocus 189547 189571 (460429) + (TGTT)n Simple_repeat 1 25 (0) 118
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 Crub_svsplocus 189547 189571 460429 + (TGTT)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 Crub_svsplocus 189547 189571 (460429) (TGTT)n#Simple_repeat 1 25 (0) c_b4s251i2
Crub_svsplocu 189547 TGTTTGTTTGTTTGTTTGTTTGTTT 189571
(TGTT)n#Simpl 1 TGTTTGTTTGTTTGTTTGTTTGTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 510 10.3 0.0 0.0 Crub_svsplocus 189733 189800 (460200) C URR1A DNA/hAT-Charlie (0) 226 159 119
ANNOTATION EVIDENCE:
510 10.29 0.00 0.00 Crub_svsplocus 189733 189800 460200 C URR1A DNA/hAT-Charlie 159 226 0
510 10.29 0.00 0.00 Crub_svsplocus 189733 189800 (460200) C URR1A#DNA/hAT-Charlie (0) 226 159 m_b4s001i26
Crub_svsplocu 189733 CAGTGGTTCTCAACCTTTCTAATGCCGTGACCCCATAATATAGTTCCCCA 189782
i i i iv i i
C URR1A#DNA/hAT 226 CAGTGGTTCTCAACCTTCCTAATGCTGCGACCCTTTAATACAGTTCCTCA 177
Crub_svsplocu 189783 TGTTGTGGTGACCCCCAA 189800
C URR1A#DNA/hAT 176 TGTTGTGGTGACCCCCAA 159
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.74
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 444 12.5 2.8 0.0 Crub_svsplocus 189867 189938 (460062) C URR1A DNA/hAT-Charlie (152) 74 1 119
ANNOTATION EVIDENCE:
444 12.50 2.78 0.00 Crub_svsplocus 189867 189938 460062 C URR1B DNA/hAT-Charlie 1 74 151
444 12.50 2.78 0.00 Crub_svsplocus 189867 189938 (460062) C URR1B#DNA/hAT-Charlie (151) 74 1 m_b4s001i27
Crub_svsplocu 189867 TGGTTT--GGCGACCCCCGTGAAATCGTCATTCGACCCCAAATGGGGTCC 189914
i -- i vv i v v v
C URR1B#DNA/hAT 74 TGGTCTTAGGCGACCCCTGTGAAAGGGTCGTTCGACCCCCAAAGGGGTCG 25
Crub_svsplocu 189915 CGACCCACAGGTTGAGAACCACTG 189938
i
C URR1B#DNA/hAT 24 CGACCCACAGGTTGAGAACCGCTG 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.73
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.01 (1 / 71), avg. gap size = 2.00 (2 / 1)
+ 342 15.1 0.0 0.0 Crub_svsplocus 189942 189994 (460006) + L3 LINE/CR1 4038 4090 (9) 114
ANNOTATION EVIDENCE:
342 15.09 0.00 0.00 Crub_svsplocus 189942 189994 460006 + L3 LINE/CR1 4038 4090 9
342 15.09 0.00 0.00 Crub_svsplocus 189942 189994 (460006) L3#LINE/CR1 4038 4090 (9) m_b4s001i28
Crub_svsplocu 189942 TAAGGGGTTGGACTAGAGGACCTCTAATGTCCCATCCAACTCTGATATTT 189991
ii i v v v v i
L3#LINE/CR1 4038 TGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCTGAGATTC 4087
Crub_svsplocu 189992 TGT 189994
L3#LINE/CR1 4088 TGT 4090
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.93
Transitions / transversions = 1.00 (4/4)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 327 19.7 0.0 0.0 Crub_svsplocus 189943 190003 (459997) + MIR3 SINE/MIR 144 204 (4) 120 *
ANNOTATION EVIDENCE:
327 19.67 0.00 0.00 Crub_svsplocus 189943 190003 459997 + MIR3 SINE/MIR 144 204 4
327 19.67 0.00 0.00 Crub_svsplocus 189943 190003 (459997) MIR3#SINE/MIR 144 204 (4) m_b4s001i29
Crub_svsplocu 189943 AAGGGGTTGGACTAGAGGACCTCTAATGTCCCATCCAACTCTGATATTTT 189992
i v i v v i i i
MIR3#SINE/MIR 144 AGGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATTCT 193
Crub_svsplocu 189993 GTTTTTGTATG 190003
i vv v
MIR3#SINE/MIR 194 ATGATTCTATG 204
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.96
Transitions / transversions = 1.00 (6/6)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 13 11.6 4.9 4.9 Crub_svsplocus 191722 191762 (458238) + (AATGTAG)n Simple_repeat 1 41 (0) 121
ANNOTATION EVIDENCE:
13 11.61 4.88 4.88 Crub_svsplocus 191722 191762 458238 + (AATGTAG)n Simple_repeat 1 41 0
13 11.61 4.88 4.88 Crub_svsplocus 191722 191762 (458238) (AATGTAG)n#Simple_repeat 1 41 (0) m_b4s252i5
Crub_svsplocu 191722 AATGTAGAATTGTAAATTGTAAGAAT-TAGATGGTA-AATGTA 191762
- i v - - vv -
(AATGTAG)n#Si 1 AATGTAGAA-TGTAGAATGT-AGAATGTAGAATGTAGAATGTA 41
Matrix = Unknown
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4)
+ 16 18.6 0.0 6.5 Crub_svsplocus 191769 191817 (458183) + (TTGTTA)n Simple_repeat 1 46 (0) 122
ANNOTATION EVIDENCE:
16 18.60 0.00 6.52 Crub_svsplocus 191769 191817 458183 + (TTGTTA)n Simple_repeat 1 46 0
16 18.60 0.00 6.52 Crub_svsplocus 191769 191817 (458183) (TTGTTA)n#Simple_repeat 1 46 (0) m_b4s252i6
Crub_svsplocu 191769 TTGTTATTGTCACTGTGATTGCTGTAGCTGTTATTATTGTTGTAATTGT 191817
i i v - - -i i i v
(TTGTTA)n#Sim 1 TTGTTATTGTTATTGTTATTG-T-TA-TTGTTATTGTTATTGTTATTGT 46
Matrix = Unknown
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3)
+ 13 19.5 0.0 2.8 Crub_svsplocus 192322 192358 (457642) + A-rich Low_complexity 1 36 (0) 123
ANNOTATION EVIDENCE:
13 19.49 0.00 2.78 Crub_svsplocus 192322 192358 457642 + (AAATTT)n Simple_repeat 1 36 0
13 19.49 0.00 2.78 Crub_svsplocus 192322 192358 (457642) (AAATTT)n#Simple_repeat 1 36 (0) m_b4s252i7
Crub_svsplocu 192322 AAATTTAATATTGAAAGAGAAATTTAAAATTGAATTT 192358
- v vvv v i
(AAATTT)n#Sim 1 AAATTTAA-ATTTAAATTTAAATTTAAATTTAAATTT 36
Matrix = Unknown
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1)
+ 5606 29.7 3.0 1.9 Crub_svsplocus 192735 194856 (455144) + L3 LINE/CR1 1958 4080 (19) 124
ANNOTATION EVIDENCE:
5606 30.29 2.71 1.93 Crub_svsplocus 192735 194841 455159 + L3 LINE/CR1 1958 4080 19
5606 30.29 2.71 1.93 Crub_svsplocus 192735 194841 (455159) L3#LINE/CR1 1958 4080 (19) m_b4s001i30
Crub_svsplocu 192735 GGAAGAGCTAATTTCAATAAACTTAGAGAGGGCTTGGGAAGGATTCCATG 192784
i vi v i i iiiv--i v v
L3#LINE/CR1 1958 GGAAAAGCAGATTTCAAAAAATTCAGAGAAAAG--AGGTATGATTCCATG 2005
Crub_svsplocu 192785 GA-TGAGAATCCTCCAGGGGAAA-ACAACGCAAGAAGCTTGGGAAATTTT 192832
v-? --- v iii - iii v i v? ii i
L3#LINE/CR1 2006 GCCNGAGA---CTCAAAAAGAAAGATGGCTCAAGAGGGNTGGGAAGCTCT 2052
Crub_svsplocu 192833 GAAAAATGAGATAGTAAAAGCC-CAGTCTAGCACAATA--CCAAGAAAGA 192879
v i vv i --- i- i - - - i-- vi i
L3#LINE/CR1 2053 TAAAAATGAAATTCTGA---CTACAAT-TA-CA-AATGATCCAATGAGGA 2096
Crub_svsplocu 192880 GGAAAAACAACAGCTC-TCAAAAAAACCAGCCGAGCTGCATAAAGAA--C 192926
i iviiv vv - iv i i vvi ? i ? --
L3#LINE/CR1 2097 AGAAAAGAGGGAGGGCATTTAAGAAACCAACGTGGCTNCATAGAGNATTC 2146
Crub_svsplocu 192927 TCTGA---CAAATTGAAAGATAAAAAGGACAGATAT-AGAAAGTAGAAAG 192972
--- i ------ v vi - ii i
L3#LINE/CR1 2147 TCTGATGTCAGATT------TTAAAAGGACATGTATCAGAAGATGGAAAG 2190
Crub_svsplocu 192973 AGGGGCACATAACTAAATTAGAATATCAACAAA-TAGCCCGAGCCTGCAA 193021
i- i i ---- i i vvi v i - ? v i i
L3#LINE/CR1 2191 AGGA-CATATAACCAA----GGACAAAGAGAGAGTANCACAAGCCTGTAA 2235
Crub_svsplocu 193022 AGATGAAATGAGGAAAGCCAAGGCTCA-AATGAACTAAGGCTTGCGACCA 193070
ii iivi v i i i i - i i vv
L3#LINE/CR1 2236 GAATAGTGTCAGGAAGGCTAAAGCCCAGAATGAGCTGAGGCTTGCGAAAA 2285
Crub_svsplocu 193071 AA---GTCAAAAATAACAAAAAAAAGCTTCTTTCAA---CATGTAAAAAA 193114
--- ii ii i ? vi - ---i vvii i
L3#LINE/CR1 2286 AAAATGCTAAGGACAACAAAAANAAGGCT-TTTCAAAGCTATGTTCGGAG 2334
Crub_svsplocu 193115 CAAGAAAAAAGTGAAGAAAACGATTGGTCCATTAGTGGGTGAAAGTGGTA 193164
ii ii --- i? iv i ii iv v v v ii ii
L3#LINE/CR1 2335 CAGAAGGAAA---AAGAAAGNGACAGGCCCGCTGCTTGGGGCAGATGGCG 2381
Crub_svsplocu 193165 AGAAGGTGACTAGCAATAGGGAGAAAGCAGAACTATTTAACTCGTTTTTT 193214
vi v v i viiii i i i i v v
L3#LINE/CR1 2382 TAATGTTAACAGATGACAGAGAGAAAGCAGAACTACTCAACTCCTATTTT 2431
Crub_svsplocu 193215 GCATCTGTCTTTAC-ACAAAGGGAAAAAA----CAGACCAACCTATCAAA 193259
v i iv - iv ii vi ---- iii--------
L3#LINE/CR1 2432 GCTTCCGTCTTCTCTATCAAGGAGAATGATCTTCAGACTGG--------A 2473
Crub_svsplocu 193260 AATAGTGCCATAAAAACAGT----ATAGAAACACAACTTAAGATAGGCAA 193305
vi ivv i v iv ---- vi viiv i ii ii
L3#LINE/CR1 2474 AAGGGTAGAACAAACATCGTTAAGAGGGAATTGAAGCCCAAGATAGGTGA 2523
Crub_svsplocu 193306 GAAAATTATAAGTGAGCACCTGTCCAGCCTAGACAAGTTCAAATCACCAG 193355
i i vi v iv ivii i ii i v
L3#LINE/CR1 2524 GGAGATAGTAAGAGAGCACCTAGCCGCTTTAAATGAGTTCAAGTCTCCAG 2573
Crub_svsplocu 193356 AACCAGATGGATTACACCACAAGGTTCTTAAGGACCTGGCAGATGTGATC 193405
iv i i i v i v v i v v
L3#LINE/CR1 2574 GCCCAGACGAATTACATCCCAGGGTACTGAAAGAACTTGCAGATGTGATC 2623
Crub_svsplocu 193406 TCAGAACCACTG-AACTATATTTTTCAGAGATCCTGGAGCACTGGAGAAC 193454
v i i -viv - i v i vi v v i iv
L3#LINE/CR1 2624 GCGGAACCGCTGTCGGTA-ATCTTTGAGAAATCACGGAGAACGGAAGAGG 2672
Crub_svsplocu 193455 TACCAGAGAACTGGAAAAGAACTGATGTAGTTCCCATCTTCAAAAAAGGA 193504
i ii i v ii vi ? ? i ?i i i
L3#LINE/CR1 2673 TGCCAGAAGACTGGAGACGGGCAAATGTNGTNCCTANTTTTAAAAAGGGA 2722
Crub_svsplocu 193505 AAAAAAATGGATCCAGGAAATTACAGACCTATCAGCCTGACCTCAATACC 193554
i i v ? i vi v i v i v
L3#LINE/CR1 2723 AAAAAGATGGATTCTGNAAACTACAGACCGGTAAGCTTGACGTCGATCCC 2772
Crub_svsplocu 193555 TGGGAAGATTCTGGAAAAGATAATCAAACAACGAATCAGCGAACACCTAG 193604
i v i i vi v i ivvii iv i i i
L3#LINE/CR1 2773 CGGCAAAATTCTAGAACGGATTATTAAACAGATGGTTTGTGAGCACTTAG 2822
Crub_svsplocu 193605 AGGCAAACAAA---GTCATTACTAAAAGCCAACATGGGTTTGTCAAAAAC 193651
--- vi --- v i ii i iiii i
L3#LINE/CR1 2823 A---AAAGGAAGCGGTGATCACTAGGAGCCAGCATGGGTTCACTAAGAAC 2869
Crub_svsplocu 193652 AGATCATGCCAGACAAACCTTATTGCATTCTTTGACCAAGTGATAAAATT 193701
ii i v i v v i ivii v iv i i
L3#LINE/CR1 2870 AAGTCATGCCAAACTAACCTCATTTCCTTTTTTGATAGGGTTACTAGACT 2919
Crub_svsplocu 193702 AGTGGATCAGAGGAATGCTGTGGACATAATTTACTTGGACTTCAGTAAGG 193751
i i i i i ? i v ii i i
L3#LINE/CR1 2920 GGTAGATCAGGGGAATGCCGTAGACANAGTGTATCTGGATTTCAGCAAGG 2969
Crub_svsplocu 193752 CATTTGATAAAGTAGATTACAACCTACTACTTGATAAGATAGAAAAATGT 193801
i vvv i ii iv v vv v i i i i
L3#LINE/CR1 2970 CATTTGACAAAGTCTCTCATGATATCCTTGTGGACAAGATGGAGAAATAT 3019
Crub_svsplocu 193802 GGGTTAGACAGAATCACCACCAGATGGATTCGTAGCTGGCTGACCGGCTG 193851
i i iiiv vi viii i i v i i
L3#LINE/CR1 3020 GGGCTGGATGATAGTACAGTTAGGTGGATTCGTAGCTGGTTGAACGACCG 3069
Crub_svsplocu 193852 TACTCAGCATGTGGTCCTCAATGGAACCACATCTACATGGAGGGAAGTGT 193901
i iv v v vv i v v ii v v i v
L3#LINE/CR1 3070 TACCCAAAAGGTGTTGATTAATGGATCGATGTCAACCTGGAGGGAGGTCT 3119
Crub_svsplocu 193902 GTAGTGGGGTTCCCCAGGGCTCTGTTCTGGGCCAAGTGCTCTTCAACATC 193951
v v v v i v vv v v i
L3#LINE/CR1 3120 CTAGTGGCGTGCCACAGGGCTCTGTCCTTGGCCCTGTCCTGTTCAACATT 3169
Crub_svsplocu 193952 TTCATCAACAATTTGGATGAGGGGATAGATAGAGAACTCATCAAATTTGC 194001
i ii i i iv vi vivi i
L3#LINE/CR1 3170 TTTATCAATGACTTGGATGAAGACATAGAAGGCATGCTTATCAAATTTGC 3219
Crub_svsplocu 194002 AGATGACACCAAGCTGTCAGGAATAGCCAACACTCCAGAAGACAGGCTTA 194051
v vv i i i v?ii v iv i
L3#LINE/CR1 3220 AGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGATGACAGAATCA 3269
Crub_svsplocu 194052 AGAAACAGGAGGATCTGGACAGACTTGAACACTGGGCGCTATCTAACAAA 194101
vv ii ? v i v iv vvv v i i
L3#LINE/CR1 3270 AGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAAACCAACAAG 3319
Crub_svsplocu 194102 ATGAAATT---CAGTGGTGA--------------ATTTAGGCAAGAAAAA 194134
--- v i i -------------- ivvi
L3#LINE/CR1 3320 ATGAAATTTAACAGGGATAAATGTAAAGTCCTGCATTTAGGTTCAAAAAA 3369
Crub_svsplocu 194135 CCAAATGCACAGGTATAGTATAGGGGGTACCTTGCTCAATAGTAGTAACT 194184
i v i i v i i i v i v i ii i vvvi
L3#LINE/CR1 3370 TCAACTGCACAAGTACAGGATGGAGAGGATCTGGCTTAGCAGCAGTTCAC 3419
Crub_svsplocu 194185 GTGAGAGGGATCTCGGAGTCCTAGTGGACAATCACTTAAATATGAGTCAG 194234
i ii i v i ii v viiv vi v i i
L3#LINE/CR1 3420 GTGAAAAAGACCTAGGGGTTTTAGTTGACCGCAAGCTCAATATGAGCCAA 3469
Crub_svsplocu 194235 CAGTGTGCTGCAGCTGCCAAAAAGGCCAACACAGTGCTAGGCTGCATTAA 194284
v ii i i ii i vi
L3#LINE/CR1 3470 CAGTGTGATGTGGCTGCCAAAAAAGCTAATGCAATCTTAGGCTGCATTAA 3519
Crub_svsplocu 194285 CAGAGGGATAGAATCAAGATCACGTGAAGTATTAATACCACTCTACAGTG 194334
i i v vi v ? v v i v i v i v vv
L3#LINE/CR1 3520 TAGAAGTATAGTGTCCAGANCAAGGGAGGTAATAGTCCCGCTGTACTCTG 3569
Crub_svsplocu 194335 CCTTGGTAAGGCCACACTTGGAATACTGCATCCAGTTTTGGTCACCATGA 194384
vi v i ii i i i i i v i iiv
L3#LINE/CR1 3570 CGCTGGTCAGACCACATCTGGAGTATTGCGTTCAGTTCTGGGCGCCACAT 3619
Crub_svsplocu 194385 TGTAAAAAAGATGTTGAGACTCTAGAAAGAGTACAGAGAAGAGCAACAAA 194434
v i ii ii v vv i iv v v i i v i
L3#LINE/CR1 3620 TTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAG 3669
Crub_svsplocu 194435 GATGATTAGGGGACTGGAGGCTAAAACATATAAGGAACGGTTGCGAGAAT 194484
i v i v ii i viv i vii i
L3#LINE/CR1 3670 GATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAAGGAAC 3719
Crub_svsplocu 194485 TGGGTATGTCTAGTTTAACGAAGAGAAGGACGAGGGGGGACATGATAGCA 194534
v i ii iiv iviv i i v
L3#LINE/CR1 3720 TGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCT 3769
Crub_svsplocu 194535 GTATTCCAATATCTCTGTGGCTGCCATAAAGAAGAGGGAATCAAGCTATT 194584
v v i vviv i ivi v vi vi
L3#LINE/CR1 3770 GTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATT 3819
Crub_svsplocu 194585 TTCCAAAGCACCTGAAGGCAGGACAAGAAGGAACGGGTGGAAACTAATCA 194634
i viivi v v i i v i vv i ii --
L3#LINE/CR1 3820 CTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTA--CA 3867
Crub_svsplocu 194635 AGGAGAAAAG---CAACCTAGAACTAAGGAGAAGCTTCCTGACAGTGAGA 194681
i iv ii--- ii ii iv - ii i i i i v
L3#LINE/CR1 3868 GGGAGGCAGATTTCGGCTCAATA-TAAGGAAGAACTTTCTAACAATCAGA 3916
Crub_svsplocu 194682 ACAATTAATCAGTGGAACAGCCTGCCTCCAAAAGCAGTAAATGCTCCAAC 194731
i vi iv vv i ii v v?i i i i iiv i iv
L3#LINE/CR1 3917 GCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTC 3966
Crub_svsplocu 194732 ACTGGAAGTTTTTAAGAAGAGACTGGACAACCATTTGTCTGAAATGGTGT 194781
i v i v i ii i v ii v
L3#LINE/CR1 3967 ACTGGAGGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGT 4016
Crub_svsplocu 194782 ---AGGGTTTCCTGCCT-GAGCAGGGGGTTGGACTAGATGACCTCCAAGG 194827
--- v v - iiii i i
L3#LINE/CR1 4017 AGAAGGGATTCCTGCATCGGATGGGAGGTTGGACTAGATGACCTCTAAGG 4066
Crub_svsplocu 194828 TCCCTTCCAACTTT 194841
i
L3#LINE/CR1 4067 TCCCTTCCAACTCT 4080
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.80
Transitions / transversions = 1.72 (396/230)
Gap_init rate = 0.03 (63 / 2106), avg. gap size = 1.56 (98 / 63)
407 15.54 8.79 1.02 Crub_svsplocus 194766 194856 455144 + CR1-3_Croc LINE/CR1 3503 3600 5
407 15.54 8.79 1.02 Crub_svsplocus 194766 194856 (455144) CR1-3_Croc#LINE/CR1 3503 3600 (5) m_b4s001i31
Crub_svsplocu 194766 TTGTCTGAAATGGT----GTAGGGTT--TCCTGCCTGAG-CAGGGGGTTG 194808
v ii ----i v -- v -
CR1-3_Croc#LI 3503 TTGTATGGGATGGTTTGGATAGGGATGATCCTGCCTCAGGCAGGGGGTTG 3552
Crub_svsplocu 194809 GACTAGATGACCTCC-AAGGTCCCTTCCAACTTTACTACTACTACTATT 194856
i-i i ii v - iv
CR1-3_Croc#LI 3553 GACTAGATGACCTCTGGAGGTCCCTTCCAGCCCTACTTCT-CTATGATT 3600
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.70
Transitions / transversions = 1.80 (9/5)
Gap_init rate = 0.06 (5 / 90), avg. gap size = 1.80 (9 / 5)
+ 643 25.1 2.8 8.9 Crub_svsplocus 195306 195519 (454481) + L3 LINE/CR1 3893 4080 (19) 125
ANNOTATION EVIDENCE:
581 25.14 2.80 8.91 Crub_svsplocus 195306 195519 454481 + Plat_L3 LINE/CR1 3364 3565 8
581 25.14 2.80 8.91 Crub_svsplocus 195306 195519 (454481) Plat_L3#LINE/CR1 3364 3565 (8) m_b4s001i32
Crub_svsplocu 195306 TAAGGAGAAACTTCCTGACAATTAACAGGAAGATTAACAAAGAACAATTA 195355
ii i vi --- iv ------ i ----
Plat_L3#LINE/ 3364 TAAGGAAGAACTTCTTGACTGT---CAGGGTGAT------AAAACA---- 3400
Crub_svsplocu 195356 ACCAGTGGAACAATCTGCCTCCAGAAGCAGTGAATGCTCCAACACTGGAA 195405
-- -- iiv i vvvi i iv i vv v v i
Plat_L3#LINE/ 3401 --C--TGGAACGGGCTACCGAGGGAGGTTGTGGAGTCTCCATCCCTGGAG 3446
Crub_svsplocu 195406 GTTTTTAAGAAGAGACCGGACAGCCATTTGTCTGAAATGGTGTAG--AGT 195453
i i i vii ? i ivii v -- v
Plat_L3#LINE/ 3447 ATCTTTAAGAAAAGAATAGACANCCATCTGTCCTGGATGGTTTAGTCATT 3496
Crub_svsplocu 195454 T-TCTGCCTGA--GCAGGGGGTTGGACTCGATGACCTC-CAAGGTCCCTT 195499
i-i i-- i iv - i
Plat_L3#LINE/ 3497 CACCTGCCTGGAGGCAGGGGGCTGGACCAGATGACCTCTCGAGGTCCCTT 3546
Crub_svsplocu 195500 CCAACTTTATTATTATTATG 195519
i i ?v -i
Plat_L3#LINE/ 3547 CCAGCTCTANGATT-CTATG 3565
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.27
Transitions / transversions = 1.88 (32/17)
Gap_init rate = 0.10 (22 / 213), avg. gap size = 1.09 (24 / 22)
643 26.70 6.82 0.00 Crub_svsplocus 195332 195507 454493 + L3 LINE/CR1 3893 4080 19
643 26.70 6.82 0.00 Crub_svsplocus 195332 195507 (454493) L3#LINE/CR1 3893 4080 (19) m_b4s001i33
Crub_svsplocu 195332 AGGAAGA-----TTAACAA--AGAACAATTAACCAGTGGAACAATCTGCC 195374
-----i -- i vi iv vv i iiiv
L3#LINE/CR1 3893 AGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCC 3942
Crub_svsplocu 195375 TCCAGAAGCAGTGAATGCTCCAACACTGGAAGTTTTTAAGAAGAGACCGG 195424
v? i i iiv i iv i v i v i i
L3#LINE/CR1 3943 TCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTGG 3992
Crub_svsplocu 195425 ACAGCCATTTGTCTGAAATGGTGTAGAG----TTTCTGCCT-GAGCAGGG 195469
iii i v ii v i---- i v - iiii i
L3#LINE/CR1 3993 ATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATCGGATGGGA 4042
Crub_svsplocu 195470 GGTTGGACTCGATGACCTCCAAGGTCCCTTCCAACTTT 195507
v i i
L3#LINE/CR1 4043 GGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCT 4080
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.97
Transitions / transversions = 2.36 (33/14)
Gap_init rate = 0.02 (4 / 175), avg. gap size = 3.00 (12 / 4)
+ 16 23.2 4.8 1.6 Crub_svsplocus 197869 197930 (452070) + GA-rich Low_complexity 1 64 (0) 126
ANNOTATION EVIDENCE:
16 23.18 4.84 1.56 Crub_svsplocus 197869 197930 452070 + (AGAGA)n Simple_repeat 1 64 0
16 23.18 4.84 1.56 Crub_svsplocus 197869 197930 (452070) (AGAGA)n#Simple_repeat 1 64 (0) m_b4s252i8
Crub_svsplocu 197869 AGAGAAGAGCAGAGAGTAGATGA-AATAAATGA-AAGACTAGAAGAAAAG 197916
v iv v - v i v - vv - i
(AGAGA)n#Simp 1 AGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAG-AGAAGAG 49
Crub_svsplocu 197917 AA-AGTAGGGAAGAG 197930
- v i
(AGAGA)n#Simp 50 AAGAGAAGAGAAGAG 64
Matrix = Unknown
Transitions / transversions = 0.50 (4/8)
Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4)
+ 12 16.0 0.0 3.5 Crub_svsplocus 198523 198552 (451448) + (ATA)n Simple_repeat 1 29 (0) 127
ANNOTATION EVIDENCE:
12 16.04 0.00 3.45 Crub_svsplocus 198523 198552 451448 + (ATA)n Simple_repeat 1 29 0
12 16.04 0.00 3.45 Crub_svsplocus 198523 198552 (451448) (ATA)n#Simple_repeat 1 29 (0) m_b4s252i9
Crub_svsplocu 198523 ATAATAATGTATAATAATAATATGAATTAT 198552
-v vv v
(ATA)n#Simple 1 ATAATAAT-AATAATAATAATAATAATAAT 29
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1)
+ 21 3.5 0.0 0.0 Crub_svsplocus 198721 198749 (451251) + (TGTTT)n Simple_repeat 1 29 (0) 128
ANNOTATION EVIDENCE:
21 3.54 0.00 0.00 Crub_svsplocus 198721 198749 451251 + (TGTTT)n Simple_repeat 1 29 0
21 3.54 0.00 0.00 Crub_svsplocus 198721 198749 (451251) (TGTTT)n#Simple_repeat 1 29 (0) m_b4s252i10
Crub_svsplocu 198721 TGTTTTGTTGTGTTTTGTTTTGTTTTGTT 198749
v
(TGTTT)n#Simp 1 TGTTTTGTTTTGTTTTGTTTTGTTTTGTT 29
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 232 22.9 0.0 0.0 Crub_svsplocus 200315 200362 (449638) C Gypsy72-I_DR LTR/Gypsy (860) 3453 3406 129
ANNOTATION EVIDENCE:
232 22.92 0.00 0.00 Crub_svsplocus 200315 200362 449638 C Gypsy-170-I_DR LTR/Gypsy 3406 3453 860
232 22.92 0.00 0.00 Crub_svsplocus 200315 200362 (449638) C Gypsy-170-I_DR#LTR/Gypsy (860) 3453 3406 m_b4s001i34
Crub_svsplocu 200315 AGAATTCCTTCCAAAATGCAGACATAAATTGCACTCCCCTATCAGAGA 200362
ivvi v i i iiv i
C Gypsy-170-I_D 3453 AGAATTCCTTCCAAAACCGGGAAACAAACTGTGGTCCCCTATCAGAAA 3406
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.06
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 888 32.8 5.3 6.7 Crub_svsplocus 201068 202201 (447799) C Gypsy72-I_DR LTR/Gypsy (1754) 2491 1602 129
ANNOTATION EVIDENCE:
473 32.34 5.64 7.42 Crub_svsplocus 201068 201972 448028 C Gypsy69-I_DR LTR/Gypsy 1602 2491 1754
473 32.34 5.64 7.42 Crub_svsplocus 201068 201972 (448028) C Gypsy69-I_DR#LTR/Gypsy (1754) 2491 1602 m_b4s001i35
Crub_svsplocu 201068 TTCTGTTTCCGTGAGTTTCTTGGATGTATATGCACAGGGTTGCAATACTC 201117
v i v v vivi viv ? v ? v v i viv
C Gypsy69-I_DR# 2491 TTCAGCTGCCGTCAGTTTGCGAGAAAAANAAGCACANGGGTGGAGTTTAC 2442
Crub_svsplocu 201118 CT---TCATCATTTTCTTCTAATAGAACAGCCCCCATGGCCACA-TCACT 201163
--- i i i v?iv v i i ? v v - i - ?vv
C Gypsy69-I_DR# 2441 CTGGGTTACCGTGNCGTTGTGACAGNACTGCCCCAATG-CCATAGTCNGA 2393
Crub_svsplocu 201164 TGCATCCACCTGTATTACGAAGGGCTTA--TCCAAGTCTGGGTGCCTTAG 201211
? i v? iv -- -- ?ii v ii i
C Gypsy69-I_DR# 2392 NGCATCCACTTCNACAACGAAGGG--TAGCTCNGGGTCGGGGTGTTTCAG 2345
Crub_svsplocu 201212 TACTGGTTCGGCAGAAAAAAGTCTCTTTAGTCTCTCAAAC------ACTG 201255
v iv v ? ii vi ivvvv v i ------
C Gypsy69-I_DR# 2344 AATGGGTGCNGTGGTGAAGCTGGTCTTAAGTTTCTCAAACGATTTGACTG 2295
Crub_svsplocu 201256 CTTGGCACTCCATTGTCCATGTTAGTGGCTGGCTAGGTTTCACTGAAGAT 201305
---- vv -- iv i --- vi??v v---------
C Gypsy69-I_DR# 2294 CTT----CTGGATT--CCACTTCAG---CTTANNTGGTTTA--------- 2263
Crub_svsplocu 201306 GCTCCCTTCATTTTTAGTAAGTTAGTGAGGGGCAAGGCTAT--CTGGGCA 201353
--- ? vi--- i --- --- ii?--i i -
C Gypsy69-I_DR# 2262 ---CCCTTNAGC---AGTGAG---GTGAGGGG---GGCCGNAATTAGGC- 2226
Crub_svsplocu 201354 AATGAGG-----GATGAATTGGCGGTAAAAGTTTGTAAAGCCCAGGAAAC 201398
-- vi -----? ii i v ii v i i v
C Gypsy69-I_DR# 2225 --TGTAGTTTCTNATGAACCGGCGATAAAAGTTGGCGAACCCTAGAAATC 2178
Crub_svsplocu 201399 TTTGTAGTTGCTTTCTTG-TGTGGGGTGGTGCCCAATCTAAT-ACTGCTC 201446
v ivi - v v iv -- ? i i - -
C Gypsy69-I_DR# 2177 TTTGTAGTTCCTTCACTGTTTTGGGGAGAGGCC--ANCCAGTGACTGC-C 2131
Crub_svsplocu 201447 TGACCTTCTCTGG----GTCCATTTCAATGCCCTGGGGG--GAT-ATGCG 201489
v i --- ---- v iv v iv -- - --
C Gypsy69-I_DR# 2130 TGAACCT---TGGNGTCGTCCATTTCCACTCCGTGATGGCTGATAATG-- 2086
Crub_svsplocu 201490 ATAACCTAGGTAGTCTATCCTTTCCTGGTGGAATTCGTATTTCGAGAGTT 201539
- v i v vvvvi i vvv vv ii i vvvi i
C Gypsy69-I_DR# 2085 -TATCCCAGGAACGAGGTCTTGGACACGTGGAATTCACACTTCTCCGGCT 2037
Crub_svsplocu 201540 TGGCATATAGATGGGCGGCTCGCAGTTTCTTTAAAACCACTCTGACTAGG 201589
i v v vivv i i i?iviv i viii vvvv
C Gypsy69-I_DR# 2036 TGGCGTAGAGTTGGTTTTCTTGTAANCGTGTCAAAACAGTCCTGACGTCC 1987
Crub_svsplocu 201590 TTGACATGTTCCTCTTTTGTTTCAGTGA--AGATAAGAATGTTCTCCAAG 201637
ii vi -- v v vi v -- v i iv ? vi
C Gypsy69-I_DR# 1986 TTGATGTGTTGTTC--TAGGTTGGGGGAATAGATCAGGATGTCATCNATA 1939
Crub_svsplocu 201638 TAAACAAGGAC---TTCCTTAAACAGGTGCTCCCTTAGAACATCATTAAT 201684
ii i v --- iv v i ii--- i v i iv ---
C Gypsy69-I_DR# 1938 TAGGCGATGACACATTTGTTCAGCAAA---TCTCTGAAAATTTCATT--- 1895
Crub_svsplocu 201685 TGCATAAAT-ACTGCAGGGCCCC-------CTTG-TAATCCAAATGGCAA 201725
--? i - v i i ?v -------i ? -? i? v v v
C Gypsy69-I_DR# 1894 --NATGAATGACTGGAAGACNGCTGGNGAGTTNGCNAGNCCATAGGGCAT 1847
Crub_svsplocu 201726 GACTTTGAATTGATAGCACCCCATGG-GG-CAGTTAAATGCAGTCTTCCA 201773
i ?vv v v ii v i - - --i i i i
C Gypsy69-I_DR# 1846 AACNAGGTATTCATAGTGCCCCCTAGTGGTCAG--GAACGCGGTTTTCCA 1799
Crub_svsplocu 201774 TTCGTCCCCTTCCTTAATTCTCACGTGATAGTAAGCTTCCCTTAGGTCTA 201823
i i i ivi ? vv i?v i vi viii v v
C Gypsy69-I_DR# 1798 CTCGTCTCCCTCCCGGATNCGAATNAGGTTATAAGCACTTCTGAGGTCAA 1749
Crub_svsplocu 201824 ATTTAG---AAA-ACAAATTTTCCCTTTCGATAGGTGT--GACAGCATGT 201867
i i --- i - iiii iv ------i v --? vi v -
C Gypsy69-I_DR# 1748 GTTTGGTGTAGATACGGGCTTCAC------GTAGTTGTTCNAGGGCAGG- 1706
Crub_svsplocu 201868 CTTTCATGAGGGGCAGCGGGTATAGGTTGCTTT-CACTGATTGTATTCAG 201916
-?vvv iv i v v - v v i v- v ivv i
C Gypsy69-I_DR# 1705 -NGGGACCAAGGGAAGAGGGTA-ACGATACTTGACAGTGACGTTATTCAA 1658
Crub_svsplocu 201917 GGCCCTATAATCCACGCATAAACGTAAAGAGCCATCCTTCTTCTCTCTAA 201966
?v i vi i v i ?ii v i vvv ivii
C Gypsy69-I_DR# 1657 NCCTCGGTAGTCGATGCANGGACGGAGACCTCCATCCTTCTTCTCCACGA 1608
Crub_svsplocu 201967 AAAGGA 201972
i i
C Gypsy69-I_DR# 1607 AGAAGA 1602
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.36
Transitions / transversions = 1.04 (138/133)
Gap_init rate = 0.10 (88 / 904), avg. gap size = 1.33 (117 / 88)
888 33.15 3.75 3.24 Crub_svsplocus 201361 201974 448026 C Gypsy72-I_DR LTR/Gypsy 1678 2294 2003
888 33.15 3.75 3.24 Crub_svsplocus 201361 201974 (448026) C Gypsy72-I_DR#LTR/Gypsy (2003) 2294 1678 m_b4s001i36
Crub_svsplocu 201361 GATGAATTGGCGGTAAAAGTTTGTAAAGCCCAGGAAACTTTGTAGTTGCT 201410
i v i v ii v vi iivv
C Gypsy72-I_DR# 2294 GATGAATCGCCGGTAAAAATTGGCGAAGCCCAGGAACCGCTGTAACGCCT 2245
Crub_svsplocu 201411 TTCTTGTGTGGGGTGGTGCCCAATCTAATACTGCTCTGACCTTCTCTGGG 201460
vv v v i v i vi v v i i v v
C Gypsy72-I_DR# 2244 TTCGGGAGTCGGGTGGCGGCCAGTCGGAGACAGCCCTAACCTTCGCAGGG 2195
Crub_svsplocu 201461 TCCATTTCAATGCCCTGGGGGGA---TATGCGATAACCTAGGTAGTCTAT 201507
viv vv viivv --- --- iv i i v vvv i
C Gypsy72-I_DR# 2194 TCCATGCGAAGTCCCTCAACTGAAATTATG---TGTCCCAAGAAGGAAAC 2148
Crub_svsplocu 201508 CCTTTCCTGG---TGGAATTCGTATTTCGAGAGTTTGGCATATAGATGGG 201554
--- vv --- i i vvvivi vi i v iv
C Gypsy72-I_DR# 2147 ---TGACTGGACATGGAATTCGCACTTCTCCGCCTTTACATACAGCTGAT 2101
Crub_svsplocu 201555 CGGCTCGCAGTTTCTTTAAAACCACTCTGACTAGGTTG-ACATGTTCCTC 201603
ivv iv iivi v iv i- v i viiv - v
C Gypsy72-I_DR# 2100 TCTCCAGCAGCCGTTGTAGCACT-CGCCGAACGTGTTGGACATGTTCCTG 2052
Crub_svsplocu 201604 TTTTGTTTCAGTGAAGATAAGAATGTTCTCCAAGTAAACAAGGAC---TT 201650
iv v ivvv vi i iv i ii ---
C Gypsy72-I_DR# 2051 CATGGCGGAAGAAAAAATAAGAATGTCATCCAAATAAACAAAAACAAATT 2002
Crub_svsplocu 201651 CCTTAAACAGGTGCTCCCTTAGAACATCATTAAT---TGCAT-AAATACT 201696
vv v v --- i vv v i i i--- v - v
C Gypsy72-I_DR# 2001 GATTAATCATGT---CTCGGAGTACATCGTTGACGAGTGCCTGAAAGACT 1955
Crub_svsplocu 201697 GCAGG-GCCCCCTTGTAATCCAAATGGCAAGACTTTGAATTGATAGCACC 201745
v - viivv - ii i vvviv v v iii
C Gypsy72-I_DR# 1954 GCTGGAGCATTGGTG-AGCCCAAATGGCAGGACAAGATATTCAAAATGCC 1906
Crub_svsplocu 201746 CCATGGGGCAGTTAAATGCAGTCTTCCATTCGTCCCCTTCCTTAATTCTC 201795
vi vvv i i v i i v v vv
C Gypsy72-I_DR# 1905 CAGTGGGCGTGTTGAATGCGGTCTTCCATTCGTCACCCTCCCTCATACGG 1856
Crub_svsplocu 201796 ACGTGATAGTAAGCTTCCCTTAGGTCTAATTTAGAAAACAAATTTT--CC 201843
v i v iv v i i v vi - i --
C Gypsy72-I_DR# 1855 ACGAGATGGTAAGCATTGCGTAGGTCCAACTTTGTGAA-AAATCTTGCCC 1807
Crub_svsplocu 201844 CTTTCGATAGGTGTGACAGC--ATGTCTTTCATGAGGGGCAGCGGGTATA 201891
i v i v i -i vi -- v ----v i v i v iv
C Gypsy72-I_DR# 1806 CCTGCAAGAGAT-CGAAGGCCGAAG----ACATAAGCGGTAGGGGGTACC 1762
Crub_svsplocu 201892 GGTTGCTTTCACTGATTGT---ATTCAGGGCCCTATAATCCACGCATAAA 201938
i --- i v i i --- iiv i v i i i viii
C Gypsy72-I_DR# 1761 GAT---TTTTAATGGTTATGTCATTCAAACCTCGATAGTCTATGCAGGGG 1715
Crub_svsplocu 201939 CGTAAAGAGCCATCCTTCTTC-TCTCTAAAAAGGACC 201974
i i i i - v v i i
C Gypsy72-I_DR# 1714 CGCAGAGAACCATCCTTTTTCTTCACAAAGAAGAACC 1678
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.27
Transitions / transversions = 0.93 (95/102)
Gap_init rate = 0.05 (31 / 613), avg. gap size = 1.39 (43 / 31)
681 34.50 3.81 4.06 Crub_svsplocus 201362 202201 447799 C Gypsy138-I_DR LTR/Gypsy 3563 4400 7010
681 34.50 3.81 4.06 Crub_svsplocus 201362 202201 (447799) C Gypsy138-I_DR#LTR/Gypsy (7010) 4400 3563 m_b4s001i37
Crub_svsplocu 201362 ATGAATTGGCGGTAAAAGTTTGTAAAGCCCAGGAAACTTTGTAGTTGCTT 201411
i ivv i i v i v ii v v vi vi
C Gypsy138-I_DR 4400 ATAAATCTCCGATAAAAATTGGCAAACCCCAAAAATCGTTGTACCTCTTT 4351
Crub_svsplocu 201412 TCTTGTGTGGGGTGGTGCCCAATCTAATACTGCTCTGACCTTCTCTGGGT 201461
vvi viiiv v v i i ii i i vi v i
C Gypsy138-I_DR 4350 AACTGAACATGGTTGTGGCCAATCCAGTACTGCCTTAATCTTGCCAGGAT 4301
Crub_svsplocu 201462 CCATTTCAATGCCCTGGGGGGATATGCGAT-AACCTAGGTAGTCTATCCT 201510
i v v iviivvv -- v - i i v i- v iv
C Gypsy138-I_DR 4300 CCATCTGAAGGCTACATTTGGATA--CTATGAACCCAAGAAA-CGACACT 4254
Crub_svsplocu 201511 TTCCTGG-----TGGAATTCGTATTTCGAGAGTTTGGCATATAGATGGGC 201555
--- ----- ivi vvv i ii iv i - vv i
C Gypsy138-I_DR 4253 TT---GGAGACATGGAATTCGCTCTTCTCCAGCTTAACGAACAG-TCTGT 4208
Crub_svsplocu 201556 GGCTCG-CAGTTTCTTTAAAACCACTCTGACTAGGTTG-ACATGTTCCTC 201603
v i- ii vvvvv i vvi v - v - i i
C Gypsy138-I_DR 4207 GTCTCAACAACTGGGAGAGAACCTGCCGGAC-ATGTTGTACATGCTCTTC 4159
Crub_svsplocu 201604 TT--TTGTTTCAGTGAAGATAAGAATGTTCTCCAAGTAAACAAGGAC--- 201648
v --i ii v i-- i v iv i ii ---
C Gypsy138-I_DR 4158 ATAGCTACTTGAA--AAAATAAGTATGTCATCCAAGTAAACGAAAACAAA 4111
Crub_svsplocu 201649 TTCCTTAAACAGGTGCTCCCTTAGAACATCATTAAT---TGCAT-AAATA 201694
iiv v v--- v i --- v -i v
C Gypsy138-I_DR 4110 TCTGTTCAACAT---CTCCCTGAGGACATCATTAATGAATGCCTGGAAGA 4064
Crub_svsplocu 201695 CTGCAGGGCCCCCTTGTAA-TCCAAATGGCAAGACTTTGAATTGATAGCA 201743
v v -v vi ii -v v vv i viv v ii
C Gypsy138-I_DR 4063 CGGCTGGG-GCATTTACAAGGCCAAAGGGCATTACCTGATATTCATAGTG 4015
Crub_svsplocu 201744 CCCCATGGGGCAGTTAAATGCAGTCTTCCATTCGTCCCCTTCCTTAATTC 201793
v ii ? vv v i i i i i i
C Gypsy138-I_DR 4014 GCCTGTNGGGGTGTTAAAAGCGGTCTTCCACTCATCTCCTTCCTTGATCC 3965
Crub_svsplocu 201794 TCACGTGATAGTAAGCTTCCCTTAGGTCTAATTTAGAAAACAAATTTTC- 201842
v vv i v ii v i i v v v v v vv -
C Gypsy138-I_DR 3964 TGACCAGATGGTAAGCATTTCTGAGGTCCAACTTCGTAAAGATAGTGGCG 3915
Crub_svsplocu 201843 CCTTTCGATAGGTGTGACAGCA-TGTCTTTCATGAGGGGCAGCGGGTATA 201891
i v ii vv -ii v - --- v i ii vv
C Gypsy138-I_DR 3914 CCCTGCAGTATCT-CAAAAGCAGTG---TTCATTAGGGGTAATGGGTAAC 3869
Crub_svsplocu 201892 GGTTGCTTTCACTGAT--TGT-ATTCAGGGCCCTATAATCCACGCATAAA 201938
i - -- v i -- - iiv i v ii viiv
C Gypsy138-I_DR 3868 GATT-CTT--AATGGTGATGTGATTCAAACCTCTATAATCAATACAGGGT 3822
Crub_svsplocu 201939 CGTAAAGAGCCATCCTTCTTCTCTCTAAAAAGGACCGGGGCAGCCACTTT 201988
v i vvv vvvvvi i ---i v v iv vi
C Gypsy138-I_DR 3821 CGAAGACTCCCATCCTTCTTGGAAACAAAAAAGA---AGCCTGCTCCTGC 3775
Crub_svsplocu 201989 AGGCTTGGCT---GGCTCAATGAAACCTCTCTCTAG-GTTTTTTTTAATA 202034
ivv i --- viv v v v - ii iv i -i
C Gypsy138-I_DR 3774 AGGTGAGGTTGAAGGGCGAATGAATCCACTGTCTAGAGCCTCGTTCAA-G 3726
Crub_svsplocu 202035 AATCTTTCCATTTC--CTCCTTCTCCTTTGGGCTCATGGAGTATAATCTG 202082
v i i vv --i i vvvvv i--v v i -
C Gypsy138-I_DR 3725 TATTTCTCCATGGCAGTTCTTTCAGGAATGGA--GAGGGAGTACAATCT- 3679
Crub_svsplocu 202083 GGCTTTGGG--AGTTTTGCTCCAGGCTTGAATTCAATGGCACAGTC-TGT 202129
-i i i i --i vi ivii i i v i - i
C Gypsy138-I_DR 3678 -ACCTCGAGGTGGGCTTGCTCCAGGTACAAGTTCAATAGAACAATCATAT 3630
Crub_svsplocu 202130 GGGTCGGTGGGGGGGGGGGAAACTCATCCGCCCTCTCCTCACTGAAAACT 202179
i- i v viivi v ----v ivvvv i i i
C Gypsy138-I_DR 3629 GGA-CGATGCGGGGGTAATGAAGT----AGCCTGAGACTTACTAAAGACT 3585
Crub_svsplocu 202180 TCAGCAAGGTCTCTGTATTCCT 202201
vii i iv i
C Gypsy138-I_DR 3584 TCACTGAGATCCATGTATTCTT 3563
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 45.77
Transitions / transversions = 1.03 (141/137)
Gap_init rate = 0.06 (52 / 839), avg. gap size = 1.27 (66 / 52)
+ 275 12.2 0.0 0.0 Crub_svsplocus 205187 205227 (444773) + L1MdTf_I LINE/L1 2111 2151 (4428) 130
ANNOTATION EVIDENCE:
275 12.20 0.00 0.00 Crub_svsplocus 205187 205227 444773 + L1MdGf_II_orf2 LINE/L1 909 949 3732
275 12.20 0.00 0.00 Crub_svsplocus 205187 205227 (444773) L1MdGf_II_orf2#LINE/L1 909 949 (3732) m_b4s001i38
Crub_svsplocu 205187 ATATCCATTAATGTTAATGGTCTCAACTCTCCAATAAAAAG 205227
iv i i i
L1MdGf_II_orf 909 ATATCTCTTAATATCAATGGTCTCAACTCCCCAATAAAAAG 949
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.64
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
+ 324 36.0 4.7 3.7 Crub_svsplocus 205887 206290 (443710) C MamRTE1 LINE/RTE-BovB (318) 3494 3087 131
ANNOTATION EVIDENCE:
324 35.97 4.70 3.68 Crub_svsplocus 205887 206290 443710 C MamRTE1 LINE/RTE-BovB 3087 3494 318
324 35.97 4.70 3.68 Crub_svsplocus 205887 206290 (443710) C MamRTE1#LINE/RTE-BovB (318) 3494 3087 m_b4s001i39
Crub_svsplocu 205887 GAAGCT----TTTAACGTGTCTTTGTATCGCTTCTTTTGTCCCCCATGT- 205931
---- i ii ?i i iv v i i i i v i-
C MamRTE1#LINE/ 3494 GAAGCTGTGCTTCAGTGNATCCTTAAAGCGTTTCTTCTGCCCTCCCTGCT 3445
Crub_svsplocu 205932 ---AATCGCTTTCCTTGAGACAGCTCACCATAGAAGAGCTGTTTAGGGAT 205978
---ii i iiiv ---- i v iv i i v
C MamRTE1#LINE/ 3444 TGCGGTTGCCCCACTT----CAGCTCACCGTACAGCAGCTGCTTGGGTAT 3399
Crub_svsplocu 205979 -GTGATG--ATCTGGCATCCTTACAACATGTCCCGCCCAGCGCATCTGGG 206025
-v v -- --- i ivvv v v v v
C MamRTE1#LINE/ 3398 CCTGCTGTCATC---CATTCTCCGCACATGTCCAGCCCAGCGGAGCTGCG 3352
Crub_svsplocu 206026 CTTTCATCAACAGAGTGTAAACTGATGATAGAC---CTGC--TCTGGAGA 206070
i viviiv i vv iv v i- v i --- -- i----
C MamRTE1#LINE/ 3351 TTGCGGCGAGCATCGCTTCAG-TGCTGGTAGACTGGCTGCGTTCC----A 3307
Crub_svsplocu 206071 GGACATCTGTGTCTGGT-ATCTTATCCTGCCACCGGATCCTCAGAATTCT 206119
v vv - - i i i iivi vi v v vvi
C MamRTE1#LINE/ 3306 GGACCTCGTTGT-TGGTGATCCTGTCTTGCCATTTAATGTTAAGTATGGC 3258
Crub_svsplocu 206120 ACGAAGGCAAGTCATGTGGAAGTAGTTCAGTTGCCTAACATGCTTCCTGT 206169
v v ii vv vvi i v iv iv vv vi ii vivi
C MamRTE1#LINE/ 3257 TCGTAGGTGACGCTGATGAAACTGCTCAAGAAGCCGGATGTGACGTCTGT 3208
Crub_svsplocu 206170 -ACACTGTCCAGGTCTCACTAGCATACAATAGGGTAGTTAGCACTGCTGC 206218
-i -v viv i ? iv v i vi ? i iii
C MamRTE1#LINE/ 3207 GGCA-GGTCCAGGTCTCACAGCCGTANAGAAGGTTGGACANCGCTATCGC 3159
Crub_svsplocu 206219 CTGATAAACTTTAAGCTTGGTAGCAAGACTTATTCCACGACGGTCCCACA 206268
iivi i i v i vvvi vi v v vi iv
C MamRTE1#LINE/ 3158 TCTGTAGACCTTTAGTTTGGTCTGGAGCTTGATGCCACGTTGGCGCCACA 3109
Crub_svsplocu 206269 CGTTAGTCCG-CAATCTGCCAAA 206290
vi - i - ii v
C MamRTE1#LINE/ 3108 CTCT-GTCTGCCAGCCTCCCAAA 3087
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 46.45
Transitions / transversions = 1.15 (75/65)
Gap_init rate = 0.06 (25 / 403), avg. gap size = 1.36 (34 / 25)
+ 5923 28.7 2.2 1.8 Crub_svsplocus 206687 208666 (441334) C L3 LINE/CR1 (19) 4080 2117 132
ANNOTATION EVIDENCE:
396 18.27 8.51 0.99 Crub_svsplocus 206687 206780 443220 C CR1-3_Croc LINE/CR1 3503 3603 2
396 18.27 8.51 0.99 Crub_svsplocus 206687 206780 (443220) C CR1-3_Croc#LINE/CR1 (2) 3603 3503 m_b4s001i40
Crub_svsplocu 206687 TATAATAATAATAGTAGTAAAGTTGGAAGGGACCTT-GGAGGTCATCTAG 206735
v v i- v ii i i-i
C CR1-3_Croc#LI 3603 TAGAATCATAG-AGAAGTAGGGCTGGAAGGGACCTCCAGAGGTCATCTAG 3555
Crub_svsplocu 206736 TCCAACCCCCTGCTCG-GGCAGGA--AACCCTAC----ACCATTTCGGAC 206778
ii - -- v i---- ii iv
C CR1-3_Croc#LI 3554 TCCAACCCCCTGCCTGAGGCAGGATCATCCCTATCCAAACCATCCCATAC 3505
Crub_svsplocu 206779 AA 206780
C CR1-3_Croc#LI 3504 AA 3503
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.53
Transitions / transversions = 2.40 (12/5)
Gap_init rate = 0.05 (5 / 93), avg. gap size = 1.80 (9 / 5)
5923 29.24 1.94 1.83 Crub_svsplocus 206705 208666 441334 C L3 LINE/CR1 2117 4080 19
5923 29.24 1.94 1.83 Crub_svsplocus 206705 208666 (441334) C L3#LINE/CR1 (19) 4080 2117 m_b4s001i41
Crub_svsplocu 206705 AAAGTTGGAAGGGACCTTGGAGGTCATCTAGTCCAACCCCCTGCTCGG-G 206753
i i i iiii i-
C L3#LINE/CR1 4080 AGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCATCCGATG 4031
Crub_svsplocu 206754 CAGGAAACCCT---ACACCATTTCGGACAAATGGCTGTCCAGTCTCTTCT 206800
v --- v ii v i iii i v
C L3#LINE/CR1 4030 CAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCT 3981
Crub_svsplocu 206801 TAAAAACTTCCAGTGTTGGAGCATTTACTGCTTCTGGAGGCAAGCTGTTC 206850
i v i vi i vii i i i ?v iv ii
C L3#LINE/CR1 3980 TGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTC 3931
Crub_svsplocu 206851 CACTGATTAATTGTTCTCACTGTCAGGAAGTTTCTCCTTAGTTCTAGGTT 206900
i vv vi iv i v i i i ii - vi ii ii
C L3#LINE/CR1 3930 CATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTA-TATTGAGCC 3882
Crub_svsplocu 206901 G----CTTCTCTCCTTGATTAGTTTCCACCCGTTGCTTCTTGTCCTGCCT 206946
---- v - i -- ii i v i v i i
C L3#LINE/CR1 3881 GAAATCTGC-CTCCCTG--TAACTTCCACCCATTGGTCCTAGTTCTGCCC 3835
Crub_svsplocu 206947 TCAGGTGCTTTGGAAAATA-GCTTAATTCCCTCTTCTTTATGGCAGCCCC 206995
v v iviiv i - ii - ivi i i
C L3#LINE/CR1 3834 TCTGGAGCCACACAGAATAAGTCTAAT-CCCTCTTCCACATGACAGCCCT 3786
Crub_svsplocu 206996 TGAGATATTGGAATACTGCTATCATGTCCCCCCTTGTCCTTCTCTTCGTT 207045
v i v v v i i vivi vii
C L3#LINE/CR1 3785 TCAAATATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCC 3736
Crub_svsplocu 207046 AAACTAGACATACCCAATTCTCGCAACCGTTCCTTATATGTTTTAGCCTC 207095
ii i v i iiv i viv i ii
C L3#LINE/CR1 3735 AGGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACATGGTTTC 3686
Crub_svsplocu 207096 CAGTCCCCTAATCATCTTTATTGCTCTTCTCTGTACTCTTTCTAGAGTCT 207145
v i v i i vi i i v v vi i vv v
C L3#LINE/CR1 3685 CAGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTGT 3636
Crub_svsplocu 207146 CAACATCTTTTTTACATCGTGGTGACCAAAACTGGATGCAGTATTCCAAG 207195
ii ii i v vi i v i i i i i ii
C L3#LINE/CR1 3635 CAATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAATACTCCAGA 3586
Crub_svsplocu 207196 TGTGGCCTTACCAAGGCATTGAAGAATGGTATTAATACTTCACGTGATCT 207245
i v iv vv v v ii v i v i v v ?
C L3#LINE/CR1 3585 TGTGGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCTCCCTTGNTCT 3536
Crub_svsplocu 207246 TGATTCTATCCCTCTGTTAATGCAGCCTAGCACTGTGTTGGCCTTTTTGG 207295
v iv v i i iv i ii i i
C L3#LINE/CR1 3535 GGACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTTTTTTGG 3486
Crub_svsplocu 207296 CAGCTGCCGCACACTGCTGGCTCATATTTAAGTGATTGTCTACTAGGACT 207345
ii vv i v iv viiv v ii i
C L3#LINE/CR1 3485 CAGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAACTAAAACC 3436
Crub_svsplocu 207346 CCGAGGTCCCTCTCACAGTTACTACTATTGAGCATGGTGCCACCTATGCT 207395
v ii i ivvv i ii i vv i v ivi i v
C L3#LINE/CR1 3435 CCTAGGTCTTTTTCACGTGAACTGCTGCTAAGCCAGATCCTCTCCATCCT 3386
Crub_svsplocu 207396 GTACTTGTGCATTTGGTTTTTCTTGCCTAAATGTAGAACCTTGCTTTTTT 207445
v i ivvi i i i i v v
C L3#LINE/CR1 3385 GTACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGACTTTACATTTAT 3336
Crub_svsplocu 207446 CACCATTGAATTTCATTTTGTTAATTAGTGCCCAGTGTTCAAGTCTGTCC 207495
v ii i i ii vvv vi v i v
C L3#LINE/CR1 3335 CCCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTCCAGCCTGTCG 3286
Crub_svsplocu 207496 AGATCCTTCTGTATCTGAAGCCTGTCTTCTGGAGTGTTGGCTATTCCTGC 207545
? i v vi vi v ii?v i i i v
C L3#LINE/CR1 3285 AGATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATCCCTCC 3236
Crub_svsplocu 207546 CAGCTTGGTGTCGTCTGCAAATTTGATGAGTTCCCCATCTATCCCTTCAT 207595
v i i iviv v vi
C L3#LINE/CR1 3235 CAGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCAT 3186
Crub_svsplocu 207596 CCAAATTGTTGATGAAGATGTTGAAGAGTACTGGGCC-AGAACAGAGCCC 207644
i ii i i v v v - i
C L3#LINE/CR1 3185 CCAAGTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAGAGCCC 3136
Crub_svsplocu 207645 TGGGGCACCCCACTACACACTTCCCTCCATATAGATGCAGTTCCATTGAG 207694
v v v v i vi v iiiv v i v
C L3#LINE/CR1 3135 TGTGGCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTAAT 3086
Crub_svsplocu 207695 GACCACTCGCTGAGTACGGCCGGTCAGCCAGCTACGGATCCATCTGGTGG 207744
v v iivi i i v i i i iiiv
C L3#LINE/CR1 3085 CAACACCTTTTGGGTACGGTCGTTCAACCAGCTACGAATCCACCTAACTG 3036
Crub_svsplocu 207745 TGGTTCTGTCTACTCCACATTTTTCTATCTTGTCAAGTAGTAGGTTGTGA 207794
iv viii i vi i i i v vv v vi ii
C L3#LINE/CR1 3035 TACTATCATCCAGCCCATATTTCTCCATCTTGTCCACAAGGATATCATGA 2986
Crub_svsplocu 207795 TCTACTTTATTAAATGCCTTACTGAAGTCCAAGTAAATTATGTCCACAGC 207844
vvv i i i i ii v i ? i i
C L3#LINE/CR1 2985 GAGACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTGTCTACGGC 2936
Crub_svsplocu 207845 ATTCCTCTGATCCACTAATTTTGTCACTTGGTCAAAGAATGCAATAAGAT 207894
i i i i i v v iivi i v v i i
C L3#LINE/CR1 2935 ATTCCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGGAAATGAGGT 2886
Crub_svsplocu 207895 TTGTCTGGCATGATCTATTTTTGACAAACCCATGTTGGCTTTTAGTAATG 207944
v i ii i i iiii i ii i v
C L3#LINE/CR1 2885 TAGTTTGGCATGACTTGTTCTTAGTGAACCCATGCTGGCTCCTAGTGATC 2836
Crub_svsplocu 207945 A---CTTTGTTTGCCTCTAGGTGTTCGTTGATTCGTTGTTTGATTATCTT 207991
--- iv --- i i iivi iivvi i v iv
C L3#LINE/CR1 2835 ACCGCTTCCTTT---TCTAAGTGCTCACAAACCATCTGTTTAATAATCCG 2789
Crub_svsplocu 207992 TTCCAGGATCTTCCCAGGTATTGAGGTCAGGCTGATAGGTCTGTAATTTC 208041
i i i v i v i v i v iv i ?
C L3#LINE/CR1 2788 TTCTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTTN 2739
Crub_svsplocu 208042 CTGGATCCATTTTTTTTCCTTTTTTGAGGATGGGAACTACATCAGCTCTT 208091
v i i i i ii? i ? ? iv i v
C L3#LINE/CR1 2738 CAGAATCCATCTTTTTTCCCTTTTTAAAANTAGGNACNACATTTGCCCGT 2689
Crub_svsplocu 208092 TTCCAGTCCTCTGGTAGTTCCCCTGTGTTCCAGGATCTTTGAAAAATATA 208141
i i i vi ii i vi iv i i v i -
C L3#LINE/CR1 2688 CTCCAGTCTTCTGGCACCTCTTCCGTTCTCCGTGATTTCTCAAAGAT-TA 2640
Crub_svsplocu 208142 GTT-CAGTGGCTCCGATATCACATCTGCCAGTTCCTTGAGAACTCTGGGG 208190
viv- i i vv v i v v i i
C L3#LINE/CR1 2639 CCGACAGCGGTTCCGCGATCACATCTGCAAGTTCTTTCAGTACCCTGGGA 2590
Crub_svsplocu 208191 TGTAATCCGTGTGGTCCTGGCGATTTGAACTCATCTAGGGTGGACAGGTG 208240
i v v v i i ii i vi
C L3#LINE/CR1 2589 TGTAATTCGTCTGGGCCTGGAGACTTGAACTCATTTAAAGCGGCTAGGTG 2540
Crub_svsplocu 208241 CTCCCTAACGATTTTCTTGCCTATCTT-AACTTGTGTTTCTGTTT----- 208284
i v v i i ii -ii vvi i ivi -----
C L3#LINE/CR1 2539 CTCTCTTACTATCTCCTCACCTATCTTGGGCTTCAATTCCCTCTTAACGA 2490
Crub_svsplocu 208285 TGTTTTTTATGGCACTATTTTTAATAGGTTGGTCTG----TTTTTTCCCT 208330
v v --- iv ii -------- ---- iv ii
C L3#LINE/CR1 2489 TGTTTGTTCT---ACCCTTTCCA--------GTCTGAAGATCATTCTCCT 2451
Crub_svsplocu 208331 TTGT-GTAAAGACAGATGCAAAAAATGAGTTAAATAGTTCTGCTTTCTCC 208379
vi - vi i v v v i i i
C L3#LINE/CR1 2450 TGATAGAGAAGACGGAAGCAAAATAGGAGTTGAGTAGTTCTGCTTTCTCT 2401
Crub_svsplocu 208380 CTGTTGCTTGTCACCTTCTTGCCGCTTCCACCCACTAATGGACCAATCAT 208429
iiii i v v ivi iii v v v vi ii i vi ?i
C L3#LINE/CR1 2400 CTGTCATCTGTTAACATTACGCCATCTGCCCCAAGCAGCGGGCCTGTCNC 2351
Crub_svsplocu 208430 TTCCTTCACTTTTTTCTTGTTTTTTACATG---TTGAAAGAAGC--TTTT 208474
i --- ii ii i iivv i--- -- -- ?
C L3#LINE/CR1 2350 TTTCTT---TTTCCTTCTGCTCCGAACATAGCTTTGAA--AAGCCTTNTT 2306
Crub_svsplocu 208475 TTTGTTATTTTTGAC---TTTGGTCGCAAACCTTAGTTCATTTTGAGCCT 208521
i ii ii --- vv i i i i i i
C L3#LINE/CR1 2305 TTTGTTGTCCTTAGCATTTTTTTTCGCAAGCCTCAGCTCATTCTGGGCTT 2256
Crub_svsplocu 208522 TGGCTTTCTTCACTTCATCTTTGCAGGCTCGGGCTATTTGC-CGATATTC 208570
i i i v vii ii i i v ? i iv - vv i i
C L3#LINE/CR1 2255 TAGCCTTCCTGACACTATTCTTACAGGCTTGTGNTACTCTCTCTTTGTCC 2206
Crub_svsplocu 208571 TGACTTAGTTATGTTCCCCTCTTTCCACTTTCT-ATACTTGTCCTTTTTA 208619
viv -- --- ii - v v
C L3#LINE/CR1 2205 TTGGTTA--TATGT---CCTCTTTCCATCTTCTGATACATGTCCTTTTAA 2161
Crub_svsplocu 208620 TCTTTCAATTTG---TCAGAGAGTTCTTTATGCAGCCATGCTGGTTTCTT 208666
------ i --- i ? i ? i i
C L3#LINE/CR1 2160 ------AATCTGACATCAGAGAATNCTCTATGNAGCCACGTTGGTTTCTT 2117
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 36.92
Transitions / transversions = 1.81 (363/200)
Gap_init rate = 0.03 (53 / 1961), avg. gap size = 1.40 (74 / 53)
+ 5264 27.8 1.5 0.7 Crub_svsplocus 208926 210455 (439545) + L3 LINE/CR1 2553 4077 (22) 133
ANNOTATION EVIDENCE:
5264 28.48 0.99 0.72 Crub_svsplocus 208926 210446 439554 + L3 LINE/CR1 2553 4077 22
5264 28.48 0.99 0.72 Crub_svsplocus 208926 210446 (439554) L3#LINE/CR1 2553 4077 (22) m_b4s001i42
Crub_svsplocu 208926 TAGATGAGTTCAAATCGCCAGGACCAGATGGATTACACCCCAGAGTTCTC 208975
i i v v i i i i v v
L3#LINE/CR1 2553 TAAATGAGTTCAAGTCTCCAGGCCCAGACGAATTACATCCCAGGGTACTG 2602
Crub_svsplocu 208976 AAGGAACTGGCAGATGTGATATCGGAGCCACTG-AACTATATTTTTCAAA 209024
i v vv i i -viv - i v i
L3#LINE/CR1 2603 AAAGAACTTGCAGATGTGATCGCGGAACCGCTGTCGGTA-ATCTTTGAGA 2651
Crub_svsplocu 209025 GATCCTGGAACACAGGGGAACTACCAGAGGACTGGAAAAGAGCTGATGTA 209074
i vi iv i ii iv i i i v i vi ?
L3#LINE/CR1 2652 AATCACGGAGAACGGAAGAGGTGCCAGAAGACTGGAGACGGGCAAATGTN 2701
Crub_svsplocu 209075 GTTCCCATCCTCAAAAAAGGAAAAAAAATGGATCCAGGAAATTACAGACC 209124
? i ?ii i i i i v ? i
L3#LINE/CR1 2702 GTNCCTANTTTTAAAAAGGGAAAAAAGATGGATTCTGNAAACTACAGACC 2751
Crub_svsplocu 209125 TATCAGCCTGACCTCAATACCTGGGAAGACCCTGGAAAAGATAATCAAAC 209174
vi v i v i v i v i ii i vi v i
L3#LINE/CR1 2752 GGTAAGCTTGACGTCGATCCCCGGCAAAATTCTAGAACGGATTATTAAAC 2801
Crub_svsplocu 209175 A-ATGAATCAACAAACACTTAGAGGCAAACAAAA---TCATTACTAAAAG 209220
- iv ii-ii i --- vi i--- v i ii
L3#LINE/CR1 2802 AGATGGTTTG-TGAGCACTTAGA---AAAGGAAGCGGTGATCACTAGGAG 2847
Crub_svsplocu 209221 CCAACACGGGTTTGTCAAAAATAGATCATGCCAGACAAATCTTATTGCAT 209270
i i iiii i i ii i v i i v v
L3#LINE/CR1 2848 CCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTAACCTCATTTCCT 2897
Crub_svsplocu 209271 TCTTTGACCAAGTGACAAAATTAGTGGATCAGAGGAATGCTGTGGACATA 209320
i ivii v v i i i i i i i ?
L3#LINE/CR1 2898 TTTTTGATAGGGTTACTAGACTGGTAGATCAGGGGAATGCCGTAGACANA 2947
Crub_svsplocu 209321 ATTTATTTGGACTTCAGTAAGGCATTTGATAAAGTAGATCACAACCTACT 209370
i v i i i i vvv ii iv v
L3#LINE/CR1 2948 GTGTATCTGGATTTCAGCAAGGCATTTGACAAAGTCTCTCATGATATCCT 2997
Crub_svsplocu 209371 ACATG-ACAAGATAGAAAAATGTGGGGTAGACAGAACCACCACCAGATGG 209419
-ii - i i i v i iiiv vi viii i
L3#LINE/CR1 2998 -TGTGGACAAGATGGAGAAATATGGGCTGGATGATAGTACAGTTAGGTGG 3046
Crub_svsplocu 209420 ATCCATAGCTGGCTGACCGGCCGTACTCAGCGAGTGGTCCTCAATGGAAC 209469
i i i v i i ivii v vv i v
L3#LINE/CR1 3047 ATTCGTAGCTGGTTGAACGACCGTACCCAAAAGGTGTTGATTAATGGATC 3096
Crub_svsplocu 209470 TGCATCTATATGGAGGGAAGTGTGTAGTGGGGTGCCCCAGGGCTCTGTTC 209519
viii v iv i v v v v i
L3#LINE/CR1 3097 GATGTCAACCTGGAGGGAGGTCTCTAGTGGCGTGCCACAGGGCTCTGTCC 3146
Crub_svsplocu 209520 TGGGTCCAGTACTCTTCAACATCTTCATCAACGATTTGGATGAAGGGATA 209569
v i v v v i i i i iv
L3#LINE/CR1 3147 TTGGCCCTGTCCTGTTCAACATTTTTATCAATGACTTGGATGAAGACATA 3196
Crub_svsplocu 209570 GATGGGGAACTCATCAAATTTGCAGACGACACCAAGCTGGCAGGAATAGC 209619
v vivi i i v v i
L3#LINE/CR1 3197 GAAGGCATGCTTATCAAATTTGCAGATGACACAAAGCTGGGAGGGATAGC 3246
Crub_svsplocu 209620 CAACACTCCAGAAGACAGGCTTCAGATACAGAAGGATCTGGACAGACTTG 209669
i i v?ii v iv iv v i ? v i v
L3#LINE/CR1 3247 TAATACGNTGGATGACAGAATCAAGATTCAAAANGATCTCGACAGGCTGG 3296
Crub_svsplocu 209670 AACACTGGGCACTAACTAACAAAATGAAATTCAATGGTGAAAAAAGCAAG 209719
iv vvv i i i ii v v v i i
L3#LINE/CR1 3297 AACGATGGGCCGAAACCAACAAGATGAAATTTAACAGGGATAAATGTAAA 3346
Crub_svsplocu 209720 GTTCTACATTTAGGCAAGAAAAACCAAATGCACAAGTACAGCATAGGTGG 209769
i i ivvi i v v i ivi
L3#LINE/CR1 3347 GTCCTGCATTTAGGTTCAAAAAATCAACTGCACAAGTACAGGATGGAGAG 3396
Crub_svsplocu 209770 CACCGTGCTCAATAGTAGTAACTGTGAGAGGGACCTCGGAGTTCTAGTAG 209819
v i vv i ii i vvvi i ii v i i v
L3#LINE/CR1 3397 GATCTGGCTTAGCAGCAGTTCACGTGAAAAAGACCTAGGGGTTTTAGTTG 3446
Crub_svsplocu 209820 ACAATCACCTAAATATGAGCCAGCAGTGTGCTGCAGCTGCCAAAAAGGCC 209869
viiv v v i v ii i i
L3#LINE/CR1 3447 ACCGCAAGCTCAATATGAGCCAACAGTGTGATGTGGCTGCCAAAAAAGCT 3496
Crub_svsplocu 209870 AACACAGTGCTAGGCTGCATTAAAAGAGGGATAGAATCAAGATCACGTGA 209919
ii i vi v i v vi v ? v v
L3#LINE/CR1 3497 AATGCAATCTTAGGCTGCATTAATAGAAGTATAGTGTCCAGANCAAGGGA 3546
Crub_svsplocu 209920 AGTATTAATACCACTCTTCAATGCCTTGGTAAGGCCACACTTGGAATACT 209969
i v i v i v v vv vi v i ii i i
L3#LINE/CR1 3547 GGTAATAGTCCCGCTGTACTCTGCGCTGGTCAGACCACATCTGGAGTATT 3596
Crub_svsplocu 209970 GCATCCAGTTTTGGTCACCACGATGTAAAAAAGATGTTGAGACTCTAGAA 210019
i i i v i iv v i ii ii v vv i i
L3#LINE/CR1 3597 GCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGACAAACTGGAG 3646
Crub_svsplocu 210020 AGAGTACAGAGAAGAGCAACAAAGATGATTAGGGGACTGGAGGCTAAAAC 210069
v v v i i v i i v i v ii i viv
L3#LINE/CR1 3647 CGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGAAACCATGTC 3696
Crub_svsplocu 210070 ATATAAGGAACGGTTGCGAGAATTGGGTATGTCTAGTTTAACGAAGAAAA 210119
i vii i v i ii iiv i
L3#LINE/CR1 3697 ATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGGAGAAGAGAA 3746
Crub_svsplocu 210120 GGACAAGGGGGGACATGATAGCAGTATTCCAATATCTCAGGGGCTGCCAT 210169
iviv i i v v v i v i i
L3#LINE/CR1 3747 GACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAGGGCTGTCAT 3796
Crub_svsplocu 210170 AAAGAAGAGGGAATTAAGC-TATTTTCCAAAGCACCTGAAGGCAGGACAA 210218
ivi - ii - i viivi v v i i v
L3#LINE/CR1 3797 GTGGAAGAGGG-ATTAGACTTATTCTGTGTGGCTCCAGAGGGCAGAACTA 3845
Crub_svsplocu 210219 GAAGCAACGGGTGGAAACTAATCAAGGAGAGAAG----CAACCTAGAACT 210264
i v i ii -- i - v ---- ii ii iv -
L3#LINE/CR1 3846 GGACCAATGGGTGGAAGTTA--CAGGGAG-GCAGATTTCGGCTCAATA-T 3891
Crub_svsplocu 210265 AAGGAGAAACTTCCTGACAATGAGAACAATTAATCAGTGGAACAGCCTGC 210314
ii i i v i vi iv vv i ii v
L3#LINE/CR1 3892 AAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAATGGGCTGC 3941
Crub_svsplocu 210315 CTCCAGAAGCAGTAAATGCTCCAACACTGGAAGTTTTTAAGAAGAGACTG 210364
v? i i i iiv i iv i v i v i
L3#LINE/CR1 3942 CTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGCAGAGGCTG 3991
Crub_svsplocu 210365 GACAGCCACTTGTCCGAAATGGTGT---AGGGTTTCCTGC-CCGAGCAGG 210410
iii v ii v --- v -i iiii
L3#LINE/CR1 3992 GATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCATCGGATGGG 4041
Crub_svsplocu 210411 GGGTTGGACTAGATGACCTCCAAGGTCCCTTCCAAC 210446
i i
L3#LINE/CR1 4042 AGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAAC 4077
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 35.34
Transitions / transversions = 1.72 (272/158)
Gap_init rate = 0.01 (19 / 1520), avg. gap size = 1.37 (26 / 19)
392 15.85 9.76 0.00 Crub_svsplocus 210374 210455 439545 + CR1-3_Croc LINE/CR1 3503 3592 13
392 15.85 9.76 0.00 Crub_svsplocus 210374 210455 (439545) CR1-3_Croc#LINE/CR1 3503 3592 (13) m_b4s001i43
Crub_svsplocu 210374 TTGTCCGAAATGGT----GTAGGGTT--TCCTGCC-CGAGCAGGGGGTTG 210416
vi ii ----i v -- - ii
CR1-3_Croc#LI 3503 TTGTATGGGATGGTTTGGATAGGGATGATCCTGCCTCAGGCAGGGGGTTG 3552
Crub_svsplocu 210417 GACTAGATGACCTCC-AAGGTCCCTTCCAACCTTACTACT 210455
i-i i i v
CR1-3_Croc#LI 3553 GACTAGATGACCTCTGGAGGTCCCTTCCAGCCCTACTTCT 3592
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.36
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.05 (4 / 81), avg. gap size = 2.00 (8 / 4)
+ 279 25.0 1.1 1.1 Crub_svsplocus 211119 211207 (438793) + L1MdTf_I LINE/L1 2924 3012 (2568) 130
ANNOTATION EVIDENCE:
279 25.00 1.12 1.12 Crub_svsplocus 211119 211207 438793 + L1-97_DR LINE/L1 2924 3012 2568
279 25.00 1.12 1.12 Crub_svsplocus 211119 211207 (438793) L1-97_DR#LINE/L1 2924 3012 (2568) m_b4s001i45
Crub_svsplocu 211119 AAAGCACCTGGGCCAGATGGTCTACCTGTAGAA-TGTATAAAATCATACA 211167
i v v v - v i vvv i
L1-97_DR#LINE 2924 AAGGCTCCTGGGCCCGATGGTATACCTGTAGAATTTTACAAAAAATTGCA 2973
Crub_svsplocu 211168 AGAACTCTTAAGCCCAATAATGTTGGAACTATTTAATGAG 211207
i v vv v v i-v ii v v
L1-97_DR#LINE 2974 GGTAAACTTATGCCCCAC-TTACTTGAAGTATTTAATGAG 3012
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.41
Transitions / transversions = 0.47 (7/15)
Gap_init rate = 0.02 (2 / 88), avg. gap size = 1.00 (2 / 2)
+ 268 30.9 6.8 7.1 Crub_svsplocus 211208 211716 (438284) + Nimb-4_DR LINE/I 5089 5683 (3978) 134 *
ANNOTATION EVIDENCE:
268 30.86 6.75 7.11 Crub_svsplocus 211110 211716 438284 + Nimb-4_DR LINE/I 5079 5683 3978
268 30.86 6.75 7.11 Crub_svsplocus 211110 211716 (438284) Nimb-4_DR#LINE/I 5079 5683 (3978) m_b4s001i44
Crub_svsplocu 211110 AAAAATAATAAAGCACCTGGGCCA--GATGGTCTACCTGTAGAATGTATA 211157
i i -- -- viv vv v
Nimb-4_DR#LIN 5079 AAAAATAATAAAACACCCGG--CAATGATGGTCTACCTTCTGAATGGTTC 5126
Crub_svsplocu 211158 AAATCAT----ACAAGAACTCTTAAGCCCAATAATGTTGGAACTATTTAA 211203
v ---- v iv i vvi ivv v i i--- ii
Nimb-4_DR#LIN 5127 AAAACATTTAAAAAAGAGATCTCACCTCTTCTTATATC---ATCATTTAA 5173
Crub_svsplocu 211204 TGAGGT-CTTAACAAAAGCTAAAATACTGGCTTCATGGGAAGAAGC--TC 211250
vi ii- - i i vi v ivv v iii -- i
Nimb-4_DR#LIN 5174 TTGGACACTTAA-AGAGGCAGAAATTCCCCCTTCTTGGAGGGAAGCAATT 5222
Crub_svsplocu 211251 TCCTTACTCTGATTCCTAA-----GGAAAAAGCAGACCTGGCGCATATTA 211295
vi i v -- v ----- ii vv i iivvi i -i v
Nimb-4_DR#LIN 5223 ATCTCAGTC--ATACCTAAAGAGGGGAAGGATAAAACTCTTTGTA-GTTC 5269
Crub_svsplocu 211296 AAAACTATAGACCCATTTCATTATTAAACTCAGACTATAAGATCTTTATG 211345
---- v ii v vv v ivi iv v iiv
Nimb-4_DR#LIN 5270 A----TTTAGACCTGTGTCTGTTTTAAATGTAGACTATAAATTATTTGCC 5315
Crub_svsplocu 211346 CCTATAATGGCACAAAGACTTGAAAGATTTCTAGCAGATTTTATACACTT 211395
i vv i vv i v i v v v v v
Nimb-4_DR#LIN 5316 TCTATTTTAGCCAAGAGACTTGAAACATTTTTACCTGATTTGATAGACAT 5365
Crub_svsplocu 211396 TGATCAAA-ATGGCTTTTTATCAAAAAGATATATAAGAAATAATGT--TA 211442
v - v i v -v ii v ii v ivvi i i --v
Nimb-4_DR#LIN 5366 AGATCAAACAGGGTTTATTA-GAGGACGGCAGACTCAAGATAATATAGAA 5414
Crub_svsplocu 211443 GGATTGTTT-TGGATATACTGGAGTATT--ATGAGGTGCACAATGAAAAG 211489
ivv i- v - viv i- -- vi i - v --
Nimb-4_DR#LIN 5415 GGACACTTCATGCA-ATACGACAA-ATTAAAAAAGAT-CACATT--AAAG 5459
Crub_svsplocu 211490 CAAGTGAGTTTAATCTTTCTTGATGCATAAAAAGCTTTCGACAATGTGAA 211539
---- v i ivvi v v i i vi i
Nimb-4_DR#LIN 5460 CA----ATTTTAGTTAGCCTAGATGCAGAGAAAGCTTTTGACTGTGTAAA 5505
Crub_svsplocu 211540 ATGGGATTTTATGTTTAATCAAT-TGTCATATA----TGGACTT-CGGGG 211583
v ---- i v i - v v ---- i - i ii
Nimb-4_DR#LIN 5506 TTGGGA----ATATTTATTTAATGTTTAATATAGATTTGGATTTACAGAA 5551
Crub_svsplocu 211584 AAAAC-TTTATAAATATGTTTAAATCAGTCTAT-TTTAA--TCAGGAGCG 211629
v -v v ii--- v -- i - i --i ii v
Nimb-4_DR#LIN 5552 AATACAGTTAGAAGC---TTTCAAT--GTTTATATTCAAACCCAGAGGCT 5596
Crub_svsplocu 211630 AAAGTAATAATTAATGG----------AGAAATGACCGATAGCTTTCCAA 211669
iii v v i ---------- i ----- i------
Nimb-4_DR#LIN 5597 AGGATAAAAATAAACGGTTGTCTTTCAAAAAA-----GATAA------AA 5635
Crub_svsplocu 211670 TT-GAAAAAGGTACAAGGCAAGGTTGTCCGTTATCGCCATTGTTGTTT 211716
i - v v i vi v v vi v
Nimb-4_DR#LIN 5636 CTAGAAAAAGGAACTAGGCAGGGTTGTCCCCTCTCTCCCCTGATGTTT 5683
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.73
Transitions / transversions = 1.02 (88/86)
Gap_init rate = 0.10 (60 / 606), avg. gap size = 1.40 (84 / 60)
+ 321 34.6 2.8 1.5 Crub_svsplocus 211503 211838 (438162) + L1MdTf_I LINE/L1 3127 3383 (1917) 130
ANNOTATION EVIDENCE:
321 37.55 1.56 1.17 Crub_svsplocus 211503 211758 438242 + L1-109_DR LINE/L1 3127 3383 1917
321 37.55 1.56 1.17 Crub_svsplocus 211503 211758 (438242) L1-109_DR#LINE/L1 3127 3383 (1917) m_b4s001i46
Crub_svsplocu 211503 TCTTTCTTGATGCATAAAAAGCTTTCGACAATGTGAAATGGGATTTTATG 211552
iv v i v i i i viv vi i--iv v
L1-109_DR#LIN 3127 TCTCACTAGACGCAGAGAAAGCCTTTGACCGGGTCGAATGGA--CATATC 3174
Crub_svsplocu 211553 TTTAATCAATTGTCA--TATATGGACTTCGGGGAAAACTTTATAAATATG 211600
i ii i v v -- i v i i vvv i v
L1-109_DR#LIN 3175 TCTGGTCAGTTTTGAAGTGTCTGGGCTTTGGTCCAAATTTTATACATATG 3224
Crub_svsplocu 211601 TTTAAATCAGTCTATTTTAAT-CAGGAGCGAAAGTAATAATTAATGGAGA 211649
v vv v vv v iv - vv i ii ivi i- iv vv
L1-109_DR#LIN 3225 GTACAAACTCTGTATCGTAATTCAGCTGCAAGGGTGTCAAC-AGGGTTGA 3273
Crub_svsplocu 211650 AATGACCGATAGCTTTCCAATTGAA-AAAGGTACAAGGCAAGGTTGTCCG 211698
iv vi i vv i vii ii- i i i i i i i
L1-109_DR#LIN 3274 GCTGCTCAAGTGCTTTTCTGCTGGGCAGAGGCACAAGACAGGGCTGCCCA 3323
Crub_svsplocu 211699 TTATCGCCATTGTTGTTTATATTATCCCTAGAGGCATTGATCAGAGTAAT 211748
i i ? iivi v vi v v ii vii i
L1-109_DR#LIN 3324 TTGTCACCATTGTTGNTTGCCCTTTCGTTAGAGCCTTTGGCCCAGGCAAT 3373
Crub_svsplocu 211749 TTGAAAAGAT 211758
i vv i
L1-109_DR#LIN 3374 TCGTCAGGAT 3383
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 50.24
Transitions / transversions = 1.26 (53/42)
Gap_init rate = 0.02 (6 / 255), avg. gap size = 1.17 (7 / 6)
307 33.47 3.25 1.60 Crub_svsplocus 211593 211838 438162 + L1MdTf_I_orf2 LINE/L1 2758 3007 1674
307 33.47 3.25 1.60 Crub_svsplocus 211593 211838 (438162) L1MdTf_I_orf2#LINE/L1 2758 3007 (1674) m_b4s001i47
Crub_svsplocu 211593 TAAATATGTTTAAATCAGTCTATTTTAA-TCAGGAGCGAAAGTAATAATT 211641
i v v v i ivvi -i v v vi v v i v
L1MdTf_I_orf2 2758 TAAACATGATAAAAGCAATCTACAGCAAACCAGTAGCCAACATCAAAGTA 2807
Crub_svsplocu 211642 AATGGAGAAATGACCGATAGCTTTCCAATTGAAA-AAGGTACAAGGCAAG 211690
i v - i iv vv v i i -v v v i
L1MdTf_I_orf2 2808 AATGGAGAGAAG-CTGGAAGCAATCCCACTAAAATCAGGGACTAGACAAG 2856
Crub_svsplocu 211691 GTTGTCCGTTATCGCCATTGTTGTTTA---TATTATCCCTAGAGGCATTG 211737
i i ii v v v vvi v i --- v --- v i i i
L1MdTf_I_orf2 2857 GCTGCCCACTTTCTCCCTACCTTTTCAACATAGTA---CTTGAAGTATTA 2903
Crub_svsplocu 211738 ATCAGAGTAATTTGAAAAGATAGACAGATCAAAGGTTTACAGATCAAGAA 211787
ii i i v v v iiv i vv i iiii
L1MdTf_I_orf2 2904 GCCAGAGCAATTCGACAACAAAAGGAGATCAAGGGGATACAAATTGGAAA 2953
Crub_svsplocu 211788 AGAAACATTTAAAATGCAAGCTTTTGCAGACGAT-T--TAGTTTTTATAA 211834
iiv v i iiv vi i - -- v v
L1MdTf_I_orf2 2954 AGAGGAAGTCAAAATATCACTTTTTGCAGATGATATGATAGTATATATAA 3003
Crub_svsplocu 211835 TTGA 211838
v
L1MdTf_I_orf2 3004 GTGA 3007
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.36
Transitions / transversions = 1.02 (41/40)
Gap_init rate = 0.04 (9 / 245), avg. gap size = 1.33 (12 / 9)
+ 416 31.7 2.4 3.8 Crub_svsplocus 212059 212353 (437647) + L1-88_DR LINE/L1 3788 4078 (1348) 135
ANNOTATION EVIDENCE:
416 31.71 2.37 3.78 Crub_svsplocus 212059 212353 437647 + L1-88_DR LINE/L1 3788 4078 1348
416 31.71 2.37 3.78 Crub_svsplocus 212059 212353 (437647) L1-88_DR#LINE/L1 3788 4078 (1348) m_b4s001i48
Crub_svsplocu 212059 AATTATGATAAACTAATTGAACAGATTAAAGCTGATTTAGATACTTGGAC 212108
i v ii v iiiv i i i ii vv- i
L1-88_DR#LINE 3788 AATCATGAAAAGTTATTTAGGGAAATTAAAACCGATTTGAATAGA-GGAT 3836
Crub_svsplocu 212109 CAACTTACAGCTTTCCTTCATGGGCAGAATAGCCATAATTAAAATGAATG 212158
vv v - ii v i v v vv vv i
L1-88_DR#LINE 3837 ATACTTCCA-CTTTCTCTCCTAGGAAGAATTGAAAGTATTAGAATGAATG 3885
Crub_svsplocu 212159 TGTTACCAAAGATCTTATTTCTGTTTCAATGTACACCCATAAAATTGGAT 212208
vi iiv v i iv v v iviv ii vi-- v i
L1-88_DR#LINE 3886 TTCTACCAAGATTATTGTTCATTTTTCAAAGCCTTCCTGTTG--TTGTAC 3933
Crub_svsplocu 212209 AACAATTTTT-TTCAAAACCTTAACAAAATT--ATTCTCAAATTTATTTG 212255
v i vi- v v - v -- iiv
L1-88_DR#LINE 3934 CACAATCTGCATTCAAATCATTA-CAAAAGTGCATTTCAAAATTTATTTG 3982
Crub_svsplocu 212256 GCAAGGGAAAAAAAAGCAAGGA--CCAAATTAAAATTAT--TGCAGGATT 212301
--- v i v i --v ivv v -- ivi -
L1-88_DR#LINE 3983 GCA---GAACAAAAGGCCAAGAGTGCGCCTTAAAATTCTGATGTCAGAT- 4028
Crub_svsplocu 212302 CAAAGGAGAGGGGGGGACTTGGCCTCCCTGACATGGAAAAATACTATCGG 212351
-- iv iv v v v v v i ii vi i i
L1-88_DR#LINE 4029 --AAGGGTAATGGTGGTCTGGGGCTGCCTAACATAAAAATGTATTATTGG 4076
Crub_svsplocu 212352 GC 212353
L1-88_DR#LINE 4077 GC 4078
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.52
Transitions / transversions = 0.96 (44/46)
Gap_init rate = 0.05 (15 / 294), avg. gap size = 1.20 (18 / 15)
+ 655 31.9 3.5 3.5 Crub_svsplocus 214933 215721 (434279) + Gypsy-168-I_DR LTR/Gypsy 1428 2304 (1995) 136
ANNOTATION EVIDENCE:
469 32.62 5.34 5.34 Crub_svsplocus 214933 215719 434281 + Gypsy69-I_DR LTR/Gypsy 1428 2214 2031
469 32.62 5.34 5.34 Crub_svsplocus 214933 215719 (434281) Gypsy69-I_DR#LTR/Gypsy 1428 2214 (2031) m_b4s001i49
Crub_svsplocu 214933 TACCACCTCACCGAC---GGACAGATTGTTCAATCGAACTTGCTCCTGGG 214979
? i ? --- --- i v ? i - v ----
Gypsy69-I_DR# 1428 TACCNCCTCATCGNCCTTGG---GACTGTGCNATTGAACT-GCTAC---- 1469
Crub_svsplocu 214980 GCCAAGCTG------CCTAAACCCAGAATGTACCCTATGAC-CTTCGCAG 215022
- vv ------ vv i i v ?v v - v v ii
Gypsy69-I_DR# 1470 -CCAATATGTCCCCACCTAAAAGCAAAGTTTACCCNCTGTCTCGTCCCGA 1518
Crub_svsplocu 215023 AATTGCAAGAATTGAGAAAGTACATTGATAAGAACTTGGCTAGGGGCTTC 215072
i - vvv ii vi i vi iv i i ?vvv i v
Gypsy69-I_DR# 1519 AACT-CAAGCCATGGAAACATACATCGAGGAGGCCCTAGCNTCTGGTTAC 1567
Crub_svsplocu 215073 ATAGAGCCAGC-ACGCTCGAGGATAGCAGCCCCAGTCATATTCCAGGGGA 215121
vvii ?v - ?- ivv?ii? vvv v v v vv i
Gypsy69-I_DR# 1568 ATTCGACCNTCTACN-TCACCNGCNGCAGCAGGATTCTTCTTCGTGGAGA 1616
Crub_svsplocu 215122 AAAAGGACGGGAGATTACGACTGTGTGTAGACTTCCGAGGCCTGAA---- 215167
i i ii vi v v i? ii v v ?i ----
Gypsy69-I_DR# 1617 AGAAGGATGGAGGTCTCCGTCCNTGCATCGACTACCGAGGNTTGAATAAC 1666
Crub_svsplocu 215168 --CACTGT-GTGTATAGACCAGGTTTATCCCCTGCCGCTTATGAAAGACC 215214
-- -iv v ------- i i v - i----- v
Gypsy69-I_DR# 1667 GTCACTGTCAAGTATCG-------TTACCCTCTTCC-CTTG-----GTCC 1703
Crub_svsplocu 215215 TACTTACCCATTTGGCAGCT--GGGAAA-----ATCTTTACAAAACTAGA 215257
i? i i - ?vii i -- v i----- vi v v
Gypsy69-I_DR# 1704 CNCCTGCCC-TNGAACAACTACGTGAAGCCCGTATCTACACCAAACTTGA 1752
Crub_svsplocu 215258 CCTCCGTGAGGCATACTATAGGGTACGAATCAGAGAAGGGGATGAGTGGA 215307
v viiv v iv ivv?i v ? v i i i i
Gypsy69-I_DR# 1753 CCTCAGAAGTGCTTATAACCTNATTCGNATCCGGGAGGGAGACGAGTGGA 1802
Crub_svsplocu 215308 AAACAGCGTTCAACTGTCCCCTGGGTAG--CTACCAATTCAAGGTGATGC 215355
v -- v v i vi -- iv v vv? v
Gypsy69-I_DR# 1803 AAACCGCGTTC--CTGACCACTAGGGGGCACTATGAATACCTNGTTATGC 1850
Crub_svsplocu 215356 CCTTCGGATTACAAGGAGCGCCGGCTGTATTTATGCAACTGATCAACGGA 215405
vi ?i ?vv?iivv ? i ? v ivv iv i v ? i i
Gypsy69-I_DR# 1851 CCTATGGNCTNGCNAACTCNCCAGCNGTCTTCCAGTCATTCATNAATGAA 1900
Crub_svsplocu 215406 GTGTTGCATGACCATCTATATAGAGGCGTCCTTGTATATCTGGATGACAT 215455
i v vviv iivv iv i i v i v i iv v ?
Gypsy69-I_DR# 1901 ATTTTCAGAGATTTGCTGAACAAATGTGTCATCGCCTATATNGATGACAT 1950
Crub_svsplocu 215456 ACTGATCTACTCACAGACGTTGGAAGACCATATACAATTA-GTACGGACA 215504
v i v vv vvi i v v i - vv - vv v
Gypsy69-I_DR# 1951 CCTGATCTATTCCCCCAACCTAGAACAACACAT-CAAGGACGTCAGGACT 1999
Crub_svsplocu 215505 GTACTGCGAAAATTACTAG-ATGCCAAC-CTATACTGTAAGTTGTCGAAG 215552
vi vv vi? v - vi - ii --i ii vv
Gypsy69-I_DR# 2000 GTTTTGACACGNTTACAAGAAAACCAACTCTACGC--CAAGCCGGAGAAG 2047
Crub_svsplocu 215553 TGCGAGTTTCA------CAAGA-CTCGGATTGACTATTTAGGGTTCAGAG 215595
i i i ------ - -- -----ii i i v vvi
Gypsy69-I_DR# 2048 TGTGAATTCCACGTGTCCAAGACCTCG--TT-----CCTGGGATACATTA 2090
Crub_svsplocu 215596 TC-TCCGCCACAGAGATAGAAATGGATCCTAGTAAAGTTC--GCAGTGTC 215642
-v ii i - i ivvi?vi i -- vv
Gypsy69-I_DR# 2091 TCAGCCATCACGGAG-TGGAAATGGACGACNCCAAGGTTCAGGCAGTCAC 2139
Crub_svsplocu 215643 TTAGAATGGCA-GGCCCCAAGGACCCGT-CGTCAACTGCAGAGATTCTTG 215690
-- i? v-vv -- v v -vivv i i ii i
Gypsy69-I_DR# 2140 T--GGNTGGCCTCTCCCCAA--AACAGTGAAGGAACTACAAAGATTTCTA 2185
Crub_svsplocu 215691 GGGTTTGCCAATTTCTACCAGCAGTTCAT 215719
i i i i iv i
Gypsy69-I_DR# 2186 GGGTTCGCCAACTTTTATCGCCGGTTCAT 2214
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.33
Transitions / transversions = 0.93 (117/126)
Gap_init rate = 0.08 (61 / 786), avg. gap size = 1.38 (84 / 61)
633 31.71 5.32 5.32 Crub_svsplocus 215139 215721 434279 + Gypsy-28-I_DR LTR/Gypsy 1722 2304 1995
633 31.71 5.32 5.32 Crub_svsplocus 215139 215721 (434279) Gypsy-28-I_DR#LTR/Gypsy 1722 2304 (1995) m_b4s001i50
Crub_svsplocu 215139 CGACTGTGTGTAGACTTCCGAGGCCTGAACACTGT----GTGTATAGACC 215184
v i ii vi v vii ---- - - vi
Gypsy-28-I_DR 1722 CGTCCGTGCATAGACTATCGAGGGCTGAACAGCATCACGGT-TA-AGAAT 1769
Crub_svsplocu 215185 AGGTTTATCCCCTGCCGCTTATGAAAGACCTACTTACCCATTTGGCAGCT 215234
--i ii v -----i -- i v v ivi iv
Gypsy-28-I_DR 1770 A--CTTATCCTTTGCCGCTGATG-----TCT--TCAGCCTTCGAGCGCCT 1810
Crub_svsplocu 215235 G-----GGAAAATCTTT--ACAAAACTAGACCTCCGTGAGGCATACTATA 215277
----- vi ii -- i i i ii v v ii v
Gypsy-28-I_DR 1811 GCAGGGGGCGAACTTTTTCACAAAATTAGATCTTCGCAATGCTTATCATT 1860
Crub_svsplocu 215278 GGGTACGAATCAGAGAAGGGGATGAGTGGAAAACAGCGTTCAACTGTCCC 215327
v v v v vvv i --v
Gypsy-28-I_DR 1861 TGGTTCGCATAAGACCCGGGGATGAGTGGAAAACAGCGTTTAAC--ACCC 1908
Crub_svsplocu 215328 CTGGGTAGCTACCAATTCAAG------GTGATGCCCTTCGGA--TTACAA 215369
i ivi ---- v ii ------ vv v-- v
Gypsy-28-I_DR 1909 CTAGAGGG----CATTTTGAGTACTGCGTTCTGCCCTTCGGCCTTTCCAA 1954
Crub_svsplocu 215370 GGAGCGCCGGCTGTATT-TATGCAACTGATCAACGGAGTGTTGCATGACC 215418
--v v v -i v - vi i iv viv --
Gypsy-28-I_DR 1955 --CGCTCCGGCTGTTTTCCAGGC-ACTCGTCAATGACGTGTTGAGAGA-- 1999
Crub_svsplocu 215419 ATCTAT-ATAGA--GGCGTCCT--TGTATATCTGGATGACATACTGATCT 215463
--- - --i iv vi -- v i v i
Gypsy-28-I_DR 2000 ---TATGATAGATCAGTTTATTTATGTCTACCTGGATGACATTCTGATTT 2046
Crub_svsplocu 215464 ACTCACAGACGTTGGAAGACCATATACAATTAGTACGGAC-AGTACTGCG 215512
vi v vv vi vv i v i v ivv - i - ii i
Gypsy-28-I_DR 2047 TTTCCCACTCTCTCCAGGAGCACATTCAACATGT-CAGACGAGTGTTGCA 2095
Crub_svsplocu 215513 AAAATTACTAGATGCCAACCTATACTGT-AAGTTGTCGAAGTGCGAGTTT 215561
i iii i viviiiv v - - vi vv i vv
Gypsy-28-I_DR 2096 GAGGCTGCTAGAGAATGGGCTTTA-TGTCAAGGCGGAGAAATGCGTTTTT 2144
Crub_svsplocu 215562 CACA-AGACTCGGATTGACTATTTAGGGTTCAGAGTCTCCGCCACAGAGA 215610
ii- v v - v v vi i iivi vv v v i ivi i
Gypsy-28-I_DR 2145 CATGCACAGTCGG-TTCAGTTCTTGGGACATATCGTGTCAGTCGAGGGGA 2193
Crub_svsplocu 215611 TAGAAATGGATCCTAGTAAAG-TTCGCAGTGTCTTAGAATGGCAGGCCCC 215659
iviv - vi - iviv vv v vii
Gypsy-28-I_DR 2194 TGCGCATGGATCC-AGAGAAGATTCAGGCTGTGGTAGATTGGCCAACCCC 2242
Crub_svsplocu 215660 AAGGACCCGT--CGTCAACTGCAGAGATTCTTGGGGTTTGCCAATTTCTA 215707
iivv --v i -- i ii v i
Gypsy-28-I_DR 2243 AGATTCCCGTAAGGCC--CTGCAGAGGTTTCTGGGTTTTGCCAATTTTTA 2290
Crub_svsplocu 215708 CCAGCAGTTCATCC 215721
i iv i i
Gypsy-28-I_DR 2291 CCGGCGTTTTATTC 2304
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.86
Transitions / transversions = 1.06 (90/85)
Gap_init rate = 0.08 (45 / 582), avg. gap size = 1.38 (62 / 45)
655 31.84 2.30 2.30 Crub_svsplocus 215243 215721 434279 + Gypsy-168-I_DR LTR/Gypsy 1791 2269 2022
655 31.84 2.30 2.30 Crub_svsplocus 215243 215721 (434279) Gypsy-168-I_DR#LTR/Gypsy 1791 2269 (2022) m_b4s001i51
Crub_svsplocu 215243 CTTTACAAAACTAGACCTCCGTGAGGCATACTATAGGGTACGAATCAGAG 215292
v v i i iiiv v v ivvvi ? v - i
Gypsy-168-I_D 1791 CTTTACCAAACTTGATCTTCGCAGTGCCTACAACCTCATNCGCAT-AAAG 1839
Crub_svsplocu 215293 AAGGG-GATGAGTGGAAAACAGCGT--TCAACTGTCCCCTGGGTAGCTAC 215339
vi - i v v -- ? - v v i vi - i
Gypsy-168-I_D 1840 CGGGGTGACGAGTGGAAAACCGGGTTCTCNAC-GACCACCGGCCA-CTAT 1887
Crub_svsplocu 215340 CAATTCAAGGTGATGCCCTTCGGATT-ACAAGGAGCGCCGGCTGTATT-T 215387
v v vi vi -i iv i- vv i v -i
Gypsy-168-I_D 1888 GAATACCGGGTGATGCCCTTCGGCCTGGCAAACAGT-CCTTCCGTCTTCC 1936
Crub_svsplocu 215388 ATGCAACTGATCAACGGAGTGTTGCATGACCAT-CTATATAGAGGCGTCC 215436
v - i v ? ii i v iv - -i iv ivi v v v
Gypsy-168-I_D 1937 AAGC-ATTCATNAACGAGGTATTTCGAGA-CATGTTGAACCAATGGGTCA 1984
Crub_svsplocu 215437 TTGTATATCTGGATGACATACTGATCTACTCACAGACGTTGGAAGACCAT 215486
? iv v v vi v ? vi ? ? i
Gypsy-168-I_D 1985 TTGTNTACATTGATGACATCCTCGTCTACTCAGANACCCTNGAAGANCAC 2034
Crub_svsplocu 215487 ATACAATTAGTACGGACAGTACTGCGAAAATTACTAGATGCCAACCTATA 215536
v ivivv vv ii v ? ? ii i i ?v v viv v v ?
Gypsy-168-I_D 2035 ATTCGCCACGTCAGAGCCGTNCTNCAGAGACTNATCGAGAACCAGCTNTA 2084
Crub_svsplocu 215537 CTGTAAGTTGTCGAAGTGCGAGTTTCACAAGACTCGGATTGACTATTTAG 215586
vvi i v v ?i v iivv vii i
Gypsy-168-I_D 2085 CGCCAAATTGTCCAAGTGCGAGTTTCACCAGACNTGCACCTCCTTCCTGG 2134
Crub_svsplocu 215587 GGTTCAGAGTCTCCGCCACAGAGATAGAAATGGATCCTAGTAAAGTTCGC 215636
i v v?i vv viv? iii i v? ivvv ? i vvi
Gypsy-168-I_D 2135 GATACATNATCAGCGCAGANGGAGTGGCNATGGACGAAAGNAAGGTAAAC 2184
Crub_svsplocu 215637 AGTGTCTTAGAATGGCAGGCCCCAAGGACCCGTCGTCAA----CTGCAGA 215682
iv ?? ii v viivv ? i? ----? v ----? iv
Gypsy-168-I_D 2185 GCTGTNNTGAATTGGCCAAAACCNAANAC----NGTGAAGGAGNTGCAAC 2230
Crub_svsplocu 215683 GATTCTTGGGGTTTGCCAATTTCTACCAGCAG-TTCATCC 215721
v ii i - ? - ?
Gypsy-168-I_D 2231 GCTTTCTGGGGTTCGCCAATTTCTA-CAGNAGATTCATNC 2269
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.76
Transitions / transversions = 0.89 (70/79)
Gap_init rate = 0.04 (18 / 478), avg. gap size = 1.22 (22 / 18)
+ 293 26.1 3.5 3.5 Crub_svsplocus 216075 216268 (433732) + Gypsy-168-I_DR LTR/Gypsy 2606 2667 (1615) 136
ANNOTATION EVIDENCE:
283 27.72 5.15 5.15 Crub_svsplocus 216075 216268 433732 + SUSHIIDR1 LTR/Gypsy 2838 3031 1999
283 27.72 5.15 5.15 Crub_svsplocus 216075 216268 (433732) SUSHIIDR1#LTR/Gypsy 2838 3031 (1999) m_b4s001i52
Crub_svsplocu 216075 TGGCGCCATTTATTGGAAGGTGCACAGCACCCCTTCGAGGTGTGGACGGA 216124
i i vii i ? ivv vv v
SUSHIIDR1#LTR 2838 TGGCGTCACTGGCTGGAGGGNGCGGCGCACCCCTTCTTGGTCTGGACGGA 2887
Crub_svsplocu 216125 CCACCGGAACCT--AATG-GTCC-TCCAGACGCCGAGGAGATTG-GCGCC 216169
ivi -- i i- - i i--- - i i - -
SUSHIIDR1#LTR 2888 CCATAAGAACCTTGAGTATGTCCGTTCG---GCC-AAGAGGTTGAGCG-C 2932
Crub_svsplocu 216170 AAAACACGTTCGCTGGGCGCAGTATTTCCAGCGTTTCAGATTTAGCCTGA 216219
viv v i i vv vi iviv v iv iiv --
SUSHIIDR1#LTR 2933 ACGCCAGGCTCGCTGGGCACTCTTCTTTGGTCGGTTCAACTTCGTCCT-- 2980
Crub_svsplocu 216220 AGGTAGTACCCGG--AGGG---AAGAACTTCTTAGCAGATGCACTCTCCC 216264
--v v - -- --- ivi vv v v v ?
SUSHIIDR1#LTR 2981 --CTCGTA-CCGGCCAGGGTCNAAGAATACCAAACCTGATGCCCTCTCNC 3027
Crub_svsplocu 216265 GGCT 216268
SUSHIIDR1#LTR 3028 GGCT 3031
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.07
Transitions / transversions = 0.96 (25/26)
Gap_init rate = 0.08 (16 / 193), avg. gap size = 1.25 (20 / 16)
293 22.58 0.00 0.00 Crub_svsplocus 216075 216136 433864 + Gypsy105-I_Dr LTR/Gypsy 2606 2667 1615
293 22.58 0.00 0.00 Crub_svsplocus 216075 216136 (433864) Gypsy105-I_Dr#LTR/Gypsy 2606 2667 (1615) m_b4s001i53
Crub_svsplocu 216075 TGGCGCCATTTATTGGAAGGTGCACAGCACCCCTTCGAGGTGTGGACGGA 216124
vii i i v v i i v v i
Gypsy105-I_Dr 2606 TGGCGCCATTGGCTGGAGGGCGCAGAGCAGCCTTTTGTGGTCTGGACAGA 2655
Crub_svsplocu 216125 CCACCGGAACCT 216136
v i
Gypsy105-I_Dr 2656 CCACAGAAACCT 2667
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.09
Transitions / transversions = 1.33 (8/6)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0)
+ 254 32.6 2.0 2.0 Crub_svsplocus 216702 216848 (433152) + Gypsy-168-I_DR LTR/Gypsy 3238 3384 (951) 136
ANNOTATION EVIDENCE:
254 32.64 2.04 2.04 Crub_svsplocus 216702 216848 433152 + Gypsy164B-I_DR LTR/Gypsy 3238 3384 951
254 32.64 2.04 2.04 Crub_svsplocus 216702 216848 (433152) Gypsy164B-I_DR#LTR/Gypsy 3238 3384 (951) m_b4s001i54
Crub_svsplocu 216702 CGGCCCTGGCAGGACATCGGGATGGATTTCCTCGTTGAGTTACCAAACGT 216751
i iviv v v i iv ii i vvvvvi
Gypsy164B-I_D 3238 CGACCCTGGTCACACATAGCGATGGACTTTGTCACTGGGTTACCCCCATC 3287
Crub_svsplocu 216752 CAGGGGTTACACGGTCATATGGACGGTTGTTGACTTATTCTCGAAACAGG 216801
v iv i vi vivv v v v vv ivv
Gypsy164B-I_D 3288 CAGTGGCAACACAGTAGTCCTCACTGTGGTGGACAGATTCTCGAAGGCGG 3337
Crub_svsplocu 216802 CACACTTTG-TCCCCT--GCAAGGGGTTGCCGTCTGCGAGGAGGTTAGCA 216848
i- --v ---i i v v ii vi
Gypsy164B-I_D 3338 CACACTTTATTCCCCTCCCCAA---ATTACCTTCAGCGAGGGAGACAGCA 3384
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.05
Transitions / transversions = 0.74 (20/27)
Gap_init rate = 0.03 (5 / 146), avg. gap size = 1.20 (6 / 5)
+ 284 30.9 2.4 3.0 Crub_svsplocus 217344 217513 (432487) + Gypsy-168-I_DR LTR/Gypsy 3832 4000 (297) 136
ANNOTATION EVIDENCE:
284 30.92 2.35 2.96 Crub_svsplocus 217344 217513 432487 + Gypsy72-I_DR LTR/Gypsy 3832 4000 297
284 30.92 2.35 2.96 Crub_svsplocus 217344 217513 (432487) Gypsy72-I_DR#LTR/Gypsy 3832 4000 (297) m_b5s001i3
Crub_svsplocu 217344 GTGGGTGACCGGGTGTACCTGTCAACCAAATATGTTAAGT--TACAGGTA 217391
ii - ivi i i v -i vv -- - v
Gypsy72-I_DR# 3832 GTGGGCAAC-GGGTGTGGTTATCAACTAAAGAT-CTACCTCTTA-AGGTT 3878
Crub_svsplocu 217392 CCATGCAAGAAG-CTAGTGCCAAAATACATTGGGCCCTTCCGTA-TAGTA 217439
i - i i-i i ii v vi v vi -
Gypsy72-I_DR# 3879 TCA-GCAGGAAAATTGGCACCTAAATTTATTGGGCCCTACCCCATTAGTA 3927
Crub_svsplocu 217440 CGCATCATCAACCCTGTTACAGTGCAGCTTCAGTTGCCGGAATTGCTTGG 217489
v - v i v v v v iv i i vvv ivv iv
Gypsy72-I_DR# 3928 AG-ATCATGAGCCCGGTGACTGTCCGCCTTCGGCTGCCCTTACACCTCTG 3976
Crub_svsplocu 217490 TAAAATACACCCAGTGTTCCATGT 217513
vivi v v i
Gypsy72-I_DR# 3977 TCGTGTACACCCTGTCTTTCATGT 4000
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.38
Transitions / transversions = 0.96 (25/26)
Gap_init rate = 0.05 (8 / 169), avg. gap size = 1.12 (9 / 8)
+ 12 21.2 7.1 1.7 Crub_svsplocus 218846 218901 (431099) + (TTTCTA)n Simple_repeat 1 59 (0) 137
ANNOTATION EVIDENCE:
12 21.20 7.14 1.69 Crub_svsplocus 218846 218901 431099 + (TTTCTA)n Simple_repeat 1 59 0
12 21.20 7.14 1.69 Crub_svsplocus 218846 218901 (431099) (TTTCTA)n#Simple_repeat 1 59 (0) m_b5s252i0
Crub_svsplocu 218846 TTTCTATTTCTATTTGTAGGTC--TTTGTATTT-TGTTATCT-TCTCCAG 218891
v vv -- v - i - - i i v
(TTTCTA)n#Sim 1 TTTCTATTTCTATTTCTATTTCTATTTCTATTTCTATT-TCTATTTCTAT 49
Crub_svsplocu 218892 TTCTTTCTCT 218901
v i
(TTTCTA)n#Sim 50 TTCTATTTCT 59
Matrix = Unknown
Transitions / transversions = 0.67 (4/6)
Gap_init rate = 0.07 (4 / 55), avg. gap size = 1.25 (5 / 4)
+ 347 26.1 7.2 3.5 Crub_svsplocus 220097 220263 (429737) C Mam_R4 LINE/Dong-R4 (1546) 2263 2091 138
ANNOTATION EVIDENCE:
347 26.05 7.19 3.47 Crub_svsplocus 220097 220263 429737 C Mam_R4 LINE/Dong-R4 2091 2263 1546
347 26.05 7.19 3.47 Crub_svsplocus 220097 220263 (429737) C Mam_R4#LINE/Dong-R4 (1546) 2263 2091 m_b5s001i4
Crub_svsplocu 220097 CATACAGCTTCAGATCATCCATGTAAAGGAGGTGG--GATAGTCTTGCAG 220144
v i i i v ii -- ii v ----
C Mam_R4#LINE/D 2263 CATAGAGCTTCAGATCGTCCACGTAGAGCAAATGGCTGATGATAT----G 2218
Crub_svsplocu 220145 ATGTTT---TTGATGTTTGAT-----AGCCATGTCCTGAGTTATTCAGTA 220186
i---i vi v ----- v v vi i v
C Mam_R4#LINE/D 2217 ATGTTCATCCTCGTGTTTTATCTTAAAGCCATGACCGGTATTATTTAGTT 2168
Crub_svsplocu 220187 TTGTTGACAGAGGAAACAGTGCAATGACA-AATAGTAATGGTGATAA-TG 220234
v vvvi i vv v v -i - ivi -iv -i
C Mam_R4#LINE/D 2167 TTCTGCTTAGGGGATTCAGTCCCA-AACAGAACCATAATGG-ACTAAGCG 2120
Crub_svsplocu 220235 AATCTCCTTGAAATATTCCTCTCTTGATA 220263
i i v v
C Mam_R4#LINE/D 2119 AGTCTCCTTGAAATATTCCCCGCTTTATA 2091
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.83
Transitions / transversions = 1.00 (21/21)
Gap_init rate = 0.07 (11 / 166), avg. gap size = 1.64 (18 / 11)
+ 125 0.0 0.0 0.0 Crub_svsplocus 220284 220391 (429609) + (ATT)n Simple_repeat 1 108 (0) 139
ANNOTATION EVIDENCE:
125 0.00 0.00 0.00 Crub_svsplocus 220284 220391 429609 + (ATT)n Simple_repeat 1 108 0
125 0.00 0.00 0.00 Crub_svsplocus 220284 220391 (429609) (ATT)n#Simple_repeat 1 108 (0) c_b5s251i0
Crub_svsplocu 220284 ATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAT 220333
(ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAT 50
Crub_svsplocu 220334 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTA 220383
(ATT)n#Simple 51 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTA 100
Crub_svsplocu 220384 TTATTATT 220391
(ATT)n#Simple 101 TTATTATT 108
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 107), avg. gap size = 0.0 (0 / 0)
+ 17 3.6 3.2 3.2 Crub_svsplocus 224896 224926 (425074) + (CCTC)n Simple_repeat 1 31 (0) 140
ANNOTATION EVIDENCE:
17 3.57 3.23 3.23 Crub_svsplocus 224896 224926 425074 + (CCTC)n Simple_repeat 1 31 0
17 3.57 3.23 3.23 Crub_svsplocus 224896 224926 (425074) (CCTC)n#Simple_repeat 1 31 (0) m_b5s252i1
Crub_svsplocu 224896 CCT-CCTCCACCCCCTCCCTCCCTCCCTCCCT 224926
- - i
(CCTC)n#Simpl 1 CCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCT 31
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2)
+ 243 17.9 0.0 0.0 Crub_svsplocus 231801 231839 (418161) + hAT-N53_DR DNA/hAT-Ac 2762 2800 (3019) 141
ANNOTATION EVIDENCE:
243 17.95 0.00 0.00 Crub_svsplocus 231801 231839 418161 + hAT-N53_DR DNA/hAT-Ac 2762 2800 3019
243 17.95 0.00 0.00 Crub_svsplocus 231801 231839 (418161) hAT-N53_DR#DNA/hAT-Ac 2762 2800 (3019) m_b5s001i5
Crub_svsplocu 231801 GTATATGTGTGTGTATATACATATAAACACACACACATA 231839
i i i i i v i
hAT-N53_DR#DN 2762 GTGTGTGTGTGTGTATACACACACACACACACACACACA 2800
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.59
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 12 12.1 0.0 6.9 Crub_svsplocus 233311 233341 (416659) + (GTT)n Simple_repeat 1 29 (0) 142
ANNOTATION EVIDENCE:
12 12.09 0.00 6.90 Crub_svsplocus 233311 233341 416659 + (GTT)n Simple_repeat 1 29 0
12 12.09 0.00 6.90 Crub_svsplocus 233311 233341 (416659) (GTT)n#Simple_repeat 1 29 (0) m_b5s252i2
Crub_svsplocu 233311 GTTGTTGTTGTTAACTTGTTGTTTTTCTTGT 233341
--v v v
(GTT)n#Simple 1 GTTGTTGTTGTT--GTTGTTGTTGTTGTTGT 29
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2)
+ 474 13.0 0.2 0.0 Crub_svsplocus 236592 236675 (413325) + URR1B DNA/hAT-Charlie 1 157 (153) 143
ANNOTATION EVIDENCE:
294 26.19 1.19 0.00 Crub_svsplocus 236592 236675 413325 + hAT-N8b_Testu DNA/hAT-Charlie 73 157 153
294 26.19 1.19 0.00 Crub_svsplocus 236592 236675 (413325) hAT-N8b_Testu#DNA/hAT-Charlie 73 157 (153) m_b5s001i6
Crub_svsplocu 236592 TCTAAAACAGTGGTTCTCAACCTGTGGGTCGGGACCCCATTTGGGGTCGA 236641
i v v v v vvvv v
hAT-N8b_Testu 73 TCTAGATCAGTGTTTCTCAACCTGGGGGTCGCGACCCCCAGGGGGGTCGC 122
Crub_svsplocu 236642 ACGACCATTTCACGGGGGTCGCCAA-ACAAGGCTG 236675
iv viv i v v i-i i i
hAT-N8b_Testu 123 GGGACGGGTTTAGGGGGGTCGCAAGTGCAGGGCCG 157
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.00
Transitions / transversions = 0.57 (8/14)
Gap_init rate = 0.01 (1 / 83), avg. gap size = 1.00 (1 / 1)
474 10.14 0.00 0.00 Crub_svsplocus 236599 236667 413333 + URR1B DNA/hAT-Charlie 1 69 156
474 10.14 0.00 0.00 Crub_svsplocus 236599 236667 (413333) URR1B#DNA/hAT-Charlie 1 69 (156) m_b5s001i7
Crub_svsplocu 236599 CAGTGGTTCTCAACCTGTGGGTCGGGACCCCATTTGGGGTCGAACGACCA 236648
i v v v v
URR1B#DNA/hAT 1 CAGCGGTTCTCAACCTGTGGGTCGCGACCCCTTTGGGGGTCGAACGACCC 50
Crub_svsplocu 236649 TTTCACGGGGGTCGCCAAA 236667
i v
URR1B#DNA/hAT 51 TTTCACAGGGGTCGCCTAA 69
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.42
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
+ 525 9.9 0.0 0.0 Crub_svsplocus 236734 236804 (413196) + URR1A DNA/hAT-Charlie 156 226 (0) 144
ANNOTATION EVIDENCE:
525 9.86 0.00 0.00 Crub_svsplocus 236734 236804 413196 + URR1A DNA/hAT-Charlie 156 226 0
525 9.86 0.00 0.00 Crub_svsplocus 236734 236804 (413196) URR1A#DNA/hAT-Charlie 156 226 (0) m_b5s001i8
Crub_svsplocu 236734 TGGTTTGGGGTCACCACAACATGGGGAACTATATTATGGGGTCGCGGCAT 236783
v i i vi i
URR1A#DNA/hAT 156 TGGTTGGGGGTCACCACAACATGAGGAACTGTATTAAAGGGTCGCAGCAT 205
Crub_svsplocu 236784 TAGAAAGGTTGAGAACCACTG 236804
i
URR1A#DNA/hAT 206 TAGGAAGGTTGAGAACCACTG 226
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.71
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 400 9.6 8.0 2.5 Crub_svsplocus 236738 236812 (413188) C CYRA11_Mm Satellite/Y-chromosome (375) 242 164 145 *
ANNOTATION EVIDENCE:
400 9.57 8.00 2.53 Crub_svsplocus 236738 236812 413188 C CYRA11_Mm Satellite/Y-chromosome 164 242 375
400 9.57 8.00 2.53 Crub_svsplocus 236738 236812 (413188) C CYRA11_Mm#Satellite/Y-chromosome (375) 242 164 m_b5s001i9
Crub_svsplocu 236738 TTGGGGTCACCACA--ACATGGGGAACTATAT-TAT---GGGGTCGCGGC 236781
- -- i i - --- ?i i
C CYRA11_Mm#Sat 242 TTGGGG-CACCACACAACATGAGGAACTGTATNTATAAAGGGNCCGCAGC 194
Crub_svsplocu 236782 ATTAGAAAGGTTGAGAACCACTGCTCTAAAA 236812
i - ii
C CYRA11_Mm#Sat 193 ATTAGGAAGGTTGAGAACCACT-CTCTGGAA 164
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.81
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.07 (5 / 74), avg. gap size = 1.60 (8 / 5)
+ 19 10.3 2.1 6.5 Crub_svsplocus 237024 237071 (412929) + A-rich Low_complexity 1 46 (0) 146
ANNOTATION EVIDENCE:
19 10.26 2.08 6.52 Crub_svsplocus 237024 237071 412929 + (AAATCTA)n Simple_repeat 1 46 0
19 10.26 2.08 6.52 Crub_svsplocus 237024 237071 (412929) (AAATCTA)n#Simple_repeat 1 46 (0) m_b5s252i3
Crub_svsplocu 237024 AAATATAAAACCTGAAATTTAAAA-CTAAAATCTGAATAAATCTAAAAT 237071
v i i i - -- -
(AAATCTA)n#Si 1 AAATCTAAAATCTAAAATCTAAAATCTAAAATCT--A-AAATCTAAAAT 46
Matrix = Unknown
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4)
+ 11 17.3 7.7 0.0 Crub_svsplocus 238311 238349 (411651) + A-rich Low_complexity 1 42 (0) 147
ANNOTATION EVIDENCE:
11 17.30 7.69 0.00 Crub_svsplocus 238311 238349 411651 + (TAAAAG)n Simple_repeat 1 42 0
11 17.30 7.69 0.00 Crub_svsplocus 238311 238349 (411651) (TAAAAG)n#Simple_repeat 1 42 (0) m_b5s252i4
Crub_svsplocu 238311 TAAAAGT-AAA-T-AAATTACAAAAAAAAGGAAAAGAAAAAG 238349
- - - v v iv v v
(TAAAAG)n#Sim 1 TAAAAGTAAAAGTAAAAGTAAAAGTAAAAGTAAAAGTAAAAG 42
Matrix = Unknown
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3)
+ 586 22.6 2.5 2.6 Crub_svsplocus 239092 239201 (410799) + L3 LINE/CR1 3927 4077 (19) 148
ANNOTATION EVIDENCE:
586 28.48 1.99 0.00 Crub_svsplocus 239092 239242 410758 + L3 LINE/CR1 3927 4080 19
586 28.48 1.99 0.00 Crub_svsplocus 239092 239242 (410758) L3#LINE/CR1 3927 4080 (19) m_b5s001i10
Crub_svsplocu 239092 AGTGGAACAATCTGCCTCCAGAAGCTGTGAATGCTCCAACAATGGAAGTT 239141
i iiiv v? i iv iiv i iv v i v
L3#LINE/CR1 3927 AATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTG 3976
Crub_svsplocu 239142 TTTAAGAAGAGACTGGACAGCCATTTGTCTGAAATGGTATAG---GATTT 239188
i v i iii i v ii v i --- iv
L3#LINE/CR1 3977 TTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATT 4026
Crub_svsplocu 239189 CCTGCCTGAGCAGGGGGGTTGAACTAGATGACCTTCAAGTTCCCTTCCAA 239238
v vi vv i i ii v
L3#LINE/CR1 4027 CCTGCATCGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAA 4076
Crub_svsplocu 239239 CTTT 239242
i
L3#LINE/CR1 4077 CTCT 4080
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 35.23
Transitions / transversions = 1.69 (27/16)
Gap_init rate = 0.01 (1 / 150), avg. gap size = 3.00 (3 / 1)
262 13.59 3.17 6.56 Crub_svsplocus 239189 239251 410749 + CR1L_fAlb LINE/CR1 33 93 6
262 13.59 3.17 6.56 Crub_svsplocus 239189 239251 (410749) CR1L_fAlb#LINE/CR1 33 93 (6) m_b5s001i11
Crub_svsplocu 239189 CCTGCCT-GAGCAGGGGGGTTGAACTAGATGACCTTC-AAGTTCCCTTCC 239236
i - i - i - i -i v
CR1L_fAlb#LIN 33 CCTGCTTTGAGCAGGAGG-TTGGACTAGA-GACCTCCTGAGGTCCCTTCC 80
Crub_svsplocu 239237 AACTTTATTATTATT 239251
i v --
CR1L_fAlb#LIN 81 AACCTGA--ATTATT 93
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.30
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.10 (6 / 62), avg. gap size = 1.00 (6 / 6)
+ 272 21.3 0.0 0.0 Crub_svsplocus 239202 239248 (410752) + MIR3 SINE/MIR 145 191 (17) 149
ANNOTATION EVIDENCE:
272 21.28 0.00 0.00 Crub_svsplocus 239202 239248 410752 + MIR3 SINE/MIR 145 191 17
272 21.28 0.00 0.00 Crub_svsplocus 239202 239248 (410752) MIR3#SINE/MIR 145 191 (17) m_b5s001i12
Crub_svsplocu 239202 GGGGGTTGAACTAGATGACCTTCAAGTTCCCTTCCAACTTTATTATT 239248
i i ii v i i ivi
MIR3#SINE/MIR 145 GGGGGTTGGACTAGATGATCTCTAAGGTCCCTTCCAGCTCTGACATT 191
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.37
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 428 31.5 2.4 2.8 Crub_svsplocus 240420 240776 (409224) C L1-21_DR LINE/L1 (1714) 4300 3945 150
ANNOTATION EVIDENCE:
428 30.24 1.82 2.28 Crub_svsplocus 240420 240639 409361 C L1-21_DR LINE/L1 4082 4300 1714
428 30.24 1.82 2.28 Crub_svsplocus 240420 240639 (409361) C L1-21_DR#LINE/L1 (1714) 4300 4082 m_b5s001i13
Crub_svsplocu 240420 GCCTGGTAGTATTTCTCCAAGTCTGGAAGGCCAAATCCCCCCCCTTTCCT 240469
i i i iiv v ivvi i ii v iii
C L1-21_DR#LINE 4300 GCTTGGTAATACTTCTCCAAACATGGCAATGTAAATCCTCCTTCGTCTTT 4251
Crub_svsplocu 240470 TTG-AATCCTGCAATAATTTTAGTTTAATTCTTGCTCTTTTTCCTTGCCA 240518
i - -- i iiiv v i v i i
C L1-21_DR#LINE 4250 CTGTAAT--TGTAGCGTTTTAAATTTAATTCTTGGTTTTTTCCCTTGCCA 4203
Crub_svsplocu 240519 GAT-AAATTTGAGCATCATTTTATTCAAATTTTGAAAAAAATTCTTTTC- 240566
v - iv i- iv i i -v i v vii v v -
C L1-21_DR#LINE 4202 TATAAAACGTGAA-ATCGATCTATCC-CATTCTGTAAAATGCTGTTTACT 4155
Crub_svsplocu 240567 TAGTTTTATAGGTATGCATTGGAACAAGA-ATAAGATTTTCTGCAATACG 240615
v i - ii v v - i v iviv v i i
C L1-21_DR#LINE 4154 TATTTCTATAGGTA-GTGTTTGAAAAAGATATAAAAATCGTGGGAGTATG 4106
Crub_svsplocu 240616 TTCATTTTAATCACTGCAATTCTG 240639
? iiv v v
C L1-21_DR#LINE 4105 TTNATTTTAATTGATTCTATTCTG 4082
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 36.98
Transitions / transversions = 1.50 (39/26)
Gap_init rate = 0.04 (9 / 219), avg. gap size = 1.00 (9 / 9)
257 33.43 3.42 3.71 Crub_svsplocus 240426 240776 409224 C L1-50_DR LINE/L1 3945 4294 1540
257 33.43 3.42 3.71 Crub_svsplocus 240426 240776 (409224) C L1-50_DR#LINE/L1 (1540) 4294 3945 m_b5s001i14
Crub_svsplocu 240426 TAGTATTTCTCCAAGTCTGGAAGGCCAAATCCCCCCCCTTTCCTTTG--A 240473
i v i iivi vvv i i - --
C L1-50_DR#LINE 4294 TAATAATCCTCCAAACACGGAAGGGACAGTCCTCCCC-TTTCCTTTGTTA 4246
Crub_svsplocu 240474 ATCCTGCAATAATTTTAGTTTAATTCTTGCTCTT--TTTCCTTGCCAGAT 240521
-- i i iv v i v i v v i i--v i -- v
C L1-50_DR#LINE 4245 AT--TGTAGTGTTTTAAGTCTCACTCTGGGTTTCAGATTCTT--CCATAT 4200
Crub_svsplocu 240522 AAATTTGAGCATCATTTTATTCAAATTTTGAAAAAAATTCTTTTCTAGTT 240571
i viiv v v iv v vviv i vv v
C L1-50_DR#LINE 4199 AAATCTCGAAATCATTTGATTCCAATCATTAAATTGTTTTTTTGGTATTT 4150
Crub_svsplocu 240572 TTATAGGTATGCATTGGAACAAGAATAAGATTTTCTGCAATACGTTCATT 240621
iv viv v ii i iv v iv v iv i i
C L1-50_DR#LINE 4149 CAATAGGTAGAGATTGGAAAAGAAACAGCAGTCGCGGCAGAACATTCATC 4100
Crub_svsplocu 240622 TTAATCACTGCAATTCTGCC-CATAAA-GGAGAGCTGTAGGTTAGACCAA 240669
v v i v v v ii-i -vv i -- vvv v
C L1-50_DR#LINE 4099 TTTATAATTTCTATTCGGTTATATAAACTTAAAG--GTAGGGGTGTCCAA 4052
Crub_svsplocu 240670 ATATCAAGATCTTTTTGGATCTGTTCTATTAACTTATCATAAT------T 240713
v v i v vv vi i i i vvvvii ------
C L1-50_DR#LINE 4051 CTATCCAGGTCTGTTTTTATCTCCTTTGTCATAGGGCCATAATTAGTTGT 4002
Crub_svsplocu 240714 ATCCTTTTTAAGTGTAGCACATCTGGCAGTCAATTGTATCCCTAAATATC 240763
v v - ---- v iivvvi vv i- i i
C L1-50_DR#LINE 4001 ATACATTTT-AGT----CAAATTCTTAGGTATATTA-ATCCCTAGATATT 3958
Crub_svsplocu 240764 TAATTTTGTTTGT 240776
v v
C L1-50_DR#LINE 3957 TAATATTCTTTGT 3945
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.02
Transitions / transversions = 0.77 (49/64)
Gap_init rate = 0.05 (18 / 350), avg. gap size = 1.39 (25 / 18)
+ 247 26.1 3.3 0.0 Crub_svsplocus 240933 241024 (408976) C L1MdTf_I LINE/L1 (2370) 4209 4115 151
ANNOTATION EVIDENCE:
247 26.09 3.26 0.00 Crub_svsplocus 240933 241024 408976 C L1MdTf_I_orf2 LINE/L1 2913 3007 1674
247 26.09 3.26 0.00 Crub_svsplocus 240933 241024 (408976) C L1MdTf_I_orf2#LINE/L1 (1674) 3007 2913 m_b5s001i15
Crub_svsplocu 240933 TCAATTATAAAAACTA--A-ATCATCTGCAAAGGCTTGTATTTTGAATGT 240979
v v v -- - iiv vi v vi
C L1MdTf_I_orf2 3007 TCACTTATATATACTATCATATCATCTGCAAAAAGTGATATTTTGACTTC 2958
Crub_svsplocu 240980 CTCTTTCTTAATCTCTAAACCTTTGATCTGTTCATCTTGTCGAAT 241024
iii i v vv i vi iv v
C L1MdTf_I_orf2 2957 CTCTTTTCCAATTTGTATCCCCTTGATCTCCTTTTGTTGTCGAAT 2913
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.24
Transitions / transversions = 0.85 (11/13)
Gap_init rate = 0.02 (2 / 91), avg. gap size = 1.50 (3 / 2)
+ 16 16.1 0.0 0.0 Crub_svsplocus 241278 241305 (408695) + A-rich Low_complexity 1 28 (0) 152
ANNOTATION EVIDENCE:
16 16.12 0.00 0.00 Crub_svsplocus 241278 241305 408695 + (A)n Simple_repeat 1 28 0
16 16.12 0.00 0.00 Crub_svsplocus 241278 241305 (408695) (A)n#Simple_repeat 1 28 (0) m_b5s252i5
Crub_svsplocu 241278 AAATAAAAAAAAATAAATTAAAAAAAAA 241305
v v vv
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA 28
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 314 28.6 1.6 1.6 Crub_svsplocus 243185 243319 (406681) C Gypsy-176_DR-I LTR/Gypsy (1364) 2311 2237 153
ANNOTATION EVIDENCE:
241 29.23 3.70 3.70 Crub_svsplocus 243185 243319 406681 C Gypsy-175_DR-I LTR/Gypsy 1486 1620 1343
241 29.23 3.70 3.70 Crub_svsplocus 243185 243319 (406681) C Gypsy-175_DR-I#LTR/Gypsy (1343) 1620 1486 m_b5s001i16
Crub_svsplocu 243185 GCCTTCATCCGGACTATTCCTGGATGTCCCTCATGCAGAGAGAACAAGAC 243234
i v v iv ivi v ?vvviii iv
C Gypsy-175_DR- 1620 GCCTTCATTCGCACGACACCTGGATGTCCTGTATGAANTTCAGGCAGCAC 1571
Crub_svsplocu 243235 TCTAGTCCTCAA-TGAGGCTGGGATGACTACCCTGCTACCCCATAGGACA 243283
i i vi v - v v- i i v v i vi v
C Gypsy-175_DR- 1570 CCTGGATCGCAATTTAGGA-GGAATAACTACCCTCCTTCCCCACATAAGA 1522
Crub_svsplocu 243284 CACCCCTTGAAGGTGGAT----AGCTCATGCTTCCTCTTC 243319
v i ---- v ---- v i v
C Gypsy-175_DR- 1521 CAGCCTT----GTTGGATTGTCAGCTCATCCTTTCTATTC 1486
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.63
Transitions / transversions = 0.81 (17/21)
Gap_init rate = 0.05 (7 / 134), avg. gap size = 1.43 (10 / 7)
314 28.00 0.00 0.00 Crub_svsplocus 243199 243273 406727 C Gypsy-176_DR-I LTR/Gypsy 2237 2311 1364
314 28.00 0.00 0.00 Crub_svsplocus 243199 243273 (406727) C Gypsy-176_DR-I#LTR/Gypsy (1364) 2311 2237 m_b5s001i17
Crub_svsplocu 243199 TATTCCTGGATGTCCCTCATGCAGAGAGAACAAGACTCTAGTCCTCAATG 243248
ii v ivvv i i ivii i v i
C Gypsy-176_DR- 2311 TATTCCCAGATGGCCCTCATGCAACTTGGACAGGATGTCAGCCCTGAGTG 2262
Crub_svsplocu 243249 AGGCTGGGATGACTACCCTGCTACC 243273
vi ii i
C Gypsy-176_DR- 2261 ACACTGGGATGACTATTCTGCTGCC 2237
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 36.60
Transitions / transversions = 2.00 (14/7)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 15 17.8 2.1 4.3 Crub_svsplocus 243569 243616 (406384) + (AACAACA)n Simple_repeat 1 47 (0) 154
ANNOTATION EVIDENCE:
15 17.77 2.08 4.26 Crub_svsplocus 243569 243616 406384 + (AACAACA)n Simple_repeat 1 47 0
15 17.77 2.08 4.26 Crub_svsplocus 243569 243616 (406384) (AACAACA)n#Simple_repeat 1 47 (0) m_b5s252i6
Crub_svsplocu 243569 AACAATAAAAAAACACATAAAACATAACAAACAACAATACAA-AAACAA 243616
-v v v i v v i - -
(AACAACA)n#Si 1 AACAA-CAAACAACAAACAACAAACAACAAACAACAA-ACAACAAACAA 47
Matrix = Unknown
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3)
+ 375 32.1 2.8 2.8 Crub_svsplocus 243876 244300 (405700) C Gypsy56-I_DR LTR/Gypsy (1757) 2799 2223 155
ANNOTATION EVIDENCE:
375 28.04 0.00 0.00 Crub_svsplocus 243876 243982 406018 C Gypsy56-I_DR LTR/Gypsy 2693 2799 1757
375 28.04 0.00 0.00 Crub_svsplocus 243876 243982 (406018) C Gypsy56-I_DR#LTR/Gypsy (1757) 2799 2693 m_b5s001i18
Crub_svsplocu 243876 TGGTCTATAAAGACCGTGAAATGGCGGCCATAAAGAAAGTCATGGAATTT 243925
i i i vi v vv v i i v v v
C Gypsy56-I_DR# 2799 TGATCTGTGAAGAGTGTGAATTTTCGTCCGTAGAGATACTGATGGAATTT 2750
Crub_svsplocu 243926 CTTTATGCCAGCCACTATGGCCAAAGCTTCCCTATCTATCTGCGCGTAAT 243975
ivv iv iv v v i i v vv v
C Gypsy56-I_DR# 2749 CCGAACTCCAAACACAATTGCCAGAGCCTCGCGCTCAATCTGCGCGTAAT 2700
Crub_svsplocu 243976 TGTGTTC 243982
v
C Gypsy56-I_DR# 2699 TCTGTTC 2693
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.47
Transitions / transversions = 0.58 (11/19)
Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.0 (0 / 0)
315 30.36 0.00 0.00 Crub_svsplocus 243903 244014 405986 C Gypsy-110_DR-I LTR/Gypsy 2381 2492 2071
315 30.36 0.00 0.00 Crub_svsplocus 243903 244014 (405986) C Gypsy-110_DR-I#LTR/Gypsy (2071) 2492 2381 m_b5s001i19
Crub_svsplocu 243903 CCATAAAGAAAGTCATGGAATTTCTTTATGCCAGCCACTATGGCCAAAGC 243952
v v v vi ii viv iv iiiv
C Gypsy-110_DR- 2492 CCATAAACATACTGGTGGAATTTTCTTAGAGCAAACACTATGGCCAGGAG 2443
Crub_svsplocu 243953 TTCCCTATCTATCTGCGCGTAATTGTGTTCATCAGATGATAGGGTCCTAG 244002
ii v v v v v v vv v ii v
C Gypsy-110_DR- 2442 TTCTTTTTCTATCTGAGCGTAATTCTTTTCAGCTGCAGATAGTGCTCTTG 2393
Crub_svsplocu 244003 AATAGTAGGCTA 244014
vvv v
C Gypsy-110_DR- 2392 ACGCGTATGCTA 2381
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.92
Transitions / transversions = 0.55 (12/22)
Gap_init rate = 0.00 (0 / 111), avg. gap size = 0.0 (0 / 0)
305 33.79 4.18 4.18 Crub_svsplocus 243918 244300 405700 C Gypsy158-I_DR LTR/Gypsy 2223 2605 1786
305 33.79 4.18 4.18 Crub_svsplocus 243918 244300 (405700) C Gypsy158-I_DR#LTR/Gypsy (1786) 2605 2223 m_b5s001i20
Crub_svsplocu 243918 TGGAATTTCTTTATGCCAGCCACTATGGCCAAAGCTTCCCTATCTATCTG 243967
iv iiv vv i v i i i v
C Gypsy158-I_DR 2605 TGGAATTTCTTTACCCCGAACAGGACGGCCAAACCCTCCTTATCCAACTG 2556
Crub_svsplocu 243968 CGCGTAATTGTGTTCATCAG-ATGATAGGGTCCTAGA-ATAGTAGGCTAC 244015
v v v vv v - v- iv vv - i i- vv i
C Gypsy158-I_DR 2555 CGAGTAATTCTTTTCTGCTGCATT-TAACGTCCGTGACACAA-ATCCTAT 2508
Crub_svsplocu 244016 AGGGACTTGTGTCCCATTAGCCTTCAAGTTTCTTAACACAGCCCCAATCC 244065
v vvi? vv i ivv v vv v?vvi v v i
C Gypsy158-I_DR 2507 TGGTCTNTCAGTCCCGTCTTCCATCCTGTGNGACAAAACAGCCCCTACCC 2458
Crub_svsplocu 244066 CATAAAAGGATGCATCACAGGCTATGCATACAGGCAATTGCT--CATTGA 244113
viiv v v i v - - iviv v --v i v
C Gypsy158-I_DR 2457 CATATGGCGAAGCATCACACGCCAAG-ATA-AGAGGTTTGGTAGGATCGT 2410
Crub_svsplocu 244114 AATGCGCTAGAACCGCATTTGA--AGATAGGAAGGCC--TTGACCTC-TG 244158
i i v vv v? --i --- vi -- i -i
C Gypsy158-I_DR 2409 AGTGCACTAGTAAAGCAGNTGACTGGA---GAAGCTCTTTTGACTTCGCG 2363
Crub_svsplocu 244159 CAAAACTCCTTTTGT---GGACTTTTGTCCATAGCCATGGAGCCTGTTTA 244205
v i i i ii i--- ii -----i iv ivvv ii vi v
C Gypsy158-I_DR 2362 AAAGATTCTTCCTGCTCAGAGC-----CCCATGTCCACTTTGTTTCCTTC 2318
Crub_svsplocu 244206 TCCAAGAGCCGGTGTAGCGGCTCAGCCACTG----CAGCCTTGTGAGGGA 244251
i v i v i iv iv viv ---- v ----i v
C Gypsy158-I_DR 2317 TTCAACAACCTGTGCAAGGGTGCCAACACTGTGGACAGACT----GGGCA 2272
Crub_svsplocu 244252 GGAATGAATGATAAAAGTTTAACAGTCCCAGAAAAACCTGGAGTTCACT 244300
i ivv v iv i v i vv
C Gypsy158-I_DR 2271 GAAACTTATGATAATAGTTTAACAAGCCTAGATAAGCCTTCAGTTCACT 2223
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.35
Transitions / transversions = 0.77 (54/70)
Gap_init rate = 0.06 (24 / 382), avg. gap size = 1.33 (32 / 24)
+ 1041 5.0 3.6 4.2 Crub_svsplocus 244864 245030 (404970) + CYRA11_Mm Satellite/Y-chromosome 155 320 (297) 156 *
ANNOTATION EVIDENCE:
1041 5.00 3.59 4.22 Crub_svsplocus 244864 245030 404970 + CYRA11_Mm Satellite/Y-chromosome 155 320 297
1041 5.00 3.59 4.22 Crub_svsplocus 244864 245030 (404970) CYRA11_Mm#Satellite/Y-chromosome 155 320 (297) m_b5s001i21
Crub_svsplocu 244864 TTTTGAAAATATCTAGAGCAGTGGTTCTCAACCTTCCTAATGCCATG-AC 244912
v i - i - iii -?
CYRA11_Mm#Sat 155 TTTTCAAAGT-TCCAGAG-AGTGGTTCTCAACCTTCCTAATGCTGCGGNC 202
Crub_svsplocu 244913 CCTTTA---ATACAGTTCCTCATGTTGTG--GTGACCCCCAACCATACAA 244957
--- -- -- v
CYRA11_Mm#Sat 203 CCTTTATANATACAGTTCCTCATGTTGTGTGGTG--CCCCAACCATAAAA 250
Crub_svsplocu 244958 TTATTTTCATTGCTACTTCATAACTATAATTTTGCTACTGTTATGAATCG 245007
-- i -
CYRA11_Mm#Sat 251 TTATTTT--TTGCTACTTCATAACTGTAATTTT-CTACTGTTATGAATCG 297
Crub_svsplocu 245008 TAATGTAAATATCTGATATGCAG 245030
CYRA11_Mm#Sat 298 TAATGTAAATATCTGATATGCAG 320
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.63
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.06 (10 / 166), avg. gap size = 1.30 (13 / 10)
+ 1285 5.2 0.0 0.0 Crub_svsplocus 244882 245035 (404965) C URR1A DNA/hAT-Charlie (0) 226 73 157
ANNOTATION EVIDENCE:
1285 5.19 0.00 0.00 Crub_svsplocus 244882 245035 404965 C URR1A DNA/hAT-Charlie 73 226 0
1285 5.19 0.00 0.00 Crub_svsplocus 244882 245035 (404965) C URR1A#DNA/hAT-Charlie (0) 226 73 m_b5s001i22
Crub_svsplocu 244882 CAGTGGTTCTCAACCTTCCTAATGCCATGACCCTTTAATACAGTTCCTCA 244931
iii
C URR1A#DNA/hAT 226 CAGTGGTTCTCAACCTTCCTAATGCTGCGACCCTTTAATACAGTTCCTCA 177
Crub_svsplocu 244932 TGTTGTGGTGACCCCCAACCATACAATTATTTTCATTGCTACTTCATAAC 244981
v i
C URR1A#DNA/hAT 176 TGTTGTGGTGACCCCCAACCATAAAATTATTTTCGTTGCTACTTCATAAC 127
Crub_svsplocu 244982 TATAATTTTGCTACTGTTATGAATCGTAATGTAAATATCTGATATGCAGG 245031
i
C URR1A#DNA/hAT 126 TGTAATTTTGCTACTGTTATGAATCGTAATGTAAATATCTGATATGCAGG 77
Crub_svsplocu 245032 GTGT 245035
i i
C URR1A#DNA/hAT 76 ATAT 73
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 4.17
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 153), avg. gap size = 0.0 (0 / 0)
+ 161 13.1 4.5 2.8 Crub_svsplocus 245143 245495 (404505) + GA-rich Low_complexity 1 359 (0) 158
ANNOTATION EVIDENCE:
161 13.07 4.53 2.79 Crub_svsplocus 245143 245495 404505 + (GGAA)n Simple_repeat 1 359 0
161 13.07 4.53 2.79 Crub_svsplocus 245143 245495 (404505) (GGAA)n#Simple_repeat 1 359 (0) m_b5s252i7
Crub_svsplocu 245143 GGAGGGAAGGAAGG-A-GAAGGAAGGAA-GATTGAAGG-GGAAAGGAAGG 245188
i - - - vv -i i
(GGAA)n#Simpl 1 GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG 50
Crub_svsplocu 245189 AGATGGA-GAAGGAAGGAGATTGAAGG--GGAAGGAAGGAAGGAAGGAAG 245235
- v i - - -v --
(GGAA)n#Simpl 51 A-AGGAAGGAAGGAAGGA-A-GGAAGGAAGGAAGGAAGGAAGGAAGGAAG 97
Crub_svsplocu 245236 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 245285
(GGAA)n#Simpl 98 GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA 147
Crub_svsplocu 245286 AGGAAGGAAGG-AGAGAGAAATTGAAGG-TGAAGGGAAGGAGATGGA-GA 245332
- ii i -v -v i i - v i -
(GGAA)n#Simpl 148 AGGAAGGAAGGAAGGAAGGAA-GGAAGGAAGGAAGGAAGGA-AGGAAGGA 195
Crub_svsplocu 245333 TGGAAGGAAGGAAGGAA-GATTGAAGGGGGGAA--AAGGAGATGGA-GAA 245378
v - vv ii -- - v i -
(GGAA)n#Simpl 196 AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA-AGGAAGGAA 244
Crub_svsplocu 245379 GGAAGGAGATTAAGGGGGAAAGGAAGGAAAGAAGGAAGGAAGGAAGCAAG 245428
- vv ii i i v
(GGAA)n#Simpl 245 GGAAGGA-AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG 293
Crub_svsplocu 245429 CAAGCAAGGAGAGATTGAAGG--GGAAGGGAAGGAGATGGATGGATGGAA 245476
v v ii vv -- - - - v v
(GGAA)n#Simpl 294 GAAGGAAGGAAGGAAGGAAGGAAGGAA-GGAAGGA-A-GGAAGGAAGGAA 340
Crub_svsplocu 245477 AGAAGGAAGGAAGGAAGGA 245495
i
(GGAA)n#Simpl 341 GGAAGGAAGGAAGGAAGGA 359
Matrix = Unknown
Transitions / transversions = 1.00 (20/20)
Gap_init rate = 0.07 (23 / 352), avg. gap size = 1.13 (26 / 23)
+ 682 9.9 2.2 0.0 Crub_svsplocus 246712 246802 (403198) C URR1B DNA/hAT-Charlie (132) 93 1 159
ANNOTATION EVIDENCE:
682 9.89 2.20 0.00 Crub_svsplocus 246712 246802 403198 C URR1B DNA/hAT-Charlie 1 93 132
682 9.89 2.20 0.00 Crub_svsplocus 246712 246802 (403198) C URR1B#DNA/hAT-Charlie (132) 93 1 m_b5s001i23
Crub_svsplocu 246712 AAATAT--GTGTTTTCCAATGGTCTTAGGCGACCCCTGTGAAAGCATTGT 246759
-- i vi i
C URR1B#DNA/hAT 93 AAATATCTGTGTTTTCCGATGGTCTTAGGCGACCCCTGTGAAAGGGTCGT 44
Crub_svsplocu 246760 TCGACCCCCAAAAGGGTTGTGACCCACAGGTTGACAACTGCTG 246802
i i i v i
C URR1B#DNA/hAT 43 TCGACCCCCAAAGGGGTCGCGACCCACAGGTTGAGAACCGCTG 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 5.13
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.01 (1 / 90), avg. gap size = 2.00 (2 / 1)
+ 43 2.5 0.0 0.0 Crub_svsplocus 251774 251814 (398186) + (AC)n Simple_repeat 1 41 (0) 160
ANNOTATION EVIDENCE:
43 2.50 0.00 0.00 Crub_svsplocus 251774 251814 398186 + (AC)n Simple_repeat 1 41 0
43 2.50 0.00 0.00 Crub_svsplocus 251774 251814 (398186) (AC)n#Simple_repeat 1 41 (0) c_b5s251i1
Crub_svsplocu 251774 ACACACACACACACACATACACACACACACACACACACACA 251814
i
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACA 41
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
+ 26 17.1 7.9 2.1 Crub_svsplocus 252724 252813 (397187) + (CTCTC)n Simple_repeat 1 95 (0) 161
ANNOTATION EVIDENCE:
15 13.07 11.90 0.00 Crub_svsplocus 252724 252765 397235 + (TC)n Simple_repeat 1 47 0
15 13.07 11.90 0.00 Crub_svsplocus 252724 252765 (397235) (TC)n#Simple_repeat 1 47 (0) m_b5s252i8
Crub_svsplocu 252724 TCTCTC-CTCAC-CTCAC-CTCTCTCTC-CCCTCCCCCTCTC-CTCT 252765
- v - v - - i i i -
(TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 47
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.12 (5 / 41), avg. gap size = 1.00 (5 / 5)
26 17.07 7.87 2.13 Crub_svsplocus 252725 252813 397187 + (CTCTC)n Simple_repeat 1 94 0
26 17.07 7.87 2.13 Crub_svsplocus 252725 252813 (397187) (CTCTC)n#Simple_repeat 1 94 (0) m_b5s252i9
Crub_svsplocu 252725 CTCTCCTCACCTCACCTCT-CTCTCCCCTCC-C-CCTCTCCTCTTACCAA 252771
v v - i - - ivi vv
(CTCTC)n#Simp 1 CTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTC 50
Crub_svsplocu 252772 C-CTACT-TCCTC-CCTACCCTTCCTCCTCCCCTCTCGTC-CCTCT 252813
- v - - - i i - i v -
(CTCTC)n#Simp 51 CTCTCCTCTCCTCTCCT-CTCCT-CTCCTCTCCTCTCCTCTCCTCT 94
Matrix = Unknown
Transitions / transversions = 0.86 (6/7)
Gap_init rate = 0.10 (9 / 88), avg. gap size = 1.00 (9 / 9)
+ 267 17.5 0.0 0.0 Crub_svsplocus 254563 254602 (395398) + AmnSINE2 SINE/tRNA-Deu 80 119 (239) 162
ANNOTATION EVIDENCE:
267 17.50 0.00 0.00 Crub_svsplocus 254563 254602 395398 + AmnSINE2 SINE/tRNA-Deu 80 119 239
267 17.50 0.00 0.00 Crub_svsplocus 254563 254602 (395398) AmnSINE2#SINE/tRNA-Deu 80 119 (239) m_b5s001i24
Crub_svsplocu 254563 CAAGGTTGACTCAGCCTTCCATCCTTTTGAGGTTGATAAA 254602
i i i i ii v
AmnSINE2#SINE 80 CAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAGATAAA 119
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.68
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 875 34.2 3.6 3.7 Crub_svsplocus 257779 258687 (391313) + Gypsy72-I_DR LTR/Gypsy 1413 2320 (2000) 163
ANNOTATION EVIDENCE:
636 34.68 4.40 4.52 Crub_svsplocus 257779 258687 391313 + Gypsy-194_DR-I LTR/Gypsy 1413 2320 2000
636 34.68 4.40 4.52 Crub_svsplocus 257779 258687 (391313) Gypsy-194_DR-I#LTR/Gypsy 1413 2320 (2000) m_b5s001i25
Crub_svsplocu 257779 CAGAAATACCAGAGGAATATAGAGACCTTGCTGAAGTCTTCAGTGAGGAG 257828
i v v i viv vi i iv ii v i
Gypsy-194_DR- 1413 CGGAAATTCCTGAAGAATATCACGACCTGACCGAAGCATTCAACGAGCAA 1462
Crub_svsplocu 257829 AGGGCGAATGAGCTTCCCCCCCACCAACCCACA-GACTGTACCATTGAAT 257877
i v vi i v v v i-ivvii - i v ii
Gypsy-194_DR- 1463 AAGGCCACCGAGTTACCACCGCACCG-TGAGTATGACTGTGCAATTGAGC 1511
Crub_svsplocu 257878 TCAAGCCTGGGGCAAAATTCCCGAAGCCCAGATTATACTCCATGAGCCCA 257927
ivv i ii i vvii ivi vvv v v - v v v
Gypsy-194_DR- 1512 TTTTGCCCGGAACGACCCCCCCACGGGGAAGAATATTC-CCTTTATCCCA 1560
Crub_svsplocu 257928 AAG-GAGAAGGAGGAAATGGAAAGATTTATAAAAAAAAAACCTAGAGAGA 257976
v- i vv iivv i viv vi vi ii ii ii - ii
Gypsy-194_DR- 1561 AACTGAAACCGAAACCATGAACGCATACATTGAGGAGGAACTCA-AGAAG 1609
Crub_svsplocu 257977 GGTTTCATTGAGGCAGCCAAGCCTAAAGTGGCTGCCCCAGTC-----CTT 258021
v i ?---- iv -- vi viviiv vi i -----
Gypsy-194_DR- 1610 GGATTTATN----CGTC--ATTCTACGTCACCTGCATCAGCCGGTTTCTT 1653
Crub_svsplocu 258022 TTTAG-AGAGAAGAAGGATGGCTCGTTACGTTTATGCGTGGATTATAGGG 258070
i v -i i ivvi iii ii v i iv
Gypsy-194_DR- 1654 CTTCGTGGAGAAGAAGGACGGTGGATTACGCCCATGTATCGACTACCGGG 1703
Crub_svsplocu 258071 CCCTGAATACAAT--CAGTGAAAGCAACCTATACCCTCTGCCCTTCATGA 258118
vv v i -- v iv-- vvi ii vi vv
Gypsy-194_DR- 1704 GGCTCAATGCAATTACAGTCAAGT--ACAGGTACCCTCTGCCTCTAGTCC 1751
Crub_svsplocu 258119 AAGACATGCTGTCACACCTAT--CGAAAGGGAAAATTTTTT-CTAAACTA 258165
vi - - v - v v ? -- v vv vv vi - i v
Gypsy-194_DR- 1752 CGG-CA-GCTCT-AGAACNATTACGCACTGCCAAATACTTTACTAAGCTC 1798
Crub_svsplocu 258166 GACCTAAGGGAAGCTTACTATCGCGTGAGAATTAAGGAAGGGGACGAATG 258215
i vv viiv v ivvi v v i i vv i i
Gypsy-194_DR- 1799 GATCTCCGTAGTGCTTACAATTTGATTAGAATAAAGAAGGGCCATGAGTG 1848
Crub_svsplocu 258216 GAAGACTGCATT------TAACTGCCCCATGGGGTGCTATCAATTCAAAG 258259
i ? i ------ iiv ------ vii v v vvi
Gypsy-194_DR- 1849 GAAAACNGCGTTCTCTACTAGTAGC------GGCCACTATGAATACTTGG 1892
Crub_svsplocu 258260 TCTTGCCATTTGGATTA-CAAGGGGGCCCTGCAGTCTTT-ATGCAATTAA 258307
v v i i - ivi v - v v i- v v -
Gypsy-194_DR- 1893 TCATGCCCTTCGGACTAGCAAACAGTCCCT-CTGTGTTCCAAGCATTTA- 1940
Crub_svsplocu 258308 TCAATGACGT--TCTAAGGGAGCACCTGTTTAAG-G--GGGTCCTTGTTT 258352
i -- ii ----- v i v- -- v i
Gypsy-194_DR- 1941 TTAATGACGTCTTCCGAG-----ACATGCTTAATCGCTGGGTCATTGTCT 1985
Crub_svsplocu 258353 ACTTGGACGACATTCTTATCTTTACTGAAACAAAAGAGGAACACGTCAAC 258402
v v i i v v v v vvv i i iii
Gypsy-194_DR- 1986 ACATCGATGACATCCTGATCTATTCTGAATCCCTAGAAGAACACATCGGT 2035
Crub_svsplocu 258403 CTTGTCAGAGCGGT--TTTAAAGAAGCTGCGAGCCGCCCACC---TATAT 258447
vi v i i -- i v ----- v ii vv ---
Gypsy-194_DR- 2036 CACGTAAGGGCAGTGCTTCAACGA-----CTAATCGAACACCGATTATAT 2080
Crub_svsplocu 258448 ACCAAACTCTCAAAATGCGAATTCCACCAGGAAAGGATAGACTACCTAGG 258497
i v vvvi i i iiv vvv vvv v i
Gypsy-194_DR- 2081 GCAAAACTAGAGAAGTGTGAATTCCACCAAACATCCATCTCCTTCCTGGG 2130
Crub_svsplocu 258498 CTATTGCA-TATCCCCAC--AGGGCATTGAAATGGACCCAGAGAAGGTCA 258544
v --- - ivv -- i v vv ivviv vv
Gypsy-194_DR- 2131 ATA---CATTATTGGCACTGAGGGCGTGGCCATGGATGAGCAGAAGGTGC 2177
Crub_svsplocu 258545 AAGCAGTATTAGATTGGGCGCCACCCCGCACAAGAAAGCAACTACAAAGT 258594
i v v vvv v v v vv iv i v v
Gypsy-194_DR- 2178 AAGCAGTATTAAAATGGCCCAAACCCAGAACCATTAAAGAGCTCCAAAGA 2227
Crub_svsplocu 258595 TTCCTGGGCTTTGCAAACTTTTACCGCCAATTCATCC----CCTCA-TTT 258639
i v i i i iv v iv i ---- i -
Gypsy-194_DR- 2228 TTTCTTGGCTTCGCAAATTTCTATAGACGTTTCATTCGAAACTTCAGTTT 2277
Crub_svsplocu 258640 GCCCAGATAGCCTTGCCCCTCACTAACTT-ACTAAAAACGAAGGGAGCA 258687
----- i v i iv v i ii - i i ii- i v
Gypsy-194_DR- 2278 -----GGTTGCTTCCCCACTCACCAGTTTGACCAGAGG-GAAAGGATCA 2320
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.07
Transitions / transversions = 0.92 (144/157)
Gap_init rate = 0.07 (61 / 908), avg. gap size = 1.33 (81 / 61)
875 34.01 3.26 3.26 Crub_svsplocus 258017 258630 391370 + Gypsy72-I_DR LTR/Gypsy 1681 2294 2003
875 34.01 3.26 3.26 Crub_svsplocus 258017 258630 (391370) Gypsy72-I_DR#LTR/Gypsy 1681 2294 (2003) m_b5s001i26
Crub_svsplocu 258017 TCCTTTTTAGAGAGAAGAAGGATGGCTCGTTACGTTTATGCGTGGATTAT 258066
i i ivii i i vi i iiiv i i i
Gypsy72-I_DR# 1681 TCTTCTTTGTGAAGAAAAAGGATGGTTCTCTGCGCCCCTGCATAGACTAT 1730
Crub_svsplocu 258067 AGGGCCCTGAAT---ACAATCAGTGAAAGCAACCTATACCCTCTGCCCTT 258113
v i vii --- i i v i --- i vi i i vi
Gypsy72-I_DR# 1731 CGAGGTTTGAATGACATAACCATTAAAA---ATCGGTACCCCCTACCGCT 1777
Crub_svsplocu 258114 CATGAAAGACAT--GCTGTCACACCTATCGAAAGGG--AAAATTTTTTCT 258159
i v---- v -- iv i- i v i v i -- i ivi
Gypsy72-I_DR# 1778 TATGT----CTTCGGCCTTCG-ATCTCTTGCAGGGGGCAAGATTTTTCAC 1822
Crub_svsplocu 258160 AAA-CTAGACCTAAGGGAAGCTTACTATCGCGTGAGAATTAAGGAAGGGG 258208
-i i v vi v i v vv v v i i v
Gypsy72-I_DR# 1823 AAAGTTGGACCTACGCAATGCTTACCATCTCGTCCGTATGAGGGAGGGTG 1872
Crub_svsplocu 258209 ACGAATGGAAGACTGCATTTAACTGCCCCATGGGGTGCTATCAATTCAAA 258258
i i vvv iv iii v v vivvv
Gypsy72-I_DR# 1873 ACGAATGGAAGACCGCATTCAACACGCCCACTGGGCATTTTGAATATCTT 1922
Crub_svsplocu 258259 GTCTTGCCATTTGGATTACAAGGGGGC-CCTGCAGTCTTT-ATGCAATTA 258306
i ii - vviiv - v - v - i v
Gypsy72-I_DR# 1923 GTCCTGCCATTTGGGCT-CACCAATGCTCCAGCAGTCTTTCAGGC-ACTC 1970
Crub_svsplocu 258307 ATCAATGACGTTCTAAGGGAGCACCTGTTTAAGGGG---GTCCTTGTTTA 258353
i i i v vv i --- v v vvii--- ii
Gypsy72-I_DR# 1971 GTCAACGATGTACTCCGAG---ACATGATTAATCAATTTGTTTTTGTTTA 2017
Crub_svsplocu 258354 CTTGGACGACATTCTTATCTTTACTGAAACAAAAGAGGAACACGTCAACC 258403
i i i v vvvi v viv i v v
Gypsy72-I_DR# 2018 TTTGGATGACATTCTTATTTTTTCTTCCGCCATGCAGGAACATGTCCAAC 2067
Crub_svsplocu 258404 TTGTCAGAGCG-GTTTTAAAGAAGCTGCGAGCCGCCCACCTATATACCAA 258452
vi iv - - vi v ivi vi vvivi v i iiv
Gypsy72-I_DR# 2068 ACGTTCG-GCGAGTGCTACAACGGCTGCTGGAGAATCAGCTGTATGTAAA 2116
Crub_svsplocu 258453 ACTCTCAAAATGCGAATTCCA---CCAGGAAAGGATAGACTACCTAGGCT 258499
ivivvvi i --- vv ---i vvv v i i vi
Gypsy72-I_DR# 2117 GGCGGAGAAGTGCGAATTCCATGTCCAGTCA---GTTTCCTTCTTGGGAC 2163
Crub_svsplocu 258500 ATTGCATATCCCCA---CAGGGCATTGAAATGGACCCAGAGAAGGTCAAA 258546
--- viii ---v vv viv v v i ii
Gypsy72-I_DR# 2164 A---CATAATTTCAGTTGAGGGACTTCGCATGGACCCTGCGAAGGTTAGG 2210
Crub_svsplocu 258547 GCAGTATTAGATTGGGCGCCACCCCGCACAAGAAAGCAACTACAAAGTTT 258596
v v iv i v vi v vv vvii iv v
Gypsy72-I_DR# 2211 GCTGTCTCCGACTGGCCGCCACCCGACTCCCGAAAGGCGTTACAGCGGTT 2260
Crub_svsplocu 258597 CCTGGGCTTTGCAAACTTTTACCGCCAATTCATC 258630
i v i v i
Gypsy72-I_DR# 2261 CCTGGGCTTCGCCAATTTTTACCGGCGATTCATC 2294
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.56
Transitions / transversions = 1.04 (103/99)
Gap_init rate = 0.05 (30 / 613), avg. gap size = 1.33 (40 / 30)
+ 348 29.9 3.3 3.4 Crub_svsplocus 258718 259119 (390881) + Gypsy-115-I_DR LTR/Gypsy 2605 2742 (1540) 164
ANNOTATION EVIDENCE:
323 29.60 1.94 1.94 Crub_svsplocus 258718 258872 391128 + Gypsy39-I_DR LTR/Gypsy 4471 4625 424
323 29.60 1.94 1.94 Crub_svsplocus 258718 258872 (391128) Gypsy39-I_DR#LTR/Gypsy 4471 4625 (424) m_b5s001i27
Crub_svsplocu 258718 TGGACAATGGAGTGCCAAGCA-GCGTTTGAGAG-ACTAAATAGACTTTTT 258765
v vi? i - - v i - i -iv i v
Gypsy39-I_DR# 4471 TGGTCATCNGAATGCCA-GCATGCCTTTGAAAGTATTAAA-GCACTTCTG 4518
Crub_svsplocu 258766 TCTGCCGAACCAGTACTAA-GGCACCCAGACATGGACAAGCCCTTCGTAA 258814
v vv vv ii - -i i iv v v i iiv
Gypsy39-I_DR# 4519 TGTGAAGCTCCAGTGTTAATGGC-TCCAAATTTCGAAAAGCCTTTTAAAA 4567
Crub_svsplocu 258815 TACAGGCAGATGCAAGTGATGTGGCAGTGGGGGCTGTGCTATTACAAGAA 258864
iv i v i v iv v v ii i i
Gypsy39-I_DR# 4568 TGGAGGTAGATGCAAGTGCTGTAGGAGCTGGCGCTGTCCTGCTGCAGGAA 4617
Crub_svsplocu 258865 AATGATGA 258872
i i v
Gypsy39-I_DR# 4618 GATAAGGA 4625
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.68
Transitions / transversions = 1.14 (24/21)
Gap_init rate = 0.04 (6 / 154), avg. gap size = 1.00 (6 / 6)
286 31.10 5.79 5.24 Crub_svsplocus 258740 259119 390881 + Gypsy69-I_DR LTR/Gypsy 2304 2685 1560
286 31.10 5.79 5.24 Crub_svsplocus 258740 259119 (390881) Gypsy69-I_DR#LTR/Gypsy 2304 2685 (1560) m_b5s001i28
Crub_svsplocu 258740 CGTTTGAGAGACTAAATAGACT--TTTTTCTGCCGAACCAGTACTAAGGC 258787
i v -- i--i iv ii ? v vi v i ii
Gypsy69-I_DR# 2304 CGTTTGAGAAACTTAA--GACCAGCTTCACCACNGCACCCATTCTGAAAC 2351
Crub_svsplocu 258788 ACCCAGACATGGACAAGCCCTTCGTAATACAGGCAGATGCAAGTGA-TGT 258836
v vi? vvvi vi ?v i ii ?vv? - i
Gypsy69-I_DR# 2352 ACCCCGACCCNGAGCTACCCTTCGTTGTNGAAGTGGATGCNTCNGACTAT 2401
Crub_svsplocu 258837 GGCAGTGGGGGCTGTGCTATTACAAGAAAATGATGATGCAGT---ATTGC 258883
v - v ? i i vi?v i i i iv v--- i v
Gypsy69-I_DR# 2402 GGCATTGGGG-CAGTNCTGTCACAACGNCACGGTAACCCAGGTAAACTCC 2450
Crub_svsplocu 258884 AACCCTGTGCATATACATCCAAGAAACTCACGGAAAC----AGAA-CAGT 258928
v ? v ? viv iviv v v i ---- - vi
Gypsy69-I_DR# 2451 ACCCNTGTGCTTNTTTTTCTCGCAAACTGACGGCAGCTGAAAGAAACTAT 2500
Crub_svsplocu 258929 G--GTGGCCCGTATGGGAGAAGGAG--GCTT---ATGGGATACGTTGGGC 258971
-- --- ---- v i--i --- i--- v i--
Gypsy69-I_DR# 2501 GACGTGG---GTA----ACAAGGAACTACTTTCNATGA---AGGC--GGC 2538
Crub_svsplocu 258972 ATTACTCACGTGGCGACAGTTCCTGGAAGGCAACAAAATCC---CCTTCC 259018
i ivvvivi ? v vv ? i viv i--- --- ?
Gypsy69-I_DR# 2539 ACTGGAAGAATGGCGNCACTGGCTNGAGGGAGCCG---TCCATCCNTTCC 2585
Crub_svsplocu 259019 AGGTGTGGACTGATCACAAAAACTTAGAAGCCCTGAAAACTTCCAGGAAA 259068
i vvvv v i i ? ivviv v v v v ivi
Gypsy69-I_DR# 2586 AGATTATCACAGACCACAAAAACCTNGAGTATATCAAAAGTGCCCGACGA 2635
Crub_svsplocu 259069 CTCAATCCCAAACAAGCCCGCTGGTCCCAGCATT-TTCACCAGTTCCAAT 259117
v i i i i ? ii--i - v ? i
Gypsy69-I_DR# 2636 CTAAACCCCAGACAGGCTCGNTGGTCTT--TATTCTTCACCCGNTTCAAT 2683
Crub_svsplocu 259118 TT 259119
Gypsy69-I_DR# 2684 TT 2685
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.22
Transitions / transversions = 1.00 (56/56)
Gap_init rate = 0.08 (30 / 379), avg. gap size = 1.40 (42 / 30)
348 28.68 1.44 2.17 Crub_svsplocus 258981 259119 390881 + Gypsy105-I_Dr LTR/Gypsy 2605 2742 1540
348 28.68 1.44 2.17 Crub_svsplocus 258981 259119 (390881) Gypsy105-I_Dr#LTR/Gypsy 2605 2742 (1540) m_b5s001i29
Crub_svsplocu 258981 GTGGCGACAGTTCCTGGAAGGCAACAAAATCCCCTTCCA-GGTGTGGACT 259029
v v vv i i- i iivv iii- v v
Gypsy105-I_Dr 2605 GTGGCGCCATTGGCTGGAGGGCG-CAGAGCAGCCTTTTGTGGTCTGGACA 2653
Crub_svsplocu 259030 GATCACAAAAACTTAGAAGCCCTGAAAACTTCCAGGAAACTCAATCCCAA 259079
i i i v vv v i vv v ii ii v v i
Gypsy105-I_Dr 2654 GACCACAGAAACCTTGAATACATAAACTCTGCCAAAAGGCTCAATGCAAG 2703
Crub_svsplocu 259080 ACAAGCCCGCTGGTCCCAGCATTTTCA-CCAGTTCCAATTT 259119
i -v v i - i -
Gypsy105-I_Dr 2704 ACAAGCCCGCTGGTCTC-TCTTCTTCAGCCGGTT-CAATTT 2742
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.35
Transitions / transversions = 1.05 (20/19)
Gap_init rate = 0.04 (5 / 138), avg. gap size = 1.00 (5 / 5)
+ 231 26.4 0.0 0.0 Crub_svsplocus 259454 259506 (390494) + Gypsy-115-I_DR LTR/Gypsy 3076 3128 (1190) 164
ANNOTATION EVIDENCE:
231 26.42 0.00 0.00 Crub_svsplocus 259454 259506 390494 + Gypsy97-I_DR LTR/Gypsy 3076 3128 1190
231 26.42 0.00 0.00 Crub_svsplocus 259454 259506 (390494) Gypsy97-I_DR#LTR/Gypsy 3076 3128 (1190) m_b5s001i30
Crub_svsplocu 259454 ACTTTACATTTAATTAAACGGCAATTTTGGTGGCCATCCATGAAAAAGGA 259503
v iv ii i i i v i iv vi
Gypsy97-I_DR# 3076 ACATTATTTTTGGTTAAACAGCGATTCTGGTGGCCAGCTATGGCACGGGA 3125
Crub_svsplocu 259504 CAT 259506
Gypsy97-I_DR# 3126 CAT 3128
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.02
Transitions / transversions = 1.80 (9/5)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 353 32.7 2.5 2.5 Crub_svsplocus 259651 259905 (390095) + Gypsy-115-I_DR LTR/Gypsy 3276 3534 (790) 164
ANNOTATION EVIDENCE:
332 35.74 2.35 2.35 Crub_svsplocus 259651 259905 390095 + Gypsy-193_DR-I LTR/Gypsy 3280 3534 790
332 35.74 2.35 2.35 Crub_svsplocus 259651 259905 (390095) Gypsy-193_DR-I#LTR/Gypsy 3280 3534 (790) m_b5s001i32
Crub_svsplocu 259651 CAATGGGAATACTGTGGTCTGGACAGTCACGGACTTGTTTTCCAAACAGG 259700
i v i v i i vi v vii iv i v ivvv
Gypsy-193_DR- 3280 CAACGGCAACACGGTGATTTTAACCGTAGTGGACCGGTTCTCGAAGGCTG 3329
Crub_svsplocu 259701 TGCACTTTATCCCT-TGCCAAAAGATTCCCA-CTGCAAAAGCCTTAGCAA 259748
iv i ii - v -- v i- v v i vvvi ii
Gypsy-193_DR- 3330 CTCATTTCGTCCCTCTGCCCAAA--TTACCGTCAGCCAGAGAGACAGCGG 3377
Crub_svsplocu 259749 AACTTTTCATCCAACACAT-TTACAGATTGCATGGGGCACCCCAACG--C 259795
vvvi v iv v i - v iv - -- vi i --
Gypsy-193_DR- 3378 TTGCTGTCATTAATCACGTCTTTCGCATT-CATGG--CCTCCCGACGGAC 3424
Crub_svsplocu 259796 ATCATCTCTGACAGGGGGGTGCAATTTACGTCTGCATTTTGGAAGGAATT 259845
i vi i viv i iv iv i -
Gypsy-193_DR- 3425 GTGGTTTCTGACAGGGGGCCTCAGTTTATCTCTAAATTTTGGAGGGAA-T 3473
Crub_svsplocu 259846 TTTATC-CTTCTTAGGAACCACTCAGGGACTGACATCTAGCCACCACCCT 259894
i i -i v i ii vv i v vv i i ivi i i
Gypsy-193_DR- 3474 TCTGTCGTTTATTGGGGGCCACTGTGAGTCTTTCGTCTGGCTTTCATCCC 3523
Crub_svsplocu 259895 CAAGGAAATGG 259905
ii v i
Gypsy-193_DR- 3524 CAGAGTAACGG 3534
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.80
Transitions / transversions = 1.23 (49/40)
Gap_init rate = 0.04 (11 / 254), avg. gap size = 1.09 (12 / 11)
353 31.77 2.54 2.54 Crub_svsplocus 259651 259847 390153 + Gypsy-115-I_DR LTR/Gypsy 3276 3472 849
353 31.77 2.54 2.54 Crub_svsplocus 259651 259847 (390153) Gypsy-115-I_DR#LTR/Gypsy 3276 3472 (849) m_b5s001i31
Crub_svsplocu 259651 CAATGGGAATACTGTGGTCTGGACAGTCACGGACTTGTTTTCCAAACAGG 259700
i v i i v v vii iv v vvvi
Gypsy-115-I_D 3276 CAACGGGAATACGGTGATTTTGACCGTAGTGGACCGGTTTTCGAAAGCCA 3325
Crub_svsplocu 259701 TGCACTTTATCCCT-TGCCAAAAGATTCCCA-CTGCAAAAGCCTTAGCAA 259748
iv - v -- v - v v i vvvi ii
Gypsy-115-I_D 3326 CTCACTTTATCCCTCTGCCCAA--ATTACCATCAGCCAGAGAGACAGCGG 3373
Crub_svsplocu 259749 AACTTTTCATCCAACACAT-TTACAGATTGCATGGGGCACCCCAACGCA- 259796
vvvi v iv v ii - v iv - -- vi i v -
Gypsy-115-I_D 3374 CTGCTGTCATTGACCATGTCTTTCGTATT-CAT--GGCCTCCCGACGGAT 3420
Crub_svsplocu 259797 -TCATCTCTGACAGGGGGGTGCAATTTACGTCTGCATTTTGGAAGGAATT 259845
- vi i viv i i iv iv ii i
Gypsy-115-I_D 3421 GTGGTTTCTGACAGGGGGCCTCAGTTCATCTCTAAATTTTGGAGAGAGTT 3470
Crub_svsplocu 259846 TT 259847
Gypsy-115-I_D 3471 TT 3472
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.53
Transitions / transversions = 0.91 (29/32)
Gap_init rate = 0.05 (10 / 196), avg. gap size = 1.00 (10 / 10)
+ 17 9.7 2.9 2.9 Crub_svsplocus 262741 262775 (387225) + (CCTC)n Simple_repeat 1 35 (0) 165
ANNOTATION EVIDENCE:
17 9.67 2.86 2.86 Crub_svsplocus 262741 262775 387225 + (CCTC)n Simple_repeat 1 35 0
17 9.67 2.86 2.86 Crub_svsplocus 262741 262775 (387225) (CCTC)n#Simple_repeat 1 35 (0) m_b5s252i10
Crub_svsplocu 262741 CCT-CCTCCACCCCCTCCCGACCTCCCTCCCTCCCT 262775
- - i vv
(CCTC)n#Simpl 1 CCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCTCCCT 35
Matrix = Unknown
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2)
+ 17 11.2 0.0 0.0 Crub_svsplocus 268262 268291 (381709) + (CACA)n Simple_repeat 1 30 (0) 166
ANNOTATION EVIDENCE:
17 11.16 0.00 0.00 Crub_svsplocus 268262 268291 381709 + (CACA)n Simple_repeat 1 30 0
17 11.16 0.00 0.00 Crub_svsplocus 268262 268291 (381709) (CACA)n#Simple_repeat 1 30 (0) m_b5s252i11
Crub_svsplocu 268262 CACATACATACACACACACACACATACACA 268291
i i i
(CACA)n#Simpl 1 CACACACACACACACACACACACACACACA 30
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 267 17.5 0.0 0.0 Crub_svsplocus 270635 270674 (379326) + AmnSINE2 SINE/tRNA-Deu 80 119 (239) 167
ANNOTATION EVIDENCE:
267 17.50 0.00 0.00 Crub_svsplocus 270635 270674 379326 + AmnSINE2 SINE/tRNA-Deu 80 119 239
267 17.50 0.00 0.00 Crub_svsplocus 270635 270674 (379326) AmnSINE2#SINE/tRNA-Deu 80 119 (239) m_b5s001i33
Crub_svsplocu 270635 CAAGGTTGACTCAGCCTTCCATCCTTTTGAGGTTGATAAA 270674
i i i i ii v
AmnSINE2#SINE 80 CAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAGATAAA 119
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.68
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 540 32.8 2.7 2.5 Crub_svsplocus 277939 278494 (371506) C MamGypsy2-I LTR/Gypsy (630) 3536 3020 168
ANNOTATION EVIDENCE:
540 33.93 3.10 2.90 Crub_svsplocus 277939 278454 371546 C MamGypsy2-I LTR/Gypsy 3020 3536 630
540 33.93 3.10 2.90 Crub_svsplocus 277939 278454 (371546) C MamGypsy2-I#LTR/Gypsy (630) 3536 3020 m_b6s001i1
Crub_svsplocu 277939 ATCCTCTTGAGAGCATCTTTGGTTGTGCATACCATACACTCAGCTTGTCC 277988
v v i i i v viii v vi i v
C MamGypsy2-I#L 3536 ATCCGCTTCAGGGCATCCTTAGTAGTCTGCACCATCCTTTCAGCCTGACC 3487
Crub_svsplocu 277989 ATTGGACGCAAGATGAAAAGGTGCTGACG-TGGCATGATGGATCAG-TTG 278036
v vivv i i vi i - i - i vvvi v - -
C MamGypsy2-I#L 3486 ATTTGCTTGAGGGTGATGAGGCGC-GATGGTGACAGCTCGGATAAGGTT- 3439
Crub_svsplocu 278037 GCCGGT--AGAAAAGCCTGAAACTCACAAGAAGTGAATTGGGATCTGTTG 278084
- v -- v vv v vvv i i vvi i ii
C MamGypsy2-I#L 3438 -CCTGTCCACAAATTCCTTAAACTCAACTGAGGTAAATGCAGACCCATTG 3390
Crub_svsplocu 278085 TCAGAGACAAGGACATCTGGAAGTCCATGAGAAGTGAAGATTCCT--CTC 278132
i i viiii v i i v --v v i vv -- v
C MamGypsy2-I#L 3389 TCAGAAACGATAGTGTCTGGCAATCCGTGTG--TTGCAAATAACTGGCGC 3342
Crub_svsplocu 278133 AACACCTG-GATGGTCCTGGCAGTGGTA-GAGAAGGAGACAGGAACAACC 278180
i- v - v ivii v v- v ivi i - i
C MamGypsy2-I#L 3341 AG-AGCTGTGATTGTTGCAGCAGAGGTTTGAGATGGAACTAGGAGCA-CT 3294
Crub_svsplocu 278181 TCTAGCCACTTGGAATGGCTGTCCGCAAGAAGAAGGAAGAATTGCCCCTG 278230
v i v ivi vv ii v v vv i vvi v
C MamGypsy2-I#L 3293 TCGAGCCATTTTGAGAAGGAGTCTACCACAATCAAGAAGTTCTTCCCCTG 3244
Crub_svsplocu 278231 AAAGGGCCCAGCGTAGTCGATATGAACCCTTGACCAAGGGGCTTGT--GT 278278
i v i v iv i i i ii -- v --
C MamGypsy2-I#L 3243 GAATGGTCCTGCAAAATCAATATGGATTCTTGACCAAGG--CTTCTTGGT 3196
Crub_svsplocu 278279 CTCCTCCCACCTATGTACAGGAGCTTGAGGCAT-TTCTG--GACTAGACT 278325
v i i ivv vivii v i vv iv- v -- v - -
C MamGypsy2-I#L 3195 CACTTTCCATGGAAAAGTAGGTGCCTTTGGCGGGTTATGCCGAGTAG-C- 3148
Crub_svsplocu 278326 GCTGGCAAACACTACACTCATGGACCTGGGCCT---CGATCTCTTTATCG 278372
- viii v vv ---i i --- i v vvv i
C MamGypsy2-I#L 3147 -CTGGCATGTGCTACACTCCTTTAC---AGTCTTTTCAATATCAGAATCA 3102
Crub_svsplocu 278373 AGCCCAGGCCACCAAAGATGGCTGTGTGCAAACACCTTCATCCGGACTAT 278422
vi i v i vivv v ii i v i v
C MamGypsy2-I#L 3101 ATTCCAGGCCACCAGACATAGCTTCTAGCCAATGCTTTCATGCGAACAAT 3052
Crub_svsplocu 278423 TCCTGGATGTCCCTCATGCAGAGAGAACAAGA 278454
i v iv i v v iv
C MamGypsy2-I#L 3051 TCCCGGATGTGCTGCATGTAGTGTGGCCAAGA 3020
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.62
Transitions / transversions = 0.91 (81/89)
Gap_init rate = 0.05 (25 / 515), avg. gap size = 1.24 (31 / 25)
347 25.33 0.00 0.00 Crub_svsplocus 278420 278494 371506 C Gypsy-176_DR-I LTR/Gypsy 2237 2311 1364
347 25.33 0.00 0.00 Crub_svsplocus 278420 278494 (371506) C Gypsy-176_DR-I#LTR/Gypsy (1364) 2311 2237 m_b6s001i2
Crub_svsplocu 278420 TATTCCTGGATGTCCCTCATGCAGAGAGAACAAGACTCTAGTCCTCAATG 278469
ii v ivvv i i ivii i v i
C Gypsy-176_DR- 2311 TATTCCCAGATGGCCCTCATGCAACTTGGACAGGATGTCAGCCCTGAGTG 2262
Crub_svsplocu 278470 AGGCTGGGATGACTATCCTGCTGCC 278494
vi i
C Gypsy-176_DR- 2261 ACACTGGGATGACTATTCTGCTGCC 2237
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.83
Transitions / transversions = 1.71 (12/7)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 1879 35.3 2.1 2.0 Crub_svsplocus 278863 280165 (369835) C MamGypsy2-I LTR/Gypsy (1433) 2733 1429 169
ANNOTATION EVIDENCE:
1879 35.31 2.15 1.99 Crub_svsplocus 278863 280165 369835 C MamGypsy2-I LTR/Gypsy 1429 2733 1433
1879 35.31 2.15 1.99 Crub_svsplocus 278863 280165 (369835) C MamGypsy2-I#LTR/Gypsy (1433) 2733 1429 m_b6s001i3
Crub_svsplocu 278863 GCTGAGGCCATCTGCATG-GCCATTTCTTTGCCTGGTTTGTGAACCAGTG 278911
v v v v- vi v i v v i ii v i
C MamGypsy2-I#L 2733 GCTCAGGGCATCAGCATTCGATATTGCTCTTCCAGGCTTGTAGACAAGCG 2684
Crub_svsplocu 278912 TGTAGTCATATACAGACAGGAAAATAGACCATCTCAGCATTCTAGGAGAG 278961
i vi vvv v v vv v v v v vv v v
C MamGypsy2-I#L 2683 CGTAGTCATAAGCACTGAGCAAAAGACTCCAGCGCTGCATACGTGGTGAC 2634
Crub_svsplocu 278962 ATGATGTGTGGG-GTTTGCTTATTGGTTTGAACAA---CCCCAACAGTGG 279007
i - iv - vv iv- v v i--- - v
C MamGypsy2-I#L 2633 ATAAT-TAAGGGCGTAGGCTTATCC-TTAGAAAAGAGTCCCCAA-AGAGG 2587
Crub_svsplocu 279008 CTTATGGTCTGTAAAGAACATGAAATGGGGGCCATAAAGAAAGTCATGGA 279057
i i v v i vii i ivviv i i iv ii
C MamGypsy2-I#L 2586 CTTGTGATCAGTACAAATTGTAAAGGCACGGCCGTAGAGGTAGTTGTGGA 2537
Crub_svsplocu 279058 ATTTCTTTATGCCAGCCACTATGGCCAAGGTTTCCCTATCTATCTGTGCG 279107
i v iv v v iv ii v i i ii i v i ii
C MamGypsy2-I#L 2536 ACTTCTTGACTCCCGCGATAACAGCAAGGGCTTCTTTGTCAATTTGTGTA 2487
Crub_svsplocu 279108 TAATTACGTTCAGCAAATGATAGAACAGTCCTAGAATAGTAGGCTATAGG 279157
i v v i i i ---iv i v i i v v
C MamGypsy2-I#L 2486 TAGTTCCGTTCTGTAGATGACA---TTGTTCTTGAGTAGTAAGCAATTGG 2440
Crub_svsplocu 279158 GACTTGTGTCCCATCAGCCTTCAAGTGGCTCAACTCAGCCCCAATCCTAT 279207
vi i vv v v v v ivv v i v i iiv ii
C MamGypsy2-I#L 2439 TGCCTCAGTGCCATCTGGCATTTTGTGGCTAAGCACAGCTCCAGCACCGT 2390
Crub_svsplocu 279208 AAGGGGATGCATCACAGGCTATGCATACAGGCAATT--GCTCATTGAAAT 279255
v v i vv - v v - vviv -- i i v
C MamGypsy2-I#L 2389 AAGGTGAAGCGTCAGTGG-TAAGAA-ACAGTGGTTTATGTTCATCGTAAT 2342
Crub_svsplocu 279256 GCACTAGAACTGCATTTGAAGATAGGAAGGCCTTGAC-CTCTGCAAAAC- 279303
i v v vv iv vi iv vvv -i i v i -
C MamGypsy2-I#L 2341 GTACTAGCACAGACTCGGAAGTCAATAACTGCTTGACATTCCGGAAAGCG 2292
Crub_svsplocu 279304 TCCTTTTGTGGACCTTTGTCCACAGCCATGGAGCCTGTTTATCCAAGAGC 279353
iv iv i vv-- vv i i viv vi iv v
C MamGypsy2-I#L 2291 TCCTCATGCTGGCGA--GTCCAACGCCACGGAACGCCTTTTCCCAGTAGG 2244
Crub_svsplocu 279354 CAGTGTAACAGCTCAGCCACTGCAGCCTTGTGAGGGAAAAATGAATGGTA 279403
ii v iii v iv iv v v i i viv
C MamGypsy2-I#L 2243 CGATGAAGTGGCTCAGCAATGGTTGCCTTTTGTGGAAGAAAAACATGGTA 2194
Crub_svsplocu 279404 AAAGTTTAACAGTCCCAGAAAAGCCTGGAGTTC--ACTTTTGGACGTGGG 279451
i i v ii i i i i i i --i -- viv v
C MamGypsy2-I#L 2193 GAAATTGAGTAGCCCCAGGAAGGCTTGAAGCTCTTGCTTT--GTTTTTGG 2146
Crub_svsplocu 279452 ACTTGGGGCCTGCGGAATTGCTTTAAGCTTAGATTCAGCAGGGTGCATGC 279501
v v v v vvv i vivv v vv v ii v i
C MamGypsy2-I#L 2145 AGTAGGCGCGTCATGGATTGCACGTACCTTATCTTGAGTGGGGTGAATAC 2096
Crub_svsplocu 279502 CTTCAGCATCAATACGGAATCCCA-GAAATT--CTGTGGAAATGACTCCG 279548
vv ii i v v i - iv -- vv i ---
C MamGypsy2-I#L 2095 CAGCAGCATTGATGCGGTAGCCTAAGAAGGTGACACTGGAAGT---TCCG 2049
Crub_svsplocu 279549 ATTTTACATTTATCTTGCTTTAGTTTTAGCCCCACTTGGCG----GAAAT 279594
i v i vi i v ivv ----i i ii ---- i
C MamGypsy2-I#L 2048 ATTTCACATTTCTCCTTTTTCACTCGGA----TACCTGATGTATCGAAAC 2003
Crub_svsplocu 279595 GCAGCAAGACAGCTCTAAGCCTTTTTGCCAG---ATTTTCAGATGATTCC 279641
vv i i vv iiv i ii v --- ii v v --
C MamGypsy2-I#L 2002 GATGTAGGACTTCCTGAAGTCTTTCCGCGAGTTCATCCTCTGTTGAT--C 1955
Crub_svsplocu 279642 CCAGCGATGAGGACATCATCAAAGTACGGGCAAACACCTGGAATATCGCA 279691
-i v i i i vvvv viiiv
C MamGypsy2-I#L 1954 CCA-TGATCAGGACATCATCGAAATATGGTACCACACCTGGAATCCTAGA 1906
Crub_svsplocu 279692 GAGC---GTTCGCTCCATCACACATTGGAAGATGCCAGGGGCTACATTAA 279738
i --- --- v vi i i v v vv
C MamGypsy2-I#L 1905 AAGCAGGGT---CTCCATGAAGCACTGGAAAATTCCAGGGGCAACAGAAA 1859
Crub_svsplocu 279739 CCCCAAACTGCAGCCTTTTGACTTTAAATGCACCCCGGTGTGTTACAGTT 279788
ii i v v vi i ivi v i i v v iii
C MamGypsy2-I#L 1858 TTCCGAACTGAAGGCGCTTAACTCGGAATGCCCCTCGATGAGTGATGATT 1809
Crub_svsplocu 279789 GTTTGAGCCTTTGCTGTTGCCTCATCAACTGAT-AATTGTTGATAGGCCT 279837
i v i v v v i i - - ii i i
C MamGypsy2-I#L 1808 GTTTGGGCGTCTGCAGTAGCATCACCGAC-GATCAGCTGTTGATAAGCTT 1760
Crub_svsplocu 279838 GGGCCAAGTGAAGTTTGGCAAAAACACGCCCTCCTTTGAGGGAGGCCTGG 279887
v i v v i vivii i vvii iivi vv
C MamGypsy2-I#L 1759 GGGCAAGGTCAAGTTTTGCAAAGACCTTTTCCCCAGCAAGAACAGCAAGG 1710
Crub_svsplocu 279888 ATGTGGCTCACCACTGGCAACGGGTATGAGTGCTGCTGCAATGCTTTA-- 279935
vv ii v ii v vi i i vv i i --
C MamGypsy2-I#L 1709 AGTTGATTGACTGCAGGCACTGGATATGGGTGCTGCTTAAGTGCCTTATT 1660
Crub_svsplocu 279936 -AGTGTGCACTTATAGTCCGCACAAATTCGGACTTCTCCATTGGCCTTCA 279984
- vv i iv v vv i iv i v i
C MamGypsy2-I#L 1659 CACAGTGCACTTGTAGTCTCCACAAAGTCTCACCTTACCATTAGGCTTTA 1610
Crub_svsplocu 279985 GTGGCCTTACTATGGGGGTTTCCCATGGACTGCAGTCCATAGGTTCTAAA 280034
iv vvii v v vi vv iv iv iiivviv iv v ii
C MamGypsy2-I#L 1609 GTACCGGCGCAATTGGTATAGCCCACCGGGTATGTGTAACTGGTTCGAGG 1560
Crub_svsplocu 280035 ATGCCCTGCTGGAGCAGCTTGTCCAGCTCTGCATTAATTTTATTCTTCAA 280084
iii i i v vi v vv v v v i ? v i i i
C MamGypsy2-I#L 1559 GCACCTTGTTTGATTAGATGCTCAAGCTCTTCTTCANTTTTTTTCCTTAG 1510
Crub_svsplocu 280085 TGCGAAGGGCACCCATCTAGGCTTAATCCTAATGGGTGCAATGGCTGGGT 280134
v i i i viv vi v vviv v i
C MamGypsy2-I#L 1509 AGCAAAAGGTACATTTCTAGCTTTCAAGTGAATTGGTGCAATGGCTGGAT 1460
Crub_svsplocu 280135 CTAAACATAAAGAAATGGGAGGCCCCTTGTA 280165
i i iiv v v iv vvv i
C MamGypsy2-I#L 1459 CCAGATGGAATGACACTGGCTCCCTCTTGTA 1429
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 45.75
Transitions / transversions = 0.94 (219/232)
Gap_init rate = 0.03 (41 / 1302), avg. gap size = 1.32 (54 / 41)
+ 350 35.9 2.6 2.6 Crub_svsplocus 285712 286014 (363986) C Gypsy72-I_DR LTR/Gypsy (742) 3582 3280 170
ANNOTATION EVIDENCE:
350 35.93 2.64 2.64 Crub_svsplocus 285712 286014 363986 C Gypsy-193_DR-I LTR/Gypsy 3280 3582 742
350 35.93 2.64 2.64 Crub_svsplocus 285712 286014 (363986) C Gypsy-193_DR-I#LTR/Gypsy (742) 3582 3280 m_b6s001i4
Crub_svsplocu 285712 AAACATCTTAAATAT-TGCTTAAG-TACGGAGTTCATTTTTTCAGCCCCC 285759
vi - i -i i - v v - vii i i i i ivv
C Gypsy-193_DR- 3582 AAACATCGCAA-TGTGCGCTCAAGATCCTGA-TTGGCTCTCTCGGTCTGA 3535
Crub_svsplocu 285760 CCATTTCCTTGAGGGTGGTGGCTAGATGTCAGTCCCTGAGTGGTTCCTAA 285809
i v ii i i ivi i i vv v i vv ii i
C Gypsy-193_DR- 3534 CCGTTACTCTGGGGATGAAAGCCAGACGAAAGACTCACAGTGGCCCCCAA 3485
Crub_svsplocu 285810 GAGG-GATAAAAATTCCTTCCAAAATGCAGACGTAAATTGCACCCCCCTG 285858
v ii- i i - i vi vi i viv
C Gypsy-193_DR- 3484 TAAACGACAGAA-TTCCCTCCAAAATTTAGAGATAAACTGAGGCCCCCTG 3436
Crub_svsplocu 285859 TCAGAGATGATG--CGTTGGGGTGCCCCATGCAATCTGTAA-ATGTGTTG 285905
i iv i -- i iv -- - vi v - i v v
C Gypsy-193_DR- 3435 TCAGAAACCACGTCCGTCGGGAGG--CCATG-AATGCGAAAGACGTGATT 3389
Crub_svsplocu 285906 GATGAAAAGTTTTGCTAAGGCTTTTGCAG-TGGGAATCTTTTGGCA-AGG 285953
i v ivvvii ivvv i v v -i v -- v -
C Gypsy-193_DR- 3388 AATGACAGCAACCGCTGTCTCTCTGGCTGACGGTAA--TTTGGGCAGAGG 3341
Crub_svsplocu 285954 GATAAAATGCACCTGTTTGGAAAACAAGTCCGTGACCGTCCAGACCACAG 286003
ii vi vvvi v i vi iiv v iv i i v
C Gypsy-193_DR- 3340 GACGAAATGAGCAGCCTTCGAGAACCGGTCCACTACGGTTAAAATCACCG 3291
Crub_svsplocu 286004 TATTCCCATTG 286014
i v i
C Gypsy-193_DR- 3290 TGTTGCCGTTG 3280
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.30
Transitions / transversions = 1.30 (60/46)
Gap_init rate = 0.05 (15 / 302), avg. gap size = 1.07 (16 / 15)
+ 231 26.4 0.0 0.0 Crub_svsplocus 286159 286211 (363789) C Gypsy72-I_DR LTR/Gypsy (1190) 3128 3076 170
ANNOTATION EVIDENCE:
231 26.42 0.00 0.00 Crub_svsplocus 286159 286211 363789 C Gypsy97-I_DR LTR/Gypsy 3076 3128 1190
231 26.42 0.00 0.00 Crub_svsplocus 286159 286211 (363789) C Gypsy97-I_DR#LTR/Gypsy (1190) 3128 3076 m_b6s001i5
Crub_svsplocu 286159 ATGTCCTTTTTCATGGATGGCCACCAAAATTGCCGTTTAATTAAATGTAA 286208
iv vi i v i i i ii vi
C Gypsy97-I_DR# 3128 ATGTCCCGTGCCATAGCTGGCCACCAGAATCGCTGTTTAACCAAAAATAA 3079
Crub_svsplocu 286209 AGT 286211
v
C Gypsy97-I_DR# 3078 TGT 3076
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.02
Transitions / transversions = 1.80 (9/5)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 422 32.5 1.1 1.1 Crub_svsplocus 286515 286710 (363290) C Gypsy72-I_DR LTR/Gypsy (1473) 2848 2605 170
ANNOTATION EVIDENCE:
422 33.12 0.00 0.00 Crub_svsplocus 286515 286671 363329 C Gypsy64-I_DR LTR/Gypsy 2637 2793 1475
422 33.12 0.00 0.00 Crub_svsplocus 286515 286671 (363329) C Gypsy64-I_DR#LTR/Gypsy (1475) 2793 2637 m_b6s001i6
Crub_svsplocu 286515 CATGCGAGATAGAGCATCAGCCAGGAAGTTCTTTCTCCCTGGTAAATGTT 286564
v v i v vv iv vv ivvi iiv
C Gypsy64-I_DR# 2793 CATGCGAGAGAGAGAATCGGGCTTGGTGTTCTTTGACCCTGGCCTGTACG 2744
Crub_svsplocu 286565 TGAGCTTAAACTGGAATTGGTGAAAATGCTGAGACCAGCGGGCTTGTTTG 286614
v iv v v i iiv ivv i i i i
C Gypsy64-I_DR# 2743 AGAGTGTAAAGTTGAATCGACTAAAATAAAGGGACCAGCGGGCCTGTCTA 2694
Crub_svsplocu 286615 GGATTGAGTTTCCTGGACGTTTTCAGGGCTTCTAAATTTTTGTGATCGGT 286664
i i v ii ii v vi v vivv i i v
C Gypsy64-I_DR# 2693 GAACTCAGCCTTTTGGCCGTGCTAATATATTCTAAATTCTTGTGGTCTGT 2644
Crub_svsplocu 286665 CCACACC 286671
v
C Gypsy64-I_DR# 2643 CCAGACC 2637
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.98
Transitions / transversions = 0.93 (25/27)
Gap_init rate = 0.00 (0 / 156), avg. gap size = 0.0 (0 / 0)
293 34.23 2.09 2.09 Crub_svsplocus 286519 286709 363291 C Gypsy3-I_DR LTR/Gypsy 2658 2848 1473
293 34.23 2.09 2.09 Crub_svsplocus 286519 286709 (363291) C Gypsy3-I_DR#LTR/Gypsy (1473) 2848 2658 m_b6s001i7
Crub_svsplocu 286519 CGAGATAGAGCATCAG---CCAGGAAGTTCTTTCTCCCTGGTAAATGTTT 286565
i i v ---i i--- vvvi vvi ivv
C Gypsy3-I_DR#L 2848 CGGGACAGTGCATCAGGTTTCAGA---TTCTTAGATCCTGGACGATAGGT 2802
Crub_svsplocu 286566 GAGCTTAAACTGGAATTGGTGAAAATGCTGAGACCAGCGGGCTTGTTTGG 286615
iv i v i v iviiv i v viv
C Gypsy3-I_DR#L 2801 GAGTGTGAAGTGGAATCGGTTAAAGAATAGAGACCAACGTGCTTGGCGGG 2752
Crub_svsplocu 286616 GATTGAGTTTCCTGGACGTTTTCAGGGCTTCTAAATTTTTGTGATCGGTC 286665
i ivii v vv vv vivv i i i v
C Gypsy3-I_DR#L 2751 GATTAAGTCGTTTGGCCTGTTGGATATATTCTAAATTCTTGTGGTCAGTA 2702
Crub_svsplocu 286666 CACACCTGGAA-GGGGATTTTGTTGCCTTCCAGGAACTGTCGCCA 286709
viv i - vi i ii- i v vv v v
C Gypsy3-I_DR#L 2701 AGAACTTGGAATGGGTGTTTCGCC-CCCTCGAGCCAGTGTCTCCA 2658
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.61
Transitions / transversions = 0.88 (30/34)
Gap_init rate = 0.03 (6 / 190), avg. gap size = 1.33 (8 / 6)
306 32.16 1.38 1.38 Crub_svsplocus 286566 286710 363290 C Gypsy105-I_Dr LTR/Gypsy 2605 2749 1533
306 32.16 1.38 1.38 Crub_svsplocus 286566 286710 (363290) C Gypsy105-I_Dr#LTR/Gypsy (1533) 2749 2605 m_b6s001i8
Crub_svsplocu 286566 GAGCTTAAACTGGAATTGG-TGAAAATGCTGAGACCAGCGGGCTTGTTTG 286614
iv i v v ii - i v v- i v
C Gypsy105-I_Dr 2749 GAGTGTGAAATTGAACCGGCTGAAGAAGA-GAGACCAGCGGGCTTGTCTT 2701
Crub_svsplocu 286615 GGATTGAGTTTCCTGGACGTTTTCAGGGCTTCTAAATTTTTGTGATCGGT 286664
v ii ii vv vv i v vv v ii i i v
C Gypsy105-I_Dr 2700 GCATTGAGCCTTTTGGCAGAGTTTATGTATTCAAGGTTTCTGTGGTCTGT 2651
Crub_svsplocu 286665 CCACACC-TGGAAGGGGATTTTGTTGCCTTCCAGGAACTGTCGCCAC 286710
v -iii vvii i -i i vv v v
C Gypsy105-I_Dr 2650 CCAGACCACAAAAGGCTGCTCTG-CGCCCTCCAGCCAATGGCGCCAC 2605
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.27
Transitions / transversions = 1.00 (23/23)
Gap_init rate = 0.03 (4 / 144), avg. gap size = 1.00 (4 / 4)
+ 392 27.0 1.9 1.9 Crub_svsplocus 286819 286973 (363027) C Gypsy39-I_DR LTR/Gypsy (424) 4625 4471 171
ANNOTATION EVIDENCE:
392 26.97 1.94 1.94 Crub_svsplocus 286819 286973 363027 C Gypsy39-I_DR LTR/Gypsy 4471 4625 424
392 26.97 1.94 1.94 Crub_svsplocus 286819 286973 (363027) C Gypsy39-I_DR#LTR/Gypsy (424) 4625 4471 m_b6s001i9
Crub_svsplocu 286819 TCATTATTTTCTTGTAATAGCACAGCCCCCACTGCCACATCACTTGCATC 286868
v i i i ii v v vi v i v
C Gypsy39-I_DR# 4625 TCCTTATCTTCCTGCAGCAGGACAGCGCCAGCTCCTACAGCACTTGCATC 4576
Crub_svsplocu 286869 TGCCTGTATTATGAAGGGCTTGTCCATATCTGGGTGCC-TTAGTACTGGT 286917
i vi v i i v v v i i- - ii v
C Gypsy39-I_DR# 4575 TACCTCCATTTTAAAAGGCTTTTCGAAATTTGGA-GCCATTAACACTGGA 4527
Crub_svsplocu 286918 TCGGCAGAAAAAAGTCTCTTTAGT-CTCTCAAACGC-TGCTTGGCACTCC 286965
v vv v v i -v i - i v - - i ?
C Gypsy39-I_DR# 4526 GCTTCACACAGAAGT-GCTTTAATACTTTCAAAGGCATGC-TGGCATTCN 4479
Crub_svsplocu 286966 ATTGTCCA 286973
iv v
C Gypsy39-I_DR# 4478 GATGACCA 4471
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.02
Transitions / transversions = 0.95 (20/21)
Gap_init rate = 0.04 (6 / 154), avg. gap size = 1.00 (6 / 6)
+ 933 31.0 3.5 4.3 Crub_svsplocus 286996 287902 (362098) C Gypsy72-I_DR LTR/Gypsy (1978) 2317 1682 170
ANNOTATION EVIDENCE:
257 15.98 4.24 9.82 Crub_svsplocus 286996 287113 362887 C Gypsy172-I_Dr LTR/Gypsy 2120 2231 1985
257 15.98 4.24 9.82 Crub_svsplocus 286996 287113 (362887) C Gypsy172-I_Dr#LTR/Gypsy (1985) 2231 2120 m_b6s001i10
Crub_svsplocu 286996 ACTGAGGATGCTCCCTTCGTTTTTAGTA-AGTTAGTGAGGGGCAAGGCTA 287044
v -- i --- vi -? ? - ? ??iv ?
C Gypsy172-I_Dr 2231 ACTGTGG--GCTCCTTTC---TTTACCATNGNT-GTNAGGGGNNGTGCNA 2188
Crub_svsplocu 287045 TCTGGGCAAATGAGG----GGATGAATTGGCGGTAAAAGTTTGCAAAGCC 287090
- v i --- i ---- ?i v ? v i ?
C Gypsy172-I_Dr 2187 -CGGAGC---TGAAGTTCCGGATGAANCGTCNGTAAAAGTTGGCGAANCC 2142
Crub_svsplocu 287091 CAGGAAACTTTGTAGTTGCTTTC 287113
? i i v ? i -
C Gypsy172-I_Dr 2141 NAGAAAGCGTTGNAATT-CTTTC 2120
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.91
Transitions / transversions = 1.43 (10/7)
Gap_init rate = 0.11 (13 / 117), avg. gap size = 1.23 (16 / 13)
356 29.63 2.42 1.81 Crub_svsplocus 287021 287185 362815 C Gypsy164-I_DR LTR/Gypsy 1741 1906 1957
356 29.63 2.42 1.81 Crub_svsplocus 287021 287185 (362815) C Gypsy164-I_DR#LTR/Gypsy (1957) 1906 1741 m_b6s001i11
Crub_svsplocu 287021 GTAAG-TTAGTGAGGGGCAAGGCTATCTGGGCAAATGAGGGGATGAATTG 287069
- v i i ii v i ivi vvv v i ii
C Gypsy164-I_DR 1906 GTAAGATTAGTCAGAGGTAGAGCAACCTGACTAAAATTGCGAATGAACCG 1857
Crub_svsplocu 287070 GCGGTAAAAGTTTGCAAAGCCCAGGAAACTTTGTAGTTGCTTT-C--TTG 287116
v v i v v i v vi -i ii i - --i
C Gypsy164-I_DR 1856 TCTGTAAAAATTGGCAAACCCCAGAAATCGCTG-GGCCGCCTTGCGACTG 1808
Crub_svsplocu 287117 TGCGGGGTGGCGCCCAATCTAATACTGCTTTGACCTTCTCTGGATCCATT 287166
vi - - ivv v i vv v
C Gypsy164-I_DR 1807 TCTGGGGTGG-GCC-AATCTGCAACTGCTTTCACTTTGGCAGGATCCATT 1760
Crub_svsplocu 287167 TCAATGCCCTCTGGGGATA 287185
ivv iv v i
C Gypsy164-I_DR 1759 CGCACTCCCTCTGGCGACA 1741
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 35.26
Transitions / transversions = 1.00 (24/24)
Gap_init rate = 0.04 (6 / 164), avg. gap size = 1.17 (7 / 6)
384 26.77 2.04 3.45 Crub_svsplocus 287031 287177 362823 C Gypsy70-I_DR LTR/Gypsy 2173 2317 1978
384 26.77 2.04 3.45 Crub_svsplocus 287031 287177 (362823) C Gypsy70-I_DR#LTR/Gypsy (1978) 2317 2173 m_b6s001i12
Crub_svsplocu 287031 GAGGGGCAAGGCTATCTGG--GCAAATGAGGGGATGAATTGGCGGTAAAA 287078
v-- i -- i iv v i-- vi v vi i
C Gypsy70-I_DR# 2317 GAGGGGCC--GCTACCTGGCTGTAGTTGCGA--ATGAAACGCCTATAGAA 2272
Crub_svsplocu 287079 GTTTGCAAAGCCCAGGAAACTTTGTAGTTGCTTT-CTTGTGCGGGGTGGC 287127
i i i viv v- - v v vi viv
C Gypsy70-I_DR# 2271 ATTCGCAAAGCCCAAGAATTGTTGTAGA-GCTTTGCGTGAGCCAGGAACC 2223
Crub_svsplocu 287128 GCCCAATCTAATACTGCTTTGACCTTCTCTGGATCCATTTCAATGCCCTC 287177
v i vi v v i v i iv
C Gypsy70-I_DR# 2222 GGCCAGTCGGAGACAGCTCTTACCTTTTCTGGATCCATTCGAATGCCCTC 2173
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.30
Transitions / transversions = 0.90 (18/20)
Gap_init rate = 0.05 (7 / 146), avg. gap size = 1.14 (8 / 7)
933 33.55 3.26 3.26 Crub_svsplocus 287061 287673 362327 C Gypsy72-I_DR LTR/Gypsy 1682 2294 2003
933 33.55 3.26 3.26 Crub_svsplocus 287061 287673 (362327) C Gypsy72-I_DR#LTR/Gypsy (2003) 2294 1682 m_b6s001i13
Crub_svsplocu 287061 GATGAATTGGCGGTAAAAGTTTGCAAAGCCCAGGAAACTTTGTAGTTGCT 287110
i v i v i v vi iivv
C Gypsy72-I_DR# 2294 GATGAATCGCCGGTAAAAATTGGCGAAGCCCAGGAACCGCTGTAACGCCT 2245
Crub_svsplocu 287111 TTCTTGTGCGGGGTGGCGCCCAATCTAATACTGCTTTGACCTTCTCTGGA 287160
vv v iv v i vi v v ii i v v i
C Gypsy72-I_DR# 2244 TTCGGGAGTCGGGTGGCGGCCAGTCGGAGACAGCCCTAACCTTCGCAGGG 2195
Crub_svsplocu 287161 TCCATTTCAATGCCCTC---TGGGGATATGCGATAGCCTAGGTAGTCTAT 287207
viv vv --- iiiv --- iv i i v vvv i
C Gypsy72-I_DR# 2194 TCCATGCGAAGTCCCTCAACTGAAATTATG---TGTCCCAAGAAGGAAAC 2148
Crub_svsplocu 287208 CCTTTCCTGG---TGGAATTCGCATTTTGAGAGTTTGGCATATAGGTGAG 287254
--- vv --- i ivvvivi vi i v v
C Gypsy72-I_DR# 2147 ---TGACTGGACATGGAATTCGCACTTCTCCGCCTTTACATACAGCTGAT 2101
Crub_svsplocu 287255 CGGCTCGCAGCTTCTTTAAAAC-CGCTCTGACAAGTTTGACGTGTTCTTC 287303
ivv iv ivi v iv - - vi iv v i i v
C Gypsy72-I_DR# 2100 TCTCCAGCAGCCGTTGTAGCACTCGC-CGAACGTGTTGGACATGTTCCTG 2052
Crub_svsplocu 287304 TTTTGTTTCAGTAAAGATAAGAATGTCGTCCAAGTAAACAAGGAC---CC 287350
iv v ivvv v i i i ii ---ii
C Gypsy72-I_DR# 2051 CATGGCGGAAGAAAAAATAAGAATGTCATCCAAATAAACAAAAACAAATT 2002
Crub_svsplocu 287351 CCTTAAACAGGTGCTCCCTTAGAACGTCATTGATTAATTGCAT-AAAGAC 287399
vv v v --- i vv v i i iv i - v -
C Gypsy72-I_DR# 2001 GATTAATCATGT---CTCGGAGTACATCGTTGACGAGT-GCCTGAAAGAC 1956
Crub_svsplocu 287400 TGCAGG-GCCCCCTTGTAATCCAAATGGCAAGACTTTGAATTGATAGCAC 287448
v - viivv - ii i vvviv v v iii
C Gypsy72-I_DR# 1955 TGCTGGAGCATTGGTG-AGCCCAAATGGCAGGACAAGATATTCAAAATGC 1907
Crub_svsplocu 287449 CCCATGGGGCAGTTAAATGCAGTCTTCCATTCATCCCCTTCCTTAATTCT 287498
vi vvv i i i v i i v v v
C Gypsy72-I_DR# 1906 CCAGTGGGCGTGTTGAATGCGGTCTTCCATTCGTCACCCTCCCTCATACG 1857
Crub_svsplocu 287499 TACGCGATAGTAAGCTTCCCTTAGGTCTAG-TTTAGAAAAAATTTT--CC 287545
v v i v iv v i i- ivi i --
C Gypsy72-I_DR# 1856 GACGAGATGGTAAGCATTGCGTAGGTCCAACTTTGTGAAAAATCTTGCCC 1807
Crub_svsplocu 287546 CTTTCGATAGGTGTGACAGC--ATGTCTTTCATGAGGGGCAGCGGGTATA 287593
i v i v i -i vi -- v ----v i v i v iv
C Gypsy72-I_DR# 1806 CCTGCAAGAGAT-CGAAGGCCGAAG----ACATAAGCGGTAGGGGGTACC 1762
Crub_svsplocu 287594 GGTTGCTTTCACTGATTGT---ATTCAGGACCCTATAATCCACGCATAAA 287640
i --- i v i i --- iiv i v i i i viii
C Gypsy72-I_DR# 1761 GAT---TTTTAATGGTTATGTCATTCAAACCTCGATAGTCTATGCAGGGG 1715
Crub_svsplocu 287641 CGTAAAGAGCCATCCTTCTTCTCTCTAAAAAGG 287673
i i i i iivi i i
C Gypsy72-I_DR# 1714 CGCAGAGAACCATCCTTTTTCTTCACAAAGAAG 1682
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.47
Transitions / transversions = 1.05 (102/97)
Gap_init rate = 0.05 (30 / 612), avg. gap size = 1.33 (40 / 30)
802 33.67 3.92 4.30 Crub_svsplocus 287062 287902 362098 C Gypsy138-I_DR LTR/Gypsy 3563 4400 7010
802 33.67 3.92 4.30 Crub_svsplocus 287062 287902 (362098) C Gypsy138-I_DR#LTR/Gypsy (7010) 4400 3563 m_b6s001i14
Crub_svsplocu 287062 ATGAATTGGCGGTAAAAGTTTGCAAAGCCCAGGAAACTTTGTAGTTGCTT 287111
i ivv i i v v ii v v vi vi
C Gypsy138-I_DR 4400 ATAAATCTCCGATAAAAATTGGCAAACCCCAAAAATCGTTGTACCTCTTT 4351
Crub_svsplocu 287112 TCTTGTGCGGGGTGGCGCCCAATCTAATACTGCTTTGACCTTCTCTGGAT 287161
vvi vi iv v i v i i i i i vi v
C Gypsy138-I_DR 4350 AACTGAACATGGTTGTGGCCAATCCAGTACTGCCTTAATCTTGCCAGGAT 4301
Crub_svsplocu 287162 CCATTTCAATGC--CCTCTGGGGA-TATGCGATAGCCTAGGTAGTCTATC 287208
i v v -- v i iv - ---- i i i v i- v iv
C Gypsy138-I_DR 4300 CCATCTGAAGGCTACATTTGGATACTATG----AACCCAAGAAA-CGACA 4256
Crub_svsplocu 287209 CTTTCCTGG-----TGGAATTCGCATTTTGAGAGTTTGGCATATAGGTGA 287253
--- ----- vi ivvv i ii iv i - vv
C Gypsy138-I_DR 4255 CTTT---GGAGACATGGAATTCGCTCTTCTCCAGCTTAACGAACAG-TCT 4210
Crub_svsplocu 287254 GCGGCTCG-CAGCTTCTTTAAAACCGCTCTGACAAGTTTGACGTGTTCTT 287302
i v i- i vvvvv i vvi v v vv i i
C Gypsy138-I_DR 4209 GTGTCTCAACAACTGGGAGAGAACCTGCCGGACATGTTGTACATGCTCTT 4160
Crub_svsplocu 287303 CTT--TTGTTTCAGTAAAGATAAGAATGTCGTCCAAGTAAACAAGGAC-- 287348
v --i ii v -- i v i i ii --
C Gypsy138-I_DR 4159 CATAGCTACTTGA--AAAAATAAGTATGTCATCCAAGTAAACGAAAACAA 4112
Crub_svsplocu 287349 -CCCCTTAAACAGGTGCTCCCTTAGAACGTCATTGATTAATTGCAT-AAA 287396
-i iv v ---v v i i i v - v -i
C Gypsy138-I_DR 4111 ATCTGTTCAACA---TCTCCCTGAGGACATCATTAATGAA-TGCCTGGAA 4066
Crub_svsplocu 287397 GACTGCAGGGCCCCCTTGTAA-TCCAAATGGCAAGACTTTGAATTGATAG 287445
v v -v vi ii -v v vv i viv v
C Gypsy138-I_DR 4065 GACGGCTGGG-GCATTTACAAGGCCAAAGGGCATTACCTGATATTCATAG 4017
Crub_svsplocu 287446 CACCCCATGGGGCAGTTAAATGCAGTCTTCCATTCATCCCCTTCCTTAAT 287495
iiv ii ? vv v i i i i
C Gypsy138-I_DR 4016 TGGCCTGTNGGGGTGTTAAAAGCGGTCTTCCACTCATCTCCTTCCTTGAT 3967
Crub_svsplocu 287496 TCTTACGCGATAGTAAGCTTCCCTTAGGTCTAGTTTAGAAAAAAT--TTT 287543
i v vv i v ii v i ii v v i -- vv
C Gypsy138-I_DR 3966 CCTGACCAGATGGTAAGCATTTCTGAGGTCCAACTTCGTAAAGATAGTGG 3917
Crub_svsplocu 287544 C-CCTTTCGATAGGTGTGACAGCA-TGTCTTTCATGAGGGGCAGCGGGTA 287591
- i v ii vv -ii v - --- v i ii
C Gypsy138-I_DR 3916 CGCCCTGCAGTATCT-CAAAAGCAGTG---TTCATTAGGGGTAATGGGTA 3871
Crub_svsplocu 287592 TAGGTTGCTTTCACTGAT--TGT-ATTCAGGACCCTATAATCCACGCATA 287638
vv i - -- v i -- - iiv i v ii vi
C Gypsy138-I_DR 3870 ACGATT-CTT--AATGGTGATGTGATTCAAACCTCTATAATCAATACAGG 3824
Crub_svsplocu 287639 AACGTAAAGAGCCATCCTTCTTCTCTCTAAAAAGGGCCGGGGCAGCCACT 287688
iv v i vvv vvvvvi i ---ii v v iv
C Gypsy138-I_DR 3823 GTCGAAGACTCCCATCCTTCTTGGAAACAAAAAAG---AAGCCTGCTCCT 3777
Crub_svsplocu 287689 TTAGGCTTGGCT---GGCTCAATGAAACCTCTCTCTAGGTTTTTTTTTAT 287735
vi ivv i --- viv v v v ivii iv i v
C Gypsy138-I_DR 3776 GCAGGTGAGGTTGAAGGGCGAATGAATCCACTGTCTAGAGCCTCGTTCAA 3727
Crub_svsplocu 287736 AAATCTTTCCATTTC--CTCCTTCTCCTTTGGGCTCATGGAGTATAATCT 287783
iv i i vv --i i vvvvv i--v v i
C Gypsy138-I_DR 3726 GTATTTCTCCATGGCAGTTCTTTCAGGAATGGA--GAGGGAGTACAATCT 3679
Crub_svsplocu 287784 GGGCTTCGGG--AGTTTTGCCCCAGGCTTGAATTCAATGGTACAGTC-TG 287830
--i i i --i vi i ivii i i v i - i
C Gypsy138-I_DR 3678 --ACCTCGAGGTGGGCTTGCTCCAGGTACAAGTTCAATAGAACAATCATA 3631
Crub_svsplocu 287831 TGGGTCGGTGGGGGGG--GGGGAGCTCATTCGCCCTCTCCTCACTGAAGA 287878
i- i v --iv i ----- v ivvvv i i
C Gypsy138-I_DR 3630 TGGA-CGATGCGGGGGTAATGAAG-----TAGCCTGAGACTTACTAAAGA 3587
Crub_svsplocu 287879 CTTCAGCAAGGTCCCTATATTCCT 287902
vii i v i i
C Gypsy138-I_DR 3586 CTTCACTGAGATCCATGTATTCTT 3563
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.48
Transitions / transversions = 1.05 (139/132)
Gap_init rate = 0.07 (55 / 840), avg. gap size = 1.25 (69 / 55)
+ 466 16.7 0.0 0.1 Crub_svsplocus 291788 292182 (357818) + IMPB_01 Satellite 1 394 (2148) 172
ANNOTATION EVIDENCE:
463 13.98 0.00 0.42 Crub_svsplocus 291788 292024 357976 + IMPB_01 Satellite 165 400 2148
463 13.98 0.00 0.42 Crub_svsplocus 291788 292024 (357976) IMPB_01#Satellite 165 400 (2148) m_b6s001i15
Crub_svsplocu 291788 ATCTCTCTCCCCCTCTTTCTTTCTCTCTCTCCCTCTCTCTCTCTCCCTCT 291837
i i i i i i
IMPB_01#Satel 165 ATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 214
Crub_svsplocu 291838 TTCTTTCTCTCTCTCCCTCTCTTTCTCTCTCTTCTCTCTCCCTCTCTTTC 291887
i i i i - i i
IMPB_01#Satel 215 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTC 263
Crub_svsplocu 291888 TCTCTCTCTCCCCCTCTCTATTTCTCTCTCCCTTTCTCTCTCCCTCTCTT 291937
i i v i i i i i
IMPB_01#Satel 264 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 313
Crub_svsplocu 291938 TCTCTCTCTCCCTCTCTCCCTCTATTTCTCCCTCTCTCTCTTTCTCTCTC 291987
i i v i i i
IMPB_01#Satel 314 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 363
Crub_svsplocu 291988 CCTCTCTCTTTGTCTCCCTCCCTCCCTCTCTCCCTCT 292024
i i v i i i i
IMPB_01#Satel 364 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 400
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.17
Transitions / transversions = 10.00 (30/3)
Gap_init rate = 0.00 (1 / 236), avg. gap size = 1.00 (1 / 1)
446 14.16 0.00 0.43 Crub_svsplocus 291820 292053 357947 + IMPB_01 Satellite 167 399 2149
446 14.16 0.00 0.43 Crub_svsplocus 291820 292053 (357947) IMPB_01#Satellite 167 399 (2149) m_b6s001i16
Crub_svsplocu 291820 CTCTCTCTCTCTCCCTCTTTCTTTCTCTCTCTCCCTCTCTTTCTCTCTCT 291869
i i i i i
IMPB_01#Satel 167 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 216
Crub_svsplocu 291870 TCTCTCTCCCTCTCTTTCTCTCTCTCTCCCCCTCTCTATTTCTCTCTCCC 291919
- i i i i v i i
IMPB_01#Satel 217 -CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 265
Crub_svsplocu 291920 TTTCTCTCTCCCTCTCTTTCTCTCTCTCCCTCTCTCCCTCTATTTCTCCC 291969
i i i i i v i i
IMPB_01#Satel 266 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 315
Crub_svsplocu 291970 TCTCTCTCTTTCTCTCTCCCTCTCTCTTTGTCTCCCTCCCTCCCTCTCTC 292019
i i i v i i i
IMPB_01#Satel 316 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 365
Crub_svsplocu 292020 CCTCTTTCTCCCTCTCCCTCTCTATTTCTCTCTC 292053
i i i i v i
IMPB_01#Satel 366 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 399
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.34
Transitions / transversions = 7.25 (29/4)
Gap_init rate = 0.00 (1 / 233), avg. gap size = 1.00 (1 / 1)
466 15.85 0.00 0.00 Crub_svsplocus 291880 292125 357875 + IMPB_01 Satellite 166 411 2137
466 15.85 0.00 0.00 Crub_svsplocus 291880 292125 (357875) IMPB_01#Satellite 166 411 (2137) m_b6s001i17
Crub_svsplocu 291880 TCTCTTTCTCTCTCTCTCCCCCTCTCTATTTCTCTCTCCCTTTCTCTCTC 291929
i i i v i i i
IMPB_01#Satel 166 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 215
Crub_svsplocu 291930 CCTCTCTTTCTCTCTCTCCCTCTCTCCCTCTATTTCTCCCTCTCTCTCTT 291979
i i i i v i i i
IMPB_01#Satel 216 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 265
Crub_svsplocu 291980 TCTCTCTCCCTCTCTCTTTGTCTCCCTCCCTCCCTCTCTCCCTCTTTCTC 292029
i i v i i i i i
IMPB_01#Satel 266 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 315
Crub_svsplocu 292030 CCTCTCCCTCTCTATTTCTCTCTCCCTCTCTTTCTCCCTCTCTCTTTCTC 292079
i i v i i i i i
IMPB_01#Satel 316 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 365
Crub_svsplocu 292080 TCTCTCTCTCTTTCTCCCTCCCTCTCTTTCTCTATTTGTCTTTCTC 292125
i i i i v v? i v
IMPB_01#Satel 366 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGNGTTTTGCTC 411
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 18.58
Transitions / transversions = 4.57 (32/7)
Gap_init rate = 0.00 (0 / 245), avg. gap size = 0.0 (0 / 0)
415 16.60 0.00 0.00 Crub_svsplocus 291922 292156 357844 + IMPB_01 Satellite 166 400 2148
415 16.60 0.00 0.00 Crub_svsplocus 291922 292156 (357844) IMPB_01#Satellite 166 400 (2148) m_b6s001i18
Crub_svsplocu 291922 TCTCTCTCCCTCTCTTTCTCTCTCTCCCTCTCTCCCTCTATTTCTCCCTC 291971
i i i i v i i
IMPB_01#Satel 166 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 215
Crub_svsplocu 291972 TCTCTCTTTCTCTCTCCCTCTCTCTTTGTCTCCCTCCCTCCCTCTCTCCC 292021
i i i v i i i i
IMPB_01#Satel 216 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 265
Crub_svsplocu 292022 TCTTTCTCCCTCTCCCTCTCTATTTCTCTCTCCCTCTCTTTCTCCCTCTC 292071
i i i v i i i i
IMPB_01#Satel 266 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 315
Crub_svsplocu 292072 TCTTTCTCTCTCTCTCTCTTTCTCCCTCCCTCTCTTTCTCTATTTGTCTT 292121
i i i i i v i v i
IMPB_01#Satel 316 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 365
Crub_svsplocu 292122 TCTCTCCCTCCCTCCTTCTCTCTTCCTCCCTCTCT 292156
i i ii ii i
IMPB_01#Satel 366 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 400
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 19.69
Transitions / transversions = 6.80 (34/5)
Gap_init rate = 0.00 (0 / 234), avg. gap size = 0.0 (0 / 0)
348 18.38 0.00 0.00 Crub_svsplocus 291949 292182 357818 + IMPB_01 Satellite 167 400 2148
348 18.38 0.00 0.00 Crub_svsplocus 291949 292182 (357818) IMPB_01#Satellite 167 400 (2148) m_b6s001i19
Crub_svsplocu 291949 CTCTCTCCCTCTATTTCTCCCTCTCTCTCTTTCTCTCTCCCTCTCTCTTT 291998
i v i i i i i
IMPB_01#Satel 167 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 216
Crub_svsplocu 291999 GTCTCCCTCCCTCCCTCTCTCCCTCTTTCTCCCTCTCCCTCTCTATTTCT 292048
v i i i i i i i v i
IMPB_01#Satel 217 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 266
Crub_svsplocu 292049 CTCTCCCTCTCTTTCTCCCTCTCTCTTTCTCTCTCTCTCTCTTTCTCCCT 292098
i i i i i i
IMPB_01#Satel 267 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 316
Crub_svsplocu 292099 CCCTCTCTTTCTCTATTTGTCTTTCTCTCCCTCCCTCCTTCTCTCTTCCT 292148
i i v i v i i i ii ii
IMPB_01#Satel 317 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 366
Crub_svsplocu 292149 CCCTCTCTCTTCCTCTCTTTCTCCTTCCCTCCCT 292182
i ii i ii i i
IMPB_01#Satel 367 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 400
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.34
Transitions / transversions = 7.60 (38/5)
Gap_init rate = 0.00 (0 / 233), avg. gap size = 0.0 (0 / 0)
+ 51 7.5 1.4 0.0 Crub_svsplocus 295497 295566 (354434) + (TC)n Simple_repeat 1 71 (0) 173
ANNOTATION EVIDENCE:
51 7.51 1.43 0.00 Crub_svsplocus 295497 295566 354434 + (TC)n Simple_repeat 1 71 0
51 7.51 1.43 0.00 Crub_svsplocus 295497 295566 (354434) (TC)n#Simple_repeat 1 71 (0) c_b6s251i0
Crub_svsplocu 295497 TCTCTCTCTCTCTCTTTCTCTC-CTCTCTCTCTCTCTCTCTCTCTCTGTG 295545
i - v v
(TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50
Crub_svsplocu 295546 TGTCCCTCTCTCTCTCTCTCT 295566
v i
(TC)n#Simple_ 51 TCTCTCTCTCTCTCTCTCTCT 71
Matrix = Unknown
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1)
+ 12 20.5 5.6 3.6 Crub_svsplocus 296421 296474 (353526) + (TTCTCC)n Simple_repeat 1 55 (0) 174
ANNOTATION EVIDENCE:
12 20.46 5.56 3.64 Crub_svsplocus 296421 296474 353526 + (TTCTCC)n Simple_repeat 1 55 0
12 20.46 5.56 3.64 Crub_svsplocus 296421 296474 (353526) (TTCTCC)n#Simple_repeat 1 55 (0) m_b6s252i0
Crub_svsplocu 296421 TTCTACTTCTCCTT-TTCTTATCCTT-T-GTTCTCCATGCCCTTGTCTGC 296467
v - i v - -v - v i i - v
(TTCTCC)n#Sim 1 TTCTCCTTCTCCTTCTCCTTCTCCTTCTCCTTCTCC-TTCTCCT-TCTCC 48
Crub_svsplocu 296468 CTCTCCT 296474
i
(TTCTCC)n#Sim 49 TTCTCCT 55
Matrix = Unknown
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.09 (5 / 53), avg. gap size = 1.00 (5 / 5)
+ 13 18.8 0.0 0.0 Crub_svsplocus 302468 302498 (347502) + (CCTTT)n Simple_repeat 1 31 (0) 175
ANNOTATION EVIDENCE:
13 18.81 0.00 0.00 Crub_svsplocus 302468 302498 347502 + (CCTTT)n Simple_repeat 1 31 0
13 18.81 0.00 0.00 Crub_svsplocus 302468 302498 (347502) (CCTTT)n#Simple_repeat 1 31 (0) m_b6s252i1
Crub_svsplocu 302468 CCTTTCCTTTCCTTCCCTTCTCTATCTTTTC 302498
i ii v i
(CCTTT)n#Simp 1 CCTTTCCTTTCCTTTCCTTTCCTTTCCTTTC 31
Matrix = Unknown
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)
+ 1521 33.1 2.9 2.9 Crub_svsplocus 303337 304259 (345741) C Gypsy63-I_DR LTR/Gypsy (1012) 5325 4403 176
ANNOTATION EVIDENCE:
1521 33.15 2.93 2.93 Crub_svsplocus 303337 304259 345741 C Gypsy63-I_DR LTR/Gypsy 4403 5325 1012
1521 33.15 2.93 2.93 Crub_svsplocus 303337 304259 (345741) C Gypsy63-I_DR#LTR/Gypsy (1012) 5325 4403 m_b6s001i20
Crub_svsplocu 303337 ACCACATACAACTGAGAGCCCCACCGATCGGCCAATTTGTGCCTCCCAGC 303386
v v i v iii i vi v i i -vi
C Gypsy63-I_DR# 5325 ACAACATAAAGCTCAGAATTCCATCTGTCTGCCAATTTGTGCTTTCC-TT 5277
Crub_svsplocu 303387 AGGGCCCAA-ATTTCTTAACAGCACTCAGTCCCCA--AAC----TGTAAA 303429
i i i - v v iv iv -- ---- vi
C Gypsy63-I_DR# 5276 GGAGTCCAAGATTTCGTATCAAGACTTTGTCCCCAGGAACCAGGTGAGAA 5227
Crub_svsplocu 303430 TCCTGGACCCTTACTCTCAGATCATAATTTCTTTTGTTCCGCTGC----- 303474
vv ------i v v vi i i i - -----
C Gypsy63-I_DR# 5226 TAATG------CAATCTCTGATCATATCTTCTCTTATTTC-CTGCATTTT 5184
Crub_svsplocu 303475 ---TCCCGGACCCCTGTGGCCTCTGC-GGCTTTTTCATAAGCCCCCTTTA 303520
--- i i -- vi v -- -i v---- vvv- v
C Gypsy63-I_DR# 5183 TCTTCTCAG--CATTTT--CCTCTGCTAGCTG----ATAAGCAGA-TTTC 5143
Crub_svsplocu 303521 AGCTCTTCCT-CAACCTGTCCACATAATTAC-GGTGAGACTTAAAAGAGG 303568
i v i - v i v ii i- iiii- i i v v i
C Gypsy63-I_DR# 5142 AGTTCGTTCTGCATCTTCTTTACG-AACCGTTGGTAAGACCTTACAGAAG 5094
Crub_svsplocu 303569 TCTCGTCCATTGAGGTACCAAAAGCCAGGTCCACCGGTAGGCGGGCTTCC 303618
vi i vv vii vi i v iv i v v
C Gypsy63-I_DR# 5093 TACCATCACTTGACACACCAAAACTCAAGTCAATGGGCAGCCTGGCTTCC 5044
Crub_svsplocu 303619 CTGCCAAACATTAGCCGGTACGGGGAATACCCGGTGACGTCACTCCTTGT 303668
v vvi v v i i v vv
C Gypsy63-I_DR# 5043 CTGCCAAACATAAGAAAGTAAGGGGAATACCCTGTGGCGTCATTCATGCT 4994
Crub_svsplocu 303669 GTTCTTATAGGTGTGCATGACGGTG-GAGATATGTTGGGTCCAATGCTGT 303717
ivv i viii ii - i -vvi i i iv v i
C Gypsy63-I_DR# 4993 GCAATTGTACACATGCACAA-GATGTCCAATGTGTCGACTCCACTGTTGT 4945
Crub_svsplocu 303718 TTCTGCACTTCAGT-GAGAGTTCCCACCATGTCAAAGAGACTGTGGTTAA 303766
- v i -v i i v i v i vv vi i
C Gypsy63-I_DR# 4944 TTCTGC-CTTGAATCCAGGGTCCCCAGCATATCTAAAAGCGTTCGGTTGA 4896
Crub_svsplocu 303767 ATCTCTCGGGCTGTGAATCGCCTTGCGGGTGGTACGGGGTGGTGCGGGAC 303816
i vi i i i i i i i v v v i
C Gypsy63-I_DR# 4895 ACCGTTCAGGCTGCGGATCACCCTGCGGATGATACGGTGTTGTTCGGGAT 4846
Crub_svsplocu 303817 TTCCGAATACCCAACAAGCCCAGCAATTGCTTGATCAGTCAACTTTTAAA 303866
ivv iv i i i i v i i vv v v iivi i ii
C Gypsy63-I_DR# 4845 TTCTCTACTCCTAATAGGTCAAACAACTCATGGATGAGCTTGCTCTCGAA 4796
Crub_svsplocu 303867 ATCCCTCTCTTGGTCAGAATGTATGCGCTGAGGTAGCCCATAGTGTATGA 303916
vvi v i i v vi v i i i v
C Gypsy63-I_DR# 4795 ATCCCGACCTTGGTCTGAGTGCATTCTTTTAGGCAGTCCGTAGTGAATGA 4746
Crub_svsplocu 303917 AAAAATTCTCCACTAATACTTTGGCCACTGTAACAGCGCGCTGGTCTTTC 303966
iv v i vvi iv v v iiiv viv i v
C Gypsy63-I_DR# 4745 AGTATTTTTCCCACAGAACTTTCGCAACTGTGGTTGCCTTCTGATCTTTA 4696
Crub_svsplocu 303967 GTTGGGAAGGCCTGGGCATAACACGTAAAGTGATCGGTCACAACCAACAC 304016
i v v vi iv i v v ii v iv
C Gypsy63-I_DR# 4695 GTTGGAAAGGCCTGTGCATACCTTGTGTAGTGGTCCGTGATGACAAGGAC 4646
Crub_svsplocu 304017 ATTTCCT-TGTCCACTGGCATCCAGTTCTAAGGAAAGGAAATTGATGCAG 304065
v vv- ii-i v ii i v v i iv i v
C Gypsy63-I_DR# 4645 ATTACAGATGTTT-TTGGAATCTGGCTCTATGGATAGAAAATCCATACAT 4597
Crub_svsplocu 304066 ACCAAGTCCAAGTGCCTATGACTTTGTAAATGGCTCACTGGCGCAG---T 304112
v ii vvv i i v vvii vvv vv i ---
C Gypsy63-I_DR# 4596 ACAAGATCCATCGGTCCATTACTAGACAAATGTGACAAGGGTGCAGCTTT 4547
Crub_svsplocu 304113 TCTAGATGGCAGAGTTTTTCTCTGAATACAAT--GCAGATAAGATCT-AC 304159
--- i i i i i vi-- v ---i -i
C Gypsy63-I_DR# 4546 TCTA---GGCAAAGTCTTTCTTTGGACACACCTGGCACAT---GTCTGGC 4503
Crub_svsplocu 304160 AGTAGTCCCCGACTTCCTTCTTCATGCCGGGCCAGTAGAACTGATCCACT 304209
i v i i i v vvi v v i iiv iivii
C Gypsy63-I_DR# 4502 AATATTTCTCAACATCAACCTTCATTCGGGGCCAGTAAAATCTATTTCTC 4453
Crub_svsplocu 304210 ACTAAATTAAAAGTCTTTTCTGGCCCCAAATGCCCATGCTCATCGTGGAG 304259
v ii v i v vii vi v vviv i i
C Gypsy63-I_DR# 4452 ACAAAACCATAGGTCTTGTCAAACCCCATGTGACCTGAATCATCATGAAG 4403
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.34
Transitions / transversions = 1.17 (160/137)
Gap_init rate = 0.04 (41 / 922), avg. gap size = 1.32 (54 / 41)
+ 2863 32.2 2.5 2.1 Crub_svsplocus 304781 306078 (343922) C Gypsy63-I_DR LTR/Gypsy (2482) 3855 2553 176
ANNOTATION EVIDENCE:
2863 32.18 2.47 2.07 Crub_svsplocus 304781 306078 343922 C Gypsy63-I_DR LTR/Gypsy 2553 3855 2482
2863 32.18 2.47 2.07 Crub_svsplocus 304781 306078 (343922) C Gypsy63-I_DR#LTR/Gypsy (2482) 3855 2553 m_b6s001i21
Crub_svsplocu 304781 GCATCAAATTTAGCAGTGGTGAGCAAATACGTAAGTGGATTATTGTCTAT 304830
v ii i v v v v v v v i i i
C Gypsy63-I_DR# 3855 GCATCCAGCTTGGCTGTTGTCAGAACATAAGTTAGCGGGTTATTGTCTGT 3806
Crub_svsplocu 304831 TTTAACTTCAAACTCTGCCCCATACAAATAATCCCTTAACTTATCCACAA 304880
i vi i i ivi v i i viv i i v
C Gypsy63-I_DR# 3805 CTGGACCTCAAATTTAACCCCATAGAGATAGTCATGTAGCTTGTCAACAA 3756
Crub_svsplocu 304881 CCACCCACTTGAGTGCCCAAAATTCCAACTTATGGGTTGGATAATTCTTT 304930
i i v i v i i v ii i iiv i i
C Gypsy63-I_DR# 3755 CCGCCCATTTTAATGCCAAGAACTCAAGTTTGTGGACGGGGTAGTTCTTT 3706
Crub_svsplocu 304931 TCCCAGGGAGTTAAACCCCTACTGATATATGCAATGGGCTTTAAATGTTG 304980
vv i v i ii i i v v iv i vivi v
C Gypsy63-I_DR# 3705 TCAGAAGGCGTCAAACTTCTGCTGACAAATGCCACTGGTTTTAACCCCTC 3656
Crub_svsplocu 304981 ATCATGCTCCTGATATAACACCTTCCCAAGGCCATCCCGACTGGCATCTA 305030
vi v v i i viiv v v v i v i v
C Gypsy63-I_DR# 3655 TCCTTGATCCTGGTACAACACGCCACCAAGTCCTTCACAACAGGCGTCGA 3606
Crub_svsplocu 305031 CATGTAATTCATATGG---CTGATTGGGGTCGGCATAAGCTAAGACTGGA 305077
v v --- --- i iv v ii i
C Gypsy63-I_DR# 3605 CATGTAATACATAGGGGAGCTGA---GGATTTGCAAAGACCAAGACTGGA 3559
Crub_svsplocu 305078 GTGTTTGTAAACCTTCACTTCAGCTGATCAAAAGCCTGTTCACAACGC-T 305126
iv iv v i ivv i i vv i i vvv i -i -
C Gypsy63-I_DR# 3558 GCTTCAGTTAATCTCACCTTTAACTCTTTAAAGGCAGTTTCGCA-TGCAT 3510
Crub_svsplocu 305127 CAGTCCATTCTGC-CTGAATAGACTCTCGTGACTTCCTGGGCCCCCTAGT 305175
- i - iv v iv -v ii i---- iv v i
C Gypsy63-I_DR# 3509 CAGTCCA-TCTACTCCCAAAAGGGTC-AGTAGCTTT----GTACGCTAAT 3466
Crub_svsplocu 305176 T-TTATGGACTGGATTTGAATGACCCACTGTGTTCTCT-----ACCTCCT 305219
- v i ------- - v ii v v i ----- i v
C Gypsy63-I_DR# 3465 TGTTCTGGGC-------GAA-GTCCTGCTTTGATCTTTTTCAAACTTGCT 3424
Crub_svsplocu 305220 ---------CA-TTTTTTAACAACTCATTAAGCGGGTGAGCTATCTTAGC 305259
--------- -ii v v i v v i i ii v ii v v
C Gypsy63-I_DR# 3423 GCAGGCAGACAACCTTGTAAGAGCTGATTCAGTGGATAGGATACTTTTGA 3374
Crub_svsplocu 305260 AAAGCCTTCCACAAATCTTCGATAGTATGAACAAAACCCCAAAAACAACC 305309
v i i v vv i v i ii v
C Gypsy63-I_DR# 3373 ATAGTCTTTCACAAATCTTCTATAGTATCCACAGAAACCTAAAAATGAAC 3324
Crub_svsplocu 305310 GCAGTTAGCGACAC--TCTGGGGCCTAGGCCAAGAAACT-TGGCCTCAAG 305356
i v-i -- i i v vvi -ii v v
C Gypsy63-I_DR# 3323 GCAGCTC-TGACACGTTCTGAGGTCGAGGCCAAGATTTTACAGCATCAAT 3275
Crub_svsplocu 305357 CTTGGCGGGCTCCATTGCCAGTCC--CTCGGCCAAGATGTCATGCCCTAA 305404
v v ii vv vv -- i --i iivii i v v
C Gypsy63-I_DR# 3274 CTTGGAGGGGTCTGTTGAGACACCGTCTTGG--GAGACAATGTGTCCAAC 3227
Crub_svsplocu 305405 ATAGGTGAGAGATGGCTGATAAAATTGGCATTTTCCTAACGACAATTTCA 305454
i v v v v i i vvv vi i v i
C Gypsy63-I_DR# 3226 GTAGCTGACAGAGGTCTGACAGAAGGTGCATTTATCCAAAGACAACTTCA 3177
Crub_svsplocu 305455 GCCCCTCCTCCTGGAGCCTTGTCAATACCTTCTCTAAACGCTCCTCATGC 305504
ii i vii v ii vvi v i ivvi v v i
C Gypsy63-I_DR# 3176 ATCCTTCACTCTGTAATCTGTCCAAGACTTTTAGCAACCTCTCTTCATGC 3127
Crub_svsplocu 305505 TGCTCAAGTGTCTCCCCAAAGACAATGATATCATCTAAATAGACCAACAC 305554
v v i iiv v i vi i i i v i i
C Gypsy63-I_DR# 3126 TCCTCCAATGTCCTGCCAAATACGATGAGGTCGTCCAGATACACTAATAC 3077
Crub_svsplocu 305555 CTCTATCAGGTTCATGTCCCCCACTGTCCGTTCCATAAGCCTTTGAAAGG 305604
i i v i v v iv vi i
C Gypsy63-I_DR# 3076 TTCCAACAAGTTCATGTCCCCAACGGTCTTTTCCATAACTCTTTGAAAAG 3027
Crub_svsplocu 305605 TTGCTGGAGCCCCTGACAA--CCCTTGTGGCATTTGATTGAATTCATAAA 305652
i v i -- -- i ivv v i v i
C Gypsy63-I_DR# 3026 TCGATGGAGCTCC--ACAAATCCCCTGTGGCATTCTCTGGAACTGATAGA 2979
Crub_svsplocu 305653 ATCCCAATGGGCAGATGAATGCAGTTTTGTCCCTATCCTCTGGATGCATG 305702
i v v i v iiv iv vv iv i
C Gypsy63-I_DR# 2978 ACCCCACTGGGCAGATGAATGCTGTCTTTTCTTGATCTGCTTCACTCATA 2929
Crub_svsplocu 305703 GGGATCTGATGGTAACCACTCCTTAAATCTAACACACTGAACCACTTTGC 305752
i i ii v v i i i i vvi
C Gypsy63-I_DR# 2928 GGAATCTGGTAATATCCACTCCTGAGATCCAATACACTAAACCACTTGCT 2879
Crub_svsplocu 305753 CCCTGACAAACACTGCAAAGCATCCTCTATCCGAGGAGTTGTATACTGGT 305802
vvv i vvvi iv v iiv i i i
C Gypsy63-I_DR# 2878 CCCATTCAGACAAGTTAGTGCATCCTCTATCCGTGGAACAGTGTATTGAT 2829
Crub_svsplocu 305803 CAGGGATGGTCCTCTGGTTAAGGGTACGATAATCTATACACATCCTTAGG 305852
v i i v vii v v v i ii i ---
C Gypsy63-I_DR# 2828 CTGGAATAGTACGTCGGTTTAGCGTTCGATAATCCACGCACATTCT---G 2782
Crub_svsplocu 305853 GTC---CTGTTCTTCTTTCAGACCACCTCTATAGGGGAAGCATAAGGACT 305899
i --- ii i i iv i vv v v i v
C Gypsy63-I_DR# 2781 ATCTGGCCATTCTTTTTCCGTACTACAACAATCGGAGAAGCATATGGACT 2732
Crub_svsplocu 305900 TCGAGACTCCCTAATGACCCCAGTCCTTTTTAACTCTTCTAGGTGCTCCC 305949
i vi i iv i i i v ii i ii i ivv
C Gypsy63-I_DR# 2731 CCTGGATTCTGTGATAATCCCTGCTCCTTTTAACTTCTCTAGATGTAGCC 2682
Crub_svsplocu 305950 GAAGATCATCTAAGTC-GCTCAAAGGGATCCGTCGGGACCTTTCCCTAAA 305998
vi v v i ii - -ii vi vv vv v vi v v
C Gypsy63-I_DR# 2681 TGACATCTTCCAGATCAGCT-GGAGCAAGACGTCTTGAACGCTCACGAAA 2633
Crub_svsplocu 305999 GGGTTTATCCTCCCTCAGTCAGATTTCATGTTTAGCACTCCTAGCGCAGC 306048
i i i iv i ii iiv i vi i i v vi v
C Gypsy63-I_DR# 2632 AGGTTTGTTCTCTGTCAGCCGAATCCGATGCTGGGTACTCTTTGAACATC 2583
Crub_svsplocu 306049 CTACATCAAAATCATCTCTCGAGAATAAAT 306078
v v v v vv i v
C Gypsy63-I_DR# 2582 CAACTTCAAATTCATCACAGGAGAACACAT 2553
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.07
Transitions / transversions = 1.19 (222/187)
Gap_init rate = 0.03 (40 / 1297), avg. gap size = 1.48 (59 / 40)
+ 478 29.9 3.2 3.2 Crub_svsplocus 306717 306965 (343035) C Gypsy63-I_DR LTR/Gypsy (4435) 1902 1654 176
ANNOTATION EVIDENCE:
478 29.88 3.21 3.21 Crub_svsplocus 306717 306965 343035 C Gypsy63-I_DR LTR/Gypsy 1654 1902 4435
478 29.88 3.21 3.21 Crub_svsplocus 306717 306965 (343035) C Gypsy63-I_DR#LTR/Gypsy (4435) 1902 1654 m_b6s001i22
Crub_svsplocu 306717 GCAACAGAGGGCCC---AAACGTCAGCTGTATAGGCAAACATCCATCATA 306763
---i --- vi ivi v i v
C Gypsy63-I_DR# 1902 GCAACAGA---TCCTGGAAACTCCAGCCTCAAAGACAAACAGCCATCATA 1856
Crub_svsplocu 306764 GGGGAATTTTTCAGTAC-CAATACCACAGATCTTCAAATCACCCAACTCC 306812
v v i vvi - v - v i ivi i ---ii
C Gypsy63-I_DR# 1855 TGGGTACTTTTGCATACTCAATCCC-CATATCTCCAAATTTTCTA---TT 1810
Crub_svsplocu 306813 TGTATG---GGCATATGCATCAAATACTTATCATAAAAATCCCTATATAG 306859
v v--- iv i i i i ivvi i
C Gypsy63-I_DR# 1809 GGTATCAATGGCATATGTCTCAAGTATTTGTCATAGAAGGATCTGTATAG 1760
Crub_svsplocu 306860 TAACATCACTTGCGCACCTGAATCCAAAAGAGCCTTAGTATAAATTCCTT 306909
i ivi v vv vvv i v i v i i
C Gypsy63-I_DR# 1759 CAGGGTAACTTGCGATCCACTATCTAACAAAGCCTTTGCATAGATTCCTT 1710
Crub_svsplocu 306910 CCACCTGCACCGGCACCACCGGGGAGGGGCCCACCAA-CTGCTGAGGAAA 306958
i v v v vv v iivv v i i - i -v i
C Gypsy63-I_DR# 1709 CCACTTGAACAGGAAGGACAGAACTGGGTCCTACTAACCCGCT-CGGAAG 1661
Crub_svsplocu 306959 CATTGCT 306965
v i
C Gypsy63-I_DR# 1660 AACTGCT 1654
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.92
Transitions / transversions = 1.00 (36/36)
Gap_init rate = 0.05 (12 / 248), avg. gap size = 1.33 (16 / 12)
+ 16 23.0 4.2 4.2 Crub_svsplocus 308617 308688 (341312) + (ACATA)n Simple_repeat 1 72 (0) 177
ANNOTATION EVIDENCE:
16 22.98 4.17 4.17 Crub_svsplocus 308617 308688 341312 + (ACATA)n Simple_repeat 1 72 0
16 22.98 4.17 4.17 Crub_svsplocus 308617 308688 (341312) (ACATA)n#Simple_repeat 1 72 (0) m_b6s252i2
Crub_svsplocu 308617 ACA-AAAAGAACAAAACCAT-ACAAAGACAAAAAACAACATATACA-AAA 308663
- v v v - - v - v v i - - v
(ACATA)n#Simp 1 ACATAACATAACATAA-CATAACATA-ACATAACATAACATA-ACATAAC 47
Crub_svsplocu 308664 AAAACTAAACATTACATAACAAAAC 308688
v vv v v
(ACATA)n#Simp 48 ATAACATAACATAACATAACATAAC 72
Matrix = Unknown
Transitions / transversions = 0.08 (1/12)
Gap_init rate = 0.08 (6 / 71), avg. gap size = 1.00 (6 / 6)
+ 29 0.0 0.0 0.0 Crub_svsplocus 308819 308843 (341157) + (AT)n Simple_repeat 1 25 (0) 178
ANNOTATION EVIDENCE:
29 0.00 0.00 0.00 Crub_svsplocus 308819 308843 341157 + (AT)n Simple_repeat 1 25 0
29 0.00 0.00 0.00 Crub_svsplocus 308819 308843 (341157) (AT)n#Simple_repeat 1 25 (0) c_b6s251i1
Crub_svsplocu 308819 ATATATATATATATATATATATATA 308843
(AT)n#Simple_ 1 ATATATATATATATATATATATATA 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 348 27.0 6.5 6.5 Crub_svsplocus 310014 310245 (339755) C L1-18_DR LINE/L1 (1527) 4187 4076 179
ANNOTATION EVIDENCE:
277 26.98 6.52 6.52 Crub_svsplocus 310014 310243 339757 C L1-1_Testu LINE/L1 4795 5024 1308
277 26.98 6.52 6.52 Crub_svsplocus 310014 310243 (339757) C L1-1_Testu#LINE/L1 (1308) 5024 4795 m_b6s001i23
Crub_svsplocu 310014 AGTCCACCCCTCTCACGGAAGTCT-TGCATAATTTTA-AACTTAACCCTT 310061
v i-i v i ii - i v i - i v i
C L1-1_Testu#LI 5024 AGTCCACCCCACTT-TGTAGGCTTATACAGAACTTTAGAACTCACCCTTT 4976
Crub_svsplocu 310062 GGCTTTTTTCCTGCCCAAATAAATTTGTTAA-GGC-CTTTCTGCCATTCG 310109
v v vi -i v i -- -i - v i --
C L1-1_Testu#LI 4975 GTCTTTTATGTT-TCCATATGAATTT--TAATAGCGCATCCTGCCAT--G 4931
Crub_svsplocu 310110 CTTAGATTAATCTCATTCTTCAA-------AATCGGTA-GCATTTGAAAC 310151
i --- v v-- i------- iv v - i -
C L1-1_Testu#LI 4930 TTT---TTAATGTCATG--TCAGGGATACCAACAGGGATGCACT-GAAAC 4887
Crub_svsplocu 310152 AAAAAGAGAAACTTGGGTAGAATATTCATTTTTATCACTGCAATTCTTCC 310201
v iv v v i i i i ivv v ii v
C L1-1_Testu#LI 4886 AAAAATAATAACTTTGGGAGGACATTCATCTTTACCGAGGCTACCCTACC 4837
Crub_svsplocu 310202 CA--TAAGGGATAATTGCA-ACTTCTCCCAATTCTTCAGGTCTTT 310243
i --i i--- v - i v i v i i i
C L1-1_Testu#LI 4836 TAGCCAAGA---AATTTCATATTTGTTCCATTCCTCCAAGTCTTT 4795
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.51
Transitions / transversions = 1.42 (34/24)
Gap_init rate = 0.10 (23 / 229), avg. gap size = 1.30 (30 / 23)
348 32.14 0.00 0.00 Crub_svsplocus 310134 310245 339755 C L1-18_DR LINE/L1 4076 4187 1527
348 32.14 0.00 0.00 Crub_svsplocus 310134 310245 (339755) C L1-18_DR#LINE/L1 (1527) 4187 4076 m_b6s001i24
Crub_svsplocu 310134 ATCGGTAGCATTTGAAACAAAAAGAGAAACTTGGGTAGAATATTCATTTT 310183
v vivi i i ii i i i
C L1-18_DR#LINE 4187 ATGGGTAGGGACTGAAATAAAAAAAGAAATCTAGGTAAAATATTCATTCT 4138
Crub_svsplocu 310184 TATCACTGCAATTCTTCCCATAAGGGATAATTGCAACTTCTCCCAATTCT 310233
iii v i v v vv iv i v i i vi vi
C L1-18_DR#LINE 4137 TATTGTTTCAATCCTACCAAACAATGATAGTGGTAGCACCTCCCACCTCT 4088
Crub_svsplocu 310234 TCAGGTCTTTCT 310245
v ii i i
C L1-18_DR#LINE 4087 GCAAATCCTTTT 4076
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.01
Transitions / transversions = 1.77 (23/13)
Gap_init rate = 0.00 (0 / 111), avg. gap size = 0.0 (0 / 0)
+ 404 34.4 3.3 4.0 Crub_svsplocus 310578 311353 (338647) C L1-1_Testu LINE/L1 (2090) 4242 3173 180
ANNOTATION EVIDENCE:
280 28.22 0.00 2.56 Crub_svsplocus 310578 310657 339343 C L1-1_Testu LINE/L1 4375 4452 1880
280 28.22 0.00 2.56 Crub_svsplocus 310578 310657 (339343) C L1-1_Testu#LINE/L1 (1880) 4452 4375 m_b6s001i25
Crub_svsplocu 310578 TCTCGAATTTTGATTAACAATATTTCCAATGTTAAAACAAACAGCAACGG 310627
iv -- ivv ivi v ii i iv
C L1-1_Testu#LI 4452 TCTCACATTT--ATTGCAAATGGCTCCATTGCCAAAGCAAACAGCAGGGG 4405
Crub_svsplocu 310628 TGATAATGGACATCCCTGCCTGGTACCTTT 310657
v i i v i v ii
C L1-1_Testu#LI 4404 GGATAACGGGCAACCCTGTCTCGTACCCCT 4375
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.28
Transitions / transversions = 1.44 (13/9)
Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2)
287 35.38 2.94 3.55 Crub_svsplocus 310602 311111 338889 C L1-21_DR LINE/L1 3173 3679 2335
287 35.38 2.94 3.55 Crub_svsplocus 310602 311111 (338889) C L1-21_DR#LINE/L1 (2335) 3679 3173 m_b6s001i26
Crub_svsplocu 310602 TCCAATGTTAAAACAAACAGCAACGGTGATAATGGACATCCCTGCCTGGT 310651
vivi i i ii ii v vv v i i i ivv
C L1-21_DR#LINE 3679 TCCAAAAACAAAGCGAACAATAGTGGAGAACAGGGGCATCCTTGTCTACA 3630
Crub_svsplocu 310652 ACCTTTCTCTATTGTAAAAACCTCTGACAACCCTCCATTAACAATAAGTT 310701
vv i i vvi vivi i v iv i ivv i v i
C L1-21_DR#LINE 3629 AGATCTTTCTAGAATAAATGATTTTGAGAGGCTTCCATTAATTTTGATTC 3580
Crub_svsplocu 310702 GTGCCGTTTGTTTTTGATATATTACT-GTAAGAGCTTGTACTATCTTTTC 310750
vv i v iv vi i - - vv iv vv vv
C L1-21_DR#LINE 3579 TAGCTGTTGGTTCGTTGTATATTGCTTGTA-GAGCTTTAATGATAATTGG 3531
Crub_svsplocu 310751 ACCAAAATTCATCTCCTCCATTACTCTTAACATAAA---ATGCCAATTCA 310797
ivi iiv vi i i ---- --- iv v ii
C L1-21_DR#LINE 3530 ATGGAAACCAAATTTCTCCATTACTTT----ATAAAGATATAACCATCTA 3485
Crub_svsplocu 310798 ATTG-ATCAAAAGCCTTTTCAGCATCTAAAAATATCAACCCTGCAGGGAC 310846
i - i i v i --- i vi vvi-- v i
C L1-21_DR#LINE 3484 ACTGTATCAAAGGCTTTTTCTGCGTCT---AGTCCCAAGAT--CAGTGAT 3440
Crub_svsplocu 310847 TTGGTTGTTCTTGTCTAAATATTC--TAATAAGT-TAATAATTTGTCTAA 310893
ivi iv vvi iv i v -- v v - - i i
C L1-21_DR#LINE 3439 TCTATCTTTCTTTGTTGTATGTGCGATAAGATGTGTAA-AGTTCGTCTAA 3391
Crub_svsplocu 310894 CATTATTTTTCATATACCTTCCAGT--TATAAATCCAGATTGATCTTTAT 310941
i i i i vvi v ii i-- -- v v vvv
C L1-21_DR#LINE 3390 TACTGTCTTGGGTTTGTCTTT--GTCGTATAAATCCTGTTTGATCTAGTT 3343
Crub_svsplocu 310942 GCACAAGA--TGATGCACA-ACCCTCATAAGCCTATTTACTAAAATTTTT 310988
i i i-- i i- i - ii? - - i v i i vv
C L1-21_DR#LINE 3342 GTATAAGGTCTGGTA-ATATATTNTC-T-AGTCTTTTTGCCAAAATTGAT 3296
Crub_svsplocu 310989 ACAAATATCTTATAATCCACATTTAGAAGAGATATAGGCCTATAATTCTT 311038
iiiv i i i i vv v v v v i
C L1-21_DR#LINE 3295 GTGTATATTTTATAATCTATATTTAAAACCGAAATTGGGCGATAATTTTT 3246
Crub_svsplocu 311039 TGGTAAAGTAA--GATCTTGATCCTCTTTTGGAATCAGTGATATAAAAGC 311086
--ii vv --vi vvi v v v v vv vivv
C L1-21_DR#LINE 3245 --ACACTGTAATTTGTCTTTCCCATCTTTAGGAATAATTGTAATTGTCGC 3198
Crub_svsplocu 311087 ACTACGCCATGAAGGAGGAATCTCT 311111
viiv v v i
C L1-21_DR#LINE 3197 TTCTCTCCAAGAAGGAGGAATTTCT 3173
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 47.43
Transitions / transversions = 1.05 (89/85)
Gap_init rate = 0.05 (27 / 509), avg. gap size = 1.22 (33 / 27)
404 34.58 4.96 5.15 Crub_svsplocus 310790 311353 338647 C L1-1_Testu LINE/L1 3680 4242 2090
404 34.58 4.96 5.15 Crub_svsplocus 310790 311353 (338647) C L1-1_Testu#LINE/L1 (2090) 4242 3680 m_b6s001i27
Crub_svsplocu 310790 CCAATTCAATTGATCAAAAGCCTTTTCAGCATCTAAAAATATCAACCCTG 310839
v i iii i i i i i i i v v i v -i
C L1-1_Testu#LI 4242 CCACTCCAGCCGGTCGAAGGCTTTCTCAGCATCCAAAGAAAGCAGCGC-A 4194
Crub_svsplocu 310840 CAGG--GACTTGGTTGTTCTTGTCTAAATATTCTA-AT-AAGTTAATAAT 310885
-- v ------ v vv v i v - - i v v i
C L1-1_Testu#LI 4193 CAGGAAGAATTG------CTAGAATTAACATTATAGATCAAATTCAGAGT 4150
Crub_svsplocu 310886 TTGTCTAACATTATTTTTCATATACCTTCCAGTTATAAATCCAGATTGAT 310935
iv i i ivvvi v i v iv ii i i
C L1-1_Testu#LI 4149 TCTTCTGATATTATCAGATAGATGCCTGCCAGCAACGAACCCAGATTGGT 4100
Crub_svsplocu 310936 C----------TTTATGCACAAGATGATGCACAACCCTCATAAGCCTATT 310975
---------- v v vi ii v i ---------- i
C L1-1_Testu#LI 4099 CAGGGTGAACATATTTGGGCAAGATGACACTCAATC----------TGTT 4060
Crub_svsplocu 310976 TACTAAAATTTTTACAAATATCTTATAATCCACATTTAGAAGAGATATAG 311025
i iv ii vi v v i vv v vv i v
C L1-1_Testu#LI 4059 TGCTAGCACCTTGGCATAAATTTTAGCATCCACATTAATTAAAGAAATAG 4010
Crub_svsplocu 311026 GCCTATA--ATTCTTTGGTAA--AGTAAGATCTTGATCCTCTTTTGGAAT 311071
i i -- v ----ii --i vvi i v -
C L1-1_Testu#LI 4009 GTCTGTATGATGC----ACAATTGGTAAGATCTTTTCCTTCTTTAGGAA- 3965
Crub_svsplocu 311072 CAGTGATATAAAA-----GCACTACGCCATGAAGGAGGAATCTCTAGACC 311116
--- i-i v ----- viiviv vvv vvvv
C L1-1_Testu#LI 3964 ---TGAC-CACAATTTTTGCCTCTTTCCATGAATCTGGAATCTCGTTCCC 3919
Crub_svsplocu 311117 CTGTAAAATATCATTAAAAAGATTACCT--AATGGCTGAATCATCTCCTC 311164
i v i v iv i vi -- i -- i i v v i v
C L1-1_Testu#LI 3918 CTGCAATATACCATTAAACAATTCAGTTAAAATAG--GGACCAACACTTG 3871
Crub_svsplocu 311165 CATTAAAGCTTTATAATAAACAGCTGTTAACCCATCCGTACCCGGTGCTT 311214
v i i vv vv v vv v v i v
C L1-1_Testu#LI 3870 CTTTAGAGCTCTATAATACTCCCCAGAAAACCCATCGGGACCTGGAGCTT 3821
Crub_svsplocu 311215 TCCCTGGTTTCAATTGCTGAATTGCTAACACAATTTCCTCCTTAGTAATT 311264
viiv i i v v v i v viv i ivi i
C L1-1_Testu#LI 3820 TATTGGATTTTAAATTCTTAATTACAACTTCAACTTCCTCTGCAGCAATT 3771
Crub_svsplocu 311265 AAGCCATTAATTTCCTGCTTC-TGATCCTCTGTCAATTTGGGAAAACTAG 311313
viv i i -vvv iv - v vv ii vi v ivi vi
C L1-1_Testu#LI 3770 TGCCTATCAA-GAGCTGCCACATCATCCTCTGAGAGCTGAGGTAGTTTCA 3722
Crub_svsplocu 311314 CCTCGTTTAAATATTTATTTATA--TCTAAAATTTGAACATT 311353
viivi i i -- ii ii i ii
C L1-1_Testu#LI 3721 CACTTCTCAAATATCTATTTATAAGTTCAGGATTTGGATGTT 3680
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 46.22
Transitions / transversions = 1.06 (95/90)
Gap_init rate = 0.07 (39 / 563), avg. gap size = 1.46 (57 / 39)
+ 232 26.1 7.1 5.8 Crub_svsplocus 311742 312049 (337951) C L1-53_DR LINE/L1 (3551) 2895 2854 181
ANNOTATION EVIDENCE:
226 28.55 7.79 6.75 Crub_svsplocus 311742 312049 337951 C L1-25_DR LINE/L1 2174 2484 3227
226 28.55 7.79 6.75 Crub_svsplocus 311742 312049 (337951) C L1-25_DR#LINE/L1 (3227) 2484 2174 m_b6s001i28
Crub_svsplocu 311742 GCTTTACCTGCATCCCATACCATTGACATTGAAG----TCCCCTTATACA 311787
v vi - vv i ---- v v i -
C L1-25_DR#LINE 2484 GCTTTTCCTGCATCCCATAATATTGA-AGGGGAGACATTACCATCAT-CA 2437
Crub_svsplocu 311788 T-ATTTAAAGCAAAATAATCCTTTAAACACTCCTTTAACTTTTGAACATT 311836
- v --- i v i ---- v i----- v i-
C L1-25_DR#LINE 2436 TTAATTAAA---AAGTATTCTTTTAA----TGCTTC-----TTGTAT-TT 2400
Crub_svsplocu 311837 CTTTTCTTGTCTAAATAAATTTT----------CATTCACTCTCCAGGAT 311876
i i i i ivv v ---------- v iv
C L1-25_DR#LINE 2399 CTTTTTTTGTTTGAGTGTTTGTTAACAATGAGACATTCAATCTCCAATAT 2350
Crub_svsplocu 311877 CTTCTCTCC---TCTTTTTCTTGGGTCAGCTCCATCCAAACTGGGCTATG 311923
vvv v --- vv i iv v v vi i vvv ii i
C L1-25_DR#LINE 2349 CTAAACTGCGTGTCTAGTCCCAGGTTAATTTTCATAATAACTGGATTGTG 2300
Crub_svsplocu 311924 ATCCGTCA--GCGACCTAGGAAAAATCTTTACATTCTTT-ACTCTATTAT 311970
i i vv -- i i i-- vvv - i i - i -
C L1-25_DR#LINE 2299 GTCTGAAATGGTGGCT--GGTTCAAT-TCTACACTCTTTTACTTTAT-AT 2254
Crub_svsplocu 311971 ATAAGTCCG---TTGTAATAAAAAAAAAGTCAATTCTTGAGAAGGATTGG 312017
-- i --- vv v v v v vv iv
C L1-25_DR#LINE 2253 ATA--TCTGCTTTTGGTATACAAAAATAGTCTATTCTTGAGTAGCTTCCG 2206
Crub_svsplocu 312018 TGTCTATCTGAGAAAAAGGTGAAATCTCTCTC 312049
ivi v i i v i i i
C L1-25_DR#LINE 2205 TGCACATGTGAAAAGAATGTAAAGTCTCTTTC 2174
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 36.18
Transitions / transversions = 0.82 (37/45)
Gap_init rate = 0.09 (28 / 307), avg. gap size = 1.61 (45 / 28)
232 9.76 2.44 0.00 Crub_svsplocus 311979 312019 337981 C L1-53_DR LINE/L1 2854 2895 3551
232 9.76 2.44 0.00 Crub_svsplocus 311979 312019 (337981) C L1-53_DR#LINE/L1 (3551) 2895 2854 m_b6s001i29
Crub_svsplocu 311979 GTTGT-AATAAAAAAAAAGTCAATTCTTGAGAAGGATTGGTG 312019
- v i v i
C L1-53_DR#LINE 2895 GTTGTCAATCAGAAAAAAGTCAATTCTGGAAAAGGATTGGTG 2854
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.48
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1)
+ 278 31.2 0.0 0.0 Crub_svsplocus 312465 312589 (337411) C L1-72_DR LINE/L1 (3882) 1585 1461 182
ANNOTATION EVIDENCE:
278 31.20 0.00 0.00 Crub_svsplocus 312465 312589 337411 C L1-72_DR LINE/L1 1461 1585 3882
278 31.20 0.00 0.00 Crub_svsplocus 312465 312589 (337411) C L1-72_DR#LINE/L1 (3882) 1585 1461 m_b6s001i30
Crub_svsplocu 312465 TGATCCTTAAGTAAAATATGAGTTTCCTGTAAACAAATAACATCATTGTT 312514
viv v v v iiv v ii vvv
C L1-72_DR#LINE 1585 TGATCCTTAAGTCGCAGATGTGTTTCCTGAAGGAATATAATGTCAGGTTT 1536
Crub_svsplocu 312515 ATGTTGCTTCAAATAATAGAAGATTTTTTTCCTTTTCTGAGGAGAATTCA 312564
v v i vvv i i vvvi vvv vv v
C L1-72_DR#LINE 1535 TTGTAGCTTCAAATGAGTCAAAACTTTAGATCTTTTAATAGGACCATTGA 1486
Crub_svsplocu 312565 ATCCGTTAACATTCCAGGTCAGAAA 312589
i v iv ii
C L1-72_DR#LINE 1485 GTCCTTTAACATTCCAACTCAAGAA 1461
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.12
Transitions / transversions = 0.50 (13/26)
Gap_init rate = 0.00 (0 / 124), avg. gap size = 0.0 (0 / 0)
+ 12 26.9 1.6 4.9 Crub_svsplocus 313936 313998 (336002) + A-rich Low_complexity 1 61 (0) 183
ANNOTATION EVIDENCE:
12 26.89 1.59 4.92 Crub_svsplocus 313936 313998 336002 + (AAAAGC)n Simple_repeat 1 61 0
12 26.89 1.59 4.92 Crub_svsplocus 313936 313998 (336002) (AAAAGC)n#Simple_repeat 1 61 (0) m_b6s252i3
Crub_svsplocu 313936 AAAATCCAAAG-AAGAAAAAAAGAAAAAAGTCAAAAGAAAAATCCAGTGC 313984
v v - i iv -v - v v v iv -
(AAAAGC)n#Sim 1 AAAAGCAAAAGCAAAAGCAAAAG-CAAAAG-CAAAAGCAAAAGCAAAAG- 47
Crub_svsplocu 313985 CAAGAGCAAAATCA 313998
i v
(AAAAGC)n#Sim 48 CAAAAGCAAAAGCA 61
Matrix = Unknown
Transitions / transversions = 0.44 (4/9)
Gap_init rate = 0.06 (4 / 62), avg. gap size = 1.00 (4 / 4)
+ 502 9.5 2.5 1.1 Crub_svsplocus 318906 318996 (331004) + URR1B DNA/hAT-Charlie 1 128 (91) 184
ANNOTATION EVIDENCE:
248 14.06 1.67 5.17 Crub_svsplocus 318906 318965 331035 + Charlie-N1b_Cpb DNA/hAT-Charlie 71 128 91
248 14.06 1.67 5.17 Crub_svsplocus 318906 318965 (331035) Charlie-N1b_Cpb#DNA/hAT-Charlie 71 128 (91) m_b6s001i31
Crub_svsplocu 318906 GTTGTTGTTAGGCGTAGAGCAGTGGTTCTCAACCTGTGGGTCG-GGACCC 318954
i v- i i i vi -
Charlie-N1b_C 71 GTTGTCGTTAC-CATAGAACAGTGGTTTTCAACCTGTGGTCCGCGGACCC 119
Crub_svsplocu 318955 CATTTGGGGTC 318965
-- v
Charlie-N1b_C 120 C--TGGGGGTC 128
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.72
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.07 (4 / 59), avg. gap size = 1.00 (4 / 4)
502 8.33 2.78 0.00 Crub_svsplocus 318925 318996 331004 + URR1B DNA/hAT-Charlie 1 74 151
502 8.33 2.78 0.00 Crub_svsplocus 318925 318996 (331004) URR1B#DNA/hAT-Charlie 1 74 (151) m_b6s001i32
Crub_svsplocu 318925 CAGTGGTTCTCAACCTGTGGGTCGGGACCCCATTTGGGGTCGAACGACCA 318974
i v v v v
URR1B#DNA/hAT 1 CAGCGGTTCTCAACCTGTGGGTCGCGACCCCTTTGGGGGTCGAACGACCC 50
Crub_svsplocu 318975 TTTCACAGGGGTCGCC--AAACCA 318996
-- i
URR1B#DNA/hAT 51 TTTCACAGGGGTCGCCTAAGACCA 74
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.45
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.01 (1 / 71), avg. gap size = 2.00 (2 / 1)
+ 521 8.8 0.0 0.0 Crub_svsplocus 319064 319131 (330869) + URR1A DNA/hAT-Charlie 159 226 (0) 185
ANNOTATION EVIDENCE:
521 8.82 0.00 0.00 Crub_svsplocus 319064 319131 330869 + URR1A DNA/hAT-Charlie 159 226 0
521 8.82 0.00 0.00 Crub_svsplocus 319064 319131 (330869) URR1A#DNA/hAT-Charlie 159 226 (0) m_b6s001i33
Crub_svsplocu 319064 TTGGGGGTCACCACAACATGGGGAACTGTATTATGGGGTCACGGCATTAG 319113
i vi i i
URR1A#DNA/hAT 159 TTGGGGGTCACCACAACATGAGGAACTGTATTAAAGGGTCGCAGCATTAG 208
Crub_svsplocu 319114 AAAGGTTGAGAACCACTG 319131
i
URR1A#DNA/hAT 209 GAAGGTTGAGAACCACTG 226
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.01
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 273 18.2 0.0 3.6 Crub_svsplocus 319482 319505 (330495) C TDR19 DNA/hAT-Charlie (81) 311 290 186
ANNOTATION EVIDENCE:
273 18.20 0.00 3.64 Crub_svsplocus 319482 319538 330462 C TDR19 DNA/hAT-Charlie 257 311 81
273 18.20 0.00 3.64 Crub_svsplocus 319482 319538 (330462) C TDR19#DNA/hAT-Charlie (81) 311 257 m_b6s001i34
Crub_svsplocu 319482 GTTTAATCTCCTCATGGTTTAGAGCAGGGGTGTCAAACTCAATTTCATTG 319531
iiv v - i i ? ii i - v
C TDR19#DNA/hAT 311 GTTTGGACACCT-ACGGTCTAGANCAGGGGTGTCAAACTCGGTTCC-TGG 264
Crub_svsplocu 319532 AGGGCCG 319538
C TDR19#DNA/hAT 263 AGGGCCG 257
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.21
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.04 (2 / 56), avg. gap size = 1.00 (2 / 2)
+ 265 10.8 0.0 0.0 Crub_svsplocus 319506 319542 (330458) C hAT-N103_DR DNA/hAT-Charlie (0) 687 651 187
ANNOTATION EVIDENCE:
265 10.81 0.00 0.00 Crub_svsplocus 319506 319542 330458 C hAT-N103_DR DNA/hAT-Charlie 651 687 0
265 10.81 0.00 0.00 Crub_svsplocus 319506 319542 (330458) C hAT-N103_DR#DNA/hAT-Charlie (0) 687 651 m_b6s001i35
Crub_svsplocu 319506 CAGGGGTGTCAAACTCAATTTCATTGAGGGCCGCATC 319542
v i i v
C hAT-N103_DR#D 687 CAGGGGTGTCAAACTCATTTTCACTGAGGGCCACTTC 651
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.71
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 244 17.8 0.0 12.3 Crub_svsplocus 321215 321230 (328770) C hAT-N71_DR DNA/Zisupton (1842) 1472 1417 188
ANNOTATION EVIDENCE:
244 17.81 0.00 12.28 Crub_svsplocus 321215 321278 328722 C hAT-N71_DR DNA/Zisupton 1416 1472 1842
244 17.81 0.00 12.28 Crub_svsplocus 321215 321278 (328722) C hAT-N71_DR#DNA/Zisupton (1842) 1472 1416 m_b6s001i36
Crub_svsplocu 321215 ATTCTGATGCCCTTTCTCAAAAGTGTATGTTTGTATACACACACACACAT 321264
- i i v ------ i viii i i
C hAT-N71_DR#DN 1472 ATTCTG-TACTCTTTATCA------TGTGTACACACACACACACACACAC 1430
Crub_svsplocu 321265 ACACACACACACAG 321278
C hAT-N71_DR#DN 1429 ACACACACACACAG 1416
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.79
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.11 (7 / 63), avg. gap size = 1.00 (7 / 7)
+ 309 7.3 0.0 0.0 Crub_svsplocus 321237 321277 (328723) + hAT-N53_DR DNA/hAT-Ac 2764 2804 (3015) 189
ANNOTATION EVIDENCE:
309 7.32 0.00 0.00 Crub_svsplocus 321237 321277 328723 + hAT-N53_DR DNA/hAT-Ac 2764 2804 3015
309 7.32 0.00 0.00 Crub_svsplocus 321237 321277 (328723) hAT-N53_DR#DNA/hAT-Ac 2764 2804 (3015) m_b6s001i38
Crub_svsplocu 321237 GTGTATGTTTGTATACACACACACACATACACACACACACA 321277
i v i
hAT-N53_DR#DN 2764 GTGTGTGTGTGTATACACACACACACACACACACACACACA 2804
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.75
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
+ 228 8.6 0.0 0.0 Crub_svsplocus 321249 321283 (328717) + hAT-N131_DR DNA/hAT-Ac 289 323 (1741) 190 *
ANNOTATION EVIDENCE:
228 8.57 0.00 0.00 Crub_svsplocus 321249 321283 328717 + hAT-N131_DR DNA/hAT-Ac 289 323 1741
228 8.57 0.00 0.00 Crub_svsplocus 321249 321283 (328717) hAT-N131_DR#DNA/hAT-Ac 289 323 (1741) m_b6s001i39
Crub_svsplocu 321249 ATACACACACACACATACACACACACACAGTATGT 321283
i i i
hAT-N131_DR#D 289 ACACACACACACACACACACACACACACAGTATAT 323
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.40
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0)
+ 1616 28.7 1.2 1.2 Crub_svsplocus 321806 322305 (327695) + L3 LINE/CR1 2528 3027 (1072) 191
ANNOTATION EVIDENCE:
1616 28.74 1.20 1.20 Crub_svsplocus 321806 322305 327695 + L3 LINE/CR1 2528 3027 1072
1616 28.74 1.20 1.20 Crub_svsplocus 321806 322305 (327695) L3#LINE/CR1 2528 3027 (1072) m_b6s001i40
Crub_svsplocu 321806 ATGGTAAGTGAGCACTTGTCCAGCCTAGATGAGTTAAAATCACCAGGATC 321855
i v i iv ivii i v i v vi
L3#LINE/CR1 2528 ATAGTAAGAGAGCACCTAGCCGCTTTAAATGAGTTCAAGTCTCCAGGCCC 2577
Crub_svsplocu 321856 AGATGTATTACACCCCAAGGTTCTCAAAGAACTGGCAGATTTGATCTCAG 321905
i v i i v v v v v i
L3#LINE/CR1 2578 AGACGAATTACATCCCAGGGTACTGAAAGAACTTGCAGATGTGATCGCGG 2627
Crub_svsplocu 321906 AACCACTG-AGCTATATTTTTCAAAGATCCTGGAGCACTGGGGAACTACC 321954
i -v v - i v i i vi v v ii iv i
L3#LINE/CR1 2628 AACCGCTGTCGGTA-ATCTTTGAGAAATCACGGAGAACGGAAGAGGTGCC 2676
Crub_svsplocu 321955 AGAGGACAGGAAAAGAGCTGATGTAGTTCCCATCTTCCAAAAAGAAAAAA 322004
i v i v i vi ? ? i ?i iv i i
L3#LINE/CR1 2677 AGAAGACTGGAGACGGGCAAATGTNGTNCCTANTTTTAAAAAGGGAAAAA 2726
Crub_svsplocu 322005 A-ATGGATCCGGGAAATTACAGACCTATCAGCCTAACCTCAATACCTGGG 322053
- i v ? i vi v i i v i v i v
L3#LINE/CR1 2727 AGATGGATTCTGNAAACTACAGACCGGTAAGCTTGACGTCGATCCCCGGC 2776
Crub_svsplocu 322054 AAGATTCTGGAAAAGATAATCAAACA-ATGAATCAGCAAACACCTAGAGG 322102
i i vi v i - iv i- ii i i --
L3#LINE/CR1 2777 AAAATTCTAGAACGGATTATTAAACAGATGGTTT-GTGAGCACTTAGA-- 2823
Crub_svsplocu 322103 CAAACGAAG---TCATTACTGAAAGCCAACATGGGTTTGTCAAAAACAGA 322149
- v --- v i iii i iiii i ii
L3#LINE/CR1 2824 -AAAGGAAGCGGTGATCACTAGGAGCCAGCATGGGTTCACTAAGAACAAG 2872
Crub_svsplocu 322150 TCATGTGAGACAAATCTTATTGCATACTTTGACCAAGTGACAAAATTAGT 322199
iv i v i i v v vi ivii v v i i i
L3#LINE/CR1 2873 TCATGCCAAACTAACCTCATTTCCTTTTTTGATAGGGTTACTAGACTGGT 2922
Crub_svsplocu 322200 GGATCAGAGGAATGCTGTGGATATAATTTACTTGGGACTTCAGTAAGGCA 322249
i i i i i ? i v ii - i i
L3#LINE/CR1 2923 AGATCAGGGGAATGCCGTAGACANAGTGTATCTGG-ATTTCAGCAAGGCA 2971
Crub_svsplocu 322250 TTTGATAAAGTAGATCACAACGTACTACTTGATAAGATAGAAAAATGTGG 322299
i vvv ii ii v vv v i i i i
L3#LINE/CR1 2972 TTTGACAAAGTCTCTCATGATATCCTTGTGGACAAGATGGAGAAATATGG 3021
Crub_svsplocu 322300 GTTAGA 322305
i i
L3#LINE/CR1 3022 GCTGGA 3027
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 35.19
Transitions / transversions = 1.84 (92/50)
Gap_init rate = 0.02 (10 / 499), avg. gap size = 1.20 (12 / 10)
+ 13 17.1 0.0 5.7 Crub_svsplocus 322713 322749 (327251) + (GTT)n Simple_repeat 1 35 (0) 192
ANNOTATION EVIDENCE:
13 17.10 0.00 5.71 Crub_svsplocus 322713 322749 327251 + (GTT)n Simple_repeat 1 35 0
13 17.10 0.00 5.71 Crub_svsplocus 322713 322749 (327251) (GTT)n#Simple_repeat 1 35 (0) m_b6s252i4
Crub_svsplocu 322713 GTTGTTGTTGTTAACTTGTTGTTGTTTGTCTTGTAGT 322749
--v vv v v
(GTT)n#Simple 1 GTTGTTGTTGTT--GTTGTTGTTGTTGTTGTTGTTGT 35
Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2)
+ 12 26.3 0.0 4.3 Crub_svsplocus 326654 326702 (323298) + A-rich Low_complexity 1 47 (0) 193
ANNOTATION EVIDENCE:
12 26.32 0.00 4.26 Crub_svsplocus 326654 326702 323298 + (AAATTTA)n Simple_repeat 1 47 0
12 26.32 0.00 4.26 Crub_svsplocus 326654 326702 (323298) (AAATTTA)n#Simple_repeat 1 47 (0) m_b7s252i0
Crub_svsplocu 326654 AAATAAAAAACCTGAAATTTAAAACTCAAATCTGAATAAATTTAAAATT 326702
vv ii i i i -v vv -
(AAATTTA)n#Si 1 AAATTTAAAATTTAAAATTTAAAATTTAAA-ATTTA-AAATTTAAAATT 47
Matrix = Unknown
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2)
+ 543 22.1 2.9 1.9 Crub_svsplocus 329120 329276 (320724) + L3 LINE/CR1 3929 4080 (19) 194
ANNOTATION EVIDENCE:
543 27.70 2.70 0.00 Crub_svsplocus 329120 329267 320733 + L3 LINE/CR1 3929 4080 19
543 27.70 2.70 0.00 Crub_svsplocus 329120 329267 (320733) L3#LINE/CR1 3929 4080 (19) m_b7s001i0
Crub_svsplocu 329120 TGGAACAACCTGTCTCCAGAAGCTGTGAATGCTCTAACAATGGAAGTTTT 329169
iiiv i v? i iv iiv i iiv v i v
L3#LINE/CR1 3929 TGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTT 3978
Crub_svsplocu 329170 TAAGAAGAGACTGGACAGCCATTTGTCTGAAATGGTATAG---GGTTTCC 329216
i v i iii i v ii v i --- v
L3#LINE/CR1 3979 CAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCC 4028
Crub_svsplocu 329217 TGCCT-GAGTAGGGGGTTGGACTAGATGACTTTCAAGGTCCCTTCCAACT 329265
v - ii i i i ii
L3#LINE/CR1 4029 TGCATCGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACT 4078
Crub_svsplocu 329266 TT 329267
i
L3#LINE/CR1 4079 CT 4080
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 35.51
Transitions / transversions = 2.42 (29/12)
Gap_init rate = 0.01 (2 / 147), avg. gap size = 2.00 (4 / 2)
274 13.57 3.23 4.92 Crub_svsplocus 329215 329276 320724 + CR1L_fAlb LINE/CR1 33 93 6
274 13.57 3.23 4.92 Crub_svsplocus 329215 329276 (320724) CR1L_fAlb#LINE/CR1 33 93 (6) m_b7s001i1
Crub_svsplocu 329215 CCTGCCT-GAGTAGGGGGTTGGACTAGATGACTTTC-AAGGTCCCTTCCA 329262
i - i i - i i -i
CR1L_fAlb#LIN 33 CCTGCTTTGAGCAGGAGGTTGGACTAGA-GACCTCCTGAGGTCCCTTCCA 81
Crub_svsplocu 329263 ACTTTATTATTATT 329276
i v --
CR1L_fAlb#LIN 82 ACCTGA--ATTATT 93
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 15.53
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.08 (5 / 61), avg. gap size = 1.00 (5 / 5)
+ 616 33.5 4.2 3.9 Crub_svsplocus 331839 332682 (317318) + Gypsy72-I_DR LTR/Gypsy 1426 2294 (2003) 195
ANNOTATION EVIDENCE:
423 35.28 2.96 2.96 Crub_svsplocus 331839 332682 317318 + Gypsy-168-I_DR LTR/Gypsy 1426 2269 2022
423 35.28 2.96 2.96 Crub_svsplocus 331839 332682 (317318) Gypsy-168-I_DR#LTR/Gypsy 1426 2269 (2022) m_b7s001i2
Crub_svsplocu 331839 CCAGAGGAATACAGAGACCTTACTGAAATTTTCAGTGAGGAGAGGGCGAA 331888
v ? i ii ?i i iiv ii i i ii v v
Gypsy-168-I_D 1426 CCCGANGAGTACAAGGACCTNGCCGAAGCATTCAGCAAGAAAAAAGCCAC 1475
Crub_svsplocu 331889 TGAGCTCCCCCCCCCACCG-ACCCACAGACTGTGCCATTGAATTCAAGCC 331937
ii i v i - -ivvi - i i ? vvv
Gypsy-168-I_D 1476 CAAACTCCCACCTC-ACCGTGAGTAC-GATTGCGCCATTGANTTACTGCC 1523
Crub_svsplocu 331938 TGGGGCAAAACTCCC-----GAAGCCCAGATTATACTCCATGAGCCCAAA 331982
vi ? vi i ----- i --- ivi v v ii --- i
Gypsy-168-I_D 1524 TGGTACNACGCCCCCTCGTGGGAG---AATCTTTCCTCTGT---CTCAAA 1567
Crub_svsplocu 331983 GGAGAAGGAGGAA--ATGGAAAGATTCATAAAAAAAAAACCTAGAGAGGG 332030
v- ivv i -- i viv? v v ii ii ii- i ii
Gypsy-168-I_D 1568 C-AGAAACCGAAACCATGAACGCNTACATTAAGGAGGAGT-TGGAGAAAG 1615
Crub_svsplocu 332031 GTTTCATTGAGCCAGCCAAGCCTAAAGTGGCTTCCCCGG---TCCTTTTT 332077
v ?viv iv ? v i --- viv v v ? --- i i
Gypsy-168-I_D 1616 GATTCATNCGCCCGTCNACGTC---ACCCGCATCCGCNGGCTTCTTCTTT 1662
Crub_svsplocu 332078 AGAGAGAAGAAGGATGGCTCTTTACGCTTATGCGTGGATTATAGGGCCCT 332127
ivi vvvii iiv i v i i vii
Gypsy-168-I_D 1663 GTGGAGAAGAAGGATGGAAGCCTACGCCCCTGCATCGACTATAGAGGTTT 1712
Crub_svsplocu 332128 GAATACAATCAGTG-AAAGCAACCTATACCCTCTGCCCCTCATGAAAGAC 332176
iiv v? -? i- vv i ?i i vi vvv v?
Gypsy-168-I_D 1713 GAACGAAATCACNGTNAAGT-ACCGCTATCCNTTGCCTCTGGTCCCAGCN 1761
Crub_svsplocu 332177 ATGCTGTCACACCT---CTCGAAAGGGAAATTTTTTTCTCAACTAGACCT 332223
iiv vv vi --- --- vv ii vi v iv v i
Gypsy-168-I_D 1762 GCCCTGGAACAATTACGCTC---AGCCAGGTACTTTACCAAACTTGATCT 1808
Crub_svsplocu 332224 AAGGGAAGCGTACTATCGCGTGAGAATTAAGGAAGGGGATGAATGGAAGA 332273
vv viiv v v i v i ?v v v vii v i i i
Gypsy-168-I_D 1809 TCGCAGTGCCTACAACCTCATNCGCATAAAGCGGGGTGACGAGTGGAAAA 1858
Crub_svsplocu 332274 CCGCAT--TTAACTGCCCCATGGGATGCTATCAATTCAAAGTCTTGCCAT 332321
vi -- i? vi-- iv vii v v vii vv v
Gypsy-168-I_D 1859 CCGGGTTCTCNACGA--CCACCGGCCACTATGAATACCGGGTGATGCCCT 1906
Crub_svsplocu 332322 TTGGATTACAAGGGGGCCCTGCAGTCTT-TATGCAATTAATCAATGACGT 332370
i vi ivv iivi i v v -i v - v ? i v
Gypsy-168-I_D 1907 TCGGCCTGGCAAACAGTCCTTCCGTCTTCCAAGC-ATTCATNAACGAGGT 1955
Crub_svsplocu 332371 TCTAAGGGAGCACCTGTTTA---AGGGGGTCCTTGTTTACTTGGATGACA 332417
vi vv i --- v v --- iv v ? v v
Gypsy-168-I_D 1956 ATTTCGAG---ACATGTTGAACCAATGGGTCATTGTNTACATTGATGACA 2002
Crub_svsplocu 332418 TTCTTATCTTCACCGAAACAAAAGAGGAACATGTCAACCTTGTCAGAGCA 332467
i ii v v v ? vvv? i ? ii ivi vi v
Gypsy-168-I_D 2003 TCCTCGTCTACTCAGANACCCTNGAAGANCACATTCGCCACGTCAGAGCC 2052
Crub_svsplocu 332468 GTTTTAAAGAAACTG--CGAGCCGCCCACCTATATGCCAAACTCTCAAAA 332515
?i ?v i ?-- --iv v ? i i v v i
Gypsy-168-I_D 2053 GTNCTNCAGAGACTNATCGAG--AACCAGCTNTACGCCAAATTGTCCAAG 2100
Crub_svsplocu 332516 TGCAAATTCCACCAGGAAGGGATAGACTACCTAGGTTATCGCAT-ATCCC 332564
i i i iv?v v ivvv v i v ivv? - v v
Gypsy-168-I_D 2101 TGCGAGTTTCACCAGACNTGCACCTCCTTCCTGGGATACATNATCAGCGC 2150
Crub_svsplocu 332565 CCAGGGCATTGAAATGGACCCAGAGAAGATCAGAGCAGTATTAGATTGGG 332614
vv ? vi v v? vv ii? i v iv v ?? ii v
Gypsy-168-I_D 2151 AGANGGAGTGGCNATGGACGAAAGNAAGGTAAACGCTGTNNTGAATTGGC 2200
Crub_svsplocu 332615 CACCACCCCGCACAAGAAAGCAACTACAAAGTTTCCTGGGCTTTGCATAC 332664
vv ?vi? ?ivi v i? i v i i v i vv i
Gypsy-168-I_D 2201 CAAAACCNAANACNGTGAAGGAGNTGCAACGCTTTCTGGGGTTCGCCAAT 2250
Crub_svsplocu 332665 TTTT-CTGCCAATTCATCC 332682
i - v ?vi ?
Gypsy-168-I_D 2251 TTCTACAGNAGATTCATNC 2269
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 47.35
Transitions / transversions = 0.99 (144/145)
Gap_init rate = 0.04 (37 / 843), avg. gap size = 1.35 (50 / 37)
616 32.81 4.72 4.21 Crub_svsplocus 332068 332681 317319 + Gypsy72-I_DR LTR/Gypsy 1678 2294 2003
616 32.81 4.72 4.21 Crub_svsplocus 332068 332681 (317319) Gypsy72-I_DR#LTR/Gypsy 1678 2294 (2003) m_b7s001i3
Crub_svsplocu 332068 GGTCCTTTTTAGAGA-GAAGAAGGATGGCTCTTTACGCTTATGCGTGGAT 332116
i i v v - i i i i iiv i i i
Gypsy72-I_DR# 1678 GGTTCTTCTTTGTGAAGAAAAAGGATGGTTCTCTGCGCCCCTGCATAGAC 1727
Crub_svsplocu 332117 TATAGGGCCCTGAAT---ACAATCAGTGAAAGCAACCTATACCCTCTGCC 332163
v i vii --- i i v i --- i vi i i
Gypsy72-I_DR# 1728 TATCGAGGTTTGAATGACATAACCATTAAAA---ATCGGTACCCCCTACC 1774
Crub_svsplocu 332164 CCTCATGAAAGACAT--GCTGTCACACCTCTCGAAAGGGA-AATTTTTTT 332210
v i v---- v -- iv i- i i v i i- vv
Gypsy72-I_DR# 1775 GCTTATGT----CTTCGGCCTTCG-ATCTCTTGCAGGGGGCAAGATTTTT 1819
Crub_svsplocu 332211 CTCAA--CTAGACCTAAGGGAAGCGTACTATCGCGTGAGAATTAAGGAAG 332258
v --i i v vi v v i v vv v v i i
Gypsy72-I_DR# 1820 CACAAAGTTGGACCTACGCAATGCTTACCATCTCGTCCGTATGAGGGAGG 1869
Crub_svsplocu 332259 GGGATGAATGGAAGACCGCATTTAAC-TGCCCCATGGGATGCTATCAATT 332307
v i i -i vv ------- v
Gypsy72-I_DR# 1870 GTGACGAATGGAAGACCGCATTCAACACGCCCACTGGG-------CATTT 1912
Crub_svsplocu 332308 CAAA------GTCTTGCCATTTGGATTACAAGGGGGC-CCTGCAGTCTTT 332350
ii ------ i ii - vviiv - v
Gypsy72-I_DR# 1913 TGAATATCTTGTCCTGCCATTTGGGCT-CACCAATGCTCCAGCAGTCTTT 1961
Crub_svsplocu 332351 -ATGCAATTAATCAATGACGTTCTAAGGGAGCACCTGTTTAAGGGG---G 332396
- v - i vi i i v vv i --- v v vvii---
Gypsy72-I_DR# 1962 CAGGC-ACTCGTCAACGATGTACTCCGAG---ACATGATTAATCAATTTG 2007
Crub_svsplocu 332397 TCCTTGTTTACTTGGATGACATTCTTATCTTCACCGAAACAAAAGAGGAA 332446
ii i i iv ivvvi v viv
Gypsy72-I_DR# 2008 TTTTTGTTTATTTGGATGACATTCTTATTTTTTCTTCCGCCATGCAGGAA 2057
Crub_svsplocu 332447 CATGTCAACCTTGTCAGAGCAGTTTTAAAGAAACTGCGAGCCGCCCACCT 332496
v v vi iv ivv vi v ivii vi vvivi v
Gypsy72-I_DR# 2058 CATGTCCAACACGTTCGGCGAGTGCTACAACGGCTGCTGGAGAATCAGCT 2107
Crub_svsplocu 332497 ATATGCCAAACTCTCAAAATGCAAATTCCA---CCAGGAAGGGATAGACT 332543
i iv ivivvvi i i --- vv --- vvv
Gypsy72-I_DR# 2108 GTATGTAAAGGCGGAGAAGTGCGAATTCCATGTCCAGTCAG---TTTCCT 2154
Crub_svsplocu 332544 ACCTAGGTTATCGCATA--TCC--CCCAGGGCATTGAAATGGACCCAGAG 332589
v i i vi --- -- i --iiv vv viv v v
Gypsy72-I_DR# 2155 TCTTGGGACA---CATAATTTCAGTTGAGGGACTTCGCATGGACCCTGCG 2201
Crub_svsplocu 332590 AAGATCAGAGCAGTATTAGATTGGGCACCACCCCGCACAAGAAAGCAACT 332639
i i i v v iv i v i vi v vv vvii
Gypsy72-I_DR# 2202 AAGGTTAGGGCTGTCTCCGACTGGCCGCCACCCGACTCCCGAAAGGCGTT 2251
Crub_svsplocu 332640 ACAAAGTTTCCTGGGCTTTGCATACTTTT-CTGCCAATTCATC 332681
iv v i vv i - i v i
Gypsy72-I_DR# 2252 ACAGCGGTTCCTGGGCTTCGCCAATTTTTACCGGCGATTCATC 2294
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 39.25
Transitions / transversions = 1.01 (97/96)
Gap_init rate = 0.07 (40 / 613), avg. gap size = 1.38 (55 / 40)
+ 252 28.3 7.0 3.6 Crub_svsplocus 333212 333398 (316602) + Gypsy72-I_DR LTR/Gypsy 3248 3440 (858) 195
ANNOTATION EVIDENCE:
252 28.30 6.95 3.63 Crub_svsplocus 333212 333398 316602 + Gypsy-166-I_DR LTR/Gypsy 3248 3440 858
252 28.30 6.95 3.63 Crub_svsplocus 333212 333398 (316602) Gypsy-166-I_DR#LTR/Gypsy 3248 3440 (858) m_b7s001i4
Crub_svsplocu 333212 GGGAATACTGTTGTCTGGACGGTGACGGACTTGTTTTCCAAACAGGTGCA 333261
v i i i v ii ivv i ivv? iv
Gypsy-166-I_D 3248 GGTAACACCGTTGTTTTGACGGTGGTGGACCGCTTCTCCAAGGCNGCCCA 3297
Crub_svsplocu 333262 TTTTATCCC-TTGCCAAAAGATTCCCA-CCGCAAA--AGCCTTAGCAAAA 333307
- i v -- i i- v -- v -- vv i
Gypsy-166-I_D 3298 TTTTATCCCTTTACCCAA--ACTCCCGTCCGCCAAGGAGACT--GCTCAG 3343
Crub_svsplocu 333308 CTTTTCATCCAGCACAT-TTACAGATTGCATGGGGCACCCCAAC--ACAT 333354
v vv v iv v ?i - v i - ? -- vii ? i-- i
Gypsy-166-I_D 3344 GTGGTGATTGACCANGTCTTTCGGA-TNCAT--GGCCTTCCNATGGACGT 3390
Crub_svsplocu 333355 CATCTCTGACAGGGGGGTGCAATTTAC------ATTTTGGAAGGAATTTT 333398
vi i vi? ii------i i i i
Gypsy-166-I_D 3391 GGTCTCTGACAGAGGGCCNCAATTTGTCTCCCGGTTTTGGAAAGAGTTCT 3440
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 33.26
Transitions / transversions = 1.32 (29/22)
Gap_init rate = 0.07 (13 / 186), avg. gap size = 1.54 (20 / 13)
+ 13 21.6 4.7 0.0 Crub_svsplocus 342096 342138 (307862) + (ATTT)n Simple_repeat 1 45 (0) 196
ANNOTATION EVIDENCE:
13 21.59 4.65 0.00 Crub_svsplocus 342096 342138 307862 + (ATTT)n Simple_repeat 1 45 0
13 21.59 4.65 0.00 Crub_svsplocus 342096 342138 (307862) (ATTT)n#Simple_repeat 1 45 (0) m_b7s252i1
Crub_svsplocu 342096 ATTTATTTATTTATTT-TTTGGTAAGAGTTTTATTGATTT-TTTA 342138
- iv v vvvv v -
(ATTT)n#Simpl 1 ATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTA 45
Matrix = Unknown
Transitions / transversions = 0.14 (1/7)
Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2)
+ 16 22.5 8.1 1.3 Crub_svsplocus 342209 342282 (307718) + (AATT)n Simple_repeat 1 79 (0) 197
ANNOTATION EVIDENCE:
16 22.48 8.11 1.27 Crub_svsplocus 342209 342282 307718 + (AATT)n Simple_repeat 1 79 0
16 22.48 8.11 1.27 Crub_svsplocus 342209 342282 (307718) (AATT)n#Simple_repeat 1 79 (0) m_b7s252i2
Crub_svsplocu 342209 AATCAA-TA-TTAGTTAATTAA-GAGTCAA-TAA-TAATTAATTTTTATA 342253
i - - i -v i i - - vv -
(AATT)n#Simpl 1 AATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAATTAAT-TA 49
Crub_svsplocu 342254 TTTCCATAATTAGTAAATTAATTGA-TAAT 342282
v vvv i v i -
(AATT)n#Simpl 50 ATTAATTAATTAATTAATTAATTAATTAAT 79
Matrix = Unknown
Transitions / transversions = 0.75 (6/8)
Gap_init rate = 0.10 (7 / 73), avg. gap size = 1.00 (7 / 7)
+ 21 16.6 2.4 0.0 Crub_svsplocus 343764 343804 (306196) + (TA)n Simple_repeat 1 42 (0) 198
ANNOTATION EVIDENCE:
21 16.57 2.44 0.00 Crub_svsplocus 343764 343804 306196 + (TA)n Simple_repeat 1 42 0
21 16.57 2.44 0.00 Crub_svsplocus 343764 343804 (306196) (TA)n#Simple_repeat 1 42 (0) m_b7s252i3
Crub_svsplocu 343764 TATATAGTTCT-TATCTTTATATATATATATATATATTTATA 343804
vv v - v v v
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATA 42
Matrix = Unknown
Transitions / transversions = 0.00 (0/6)
Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1)
+ 19 0.0 0.0 0.0 Crub_svsplocus 345890 345910 (304090) + (AG)n Simple_repeat 1 21 (0) 199
ANNOTATION EVIDENCE:
19 0.00 0.00 0.00 Crub_svsplocus 345890 345910 304090 + (AG)n Simple_repeat 1 21 0
19 0.00 0.00 0.00 Crub_svsplocus 345890 345910 (304090) (AG)n#Simple_repeat 1 21 (0) m_b7s252i4
Crub_svsplocu 345890 AGAGAGAGAGAGAGAGAGAGA 345910
(AG)n#Simple_ 1 AGAGAGAGAGAGAGAGAGAGA 21
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
+ 23 8.1 2.6 0.0 Crub_svsplocus 345923 345961 (304039) + (ATAGTA)n Simple_repeat 1 40 (0) 200
ANNOTATION EVIDENCE:
23 8.12 2.56 0.00 Crub_svsplocus 345923 345961 304039 + (ATAGTA)n Simple_repeat 1 40 0
23 8.12 2.56 0.00 Crub_svsplocus 345923 345961 (304039) (ATAGTA)n#Simple_repeat 1 40 (0) m_b7s252i5
Crub_svsplocu 345923 ATA-TAATAGTAATAGTAATAGTAAAAGTAAAAGTAACAG 345961
- v v i
(ATAGTA)n#Sim 1 ATAGTAATAGTAATAGTAATAGTAATAGTAATAGTAATAG 40
Matrix = Unknown
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1)
+ 2656 31.3 1.3 1.7 Crub_svsplocus 345962 347024 (302976) C L3 LINE/CR1 (38) 4061 3003 201
ANNOTATION EVIDENCE:
2656 31.29 1.32 1.70 Crub_svsplocus 345962 347024 302976 C L3 LINE/CR1 3003 4061 38
2656 31.29 1.32 1.70 Crub_svsplocus 345962 347024 (302976) C L3#LINE/CR1 (38) 4061 3003 m_b7s001i5
Crub_svsplocu 345962 GAGGTCTTCTAATCCAACCCCCTGCTC-AGGCAGGAA-ACCTTATAC--C 346007
v i i iiii - v -v v --
C L3#LINE/CR1 4061 GAGGTCATCTAGTCCAACCTCCCATCCGATGCAGGAATCCCTTCTACAAC 4012
Crub_svsplocu 346008 ATTTCAAACAAATGGCTGTCCAGTCCCTTCTTAAAAACTTCCAGTGTTGG 346057
ii vi i iii i i v i v i vi
C L3#LINE/CR1 4011 ATCCCTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGG 3962
Crub_svsplocu 346058 AGCATTCACCGCTTCTGGAGGCAGGTTGTTCCACTGGTTAATTGTCCTAA 346107
i vii ii i ?v viii i vv vi iv ii i
C L3#LINE/CR1 3961 GGAGCTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGA 3912
Crub_svsplocu 346108 CTGTCAGGAAGTTTCTCCTTA-GTT----CTAGAT-TGCTTCTCTCCTTG 346151
i i i ii -i ---- v i - ---- i
C L3#LINE/CR1 3911 TTGTTAGAAAGTTCTTCCTTATATTGAGCCGAAATCTGC----CTCCCTG 3866
Crub_svsplocu 346152 ATCAATTTCCATCCATTGCTTCTTGTCCTGCCTTCAGGCACCTTGGAAAA 346201
--i i i v i v i i v vi viiv i
C L3#LINE/CR1 3865 --TAACTTCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAA 3818
Crub_svsplocu 346202 TAGCTTCACTCCGTCTTCTTTGGGGCAGCCCCTGAGATACTGGAACACTG 346251
iv ii v v iviiv i i v i i v v v
C L3#LINE/CR1 3817 TAAGTCTAATCCCTCTTCCACATGACAGCCCTTCAAATATTTGAAGACAG 3768
Crub_svsplocu 346252 CTATCATGTCCCCACTCGTCCTTCTCTTCATTAAACTAGACATACCCAAT 346301
i v vivi vii ii i v i
C L3#LINE/CR1 3767 CTATCATGTCTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGT 3718
Crub_svsplocu 346302 TCCAGCAGCCGTTCCTTATATGTTTAAGCCTCCAGTCCCCTAATCATCTT 346351
vv i i vivvi ii v i v i i
C L3#LINE/CR1 3717 TCCTTCAACCGTTCCTCATATGACATGGTTTCCAGACCCTTCACCATCCT 3668
Crub_svsplocu 346352 TGTTGCTCTTCTCTGTACTCTTTCTAGAGTCTCAACATCTTTTTTACATT 346401
v i i v v vi i vv v ii ii i v v
C L3#LINE/CR1 3667 GGTCGCTCTCCTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAAT 3618
Crub_svsplocu 346402 ATGGTGACCAAAACTGGATGCAGTATTCCAAGTATGGCCTTACCAAGGCA 346451
i i v i i i i i ii i i v iv
C L3#LINE/CR1 3617 GTGGCGCCCAGAACTGAACGCAATACTCCAGATGTGGTCTGACCAGCGCA 3568
Crub_svsplocu 346452 TTGTAAAGTGGCATTAATACTTCATGTGATCTTGATTCTATCCCTCTGTT 346501
vv v i v i v i viv ? v iv v i i
C L3#LINE/CR1 3567 GAGTACAGCGGGACTATTACCTCCCTTGNTCTGGACACTATACTTCTATT 3518
Crub_svsplocu 346502 AATGCAGCCTAGAACTGTGTTGGCCTTTTTGGCAGCTGCAGCACACTGTT 346551
ii i ii i i ii v
C L3#LINE/CR1 3517 AATGCAGCCTAAGATTGCATTAGCTTTTTTGGCAGCCACATCACACTGTT 3468
Crub_svsplocu 346552 GGCTCACATTTAAGTGATTGTCCACTAGGACTTCGAAGTCCCTCTCACAG 346601
i v iv viiv v ii ii v i ii i iv
C L3#LINE/CR1 3467 GGCTCATATTGAGCTTGCGGTCAACTAAAACCCCTAGGTCTTTTTCACGT 3418
Crub_svsplocu 346602 TTACTACTATTGAGCAAGGTACCCCCTATACTATAACTGTACATTTGGTT 346651
vv i ii i v i v i i i v i vi i v i
C L3#LINE/CR1 3417 GAACTGCTGCTAAGCCAGATCCTCTCCATCCTGTACTTGTGCAGTTGATT 3368
Crub_svsplocu 346652 TTTCTTGCCTAAATGTAGAACCTTACTTTTTTCACCATTGAATTTCATTT 346701
ivvi i i i v v v ii i i
C L3#LINE/CR1 3367 TTTTGAACCTAAATGCAGGACTTTACATTTATCCCTGTTAAATTTCATCT 3318
Crub_svsplocu 346702 TGTTAGATAGCGCCCAGTGTTGAAGTCTGTCCAGATCCTCCTGTATCTTA 346751
i v vvv vi vv i v ? ii v i
C L3#LINE/CR1 3317 TGTTGGTTTCGGCCCATCGTTCCAGCCTGTCGAGATCNTTTTGAATCTTG 3268
Crub_svsplocu 346752 AGCCTGTCTTCTGGAGTGTTGGCTATTCTTGTCAGCTTGGTGTCATCTGC 346801
vi v ii?v i i i i vi v
C L3#LINE/CR1 3267 ATTCTGTCATCCANCGTATTAGCTATCCCTCCCAGCTTTGTGTCATCTGC 3218
Crub_svsplocu 346802 AAATTTGATAATTTCCCCATCTATCCCCTCGTCCAAATTGTTGATGAAGA 346851
viviv v vi i i i ii i i
C L3#LINE/CR1 3217 AAATTTGATAAGCATGCCTTCTATGTCTTCATCCAAGTCATTGATAAAAA 3168
Crub_svsplocu 346852 GATTGAAGTGCACTGGGCCCAGAACAGAGCCCTGGGGCACCCCACTACAC 346901
vi vv v v v i v v --------
C L3#LINE/CR1 3167 TGTTGAACAGGACAGGGCCAAGGACAGAGCCCTGTGGCACGC-------- 3126
Crub_svsplocu 346902 ACTACACTACACACTTCCCTCCATGTAGATGCAGTTCCATTGAGGATCAC 346951
---- v v i v v iiiv v i vv v
C L3#LINE/CR1 3125 ----CACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTAATCAACAC 3080
Crub_svsplocu 346952 ACGCTGAGTATGG----CCAGCCATCTACGAATCCATCTGGTGGTAATGC 346997
vivi i i ----i i v i iiiv v ii
C L3#LINE/CR1 3079 CTTTTGGGTACGGTCGTTCAACCAGCTACGAATCCACCTAACTGTACTAT 3030
Crub_svsplocu 346998 TGTCTAACCCACATTTTTCTATCTTAT 347024
ii i i i i i i
C L3#LINE/CR1 3029 CATCCAGCCCATATTTCTCCATCTTGT 3003
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 40.76
Transitions / transversions = 1.60 (201/126)
Gap_init rate = 0.02 (25 / 1062), avg. gap size = 1.28 (32 / 25)
+ 64 1.7 0.0 0.0 Crub_svsplocus 347025 347083 (302917) + (AC)n Simple_repeat 1 59 (0) 202
ANNOTATION EVIDENCE:
64 1.72 0.00 0.00 Crub_svsplocus 347025 347083 302917 + (AC)n Simple_repeat 1 59 0
64 1.72 0.00 0.00 Crub_svsplocus 347025 347083 (302917) (AC)n#Simple_repeat 1 59 (0) c_b7s251i0
Crub_svsplocu 347025 ACACATACACACACACACACACACACACACACACACACACACACACACAC 347074
i
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50
Crub_svsplocu 347075 ACACACACA 347083
(AC)n#Simple_ 51 ACACACACA 59
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 58), avg. gap size = 0.0 (0 / 0)
+ 17 17.0 2.0 4.1 Crub_svsplocus 347954 348003 (301997) + A-rich Low_complexity 1 49 (0) 203
ANNOTATION EVIDENCE:
17 17.00 2.00 4.08 Crub_svsplocus 347954 348003 301997 + (CATAAAA)n Simple_repeat 1 49 0
17 17.00 2.00 4.08 Crub_svsplocus 347954 348003 (301997) (CATAAAA)n#Simple_repeat 1 49 (0) m_b7s252i6
Crub_svsplocu 347954 CATAAGAAAAT-AAATTTAAAAAAAAAATCAGTAAAACATAAAAGATAAA 348002
- v - iv v v v - v
(CATAAAA)n#Si 1 CATAA-AACATAAAACATAAAACATAAAACA-TAAAACATAAAACATAAA 48
Crub_svsplocu 348003 A 348003
(CATAAAA)n#Si 49 A 49
Matrix = Unknown
Transitions / transversions = 0.17 (1/6)
Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3)
+ 12 12.1 0.0 6.9 Crub_svsplocus 348892 348922 (301078) + (GTT)n Simple_repeat 1 29 (0) 204
ANNOTATION EVIDENCE:
12 12.09 0.00 6.90 Crub_svsplocus 348892 348922 301078 + (GTT)n Simple_repeat 1 29 0
12 12.09 0.00 6.90 Crub_svsplocus 348892 348922 (301078) (GTT)n#Simple_repeat 1 29 (0) m_b7s252i7
Crub_svsplocu 348892 GTTGTTGTTGTTAACTTGTTGTTTTTCTTGT 348922
--v v v
(GTT)n#Simple 1 GTTGTTGTTGTT--GTTGTTGTTGTTGTTGT 29
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2)
+ 522 25.3 4.4 0.0 Crub_svsplocus 352838 352995 (297005) + Plat_L3 LINE/CR1 3396 3560 (13) 205
ANNOTATION EVIDENCE:
522 25.32 4.43 0.00 Crub_svsplocus 352838 352995 297005 + Plat_L3 LINE/CR1 3396 3560 13
522 25.32 4.43 0.00 Crub_svsplocus 352838 352995 (297005) Plat_L3#LINE/CR1 3396 3560 (13) m_b7s001i6
Crub_svsplocu 352838 AACCAGTGGAACAATCTGCCTCCAGAAGCTGTGAATGCTCCAACAATGGA 352887
v v iiv i vvvi i i i vv v vv
Plat_L3#LINE/ 3396 AAACACTGGAACGGGCTACCGAGGGAGGTTGTGGAGTCTCCATCCCTGGA 3445
Crub_svsplocu 352888 AGTTTTTAAGAA--GACTGGACAGCCATTTGTCTGAAATGGTATAGGGTT 352935
ii i -- v i ? i ivii v vvv
Plat_L3#LINE/ 3446 GATCTTTAAGAAAAGAATAGACANCCATCTGTCCTGGATGGTTTAGTCAT 3495
Crub_svsplocu 352936 TC--CTGCCTGA--GCAGGGGATTGGACTAGATGACCT-TCAAGGTCCCT 352980
-- i-- ii i - i
Plat_L3#LINE/ 3496 TCACCTGCCTGGAGGCAGGGGGCTGGACCAGATGACCTCTCGAGGTCCCT 3545
Crub_svsplocu 352981 TCCAACTTTATTATT 352995
i i ?v
Plat_L3#LINE/ 3546 TCCAGCTCTANGATT 3560
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 30.01
Transitions / transversions = 1.22 (22/18)
Gap_init rate = 0.03 (4 / 157), avg. gap size = 1.75 (7 / 4)
+ 30 0.0 0.0 0.0 Crub_svsplocus 354320 354347 (295653) + (CCCT)n Simple_repeat 1 28 (0) 206
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 Crub_svsplocus 354320 354347 295653 + (CCCT)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 Crub_svsplocus 354320 354347 (295653) (CCCT)n#Simple_repeat 1 28 (0) c_b7s251i1
Crub_svsplocu 354320 CCCTCCCTCCCTCCCTCCCTCCCTCCCT 354347
(CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 1119 34.1 2.2 1.9 Crub_svsplocus 355761 356569 (293431) + MamGypsy2-I LTR/Gypsy 1780 2591 (1575) 207
ANNOTATION EVIDENCE:
1119 34.13 2.22 1.85 Crub_svsplocus 355761 356569 293431 + MamGypsy2-I LTR/Gypsy 1780 2591 1575
1119 34.13 2.22 1.85 Crub_svsplocus 355761 356569 (293431) MamGypsy2-I#LTR/Gypsy 1780 2591 (1575) m_b7s001i7
Crub_svsplocu 355761 GTTGATGAGGTATCTGCAGAGGCCCAGACTATTGTAACTCACAGGGGGGC 355810
i i v ivv v i v ii v iv i
MamGypsy2-I#L 1780 GTCGGTGATGCTACTGCAGACGCCCAAACAATCATCACTCATCGAGGGGC 1829
Crub_svsplocu 355811 CTTCAAGGTCAAAAGACTGCAATTTGGGGTAAATGTAGCCCCTGGCATAT 355860
v vii i iv v v i i ii vvv v v v
MamGypsy2-I#L 1830 ATTCCGAGTTAAGCGCCTTCAGTTCGGAATTTCTGTTGCCCCTGGAATTT 1879
Crub_svsplocu 355861 TCCAAAGTGTTATGGAGAGCACACTT-CGAGGTATTCCTGGAGTCTGTCC 355909
iv iv i v vii - v - v v v- v
MamGypsy2-I#L 1880 TCCAGTGCTTCATGGAGACCCTGCTTTCTAGG-ATTCCAGGTGTG-GTAC 1927
Crub_svsplocu 355910 C-TACTTTGATGATGTCCTCGTTGCTGGGGAGTCATCTCAAAAT---TTA 355955
- i i vi iii-- - v vv ii ---i v
MamGypsy2-I#L 1928 CATATTTCGATGATGTCCTGATCAT--GGGA-TCAACAGAGGATGAACTC 1974
Crub_svsplocu 355956 GCAGAAAGG-TTAAGGACTGTCTTGCTTCATTTTCAAAAAGCAGGCCTTA 356004
i i- v v- i i v i iv v v v iv iv
MamGypsy2-I#L 1975 GCGGAAAGACTTCAGGAA-GTCCTACATCGTTTCGATACATCAGGTATCC 2023
Crub_svsplocu 356005 AATTAAAGCAGAATAAATGCAAGATAGGAGTCACTTCTACTG--AC---- 356048
i v i iv i v ii i v --- i v -- ----
MamGypsy2-I#L 2024 GAGTGAAAAAGGAGAAATGTGAAATCGGA---ACTTCCAGTGTCACCTTC 2070
Crub_svsplocu 356049 TTAGAGTTCAGGATTGATGCCCAAGGCATTCAACCTGCTGAATCAAAGCT 356098
iv v v v ii ivvv i v ii v vvv v
MamGypsy2-I#L 2071 TTAGGCTACCGCATCAATGCTGCTGGTATTCACCCCACTCAAGATAAGGT 2120
Crub_svsplocu 356099 GCAAACTATTCAGCAGGCCCCAAGCCTCAAGTCCAAAA-GTGAGCTTCAA 356147
i ivi v i vv v v v - ii ivv i-iv
MamGypsy2-I#L 2121 ACGTGCAATCCATGACGCGCCTA-CTCCAAAAACAAAGCAAGAGCTTCAA 2169
Crub_svsplocu 356148 GCCTTCTTGGGACTCTTAAATTTTTACCATGGATTTCTCCCACATAAGGC 356197
i i vi v i vv i v
MamGypsy2-I#L 2170 GCCTTCCTGGGGCTACTCAATTTCTACCATGTTTTTCTTCCACAAAAGGC 2219
Crub_svsplocu 356198 TGCAGTGGCAGAGCCATTACACAGGCTCTTAGATAAGCAGGTTCCATGGC 356247
vi vi v v i v iv v vi i iv iviv i
MamGypsy2-I#L 2220 AACCATTGCTGAGCCACTTCATCGCCTACTGGGAAAAGGCGTTCCGTGGC 2269
Crub_svsplocu 356248 AGTGGACTAAAGTC--CATGACAGGAGTTTCAATGAGGTTAAGGCCTTGC 356295
iv --v i -- viiviv vivi v i vvv ii
MamGypsy2-I#L 2270 GTTGGACT--CGCCAGCATGAGGACGCTTTCCGGAATGTCAAGCAGTTAT 2317
Crub_svsplocu 356296 TCACTTCAAATGCTGTTTTAGCACATTTCAATGAGC---AACTGCCTGTT 356342
v vi vv vi i v i i --- ii-
MamGypsy2-I#L 2318 TGACTTCCGAGTCTGTGCTAGTACATTACGATGAACATAAACCA-CTGTT 2366
Crub_svsplocu 356343 TGCATCGCATGCGATGCATCTCCTTATGGGGTGGGAGCAGTACTTAGTCA 356392
- v vv i-i i v v i v iv v i i
MamGypsy2-I#L 2367 T-CTTACCAC-TGACGCTTCACCTTACGGTGCTGGAGCTGTGCTTAGCCA 2414
Crub_svsplocu 356393 CCTGAAGGTTGATGGGACACAAGTCCCTGTGGCCTACTACTCAAGGACTC 356442
vvi v viv v vv i iv vi v i i vv
MamGypsy2-I#L 2415 CAAAATGCCAGATGGCACTGAGGCACCAATTGCTTACTACTCAAGAACAA 2464
Crub_svsplocu 356443 TGTCATCTGCAGAGTGGAATTACGCTCAGATTGACAGAGAAGCCTTGGCC 356492
i ii i ii v i i i v i
MamGypsy2-I#L 2465 TGTCATCTACAGAACGGAACTATACACAAATTGACAAAGAAGCCCTTGCT 2514
Crub_svsplocu 356493 ATCATGGCTGGCATAAAGAAATTCCATGATTTCTTATATGGCTGCCACTT 356542
i i v v vi v i ii i v i v i i ivv
MamGypsy2-I#L 2515 GTTATCGCGGGAGTCAAGAAGTTCCACAACTACCTCTACGGCCGTGCCTT 2564
Crub_svsplocu 356543 CATGGTCTATACAGACCATAAGCCTCT 356569
i iii i i v i i
MamGypsy2-I#L 2565 TACAATTTGTACTGATCACAAGCCTCT 2591
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 41.90
Transitions / transversions = 1.02 (137/134)
Gap_init rate = 0.03 (24 / 808), avg. gap size = 1.38 (33 / 24)
+ 316 5.1 0.0 0.0 Crub_svsplocus 360312 360350 (289650) + hAT-N53_DR DNA/hAT-Ac 2760 2798 (3021) 208
ANNOTATION EVIDENCE:
316 5.13 0.00 0.00 Crub_svsplocus 360312 360350 289650 + hAT-N53_DR DNA/hAT-Ac 2760 2798 3021
316 5.13 0.00 0.00 Crub_svsplocus 360312 360350 (289650) hAT-N53_DR#DNA/hAT-Ac 2760 2798 (3021) m_b7s001i8
Crub_svsplocu 360312 GTGTATGTGTGTGTGTATACACACACACACACACACACA 360350
i i
hAT-N53_DR#DN 2760 GCGTGTGTGTGTGTGTATACACACACACACACACACACA 2798
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 2.90
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 17 17.0 2.0 4.1 Crub_svsplocus 363714 363763 (286237) + A-rich Low_complexity 1 49 (0) 209
ANNOTATION EVIDENCE:
17 17.00 2.00 4.08 Crub_svsplocus 363714 363763 286237 + (CATAAAA)n Simple_repeat 1 49 0
17 17.00 2.00 4.08 Crub_svsplocus 363714 363763 (286237) (CATAAAA)n#Simple_repeat 1 49 (0) m_b7s252i8
Crub_svsplocu 363714 CATAAGAAAAT-AAATTTAAAAAAAAAATCAGTAAAACATAAAAGATAAA 363762
- v - iv v v v - v
(CATAAAA)n#Si 1 CATAA-AACATAAAACATAAAACATAAAACA-TAAAACATAAAACATAAA 48
Crub_svsplocu 363763 A 363763
(CATAAAA)n#Si 49 A 49
Matrix = Unknown
Transitions / transversions = 0.17 (1/6)
Gap_init rate = 0.06 (3 / 49), avg. gap size = 1.00 (3 / 3)
+ 249 17.5 0.0 0.0 Crub_svsplocus 366127 366166 (283834) + AmnSINE2 SINE/tRNA-Deu 80 119 (239) 210
ANNOTATION EVIDENCE:
249 17.50 0.00 0.00 Crub_svsplocus 366127 366166 283834 + AmnSINE2 SINE/tRNA-Deu 80 119 239
249 17.50 0.00 0.00 Crub_svsplocus 366127 366166 (283834) AmnSINE2#SINE/tRNA-Deu 80 119 (239) m_b7s001i9
Crub_svsplocu 366127 CAAGGTTGACTCAGCCTTCCATCCTTTTGAGGTTGATAAA 366166
i i i i ii v
AmnSINE2#SINE 80 CAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAGATAAA 119
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 14.68
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 402 13.8 0.0 0.0 Crub_svsplocus 367054 367118 (282882) + URR1A DNA/hAT-Charlie 1 65 (161) 211
ANNOTATION EVIDENCE:
402 13.85 0.00 0.00 Crub_svsplocus 367054 367118 282882 + URR1A DNA/hAT-Charlie 1 65 161
402 13.85 0.00 0.00 Crub_svsplocus 367054 367118 (282882) URR1A#DNA/hAT-Charlie 1 65 (161) m_b7s001i10
Crub_svsplocu 367054 CAGCTGTTCTCAACCTATGGGTCGCGACCCCATTTGGGGTCGAATGACCA 367103
v i v v i v
URR1A#DNA/hAT 1 CAGCGGTTCTCAACCTGTGGGTCGCGACCCCTTTGGGGGTCGAACGACCC 50
Crub_svsplocu 367104 TTTTATGGGGGTCGC 367118
i ii
URR1A#DNA/hAT 51 TTTCACAGGGGTCGC 65
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 13.68
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0)
+ 1488 32.6 3.0 3.3 Crub_svsplocus 368423 369851 (280149) + RTE1_ChrAsi LINE/RTE-BovB 89 1513 (1723) 212
ANNOTATION EVIDENCE:
1488 32.56 3.01 3.30 Crub_svsplocus 368423 369851 280149 + RTE1_ChrAsi LINE/RTE-BovB 89 1513 1723
1488 32.56 3.01 3.30 Crub_svsplocus 368423 369851 (280149) RTE1_ChrAsi#LINE/RTE-BovB 89 1513 (1723) m_b7s001i11
Crub_svsplocu 368423 GCAGGGCCACCCAAGACGGACAGGTTATAGCAGAGAGTTCTGACAAAATG 368472
i v ii vi vv vv i v i ---
RTE1_ChrAsi#L 89 GCAGGGTCACCCATGGTGGACAGGTTTCAGATGAGCTTCCAGACGAA--- 135
Crub_svsplocu 368473 TGATCCACT-GGAGAAGGAAATGGCAAACCACTCCAGTATCTTT-GCCA- 368519
- ivv - ii i i i i i i i v v v - i -
RTE1_ChrAsi#L 136 -GACAGACTAGGAAGAAGGAGTGACGAACTACTTCCGAATATTTAGTCAC 184
Crub_svsplocu 368520 TGAAAACCCCATGGACAGTACTAAAAGGAAAAA-----AGATATGACGCT 368564
ii i i i -----ii v ----- iii i
RTE1_ChrAsi#L 185 TGAAAACCTTATGAATAGCA-----GAGAAACACTGTCAGATATAGTGCC 229
Crub_svsplocu 368565 GGAAGATGAGCCCCTCAGGTCGGAAGGTGTCCAATGTGCTACTGGGGAAG 368614
i i iiii vi v
RTE1_ChrAsi#L 230 GGAAAATGAGCCCCTCAGGTTGGAAGGCACTCAAAATGCGACTGGGGAAG 279
Crub_svsplocu 368615 AGCGGAGGGCTAGTACTAGTAGCGCCAGAAAGAATGAAGCGACTGGGCCA 368664
v v--- vv vvv v iiiivvivi v v ivi
RTE1_ChrAsi#L 280 AGCTGC---CTCCTCAAAGTAGAGTTGACCGTGATGACGCGAATGGAGTA 326
Crub_svsplocu 368665 AAGCCGAAAGGACGCTCA---GCTG--TGGATATATCTGGTGGTGAAAGG 368709
vivi vi --- --v ii i v vivii ii
RTE1_ChrAsi#L 327 AAGCCCGCGGGACCTTCATTTGCTGATGGGGCACAACTCAAAATGAAGAG 376
Crub_svsplocu 368710 AAAGTCCGATGCTGTAAAGATTTTTTCTCCATAGGAACCTGGAATGTAAG 368759
--- i-- v iiv vv?v v v v
RTE1_ChrAsi#L 377 AAA---CA--GCTGTAAACATCCATTGANAATCGGAACATGGAATGTACG 421
Crub_svsplocu 368760 ATCCATGAATCAAGGCAAGCTAGACGTAGTCAAAAAAGAGATGACAAGAC 368809
vvi vi v ii i v v v i iv v vv
RTE1_ChrAsi#L 422 AAGTATGAATCTGGGAAAATTGGAAGTTGTCAAAAATGAAATGGAACGCA 471
Crub_svsplocu 368810 TGAACATCGACATCTTAGGAATCAGCGAACTAAAATGGACAGGAATGGGT 368859
i i v i i i i v v v i
RTE1_ChrAsi#L 472 TAAACATCGATATCTTAGGCATTAGTGAGCTGAAATGGACTGGTATTGGC 521
Crub_svsplocu 368860 GAATTTAACTCAGATGACCATCAAGTATACTACTGTGGGCAA----GAAT 368905
v v i v v i ivvi v - iv v ----i
RTE1_ChrAsi#L 522 CATTTTGAATCTGACGACCACATGGTTTACTA-TGCCGGGAATGACAAAT 570
Crub_svsplocu 368906 CCCTCAGAAGAAATGGAGTAGCCTTCATAGTCAATAAAAGAATAGGAAAA 368955
--- v ii i v v v v v i iv vvv i
RTE1_ChrAsi#L 571 ---TGAAGAGGAATGGTGTTGCATTCATCGTCAAAAAGAACATATCCAGA 617
Crub_svsplocu 368956 GCAATACTGGGATACAATCCCCAAAATGACAGATTGATCTCAATTCGAAT 369005
v i vv i i iv ivvvvi i iv i v v v vv
RTE1_ChrAsi#L 618 TCAGTCATGAGGTACAACGCTGTCTGTGATAGGATAATATCCATGCGCCT 667
Crub_svsplocu 369006 CCAAGGCAAACCATTCAATATCACAATAGTCCAAATCTATGCCCCAACCA 369055
v i v i? v i i v vi i i i v
RTE1_ChrAsi#L 668 ACAGGGAAGNCCAGTTAATACCACTATTATTCAAATTTACGCACCAACCA 717
Crub_svsplocu 369056 CTGGTGCTGAAGAGGATGAAATTGACCGGTTCTATGAAGCCCTACAGCAC 369105
iiv iiiv v vvii iv vii v -- i
RTE1_ChrAsi#L 718 CTAAAGCCAGTGAGGATGAAATAGAAGAATTCTACCAACTTCTTCA--AT 765
Crub_svsplocu 369106 CTTATAGAATT-----AACACCCAAAAATGATGTCCTTATCATCATGGGG 369150
v --- ----- iv vv v vi v i iv v
RTE1_ChrAsi#L 766 CTGA---AATTGATCAAACATGCAATCAAGATGTATTGATCATTACTGGT 812
Crub_svsplocu 369151 GATTGGAATGCTAAGGTAGGAAGCCAAAAG--ATAACCGGAATAACAGGC 369198
v v i v i -- vi i -- i iiv v
RTE1_ChrAsi#L 813 GATTGGAATGCAAAGGTTGGGAGCAAAGAGGAAGGATC--AGTAGTTGGA 860
Crub_svsplocu 369199 AAGCTTGGCCTTGGAG-TACAAAATGAAGCAGGGCACAGGCTAATAGAAT 369247
iiv v - -i v v iv ?v vv i
RTE1_ChrAsi#L 861 AAATATGGCCTTGGTGATA-GAAATGATGCTGGAGANCGCATGATAGAAT 909
Crub_svsplocu 369248 TTTGTCAAGAGAATACGATGGTCATAACAAACACTCTTTTCCAACAACCC 369297
i iv ivv ivvv v vv i ii i ivi i vi
RTE1_ChrAsi#L 910 TCTGCAAAACCAATGATTTGTTCATTTCAAATACCTTCTTTAGACAGCAT 959
Crub_svsplocu 369298 AAGAGACGGCTCTACACATGGACATCACCAGACGGTCAACATAGAAATCA 369347
i v v i vvv i
RTE1_ChrAsi#L 960 AAGAGACGACTATACACATGGACCTCACCAGATGGAATACACAGAAATCA 1009
Crub_svsplocu 369348 GATTGACTATGTGCTCTGCAGCCAAA---GATGGAGAAGCTGTATACAGG 369394
i ii--- i vv i --- i vi iviv
RTE1_ChrAsi#L 1010 AATTGACTACA---TCTGCGGAAAGAGACGATGGAAAAGCTCCATATCAT 1056
Crub_svsplocu 369395 CAGTAAAAACAAGACCAGGAGCTGACTGTGGCTCAGATCATGATCTTCTC 369444
v i i v vv i v vi v
RTE1_ChrAsi#L 1057 CAGTCAAAACAAGGCCAGGGGCAGACTGTGGAACAGACCATCAATTGCTC 1106
Crub_svsplocu 369445 GT-TGCAAAATTTAGGCTTAAATTAAAAAAAGTAGGGAAAAG--CACTAG 369491
i - - i ii v ii i i i iiii v -- v
RTE1_ChrAsi#L 1107 ATATGC-AAATTCAAACTGAAGCTGAAGAAAATGAAAACAAGTCCACGAG 1155
Crub_svsplocu 369492 -GCCACTCAGGTATGAACTAAATCATATTCCTGATGAATATACAGTAGAG 369540
- --- ii v vi vi i vvv v v vvv v
RTE1_ChrAsi#L 1156 AGCCA---AAATATGACCTTGAATATATCCCACCTGAATTTAGAGATCAT 1202
Crub_svsplocu 369541 GTGACAAATAGATTTAAGGAACTGGAT-CTGATAGACAGAATGCCTGAAG 369589
v vi i i viv i ii i- i - v vi v
RTE1_ChrAsi#L 1203 CTGAAGAACAGATTTGATACATTAAACACTAA-AGACCGAAGACCAGAAG 1251
Crub_svsplocu 369590 AACTATGGATGGAAGTTCGCAACATTGTACAAG-AGGTAGCAACTAAAAC 369638
ii i ivv vi iviv ii v - iv -- ii
RTE1_ChrAsi#L 1252 AGTTGTGGGATGACATCAAGAACATCATACATGAAGAAAGCAA--AAAGT 1299
Crub_svsplocu 369639 CATCCCAAAGA-AAAAGAAATGCAAGAAAGCAAAATGGCTGTCTGAGGAA 369687
ivvi - i i i v v i iiv v v i i
RTE1_ChrAsi#L 1300 CATTAAGAAGACAAGAAAGAAGGAAAAGGTCAAAATGGATGTCAGAAGAG 1349
Crub_svsplocu 369688 GCTTTGCAAATAGCTGAGGAAAGAAGGGAAGCGAAAGGCAAA--GGAGAA 369735
i vi v v v vvvv iv v i v v - -- i
RTE1_ChrAsi#L 1350 ACACTGAAACTTGCTCTCCAGCGTAGAGATGCTAAA-GCAAATGGAAGAA 1398
Crub_svsplocu 369736 AGAGAAAGATACACCCAATTGAATGCAGAATTCCAGAGAGTAGCTAGAAG 369785
viiii i -vv ii iiv i i i ivi v ii
RTE1_ChrAsi#L 1399 ATGAGGAGGTACA-AGAGCTGAACAGAAAATTTCAAAGGTCAGCTCGAGA 1447
Crub_svsplocu 369786 AGATAAGAATGCC--TTCTTA-AATGAACAGTGCAAAGAAATAGA---AG 369829
i i--- --v v - i vv vv i ---
RTE1_ChrAsi#L 1448 AGACAAA---GCCAAATATTACAACGAAATGTGCAAAGATCTGGAGTCAG 1494
Crub_svsplocu 369830 AAAACAACAGAATAGGGAGGAC 369851
-- i - i i
RTE1_ChrAsi#L 1495 AAAAC--CAAAA-AGGAAGAAC 1513
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 42.23
Transitions / transversions = 1.07 (233/217)
Gap_init rate = 0.05 (67 / 1428), avg. gap size = 1.34 (90 / 67)
+ 2218 31.6 2.9 2.6 Crub_svsplocus 370174 371574 (278426) + RTE1_ChrAsi LINE/RTE-BovB 1832 3236 (0) 212
ANNOTATION EVIDENCE:
2218 31.57 2.86 2.56 Crub_svsplocus 370174 371574 278426 + RTE1_ChrAsi LINE/RTE-BovB 1832 3236 0
2218 31.57 2.86 2.56 Crub_svsplocus 370174 371574 (278426) RTE1_ChrAsi#LINE/RTE-BovB 1832 3236 (0) m_b7s001i12
Crub_svsplocu 370174 CACTCA-ATTTGCCAGCAAATTTGGAAAACTCAACAGT--GGCCACAGGA 370220
-v ? iv i -- vi -- ivvv
RTE1_ChrAsi#L 1832 CACTCATCTNTGCCAAGAAATTTGGAAGAC--AACTATCTGGCCGACTGA 1879
Crub_svsplocu 370221 TTGGAAAAGGTCAGTTTACATTCCAATTCCAAAGAAAGGCAATGCCAA-A 370269
i i v v vii v v i ii i- -i
RTE1_ChrAsi#L 1880 TTGGAAGAGATCCGTATTTGTGCCCATTCCAAAGAGAGGTGAC-CCAACG 1928
Crub_svsplocu 370270 GAATGTTCAAACTATCGCACCATTGCACTCATTTCACATGCTAGTAAAGT 370319
ivv ii v v ?v vi v v v v
RTE1_ChrAsi#L 1929 GAATGCGGAAATCATCGGACAATNTCTTTGATATCCCATGCGAGTAAAGT 1978
Crub_svsplocu 370320 TATGCTTAAAATCCTACAAGCTAGACTCCA-GCAGTATGTGGATCGAGAA 370368
v i v ii vv iivvv i v - - ii v iv
RTE1_ChrAsi#L 1979 TTTACTAAAGGTAATACAGAAACGGCTGCAAGCA-TACATTGACAGAGAA 2027
Crub_svsplocu 370369 CTACCAGAAGTACAGGCAGGATTTCGAAGAGGCAGAGGAACTAGAGATCA 370418
v i v i v iv v v v i vv
RTE1_ChrAsi#L 2028 CTTCCAGAGGTTCAAGCCGGATTCAGAAGAGGCCGTGGAACGAGGGATAT 2077
Crub_svsplocu 370419 AATTGCCAACATACGCTGGATCATGGA-GAAAGCTAGGGAGTTCCAGAAA 370467
v ii ii v v v v- - i i v
RTE1_ChrAsi#L 2078 CATTGCTGATGTCCGATGGATCTTGGCTGAAAGC-AGAGAATACCAGAAA 2126
Crub_svsplocu 370468 AACATCTACTTCTGCTTCATTGACTATGCTAAAGCCTTTGATTGTGTGGA 370517
i ii i i v i i v i i i
RTE1_ChrAsi#L 2127 GATGTTTACCTGTGCTTTATTGACTACGCAAAGGCTTTCGATTGTGTGGA 2176
Crub_svsplocu 370518 TCACAACAAATTGTGG-CAAGTTCTTAAAGAGATGGGAGTA--CCAGACC 370564
ii ii i - vv ivii --- iv -- i v
RTE1_ChrAsi#L 2177 TCATGACAAGCTATGGACAACATTGCGAAG---TATGAGTATTCCGGAAC 2223
Crub_svsplocu 370565 ATCTCATTTGT-CTCTTGAGAAACCTATATGCGGGTCAAGAAGCAACAGT 370613
- i v - v i i i iii ii i iiv
RTE1_ChrAsi#L 2224 A-CTTAATTGTGCTCATGAGGAATCTGTACATGGACCAAGAGGCAGTTGT 2272
Crub_svsplocu 370614 GAGAACCGAACACGGAACCACTGATTGGTTCAAAATTGGAAAAGGAGTCC 370663
vv v i i v v i iii v v
RTE1_ChrAsi#L 2273 TCGAACAGAACATGGGAACACTGAATGGTTTAAAATTAAGAAAGGTGTGC 2322
Crub_svsplocu 370664 GGCAAGGCTGTATACTGTCGCCCTGCCTATTTAACTTATATGCAGAGCAC 370713
i i i v v i v i i i i i v v
RTE1_ChrAsi#L 2323 GACAGGGTTGTATTCTTTCACCATACTTATTCAACCTGTATGCTGAGCAA 2372
Crub_svsplocu 370714 ATCATGAGAAAGGCAGGGCTAGATGAATCAAAAGTTGGAATTAAGATTGC 370763
v vv i i v i v vv vv v i i v
RTE1_ChrAsi#L 2373 ATAATCCGAGAAGCTGGGTTATATGAAGAAAAACGTGGCATCAGGATTGG 2422
Crub_svsplocu 370764 CGGGAGAAATATCAACAACCTAAGATATGCAGATGATACCACTCTAATGG 370813
v i vvi i iv v ii iv v
RTE1_ChrAsi#L 2423 AGGAAGACTCATTAACAACCTGCGATATGCAGATGATACAACCTTGCTTG 2472
Crub_svsplocu 370814 CAGAAAGTGAAGAGGAACTAAAGAGCCTCTTGATGCAGGTGAAGAAGGAG 370863
v vi iviii vi v i v ii v v
RTE1_ChrAsi#L 2473 CTGAAAGTGAAGAGGACTTAAAATATTTACTGATGAAGATCAAAGAGCAC 2522
Crub_svsplocu 370864 AG--TGCAAAAGTTGGCTTGAAACTCAACATTAAGAAAACCAAAATCATG 370911
-- v iiv -- v v v ii v v v v
RTE1_ChrAsi#L 2523 AGCCTTCGGTA--TGGATTGCATCTCAATGTAAAGAAAACAAAAATCCTC 2570
Crub_svsplocu 370912 GCATCCGGCCCTCT---CA--ATTCCTGGCAAATAGATGGGGAAGAAATG 370956
i vv i v vv --- -- i iv ----- i i i i v
RTE1_ChrAsi#L 2571 ACCACTGGACCAATAAACAACATTCTTATCA-----ACGGAGAAAAGATT 2615
Crub_svsplocu 370957 GAGGTAGTGACAGATTTTATCTTTCTGGGCTCAAAGATTACCTCAGATGG 371006
i v v vi i i ii v v vv i v v vv i
RTE1_ChrAsi#L 2616 GAAGTTGTCAAGGACTTCATTCTTCTTGGATCAACTATCAACACTCACGG 2665
Crub_svsplocu 371007 GGACTGCAGCCAAGAAATTAAAAGACGC-TTGCTCCTGGGGAGGAAAGCT 371055
iii v i i v i- -vi i --- v v
RTE1_ChrAsi#L 2666 AAGCAGCAGTCAAGAAATCAAACGACGTATTGC-ATTAG---GCAAATCT 2711
Crub_svsplocu 371056 ATGGCAAATCTAGAC------AGCATTCTAAAAAGCAGAGACATCACCCT 371099
iiv v --- ------ ivi vi i i i ii v i
RTE1_ChrAsi#L 2712 GCTGCACA---AGACCTTTTTAAAGTGTTGAAGAGCAAAGATGTCAGCTT 2758
Crub_svsplocu 371100 GCCAACAAAAGTGCGTATAGTCCAGGCCATGGTTTTCCCAGTTGCAATGT 371149
vvi v i iv iii i v ii i vi vvii
RTE1_ChrAsi#L 2759 GAGGACTAAGGTGCGCCTGACCCAAGCCATGGTATTTTCAATAACCTCAT 2808
Crub_svsplocu 371150 ATGGCTGTGAAAGTTGGACCATAAGAAAGGCTGAACGCAAAAGAATTGAG 371199
vv i i vi i iv vv v i i v
RTE1_ChrAsi#L 2809 ATGCATGCGAAAGCTGGACAGTGAATAAGGAAGACCGTAGAAGAATTGAT 2858
Crub_svsplocu 371200 GCTTTTAAACTATGGTGCTGGAGAAGACTCCTGCGAGTCCCTTGGACTGC 371249
? i ii i i v vi vi v v i
RTE1_ChrAsi#L 2859 GCNTTTGAGTTATGGTGTTGGAGGAGAATATTGAAAGTGCCATGGGCTGC 2908
Crub_svsplocu 371250 AAGGCGTTCAAACCGGTCAGTCCTAGAAGAGATCAACCCCGACTGCTCTT 371299
v iiv vv v v i v vi i ii vv v v v i
RTE1_ChrAsi#L 2909 CAAAAGAACCAACAGATCTGTGTTGGAAGAAGTGCAGCCAGAGTGCTCCT 2958
Crub_svsplocu 371300 TAGAAGGCCA-GATCCTGAAGTTGAAACTCAAGTACTTTGGCCACCTAAT 371348
- i - vviv ii vviv vvi i v iv vi
RTE1_ChrAsi#L 2959 T-GGAGGCCAGGATGGCCAAACTTCGTCTCTCATACTTCGGACATATTGT 3007
Crub_svsplocu 371349 GAGAAGGAAGGACTCACTGGAGAAGGGCCTAATGCTGGGAAAGATTGAGG 371398
v i i vv v i iiv v i v v i v
RTE1_ChrAsi#L 3008 CAGGAGGGACCAGTCGCTGGAGAAGGATATCATGTTTGGTAAGGTGGAGG 3057
Crub_svsplocu 371399 GCAATAGAAGAAGGGGACGACAGAGAATGAGATGGCTGGATGGAGTCACT 371448
iv v i i v vvvv ii v v iiii ----
RTE1_ChrAsi#L 3058 GTCAGAGAAAAAGAGGAAGACCCCCAGCGAGATGGATTGGCAAAGT---- 3103
Crub_svsplocu 371449 GAAGCAGTAGGTGTGAATTTAAATG-GACTCCAGAAGATGGTAGAGGACA 371497
--i i vvvi iii i ii - i vv ---- ? - vii
RTE1_ChrAsi#L 3104 --GGCAGCATCGATGGGCTCAAGCGTGGCAACAG----TNGT-GAGGTTG 3146
Crub_svsplocu 371498 G--GAAGACCTGGAGGAA---CGTT-----GTCCATGGGGTCGCGATGGG 371537
--v i i v vi vi--- ----- v i v i
RTE1_ChrAsi#L 3147 GCCCAGGATCGGGCAGTGTTTCGTTCTGCTGTGCATAGGGTCGCTATGAG 3196
Crub_svsplocu 371538 TCGG-ACACGACT---TCGCAATTAACAACAACAACAACAA 371574
- - --- v vi
RTE1_ChrAsi#L 3197 TCGGTAC-CGACTCGATGGCACCTAACAACAACAACAACAA 3236
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 39.86
Transitions / transversions = 1.07 (223/208)
Gap_init rate = 0.04 (56 / 1400), avg. gap size = 1.36 (76 / 56)
+ 14 13.7 4.5 4.5 Crub_svsplocus 372290 372333 (277667) + (AATCTA)n Simple_repeat 1 44 (0) 213
ANNOTATION EVIDENCE:
14 13.69 4.55 4.55 Crub_svsplocus 372290 372333 277667 + (AATCTA)n Simple_repeat 1 44 0
14 13.69 4.55 4.55 Crub_svsplocus 372290 372333 (277667) (AATCTA)n#Simple_repeat 1 44 (0) m_b7s252i9
Crub_svsplocu 372290 AATATAAACCTGAAATTTAAAACTCAAATCTGAA--TAAATCTAAA 372333
v i - i v - i --
(AATCTA)n#Sim 1 AATCTAAATCT-AAATCTAAATCT-AAATCTAAATCTAAATCTAAA 44
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.33 (4 / 3)
+ 61 0.0 1.7 0.0 Crub_svsplocus 372723 372780 (277220) + (TATG)n Simple_repeat 1 59 (0) 214
ANNOTATION EVIDENCE:
61 0.00 1.72 0.00 Crub_svsplocus 372723 372780 277220 + (TATG)n Simple_repeat 1 59 0
61 0.00 1.72 0.00 Crub_svsplocus 372723 372780 (277220) (TATG)n#Simple_repeat 1 59 (0) c_b7s251i2
Crub_svsplocu 372723 TATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTA 372772
(TATG)n#Simpl 1 TATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTATGTA 50
Crub_svsplocu 372773 TGTA-GTAT 372780
-
(TATG)n#Simpl 51 TGTATGTAT 59
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 57), avg. gap size = 1.00 (1 / 1)
+ 269 32.5 2.5 2.1 Crub_svsplocus 373643 373889 (276111) + L1M3 LINE/L1 3960 4209 (2376) 215
ANNOTATION EVIDENCE:
257 33.74 2.83 1.60 Crub_svsplocus 373643 373889 276111 + L1MdA_IV_orf2 LINE/L1 2758 3007 1674
257 33.74 2.83 1.60 Crub_svsplocus 373643 373889 (276111) L1MdA_IV_orf2#LINE/L1 2758 3007 (1674) m_b7s001i13
Crub_svsplocu 373643 TAAATATGTTTAAATCAGTCTATTTTAATCAGGCAGCGAAAGTAATAATT 373692
i v v v i ivvi v vi i v vi v v i v
L1MdA_IV_orf2 2758 TAAACATGATAAAAGCAATCTACAGCAAACCAGTAGCCAACATCAAAGTA 2807
Crub_svsplocu 373693 AATGGAGAAACAACTGATAGCTTTCCAATTGAAA-AAGGTACAAGGCAAG 373741
i - i iv vv v i i -v v v i
L1MdA_IV_orf2 2808 AATGGAGAGA-AGCTGGAAGCAATCCCACTAAAATCAGGGACTAGACAAG 2856
Crub_svsplocu 373742 GTTGTCCGTTATCGCCATTGTTGTTTA---TATTATCCCTAGAGGTATTG 373788
i i ii v v v vvi v i --- v --- v i i
L1MdA_IV_orf2 2857 GCTGCCCACTTTCTCCCTACCTCTTCAACATAGTA---CTTGAAGTATTA 2903
Crub_svsplocu 373789 ATCAGAGTAATTCGAAAAGATAGACAGATCAAAGGTTTAGAGATCAAGAA 373838
ii i v v v iiv i vv v i iiii
L1MdA_IV_orf2 2904 GCCAGAGCAATTCGACAACAAAAGGAGATCAAGGGGATACAAATTGGAAA 2953
Crub_svsplocu 373839 AGAAACGTTTAAAATGCAAGCTTTTGCAGACGAT-T--TAGTTTTTATAA 373885
iiviv i iiv vi i - -- v v
L1MdA_IV_orf2 2954 AGAGGAAGTCAAAATATCACTTTTTGCAGATGATATGATAGTATATATAA 3003
Crub_svsplocu 373886 TTGA 373889
v
L1MdA_IV_orf2 3004 GTGA 3007
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 45.57
Transitions / transversions = 1.00 (41/41)
Gap_init rate = 0.03 (8 / 246), avg. gap size = 1.38 (11 / 8)
269 31.91 2.40 2.40 Crub_svsplocus 373676 373842 276158 + L1M3_orf2 LINE/L1 1907 2073 1215
269 31.91 2.40 2.40 Crub_svsplocus 373676 373842 (276158) L1M3_orf2#LINE/L1 1907 2073 (1215) m_b7s001i14
Crub_svsplocu 373676 CAGCGAAAGTAATAATTAATGGAGAAACAACTGATAGCTTTCCAATTGAA 373725
v vi v v i v - v i vvi i i
L1M3_orf2#LIN 1907 CAGCTAACATCATACTCAATGGTGAAA-AACTGAAAGCTTTTCCTCTAAG 1955
Crub_svsplocu 373726 A-AAGGTACAAGGCAAGGTTGTCCGTTATCGCCATTGTTGTT---TATAT 373771
-v v v i ii v i vi i ---i v
L1M3_orf2#LIN 1956 ATCAGGAACAAGGCAAGGATGCCCACTCTCGCCACTTCTATTCAACATAG 2005
Crub_svsplocu 373772 TATCCCTAGAGGTATTGATCAGAGTAATTCGAAAAGATAGACAGATCAAA 373821
--- i i vi iii i v iv v i v i v
L1M3_orf2#LIN 2006 TA---CTGGAAGTCCTAGCCAGAGCAATTAGGCAAGAAAAAGAAATAAAA 2052
Crub_svsplocu 373822 GGTTTAGAGATCAAGAAAGAA 373842
iv vv i iii i
L1M3_orf2#LIN 2053 GGCATCCAAATCGGAAAGGAA 2073
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 41.56
Transitions / transversions = 1.26 (29/23)
Gap_init rate = 0.04 (6 / 166), avg. gap size = 1.33 (8 / 6)
+ 301 24.3 5.3 5.3 Crub_svsplocus 374122 374364 (275636) + L1-23_DR LINE/L1 3692 4168 (1411) 216
ANNOTATION EVIDENCE:
237 23.02 6.17 6.17 Crub_svsplocus 374122 374283 275717 + L1-19_DR LINE/L1 3916 4077 1522
237 23.02 6.17 6.17 Crub_svsplocus 374122 374283 (275717) L1-19_DR#LINE/L1 3916 4077 (1522) m_b7s001i15
Crub_svsplocu 374122 ATTGAACACATTAAAGCTGATTTAGATAC-TTGGACCAACTTACAGCTCT 374170
i v v i vv i - - --- i --- i
L1-19_DR#LINE 3916 ATTAAAAAGATTAAGGAAGATTTGGA-ACGTTGGA---ATTT---GCTCC 3958
Crub_svsplocu 374171 CC--TTCA-TG---GGCAGAATAGCTGTAATTAAAATGAATGTGTTACCG 374214
-- - --- v vivi v i i i
L1-19_DR#LINE 3959 CCATTTCACTGCTTGGAAGAATTAACGTAATAAAAATGAATATATTACCA 4008
Crub_svsplocu 374215 AAAATCTTA--TTTCTGTTTCAATGTATACCCATG-AAATTGGATAAGAA 374261
i -- -- i i viv i - -v v ii ii
L1-19_DR#LINE 4009 AGAA--TTAATTTTTTATTTCAATCCTTGCCC-TGTTACTTAAATAAAGA 4055
Crub_svsplocu 374262 TTTTTTTCAAAACCTTAACAAA 374283
iv iv
L1-19_DR#LINE 4056 TTTTTTCAAAAATGTTAACAAA 4077
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 27.14
Transitions / transversions = 1.50 (21/14)
Gap_init rate = 0.10 (16 / 161), avg. gap size = 1.25 (20 / 16)
244 32.71 0.00 0.00 Crub_svsplocus 374140 374246 275754 + L1-104_DR LINE/L1 3692 3798 1829
244 32.71 0.00 0.00 Crub_svsplocus 374140 374246 (275754) L1-104_DR#LINE/L1 3692 3798 (1829) m_b7s001i16
Crub_svsplocu 374140 GATTTAGATACTTGGACCAACTTACAGCTCTCCTTCATGGGCAGAATAGC 374189
v v vv viv i v v i viii vv
L1-104_DR#LIN 3692 GATTTACAAAGATGGAGTCACTTGCCGCTGTCTTTAGCAGGCAGAATACA 3741
Crub_svsplocu 374190 TGTAATTAAAATGAATGTGTTACCGAAAATCTTATTTCTGTTTCAATGTA 374239
vi v i i i iivvi v v i i iv
L1-104_DR#LIN 3742 AATTATCAAAATGAATGTGCTACCAAGGTATTTATATGTATTTCAGTGCC 3791
Crub_svsplocu 374240 TACCCAT 374246
i
L1-104_DR#LIN 3792 TGCCCAT 3798
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 43.53
Transitions / transversions = 0.94 (17/18)
Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.0 (0 / 0)
263 23.53 2.33 1.15 Crub_svsplocus 374152 374237 275763 + L1-11_DR LINE/L1 3744 3830 3494
263 23.53 2.33 1.15 Crub_svsplocus 374152 374237 (275763) L1-11_DR#LINE/L1 3744 3830 (3494) m_b7s001i17
Crub_svsplocu 374152 TGGACCAACTTACAGCTCTCCTTCATGGGCAGAATAGCTGTAATTAAAAT 374201
iv vi v v v v ii
L1-11_DR#LINE 3744 TGGATGAACTTACCACTATCCATCATGGGCAGAATATCAGTAACCAAAAT 3793
Crub_svsplocu 374202 GAATGTGTTACCGAAAAT--CTTATTTCTGTTTCAATG 374237
vvii ?i v i --vi v -
L1-11_DR#LINE 3794 GTCCATNCTCCCAAAAATAAACTATTTAT-TTTCAATG 3830
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 28.77
Transitions / transversions = 0.82 (9/11)
Gap_init rate = 0.02 (2 / 85), avg. gap size = 1.50 (3 / 2)
301 26.84 3.55 3.55 Crub_svsplocus 374168 374364 275636 + L1-23_DR LINE/L1 3972 4168 1411
301 26.84 3.55 3.55 Crub_svsplocus 374168 374364 (275636) L1-23_DR#LINE/L1 3972 4168 (1411) m_b7s001i18
Crub_svsplocu 374168 TCTCCTTCATGGGCAGAATAGCTGTAATTAAAATGAATGTGTTACCGAAA 374217
v iv i v iv v ii v v
L1-23_DR#LINE 3972 TCTCATTTCTAGGAAGAATAAATGTAATAAAAATGAATGTACTTCCTAAA 4021
Crub_svsplocu 374218 ATCTTATTTCTGTTTCAATGTATACCCATGAAATTGGATAAGAATT--TT 374265
v v i i i i vi i vvv v i -i -- --
L1-23_DR#LINE 4022 TTCTTATATTTATTCCAGTCCATACCTAGCTACTTAG-CA--AATTCATT 4068
Crub_svsplocu 374266 TTTCAAA-ACCTTAACAAAATTATTCTCAAA-TTTATTTGGCAAGGAAAA 374313
- i i vvi - - i v viiv
L1-23_DR#LINE 4069 TTTCAAAGATCTTAATAAACACA-TCTCAAAGTTTATCTGGAACAATAAA 4117
Crub_svsplocu 374314 AAAGCGAGGATCAAA---TTAAAATTATTGCAGGATTCGAAAGAGAGGGG 374360
i v v v i --- iv v v ---i v v
L1-23_DR#LINE 4118 AGACCGCGTATTAAAATTTCTAAATTAATGAAG---CCTAAAGACAGGGG 4164
Crub_svsplocu 374361 AGGA 374364
v
L1-23_DR#LINE 4165 TGGA 4168
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 33.40
Transitions / transversions = 0.82 (23/28)
Gap_init rate = 0.06 (11 / 196), avg. gap size = 1.27 (14 / 11)
+ 254 25.6 1.1 2.2 Crub_svsplocus 377367 377507 (272493) + Tx1-47_DR LINE/L1-Tx1 3007 3144 (2350) 217
ANNOTATION EVIDENCE:
237 31.14 2.13 4.35 Crub_svsplocus 377367 377507 272493 + Tx1-43_DR LINE/L1-Tx1 3007 3144 2350
237 31.14 2.13 4.35 Crub_svsplocus 377367 377507 (272493) Tx1-43_DR#LINE/L1-Tx1 3007 3144 (2350) m_b7s001i19
Crub_svsplocu 377367 TACCTCCGTCTTG--GAAAAGG-GCTTTTATATTGTTGATCCCAAAGGAG 377413
i v v -- v- i v i -- i ii
Tx1-43_DR#LIN 3007 TACCTTCCTCATGCAGAAAAGCTGTTTTGACATTGTTG--CCTAAAAAAG 3054
Crub_svsplocu 377414 GATCAAGATCTTACCCAGCCTAAGAATTATAGACCTATATCTCTTTTGAA 377463
---- v iv iiiv i iv i vv vi ivi
Tx1-43_DR#LIN 3055 GA----GATCTAACTGAATTAAGGAATTGGAGACCTGTTGCTCTACTATG 3100
Crub_svsplocu 377464 TACAGATTATAAGATTTTTTTGAAAATATTGGCAAATAGATTAA 377507
ii vi ii i iiv iv v i
Tx1-43_DR#LIN 3101 TACAGATTATAAAGTGCTTTCAAGAGCCTTATCTAATAGGTTAA 3144
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 41.79
Transitions / transversions = 1.62 (26/16)
Gap_init rate = 0.06 (8 / 140), avg. gap size = 1.12 (9 / 8)
254 20.00 0.00 0.00 Crub_svsplocus 377438 377507 272493 + Tx1-47_DR LINE/L1-Tx1 3010 3079 2381
254 20.00 0.00 0.00 Crub_svsplocus 377438 377507 (272493) Tx1-47_DR#LINE/L1-Tx1 3010 3079 (2381) m_b7s001i20
Crub_svsplocu 377438 AATTATAGACCTATATCTCTTTTGAATACAGATTATAAGATTTTTTTGAA 377487
v vv i i i vvii
Tx1-47_DR#LIN 3010 AATTATAGACCTTTAAGTCTTTTAAACACAGATTATAAGATTCTAACAAA 3059
Crub_svsplocu 377488 AATATTGGCAAATAGATTAA 377507
v i v v
Tx1-47_DR#LIN 3060 AATTTTAGCTAATAGAATAA 3079
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 23.31
Transitions / transversions = 0.75 (6/8)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0)
+ 229 28.3 0.9 0.9 Crub_svsplocus 377441 377554 (272446) + L1-111_DR LINE/L1 3333 3446 (2273) 218 *
ANNOTATION EVIDENCE:
229 28.32 0.88 0.88 Crub_svsplocus 377441 377554 272446 + L1-111_DR LINE/L1 3333 3446 2273
229 28.32 0.88 0.88 Crub_svsplocus 377441 377554 (272446) L1-111_DR#LINE/L1 3333 3446 (2273) m_b7s001i21
Crub_svsplocu 377441 TATAGACCTATATCTCTTTTGAATACAGATTATAAGATTTTTTTGAAAAT 377490
v v v v i v i i i i v v vii
L1-111_DR#LIN 3333 TATCGTCCAATTTCCCTATTAAACATAGATTATAAAATATATGCAAAAAT 3382
Crub_svsplocu 377491 ATTGGCAAATAGATTAATGCATGTTTTGAA-GCAATTGATCCATAGTGAT 377539
vi v i iv v v vv -i v - i i i
L1-111_DR#LIN 3383 CCTGGCCAATAGACTAACCCCTTTAATGAATACAATAG-TTCACAGCGAT 3431
Crub_svsplocu 377540 CAATCTGGATTTATA 377554
v v
L1-111_DR#LIN 3432 CAAACTGGCTTTATA 3446
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 34.40
Transitions / transversions = 0.78 (14/18)
Gap_init rate = 0.02 (2 / 113), avg. gap size = 1.00 (2 / 2)
+ 279 26.5 0.0 0.0 Crub_svsplocus 377804 377871 (272129) + L1-83_DR LINE/L1 3525 3592 (2019) 219
ANNOTATION EVIDENCE:
279 26.47 0.00 0.00 Crub_svsplocus 377804 377871 272129 + L1-83_DR LINE/L1 3525 3592 2019
279 26.47 0.00 0.00 Crub_svsplocus 377804 377871 (272129) L1-83_DR#LINE/L1 3525 3592 (2019) m_b7s001i22
Crub_svsplocu 377804 TTTAAAATTGAAAAGGATACAAGACAGGGATGTCCATTATCCCCATTGTT 377853
v ii i i i ivv v ii
L1-83_DR#LINE 3525 TTTAATATTGAAAGAGGTACAAGACAAGGATGTCCGTTGAGCCCTTTACT 3574
Crub_svsplocu 377854 ATTTGTTTTAACAATGGA 377871
v iii ii
L1-83_DR#LINE 3575 TTTTGCCCTGGCAATGGA 3592
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 32.03
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.00 (0 / 67), avg. gap size = 0.0 (0 / 0)
+ 265 23.0 3.8 3.8 Crub_svsplocus 378229 378340 (271660) + L1-83_DR LINE/L1 4794 4892 (1440) 219
ANNOTATION EVIDENCE:
265 27.55 1.01 1.01 Crub_svsplocus 378229 378327 271673 + L1-1_Testu LINE/L1 4794 4892 1440
265 27.55 1.01 1.01 Crub_svsplocus 378229 378327 (271673) L1-1_Testu#LINE/L1 4794 4892 (1440) m_b7s001i23
Crub_svsplocu 378229 AAAGGATTTAAATGATTGGAAAAAAC-TACAGTTATCTTTGCTGGGGAGA 378277
i i ii v v v i- iv i - v i v i
L1-1_Testu#LI 4794 AAAAGACTTGGAGGAATGGAACAAATATGAAATT-TCTTGGCTAGGTAGG 4842
Crub_svsplocu 378278 ATCTCAGCAGTTAAAATGAATGTTCTCCCAAAGTTTCTTTTTTTGTTTCA 378327
i vv vv i v i i vi v
L1-1_Testu#LI 4843 GTAGCCTCGGTAAAGATGAATGTCCTCCCAAAGTTATTATTTTTGTTTCA 4892
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 33.25
Transitions / transversions = 1.08 (14/13)
Gap_init rate = 0.02 (2 / 98), avg. gap size = 1.00 (2 / 2)
257 21.69 4.60 4.60 Crub_svsplocus 378254 378340 271660 + L1-83_DR LINE/L1 3972 4058 1553
257 21.69 4.60 4.60 Crub_svsplocus 378254 378340 (271660) L1-83_DR#LINE/L1 3972 4058 (1553) m_b7s001i24
Crub_svsplocu 378254 CTACAGTTATCTTTGCTGGGGAG----AATCTCAGCAGTTAAAATGAATG 378299
vi i i vv ----v ----
L1-83_DR#LINE 3972 CTACCATTATCCTTACTGGGTCGTATTCATCTCA----TTAAAATGAATG 4017
Crub_svsplocu 378300 TTCTCCCAAAGTTTCTTTTTTTGTTTCAAATGATACTTATT 378340
i viv i vi i v v i
L1-83_DR#LINE 4018 TTCTTCCACGCTTTCTCTACTTATTTCAAATGCTCCCTATT 4058
Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 24.20
Transitions / transversions = 1.00 (9/9)
Gap_init rate = 0.06 (5 / 86), avg. gap size = 1.60 (8 / 5)
+ 27 18.8 7.5 2.0 Crub_svsplocus 379573 379666 (270334) + (ATT)n Simple_repeat 1 99 (0) 220
ANNOTATION EVIDENCE:
27 18.82 7.45 2.02 Crub_svsplocus 379573 379666 270334 + (ATT)n Simple_repeat 1 99 0
27 18.82 7.45 2.02 Crub_svsplocus 379573 379666 (270334) (ATT)n#Simple_repeat 1 99 (0) m_b8s252i0
Crub_svsplocu 379573 ATTATTATTAATAAT-TTAATATGGTTGAAT-TTA-TATTATTTTTAGTA 379619
v v - v vi - v - - v v
(ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATT-ATTATTATTATTATTATTATTA 49
Crub_svsplocu 379620 TTATGGTT-TAATTA-TATTATTATT-TTAGTTTTTAAT-TTGTTAATAT 379665
vi - v - - - v v - i v
(ATT)n#Simple 50 TTATTATTATTATTATTATTATTATTATTA-TTATTATTATTATTATTAT 98
Crub_svsplocu 379666 T 379666
(ATT)n#Simple 99 T 99
Matrix = Unknown
Transitions / transversions = 0.25 (3/12)
Gap_init rate = 0.10 (9 / 93), avg. gap size = 1.00 (9 / 9)
+ 1767 35.2 2.7 2.7 Crub_svsplocus 384128 385378 (264622) + MamGypsy2-I LTR/Gypsy 1498 2748 (1418) 221
ANNOTATION EVIDENCE:
1767 35.17 2.72 2.72 Crub_svsplocus 384128 385378 264622 + MamGypsy2-I LTR/Gypsy 1498 2748 1418
1767 35.17 2.72 2.72 Crub_svsplocus 384128 385378 (264622) MamGypsy2-I#LTR/Gypsy 1498 2748 (1418) m_b8s001i3
Crub_svsplocu 384128 GTGCCCTTCGCGTTGAAGAATAAGATTAATGTAGAGCTGGACAAGCTGCT 384177
i i i vi i i v i ? i v v v vv v iv
MamGypsy2-I#L 1498 GTACCTTTTGCTCTAAGGAAAAAAANTGAAGAAGAGCTTGAGCATCTAAT 1547
Crub_svsplocu 384178 CAAGCAGGGCATCTTAGAACCTGTGG-ACAGTAGTCCATGGGAAACCCCC 384226
i i iii i v v vi- - vi vi vv iv v
MamGypsy2-I#L 1548 CAAACAAGGTGCCCTCGAACCAGTTACACA-TACCCGGTGGGCTATACCA 1596
Crub_svsplocu 384227 ATAGTAATGCCACTGAAACCTAATGGAGAAGTCCGAATATGTGCGGACTA 384276
v iivi vi i i vi i vv v v vi
MamGypsy2-I#L 1597 ATTGCGCCGGTACTAAAGCCTAATGGTAAGGTGAGACTTTGTGGAGACTA 1646
Crub_svsplocu 384277 TAAGTGTACACTTAACAAAACATTGCAGCAGCACTCGTACCAGGTGCCTG 384326
i i vv v i ii i vv i i i vi
MamGypsy2-I#L 1647 CAAGTGCACTGTGAATAAGGCACTTAAGCAGCACCCATATCCAGTGCCTG 1696
Crub_svsplocu 384327 TGGTGAGCCACATTTTGGCC--TCCTTCAAAGGAGGCCGCGTTTTTGCCA 384374
ii v ii vv ii v i-- i v vii ii--iv i v
MamGypsy2-I#L 1697 CAGTCAATCAACTCCTTGCTGTTCTTGCTGGGGAAA--AGGTCTTTGCAA 1744
Crub_svsplocu 384375 AACTTGACCTGGCTCAGGCCTATCAACAACTACTAGTTGATGAGACAACG 384424
v i i i i iv v i i vi v v
MamGypsy2-I#L 1745 AACTTGACCTTGCCCAAGCTTATCAACAGCTGATCGTCGGTGATGCTACT 1794
Crub_svsplocu 384425 GCAGAGGCCCGAACAATTGTAACACACCAGGGAGCATTTAAAGTCAAAAG 384474
v i ii v v i ii i ivi i iv
MamGypsy2-I#L 1795 GCAGACGCCCAAACAATCATCACTCATCGAGGGGCATTCCGAGTTAAGCG 1844
Crub_svsplocu 384475 GGTGCAGTTTGGGGTTAACGTAGTCCCTGGCATTTTCCAAAGTGTGATGG 384524
vv v i ii vvi v i v iv iv v
MamGypsy2-I#L 1845 CCTTCAGTTCGGAATTTCTGTTGCCCCTGGAATTTTCCAGTGCTTCATGG 1894
Crub_svsplocu 384525 AGCGAACACTCCAC-----AATATTCCAGGTGTTTGCCCTTACTTCAATG 384569
----- i ii ----- iv vvvv v i i
MamGypsy2-I#L 1895 AG-----ACCCTGCTTTCTAGGATTCCAGGTGTGGTACCATATTTCGATG 1939
Crub_svsplocu 384570 ATGTCCTCATCACTGGGGAATCATCTGAAAAT---CTGGCTGACATGCTT 384616
v - -- v v ii --- v v v vi
MamGypsy2-I#L 1940 ATGTCCTGATCA-TGGG--ATCAACAGAGGATGAACTCGCGGAAAGACTT 1986
Crub_svsplocu 384617 AGGGCCATCTTGCTGCATTTC----CGCCAAGCGGGACTGAAGCTAAAGC 384662
vi vvi i i vv i ---- ii --- v iivi - i iv
MamGypsy2-I#L 1987 CAGGAAGTCCTACATCGTTTCGATACATCA---GGTATCCGAG-TGAAAA 2032
Crub_svsplocu 384663 AAGACAAATGTAAAATTGGAGTCTCCTCCACAGAGT----TTCTGGGGTT 384708
i v i i iii ----- v ---- vi i
MamGypsy2-I#L 2033 AGGAGAAATGTGAAATCGGAACTTC-----CAGTGTCACCTTCTTAGGCT 2077
Crub_svsplocu 384709 -CCATATTGATGCTGAAGACATCCATCCTGCTGAATCCAAGCTCAAAGCA 384757
- ii ii vv ii i i ii v vvi v vviv
MamGypsy2-I#L 2078 ACCGCATCAATGCTGCTGGTATTCACCCCACTCAAGATAAGGTACGTGCA 2127
Crub_svsplocu 384758 ATTCAGCAGGCCCCAAGTCCCAACCCCAAAAGC--GAACTTCAGGCTTTT 384805
i vv v v v v v vv -- -- i i i i
MamGypsy2-I#L 2128 ATCCATGACGCGCCTACTCCAAAAAC--AAAGCAAGAGCTTCAAGCCTTC 2175
Crub_svsplocu 384806 CTGGAACTGTTAAACTTTTACCAT-TCATTCCTCCATCACAAGGCTGCAG 384854
ii ii v i i - iv i - v vi vi
MamGypsy2-I#L 2176 CTGGGGCTACTCAATTTCTACCATGTTTTTCTTCCA-CAAAAGGCAACCA 2224
Crub_svsplocu 384855 TGGCTGAGCCATTATACTGGCTCTTGGATAAACAGGCTCCATGGCAGTGA 384904
v i vi ii v vi iv viv i i iv i
MamGypsy2-I#L 2225 TTGCTGAGCCACTTCATCGCCTACTGGGAAAAGGCGTTCCGTGGCGTTGG 2274
Crub_svsplocu 384905 ACAAAAGTCCACGAAAGGA-GCTTCGCAGAG-GTCAAGGCCTTGCTGTCT 384952
--vv i vi ivi - iv i i- vvv ii v
MamGypsy2-I#L 2275 AC--TCGCCAGCATGAGGACGCTTTCCGGAATGTCAAGCAGTTATTGACT 2322
Crub_svsplocu 384953 TCAAATGCGGTTCTACCACATTTCAATGAAC---AACTGCCTGTGTGCAT 384999
vi vv v v vi v i --- ii- - v v
MamGypsy2-I#L 2323 TCCGAGTCTGTGCTAGTACATTACGATGAACATAAACCA-CTGT-TTCTT 2370
Crub_svsplocu 385000 AGC-CTGTTACGCATCCTCTTATGGGATTGGGACTGTGTTAAGTCACTTG 385048
v - -- v vi i vii ii i v i --i
MamGypsy2-I#L 2371 ACCACTG--ACGCTTCACCTTACGGTGCTGGAGCTGTGCTTAGCCAC--A 2416
Crub_svsplocu 385049 AAA-GCT-GATGGGACACAAGTCTGTGTAGCCTACTATTCTAGGACCCTA 385096
- i- v vv i ivivvi v i i v i vv i
MamGypsy2-I#L 2417 AAATGCCAGATGGCACTGAGGCACCAATTGCTTACTACTCAAGAACAATG 2466
Crub_svsplocu 385097 TCATCTGCTGAACGTAATTACACGCAGATAGATAGGGAAGCCTTGGCCAT 385146
i v v i i i i v i ii i v ii
MamGypsy2-I#L 2467 TCATCTACAGAACGGAACTATACACAAATTGACAAAGAAGCCCTTGCTGT 2516
Crub_svsplocu 385147 AGTGGCTGGCATAAAAATGTTCCATGACTATTTATATGGTCACCGTTTCA 385196
vi v v vi v i v ii ii v i i iivvi i
MamGypsy2-I#L 2517 TATCGCGGGAGTCAAGAAGTTCCACAACTACCTCTACGGCCGTGCCTTTA 2566
Crub_svsplocu 385197 CGGTCTTTACAGACCATAAGCCACTGCTGGGGTTGTTTACAACCAACAAG 385246
ii i v v i i v viv ii v v v vvi i
MamGypsy2-I#L 2567 CAATTTGTACTGATCACAAGCCTCTTTGGGGACTCTTTTCTAAGGATAAG 2616
Crub_svsplocu 385247 TAAAC-CCCACATATAATTTCTCCTAGAATGCTGAGATG--GTCAATTTT 385293
ivv - vi - v v v vv v v v v -- --
MamGypsy2-I#L 2617 CCTACGCCCTTA-ATTATGTCACCACGTATGCAGCGCTGGAGTC--TTTT 2663
Crub_svsplocu 385294 CCTTTCTGCATATGACTACACACTGGTTCATAAACCAGGCAAAGAAATGG 385343
v ivv v i i v ii i i v v i v iv
MamGypsy2-I#L 2664 GCTCAGTGCTTATGACTACGCGCTTGTCTACAAGCCTGGAAGAGCAATAT 2713
Crub_svsplocu 385344 GCCATGCAGATGGCCTCAGCAAATTACCACTACAG 385378
vvv v v v vivi i i
MamGypsy2-I#L 2714 CGAATGCTGATGCCCTGAGCCGTCTGCCACTGCAG 2748
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.97
Transitions / transversions = 1.12 (226/202)
Gap_init rate = 0.04 (51 / 1250), avg. gap size = 1.33 (68 / 51)
+ 261 29.3 0.0 0.0 Crub_svsplocus 385610 385684 (264316) + Gypsy158-I_DR LTR/Gypsy 2237 2311 (1364) 222
ANNOTATION EVIDENCE:
261 29.33 0.00 0.00 Crub_svsplocus 385610 385684 264316 + Gypsy-176_DR-I LTR/Gypsy 2237 2311 1364
261 29.33 0.00 0.00 Crub_svsplocus 385610 385684 (264316) Gypsy-176_DR-I#LTR/Gypsy 2237 2311 (1364) m_b8s001i4
Crub_svsplocu 385610 GGTAGCAGGGTAGTGATCCCAGCCTCTTTGAGGACTAGAGTCTTGCTCTT 385659
i ii v iv vi v i iivi i ii vv
Gypsy-176_DR- 2237 GGCAGCAGAATAGTCATCCCAGTGTCACTCAGGGCTGACATCCTGTCCAA 2286
Crub_svsplocu 385660 TTTGCATGAGGGACATCTTGGAATA 385684
v v v
Gypsy-176_DR- 2287 GTTGCATGAGGGCCATCTGGGAATA 2311
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.95
Transitions / transversions = 1.20 (12/10)
Gap_init rate = 0.00 (0 / 74), avg. gap size = 0.0 (0 / 0)
+ 369 31.3 3.7 1.9 Crub_svsplocus 385698 386035 (263965) + Gypsy158-I_DR LTR/Gypsy 3255 3556 (835) 222
ANNOTATION EVIDENCE:
369 31.03 4.05 1.99 Crub_svsplocus 385698 385993 264007 + Gypsy158-I_DR LTR/Gypsy 3255 3556 835
369 31.03 4.05 1.99 Crub_svsplocus 385698 385993 (264007) Gypsy158-I_DR#LTR/Gypsy 3255 3556 (835) m_b8s001i5
Crub_svsplocu 385698 TGGGAGGAGACACATGCC-CCTTGGTCGAGGGTTCATATCGACTACGCTG 385746
?i?v - - i vvi ii i i i ?
Gypsy158-I_DR 3255 TGGGAGNGNCCACA-GCCGCCCTGGAGAAGAATCCATATTGACTATGCNG 3303
Crub_svsplocu 385747 GGCCCTTTCAGAGGCAATTCTTCCTTTTCCTCATGGACAGCCATTCCAAG 385796
v ? i ii iv v v i vv i vi iivi i
Gypsy158-I_DR 3304 GTCCNTTCCAAGGAAAAATGTTTCTGATTCTGGTGGATGCTCACTCCAAG 3353
Crub_svsplocu 385797 TGGCTAGAGGTCATTCCAGTCTCCTACACTACTATTGCCAGGACTATC-- 385844
v i ? ivv? --- vv?i ? v i?v iv ?ii i --
Gypsy158-I_DR 3354 TGGATGGANGCGTNTCC---CTCGANTANTTCTACNTCTCGNGTTACCAT 3400
Crub_svsplocu 385845 CAAGT-GTTGAGAGGGATCTCT------CATGGGTTTCCAGATGTCCTTG 385887
i -?i vi vi i ------ i v v vi vv v
Gypsy158-I_DR 3401 CGAGTANCTGAGACAGAGTTTTAGCGNACATGGATTACCTGAAATGGTAG 3450
Crub_svsplocu 385888 TCTCCGACAACGGACCCCAATTCACTTCTTCTGAGTTTCAGGCTTTTCTA 385937
v v i vv?iiiv i vvv ?vv ? ?v --i
Gypsy158-I_DR 3451 TGTCGGACAATGGCANTTGTTTTACGAGTNAAGAGTTTNAGGNATT--CA 3498
Crub_svsplocu 385938 CAGGCCAACATG--ATCCAGCATGCCACATCAGCACCGTTTCATCCAGCT 385985
iii ? i?v -- ? i iv ?v ? vi ?
Gypsy158-I_DR 3499 TGAGNCGNAATGGCATCNAGCACGTGACNACAGCACCNTACCATCCANCT 3548
Crub_svsplocu 385986 TCCAATGG 385993
i
Gypsy158-I_DR 3549 TCCAACGG 3556
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.01
Transitions / transversions = 1.14 (48/42)
Gap_init rate = 0.04 (11 / 295), avg. gap size = 1.64 (18 / 11)
250 33.55 1.32 1.32 Crub_svsplocus 385885 386035 263965 + Gypsy153-I_DR LTR/Gypsy 3375 3525 874
250 33.55 1.32 1.32 Crub_svsplocus 385885 386035 (263965) Gypsy153-I_DR#LTR/Gypsy 3375 3525 (874) m_b8s001i6
Crub_svsplocu 385885 TTGTCTCCGACAACGGACCCCAATTCACTTCTTCTGAGTTTCAGGCT--T 385932
i v i i i i viv iv --i v--
Gypsy153-I_DR 3375 TTGTTTCAGACAATGGACCTCAATTTATTTCGCATGAAAT--GGGCACAT 3422
Crub_svsplocu 385933 TTCTACAGGCCAACATGATCCAGCATGCCACATCAGCACCGTTTCATCCA 385982
vv v iivii v i ii vi v v vi v
Gypsy153-I_DR 3423 TTCTACTTGCAAATGGAGTGCAACATATCAAGTCATCACCCTACCATCCT 3472
Crub_svsplocu 385983 GCTTCCAATGGCCAAGCTGAGGGTATGGTGTGCACAACCAAAGATGCTTT 386032
vv v v vv v i vv v iiv v iv v
Gypsy153-I_DR 3473 GCAACAAATGGGCTTGCGGAGAGGTTCGTGCAGACCATGAAACATGCTTT 3522
Crub_svsplocu 386033 AAA 386035
Gypsy153-I_DR 3523 AAA 3525
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.69
Transitions / transversions = 0.72 (21/29)
Gap_init rate = 0.02 (3 / 150), avg. gap size = 1.33 (4 / 3)
+ 15 7.4 3.2 3.2 Crub_svsplocus 388501 388531 (261469) + (CCTC)n Simple_repeat 1 31 (0) 223
ANNOTATION EVIDENCE:
15 7.40 3.23 3.23 Crub_svsplocus 388501 388531 261469 + (CCTC)n Simple_repeat 1 31 0
15 7.40 3.23 3.23 Crub_svsplocus 388501 388531 (261469) (CCTC)n#Simple_repeat 1 31 (0) m_b8s252i1
Crub_svsplocu 388501 CCT-CCTCCACCCCCTTCCTCCCTCCCTCCCT 388531
- - i i
(CCTC)n#Simpl 1 CCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCT 31
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.07 (2 / 30), avg. gap size = 1.00 (2 / 2)
+ 341 30.2 11.8 0.3 Crub_svsplocus 390776 391071 (258929) + Gypsy158-I_DR LTR/Gypsy 3247 3576 (815) 224
ANNOTATION EVIDENCE:
341 30.16 11.82 0.30 Crub_svsplocus 390776 391071 258929 + Gypsy158-I_DR LTR/Gypsy 3247 3576 815
341 30.16 11.82 0.30 Crub_svsplocus 390776 391071 (258929) Gypsy158-I_DR#LTR/Gypsy 3247 3576 (815) m_b8s001i7
Crub_svsplocu 390776 TACACAGGTGGGAGGATACACATGCTCCTTGGTCAAGGATTCATATTGAC 390825
vv? ?i?v vv v i vv i i
Gypsy158-I_DR 3247 TACACCCNTGGGAGNGNCCACAGCCGCCCTGGAGAAGAATCCATATTGAC 3296
Crub_svsplocu 390826 TACACTGGCCCCTTTCAGGGGCAATTCTTCTTCATTGTTGTGGACAGTCA 390875
ii ? i ? i i iv v v ii v v v iiv
Gypsy158-I_DR 3297 TATGCNGGTCCNTTCCAAGGAAAAATGTTTCTGATTCTGGTGGATGCTCA 3346
Crub_svsplocu 390876 CTCTAAA-------------------CGACTGC----------CAGG--A 390894
i i------------------- ? i?---------- i? --
Gypsy158-I_DR 3347 CTCCAAGTGGATGGANGCGTNTCCCTCGANTANTTCTACNTCTCGNGTTA 3396
Crub_svsplocu 390895 CCATCCAGGTGTTGAGGGGGATCTTCAGCTCCCATGGGCTCCCAGATGTT 390944
v vv?i ivi vi i v?v ii v v vi v
Gypsy158-I_DR 3397 CCATCGAGTANCTGAGACAGAGTTTTAGCGNACATGGATTACCTGAAATG 3446
Crub_svsplocu 390945 CTTGTCTCCAACAATGGCCCTCAATTCAC---TTCCTAGTTTCAGGCTTT 390991
v v v vi v? iiv i --- ?vvv ? ?v
Gypsy158-I_DR 3447 GTAGTGTCGGACAATGGCANTTGTTTTACGAGTNAAGAGTTTNAGGNATT 3496
Crub_svsplocu 390992 CCTACAGGC-CAATATGATCCACCATGCTACTTCAGCACCAATTCATCCA 391040
v i- ? -? ivv ? v i iv ?v ?vvi
Gypsy158-I_DR 3497 CATG-AGNCGNAATGGCATCNAGCACGTGACNACAGCACCNTACCATCCA 3545
Crub_svsplocu 391041 GCTTCCAACAGCCAAGCTGAGCGCATGGTGC 391071
? i ?ivi v i viiv
Gypsy158-I_DR 3546 NCTTCCAACGGNTTGGCAGAACGAGCTGTGC 3576
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.11
Transitions / transversions = 0.85 (41/48)
Gap_init rate = 0.02 (6 / 295), avg. gap size = 6.00 (36 / 6)
+ 13 18.0 2.5 2.5 Crub_svsplocus 393055 393094 (256906) + (TATTAGT)n Simple_repeat 1 40 (0) 225
ANNOTATION EVIDENCE:
13 17.97 2.50 2.50 Crub_svsplocus 393055 393094 256906 + (TATTAGT)n Simple_repeat 1 40 0
13 17.97 2.50 2.50 Crub_svsplocus 393055 393094 (256906) (TATTAGT)n#Simple_repeat 1 40 (0) m_b8s252i2
Crub_svsplocu 393055 TATTGGTGTATTACTTATTAGTTA-TAATTACTTGTTGTTA 393094
i - v - i i v i
(TATTAGT)n#Si 1 TATTAGT-TATTAGTTATTAGTTATTAGTTATTAGTTATTA 40
Matrix = Unknown
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2)
+ 359 30.4 6.4 5.0 Crub_svsplocus 394292 395151 (254849) C L1M4 LINE/L1 (1470) 4676 3485 226
ANNOTATION EVIDENCE:
338 26.42 0.93 0.93 Crub_svsplocus 394292 394398 255602 C L1-21_DR LINE/L1 4197 4303 1711
338 26.42 0.93 0.93 Crub_svsplocus 394292 394398 (255602) C L1-21_DR#LINE/L1 (1711) 4303 4197 m_b8s001i8
Crub_svsplocu 394292 GCTGCTTAATAATAAAGTCTCCAGTC-CGGGAGCCCAAAGCCCGCTCTGT 394340
i ii v-v iv -i v iivi v iv ii
C L1-21_DR#LINE 4303 GCCGCTTGGTAATAC-TTCTCCAAACATGGCAATGTAAATCCTCCTTCGT 4255
Crub_svsplocu 394341 CTTTAGATTCTTGTAGTAATTTAATTTTAATTCTTGCTTTTTTCCCTTGC 394390
vvi vv iiv v v
C L1-21_DR#LINE 4254 CTTTCTGTAATTGTAGCGTTTTAAATTTAATTCTTGGTTTTTTCCCTTGC 4205
Crub_svsplocu 394391 CATATAAA 394398
C L1-21_DR#LINE 4204 CATATAAA 4197
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.70
Transitions / transversions = 1.00 (14/14)
Gap_init rate = 0.02 (2 / 106), avg. gap size = 1.00 (2 / 2)
312 30.61 2.54 0.50 Crub_svsplocus 394295 394491 255509 C L1-95_DR LINE/L1 3987 4187 1396
312 30.61 2.54 0.50 Crub_svsplocus 394295 394491 (255509) C L1-95_DR#LINE/L1 (1396) 4187 3987 m_b8s001i9
Crub_svsplocu 394295 GCTTAATAATAAAGTCTCCAGTCCGGGAGCCCAAAGCCCGCTCTGTCTTT 394344
v vv iv vi ivi v v ?v vv i v
C L1-95_DR#LINE 4187 GCGTAATAATATTGTTGCAGGCATGGGAGACCTANTCCACCTTTTTCTTT 4138
Crub_svsplocu 394345 AGATTCTTGTAGTAATTTAATTTTAATTCTTGCTTTTTTCCCTTGCCATA 394394
ivv vv i iv v i v i v v i
C L1-95_DR#LINE 4137 GCTTAATTGCAGTGTTTTAAATCTTACTCTGGGTTTTTTCCCCTGCCATA 4088
Crub_svsplocu 394395 TAAATCTCATTGTTGCATTTAGATCA-TCAAAAAATTTCTGGTTTAAT-T 394442
v viv i iv? vvi - ivv vi i i -
C L1-95_DR#LINE 4087 AAAATCTAGATATTAANTTTATTCCATTCGCTAAATTGTTGATTTGATAT 4038
Crub_svsplocu 394443 TGGTG--GGAACCGTCTGAAATA-AGAAAAGGATATTAGGTAAAATGTTC 394489
vv i-- v? i - v v vi - v v
C L1-95_DR#LINE 4037 TTCTACTGGAAGNGTTTGAAATAGATACAATAAT-TTTGGTAAAATGATC 3989
Crub_svsplocu 394490 AT 394491
C L1-95_DR#LINE 3988 AT 3987
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.37
Transitions / transversions = 0.58 (22/38)
Gap_init rate = 0.03 (5 / 196), avg. gap size = 1.20 (6 / 5)
234 32.98 6.32 6.15 Crub_svsplocus 394370 394970 255030 C L1M1_orf2 LINE/L1 1966 2567 727
234 32.98 6.32 6.15 Crub_svsplocus 394370 394970 (255030) C L1M1_orf2#LINE/L1 (727) 2567 1966 m_b8s001i10
Crub_svsplocu 394370 ATTCTTGCTTTTTTCCCTTGCCATATAAATCTCA---TTGTTGCATTTAG 394416
v v i vivv v i i --- viv i v
C L1M1_orf2#LIN 2567 ATTCTGGGTCTTTTGTGGTTCCATATAAATTTTAGGATTGTTTTTTCTAT 2518
Crub_svsplocu 394417 ATCATCAAAAAATTTC--TGGTTTAATTTGGTGGGAACCGTCTGAAATAA 394464
v vvii i v -- v -- i i i ii iv vi vv
C L1M1_orf2#LIN 2517 TTCTGTGAAGAATGTCATTGGTAT--TTTGATAGGGATTGCATTGAATCT 2470
Crub_svsplocu 394465 GAAAAGGATATTAGGTAAAATGTTCATCTTAACAATCGCTATCCTTCCTA 394514
v i vviiv i iv vv i vviv i v
C L1M1_orf2#LIN 2469 GTAGATTGCTTTGGGTAGTATGGACATTTTAACAATATTGATTCTTCCAA 2420
Crub_svsplocu 394515 ACAATGATAGTTAAAGGTTTTTCCACTTTTCCAGATCTAGTTTTATTTGT 394564
v v vvi vi vi i i ivivi ivv iv v
C L1M1_orf2#LIN 2419 TCCATGAACATGGAATATCTTTCCATTTTTTGGTGTCCTCTTCAATTTCT 2370
Crub_svsplocu 394565 TTCAATAATCTTTCATAGTTATCCT---------CTTTTACTGTTATATA 394605
vi i v i v v --------- i vi -----
C L1M1_orf2#LIN 2369 TTCATCAGTGTTTTATAGTTTTCATTGTAGAGATCTTTCACTTCT----- 2325
Crub_svsplocu 394606 TTTTGATGTTAAATAGATGCCTAAATATTTGACTTT---TTTGGCTATC- 394651
-- -- i vi v ii i i --- v i-
C L1M1_orf2#LIN 2324 --TTG--GTTAAGTTAATTCCTAGGTATTTAATTTTATTTGTGGCTATTG 2279
Crub_svsplocu 394652 TGAA---GATCTATCTTTTTAACAAGTTGAAGTTTCTGTTTCTCTGTTAG 394698
i --- - ii i ---------- v ------
C L1M1_orf2#LIN 2278 TAAATGGGAT-TACTTTTTTGA----------TTTCTTTTTC------AG 2246
Crub_svsplocu 394699 ATTTTTT--TGT-ACCATA----AGTACTTTAGTCTTTTCCCTATTTATT 394741
v i-- -iv ---- i i viv vi viv i v
C L1M1_orf2#LIN 2245 ATTGTTCACTGTTGGCATATAGAAATGCTACTGATTTTTGTATGTTGATT 2196
Crub_svsplocu 394742 TTCAACCCAGCCACTCCTC-AAATTTCTCTATT--TTCTGCAAAAGTTT- 394787
vv i v v iiv -i v i i-- -- v -
C L1M1_orf2#LIN 2195 TTGTATCCTGCAACTTTACTGAATTTGTTTATCAGTTCT--AATAGTTTT 2148
Crub_svsplocu 394788 --GGTGGCTGTTGCCAATGGCTCCTCTAAGATA-AAAACCAAATCGTCTG 394834
--? v- ivii -- i ii i - - i i v i
C L1M1_orf2#LIN 2147 TTNGTGGA-GTCTTTA--GGTTTTTCCAA-ATATAAGATCATATCATCTG 2102
Crub_svsplocu 394835 CAAAAGCCTGTAATTTATATTTCTGATCTTTT--ATCTCCAATGCT-TTA 394881
vivvvi i- i -- i -- vi ivi i- v
C L1M1_orf2#LIN 2101 CAAACAAGGATAATTTG-ACTTCT--TCCTTTCCAATTTGGATGCCCTTT 2055
Crub_svsplocu 394882 ATCTCCGACTCTTGTCTAATATTCCTAGCCAGCACTTCCAATGTAAGAAT 394931
i ivv i vvii i v i iiv viv
C L1M1_orf2#LIN 2054 ATTTCTTTCTCTTGTCTGATTGCTCTAGCTAGGACTTCCAGTACTATGTT 2005
Crub_svsplocu 394932 AAATAATAAGGGCGATAGAGGGCATCCCTGTCTTGTGCC 394970
i i iv i v v i v v
C L1M1_orf2#LIN 2004 GAATAACAGTGGTGAAAGTGGGCATCCTTGTCGTGTTCC 1966
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.47
Transitions / transversions = 1.11 (98/88)
Gap_init rate = 0.09 (52 / 600), avg. gap size = 1.44 (75 / 52)
331 29.07 4.00 1.96 Crub_svsplocus 394456 394655 255345 C L1-18_DR LINE/L1 3973 4176 1538
331 29.07 4.00 1.96 Crub_svsplocus 394456 394655 (255345) C L1-18_DR#LINE/L1 (1538) 4176 3973 m_b8s001i11
Crub_svsplocu 394456 CTGAAATAAGAAAAGGATATTAGGTAAAATGTTCATCTTAACAATCGCTA 394505
i i vvi i ii v ivi iv v
C L1-18_DR#LINE 4176 CTGAAATAAAAAAAGAAATCTAGGTAAAATATTCATTCTTATTGTTTCAA 4127
Crub_svsplocu 394506 TCCTTCCTAACAATGATAGTTAAAGGTTTTTCCACTTTTCCAGATCTAGT 394555
v v viv vvii i i i v i i-v
C L1-18_DR#LINE 4126 TCCTACCAAACAATGATAGTGGTAGCACCTCCCACCTCTGCAAATCC-TT 4078
Crub_svsplocu 394556 TTTATTTGTTTCAATAATCTT-TCATAGTTATCCTCTTTTA-CTGTTATA 394603
vi v i v i - i vv vv v - v v
C L1-18_DR#LINE 4077 TTTAACTGTGTTAATTATTTTATCATAATTTGCCTGATATAGCTGTGAAA 4028
Crub_svsplocu 394604 TATTTTGATGTTAAATAG--ATGCCTAAATATTTGA----CTTTTTTGGC 394647
- i v i -- i -- iv v i ---- v i
C L1-18_DR#LINE 4027 T-TCTGGGTGT--AATGGCAACTCCTAAATATGTAAATCCCTGTTTTGAC 3981
Crub_svsplocu 394648 TATCTGAA 394655
i i
C L1-18_DR#LINE 3980 CACCTGAA 3973
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.29
Transitions / transversions = 1.04 (29/28)
Gap_init rate = 0.04 (8 / 199), avg. gap size = 1.50 (12 / 8)
283 31.30 4.77 5.21 Crub_svsplocus 394489 394970 255030 C L1M4_orf2 LINE/L1 1966 2445 849
283 31.30 4.77 5.21 Crub_svsplocus 394489 394970 (255030) C L1M4_orf2#LINE/L1 (849) 2445 1966 m_b8s001i12
Crub_svsplocu 394489 CATCTTAACAATCGCTATCCTTCCTAACAATGATAGTTAAAGGTTTTTCC 394538
vviv vi v v v vvi vii v i
C L1M4_orf2#LIN 2445 CATCTTAACAATATTAAGTCTTCCGATCCATGAACATGGGATGTCTTTCC 2396
Crub_svsplocu 394539 ACTTTTCCAGATCTAGTTTTATTTGTTTCAATAATCTTTCATAGTTATC- 394587
i v ii i vv v v i v ii v -
C L1M4_orf2#LIN 2395 ATTTATTTAGGTCTTCTTTAATTTCTTTCAACAATGTTTTGTAGTTTTCA 2346
Crub_svsplocu 394588 CTCTTTTACTGTTATATATTTTGATGTTAAATAGATGCCTAAATATTTGA 394637
v v viv v v ii i- i vv vv v i v
C L1M4_orf2#LIN 2345 GTGTACAAGTCTTGCAC-TTCTTTTGTTAAATTTATTCCTAAGTATTTTA 2297
Crub_svsplocu 394638 CT-TTTTTG--GCTATC-TGAA--GATCTATCTTTTTAACAAGTTGAAGT 394681
i - -- i- i -- vi i i i ---- vv v
C L1M4_orf2#LIN 2296 TTCTTTTTGATGCTATTGTAAATGGAATTGTTTTCTTAA----TTTCATT 2251
Crub_svsplocu 394682 TTC----TGTTTCTCTGTTAGATTTTTTTGTACCATAAGTACTTTAGTCT 394727
---- iv - i ------- -i v i vv v vi
C L1M4_orf2#LIN 2250 TTCGGATTGTTCAT-TGCTAG-------TGTA-TAGAAATACAATTGATT 2210
Crub_svsplocu 394728 TTTCCCTATTTATTTTCAACCCAGCCAC--TCCTCAAATTTCTCTATT-- 394773
viv v i vv i v v -- v -i i iv i --
C L1M4_orf2#LIN 2209 TTTGTATATTGATCTTGTATCCTGCAACCTTGCT-GAACTCGTTTATTAG 2161
Crub_svsplocu 394774 TTCTGCAAAAGTTTGGTGGCTGTTGCCAATGGCTCCTCTAAGATA-AAAA 394822
-- v vv ? iv v v vvv v ii - v - i
C L1M4_orf2#LIN 2160 TTCT--AATAGTTTTTTNGTGGATTCCTTAGGATTTTCT-ATATACAAGA 2114
Crub_svsplocu 394823 CCAAATCGTCTGCAAA---AGCCTGTAATTTATATTTCTGATCTTTT--- 394866
i vi i i --- ---i i - i -- i ---
C L1M4_orf2#LIN 2113 TCATGTCATCTGCGAATAGAG---ATAGTTT-TACTTCT--TCCTTTCCA 2070
Crub_svsplocu 394867 ATCTCCAATG-CTTTAATCTCCGACTCTTGTCTAATATTCCTAGCCAGCA 394915
-vi - v i ivvi i vvi i i v
C L1M4_orf2#LIN 2069 ATCT-GGATGCCTTTTATTTCTTTTTCTTGCCTAATTGCCCTGGCTAGAA 2021
Crub_svsplocu 394916 CTTCCAATGTAAGAATAAATAATAAGGGCGATAGAGGGCATCCCTGTCTT 394965
i i ii viv i iv iv v v i i
C L1M4_orf2#LIN 2020 CCTCCAGTACAATGTTGAATAGAAGTGGCGAGAGCGGACATCCTTGTCTT 1971
Crub_svsplocu 394966 GTGCC 394970
v
C L1M4_orf2#LIN 1970 GTTCC 1966
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.31
Transitions / transversions = 0.91 (68/75)
Gap_init rate = 0.08 (37 / 481), avg. gap size = 1.30 (48 / 37)
228 30.48 7.46 6.14 Crub_svsplocus 394736 395137 254863 C L1MdV_III_orf2 LINE/L1 2673 3079 1602
228 30.48 7.46 6.14 Crub_svsplocus 394736 395137 (254863) C L1MdV_III_orf2#LINE/L1 (1602) 3079 2673 m_b8s001i14
Crub_svsplocu 394736 TTTATTTTCAACCCAGCCACTCCTC-AAATTTCTCTATTTTCTGCAAAAG 394784
v vv i iiv -i v v i ivv vi ii
C L1MdV_III_orf 3079 TTAATTTTATATCCAGCCACTTTGCTGAAGTTGTTTATCAGCTTTAGGAG 3030
Crub_svsplocu 394785 TT---TGGTGG--CTGTTGCCAATGGCTCCTCTAAGATA-AAAACCAAAT 394828
--- --i v ----- v vii - - vi i v
C L1MdV_III_orf 3029 TTCTCTGGTGGAATTTTTG-----GGGTCACTTAAG-TATACGATCATAT 2986
Crub_svsplocu 394829 CGTCTGCAAA-AGCCTGTAATTTATATTTCTGATCTTTT---ATCTCCAA 394874
i - -- vv vv i -- i --- i vi v
C L1MdV_III_orf 2985 CATCTGCAAATAG--TGATATTTTGACTTCT--TCCTTTCCAATTTGTAT 2940
Crub_svsplocu 394875 TGCTTTAATCTCCGACTCTTGTCTAATATTCCTAGCCAGCACTTCCAATG 394924
iv i i vvi v vvii i v v i i
C L1MdV_III_orf 2939 CCCTTTGACCTCCTTTTGTTGTCTAATTGCTCTAGCTAGAACTTCAAGTA 2890
Crub_svsplocu 394925 TAAGAATAAATAATAAGGGCGATAGAGGGCATCCCTGTCTTGTGCCCT-- 394972
iv v v i ivv v v v v i v - --
C L1MdV_III_orf 2889 CTATATTGAATAGATAGGGAGAGAGTGGGCAGCCTTGTCTAGT-CCCTGA 2841
Crub_svsplocu 394973 TTTTAATATCAAAACTGTATGA------TCTCCATTTAAAAGT---ATCC 395013
i ---iii i iv v ------ --- --- vi
C L1MdV_III_orf 2840 TTTTAGT---GGGATTGCTTCAAGTTTCTCTCCATTT---AGTTTGATGT 2797
Crub_svsplocu 395014 TTGCTGATTGTTTGTTATAAATTGCTTGGATTGCATTTCTAAAGTTTCCA 395063
v iv v i i v vv i iii --- i v vvi
C L1MdV_III_orf 2796 TGGCTACTGGTTTGCTGTATATTGCTTTTACTATGTTT---AGGTATGGG 2750
Crub_svsplocu 395064 CC--AAAGTCC--ATCTCTCTCAATGGCTGGAACATAAAT---TGCC-AA 395105
--i v -- i - vivi vv i v--- i-
C L1MdV_III_orf 2749 CCTTGAATTCCTGATCTTTC-CAAGACTTTTAACATGAAGGGATGCTGAA 2701
Crub_svsplocu 395106 TTGAGATTATCAAAAGCTTTTTGTGCATCCAA 395137
---- i v vv i
C L1MdV_III_orf 2700 TT----TTGTCAAATGCTTTTTCAGCATCTAA 2673
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.17
Transitions / transversions = 0.95 (56/59)
Gap_init rate = 0.09 (38 / 401), avg. gap size = 1.45 (55 / 38)
233 30.17 7.21 5.48 Crub_svsplocus 394736 395040 254960 C L1Lx_IV_orf2 LINE/L1 2767 3076 1602
233 30.17 7.21 5.48 Crub_svsplocus 394736 395040 (254960) C L1Lx_IV_orf2#LINE/L1 (1602) 3076 2767 m_b8s001i13
Crub_svsplocu 394736 TTTATTTTCAACCCAGCCACTCCTC-AAATTTCTCTATTTTCTGCAAAAG 394784
v vv i iiv -i v v i ivv i ii
C L1Lx_IV_orf2# 3076 TTAATTTTATATCCAGCCACTTTGCTGAAGTTGTTTATCAGCTGTAGGAG 3027
Crub_svsplocu 394785 TT---TGGTGG--CTGTTGCCAATGGCTCCTCTAAGATAAAA-ACCAAAT 394828
--- --i v ----- v vii - v v- i v
C L1Lx_IV_orf2# 3026 TTCTCTGGTGGAATTTTTG-----GGGTCACTTAAG-TATACTATCATAT 2983
Crub_svsplocu 394829 CGTCTGCAAA-AGCCTGTAATTTATATTTCTGATCTTTT---ATCTCCAA 394874
i - -- vv vv i -- i --- i vi v
C L1Lx_IV_orf2# 2982 CATCTGCAAATAG--TGATATTTTGACTTCT--TCCTTTCCAATTTGTAT 2937
Crub_svsplocu 394875 TGCTTTAATCTCCGACTCTTGTCTAATATTCCTAGCCAGCACTTCCAATG 394924
iv i i vvi v vvii i i v v i i
C L1Lx_IV_orf2# 2936 CCCTTTGACCTCCTTTTGTTGTCTAATTGCTCTGGCTAGAACTTCGAGTA 2887
Crub_svsplocu 394925 TAAGAATAAATAATAAGGGCGATAGAGGGCATCCCTGTCTTGTGCCCT-- 394972
iv v v i ivv v v v v i v - --
C L1Lx_IV_orf2# 2886 CTATATTGAATAGATAGGGAGAGAGTGGGCAGCCTTGTCTAGT-CCCTGA 2838
Crub_svsplocu 394973 TTTTAATATCAAAACTGTATGA------TCTCCATTTAAAAGT---ATCC 395013
i ---iii i iv v ------ --- --- vi
C L1Lx_IV_orf2# 2837 TTTTAGT---GGGATTGCTTCAAGTTTCTCTCCATTT---AGTTTGATGT 2794
Crub_svsplocu 395014 TTGCTGATTGTTTGTTATAAATTGCTT 395040
v iv v i i v
C L1Lx_IV_orf2# 2793 TGGCTACTGGTTTGCTGTATATTGCTT 2767
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.07
Transitions / transversions = 0.93 (42/45)
Gap_init rate = 0.09 (26 / 304), avg. gap size = 1.50 (39 / 26)
242 32.54 6.01 4.69 Crub_svsplocus 394822 395137 254863 C L1_Mur2_orf2 LINE/L1 2667 2986 1689
242 32.54 6.01 4.69 Crub_svsplocus 394822 395137 (254863) C L1_Mur2_orf2#LINE/L1 (1689) 2986 2667 m_b8s001i16
Crub_svsplocu 394822 ACCAAATCGTCTGCAAA-AGC----CTGTAATTTAT--ATTTCTGATCTT 394864
i v i i - ---- v i i v --v ii -
C L1_Mur2_orf2# 2986 ATCATATCATCTGCGAATAGCGATACTTTGACTTCTTCCTTTCCAAT-TT 2938
Crub_svsplocu 394865 TTATCTCCAATGCTTTAATCTCCGACTCTTGTCTAATATTCCTAGCCAGC 394914
v i ------ i vvivv v vvii i v
C L1_Mur2_orf2# 2937 GTATCCCC------TTGATCTCCTTTAGTTGTCTTATTGCTCTAGCTAGA 2894
Crub_svsplocu 394915 ACTTCCAATGTAAGAATAAATAATAAGGGCGATAGAGGGCATCCCTGTCT 394964
v i iiv v v i ivv v v v v i
C L1_Mur2_orf2# 2893 ACTTCAAGTACTATATTGAATAGATAGGGAGAGAGTGGGCAGCCTTGTCT 2844
Crub_svsplocu 394965 TGTGCCCT--TTTTAATATCAAAACTGTATGA------TCTCCATTTAAA 395006
- -- i i---i i iv v ------ v
C L1_Mur2_orf2# 2843 TGT-CCCTGATTTTAGTG---GAATTGCTTTAAGTTTCTCTCCATTTAAT 2798
Crub_svsplocu 395007 AGTATCCTTGCTGATTGTTTGTTATAAATTGCTTGGATTGCATTTCTAAA 395056
vvv vi v iv v i i i v vv iii --- i
C L1_Mur2_orf2# 2797 TTGATGTTGGCTATTGGCTTGCTGTATATTGCTTTTATTATGTTT---AG 2751
Crub_svsplocu 395057 GTTTCCACC--AAAGTCC--ATCTCTCTCAATGGCTGGAACATAAATTGC 395102
v vii --iv vi -- - vivi vv i vv v
C L1_Mur2_orf2# 2750 GTATGTGCCTTGTATCCCTGATCTCTC-CAAGACTTTTAACATGAAGGGG 2702
Crub_svsplocu 395103 CAATTGAGATTATCAAAAGCTTTTTGTGCATCCAA 395137
iiv v vv i i vv i
C L1_Mur2_orf2# 2701 TGTTGGATTTTGTCAAAGGCTTTTTCAGCATCTAA 2667
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.51
Transitions / transversions = 0.85 (45/53)
Gap_init rate = 0.07 (22 / 315), avg. gap size = 1.55 (34 / 22)
254 30.12 6.52 4.70 Crub_svsplocus 394822 395051 254949 C L1MdV_II_orf2 LINE/L1 2759 2992 1689
254 30.12 6.52 4.70 Crub_svsplocus 394822 395051 (254949) C L1MdV_II_orf2#LINE/L1 (1689) 2992 2759 m_b8s001i15
Crub_svsplocu 394822 ACCAAATCGTCTGCAAA-AGCCTGTAATTTATATTTCTGATCTTTT---A 394867
i v i - -- vv vv i -- i ---
C L1MdV_II_orf2 2992 ATCATATCATCTGCAAATAG--TGATATTTTGACTTCT--TCCTTTCCAA 2947
Crub_svsplocu 394868 TCTCCAATGCTTTAATCTCCGACTCTTGTCTAATATTCCTAGCCAGCACT 394917
i vi viv i vvi v vvii i i v
C L1MdV_II_orf2 2946 TTTGTATCCCTTTGATCTCCTTTTGTTGTCTAATTGCTCTGGCTAGGACT 2897
Crub_svsplocu 394918 TCCAATGTAAGAATAAATAATAAGGGCGATAGAGGGCATCCCTGTCTTGT 394967
v i iiv v v i ivv v v v v i v
C L1MdV_II_orf2 2896 TCAAGTACTATATTGAATAGGTAGGGAGAGAGTGGGCAGCCTTGTCTAGT 2847
Crub_svsplocu 394968 GCCCT--TTTTAATATCAAAACTGTATGA------TCTCCATTTAAAAGT 395009
- -- i ---iii i iv v ------ ---
C L1MdV_II_orf2 2846 -CCCTGATTTTAGT---GGGATTGCTTCAAGTTTCTCTCCATTT---AGT 2804
Crub_svsplocu 395010 ---ATCCTTGCTGATTGTTTGTTATAAATTGCTTGGATTGCATTT 395051
--- vi v iv v i i v vv iii
C L1MdV_II_orf2 2803 TTGATGTTGGCTACTGGTTTGCTGTATATTGCTTTTATTATGTTT 2759
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.96
Transitions / transversions = 0.94 (32/34)
Gap_init rate = 0.07 (16 / 229), avg. gap size = 1.62 (26 / 16)
359 32.66 4.25 3.05 Crub_svsplocus 394893 395151 254849 C L1-6_DR LINE/L1 3485 3746 1947
359 32.66 4.25 3.05 Crub_svsplocus 394893 395151 (254849) C L1-6_DR#LINE/L1 (1947) 3746 3485 m_b8s001i17
Crub_svsplocu 394893 TTGTCTAATATTCCTAGCCAGCACTTCCAATGTAAGAATAAATAATAAGG 394942
vviiv iiv i v vv v i v ii
C L1-6_DR#LINE/ 3746 TTGTCTAATAAATTGAGCCAGTGGTTCTATTGATAGATTAAACAAAAGAG 3697
Crub_svsplocu 394943 GCGATAGAGGGCATCCCTGTCTTGTGCCCTTTTTAATATCAAAACTGT-- 394990
v v v i v i i iv v --
C L1-6_DR#LINE/ 3696 GAGAGAGAGGGCAACCCTGTTTTGTTCCCCTCTTAATACAAAAAGTGTCT 3647
Crub_svsplocu 394991 ---ATGATCTCCATTTAAAAGTATCCTTGCTGATTGTTT--GTTATAAAT 395035
--- i ii -i iv iv ii v ii vv v --iv i -
C L1-6_DR#LINE/ 3646 GAAATAATTCCCA-CTGTAGTTACTCTAGCCAAGGGGTTAGAGTATAGA- 3599
Crub_svsplocu 395036 TGCTTGGATTGCATTTC--TAAAGTTTCCACCAAAGTCCATCTCTCTCAA 395083
- i i -- i i-- i v vvi i i iv vv i i i
C L1-6_DR#LINE/ 3598 -GTTTGAAT--CATCTTAATGAATTGATCGCCAAAATTAAAGTTTTTCAG 3552
Crub_svsplocu 395084 TGGCTGGAACATAAATTG--CCAATTGAGATTATCAAAAGCTTTTTGTGC 395131
-- v v v -- v iv iiiv i vi
C L1-6_DR#LINE/ 3551 TG--TGTACCATAAATAGCCCCATTCCAAGCGATCAAAGGCTTTTTCCGC 3504
Crub_svsplocu 395132 ATCCAAAAGTATAAGTGCCA 395151
i v v vi -
C L1-6_DR#LINE/ 3503 ATCTATAAGGAGGAG-GCCA 3485
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.76
Transitions / transversions = 1.16 (44/38)
Gap_init rate = 0.05 (13 / 258), avg. gap size = 1.46 (19 / 13)
+ 297 33.2 3.3 4.0 Crub_svsplocus 394924 395353 (254647) C Tx1-18_DR LINE/L1-Tx1 (1952) 3272 2846 227 *
ANNOTATION EVIDENCE:
297 33.18 3.26 3.98 Crub_svsplocus 394924 395353 254647 C Tx1-18_DR LINE/L1-Tx1 2846 3272 1952
297 33.18 3.26 3.98 Crub_svsplocus 394924 395353 (254647) C Tx1-18_DR#LINE/L1-Tx1 (1952) 3272 2846 m_b8s001i18
Crub_svsplocu 394924 GTAAGAATAAATAATAAGGGCGATAGAGGGCATCCCTGTCTTGTGCCCTT 394973
ii ---- v v vi i i v v i i
C Tx1-18_DR#LIN 3272 GTAGAAATAAATAA----GGAGAAATGGGACATCCTTGGCGTATGCCCCT 3227
Crub_svsplocu 394974 TTTAATATCAAAACTGTATGA--TCTCCATTTAAAAGTATCCTTG--CTG 395019
i v ivv -- - vvv v vv --
C Tx1-18_DR#LIN 3226 TTTAACATCAAATCTAGTTGAAGTC-CCATTTTTCAGTTTAATTGAGCTG 3178
Crub_svsplocu 395020 ATTGT-TTGTTATAAATTGCTTGGATTGCATTTCTAAAGTTTCCACCAAA 395068
v v i- ii vv i i i v v ivv vv
C Tx1-18_DR#LIN 3177 TTAGCATTACTATAAAGAGTTTGAATTGCGTTACAAAAAAATGGACCAAA 3128
Crub_svsplocu 395069 GTCCATCTCTCTCAATGGCTGG--AACATAAATTGCCAATTGAGATTATC 395116
-i vvi i i - i i-- v v vviiv ii iv
C Tx1-18_DR#LIN 3127 -CCCAAACCTTTTAA-GACTGAGAAAAATAAAATTATGTTCAAGGGTATC 3080
Crub_svsplocu 395117 AAAAGCTTTTTGTGCATCCAAAAGT-ATAAGTGCCATCTGTTTCCCCAGA 395165
v ivivi i i - vi iv ----- i i v
C Tx1-18_DR#LIN 3079 AAAAGCTTTATAGAAGTCTAAAAATAATATATAAC-----TTTTCTCTGA 3035
Crub_svsplocu 395166 TACTTTTCA-----TAATATTCCAACACATTCAAAATAATCCTTAAGTTA 395210
? ---- -----v i v v iv ii i iv vi v vi i
C Tx1-18_DR#LIN 3034 NA----TCAAGTGGGAGTAATCGAGAATGTCCAAAACTAGTCTGATATTG 2989
Crub_svsplocu 395211 TTCTTTATCTGTCTTTTAGGCAAAAAGCC-ATTTTGGTCTGAATGAATAA 395259
vviv v v vvv v v -iv v i - v
C Tx1-18_DR#LIN 2988 TTAGCAATATGTCTATTCTTCATAAATCCTGATTGGGTTTG-ATCAATAA 2940
Crub_svsplocu 395260 ATTCGTTCAAAACTTTCTTCACTCTTTCTGCTATAATTGCTATAAATATT 395309
v vv ii v iv ii v v v v v ii
C Tx1-18_DR#LIN 2939 CTGAGTCTAATATATCTTTAAATCTTTCAGCAAGAATTGCTGCAAATATT 2890
Crub_svsplocu 395310 TTATAATTCACATTTAATAATGATATTGTTCTATAATTTTTAAT 395353
ivvi ivv v vvi v i
C Tx1-18_DR#LIN 2889 TTATAATCGTTATTTAATAGACATATTGGTCGCCAATTATCAAT 2846
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.39
Transitions / transversions = 0.78 (60/77)
Gap_init rate = 0.06 (24 / 429), avg. gap size = 1.29 (31 / 24)
+ 270 31.4 1.6 1.6 Crub_svsplocus 395218 395411 (254589) C L1M4 LINE/L1 (2636) 3378 3185 226 *
ANNOTATION EVIDENCE:
270 31.42 1.55 1.55 Crub_svsplocus 395218 395411 254589 C L1-21_DR LINE/L1 3185 3378 2636
270 31.42 1.55 1.55 Crub_svsplocus 395218 395411 (254589) C L1-21_DR#LINE/L1 (2636) 3378 3185 m_b8s001i19
Crub_svsplocu 395218 TCTGTCTTTTAGGCAAAAAGCCATTTTGGTCTGAATGAATAAATTCGTTC 395267
i vvv i v v vv i iiv v iv vvvi
C L1-21_DR#LINE 3378 TTTGTCTTTGTCGTATAAATCCTGTTTGATCTAGTTGTATAAGGTCTGGT 3329
Crub_svsplocu 395268 AAAACTTTCTTCACTCTTTCTGCTATAATTGCTATAAATATTTTATAATT 395317
v iv ? ii v i i v v i iv i
C L1-21_DR#LINE 3328 AATATATTNTCTAGTCTTTTTGCCAAAATTGATGTGTATATTTTATAATC 3279
Crub_svsplocu 395318 CACATTTAATAATGATATTGTTCTATAATTTTTA-ATTTGTGTAA--GGT 395364
i i v vi v vv v - i--- --v
C L1-21_DR#LINE 3278 TATATTTAAAACCGAAATTGGGCGATAATTTTTACAC---TGTAATTTGT 3232
Crub_svsplocu 395365 CAGTATCGTCTTTAAGTATAAGAGAAATATTGGCTTCTGTCCAGGAA 395411
vv vi i i v vv v vv v v i
C L1-21_DR#LINE 3231 CTTTCCCATCTTTAGGAATAATTGTAATTGTCGCTTCTCTCCAAGAA 3185
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.21
Transitions / transversions = 0.62 (23/37)
Gap_init rate = 0.03 (5 / 193), avg. gap size = 1.20 (6 / 5)
+ 235 20.6 1.4 1.4 Crub_svsplocus 395779 395847 (254153) C L1-23_DR LINE/L1 (2860) 2719 2651 228
ANNOTATION EVIDENCE:
235 20.59 1.45 1.45 Crub_svsplocus 395779 395847 254153 C L1-23_DR LINE/L1 2651 2719 2860
235 20.59 1.45 1.45 Crub_svsplocus 395779 395847 (254153) C L1-23_DR#LINE/L1 (2860) 2719 2651 m_b8s001i20
Crub_svsplocu 395779 TTCTTTTTTCAATCTG-TATGCAAGACATCTTCCTGGTTTATTGGCATTT 395827
i - - v ivv vv v i v i
C L1-23_DR#LINE 2719 TTCCTTTTT-AATCTGATATGCTAACAATCGGCCAGGTTTGTTTGCATTC 2671
Crub_svsplocu 395828 TCAAAAAAGTTCTGTTTGGA 395847
v v i
C L1-23_DR#LINE 2670 TCATAATAATTCTGTTTGGA 2651
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.07
Transitions / transversions = 0.56 (5/9)
Gap_init rate = 0.03 (2 / 68), avg. gap size = 1.00 (2 / 2)
+ 30 0.0 0.0 0.0 Crub_svsplocus 396479 396506 (253494) + (CCCT)n Simple_repeat 1 28 (0) 229
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 Crub_svsplocus 396479 396506 253494 + (CCCT)n Simple_repeat 1 28 0
30 0.00 0.00 0.00 Crub_svsplocus 396479 396506 (253494) (CCCT)n#Simple_repeat 1 28 (0) c_b8s251i0
Crub_svsplocu 396479 CCCTCCCTCCCTCCCTCCCTCCCTCCCT 396506
(CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 37 0.0 0.0 0.0 Crub_svsplocus 400258 400289 (249711) + (AC)n Simple_repeat 1 32 (0) 230
ANNOTATION EVIDENCE:
37 0.00 0.00 0.00 Crub_svsplocus 400258 400289 249711 + (AC)n Simple_repeat 1 32 0
37 0.00 0.00 0.00 Crub_svsplocus 400258 400289 (249711) (AC)n#Simple_repeat 1 32 (0) c_b8s251i1
Crub_svsplocu 400258 ACACACACACACACACACACACACACACACAC 400289
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACAC 32
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 15 20.2 2.1 2.1 Crub_svsplocus 401149 401195 (248805) + (AAGATAA)n Simple_repeat 1 47 (0) 231
ANNOTATION EVIDENCE:
15 20.24 2.13 2.13 Crub_svsplocus 401149 401195 248805 + (AAGATAA)n Simple_repeat 1 47 0
15 20.24 2.13 2.13 Crub_svsplocus 401149 401195 (248805) (AAGATAA)n#Simple_repeat 1 47 (0) m_b8s252i3
Crub_svsplocu 401149 AAGAAAATATTTAAAAAACAACA-ATAAAACATAAAAGATAAAAAGAT 401195
v v vv i i v - v -
(AAGATAA)n#Si 1 AAGATAAAAGATAAAAGATAAAAGATAAAAGATAAAAGAT-AAAAGAT 47
Matrix = Unknown
Transitions / transversions = 0.33 (2/6)
Gap_init rate = 0.04 (2 / 46), avg. gap size = 1.00 (2 / 2)
+ 16 13.2 3.0 0.0 Crub_svsplocus 401704 401736 (248264) + (TTG)n Simple_repeat 1 34 (0) 232
ANNOTATION EVIDENCE:
16 13.23 3.03 0.00 Crub_svsplocus 401704 401736 248264 + (TTG)n Simple_repeat 1 34 0
16 13.23 3.03 0.00 Crub_svsplocus 401704 401736 (248264) (TTG)n#Simple_repeat 1 34 (0) m_b8s252i4
Crub_svsplocu 401704 TTGTTGTTGTTAAT-TTGTTGTTGTTTTTCTTGT 401736
iv - v v
(TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGT 34
Matrix = Unknown
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1)
+ 234 21.4 2.5 5.2 Crub_svsplocus 402893 402971 (247029) C Tx1-30_DR LINE/L1-Tx1 (1603) 624 548 233
ANNOTATION EVIDENCE:
234 21.36 2.53 5.19 Crub_svsplocus 402893 402971 247029 C Tx1-30_DR LINE/L1-Tx1 548 624 1603
234 21.36 2.53 5.19 Crub_svsplocus 402893 402971 (247029) C Tx1-30_DR#LINE/L1-Tx1 (1603) 624 548 m_b8s001i21
Crub_svsplocu 402893 GAAGCACCACAGGTTCTTTTTTTTTTTTTTTTTTGAA--TACATGGAGAC 402940
v i v v? i ?ii -- v i
C Tx1-30_DR#LIN 624 GAAGAATCCCACNTTTTTTTTTTTTTTTTTTTTNAGATTTAAATGAAGAC 575
Crub_svsplocu 402941 CCAGTGAATTTAAAGTAACAGCAAAACTTTA 402971
i iv v i iv ----
C Tx1-30_DR#LIN 574 CTAAGGCATTTGAAAAAA----AAAACTTTA 548
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.29
Transitions / transversions = 1.29 (9/7)
Gap_init rate = 0.06 (5 / 78), avg. gap size = 1.20 (6 / 5)
+ 12 24.3 0.0 0.0 Crub_svsplocus 405777 405810 (244190) + A-rich Low_complexity 1 34 (0) 234
ANNOTATION EVIDENCE:
12 24.30 0.00 0.00 Crub_svsplocus 405777 405810 244190 + (AAAAG)n Simple_repeat 1 34 0
12 24.30 0.00 0.00 Crub_svsplocus 405777 405810 (244190) (AAAAG)n#Simple_repeat 1 34 (0) m_b8s252i5
Crub_svsplocu 405777 AAAAGTCAATAAATTACAAAAAAAGAAAAGAAAA 405810
vv v vv v i
(AAAAG)n#Simp 1 AAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAA 34
Matrix = Unknown
Transitions / transversions = 0.17 (1/6)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0)
+ 527 32.3 7.1 7.3 Crub_svsplocus 407964 408537 (241463) C Gypsy-175_DR-I LTR/Gypsy (905) 2058 1486 235
ANNOTATION EVIDENCE:
527 32.34 7.14 7.33 Crub_svsplocus 407964 408537 241463 C Gypsy-175_DR-I LTR/Gypsy 1486 2058 905
527 32.34 7.14 7.33 Crub_svsplocus 407964 408537 (241463) C Gypsy-175_DR-I#LTR/Gypsy (905) 2058 1486 m_b8s001i22
Crub_svsplocu 407964 ACCATGTGCTTACCTTGGCCATTGAAAGCCTGATGAAAGGGTGCCGAA-- 408011
i i ivv ivi vivi iv i i ?v i--
C Gypsy-175_DR- 2058 ACCATGCGTTCCGCCAAGCCATTCGTGGCTGGGTGAAAAGGTGNAGAGCG 2009
Crub_svsplocu 408012 -GTA-GCATGACGACTCATGTTGGCTTTCAGAAAGGACTGGAACTCTGAA 408059
- i- ii - i--- i v v v vvvv
C Gypsy-175_DR- 2008 TGTGTGTGTGAC-ACC---GTTAGCTTTGAGAAATGTCTGGAACTCGTCC 1963
Crub_svsplocu 408060 GAGGTGAATTGAGGTCTGTTGTCGGAGACAAGAACATCTGAGAGCCTGTG 408109
i i v v ii i vvi v v v ii v ii
C Gypsy-175_DR- 1962 AAGGTGAACTTAGGACCATTATCGCTAACCAGCACTTCTGGAAGGCCATG 1913
Crub_svsplocu 408110 AGAGGCGAAGATTCCCCTCAGCACCTGGATGGTCCTGGCAG---TAGTTG 408156
viivii v v vi i i i v ---
C Gypsy-175_DR- 1912 ATGACTAAATAATGTCCTCAGCACTTGAATGGTCTTTGCAGATGTAGTTG 1863
Crub_svsplocu 408157 ------TGGTAGACACTGGAACGGTCTCTAGCCATTTAGAGTGACTGTCC 408200
------ vii v --------- vi i v vii i
C Gypsy-175_DR- 1862 AATCCATCACACACACT---------TCGGGCCACTTTGAGTGAGCATCT 1822
Crub_svsplocu 408201 ACAACAATGAGGAAGAATTGCCCCTGAAAGGGGCTAGCATAGTCGGATAT 408250
v? i i iv viv i v v i i -v i
C Gypsy-175_DR- 1821 ACTNCGACGAGACACGTTTGTCCCTCAAATGGACCAGCATAGTC-TACAT 1773
Crub_svsplocu 408251 GAAAACTCGACCAAGGAGCATGTGTGTGCTCCCATCTATGCA-------- 408292
v v vivi vv v vviii i vvvi i --------
C Gypsy-175_DR- 1772 GCATACGTTGCCAAGGAGACTCTGGCCATTTCCAGGGGTGTAAGGGAGAA 1723
Crub_svsplocu 408293 ----CAGGAGCCTGTGGCATTT-----CAGGCCTGGAC---TA-TTGGCA 408329
---- v i v i i ----- v - --- i- i
C Gypsy-175_DR- 1722 GGTCCAGGTGCTTTTAGCGTTTGTTGGCAGGACT-GACAGTTGTTTGACA 1674
Crub_svsplocu 408330 ACTGTGGCACCCATGGAGATGGGTCTCAATCTCTTTATCAAGCCCAGGCC 408379
vvi i-------- i v vi ------------
C Gypsy-175_DR- 1673 ACTGTTCTACT--------TGAGTGTCAATGCCT------------GGCC 1644
Crub_svsplocu 408380 ACCAGAGATAGCTGCGTGCAAGCGCTTTCCTCTGGAATATGCCCGGATAC 408429
v i vv i vi i v ii v vv ii i ii
C Gypsy-175_DR- 1643 ACCAGACATAACGCCGCGCAACTGCCTTCATTCGCACGACACCTGGATGT 1594
Crub_svsplocu 408430 CCCTCATGCAG---AGACTGCAAGACTCTAGTCCTCAATGAGGTTGGGAT 408476
ivi v ?--- --- iv i i vi v vvi vv i
C Gypsy-175_DR- 1593 CCTGTATGAANTTCAG---GCAGCACCCTGGATCGCAATTTAGGAGGAAT 1547
Crub_svsplocu 408477 CACTACCCTGCTACCCCACAGGACACAACCCTTAAAGGTGGAT----AGC 408522
v v v vi v i i ---- v ----
C Gypsy-175_DR- 1546 AACTACCCTCCTTCCCCACATAAGACAGCCTT----GTTGGATTGTCAGC 1501
Crub_svsplocu 408523 TCATGCTTTCTTTTC 408537
v v
C Gypsy-175_DR- 1500 TCATCCTTTCTATTC 1486
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.44
Transitions / transversions = 1.05 (88/84)
Gap_init rate = 0.09 (54 / 573), avg. gap size = 1.54 (83 / 54)
+ 1790 36.2 2.2 1.5 Crub_svsplocus 408715 410005 (239995) C MamGypsy2-I LTR/Gypsy (1410) 2756 1457 236
ANNOTATION EVIDENCE:
1790 36.24 2.17 1.46 Crub_svsplocus 408715 410005 239995 C MamGypsy2-I LTR/Gypsy 1457 2756 1410
1790 36.24 2.17 1.46 Crub_svsplocus 408715 410005 (239995) C MamGypsy2-I#LTR/Gypsy (1410) 2756 1457 m_b8s001i23
Crub_svsplocu 408715 TCTAAGAGCTGTAAAGGCAATCTGTTAAGGCCATCTGCATGGCCCATTTC 408764
ii v i iv iv v i v v v vvvvi v
C MamGypsy2-I#L 2756 TCTGGGATCTGCAGTGGCAGACGGCTCAGGGCATCAGCATTCGATATTGC 2707
Crub_svsplocu 408765 TTTGCCTGGTTTGTGAACCAGGGAATAGTCATAGGCA--GAGAGGAAGAT 408812
i v v i ii v v vi i -- vii i
C MamGypsy2-I#L 2706 TCTTCCAGGCTTGTAGACAAGCGCGTAGTCATAAGCACTGAGCAAAAGAC 2657
Crub_svsplocu 408813 TGACCACCTCAACATTCTAGGAGAAATTGTGTGGGGGGTTTGCTTGTTTG 408862
-- v v vi v vv v v vi vvi v vv i iiv
C MamGypsy2-I#L 2656 T--CCAGCGCTGCATACGTGGTGACATAATTAAGGGCGTAGGCTTATCCT 2609
Crub_svsplocu 408863 TTGTGAACAACCCCAGCAGTGGCTTGTGGTCTGTAAAGACCGTAAAATGG 408912
v vi v ii viv v i v v i ii ivvi
C MamGypsy2-I#L 2608 TAGAAAAGAGTCCCCAAAGAGGCTTGTGATCAGTACAAATTGTAAAGGCA 2559
Crub_svsplocu 408913 CGGCCATATAAAAAGTCATGGAACTTTTTTATGCCAGCCACAATGGCCAA 408962
i v iiv ii i v iv v v i ii v i
C MamGypsy2-I#L 2558 CGGCCGTAGAGGTAGTTGTGGAACTTCTTGACTCCCGCGATAACAGCAAG 2509
Crub_svsplocu 408963 GGCTTTTGTGTCTATCTGTGCGTAATTATGCTCAGCAGAAGACAGAGTCC 409012
i v v i ii i vi i v i v vv i
C MamGypsy2-I#L 2508 GGCTTCTTTGTCAATTTGTGTATAGTTCCGTTCTGTAGATGACATTGTTC 2459
Crub_svsplocu 409013 TTGAATAGTAGGTTACAGGAACTTGTGTACCATCAGCCTTGAGGTGGCTT 409062
i i iv iv vi i vv i v v v vvv v
C MamGypsy2-I#L 2458 TTGAGTAGTAAGCAATTGGTGCCTCAGTGCCATCTGGCATTTTGTGGCTA 2409
Crub_svsplocu 409063 AAGACAGCCCCGATCCCATAAGGGGATGCATC----GCAA---AC--TGG 409103
iv i iiiv i v v i ---- i --- --
C MamGypsy2-I#L 2408 AGCACAGCTCCAGCACCGTAAGGTGAAGCGTCAGTGGTAAGAAACAGTGG 2359
Crub_svsplocu 409104 CAGCTGCTCATTGAAATGAGGTAAAACAGCATTTGAAGACAACAA-TGCT 409152
ivvv i i v viv iv vv iv v i -
C MamGypsy2-I#L 2358 TTTATGTTCATCGTAATGTACTAGCACAGACTCGGAAGTCAATAACTGCT 2309
Crub_svsplocu 409153 TTGAC-CTCAGCAACACTCTTTTCATGGACTTTTG--TCCACTTCCATGG 409199
- -i v v vi v- ii -- vvi -- viv i
C MamGypsy2-I#L 2308 T-GACATTCCGGAAAGCG-TCCTCATG--CTGGCGAGTCCAACGCCACGG 2263
Crub_svsplocu 409200 AGCCTGTTTATCCAAGAGCCAGTGTAACTGCTCTGCCACTGCAGCCTTTT 409249
i viv vi iv v ii v iiv v v iv iv
C MamGypsy2-I#L 2262 AACGCCTTTTCCCAGTAGGCGATGAAGTGGCTCAGCAATGGTTGCCTTTT 2213
Crub_svsplocu 409250 GGGGAAGGAGGGAATGGTAAAAGTTTAAAAGTCCAAGGAAGGCTTGAAGC 409299
v i iiiv i i v iv i v
C MamGypsy2-I#L 2212 GTGGAAGAAAAACATGGTAGAAATTGAGTAGCCCCAGGAAGGCTTGAAGC 2163
Crub_svsplocu 409300 TTGGTCTTCGACTTGGGACTTTGGGCCTGCTGAATTGCTTTGAGCTTGGA 409349
ivvv i vi v v vv v v vv i vivv v ivv
C MamGypsy2-I#L 2162 TCTTGCTTTGTTTTTGGAGTAGGCGCGTCATGGATTGCACGTACCTTATC 2113
Crub_svsplocu 409350 CTCAGCAGGATGGATGCCTTCAGCATCTATACAAAACCCCAGGAAT-TGA 409398
i v ii i i i vv iv i iiv v i i v-
C MamGypsy2-I#L 2112 TTGAGTGGGGTGAATACCAGCAGCATTGATGCGGTAGCCTAAGAAGGTGA 2063
Crub_svsplocu 409399 G--TGGAAGTTACTCCAATCTTGCATTTTTCCTGCTTAAGCTTCAGC--C 409444
v-- --- i i ii i vi v --i i v--
C MamGypsy2-I#L 2062 CACTGGAAGTT---CCGATTTCACATTTCTCCTTTTTCA--CTCGGATAC 2018
Crub_svsplocu 409445 CTGCTTTGCGGAAATGCAGCAAAATGGATCAAAGCCTTTCAGACAG---A 409491
v v iiv i vv i ii ivvviii i v vv ---
C MamGypsy2-I#L 2017 CTGATGTATCGAAACGATGTAGGACTTCCTGAAGTCTTTCCGCGAGTTCA 1968
Crub_svsplocu 409492 TTTTTGATTGATTACCCTGTGATGAGGATATCATCGAAATATGGG--CAA 409539
ii ivi --- ii v i v-- v
C MamGypsy2-I#L 1967 TCCTCTGTTGAT---CCCATGATCAGGACATCATCGAAATATGGTACCAC 1921
Crub_svsplocu 409540 AGTCCCAGAAGGCTACAGAGCATTTGCTCCATCACGCTTTGGAAAATGCC 409589
-- ii vv v i vvvv v v vi v
C MamGypsy2-I#L 1920 A--CCTGGAATCCTAGAAAGCAGGGTCTCCATGAAGCACTGGAAAATTCC 1873
Crub_svsplocu 409590 AGGAGCTACATTAACTCCGAATTGCAGTCTTCTGACTTTGAAAGCTCCCC 409639
i v vv i i v v vii i iv v i i
C MamGypsy2-I#L 1872 AGGGGCAACAGAAATTCCGAACTGAAGGCGCTTAACTCGGAATGCCCCTC 1823
Crub_svsplocu 409640 AATGCATTACGATAGTTTGAGCCTCTGCCATTGCATCATCAACCAGTAGC 409689
i vi v i v i v vi v i i v vi
C MamGypsy2-I#L 1822 GATGAGTGATGATTGTTTGGGCGTCTGCAGTAGCATCACCGACGATCAGC 1773
Crub_svsplocu 409690 TGTTGATAGGCCTGGGCCAAATCAAGTTTGGTGAAAACTCGGCCTCCTTT 409739
i i v ii v ii i iivvi i vvi
C MamGypsy2-I#L 1772 TGTTGATAAGCTTGGGCAAGGTCAAGTTTTGCAAAGACCTTTTCCCCAGC 1723
Crub_svsplocu 409740 AAGTGAGGCCAAAATGTGGCTCACCACAGGCACTGGATAAGCGTGCTGCT 409789
vivi v ii vv ii v ii v v
C MamGypsy2-I#L 1722 AAGAACAGCAAGGAGTTGATTGACTGCAGGCACTGGATATGGGTGCTGCT 1673
Crub_svsplocu 409790 GTAACGCTTTGTTTAGTGTGCATTTATAGTCAGCACAAATGTGGACTTCC 409839
vv ii i i i vv i i vv vvivv i iv
C MamGypsy2-I#L 1672 TAAGTGCCTTATTCACAGTGCACTTGTAGTCTCCACAAAGTCTCACCTTA 1623
Crub_svsplocu 409840 CCATTGGCCTTGAGTGGCATGACTATGGGTGTTTCCCATGGACTGCTAT- 409888
i v v iv ivvi v v i vv i--- v v -
C MamGypsy2-I#L 1622 CCATTAGGCTTTAGTACCGGCGCAATTGGTATAGCCCAC---CGGGTATG 1576
Crub_svsplocu 409889 --CCACAGGTTTCAGAATGCCTTGCTGTAGCAGTTTATCCAGCTCAGCAT 409936
--iv v iv iiii i vv vi v vv v vv v
C MamGypsy2-I#L 1575 TGTAACTGGTTCGAGGGCACCTTGTTTGATTAGATGCTCAAGCTCTTCTT 1526
Crub_svsplocu 409937 TAAACTTTTGCTTAAGCACAAAAGGCACCCGACGAGGCTTAATCCTAATC 409986
i ?vi v i v vi i vivv v vi v vviv i
C MamGypsy2-I#L 1525 CANTTTTTTTCCTTAGAGCAAAAGGTACATTTCTAGCTTTCAAGTGAATT 1476
Crub_svsplocu 409987 GGTGCAATGGAGGGATCTA 410005
vv i
C MamGypsy2-I#L 1475 GGTGCAATGGCTGGATCCA 1457
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 47.01
Transitions / transversions = 0.90 (218/243)
Gap_init rate = 0.03 (33 / 1290), avg. gap size = 1.42 (47 / 33)
+ 731 7.7 2.2 0.0 Crub_svsplocus 413321 413411 (236589) + URR1B DNA/hAT-Charlie 1 93 (132) 237
ANNOTATION EVIDENCE:
731 7.69 2.20 0.00 Crub_svsplocus 413321 413411 236589 + URR1B DNA/hAT-Charlie 1 93 132
731 7.69 2.20 0.00 Crub_svsplocus 413321 413411 (236589) URR1B#DNA/hAT-Charlie 1 93 (132) m_b8s001i24
Crub_svsplocu 413321 CAGCAGTTTTCAACCTGTGGGTTGCGACCCTTTTGGGGGTCGAACAACCC 413370
i i i i i
URR1B#DNA/hAT 1 CAGCGGTTCTCAACCTGTGGGTCGCGACCCCTTTGGGGGTCGAACGACCC 50
Crub_svsplocu 413371 TTTTACAGGGGTCGCCTAAGACCATTGGAAAACAC--ATATTT 413411
i i --
URR1B#DNA/hAT 51 TTTCACAGGGGTCGCCTAAGACCATCGGAAAACACAGATATTT 93
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.88
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.01 (1 / 90), avg. gap size = 2.00 (2 / 1)
+ 270 13.2 7.4 1.8 Crub_svsplocus 413478 413531 (236469) + DNA2-5_DR DNA/hAT-Ac 1520 1576 (246) 238
ANNOTATION EVIDENCE:
270 13.19 7.41 1.75 Crub_svsplocus 413478 413531 236469 + DNA2-5_DR DNA/hAT-Ac 1520 1576 246
270 13.19 7.41 1.75 Crub_svsplocus 413478 413531 (236469) DNA2-5_DR#DNA/hAT-Ac 1520 1576 (246) m_b8s001i25
Crub_svsplocu 413478 AGAGAGAGAGAGAGACAGAGGGGCACTTTTGCTTCCCTT----CTCTCTC 413523
v i ii - v v v ----
DNA2-5_DR#DNA 1520 AGAGAGAGAGAGAGAGAGAGAGGTGC-TGTGCGTCGCTTTGCGCTCTCTC 1568
Crub_svsplocu 413524 TCTCTCTC 413531
DNA2-5_DR#DNA 1569 TCTCTCTC 1576
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.55
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.04 (2 / 53), avg. gap size = 2.50 (5 / 2)
+ 361 34.2 2.9 2.9 Crub_svsplocus 414083 414570 (235430) C Gypsy72-I_DR LTR/Gypsy (777) 3591 3104 239
ANNOTATION EVIDENCE:
240 35.98 4.30 4.30 Crub_svsplocus 414083 414570 235430 C Gypsy89-I_DR LTR/Gypsy 3104 3591 777
240 35.98 4.30 4.30 Crub_svsplocus 414083 414570 (235430) C Gypsy89-I_DR#LTR/Gypsy (777) 3591 3104 m_b8s001i26
Crub_svsplocu 414083 CCGTTCCGTTTGTCCATCCCCTTGTGGATGATGGCTAGATGTCAGTCCCT 414132
v i i i ivvvi v i i i i v v --v
C Gypsy89-I_DR# 3591 CCTTTCTGTCTGCCCATTAGACTGGGGGTGGTAGCCAGAGGACAG--ACT 3544
Crub_svsplocu 414133 GAGTGGTC--CCTAAGAG--GGATAAAAATTCCTTCCAAAATGCAGACGT 414178
vi i v-- v v -- vvi ii -- ivii i v
C Gypsy89-I_DR# 3543 GATCGATGAGCCAATGAGCCGCCCAAAAGCT--TTCCAAAACCTGGATGA 3496
Crub_svsplocu 414179 AAATTGCACTCCCCTATCAGAGATGATGCATTGGGGTGCCCCGTGCAATC 414228
i i vivv v iv iivi v vivv i vii
C Gypsy89-I_DR# 3495 GAACTGGGGGCCCCGATCAGAGACTATATCCTGCGGGAAGCCATGCATCT 3446
Crub_svsplocu 414229 TGTAAATGTGCTGGATGAAAAGTTTTGCTAAGGCCT---TTGCAGTGGGA 414275
iv i ii iivv v iv iv --- i --- i
C Gypsy89-I_DR# 3445 TAAAGACATGTCTCATTAGTAGTTCAGCT---GTCTGGTTCGCAGTGGGA 3399
Crub_svsplocu 414276 ATCTTTTGGCAAGGGATAA--AGTG-CACCTGTTTGGAAAATAGGTCCGT 414322
v - i v - -- - v -i i i ivv ii
C Gypsy89-I_DR# 3398 AGCTTT-GGTAATGG-TAACAAGTGACACAT-CTTAGAGAACCTGTCCAC 3352
Crub_svsplocu 414323 GACTGTCCAGATAACAGTATTCCCATTGCTTTCTGGCAATTCCACTATAA 414372
v iiivvi v v i v vivvivvv i iiiv
C Gypsy89-I_DR# 3351 CACCACAAGGATTACCGTATTTCCCTGAGACGGAGGCAATCCTGTGATAA 3302
Crub_svsplocu 414373 AATCCATGGCTATTTCCCTCCAGGGGGCTGA---GGGACTTGCCACTGGT 414419
v vi vv v vvvv --i --- - v vv v v
C Gypsy89-I_DR# 3301 AATCAAGAGAAATATGGGACCAGGGG--CGACTCGGGA-TGGAAAGTGGG 3255
Crub_svsplocu 414420 TGTAATAG-CCCTGG---CGACTTCCCTTGCAACCTCTTTGCC--GATGC 414463
v iv - --- v ---- viii- i-- -
C Gypsy89-I_DR# 3254 TGAAGAAGTCCCTGGGGTCGAGTTC----GGGGT-TCTTTGCTCTGA-GC 3211
Crub_svsplocu 414464 ACAGGTTGGGCAGCTGGCAACATAACT-TTCTATGTCCTTTTTTATTGAT 414512
v i i v - - vi ii i ivi iiv
C Gypsy89-I_DR# 3210 ACAGGTGGGGCAACTAGAAACA-AACTCTTGCACATCTTTTCGCATCATT 3162
Crub_svsplocu 414513 GGCCACCAAAATTGCCGTTTAATTAAGTGTAAAGTTTTTACAAAT-CCAA 414561
i i v vivv i - v iv v i iiv - i
C Gypsy89-I_DR# 3161 GGCCACCAGAACTTCCTCAAAATCAA-TTTGTAGGTTCTGTTAATACCAG 3113
Crub_svsplocu 414562 AATGCCCTG 414570
ii i
C Gypsy89-I_DR# 3112 GGTGTCCTG 3104
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 48.00
Transitions / transversions = 1.05 (86/82)
Gap_init rate = 0.07 (32 / 487), avg. gap size = 1.31 (42 / 32)
347 33.80 3.33 3.33 Crub_svsplocus 414086 414385 235615 C Gypsy3-I_DR LTR/Gypsy 3243 3542 779
347 33.80 3.33 3.33 Crub_svsplocus 414086 414385 (235615) C Gypsy3-I_DR#LTR/Gypsy (779) 3542 3243 m_b8s001i27
Crub_svsplocu 414086 TTCCGTTTGTCCATCCCCTTGTGGATGATGGCTAGATG-TCAGTCCCTG- 414133
iivv v i ivii ii v - v -- i -
C Gypsy3-I_DR#L 3542 TTCCGTTTGTCCATTTGATTCTGGGTGGAAACCGGAGGATAAG--CTTGT 3495
Crub_svsplocu 414134 AGTGGTCCCTAAGAGGGAT---AAAAATTCCTTCCAAAATGCAGACGTAA 414180
--- ---v i iv i v i vvi v v
C Gypsy3-I_DR#L 3494 AGTGGTCCCT---AGGGATTGACAGAACGCTTGCCAGAATCGGGAGGAAA 3448
Crub_svsplocu 414181 ATTGCACTCCCCTATCAGAGATGATGCATTGGGGTGCCCCGTGCAATCTG 414230
i viv v v i ivi viiv iviv v
C Gypsy3-I_DR#L 3447 ACTGAGGTCCCCGATCTGAGACGATGTCCTGGGGAATGCCAAAGACTCTG 3398
Crub_svsplocu 414231 TAAATGTGCTGGATGAAAAGTTTTGCTAAGGCCTTTGCAGTGGGAATCTT 414280
v v ii v vv vv iv iivvv i v v -v
C Gypsy3-I_DR#L 3397 AACACATGGTTCATGACTAGTTCGGCCGTCTCTTTGGCCGTGGGAA-GTT 3349
Crub_svsplocu 414281 TTGGCAAGGG-ATAAAGTGCACCTGTTTGGAAAATAGGTCC---GTGACT 414326
v i i - i i vi vvvi v i v ---i
C Gypsy3-I_DR#L 3348 TAGACAGGGGAATGAAGCGGGCGGCCTTTGAGAATCGGTCCACTATGACT 3299
Crub_svsplocu 414327 GTCCAGATAACAGTATTCCCATTGCTTTCTGGCAATTCCACT-ATAAAAT 414375
i--- i iii i i - vvv vv v v v -
C Gypsy3-I_DR#L 3298 A---AAATAGTGGTGTTTCC-TTGGGATGGGGGAAGTCCAGTGATAAAAT 3253
Crub_svsplocu 414376 CCATGGCTAT 414385
i v
C Gypsy3-I_DR#L 3252 CCATAGATAT 3243
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.67
Transitions / transversions = 0.85 (45/53)
Gap_init rate = 0.05 (16 / 299), avg. gap size = 1.25 (20 / 16)
361 33.66 1.89 1.89 Crub_svsplocus 414135 414346 235654 C Gypsy-129_DR-I LTR/Gypsy 3286 3497 828
361 33.66 1.89 1.89 Crub_svsplocus 414135 414346 (235654) C Gypsy-129_DR-I#LTR/Gypsy (828) 3497 3286 m_b8s001i28
Crub_svsplocu 414135 GTGGTCCCTA-AGAGGGATAAAAATTCCTTCCAAAATGCAGACGTAAATT 414183
i i -i vv ii v- i v i vvi v v
C Gypsy-129_DR- 3497 GTAGCCCCTATGGACTGGCAAAAAG-CTTGCCAGAATCGGGAGGAAAATT 3449
Crub_svsplocu 414184 GCACTCCCCTATCAGAGATGATGCATTGGGGTGCCCCGTGCAATCTGTAA 414233
viv i vi v ii iv viiv iviv v v v v
C Gypsy-129_DR- 3448 GAGGTCCTCGGTCTGAGACAATGTCTTGGGGAATGCCAAAGACTCGGAAC 3399
Crub_svsplocu 414234 ATGTGCTGGATGAAAAGTTTTGCTAAGGCCTTTGCAGTGGGAATCTTTTG 414283
i v vv iv i iv ivvv i v v- v
C Gypsy-129_DR- 3398 ACGTGATTTATGGTAAGCTCGGCTGTCTCTTTGGCAGTGGGAAG-TTTGG 3350
Crub_svsplocu 414284 GCAAGGGA-TAAA--GTGCACCTGTTTGGAAAATAGGTCCGTGACTGTCC 414330
- i -- v -- v iii i ii v
C Gypsy-129_DR- 3349 GCAAGGGAATGAATCGTGCAGCT--TTGGAAAATCGGTCCACAATTACCA 3302
Crub_svsplocu 414331 AGATAACAGTATTCCC 414346
i iii
C Gypsy-129_DR- 3301 AAATAGTGGTATTCCC 3286
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.68
Transitions / transversions = 1.00 (35/35)
Gap_init rate = 0.03 (7 / 211), avg. gap size = 1.14 (8 / 7)
+ 911 34.1 3.3 4.0 Crub_svsplocus 414853 416232 (233768) C Gypsy72-I_DR LTR/Gypsy (1504) 2741 1529 239
ANNOTATION EVIDENCE:
654 34.58 3.33 4.86 Crub_svsplocus 414853 416083 233917 C Gypsy69-I_DR LTR/Gypsy 1529 2741 1504
654 34.58 3.33 4.86 Crub_svsplocus 414853 416083 (233917) C Gypsy69-I_DR#LTR/Gypsy (1504) 2741 1529 m_b8s001i29
Crub_svsplocu 414853 TGCGAGATAGAGCATCTGCCAGGAAGTTCTTTCTCCCTGGTAAATGTTTG 414902
v i vvivi v? v vvi ivv
C Gypsy69-I_DR# 2741 TGCGAGAGAGGGCATCTGCCTTACGGTTCTTGNTGCCTGGGCGATAGGTG 2692
Crub_svsplocu 414903 AGTTTAAA-CTGGAACTGGTGAA-AATGCTGAGACCAGCGGGCTTGTTTG 414950
v v -i i ? v - i--i ? i i i
C Gypsy69-I_DR# 2691 ACTGTAAAATTGAANCGGGTGAAGAATA--AAGACCANCGAGCCTGTCTG 2644
Crub_svsplocu 414951 GGATTGAGTTTCCTGG-ACGTTTTCAGGGCTTCTAAATTTTTGTGATCGG 414999
i v ivi v - - v vivvi ? ii i v
C Gypsy69-I_DR# 2643 GGGTTTAGTCGTCGGGCAC-TTTTGATATACTCNAGGTTTTTGTGGTCTG 2595
Crub_svsplocu 415000 TCCACACCTGGAAGGG---GATTTTGTTGCCTTCCAGGAACTGTCGCCAC 415046
vvvv i ? --- iv-- i - i ? vv v ? i
C Gypsy69-I_DR# 2594 TGATAATCTGGAANGGATGGACG--GCT-CCCTCNAGCCAGTGNCGCCAT 2548
Crub_svsplocu 415047 GTGAGTAATGCCCAACGTATCCCAT---AAGC--CTCCTTCTCCCATACG 415091
vivvvi i ---- iv i - --- i--i v iv vi
C Gypsy69-I_DR# 2547 TCTTCCAGTGCC----GCCTTC-ATNGAAAGTAGTTCCTTGTTACCCACG 2503
Crub_svsplocu 415092 GGCCAGCGCTGTTCTGTTTCCGTGAGTTTCTTGGATGTATATGCACAGGG 415141
vvvi iviiv v i v v vivi viv ? v ?
C Gypsy69-I_DR# 2502 TCATAGTTTCTTTCAGCTGCCGTCAGTTTGCGAGAAAAANAAGCACANGG 2453
Crub_svsplocu 415142 TTGCAAT---ACTGCATCATTATTTTCTTGTAATAGCACAGCCCCCACTG 415188
v v i ---v vi i iii v?iv i i ? v v -
C Gypsy69-I_DR# 2452 GTGGAGTTTACCTGGGTTACCGTGNCGTTGTGACAGNACTGCCCCAA-TG 2404
Crub_svsplocu 415189 CCACA-TCACTTGCATCTGCCTGTATTATGAAGGGCTTGTCCATATCTGG 415237
i - ?vv? ii i v? iv i ivvv ?ivi v
C Gypsy69-I_DR# 2403 CCATAGTCNGANGCATCCACTTCNACAACGAAGGGTAGCTCNGGGTCGGG 2354
Crub_svsplocu 415238 GTGCCTTAGTACTGGTTCGGCAGAAAAAAGTCTCTTTAGTCTCTCAAACG 415287
ii i v iv v ? ii vi ivvvv v i
C Gypsy69-I_DR# 2353 GTGTTTCAGAATGGGTGCNGTGGTGAAGCTGGTCTTAAGTTTCTCAAACG 2304
Crub_svsplocu 415288 ------CTGCTTGGCACTCCATTGTCCATGTTAG--TGGCTGGCTAGGTT 415329
------ ---- vv -- iv i -- i?? ------
C Gypsy69-I_DR# 2303 ATTTGACTGCTT----CTGGATT--CCACTTCAGCTTANNTGG------T 2266
Crub_svsplocu 415330 TTACTGAGGATGCTCCCTTCATTTTCAGTAAGTTAGTGAGGGGCAAGTC- 415378
----------- ? v--- i --- --i i -
C Gypsy69-I_DR# 2265 TTAC-----------CCTTNAG---CAGTGAG---GTGAGGGG--GGCCG 2235
Crub_svsplocu 415379 TATCTGGGCAAATGAGGG----GATGAATTGGCGGTAAAAGTTTGCAAAG 415424
? vi i --- vi v----? ii i v i v
C Gypsy69-I_DR# 2234 NAATTAGGC---TGTAGTTTCTNATGAACCGGCGATAAAAGTTGGCGAAC 2188
Crub_svsplocu 415425 CCCAGGAAACTTTGTAGTTGCTTTCTTGTGC-GGGGTGGCGCCCAATCTA 415473
i i v v ivi vi- v iv -- ? i
C Gypsy69-I_DR# 2187 CCTAGAAATCTTTGTAGTTCCTTCACTGTTTTGGGGAGAGGCC--ANCCA 2140
Crub_svsplocu 415474 AT-ACTGCTTTGACCTTCTCTGGGTCCATTTCAATGCCCTG-TGGG-GAT 415520
i - i vi vv?vvv v iv v - v-
C Gypsy69-I_DR# 2139 GTGACTGCCTGAACCTTGGNGTCGTCCATTTCCACTCCGTGATGGCTGAT 2090
Crub_svsplocu 415521 A-TGCGATAGCCTAGTTAGTCTATCCTTTCCTGGTGGAATTCGCATTTTG 415569
- --- v i vv vvvvi i vvv vv i i iv
C Gypsy69-I_DR# 2089 AATG---TATCCCAGGAACGAGGTCTTGGACACGTGGAATTCACACTTCT 2043
Crub_svsplocu 415570 AGAGTTTGGCATATAGGTGAGCGGCTCGCAGCTTCTTTAAAACCGCTCTG 415619
vvi i i v v ivivv i i i?iviv i v ii
C Gypsy69-I_DR# 2042 CCGGCTTGGCGTAGAGTTGGTTTTCTTGTAANCGTGTCAAAACAGTCCTG 1993
Crub_svsplocu 415620 ACAAGTTTGACGTGTTCTTCTTTTCTTTCAGTAAAGATAAGAATGTCGTC 415669
ivvi i v vvvi vvvi v v v i i
C Gypsy69-I_DR# 1992 ACGTCCTTGATGTGTTGTTCTAGGTTGGGGGAATAGATCAGGATGTCATC 1943
Crub_svsplocu 415670 CAAGTAAACAAGGACCCCCTTAAACAGGTGCTCCCTTAGAACGTCATTGA 415719
? vi ii i v v vi ivv vviv i v i iv ?
C Gypsy69-I_DR# 1942 NATATAGGCGATGACACATTTGTTCAGCAAATCTCTGAAAATTTCATTNA 1893
Crub_svsplocu 415720 TTAATTGCATAAAGACTGCAGGGCCCCCTTGTAATCCAAATGGCAAGACT 415769
v vi vvi ? v ?vvvii?vv? i? v v vi ?
C Gypsy69-I_DR# 1892 TGAATGACTGGAAGACNGCTGGNGAGTTNGCNAGNCCATAGGGCATAACN 1843
Crub_svsplocu 415770 TTGAATTGATAGCACCCCATGG-GG-CAGTTAAATGCAGTCTTCCATTCG 415817
vv v v ii v i - - --i i i i i
C Gypsy69-I_DR# 1842 AGGTATTCATAGTGCCCCCTAGTGGTCAG--GAACGCGGTTTTCCACTCG 1795
Crub_svsplocu 415818 TCCCCTTCCTTAATTCTCACGCGATAGTAAGCTTCCCTTAGGTCTAGTTT 415867
i i ivi ? vv i?v i vi viii v v
C Gypsy69-I_DR# 1794 TCTCCCTCCCGGATNCGAATNAGGTTATAAGCACTTCTGAGGTCAAGTTT 1745
Crub_svsplocu 415868 AGAAAAAATTTTCCCTTTCAATAGGTGT--GACAGCATGTCTTTCATGAG 415915
i viv i vivvv ivvi v --? vi v --?vvv iv i
C Gypsy69-I_DR# 1744 GGTGTAGATACGGGCTTCACGTAGTTGTTCNAGGGCAGG--NGGGACCAA 1697
Crub_svsplocu 415916 GGGCAGCGGGTATAGGTTGCTTT-CACTGATTGTATTCAGGGCCCTATAA 415964
v v - v v i v- v ivv i?v i vi i
C Gypsy69-I_DR# 1696 GGGAAGAGGGTA-ACGATACTTGACAGTGACGTTATTCAANCCTCGGTAG 1648
Crub_svsplocu 415965 TCCACGCATAAACGTAAAGAGCCATCCTTCTTCTCT-CTAAAAAGGA--C 416011
v i ?ii v i vvv i- v i i --
C Gypsy69-I_DR# 1647 TCGATGCANGGACGGAGACCTCCATCCTTCTTCTCCACGAAGAAGAATCC 1598
Crub_svsplocu 416012 TGGGGCAGCCACTTTAGGCTTGGCTGGCTCAATGAAACCTCTCTCTAGGT 416061
vv ? ?iv --- i?v i v? iiv v vvv?v v
C Gypsy69-I_DR# 1597 TGCTGCNGCNGGT---GANGTAGANGGTCGAATGTAACCAGANGCTAGGG 1551
Crub_svsplocu 416062 TTTTTTTAATAAATCTTTCCAT 416083
ii ii ii iv v
C Gypsy69-I_DR# 1550 CCTCCTCGATGTATGTTTCCAT 1529
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 45.61
Transitions / transversions = 0.86 (187/218)
Gap_init rate = 0.07 (82 / 1230), avg. gap size = 1.22 (100 / 82)
911 33.50 3.26 3.26 Crub_svsplocus 415397 416010 233990 C Gypsy72-I_DR LTR/Gypsy 1681 2294 2003
911 33.50 3.26 3.26 Crub_svsplocus 415397 416010 (233990) C Gypsy72-I_DR#LTR/Gypsy (2003) 2294 1681 m_b8s001i30
Crub_svsplocu 415397 GATGAATTGGCGGTAAAAGTTTGCAAAGCCCAGGAAACTTTGTAGTTGCT 415446
i v i v i v vi iivv
C Gypsy72-I_DR# 2294 GATGAATCGCCGGTAAAAATTGGCGAAGCCCAGGAACCGCTGTAACGCCT 2245
Crub_svsplocu 415447 TTCTTGTGCGGGGTGGCGCCCAATCTAATACTGCTTTGACCTTCTCTGGG 415496
vv v iv v i vi v v ii i v v
C Gypsy72-I_DR# 2244 TTCGGGAGTCGGGTGGCGGCCAGTCGGAGACAGCCCTAACCTTCGCAGGG 2195
Crub_svsplocu 415497 TCCATTTCAATGCCCTG---TGGGGATATGCGATAGCCTAGTTAGTCTAT 415543
viv vv v--- iiiv --- iv i ivv vvv i
C Gypsy72-I_DR# 2194 TCCATGCGAAGTCCCTCAACTGAAATTATG---TGTCCCAAGAAGGAAAC 2148
Crub_svsplocu 415544 CCTTTCCTGG---TGGAATTCGCATTTTGAGAGTTTGGCATATAGGTGAG 415590
--- vv --- i ivvvivi vi i v v
C Gypsy72-I_DR# 2147 ---TGACTGGACATGGAATTCGCACTTCTCCGCCTTTACATACAGCTGAT 2101
Crub_svsplocu 415591 CGGCTCGCAGCTTCTTTAAAAC-CGCTCTGACAAGTTTGACGTGTTCTTC 415639
ivv iv ivi v iv - - vi iv v i i v
C Gypsy72-I_DR# 2100 TCTCCAGCAGCCGTTGTAGCACTCGC-CGAACGTGTTGGACATGTTCCTG 2052
Crub_svsplocu 415640 TTTTCTTTCAGTAAAGATAAGAATGTCGTCCAAGTAAACAAGGAC---CC 415686
iv vvivvv v i i i ii ---ii
C Gypsy72-I_DR# 2051 CATGGCGGAAGAAAAAATAAGAATGTCATCCAAATAAACAAAAACAAATT 2002
Crub_svsplocu 415687 CCTTAAACAGGTGCTCCCTTAGAACGTCATTGATTAATTGCAT-AAAGAC 415735
vv v v --- i vv v i i iv i - v -
C Gypsy72-I_DR# 2001 GATTAATCATGT---CTCGGAGTACATCGTTGACGAGT-GCCTGAAAGAC 1956
Crub_svsplocu 415736 TGCAGG-GCCCCCTTGTAATCCAAATGGCAAGACTTTGAATTGATAGCAC 415784
v - viivv - ii i vvviv v v iii
C Gypsy72-I_DR# 1955 TGCTGGAGCATTGGTG-AGCCCAAATGGCAGGACAAGATATTCAAAATGC 1907
Crub_svsplocu 415785 CCCATGGGGCAGTTAAATGCAGTCTTCCATTCGTCCCCTTCCTTAATTCT 415834
vi vvv i i v i i v v v
C Gypsy72-I_DR# 1906 CCAGTGGGCGTGTTGAATGCGGTCTTCCATTCGTCACCCTCCCTCATACG 1857
Crub_svsplocu 415835 CACGCGATAGTAAGCTTCCCTTAGGTCTAG-TTTAGAAAAAATTTT--CC 415881
v v i v iv v i i- ivi i --
C Gypsy72-I_DR# 1856 GACGAGATGGTAAGCATTGCGTAGGTCCAACTTTGTGAAAAATCTTGCCC 1807
Crub_svsplocu 415882 CTTTCAATAGGTGTGACAGC--ATGTCTTTCATGAGGGGCAGCGGGTATA 415929
i v v i -i vi -- v ----v i v i v iv
C Gypsy72-I_DR# 1806 CCTGCAAGAGAT-CGAAGGCCGAAG----ACATAAGCGGTAGGGGGTACC 1762
Crub_svsplocu 415930 GGTTGCTTTCACTGATTGT---ATTCAGGGCCCTATAATCCACGCATAAA 415976
i --- i v i i --- iiv i v i i i viii
C Gypsy72-I_DR# 1761 GAT---TTTTAATGGTTATGTCATTCAAACCTCGATAGTCTATGCAGGGG 1715
Crub_svsplocu 415977 CGTAAAGAGCCATCCTTCTTCTCTCTAAAAAGGA 416010
i i i i iivi i i
C Gypsy72-I_DR# 1714 CGCAGAGAACCATCCTTTTTCTTCACAAAGAAGA 1681
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.57
Transitions / transversions = 0.99 (99/100)
Gap_init rate = 0.05 (30 / 613), avg. gap size = 1.33 (40 / 30)
819 34.20 3.35 3.35 Crub_svsplocus 415398 416232 233768 C Gypsy138-I_DR LTR/Gypsy 3566 4400 7010
819 34.20 3.35 3.35 Crub_svsplocus 415398 416232 (233768) C Gypsy138-I_DR#LTR/Gypsy (7010) 4400 3566 m_b8s001i31
Crub_svsplocu 415398 ATGAATTGGCGGTAAAAGTTTGCAAAGCCCAGGAAACTTTGTAGTTGCTT 415447
i ivv i i v v ii v v vi vi
C Gypsy138-I_DR 4400 ATAAATCTCCGATAAAAATTGGCAAACCCCAAAAATCGTTGTACCTCTTT 4351
Crub_svsplocu 415448 TCTTGTGCGGGGTGGCGCCCAATCTAATACTGCTTTGACCTTCTCTGGGT 415497
vvi vi iv v i v i i i i i vi v i
C Gypsy138-I_DR 4350 AACTGAACATGGTTGTGGCCAATCCAGTACTGCCTTAATCTTGCCAGGAT 4301
Crub_svsplocu 415498 CCATTTCAATGCCCTGTGGGGATA-TGCGATAGCCTAGTTAGTCTATCCT 415546
i v v ivii vv - ii - v v -- iv v iv
C Gypsy138-I_DR 4300 CCATCTGAAGGCTACATTTGGATACTATGA-ACCCAAG--AAACGACACT 4254
Crub_svsplocu 415547 TTCCTGG-----TGGAATTCGCATTTTGAGAGTTTGGCATATAGGTGAGC 415591
--- ----- vi ivvv i ii iv i - vv i
C Gypsy138-I_DR 4253 TT---GGAGACATGGAATTCGCTCTTCTCCAGCTTAACGAACAG-TCTGT 4208
Crub_svsplocu 415592 GGCTCG-CAGCTTCTTTAAAACCGCTCTGACAAGTTTGACGTGTTCTTCT 415640
v i- i vvvvv i vvi v v vv i i v
C Gypsy138-I_DR 4207 GTCTCAACAACTGGGAGAGAACCTGCCGGACATGTTGTACATGCTCTTCA 4158
Crub_svsplocu 415641 TTTCTTTCAGTAAAGATAAGAATGTCGTCCAAGTAAACAAGGAC---CCC 415687
vv viiv v i v i i ii ---i i
C Gypsy138-I_DR 4157 TAGCTACTTGAAAAAATAAGTATGTCATCCAAGTAAACGAAAACAAATCT 4108
Crub_svsplocu 415688 CTTAAACAGGTGCTCCCTTAGAACGTCATTGATTAATTGCAT-AAAGACT 415736
v v ---v v i i i v - v -i v
C Gypsy138-I_DR 4107 GTTCAACA---TCTCCCTGAGGACATCATTAATGAA-TGCCTGGAAGACG 4062
Crub_svsplocu 415737 GCAGGGCCCCCTTGTAA-TCCAAATGGCAAGACTTTGAATTGATAGCACC 415785
v -v vi ii -v v vv i viv v iiv
C Gypsy138-I_DR 4061 GCTGGG-GCATTTACAAGGCCAAAGGGCATTACCTGATATTCATAGTGGC 4013
Crub_svsplocu 415786 CCATGGGGCAGTTAAATGCAGTCTTCCATTCGTCCCCTTCCTTAATTCTC 415835
ii ? vv v i i i i i i v
C Gypsy138-I_DR 4012 CTGTNGGGGTGTTAAAAGCGGTCTTCCACTCATCTCCTTCCTTGATCCTG 3963
Crub_svsplocu 415836 ACGCGATAGTAAGCTTCCCTTAGGTCTAGTTTAGAAAAAAT--TTTC-CC 415882
vv i v ii v i ii v v i -- vv -
C Gypsy138-I_DR 3962 ACCAGATGGTAAGCATTTCTGAGGTCCAACTTCGTAAAGATAGTGGCGCC 3913
Crub_svsplocu 415883 TTTCAATAGGTGTGACAGCA-TGTCTTTCATGAGGGGCAGCGGGTATAGG 415931
i v i vv -ii v - --- v i ii vv i
C Gypsy138-I_DR 3912 CTGCAGTATCT-CAAAAGCAGTG---TTCATTAGGGGTAATGGGTAACGA 3867
Crub_svsplocu 415932 TTGCTTTCACTGAT--TGT-ATTCAGGGCCCTATAATCCACGCATAAACG 415978
- -- v i -- - iiv i v ii viiv
C Gypsy138-I_DR 3866 TT-CTT--AATGGTGATGTGATTCAAACCTCTATAATCAATACAGGGTCG 3820
Crub_svsplocu 415979 TAAAGAGCCATCCTTCTTCTCTCTAAAAAGGACTGGGGCAGCCACTTTAG 416028
v i vvv vvvvvi i ---i v v iv vi
C Gypsy138-I_DR 3819 AAGACTCCCATCCTTCTTGGAAACAAAAAAGA---AGCCTGCTCCTGCAG 3773
Crub_svsplocu 416029 GCTTGGCT---GGCTCAATGAAACCTCTCTCTAG-GTTTTTTTTAATAAA 416074
ivv i --- viv v v v - ii iv i -iv
C Gypsy138-I_DR 3772 GTGAGGTTGAAGGGCGAATGAATCCACTGTCTAGAGCCTCGTTCAA-GTA 3724
Crub_svsplocu 416075 TCTTTCCATTTC--CTCCTTCTCCTTTGGGCTCATGGAGTATAATCTGGG 416122
i i vv --i i vvvvv i--v v i --i
C Gypsy138-I_DR 3723 TTTCTCCATGGCAGTTCTTTCAGGAATGGA--GAGGGAGTACAATCT--A 3678
Crub_svsplocu 416123 CTTTGGG--AGTTTTGCCCCAGGTTTGAATTCAATGGTACAGTC-TGTGG 416169
i i i --i vi i vii i i v i - i
C Gypsy138-I_DR 3677 CCTCGAGGTGGGCTTGCTCCAGGTACAAGTTCAATAGAACAATCATATGG 3628
Crub_svsplocu 416170 GTCGGTGGGGGGGAAGCTCATTCGCCCTCTCCTCACTGAAGACTTCAGCA 416219
i- i v v iivv v v ivvvv i i vii
C Gypsy138-I_DR 3627 A-CGATGCGGGGGTAATGAAGTAGCCTGAGACTTACTAAAGACTTCACTG 3579
Crub_svsplocu 416220 AGGTCCTTATATT 416232
i v i
C Gypsy138-I_DR 3578 AGATCCATGTATT 3566
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 45.10
Transitions / transversions = 0.97 (136/140)
Gap_init rate = 0.05 (44 / 834), avg. gap size = 1.27 (56 / 44)
+ 603 4.3 0.0 0.0 Crub_svsplocus 418815 418884 (231116) + URR1B DNA/hAT-Charlie 156 225 (0) 240
ANNOTATION EVIDENCE:
603 4.29 0.00 0.00 Crub_svsplocus 418815 418884 231116 + URR1B DNA/hAT-Charlie 156 225 0
603 4.29 0.00 0.00 Crub_svsplocus 418815 418884 (231116) URR1B#DNA/hAT-Charlie 156 225 (0) m_b8s001i32
Crub_svsplocu 418815 GGTTAGGGGTCACCACAACATGAGAAACTGTATTAAAGGGTTGCAGCATT 418864
i i i
URR1B#DNA/hAT 156 GGTTGGGGGTCACCACAACATGAGGAACTGTATTAAAGGGTCGCAGCATT 205
Crub_svsplocu 418865 AGGAAGGTTGAGAACCACTG 418884
URR1B#DNA/hAT 206 AGGAAGGTTGAGAACCACTG 225
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 3.09
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 69), avg. gap size = 0.0 (0 / 0)
+ 32 0.0 0.0 0.0 Crub_svsplocus 421355 421384 (228616) + (CCCT)n Simple_repeat 1 30 (0) 241
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 Crub_svsplocus 421355 421384 228616 + (CCCT)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 Crub_svsplocus 421355 421384 (228616) (CCCT)n#Simple_repeat 1 30 (0) c_b8s251i2
Crub_svsplocu 421355 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 421384
(CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 30
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 256 9.1 0.0 0.0 Crub_svsplocus 422381 422413 (227587) C URR1B DNA/hAT-Charlie (0) 225 193 242
ANNOTATION EVIDENCE:
256 9.09 0.00 0.00 Crub_svsplocus 422381 422413 227587 C URR1B DNA/hAT-Charlie 193 225 0
256 9.09 0.00 0.00 Crub_svsplocus 422381 422413 (227587) C URR1B#DNA/hAT-Charlie (0) 225 193 m_b8s001i33
Crub_svsplocu 422381 CAGTGGTTCTCAACCTTTTTAATGCCGCGACCC 422413
ii i
C URR1B#DNA/hAT 225 CAGTGGTTCTCAACCTTCCTAATGCTGCGACCC 193
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.03
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 440 11.8 1.3 2.7 Crub_svsplocus 422672 422746 (227254) C URR1B DNA/hAT-Charlie (91) 128 1 242
ANNOTATION EVIDENCE:
440 13.04 0.00 0.00 Crub_svsplocus 422672 422740 227260 C URR1B DNA/hAT-Charlie 1 69 156
440 13.04 0.00 0.00 Crub_svsplocus 422672 422740 (227260) C URR1B#DNA/hAT-Charlie (156) 69 1 m_b8s001i34
Crub_svsplocu 422672 TTTGGCGACCCCCATGAAATGGTCGTTCGACCCCAAATGGGGTCCCGAGC 422721
v ii v v v v v
C URR1B#DNA/hAT 69 TTAGGCGACCCCTGTGAAAGGGTCGTTCGACCCCCAAAGGGGTCGCGACC 20
Crub_svsplocu 422722 CACAGGTTGAGAACCACTG 422740
i
C URR1B#DNA/hAT 19 CACAGGTTGAGAACCGCTG 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 12.77
Transitions / transversions = 0.50 (3/6)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
243 11.12 2.13 4.35 Crub_svsplocus 422700 422746 227254 C Charlie-N1b_Cpb DNA/hAT-Charlie 83 128 91
243 11.12 2.13 4.35 Crub_svsplocus 422700 422746 (227254) C Charlie-N1b_Cpb#DNA/hAT-Charlie (91) 128 83 m_b8s001i35
Crub_svsplocu 422700 GACCCCAAATGGGGTCC-CGAGCCACAGGTTGAGAACCACTGGTCTAT 422746
v -- - ii i v
C Charlie-N1b_C 128 GACCCCCA--GGGGTCCGCGGACCACAGGTTGAAAACCACTGTTCTAT 83
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 12.11
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3)
+ 17 13.1 0.0 0.0 Crub_svsplocus 426564 426589 (223411) + (AT)n Simple_repeat 1 26 (0) 243
ANNOTATION EVIDENCE:
17 13.12 0.00 0.00 Crub_svsplocus 426564 426589 223411 + (AT)n Simple_repeat 1 26 0
17 13.12 0.00 0.00 Crub_svsplocus 426564 426589 (223411) (AT)n#Simple_repeat 1 26 (0) m_b8s252i6
Crub_svsplocu 426564 ATATATATATACACACATATATATAT 426589
i i i
(AT)n#Simple_ 1 ATATATATATATATATATATATATAT 26
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
+ 38 2.8 0.0 0.0 Crub_svsplocus 426718 426754 (223246) + (AC)n Simple_repeat 1 37 (0) 244
ANNOTATION EVIDENCE:
38 2.78 0.00 0.00 Crub_svsplocus 426718 426754 223246 + (AC)n Simple_repeat 1 37 0
38 2.78 0.00 0.00 Crub_svsplocus 426718 426754 (223246) (AC)n#Simple_repeat 1 37 (0) c_b8s251i3
Crub_svsplocu 426718 ACACACACACACACACACACATACACACACACACACA 426754
i
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACA 37
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 14 17.0 3.0 0.0 Crub_svsplocus 427598 427630 (222370) + (TTG)n Simple_repeat 1 34 (0) 245
ANNOTATION EVIDENCE:
14 16.97 3.03 0.00 Crub_svsplocus 427598 427630 222370 + (TTG)n Simple_repeat 1 34 0
14 16.97 3.03 0.00 Crub_svsplocus 427598 427630 (222370) (TTG)n#Simple_repeat 1 34 (0) m_b8s252i7
Crub_svsplocu 427598 TTGTTGTTGTTAAT-TTCTTGTTGTTTTTCTTGT 427630
iv - v v v
(TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGT 34
Matrix = Unknown
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1)
+ 267 17.5 0.0 0.0 Crub_svsplocus 428454 428493 (221507) + AmnSINE2 SINE/tRNA-Deu 80 119 (239) 246
ANNOTATION EVIDENCE:
267 17.50 0.00 0.00 Crub_svsplocus 428454 428493 221507 + AmnSINE2 SINE/tRNA-Deu 80 119 239
267 17.50 0.00 0.00 Crub_svsplocus 428454 428493 (221507) AmnSINE2#SINE/tRNA-Deu 80 119 (239) m_b8s001i36
Crub_svsplocu 428454 CAAGGTTGACTCAGCCTTCCATCCTTTTGAGGTTGATAAA 428493
i i i i ii v
AmnSINE2#SINE 80 CAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAGATAAA 119
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.68
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 58 0.0 0.0 0.0 Crub_svsplocus 429473 429524 (220476) + (TTTAT)n Simple_repeat 1 52 (0) 247
ANNOTATION EVIDENCE:
58 0.00 0.00 0.00 Crub_svsplocus 429473 429524 220476 + (TTTAT)n Simple_repeat 1 52 0
58 0.00 0.00 0.00 Crub_svsplocus 429473 429524 (220476) (TTTAT)n#Simple_repeat 1 52 (0) c_b8s251i4
Crub_svsplocu 429473 TTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTAT 429522
(TTTAT)n#Simp 1 TTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTAT 50
Crub_svsplocu 429523 TT 429524
(TTTAT)n#Simp 51 TT 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 339 14.6 0.0 8.1 Crub_svsplocus 429621 429687 (220313) C AmnSINE2 SINE/tRNA-Deu (230) 128 67 248
ANNOTATION EVIDENCE:
339 14.61 0.00 8.06 Crub_svsplocus 429621 429687 220313 C AmnSINE2 SINE/tRNA-Deu 67 128 230
339 14.61 0.00 8.06 Crub_svsplocus 429621 429687 (220313) C AmnSINE2#SINE/tRNA-Deu (230) 128 67 m_b8s001i37
Crub_svsplocu 429621 GGTCCTCATTTTACCTACCCCGGAAGGATGGAAGGCTGAGTCAACCTTGA 429670
?v v i i i i i i --
C AmnSINE2#SINE 128 GGNACTCAATTTATCTACCTCGGAAGGATGAAGGGCTGAGTCGACCCT-- 81
Crub_svsplocu 429671 GCCGGTGAGATTTGAAC 429687
--- i
C AmnSINE2#SINE 80 GC---TGGGATTTGAAC 67
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.95
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5)
+ 14 20.0 0.0 6.8 Crub_svsplocus 430972 431018 (218982) + A-rich Low_complexity 1 44 (0) 249
ANNOTATION EVIDENCE:
14 20.04 0.00 6.82 Crub_svsplocus 430972 431018 218982 + (GAAAAA)n Simple_repeat 1 44 0
14 20.04 0.00 6.82 Crub_svsplocus 430972 431018 (218982) (GAAAAA)n#Simple_repeat 1 44 (0) m_b8s252i8
Crub_svsplocu 430972 GAGAAAGGAAATGAAAAGAGAAGTGGAGAGAAAGGAAAAGAAAAAGA 431018
i i v - --ii i i
(GAAAAA)n#Sim 1 GAAAAAGAAAAAGAAAA-AGAA--AAAGAAAAAGAAAAAGAAAAAGA 44
Matrix = Unknown
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3)
16 17.40 0.00 4.88 Crub_svsplocus 430973 431015 218985 + (AGAAA)n Simple_repeat 1 41 0
16 17.40 0.00 4.88 Crub_svsplocus 430973 431015 (218985) (AGAAA)n#Simple_repeat 1 41 (0) m_b8s252i9
Crub_svsplocu 430973 AGAAAGGAAATGAAAAGAGAAGTGGAGAGAAAGGAAAAGAAAA 431015
i v - -v i i i
(AGAAA)n#Simp 1 AGAAAAGAAAAGAAAAGA-AA-AGAAAAGAAAAGAAAAGAAAA 41
Matrix = Unknown
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2)
+ 467 14.4 0.2 0.0 Crub_svsplocus 431371 431454 (218546) + URR1B DNA/hAT-Charlie 1 157 (153) 250
ANNOTATION EVIDENCE:
281 27.38 1.19 0.00 Crub_svsplocus 431371 431454 218546 + hAT-N8b_Testu DNA/hAT-Charlie 73 157 153
281 27.38 1.19 0.00 Crub_svsplocus 431371 431454 (218546) hAT-N8b_Testu#DNA/hAT-Charlie 73 157 (153) m_b8s001i38
Crub_svsplocu 431371 TTTAGAGCAGTGGTTCTCAACCTGTGGGTCGGGACCCCATTTGGGGTCGA 431420
i v v v v vvvv v
hAT-N8b_Testu 73 TCTAGATCAGTGTTTCTCAACCTGGGGGTCGCGACCCCCAGGGGGGTCGC 122
Crub_svsplocu 431421 ACGACCATTTCACGGGGGTCACCAA-ACAAGGCTG 431454
iv viv i v i v i-i i i
hAT-N8b_Testu 123 GGGACGGGTTTAGGGGGGTCGCAAGTGCAGGGCCG 157
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.18
Transitions / transversions = 0.64 (9/14)
Gap_init rate = 0.01 (1 / 83), avg. gap size = 1.00 (1 / 1)
467 11.59 0.00 0.00 Crub_svsplocus 431378 431446 218554 + URR1B DNA/hAT-Charlie 1 69 156
467 11.59 0.00 0.00 Crub_svsplocus 431378 431446 (218554) URR1B#DNA/hAT-Charlie 1 69 (156) m_b8s001i39
Crub_svsplocu 431378 CAGTGGTTCTCAACCTGTGGGTCGGGACCCCATTTGGGGTCGAACGACCA 431427
i v v v v
URR1B#DNA/hAT 1 CAGCGGTTCTCAACCTGTGGGTCGCGACCCCTTTGGGGGTCGAACGACCC 50
Crub_svsplocu 431428 TTTCACGGGGGTCACCAAA 431446
i i v
URR1B#DNA/hAT 51 TTTCACAGGGGTCGCCTAA 69
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.59
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
+ 442 11.8 4.4 0.0 Crub_svsplocus 431512 431579 (218421) + URR1B DNA/hAT-Charlie 155 225 (0) 251
ANNOTATION EVIDENCE:
442 11.76 4.41 0.00 Crub_svsplocus 431512 431579 218421 + URR1B DNA/hAT-Charlie 155 225 0
442 11.76 4.41 0.00 Crub_svsplocus 431512 431579 (218421) URR1B#DNA/hAT-Charlie 155 225 (0) m_b8s001i40
Crub_svsplocu 431512 TAGTTGGGGGTCACCACA---TGGGAAACTGTATTATGGGGTCGCGGCAT 431558
i --- i i vi i
URR1B#DNA/hAT 155 TGGTTGGGGGTCACCACAACATGAGGAACTGTATTAAAGGGTCGCAGCAT 204
Crub_svsplocu 431559 TAGAAAGGTTTAGAACCACTG 431579
i v
URR1B#DNA/hAT 205 TAGGAAGGTTGAGAACCACTG 225
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.04
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.01 (1 / 67), avg. gap size = 3.00 (3 / 1)
+ 17 25.3 2.9 2.9 Crub_svsplocus 431800 431868 (218132) + (TTCT)n Simple_repeat 1 69 (0) 252
ANNOTATION EVIDENCE:
17 25.28 2.90 2.90 Crub_svsplocus 431800 431868 218132 + (TTCT)n Simple_repeat 1 69 0
17 25.28 2.90 2.90 Crub_svsplocus 431800 431868 (218132) (TTCT)n#Simple_repeat 1 69 (0) m_b8s252i10
Crub_svsplocu 431800 TTATTTTTTATGTTTCTTT-ACTCTTGCTCTCCTTTCTTTCTTTTTTTCT 431848
v i - v -vi v - i i
(TTCT)n#Simpl 1 TTCTTTCTT-TCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCT 48
Crub_svsplocu 431849 CACTGT-TTTATCTATTTCTT 431868
iv v - v i v
(TTCT)n#Simpl 49 TTCTTTCTTTCTTTCTTTCTT 69
Matrix = Unknown
Transitions / transversions = 0.75 (6/8)
Gap_init rate = 0.06 (4 / 68), avg. gap size = 1.00 (4 / 4)
+ 21 6.1 2.9 0.0 Crub_svsplocus 434365 434398 (215602) + (CCTC)n Simple_repeat 1 35 (0) 253
ANNOTATION EVIDENCE:
21 6.13 2.94 0.00 Crub_svsplocus 434365 434398 215602 + (CCTC)n Simple_repeat 1 35 0
21 6.13 2.94 0.00 Crub_svsplocus 434365 434398 (215602) (CCTC)n#Simple_repeat 1 35 (0) m_b9s252i0
Crub_svsplocu 434365 CCT-CCTCCACCCCTCCCTCCCTCCCTCCCTCCCT 434398
- vi
(CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 35
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1)
+ 16 14.8 2.5 2.5 Crub_svsplocus 440703 440742 (209258) + (CTTTTTT)n Simple_repeat 1 40 (0) 254
ANNOTATION EVIDENCE:
16 14.80 2.50 2.50 Crub_svsplocus 440703 440742 209258 + (CTTTTTT)n Simple_repeat 1 40 0
16 14.80 2.50 2.50 Crub_svsplocus 440703 440742 (209258) (CTTTTTT)n#Simple_repeat 1 40 (0) m_b9s252i1
Crub_svsplocu 440703 CTTTTATTCTTTCCTCTCTTTTCTTCTTTGTTTTTT-TTTT 440742
- ii i i v -
(CTTTTTT)n#Si 1 CTTTT-TTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTT 40
Matrix = Unknown
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2)
+ 15 8.8 0.0 0.0 Crub_svsplocus 440909 440932 (209068) + (CCT)n Simple_repeat 1 24 (0) 255
ANNOTATION EVIDENCE:
15 8.85 0.00 0.00 Crub_svsplocus 440909 440932 209068 + (CCT)n Simple_repeat 1 24 0
15 8.85 0.00 0.00 Crub_svsplocus 440909 440932 (209068) (CCT)n#Simple_repeat 1 24 (0) m_b9s252i3
Crub_svsplocu 440909 CCTCCACCTTCTCCTCCTCCTCCT 440932
v i
(CCT)n#Simple 1 CCTCCTCCTCCTCCTCCTCCTCCT 24
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 280 29.1 0.0 0.0 Crub_svsplocus 442472 442581 (207419) + L1-23_DR LINE/L1 2088 2197 (3382) 256
ANNOTATION EVIDENCE:
280 29.09 0.00 0.00 Crub_svsplocus 442472 442581 207419 + L1-23_DR LINE/L1 2088 2197 3382
280 29.09 0.00 0.00 Crub_svsplocus 442472 442581 (207419) L1-23_DR#LINE/L1 2088 2197 (3382) m_b9s001i0
Crub_svsplocu 442472 AAGAATTGGAGCTTATTGATATTTGGCGAGAAAGGAACACAAGTGATAGA 442521
v v iv v v v vvi v v v iv
L1-23_DR#LINE 2088 AAGAAATTGGCCTAATTGATAGTTGGAGAGAATTAAACCCTACTACTAGA 2137
Crub_svsplocu 442522 GATTTTACTTTTTATTCTGATAGACACCAGTCATTTTCAAGGATTGATTT 442571
i v v i ivv iiiv vi i v
L1-23_DR#LINE 2138 GACTATACATTTTATTCTAACCCACATTGTTCATACTCAAGAATTGATTA 2187
Crub_svsplocu 442572 TTTTTTGATT 442581
v v
L1-23_DR#LINE 2188 TATTTTTATT 2197
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 36.81
Transitions / transversions = 0.52 (11/21)
Gap_init rate = 0.00 (0 / 109), avg. gap size = 0.0 (0 / 0)
+ 530 28.4 6.8 7.5 Crub_svsplocus 443229 444112 (205888) + L1MD LINE/L1 3064 4276 (1870) 257
ANNOTATION EVIDENCE:
320 33.41 4.75 5.33 Crub_svsplocus 443229 443775 206225 + L1-1_Testu LINE/L1 3699 4242 2090
320 33.41 4.75 5.33 Crub_svsplocus 443229 443775 (206225) L1-1_Testu#LINE/L1 3699 4242 (2090) m_b9s001i1
Crub_svsplocu 443229 TATAGATAAATATTTACAACCAGTACATTTCCCTAGACTTTCAGAGGAAC 443278
i i ivi vvv iv vi v vii i --
L1-1_Testu#LI 3699 TATAAATAGATATTTGAGAAGTGTGAAACTACCTCAGCTCTCAGAGGA-- 3746
Crub_svsplocu 443279 AACAAAATGGGA----TGAATAGTTTAATTACTGTGGAGGAAATTG--GT 443322
--ii vi v ---- vi viv i ii i --
L1-1_Testu#LI 3747 --TGATGTGGCAGCTCTTGATAGGCAAATTGCTGCAGAGGAAGTTGAAGT 3794
Crub_svsplocu 443323 TTAGCTATTAAGCAGTTAAAGGTTGGAAAGTCTCCTGGAACAGATGGACT 443372
-- iv v v iviiiiv iv v vv v ii
L1-1_Testu#LI 3795 T--GTAATTAAGAATTTAAAATCCAATAAAGCTCCAGGTCCCGATGGGTT 3842
Crub_svsplocu 443373 GACTTCTAGG---TATTATAAGATCTTATCTGAAG-AAATGATAGAGCC- 443417
--- i --- - v --- i - i v i vv -
L1-1_Testu#LI 3843 ---TTCTGGGGAGTATTATA-GAGCT---CTAAAGCAAGTGTTGGTCCCT 3885
Crub_svsplocu 443418 ATT--AAAGAAACTCTTTAATAGTATTTTGTTGGGTATGCAAG-TTCCTC 443464
-- vvi i v i v iv v -i i - vv
L1-1_Testu#LI 3886 ATTTTAACTGAATTGTTTAATGGTATATTGCAGGGGA-ACGAGATTCCAG 3934
Crub_svsplocu 443465 CTTCTTGGAAAAGAGC-----TTTTATATCACTGATTATGAAGGAAGATC 443509
v v iii ----- v i-i i vv v v i --
L1-1_Testu#LI 3935 ATTCATGGAAAGAGGCAAAAATTGTG-GTCATTCCTAAAGAAGGAAAA-- 3981
Crub_svsplocu 443510 AGGATCTTACAGAGCCTAAGAATTATA--GGCCAATTTCATTATTGAATG 443557
-- vi --i iv v i -- i v v v v
L1-1_Testu#LI 3982 --GATCTTACCAA--TTGTGCATCATACAGACCTATTTCTTTAATTAATG 4027
Crub_svsplocu 443558 TTGATTATAAGATTTTTACAAAAAATTTGGCAAATAGACTAA-TG-CAGG 443605
v vv i v i v iivvi i i i i - - vv
L1-1_Testu#LI 4028 TGGATGCTAAAATTTATGCCAAGGTGCTAGCAAACAGATTGAGTGTCATC 4077
Crub_svsplocu 443606 TTATGAAAGACTTGATTCATAGTGATCAAGCAGGATTTATAACAGGGAGA 443655
iivv - iv - ivv i v v i ii vi v v i
L1-1_Testu#LI 4078 TTGCCCAA-ATATG-TTCACCCTGACCAATCTGGGTTCGTTGCTGGCAGG 4125
Crub_svsplocu 443656 TACATGAAAC--ATAATGTTAGACAAATTATTAATTTAATTGAGTACTTG 443703
-- vv v -- i i vi i v v i iv vv iv v
L1-1_Testu#LI 4126 --CATCTATCTGATAATATCAGAAGAACTCTGAATTTGATCTATAATGTT 4173
Crub_svsplocu 443704 GATAAGAATAATCAGATTCCTGTG-GCTTTTATCTTTTTGGATGCTGAAA 443752
i vvv ii iv-- - vi v -- i
L1-1_Testu#LI 4174 AATTCTAGCAATTC--TTCCTGTGCGCTGCTTTCTTT--GGATGCTGAGA 4219
Crub_svsplocu 443753 AAGCTTTTGATCAATTGGACTGG 443775
i i i iii v
L1-1_Testu#LI 4220 AAGCCTTCGACCGGCTGGAGTGG 4242
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 43.53
Transitions / transversions = 1.01 (87/86)
Gap_init rate = 0.08 (41 / 546), avg. gap size = 1.34 (55 / 41)
374 33.02 2.34 4.79 Crub_svsplocus 443464 443762 206238 + L1-102_DR LINE/L1 667 958 2044
374 33.02 2.34 4.79 Crub_svsplocus 443464 443762 (206238) L1-102_DR#LINE/L1 667 958 (2044) m_b9s001i2
Crub_svsplocu 443464 CCTTCTTGGAAAAGAGCTTTTATATCACTGATTATGAAGGAAGATCAGGA 443513
i v ---- v v v vviv ii iv i
L1-102_DR#LIN 667 CTTTCATGGAA----GCATTGATAACACTGATACCCAAAAAAGACAAAGA 712
Crub_svsplocu 443514 TCTTACAGAGCCTAAGAATTATAGGCCAATT-TCATTATTGAATGTTGAT 443562
iv v v v ivi i v-v v i- i
L1-102_DR#LIN 713 CGTAACTGATCCTGCAAACTATAGGCCAATAAGCCTTATC-AATGTTGAC 761
Crub_svsplocu 443563 TATAAGATTTTTACAAAAAATTTGGCAAATAGACTAATGCAGGTTATGAA 443612
i i v vi vvi vvv v i iiviv - v v
L1-102_DR#LIN 762 TGTAAGGTGTTGGCAAAAATACTGGCCTCTCGGCTGGAAAAGGTT-TTAC 810
Crub_svsplocu 443613 AGACT-TGATTCATAGTGATCAAGCAGGATTTATAACAGGGAGATACATG 443661
vv v - i iv i i ii v v vi i v vi
L1-102_DR#LIN 811 CCAGTATAATTCATAAAGACCAGGTGGGCTTTATTAAGGGGAGGTCCTCG 860
Crub_svsplocu 443662 AAACATAATGTTAGACAAATTATTAATTTAATTGAGTACTTGGATAAGAA 443711
iv v v v vi vv i --- iiv ii -----
L1-102_DR#LIN 861 GCAGATAATGTGAGAAAAATGGTGCATTTGAT---GCGGTTAAAT----- 902
Crub_svsplocu 443712 TAATCAGAT-----TCCTGTGGCTTTTATCTTTTTGGATGCTGAAAAAGC 443756
v i----- vi v vvi v i i i
L1-102_DR#LIN 903 TATTCAGACAATACTCCAATTGCAGCTATATCTCTGGATGCTGAAAAGGC 952
Crub_svsplocu 443757 TTTTGA 443762
i
L1-102_DR#LIN 953 CTTTGA 958
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 41.98
Transitions / transversions = 0.84 (43/51)
Gap_init rate = 0.06 (17 / 298), avg. gap size = 1.24 (21 / 17)
305 36.44 2.06 2.70 Crub_svsplocus 443479 443963 206037 + L1-35_DR LINE/L1 3028 3509 1972
305 36.44 2.06 2.70 Crub_svsplocus 443479 443963 (206037) L1-35_DR#LINE/L1 3028 3509 (1972) m_b9s001i3
Crub_svsplocu 443479 GCTTTTATATCACTGATTATGAAGGAAGATCAGGATCTTACAGAGCCTAA 443528
v vv v i viv ii v ii iviv ivi i
L1-35_DR#LINE 3028 GCTATTATTACAGTAATTCCTAAAAAAGATAAAAATCCAGAAGAAGTTGA 3077
Crub_svsplocu 443529 GAATTATAGGCCAATTTCATTATTGAATGTTGATTATAAGAT-TTTTACA 443577
ivv i v i vi vi v i v i - v vi
L1-35_DR#LINE 3078 GGCGTATAGACCTATCTCTCTCCTCAATGTTGATCAAAAAATATTGTCTA 3127
Crub_svsplocu 443578 AAAAATTTGGCAAATAGACTAATGCAGG-TTATGAAAGACTTGATTCATA 443626
v i i- v i -v i ii- v vi v i v ii
L1-35_DR#LINE 3128 AAACACTC-GCTAATAGGCT-CTGTAAATTTATCAATAAATTGGTTAACG 3175
Crub_svsplocu 443627 GTGATCAAGCAGGATTTATAACAGGGAGATACATGAAACATAATGTTAGA 443676
vv iivv vv i vi iv vv i v
L1-35_DR#LINE 3176 TAGATCAGAATGGATTTATTCCAGGAAGAAGCACTATCCATAATATAAGA 3225
Crub_svsplocu 443677 CAAATTA-TTAATTTAATTGAGTACTTGGATAAGAATAATCAGATTC-CT 443724
- i - iv v vi ii--- -ii v vv -v
L1-35_DR#LINE 3226 -AGATTATTTAACATAATTTATCACCC---TAAG-GCAATCCGAGACAAT 3270
Crub_svsplocu 443725 GTGGCTTTTATCTTTTTGGATGCTGAAAAAGCTTTTGATCAATTGGACTG 443774
v ii v v v iv i i i v i i i v v v
L1-35_DR#LINE 3271 TTGATTGTAATATCATTAGATGCCGAAAAGGCATTCGACCGAGTCGAGTG 3320
Crub_svsplocu 443775 GCAATTTTTACTCTCTTTGGTAGAGAAAATGAATTTTGGGGATAATTTC- 443823
viv vi ii v v vv i v vi v v i i-
L1-35_DR#LINE 3321 GGGTTACTTGTTCGCTGTCCTGGAGAAATTTGATTTGGGTGATGATTTTA 3370
Crub_svsplocu 443824 TTACATGCACTTAAAGCTATATATCAGCAG-CAATCTGCACAAATTGTTG 443872
v v v - v ii v i - ii - v iv ivi v vi
L1-35_DR#LINE 3371 TAACTTGGA-TAAAAATTTTGTA-CAATAGTCCATTAGCACGTGTTTTAA 3418
Crub_svsplocu 443873 TAAATGGGG-GATT---GACTGAGAATTTTAATATTCAAAAAGGGACAAG 443918
i i ii-i --- v---- v v v i i v
L1-35_DR#LINE 3419 CAAATAGAACAATTTCAGACTC----TTTTTATCTTAAAAGAGGAACCAG 3464
Crub_svsplocu 443919 ACAAGGATGTCCATTATCCCCATTGTTATTTGTTTTAACATTGGA 443963
i v i vi v v vi v i i iv i iv i
L1-35_DR#LINE 3465 ACAGGGTTGCCCTCTCTCGCCTCTTTTGTTCGCATTGACGGTAGA 3509
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 47.53
Transitions / transversions = 0.98 (85/87)
Gap_init rate = 0.04 (21 / 484), avg. gap size = 1.10 (23 / 21)
392 29.26 6.71 7.46 Crub_svsplocus 443533 443964 206036 + L1-86_DR LINE/L1 3064 3492 1935
392 29.26 6.71 7.46 Crub_svsplocus 443533 443964 (206036) L1-86_DR#LINE/L1 3064 3492 (1935) m_b9s001i4
Crub_svsplocu 443533 TATAGGCCAATTTCATTATTGAATGTTGATTATAAGATTTTTACAAAAA- 443581
v i i ii v vi i i v -
L1-86_DR#LINE 3064 TATCGGCCAATCTCACTGCTTAATTCTGATTATAAAATTCTTACCAAAAT 3113
Crub_svsplocu 443582 -ATTTGGCAAATA-GACTAATGCAGGTTATGAAAGACTTGATTCATAGTG 443629
- -- v- - vi iv i vv vvviii ii i vv
L1-86_DR#LINE 3114 GATT--GCAT-TACGTTTAGAGCGGGTACTGCCTAGTTTAGTTCACATGG 3160
Crub_svsplocu 443630 ATCAAGCAGGATTTATAACAGGGAGATACAT----GA-AACATAATGTTA 443674
i i v v v iiv v vi---- - vv --
L1-86_DR#LINE 3161 ACCAAACTGGATTTATCAGAAATAGATCCTCTTTCGATAACATACGG--A 3208
Crub_svsplocu 443675 GACAAAT---TATTAATTTAATTGAGTACTTGGATAAGAATAATCAGATT 443721
i v --- - - v i ---ii i - v i i---
L1-86_DR#LINE 3209 GGCTAATGAATATTA-TTTA-TTCAGCA---AAACAA-ATTGATT---TT 3249
Crub_svsplocu 443722 CCTGTGGCTTTTATCTTTTTGGATGCTGAAAAAGCTTTTGATCAATTGGA 443771
v ii vi v i i i v i i i i v
L1-86_DR#LINE 3250 CCGGTGATTGCTCTTTCTTTAGATGCAGAAAAAGCCTTCGACCGAGTGGA 3299
Crub_svsplocu 443772 CTGGCAATTTTTACTCTCTTTGG-----TAGAGAAAATGAATTTTGG-GG 443815
v ---- i - vv v----- v i i -vv
L1-86_DR#LINE 3300 ATGG----TCTTA-TCTGATTGCGGTTTTACAAAAAATGAATTTCGGTCC 3344
Crub_svsplocu 443816 ATAATTTCTT-ACATGCACTTAAA-GCTATAT--------ATCAGCAGCA 443855
v v v - v - i v i - i i -------- i v
L1-86_DR#LINE 3345 AAACTTTATTGAGATG-ATTAAGATGTTGTATAGGAATCCATCGGCAGCC 3393
Crub_svsplocu 443856 ATCTGCACAAATTGTTGTAAATGGGGGATTGACTGAGAATTTTAATATTC 443905
i i v v ----i ------ iv iv -- i
L1-86_DR#LINE 3394 ATCCGTACTAATTCT----GATG------TATCTGAACATTTT--TATTT 3431
Crub_svsplocu 443906 A--AAAAGGGACAAGACAAGGATGTCCATTATCCCCATTGTTATTTGTTT 443953
-- i i v i vi v ii ii v i i
L1-86_DR#LINE 3432 ATCAAGAGGAACCAGACAGGGATGTCCCCTCTCCCCGCTACTCTTTGCTC 3481
Crub_svsplocu 443954 TAACATTGGAA 443964
i iv i
L1-86_DR#LINE 3482 TAGCGGTAGAA 3492
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 34.68
Transitions / transversions = 1.25 (65/52)
Gap_init rate = 0.10 (44 / 431), avg. gap size = 1.39 (61 / 44)
530 27.39 5.14 6.23 Crub_svsplocus 443666 443957 206043 + L1-19_DR LINE/L1 3281 3569 2030
530 27.39 5.14 6.23 Crub_svsplocus 443666 443957 (206043) L1-19_DR#LINE/L1 3281 3569 (2030) m_b9s001i5
Crub_svsplocu 443666 ATAATGTTAGACAAATTATTAATT-TAATTGAGTACTTGG----ATAAGA 443710
i i - i v - vi i ----i v
L1-19_DR#LINE 3281 ACAATGTTAGACGA-TTACTAAATATAATTGACCACTCGGCCCTGTACGA 3329
Crub_svsplocu 443711 ATAATCAG-ATTCCTGTGGCTTTTATCTTTTTGGATGCTGAAAAAGCTTT 443759
i i - vv i-------- v i i i v
L1-19_DR#LINE 3330 ACAACCAGCATTAATA--------ATATCTCTGGACGCTGAAAAAGCGTT 3371
Crub_svsplocu 443760 TGATCAATTGGACTGGCAATTTTTACTCTCTTTGGTAGAGAAAATGAATT 443809
iviiv v v v vii i vv vv i v v v
L1-19_DR#LINE 3372 TGACAGGGTCGAGTGGCCATACCTATTCTCAGTTCTAAAGAAATTCAATA 3421
Crub_svsplocu 443810 TTGGGGATA-ATTTCTTACATGCACTTAAAG-CTATATATCAGCAGCAAT 443857
v - v ivi v -- - i ---- i
L1-19_DR#LINE 3422 TTGGCGATAGATGTCTTGGGTGGA--TAAAGTCTATGTAT----AGCAAC 3465
Crub_svsplocu 443858 CTGCA----CAAAT-TGTTGTAAATGGGGGATTGACTGAGAATTTTAATA 443902
i ---- - - ivvi v i i vi ii v
L1-19_DR#LINE 3466 CCGCAAGCCCAAATATG-TGTAAATGGGACTCTGTCCGAAAAACTTGGTC 3514
Crub_svsplocu 443903 TTCAAAAAGG--GACAAGACAAGGATGTCCATTATCCCCATTGTTATTTG 443950
v v i -- v -- i i i vi i i v i
L1-19_DR#LINE 3515 TGCATAGAGGATGTC--GGCAGGGATGCCCCCTGTCCCCGTTTTTATTTA 3562
Crub_svsplocu 443951 TTTTAAC 443957
v i
L1-19_DR#LINE 3563 ATTTAGC 3569
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 31.30
Transitions / transversions = 1.14 (40/35)
Gap_init rate = 0.09 (26 / 291), avg. gap size = 1.27 (33 / 26)
293 25.29 10.31 10.31 Crub_svsplocus 443743 444033 205967 + L1-1_DR LINE/L1 3489 3779 2032
293 25.29 10.31 10.31 Crub_svsplocus 443743 444033 (205967) L1-1_DR#LINE/L1 3489 3779 (2032) m_b9s001i6
Crub_svsplocu 443743 GATGCTGAAAAAGCTTTTGATCAATTGGACTGGCAAT-----TTTTACTC 443787
i i iiv v v v ----- v
L1-1_DR#LINE/ 3489 GATGCTGAGAAGGCTTTTGATCGGGTGGAGTGGGACTACCTCTTTTACAC 3538
Crub_svsplocu 443788 TCTTTGGTAGAGAAAA--TGAATTTTGGGGATAA--TTTCTTACATGCAC 443833
------ i -- i -- v i -- iv v v i
L1-1_DR#LINE/ 3539 TCTT------AAAAAATTTGGATTT--GGCACAAAGTTCATTTCATGGAT 3580
Crub_svsplocu 443834 TTAAAGC-TATA--TATCA------GCAGCAATCTGCACAAATTGTTGTA 443874
v v - --i ------ vi i --i
L1-1_DR#LINE/ 3581 TAAAATCTTATACTCATCACCTATGGCAGCAATACGTACAAATTGT--CA 3628
Crub_svsplocu 443875 AATGGGGGATTGACTGAGAATTTTAATATTC---AAAAAGGG--ACAAGA 443919
v ------ vv i----- i-- v --- i -- v
L1-1_DR#LINE/ 3629 CAT------TTCTCC-----TTTC--TTTTCGTTAGAAAGGGGAACCAGA 3665
Crub_svsplocu 443920 CAAGGATGTCCATTATCCCCATTGTTATTTGTTTTAACATTGGAAATTTT 443969
v i vi i v i iv iii v v vi i
L1-1_DR#LINE/ 3666 CAAGGCTGCCCTCTGTCCCCCTTATTATTTGCATTGGTAATTGAACCTCT 3715
Crub_svsplocu 443970 ATTGATTCAGATTTGGGA----ATCAAAGTTAATTAAGGGTGTAAAGATA 444015
i iv vv vi ii ---- -- -- i i v ---
L1-1_DR#LINE/ 3716 GTCCATTGCGATACGAAATGATATCAA--T--ATCAAGGGTATACAG--- 3758
Crub_svsplocu 444016 AGGAAGAA---TGAGTATAAA 444033
i v --- ii
L1-1_DR#LINE/ 3759 AGGGACAACTTTGAACATAAA 3779
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 29.64
Transitions / transversions = 1.20 (36/30)
Gap_init rate = 0.14 (40 / 290), avg. gap size = 1.50 (60 / 40)
234 31.58 5.00 5.00 Crub_svsplocus 443873 444112 205888 + L1M1_orf2 LINE/L1 1928 2167 1127
234 31.58 5.00 5.00 Crub_svsplocus 443873 444112 (205888) L1M1_orf2#LINE/L1 1928 2167 (1127) m_b9s001i7
Crub_svsplocu 443873 TAAATGGGGGATTGACTGAGAATTTTAATATTCAAAAA---GGGACAAGA 443919
i i v-i i iii -- vi v i --- i v
L1M1_orf2#LIN 1928 TGAATGGGGAAA-AACTGAAAGCCTT--TCCTCTAAGATCTGGAACACGA 1974
Crub_svsplocu 443920 CAAGGATGTCCATTATCCCCATTGTTATTTGTTTTAACATTGGAAATTTT 443969
i i v v i iiviv ii i i ii
L1M1_orf2#LIN 1975 CAAGGATGCCCACTTTCACCACTGTTATTCAACATAGTACTGGAAGTCCT 2024
Crub_svsplocu 443970 A--TTGAT---TCAGATTTGGGAATCAAAGTTAATTAAGGGTGT--AAA- 444011
-- v v--- ivv i -- i --- v ii -- -
L1M1_orf2#LIN 2025 AGCTAGAGCAATCAGACAAGAGAA--AGA---AATAAAGGGCATCCAAAT 2069
Crub_svsplocu 444012 -GATAAGGAAGAATGAGTATAAATTGCGGGCATTTGCGGATGATTTGGTT 444060
- iv --- -i iivvvii i v i i
L1M1_orf2#LIN 2070 TGGAAAGGAAGA---AGT-CAAATTATCCTTGTTTGCAGATGATATGATC 2115
Crub_svsplocu 444061 TTAATTTTGGAACAGCCGAATCAGGCGATTGATGGTTTATTAGAACTTAT 444110
vv v i v vv vv v i?i viivi v
L1M1_orf2#LIN 2116 TTATATTTGGAAAAACCTAAAGACTCCACNAAAAAACTATTAGAACTGAT 2165
Crub_svsplocu 444111 AA 444112
L1M1_orf2#LIN 2166 AA 2167
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 42.55
Transitions / transversions = 1.40 (42/30)
Gap_init rate = 0.08 (18 / 239), avg. gap size = 1.33 (24 / 18)
244 32.88 2.67 2.67 Crub_svsplocus 443911 444060 205940 + L1MD_orf2 LINE/L1 1966 2115 1179
244 32.88 2.67 2.67 Crub_svsplocus 443911 444060 (205940) L1MD_orf2#LINE/L1 1966 2115 (1179) m_b9s001i8
Crub_svsplocu 443911 GGGACAAGACAAGGATGTCCATTATCCCCATTGTTATTTGTTTTAACATT 443960
i i ii v v i v iiviv ii i
L1MD_orf2#LIN 1966 GGAACAAGGCAAGGATGTCCGCTCTCACCACTCTTATTCAACATAGTACT 2015
Crub_svsplocu 443961 GGAAATTTTATTGATTCAGATTTGGGAATCAAAGTTAATTAAGGGTGTAA 444010
i i viv v vvi vv v vv vv v i ii v
L1MD_orf2#LIN 2016 GGAAGTTCTAGCCAGTGCAATAAGGCAAGAAAAGGAAATAAAAGGCATAC 2065
Crub_svsplocu 444011 AGAT----AAGGAAGAATGAGTATAAATTGCGGGCATTTGCGGATGATTT 444056
---- --- i - i ivvvi i iv
L1MD_orf2#LIN 2066 AGATTGGAAAGGAAGA---AATA-AAACTGTCCCTATTTGCAGATGACAT 2111
Crub_svsplocu 444057 GGTT 444060
i
L1MD_orf2#LIN 2112 GATT 2115
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 42.90
Transitions / transversions = 1.09 (25/23)
Gap_init rate = 0.03 (5 / 149), avg. gap size = 1.60 (8 / 5)
+ 366 26.4 7.6 5.7 Crub_svsplocus 444229 444547 (205453) + L1-18_DR LINE/L1 3669 4187 (1527) 258
ANNOTATION EVIDENCE:
228 32.08 2.60 2.60 Crub_svsplocus 444229 444420 205580 + L1-104_DR LINE/L1 3596 3787 1840
228 32.08 2.60 2.60 Crub_svsplocus 444229 444420 (205580) L1-104_DR#LINE/L1 3596 3787 (1840) m_b9s001i9
Crub_svsplocu 444229 GAAAAAAAGGTTAAATAT-TTGGGAGTATA-TCTAACTGCTTCAAATAGA 444276
i i i i- v v ii - -- ivv vvv
L1-104_DR#LIN 3596 GAAAAAGAGATCAAATACCTTGGTATTGCAATC--ACTAAGTCAACACGA 3643
Crub_svsplocu 444277 AAATTGTATTAGAAC--AATTATGAACCACTATGGGCAAAAGTCCAAAAG 444324
v v ii-- -- iv vi i vvi v vvi
L1-104_DR#LIN 3644 ACAATGCG--AGAACGAAATCTTGATTCATTAACAGCAAAAGTCAAATTA 3691
Crub_svsplocu 444325 GATTTA-AGAGATTGGAAAAAATTGCAATTGTCATTGTTGGGGAGAATTT 444373
- i - ivv v vii v ivii v vi
L1-104_DR#LIN 3692 GATTTACAAAGAT-GGAGTCACTTGCCGCTGTCTTTAGCAGGCAGAATAC 3740
Crub_svsplocu 444374 CAGCCGTAAAAATGAATGTTCTACCAAAGTTTCTTTTTTTGTTTCAG 444420
v iiii v v i v i v v v i
L1-104_DR#LIN 3741 AAATTATCAAAATGAATGTGCTACCAAGGTATTTATATGTATTTCAG 3787
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 40.47
Transitions / transversions = 0.94 (29/31)
Gap_init rate = 0.05 (9 / 191), avg. gap size = 1.11 (10 / 9)
305 27.62 3.82 3.16 Crub_svsplocus 444276 444432 205568 + L1-1_Testu LINE/L1 4748 4905 1427
305 27.62 3.82 3.16 Crub_svsplocus 444276 444432 (205568) L1-1_Testu#LINE/L1 4748 4905 (1427) m_b9s001i10
Crub_svsplocu 444276 AAAATTGTATTAGAACAA-TTATGAACCACTATGGGCAAAAGTCCAAAAG 444324
iv v iii - ivvv ? i ivv i vvv i
L1-1_Testu#LI 4748 AAAATCTTTTTAAGGCAAATTACCCTCCANTGTGGAATAAAATAATAAAA 4797
Crub_svsplocu 444325 GATTTAAGAGATTGGAAAAAAT-TGCAATTGTCATTGTTGGGGAGAATTT 444373
i iiii v v - v - v v i i v ii --
L1-1_Testu#LI 4798 GACTTGGAGGAATGGAACAAATATGAAATT-TCTTGGCTAGGTAGGGT-- 4844
Crub_svsplocu 444374 CAGCC---GTAAAAATGAATGTTCTACCAAAGTTTCTTTTTTTGTTTCAG 444420
- --- i i v vi v
L1-1_Testu#LI 4845 -AGCCTCGGTAAAGATGAATGTCCTCCCAAAGTTATTATTTTTGTTTCAG 4893
Crub_svsplocu 444421 ATG-ATACCTATT 444432
- - v i
L1-1_Testu#LI 4894 -TGCATCCCTGTT 4905
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 35.26
Transitions / transversions = 1.10 (22/20)
Gap_init rate = 0.06 (9 / 156), avg. gap size = 1.22 (11 / 9)
366 29.31 0.85 0.85 Crub_svsplocus 444315 444431 205569 + L1-18_DR LINE/L1 4071 4187 1527
366 29.31 0.85 0.85 Crub_svsplocus 444315 444431 (205569) L1-18_DR#LINE/L1 4071 4187 (1527) m_b9s001i11
Crub_svsplocu 444315 AGTCCAAAAGGATTTA-AGAGATTGGAAAAAATTGCAATTGTCATTGTTG 444363
iv i- i - i iivii i v i i v
L1-18_DR#LINE 4071 AGTTAAAAAGGATTTGCAGAGGT-GGGAGGTGCTACCACTATCATTGTTT 4119
Crub_svsplocu 444364 GGGAGAATTTCAGCCGTAAAAATGAATGTTCTACCAAAGTTTCTTTTTTT 444413
v i vv i vi i i i v ii
L1-18_DR#LINE 4120 GGTAGGATTGAAACAATAAGAATGAATATTTTACCTAGATTTCTTTTTTT 4169
Crub_svsplocu 444414 GTTTCAGATGATACCTAT 444431
i vivv i
L1-18_DR#LINE 4170 ATTTCAGTCCCTACCCAT 4187
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 38.76
Transitions / transversions = 1.83 (22/12)
Gap_init rate = 0.02 (2 / 116), avg. gap size = 1.00 (2 / 2)
272 25.21 9.57 7.01 Crub_svsplocus 444320 444528 205472 + L1-86_DR LINE/L1 3831 4044 1383
272 25.21 9.57 7.01 Crub_svsplocus 444320 444528 (205472) L1-86_DR#LINE/L1 3831 4044 (1383) m_b9s001i12
Crub_svsplocu 444320 AAAAGGATTTAA--GAGAT-TGGAAAAA--------ATTGCAATTGTCAT 444358
--- -- - i -------- i i v i i
L1-86_DR#LINE 3831 AAAAGG---TAATTGAGATCTGGAAAGATGGAATCCACTACCATTATCAC 3877
Crub_svsplocu 444359 TGTTGGGGAGAATTTCAGCCG-TAAAAATGAATGTTCTACCAAAGTTTCT 444407
iv v v i --v i i - ii v v i --
L1-86_DR#LINE 3878 TAATTGGCAGGAT--AAACTGCTAAAAATGAACATTCTTCCTAAATT--T 3923
Crub_svsplocu 444408 TTTTTTGTTTCAGATGATACCTATTCTTA----AAAAAGAGGCAAATTTG 444453
v ivv v ii ---- v ----- iv v
L1-86_DR#LINE 3924 TTATTTGTTTCAGACCCTCCCTATTTCTATCCCACAAA-----AGTTTTT 3968
Crub_svsplocu 444454 GAGGAATGGCAAAAGGGTATCAAT----AATTTTATATGGGCCGGGAAGA 444499
v vv v v--- ---- v iviiii i
L1-86_DR#LINE 3969 TAGGAATCTCAACAGC---TCAATTAGAAATTTTATTTGGAATAAAAAAA 4015
Crub_svsplocu 444500 AACCAAGGGTTAAATTTAAGATATTACAG 444528
vv i i i i
L1-86_DR#LINE 4016 CTCCAAGGATTAAACTTAGGACATTACAG 4044
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 31.20
Transitions / transversions = 1.13 (26/23)
Gap_init rate = 0.10 (21 / 208), avg. gap size = 1.67 (35 / 21)
255 28.35 5.84 3.82 Crub_svsplocus 444394 444547 205453 + L1-67_DR LINE/L1 3669 3825 1543
255 28.35 5.84 3.82 Crub_svsplocus 444394 444547 (205453) L1-67_DR#LINE/L1 3669 3825 (1543) m_b9s001i13
Crub_svsplocu 444394 CTACCAAAGTTTCTTTTTTTGTTTCAGATGATACCTATTC---TTAAAAA 444440
v iii v vi i vivv i --- ivi
L1-67_DR#LINE 3669 CTTCCAAGACTGCTTTACTTATTTCAGTCTTTACCTGTTCCCCTTGCGAA 3718
Crub_svsplocu 444441 AGAGGCAAATTTGGAGGAATGG--CAAAAGGGTATCAATAATTTTATATG 444488
i i- v v -- -- i vv i v -- iv
L1-67_DR#LINE 3719 AAAA-CAATTTTCG--GAATGGGACAGACTGATCTC--TAGATTTATATG 3763
Crub_svsplocu 444489 GGCCGGG-AAGAAACCAAGGGTTAAATTTAAGATATTACA---GGATGCT 444534
- v - i v i ivi i --- i ivv
L1-67_DR#LINE 3764 G-CAGGGCAGGAAACCAAGGGTAAAATTTAAAACCCTGCAATTGGGTAAA 3812
Crub_svsplocu 444535 CGAGAAAGAGGGG 444547
vi i
L1-67_DR#LINE 3813 GAAGAAGGAGGGG 3825
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 35.26
Transitions / transversions = 1.21 (23/19)
Gap_init rate = 0.07 (10 / 153), avg. gap size = 1.50 (15 / 10)
+ 228 28.3 3.6 5.2 Crub_svsplocus 445213 445350 (204650) + L1-18_DR LINE/L1 5716 5851 (481) 258
ANNOTATION EVIDENCE:
228 28.27 3.62 5.15 Crub_svsplocus 445213 445350 204650 + L1-1_Testu LINE/L1 5716 5851 481
228 28.27 3.62 5.15 Crub_svsplocus 445213 445350 (204650) L1-1_Testu#LINE/L1 5716 5851 (481) m_b9s001i14
Crub_svsplocu 445213 AGAGAAAATTTTTATAAAATGTTCTATAGATGGCACTTAGATCC--TAAA 445260
i v ii v i iiv -- v
L1-1_Testu#LI 5716 AAAGAAAATTTTTATAAATTACTGTATAGATGGCATTTGACTCCAGTTAA 5765
Crub_svsplocu 445261 AAATTATCTTGTATGTATTCCAATATACAGCCCAAATGTTGGAGA---TG 445307
i vii --i v v v i v viv v vvvv i---
L1-1_Testu#LI 5766 GATCCATC--ATATTTTTGCTACTAGGGAGGCGCTCTGTTGGAGGGGTTG 5813
Crub_svsplocu 445308 CGGCAATAATGATGCGACATACTTTCATATTTGGTGGAATTGT 445350
vi - v -- vi v i v --
L1-1_Testu#LI 5814 CGGGGA-AAGG--GGAACATACTTGCACATGTGGTGG--TTGT 5851
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 35.59
Transitions / transversions = 0.76 (16/21)
Gap_init rate = 0.07 (9 / 137), avg. gap size = 1.33 (12 / 9)
+ 19 31.8 0.0 2.5 Crub_svsplocus 445763 445774 (204226) + (TTATTTA)n Simple_repeat 1 79 (0) 259
ANNOTATION EVIDENCE:
19 31.83 0.00 2.50 Crub_svsplocus 445763 445844 204156 + (TTATTTA)n Simple_repeat 1 80 0
19 31.83 0.00 2.50 Crub_svsplocus 445763 445844 (204156) (TTATTTA)n#Simple_repeat 1 80 (0) m_b9s252i4
Crub_svsplocu 445763 TTAATTATGATATTTTTTTCTCTTTTTTCTTTTCTTTTTTTTCTTTTTTC 445812
v v - v v i v v v v i v v v v v
(TTATTTA)n#Si 1 TTATTTATTAT-TTATTATTTATTATTTATTATTTATTATTTATTATTTA 49
Crub_svsplocu 445813 TTAATTATTATAAATTTTTTTTTTATTTATTA 445844
v vv - v v
(TTATTTA)n#Si 50 TTATTTATTATTTA-TTATTTATTATTTATTA 80
Matrix = Unknown
Transitions / transversions = 0.11 (2/18)
Gap_init rate = 0.02 (2 / 81), avg. gap size = 1.00 (2 / 2)
+ 26 22.4 0.0 1.5 Crub_svsplocus 445775 445843 (204157) + (TTCTTTT)n Simple_repeat 1 68 (0) 260
ANNOTATION EVIDENCE:
26 22.41 0.00 1.47 Crub_svsplocus 445775 445843 204157 + (TTCTTTT)n Simple_repeat 1 68 0
26 22.41 0.00 1.47 Crub_svsplocus 445775 445843 (204157) (TTCTTTT)n#Simple_repeat 1 68 (0) m_b9s252i5
Crub_svsplocu 445775 TTTTTTTCTCTTTTTTCTTTTCTTTTTTTTCTTTTTTCTTAATTATTATA 445824
i i i i vv v v v
(TTCTTTT)n#Si 1 TTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTT 50
Crub_svsplocu 445825 AATTTTTTTTTTATTTATT 445843
vv i - v
(TTCTTTT)n#Si 51 TCTTTTTTCTTT-TTTCTT 68
Matrix = Unknown
Transitions / transversions = 0.62 (5/8)
Gap_init rate = 0.01 (1 / 68), avg. gap size = 1.00 (1 / 1)
+ 13 21.3 0.0 2.6 Crub_svsplocus 445861 445900 (204100) + G-rich Low_complexity 1 39 (0) 261
ANNOTATION EVIDENCE:
13 21.28 0.00 2.56 Crub_svsplocus 445861 445900 204100 + (TGGGGGG)n Simple_repeat 1 39 0
13 21.28 0.00 2.56 Crub_svsplocus 445861 445900 (204100) (TGGGGGG)n#Simple_repeat 1 39 (0) m_b9s252i6
Crub_svsplocu 445861 TGGGAAGTGAAGGGAGGGGGGTTGGGGGTGGGAGGGAGGG 445900
ii ii v v - v
(TGGGGGG)n#Si 1 TGGGGGGTGGGGGGTGGGGGGTGGGGGGTGGG-GGGTGGG 39
Matrix = Unknown
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.03 (1 / 39), avg. gap size = 1.00 (1 / 1)
+ 16 19.2 0.0 0.0 Crub_svsplocus 445962 445991 (204009) + A-rich Low_complexity 1 30 (0) 262
ANNOTATION EVIDENCE:
16 19.25 0.00 0.00 Crub_svsplocus 445962 445991 204009 + (A)n Simple_repeat 1 30 0
16 19.25 0.00 0.00 Crub_svsplocus 445962 445991 (204009) (A)n#Simple_repeat 1 30 (0) m_b9s252i8
Crub_svsplocu 445962 AAAAAATAAAAAAAATTCAATAAAAAAAAA 445991
v vvv v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30
Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 12 21.6 3.9 3.9 Crub_svsplocus 451453 451504 (198496) + A-rich Low_complexity 1 52 (0) 263
ANNOTATION EVIDENCE:
12 21.63 3.85 3.85 Crub_svsplocus 451453 451504 198496 + (TAAAAGA)n Simple_repeat 1 52 0
12 21.63 3.85 3.85 Crub_svsplocus 451453 451504 (198496) (TAAAAGA)n#Simple_repeat 1 52 (0) m_b9s252i9
Crub_svsplocu 451453 TAAGAAAATAAATTTTAAAA-AAATCAG-TAAAACAAAAAAGATAAAAAG 451500
- i vvv - v vv - v v -
(TAAAAGA)n#Si 1 TAA-AAGATAAAAGATAAAAGATAAAAGATAAAAGATAAAAGAT-AAAAG 48
Crub_svsplocu 451501 ATAA 451504
(TAAAAGA)n#Si 49 ATAA 52
Matrix = Unknown
Transitions / transversions = 0.12 (1/8)
Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4)
+ 231 17.5 0.0 0.0 Crub_svsplocus 451749 451788 (198212) + Gypsy157-I_DR LTR/Gypsy 3879 3918 (6982) 264
ANNOTATION EVIDENCE:
231 17.50 0.00 0.00 Crub_svsplocus 451749 451788 198212 + Gypsy157-I_DR LTR/Gypsy 3879 3918 6982
231 17.50 0.00 0.00 Crub_svsplocus 451749 451788 (198212) Gypsy157-I_DR#LTR/Gypsy 3879 3918 (6982) m_b9s001i15
Crub_svsplocu 451749 TCACACAATACACATCCATGTCAAGAAAGAGATGGATTCA 451788
i v viii i
Gypsy157-I_DR 3879 TCATACAATACACATCCCTGGTGGGAAAGAGATGGATTTA 3918
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 20.47
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 1815 32.0 1.3 0.5 Crub_svsplocus 452867 453488 (196512) C L3 LINE/CR1 (42) 4057 3431 265
ANNOTATION EVIDENCE:
1815 31.98 1.29 0.48 Crub_svsplocus 452867 453488 196512 C L3 LINE/CR1 3431 4057 42
1815 31.98 1.29 0.48 Crub_svsplocus 452867 453488 (196512) C L3#LINE/CR1 (42) 4057 3431 m_b9s001i16
Crub_svsplocu 452867 TCATCTAGTCCAACCCCCTG-CTAAGGCAGGAAACCCT---ATACCATTT 452912
i ii- ii v v --- i v ii
C L3#LINE/CR1 4057 TCATCTAGTCCAACCTCCCATCCGATGCAGGAATCCCTTCTACAACATCC 4008
Crub_svsplocu 452913 CAGACAAACGGCTGTCTAGTCTCTTCTTAAAAACTTCCAGTGTTGGAGCA 452962
v ii iii i i v i v i vi i vi
C L3#LINE/CR1 4007 CTGACAAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAG 3958
Crub_svsplocu 452963 TTCACCGCTTCTGGAGGCAAGTTGTTCCAAGGTTA-ATTGTTCTAATTGT 453011
i ii i ?v iviii vvv i- iv i i
C L3#LINE/CR1 3957 CTCACTACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGT 3908
Crub_svsplocu 453012 CAGAAAGTTTCTCCTTAGTTCTAGGTTG---CTTTTCTTCTTGATTAGTT 453058
i ii - vi ii ii ---ii vi i i -- ii
C L3#LINE/CR1 3907 TAGAAAGTTCTTCCTTA-TATTGAGCCGAAATCTGCCTCCCTG--TAACT 3861
Crub_svsplocu 453059 TCCATCCATTGCTTCTTGTCCTGCCTTCAGGCACTTTGGAAAATAGCTTG 453108
i v i v i i v vi iviiv i iv iv
C L3#LINE/CR1 3860 TCCACCCATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCT 3811
Crub_svsplocu 453109 ACTCCCTCTTTTTTGTGGCAGCCTCTGAGATATTGGAACACTGCTATCAT 453158
v iivii i ii v i v v v
C L3#LINE/CR1 3810 AATCCCTCTTCCACATGACAGCCCTTCAAATATTTGAAGACAGCTATCAT 3761
Crub_svsplocu 453159 GTCCCCTCTCGTCCTTCTCTTCGTTAAACTAGACATACCCAATTCCAGCA 453208
i vivi vii ii i v i vv
C L3#LINE/CR1 3760 GTCTCCTCTAAGTCTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCA 3711
Crub_svsplocu 453209 ACCGTTCCTTATATGTTTTAGCCTCCAGTCCCCTAATCATCTTTGTTGCT 453258
i viv i ii v i v i i v i
C L3#LINE/CR1 3710 ACCGTTCCTCATATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCT 3661
Crub_svsplocu 453259 CTTCTCTGTACTCTTTCTAGAGTTTCAACATCTTTTTTACATCGTGGTGA 453308
i v v vi i vv v ii ii i v vi i v
C L3#LINE/CR1 3660 CTCCTCTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGC 3611
Crub_svsplocu 453309 CCAAAACTGGATGCAATATTCCAAGTGTGGCCTTTCCAAGGCCTTGTAAA 453358
i i i i ii i vv iv vvv v
C L3#LINE/CR1 3610 CCAGAACTGAACGCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACA 3561
Crub_svsplocu 453359 GTGGTATTAACACTTCATGTGATCTTGATTATATCCCTCTGTTAATGCAG 453408
i v i vi i viv ? v ivv v i i
C L3#LINE/CR1 3560 GCGGGACTATTACCTCCCTTGNTCTGGACACTATACTTCTATTAATGCAG 3511
Crub_svsplocu 453409 CCCAGCACTGTGTTGGCTTTTTTGGCAGCTGCAGCACACTGCTGGCTCAT 453458
i iv i ii i ii v i
C L3#LINE/CR1 3510 CCTAAGATTGCATTAGCTTTTTTGGCAGCCACATCACACTGTTGGCTCAT 3461
Crub_svsplocu 453459 ATTTAAGTGATTGTCCACTAGGACTCCGAG 453488
v iv viiv v ii i v
C L3#LINE/CR1 3460 ATTGAGCTTGCGGTCAACTAAAACCCCTAG 3431
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 41.39
Transitions / transversions = 1.71 (125/73)
Gap_init rate = 0.01 (7 / 621), avg. gap size = 1.57 (11 / 7)
+ 233 12.1 0.0 0.0 Crub_svsplocus 453722 453754 (196246) + URR1B DNA/hAT-Charlie 193 225 (0) 266
ANNOTATION EVIDENCE:
233 12.12 0.00 0.00 Crub_svsplocus 453722 453754 196246 + URR1B DNA/hAT-Charlie 193 225 0
233 12.12 0.00 0.00 Crub_svsplocus 453722 453754 (196246) URR1B#DNA/hAT-Charlie 193 225 (0) m_b9s001i17
Crub_svsplocu 453722 GGGTAACAGCATTAAAAAGGTTGAGAACCACTG 453754
vi ii
URR1B#DNA/hAT 193 GGGTCGCAGCATTAGGAAGGTTGAGAACCACTG 225
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 10.14
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 12 23.9 2.2 2.2 Crub_svsplocus 457014 457059 (192941) + (GAATAGA)n Simple_repeat 1 46 (0) 267
ANNOTATION EVIDENCE:
12 23.85 2.17 2.17 Crub_svsplocus 457014 457059 192941 + (GAATAGA)n Simple_repeat 1 46 0
12 23.85 2.17 2.17 Crub_svsplocus 457014 457059 (192941) (GAATAGA)n#Simple_repeat 1 46 (0) m_b9s252i10
Crub_svsplocu 457014 GAACAGATAAAACAG-ATAAATGGATACAAAATTGAGAATAGAGAAT 457059
i v v v - i - i v i v
(GAATAGA)n#Si 1 GAATAGAGAATAGAGAATAGA-GAATAGAGAATAGAGAATAGAGAAT 46
Matrix = Unknown
Transitions / transversions = 0.80 (4/5)
Gap_init rate = 0.04 (2 / 45), avg. gap size = 1.00 (2 / 2)
+ 13 19.4 0.0 2.8 Crub_svsplocus 457222 457258 (192742) + A-rich Low_complexity 1 36 (0) 268
ANNOTATION EVIDENCE:
13 19.39 0.00 2.78 Crub_svsplocus 457222 457258 192742 + (AGAAA)n Simple_repeat 1 36 0
13 19.39 0.00 2.78 Crub_svsplocus 457222 457258 (192742) (AGAAA)n#Simple_repeat 1 36 (0) m_b9s252i11
Crub_svsplocu 457222 AGAAAGGAAATGATAAGAGAAGCCAAGAGAAAGAAAA 457258
i v v i vv -
(AGAAA)n#Simp 1 AGAAAAGAAAAGAAAAGAAAAGAAAAGA-AAAGAAAA 36
Matrix = Unknown
Transitions / transversions = 0.50 (2/4)
Gap_init rate = 0.03 (1 / 36), avg. gap size = 1.00 (1 / 1)
+ 12 27.3 3.0 4.5 Crub_svsplocus 457848 457914 (192086) + (TTCT)n Simple_repeat 1 66 (0) 269
ANNOTATION EVIDENCE:
12 27.30 2.99 4.55 Crub_svsplocus 457848 457914 192086 + (TTCT)n Simple_repeat 1 66 0
12 27.30 2.99 4.55 Crub_svsplocus 457848 457914 (192086) (TTCT)n#Simple_repeat 1 66 (0) m_b9s252i12
Crub_svsplocu 457848 TTATTTTTTATGTTTCTTT-ACTCCTGCTCTCCTTTCTTTCTTTTTTTCA 457896
v i - v -vi i v - i i v
(TTCT)n#Simpl 1 TTCTTTCTT-TCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCT 48
Crub_svsplocu 457897 CTATTT-TATCTATTCCTT 457914
i v - v - i
(TTCT)n#Simpl 49 TTCTTTCTTTCT-TTCTTT 66
Matrix = Unknown
Transitions / transversions = 1.00 (7/7)
Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5)
+ 11 20.8 0.0 2.9 Crub_svsplocus 462601 462635 (187365) + (AGCTCC)n Simple_repeat 1 34 (0) 270
ANNOTATION EVIDENCE:
11 20.84 0.00 2.94 Crub_svsplocus 462601 462635 187365 + (AGCTCC)n Simple_repeat 1 34 0
11 20.84 0.00 2.94 Crub_svsplocus 462601 462635 (187365) (AGCTCC)n#Simple_repeat 1 34 (0) m_b9s252i13
Crub_svsplocu 462601 AGCTCCAGGATCAGCACCAAGCTCCAGCTGGAGCT 462635
vvi v - vv
(AGCTCC)n#Sim 1 AGCTCCAGCTCCAGCTCC-AGCTCCAGCTCCAGCT 34
Matrix = Unknown
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1)
+ 43 0.0 0.0 2.3 Crub_svsplocus 463104 463147 (186853) + (TTTC)n Simple_repeat 1 43 (0) 271
ANNOTATION EVIDENCE:
43 0.00 0.00 2.33 Crub_svsplocus 463104 463147 186853 + (TTTC)n Simple_repeat 1 43 0
43 0.00 0.00 2.33 Crub_svsplocus 463104 463147 (186853) (TTTC)n#Simple_repeat 1 43 (0) c_b9s251i0
Crub_svsplocu 463104 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTCTTT 463147
-
(TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC-TTTCTTTCTTT 43
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1)
+ 15 8.1 0.0 3.7 Crub_svsplocus 464413 464440 (185560) + (CCTC)n Simple_repeat 1 27 (0) 272
ANNOTATION EVIDENCE:
15 8.11 0.00 3.70 Crub_svsplocus 464413 464440 185560 + (CCTC)n Simple_repeat 1 27 0
15 8.11 0.00 3.70 Crub_svsplocus 464413 464440 (185560) (CCTC)n#Simple_repeat 1 27 (0) m_b9s252i14
Crub_svsplocu 464413 CCTCCACACCCTTCCTCCCTCCCTCCCT 464440
- v i
(CCTC)n#Simpl 1 CCTCC-CTCCCTCCCTCCCTCCCTCCCT 27
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.04 (1 / 27), avg. gap size = 1.00 (1 / 1)
+ 500 27.4 5.1 3.9 Crub_svsplocus 468203 468536 (181464) C Gypsy158-I_DR LTR/Gypsy (819) 3572 3235 273
ANNOTATION EVIDENCE:
500 27.41 5.09 3.85 Crub_svsplocus 468203 468536 181464 C Gypsy158-I_DR LTR/Gypsy 3235 3572 819
500 27.41 5.09 3.85 Crub_svsplocus 468203 468536 (181464) C Gypsy158-I_DR#LTR/Gypsy (819) 3572 3235 m_b9s001i18
Crub_svsplocu 468203 AGTTCATCCTG----GCCGTTGGAAGCTGGATGAAATGGTGCAGACATGG 468248
i i i ----? ? iv ? v v?i vi
C Gypsy158-I_DR 3572 AGCTCGTTCTGCCAANCCGTTGGAAGNTGGATGGTANGGTGCTGTNGTCA 3523
Crub_svsplocu 468249 CATGATGGAT--CATGTTGGCCTGTAGAAAATCCTGAAACTCAAAA---- 468292
i v ? -- - ?v ? -i vi v? ? vv? ----
C Gypsy158-I_DR 3522 CGTGCTNGATGCCAT-TNCGNCT-CATGAATNCCTNAAACTCTTNACTCG 3475
Crub_svsplocu 468293 -GAAACGAATTGGGGTCCGTTGTTGGAGACAAGGATATCTGGAAGTCCAT 468341
-i - ? ---- i iv v v vv v v v i
C Gypsy158-I_DR 3474 TAAAAC-AANTG----CCATTGTCCGACACTACCATTTCAGGTAATCCAT 3430
Crub_svsplocu 468342 GAAAGGCAAAGTTCCCTCTCAACACCTGGATGGT---CCTAGCAGTAG-- 468386
v?v vi ii iv i?vv v ---? v v? --
C Gypsy158-I_DR 3429 GTNCGCTAAAACTCTGTCTCAGNTACTCGATGGTAACNCGAGANGTAGAA 3380
Crub_svsplocu 468387 -TAGTGGAGGAGACTGGAATGACCTCTAGCCACTTGGAATGGCTGTCCAC 468435
- ? v ----- i? i - ? i v i ivii
C Gypsy158-I_DR 3379 NTANTCGAGG-----GANACG-CNTCCATCCACTTGGAGTGAGCATCCAC 3336
Crub_svsplocu 468436 GAGGAGAAGGAAGAATTGCCTCTGAAAGGGCCCAGTGTAGTTGATATGAA 468485
v i vv i v v vi ii i ? v ? ii ii i
C Gypsy158-I_DR 3335 CAGAATCAGAAACATTTTTCCTTGGAANGGACCNGCATAGTCAATATGGA 3286
Crub_svsplocu 468486 CCCTTGACCAAGGAGCTTGTGTCTCCTCCCACCTGTGTACAGGGGCTTGA 468535
ii vv i v vi v?i? ?vv vv ? ?i
C Gypsy158-I_DR 3285 TTCTTCTCCAGGGCGGCTGTGGNCNCTCCCANGGGTGTAATGGNGCNCGA 3236
Crub_svsplocu 468536 G 468536
C Gypsy158-I_DR 3235 G 3235
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 36.10
Transitions / transversions = 0.91 (42/46)
Gap_init rate = 0.06 (20 / 333), avg. gap size = 1.50 (30 / 20)
+ 249 26.8 4.0 4.0 Crub_svsplocus 468617 468690 (181310) C Gypsy158-I_DR LTR/Gypsy (1365) 2310 2237 273
ANNOTATION EVIDENCE:
249 26.76 4.05 4.05 Crub_svsplocus 468617 468690 181310 C Gypsy-176_DR-I LTR/Gypsy 2237 2310 1365
249 26.76 4.05 4.05 Crub_svsplocus 468617 468690 (181310) C Gypsy-176_DR-I#LTR/Gypsy (1365) 2310 2237 m_b9s001i19
Crub_svsplocu 468617 ATTCTGAGATGTCCCTCATGTAGAGACT---GCAAGACTCTAGTCCTCAA 468663
iv v i --- ---i i ivii i v i
C Gypsy-176_DR- 2310 ATTCCCAGATGGCCCTCATGCA---ACTTGGACAGGATGTCAGCCCTGAG 2264
Crub_svsplocu 468664 TGAGGCTGGGATGATTACCCTGCTACC 468690
vi i ii i
C Gypsy-176_DR- 2263 TGACACTGGGATGACTATTCTGCTGCC 2237
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 35.05
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.05 (4 / 73), avg. gap size = 1.50 (6 / 4)
+ 1856 34.4 2.4 3.8 Crub_svsplocus 468914 470308 (179692) C MamGypsy2-I LTR/Gypsy (1410) 2756 1381 274
ANNOTATION EVIDENCE:
1856 34.42 2.37 3.78 Crub_svsplocus 468914 470308 179692 C MamGypsy2-I LTR/Gypsy 1381 2756 1410
1856 34.42 2.37 3.78 Crub_svsplocus 468914 470308 (179692) C MamGypsy2-I#LTR/Gypsy (1410) 2756 1381 m_b9s001i20
Crub_svsplocu 468914 TCTGCTAACTGTAGAGGTAATCTGCTAAGGCCATCTGCATGGCCCATTTC 468963
vv v i v i iv v v v v vvvvi v
C MamGypsy2-I#L 2756 TCTGGGATCTGCAGTGGCAGACGGCTCAGGGCATCAGCATTCGATATTGC 2707
Crub_svsplocu 468964 TTTGCCTGGTTTGTGAACCAGTGTGTAGTCATATGCAGACAGGAAAATAG 469013
i v v i ii v i i v vvv v v v
C MamGypsy2-I#L 2706 TCTTCCAGGCTTGTAGACAAGCGCGTAGTCATAAGCACTGAGCAAAAGAC 2657
Crub_svsplocu 469014 ACCATCTCAGCATTCTAAGAGATATGATGTGTGGG-GTTTGCTTATTGGT 469062
v v v v v vvi v i i - iv - vv i-v
C MamGypsy2-I#L 2656 TCCAGCGCTGCATACGTGGTGACATAAT-TAAGGGCGTAGGCTTATC-CT 2609
Crub_svsplocu 469063 TTGAACAA---CCCCAACAGTGGCTTATGGTCTGTAAAGACCGTGAAATG 469109
v v i--- - v i i v v i ii i ivv
C MamGypsy2-I#L 2608 TAGAAAAGAGTCCCCAA-AGAGGCTTGTGATCAGTACAAATTGTAAAGGC 2560
Crub_svsplocu 469110 GCGGCCATAAAGAAAGTCATGGAATTTCTTTATGCCAGCCACTATGGCCA 469159
i i i iv ii i v iv v v iv ii v
C MamGypsy2-I#L 2559 ACGGCCGTAGAGGTAGTTGTGGAACTTCTTGACTCCCGCGATAACAGCAA 2510
Crub_svsplocu 469160 AGGCTTCCCTATCTATCTGTGTGTAATTACGTTCAGCAGATGATAGAACA 469209
i ii i v i i i v v i i--- iv
C MamGypsy2-I#L 2509 GGGCTTCTTTGTCAATTTGTGTATAGTTCCGTTCTGTAGATGAC---ATT 2463
Crub_svsplocu 469210 GTCCTAGAATAGTAGGCTATAGGGACTTGTGTCCCATCAGCCTTCAAGTG 469259
i v i i v v vi i vv v v v v ivv
C MamGypsy2-I#L 2462 GTTCTTGAGTAGTAAGCAATTGGTGCCTCAGTGCCATCTGGCATTTTGTG 2413
Crub_svsplocu 469260 GCTCAGCACAGCCCCAATCCCATAAGGGGATGCATCACAGGCTATGCATA 469309
v i iiv i v v i vv - v v -
C MamGypsy2-I#L 2412 GCTAAGCACAGCTCCAGCACCGTAAGGTGAAGCGTCAGTGG-TAAGAA-A 2365
Crub_svsplocu 469310 CAGGCTGTGATTTCTCTTAAAGCATCTAGTTCATTGAAATGCACTAGAAC 469359
---- i v ------------- i v i v -
C MamGypsy2-I#L 2364 CA----GTGGTTTAT-------------GTTCATCGTAATGTACTAGCA- 2333
Crub_svsplocu 469360 CACATTT-GAAGATAGCAAGGCCTTGAC-CTCTGCAAAACTCCTCTCATG 469407
v i i- vi ii vvv -i i v i vi -
C MamGypsy2-I#L 2332 CAGACTCGGAAGTCAATAACTGCTTGACATTCCGGAAAGCGTC-CTCATG 2284
Crub_svsplocu 469408 --GACCTTTGTCCACAGCCATGGACCCTGTTTATCCAAGA-GCAGTGTAA 469454
-- i v--v vv i v viv vi iv - ii v i
C MamGypsy2-I#L 2283 CTGGCG--AGTCCAACGCCACGGAACGCCTTTTCCCAGTAGGCGATGAAG 2236
Crub_svsplocu 469455 TGGCTCAGCCACTGCAGCCTTGTGAGGGAAGAATGA-ATGGTAAAAGTTT 469503
v iv iv v -v vi - i i v
C MamGypsy2-I#L 2235 TGGCTCAGCAATGGTTGCCTTTTG-TGGAAGAAAAACATGGTAGAAATTG 2187
Crub_svsplocu 469504 AACGGTCCGAGAAAAGTCTGGAGTTC--GCTTTTGGACTTGGGACTTAGG 469551
iii i v i i ii i i -- -- vi v v vi v
C MamGypsy2-I#L 2186 AGTAGCCCCAGGAAGGCTTGAAGCTCTTGCTTT--GTTTTTGGAGTAGGC 2139
Crub_svsplocu 469552 GCCTGCTGAATTGCTTTGAGCTTGGATTCAGCAGGATAGATGCCTTCAGC 469601
v vv i vivv v ivv v ii i ii i vv
C MamGypsy2-I#L 2138 GCGTCATGGATTGCACGTACCTTATCTTGAGTGGGGTGAATACCAGCAGC 2089
Crub_svsplocu 469602 ATCAATATGG-AACCCCAGAAATT----CTGTTGAAGTGACCCCAATTTT 469646
ii ii - i iv iv ---- -- ---i i i
C MamGypsy2-I#L 2088 ATTGATGCGGTAGCCTAAGAAGGTGACACTG--GAAGT---TCCGATTTC 2044
Crub_svsplocu 469647 ACATTTGTCTTGCTTTAGCTTCAGTCCCGCTTGGCG----GAAACGCAGC 469692
v i vi i - ivii v --- ii ---- vv i
C MamGypsy2-I#L 2043 ACATTTCTCCTTTTTCA-CTCGGATACC---TGATGTATCGAAACGATGT 1998
Crub_svsplocu 469693 AAGACGGCCCTAAGCCTGTCAGCCAG---ATTTTCGGATGATTCCCCAGT 469739
i vv iv i v v v --- ii v v -- -
C MamGypsy2-I#L 1997 AGGACTTCCTGAAGTCTTTCCGCGAGTTCATCCTCTGTTGAT--CCCA-T 1951
Crub_svsplocu 469740 GATGAGGACATCATCAAAGTAAGGGCAAATGCCTGGAATATTGTGGAACG 469789
v i i v vvvv ii -- iv i v
C MamGypsy2-I#L 1950 GATCAGGACATCATCGAAATATGGTACCACACCTGGA--ATCCTAGAAAG 1903
Crub_svsplocu 469790 TTCA----CTCCATCACACTTTGGAAAATGCCAGGGGCTATGTTAACCCC 469835
-- ---- v vi vi v v iivv ii
C MamGypsy2-I#L 1902 --CAGGGTCTCCATGAAGCACTGGAAAATTCCAGGGGCAACAGAAATTCC 1855
Crub_svsplocu 469836 AAACTGCA--CCCTTATGACTTTAAATGCTCCCCGGTGCATTACAAATAT 469883
i v -- v -- ivi i i i vi v ii v i
C MamGypsy2-I#L 1854 GAACTGAAGGCGCTTA--ACTCGGAATGCCCCTCGATGAGTGATGATTGT 1807
Crub_svsplocu 469884 TTGAGCCTCAGCCGTTGCCTCATCAACTGAT-AATTGTTGATAGGCCTGA 469932
i v v v v v i i - - ii i i i
C MamGypsy2-I#L 1806 TTGGGCGTCTGCAGTAGCATCACCGAC-GATCAGCTGTTGATAAGCTTGG 1758
Crub_svsplocu 469933 GCCTAGTCAAGTTTGGCAAAAACGTGGCCTCCCTTGAGGGAAGCCAGAAT 469982
vvi v i v vvi i vvii iiv v i v
C MamGypsy2-I#L 1757 GCAAGGTCAAGTTTTGCAAAGACCTTTTCCCCAGCAAGAACAGCAAGGAG 1708
Crub_svsplocu 469983 GTAGCTCACCATGGGCACCGGGTACGAGTGCTGTTGCAAGGCTTTGTTAA 470032
v iii v iiii i i i i i vv iv i i v
C MamGypsy2-I#L 1707 TTGATTGACTGCAGGCACTGGATATGGGTGCTGCTTAAGTGCCTTATTCA 1658
Crub_svsplocu 470033 GTTTACACTTATAGTCCGCACAAATTCGGACTTCTCCATTGGCCTTCAGT 470082
vvv i i iv v vv i iv i v i
C MamGypsy2-I#L 1657 CAGTGCACTTGTAGTCTCCACAAAGTCTCACCTTACCATTAGGCTTTAGT 1608
Crub_svsplocu 470083 GGCATTACTATGGGGGTTTCCCGTGGACTA-ATGTCCACAGGTTCTAAAA 470131
iv ivii v v vi vv iiv iv -i -v v v iii
C MamGypsy2-I#L 1607 ACCGGCGCAATTGGTATAGCCCACCGGGTATGTGT-AACTGGTTCGAGGG 1559
Crub_svsplocu 470132 TGCCCTGCTGGAGCAGCTTGTCCAGCTCTGCATTGATTCTATTCTTCAAA 470181
ii i i v vi v vv v v v ii? i v i i i
C MamGypsy2-I#L 1558 CACCTTGTTTGATTAGATGCTCAAGCTCTTCTTCANTTTTTTTCCTTAGA 1509
Crub_svsplocu 470182 GTGAAGGGCACCTCTCTAGGCTTAATCCTAATGGGTGCAATGGCTGGGTC 470231
ii i i v i vi v vviv v i
C MamGypsy2-I#L 1508 GCAAAAGGTACATTTCTAGCTTTCAAGTGAATTGGTGCAATGGCTGGATC 1459
Crub_svsplocu 470232 TAAATGTAATGAAATGGGAGGCC-CTTGTACGAGCCAAGCTCTGAGCTGA 470280
i i v v iv vvv - v vv v i ivv vv
C MamGypsy2-I#L 1458 CAGATGGAATGACACTGGCTCCCTCTTGTAAGCTCCCAGTTCCTCGGAGA 1409
Crub_svsplocu 470281 ACACATCAGCAAACTCCTTGCAAACTTC 470308
i v ii v iiiv vv
C MamGypsy2-I#L 1408 ATACCTTGGGAAATCTGTTGACAACTTC 1381
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 44.11
Transitions / transversions = 0.97 (228/234)
Gap_init rate = 0.05 (69 / 1394), avg. gap size = 1.23 (85 / 69)
+ 993 32.7 3.2 3.5 Crub_svsplocus 471964 472530 (177470) + MamGypsy2-I LTR/Gypsy 1498 2062 (2104) 275
ANNOTATION EVIDENCE:
993 32.73 3.17 3.54 Crub_svsplocus 471964 472530 177470 + MamGypsy2-I LTR/Gypsy 1498 2062 2104
993 32.73 3.17 3.54 Crub_svsplocus 471964 472530 (177470) MamGypsy2-I#LTR/Gypsy 1498 2062 (2104) m_b9s001i21
Crub_svsplocu 471964 GTGCCTTTTGTGCTTAAGCAAAAA-TTAATGCTGAGCTGGACAAACTGCT 472012
i iv v i v -? i v vv v vv v iv
MamGypsy2-I#L 1498 GTACCTTTTGCTCTAAGGAAAAAAANTGAAGAAGAGCTTGAGCATCTAAT 1547
Crub_svsplocu 472013 TCAGCAAGGTATTTTGGAACC---TATGGATAACAGTCCATGGAAAACAC 472059
iv i iiii v --- iiv v --- vi ivv i
MamGypsy2-I#L 1548 CAAACAAGGTGCCCTCGAACCAGTTACACATACC---CGGTGGGCTATAC 1594
Crub_svsplocu 472060 CTATAGTTATGCC---ACTGAAGGCCAACGGGAAAGTCCGCATTTGTGCT 472106
--- i ii --- i v i i v i vv vv vv
MamGypsy2-I#L 1595 C---AATTGCGCCGGTACTAAAGCCTAATGGTAAGGTGAGACTTTGTGGA 1641
Crub_svsplocu 472107 GACTATAAATGCATGCTAAACAAAGCGTTACAACAACATTCTTATCCGGT 472156
i i ivv i i i ii vv i i ii v i
MamGypsy2-I#L 1642 GACTACAAGTGCACTGTGAATAAGGCACTTAAGCAGCACCCATATCCAGT 1691
Crub_svsplocu 472157 CCCTGTGGTGAGCCA---CATT-TTGGTCTTGCTTAAAGGAGGCCGAGTT 472202
v ii v ii --- v -i v ---- i ivvii i
MamGypsy2-I#L 1692 GCCTGCAGTCAATCAACTCCTTGCTGTTCTTGCT----GGGGAAAAGGTC 1737
Crub_svsplocu 472203 TTTGCCAAACTTGACTTAGCTCAGGCCTATCAAAAGCTATTGGTTGATGA 472252
v i v i i i v iv v i i
MamGypsy2-I#L 1738 TTTGCAAAACTTGACCTTGCCCAAGCTTATCAACAGCTGATCGTCGGTGA 1787
Crub_svsplocu 472253 GGCAATGGCAGAGGCCCAGACAATCGTAACACACCGGGGAGCTTTCAAAG 472302
v v iv v i i v v i i i v vi
MamGypsy2-I#L 1788 TGCTACTGCAGACGCCCAAACAATCATCACTCATCGAGGGGCATTCCGAG 1837
Crub_svsplocu 472303 TCAGAAGACTGCAGTTTGGAGTTAACGTAGCCCTTGGCATTTTCCAAAAC 472352
i iiv v v i i vvi v i v ivi
MamGypsy2-I#L 1838 TTAAGCGCCTTCAGTTCGGAATTTCTGTTGCCCCTGGAATTTTCCAGTGC 1887
Crub_svsplocu 472353 ATTATGGAGCGAACACTG---TGTAACATTCTGGGAGTTTGCCCATATTT 472399
v i --- v --- v iv ii v vvvv
MamGypsy2-I#L 1888 TTCATGGAG---ACCCTGCTTTCTAGGATTCCAGGTGTGGTACCATATTT 1934
Crub_svsplocu 472400 CGATGATGTCCTCATTGCAGGGGAATCACCTGAAAAT---TTGGCTGAGA 472446
v -- v - v v ii ---i v v i
MamGypsy2-I#L 1935 CGATGATGTCCTGAT--CATGGG-ATCAACAGAGGATGAACTCGCGGAAA 1981
Crub_svsplocu 472447 GGCTTCGGTCTGTTTTTCTGCGTTTCCATGAAGTGGG-GTTAAAGTTTAA 472495
i i vvv ii v vv v iv vii -i ivi - v
MamGypsy2-I#L 1982 GACTTCAGGAAGTCCTACATCGTTTCGATACATCAGGTATCCGAG-TGAA 2030
Crub_svsplocu 472496 GCAAGACAAATGCAAAATTGGAGTCACTTCCACTG 472530
iv i v ii i --- v
MamGypsy2-I#L 2031 AAAGGAGAAATGTGAAATCGGA---ACTTCCAGTG 2062
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 41.96
Transitions / transversions = 1.06 (92/87)
Gap_init rate = 0.05 (28 / 566), avg. gap size = 1.36 (38 / 28)
+ 241 11.9 2.3 4.7 Crub_svsplocus 474813 474856 (175144) C DNA-8-14_DR DNA/hAT-Charlie (628) 945 903 276
ANNOTATION EVIDENCE:
241 11.91 2.27 4.65 Crub_svsplocus 474813 474856 175144 C DNA-8-14_DR DNA/hAT-Charlie 903 945 628
241 11.91 2.27 4.65 Crub_svsplocus 474813 474856 (175144) C DNA-8-14_DR#DNA/hAT-Charlie (628) 945 903 m_b9s001i22
Crub_svsplocu 474813 TAGAACAGTGGTTCTCAACCTTTTTAT-ACCGGTGACCCCGGTCA 474856
ii i - vv --
C DNA-8-14_DR#D 945 TAGGGCAGTGGTCCTCAACCTTTTTATCACCGCGGA--CCGGTCA 903
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 13.07
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3)
+ 483 10.1 0.0 0.0 Crub_svsplocus 474919 474987 (175013) C URR1B DNA/hAT-Charlie (156) 69 1 277
ANNOTATION EVIDENCE:
483 10.14 0.00 0.00 Crub_svsplocus 474919 474987 175013 C URR1B DNA/hAT-Charlie 1 69 156
483 10.14 0.00 0.00 Crub_svsplocus 474919 474987 (175013) C URR1B#DNA/hAT-Charlie (156) 69 1 m_b9s001i23
Crub_svsplocu 474919 TTTGGCAACCCCCGTGAAATGGTCATTCGACCCCAAATGGGGTCGCGACC 474968
v i i v i v v
C URR1B#DNA/hAT 69 TTAGGCGACCCCTGTGAAAGGGTCGTTCGACCCCCAAAGGGGTCGCGACC 20
Crub_svsplocu 474969 CACAGGTTGAGAACCGCTG 474987
C URR1B#DNA/hAT 19 CACAGGTTGAGAACCGCTG 1
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 7.95
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
+ 296 14.8 1.1 14.3 Crub_svsplocus 474988 475005 (174995) + CYRA11_Mm Satellite/Y-chromosome 327 403 (214) 278
ANNOTATION EVIDENCE:
296 14.75 1.15 14.29 Crub_svsplocus 474919 475005 174995 + CYRA11_Mm Satellite/Y-chromosome 327 403 214
296 14.75 1.15 14.29 Crub_svsplocus 474919 475005 (174995) CYRA11_Mm#Satellite/Y-chromosome 327 403 (214) m_b9s001i24
Crub_svsplocu 474919 TTTGGCAACCCCCGTGAAA-TGGTCATTCGACCCCAAATGGGGTCGCGAC 474967
v i - v -------- -- v
CYRA11_Mm#Sat 327 TTAGGCGACCCCCGTGAAANTTGTCA--------CAA--GGGCTCGCGAC 366
Crub_svsplocu 474968 CCACAGGTTGAGAACCGCTGTTTTAGAAACATACAAAG 475005
i v vii v - v?
CYRA11_Mm#Sat 367 CCACAGGTTGAGAACCACAGTGCCAGCAAC-TAGNAAG 403
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 14.84
Transitions / transversions = 0.57 (4/7)
Gap_init rate = 0.14 (12 / 86), avg. gap size = 1.00 (12 / 12)
+ 18 14.1 0.0 4.9 Crub_svsplocus 475761 475803 (174197) + A-rich Low_complexity 1 41 (0) 279
ANNOTATION EVIDENCE:
18 14.11 0.00 4.88 Crub_svsplocus 475761 475803 174197 + (AGAAA)n Simple_repeat 1 41 0
18 14.11 0.00 4.88 Crub_svsplocus 475761 475803 (174197) (AGAAA)n#Simple_repeat 1 41 (0) m_b9s252i16
Crub_svsplocu 475761 AGAAAGGAAACGAAAAGAGAAGCAGAGAGAAAGAAAAAGAAAA 475803
i v i v i - -
(AGAAA)n#Simp 1 AGAAAAGAAAAGAAAAGAAAAGAAAAGA-AAAG-AAAAGAAAA 41
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2)
+ 14 24.9 3.0 4.5 Crub_svsplocus 476388 476454 (173546) + (TTCT)n Simple_repeat 1 66 (0) 280
ANNOTATION EVIDENCE:
14 24.91 2.99 4.55 Crub_svsplocus 476388 476454 173546 + (TTCT)n Simple_repeat 1 66 0
14 24.91 2.99 4.55 Crub_svsplocus 476388 476454 (173546) (TTCT)n#Simple_repeat 1 66 (0) m_b9s252i17
Crub_svsplocu 476388 TTATTTTTTATGTTTCTTT-GCTCTTGCTCTCCTTTCTTTCTTTTTTTCA 476436
v i - v -vi v - i i v
(TTCT)n#Simpl 1 TTCTTTCTT-TCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCT 48
Crub_svsplocu 476437 CTATTT-TATCTATTCCTT 476454
i v - v - i
(TTCT)n#Simpl 49 TTCTTTCTTTCT-TTCTTT 66
Matrix = Unknown
Transitions / transversions = 0.86 (6/7)
Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5)
+ 367 22.5 5.6 0.0 Crub_svsplocus 477426 477514 (172486) + Plat_L3 LINE/CR1 3467 3560 (13) 281
ANNOTATION EVIDENCE:
367 22.47 5.62 0.00 Crub_svsplocus 477426 477514 172486 + Plat_L3 LINE/CR1 3467 3560 13
367 22.47 5.62 0.00 Crub_svsplocus 477426 477514 (172486) Plat_L3#LINE/CR1 3467 3560 (13) m_b9s001i25
Crub_svsplocu 477426 CAGCCATTTGTCTGAAACGGTATA--CGGTTTCCTTCCTGA--GCAGAGG 477471
? i ivii i v -- iv iv v i-- i
Plat_L3#LINE/ 3467 CANCCATCTGTCCTGGATGGTTTAGTCATTCACCTGCCTGGAGGCAGGGG 3516
Crub_svsplocu 477472 GTTGGACTAGATGACCTC-CAAGGTCCCTTCCAACTTTATTATT 477514
i i - i i i ?v
Plat_L3#LINE/ 3517 GCTGGACCAGATGACCTCTCGAGGTCCCTTCCAGCTCTANGATT 3560
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 26.82
Transitions / transversions = 2.33 (14/6)
Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.67 (5 / 3)
+ 4434 32.6 3.2 3.3 Crub_svsplocus 481431 484578 (165422) + RTE1_ChrAsi LINE/RTE-BovB 89 3233 (3) 282
ANNOTATION EVIDENCE:
4434 32.63 3.24 3.34 Crub_svsplocus 481431 484578 165422 + RTE1_ChrAsi LINE/RTE-BovB 89 3233 3
4434 32.63 3.24 3.34 Crub_svsplocus 481431 484578 (165422) RTE1_ChrAsi#LINE/RTE-BovB 89 3233 (3) m_b9s001i26
Crub_svsplocu 481431 GCAGGGCCACCCAAGACGGACAGGTTATAGCAGAGAGTTCTGACAAAATG 481480
i v ii vi vv vv i v i ---
RTE1_ChrAsi#L 89 GCAGGGTCACCCATGGTGGACAGGTTTCAGATGAGCTTCCAGACGAA--- 135
Crub_svsplocu 481481 TGATCCACT-GGAGAAGGAAATGGCAAACCACTCCAGTATCTCT-GCCA- 481527
- ivv - ii i i i i i i i v v v i - i -
RTE1_ChrAsi#L 136 -GACAGACTAGGAAGAAGGAGTGACGAACTACTTCCGAATATTTAGTCAC 184
Crub_svsplocu 481528 TGAAAACCCCATGGACAGTACTAAAAGGAAAAA-----AGATATGACACT 481572
ii i i i -----ii v ----- iiii i
RTE1_ChrAsi#L 185 TGAAAACCTTATGAATAGCA-----GAGAAACACTGTCAGATATAGTGCC 229
Crub_svsplocu 481573 GGAAGATGAGCCCCTCAGGTCGGAAGGTGTCCAATATGCTACTGGGGAAG 481622
i i iiii v v
RTE1_ChrAsi#L 230 GGAAAATGAGCCCCTCAGGTTGGAAGGCACTCAAAATGCGACTGGGGAAG 279
Crub_svsplocu 481623 AGCAGAGGGCTAGTACTAGTAGCGCCAGAAAGAATGAAGCGACTGGGCCA 481672
---v v vv vvv v iiiivvivi v v ivi
RTE1_ChrAsi#L 280 AGC---TGCCTCCTCAAAGTAGAGTTGACCGTGATGACGCGAATGGAGTA 326
Crub_svsplocu 481673 AAGCCGAAAGGACGCTCA---GCTG--TGGATATATCTGGTGGTGAAAGG 481717
vivi vi --- --v ii i v vivii ii
RTE1_ChrAsi#L 327 AAGCCCGCGGGACCTTCATTTGCTGATGGGGCACAACTCAAAATGAAGAG 376
Crub_svsplocu 481718 AAAGTCCGATGCTGAAAAGATTTTTTCTCCATAGGAACCTGGAATGTAAG 481767
--- i-- v v iiv vv?v v v v
RTE1_ChrAsi#L 377 AAA---CA--GCTGTAAACATCCATTGANAATCGGAACATGGAATGTACG 421
Crub_svsplocu 481768 ATCCATGAATCAAGGCAAGCTAGACGTAGTCAAAAAAGAGATGACAAGAC 481817
vvi vi v ii i v v v i iv v vv
RTE1_ChrAsi#L 422 AAGTATGAATCTGGGAAAATTGGAAGTTGTCAAAAATGAAATGGAACGCA 471
Crub_svsplocu 481818 TGAACATCGACATCTTAGGAATCAGCGAACTAAAATGGACAGGAATGGGT 481867
i i v i i i i v v v i
RTE1_ChrAsi#L 472 TAAACATCGATATCTTAGGCATTAGTGAGCTGAAATGGACTGGTATTGGC 521
Crub_svsplocu 481868 GAATTTAACTCAGATGACCATCAAGTATACTATTGTGGGCAAGA---ATC 481914
v v i v v i ivvi v vvi v v --- -
RTE1_ChrAsi#L 522 CATTTTGAATCTGACGACCACATGGTTTACTATGCCGGGAATGACAAAT- 570
Crub_svsplocu 481915 CCTCAGAAGAAATGGAGTAGCCTTCATAGTCAATAAAAGAATAGGAAAAG 481964
-- v ii i v v v v v i iv vvv i v
RTE1_ChrAsi#L 571 --TGAAGAGGAATGGTGTTGCATTCATCGTCAAAAAGAACATATCCAGAT 618
Crub_svsplocu 481965 CAATACTGGGATACAATCCCCAAAATGACAGAATGATCTCAGTTCGAATC 482014
i vv i i iv ivvvvi i i i v vi v vv v
RTE1_ChrAsi#L 619 CAGTCATGAGGTACAACGCTGTCTGTGATAGGATAATATCCATGCGCCTA 668
Crub_svsplocu 482015 CAAGGCAAACCATTCAATATCACAGTAGTCCAAATCTATGCCCCAACCAC 482064
i v i? v i i vi vi i i i v
RTE1_ChrAsi#L 669 CAGGGAAGNCCAGTTAATACCACTATTATTCAAATTTACGCACCAACCAC 718
Crub_svsplocu 482065 TGGTGCTGAAGAGGATGAAATTGACCAGTTCTATGAAGCCCTACAGCACC 482114
iiv iiiv v vv i iv vii v -- i
RTE1_ChrAsi#L 719 TAAAGCCAGTGAGGATGAAATAGAAGAATTCTACCAACTTCTTCA--ATC 766
Crub_svsplocu 482115 TTATAGAATT-----AACAC-CAAAAAATGATGTTCTTATCATCATGGGG 482158
v --- ----- i- vv - vi v i iv v
RTE1_ChrAsi#L 767 TGA---AATTGATCAAACATGCAATCAA-GATGTATTGATCATTACTGGT 812
Crub_svsplocu 482159 GATTGGAATGCTAAGGTAGGAAGCCAAAAG--ATAACCGGAATAACAGGC 482206
v v i v i -- vi i -- i iiv v
RTE1_ChrAsi#L 813 GATTGGAATGCAAAGGTTGGGAGCAAAGAGGAAGGATC--AGTAGTTGGA 860
Crub_svsplocu 482207 AAGTTTGGCCTTGGAG-TACAAAATGAAGCAGGGCACAGGCTAATAGAAT 482255
i v v - -i v v iv ?v vv i
RTE1_ChrAsi#L 861 AAATATGGCCTTGGTGATA-GAAATGATGCTGGAGANCGCATGATAGAAT 909
Crub_svsplocu 482256 TTTGTCAAGAGAATACAATGGTCATAACAAACACTCTTTTCCAACAACCC 482305
i iv ivv ivvv v vv i ii i ivi i vi
RTE1_ChrAsi#L 910 TCTGCAAAACCAATGATTTGTTCATTTCAAATACCTTCTTTAGACAGCAT 959
Crub_svsplocu 482306 AAGAGACGGCTCTACACATGGACATCACCAGATGGTCAACATAGAAATCA 482355
i v v vvv i
RTE1_ChrAsi#L 960 AAGAGACGACTATACACATGGACCTCACCAGATGGAATACACAGAAATCA 1009
Crub_svsplocu 482356 GATTGACTATGTGCTCTGCAGCCAAAGA---TGGAGAAGCTGTATACAGT 482402
i ii --- i vv i --- i vi ivi
RTE1_ChrAsi#L 1010 AATTGACTACAT---CTGCGGAAAGAGACGATGGAAAAGCTCCATATCAT 1056
Crub_svsplocu 482403 CAGTAAAAACAAGACCAGGAGCTGACTGTGGCTCAGATCATGAGCTTCTC 482452
v i i v vv i v ii v
RTE1_ChrAsi#L 1057 CAGTCAAAACAAGGCCAGGGGCAGACTGTGGAACAGACCATCAATTGCTC 1106
Crub_svsplocu 482453 GT-TGCAAAATTTAGGCTTAAATTGAAAAAAGTAGGGAAAAG--CACTAG 482499
i - - i ii v ii i i iiii v -- v
RTE1_ChrAsi#L 1107 ATATGCAAA-TTCAAACTGAAGCTGAAGAAAATGAAAACAAGTCCACGAG 1155
Crub_svsplocu 482500 -GCCACTCAGGTATGAACTAAATCATATTCCGGATGAATATACAGTAGAG 482548
- --- ii v vi vi i ivv v v vvv v
RTE1_ChrAsi#L 1156 AGCCA---AAATATGACCTTGAATATATCCCACCTGAATTTAGAGATCAT 1202
Crub_svsplocu 482549 GTGACAAATAGATTTAAGGAACTGGAT-CTGATAGACAGAGTGCCTGAAG 482597
v vi i i viv i ii i- i - v ivi v
RTE1_ChrAsi#L 1203 CTGAAGAACAGATTTGATACATTAAACACTAA-AGACCGAAGACCAGAAG 1251
Crub_svsplocu 482598 AACTATGGATGGAAGTTCGCAACATTGTACAAGAGGTA-GCAACTAAAAC 482646
ii i ivv vi iviv ii v i v - -- ii
RTE1_ChrAsi#L 1252 AGTTGTGGGATGACATCAAGAACATCATACATGAAGAAAGCAA--AAAGT 1299
Crub_svsplocu 482647 CATCCCAAAGA-AAAAGAAATGCAAGAAAGCAAAATGGCTGTCTGAGGAA 482695
ivvi - i i i v v i iiv v v i i
RTE1_ChrAsi#L 1300 CATTAAGAAGACAAGAAAGAAGGAAAAGGTCAAAATGGATGTCAGAAGAG 1349
Crub_svsplocu 482696 GCTTTGCAAATAGCTGAGGAAAGAAGGGAAGTGAAAGGCAAA--GGAGAA 482743
i vi v v v vvvv iv v i v iv - -- i
RTE1_ChrAsi#L 1350 ACACTGAAACTTGCTCTCCAGCGTAGAGATGCTAAAG-CAAATGGAAGAA 1398
Crub_svsplocu 482744 AGAGAAAGATACACCCAATTGAATGCAGAATTCCAGAGAGTAGCTAGAAG 482793
viiii i vv- ii iiv i i i ivi v ii
RTE1_ChrAsi#L 1399 ATGAGGAGGTACAAG-AGCTGAACAGAAAATTTCAAAGGTCAGCTCGAGA 1447
Crub_svsplocu 482794 AGATAAGAATGCCT--TCTTA-AATGAACAGTGCAAAGAAATAGA---AG 482837
i i--- v-- v - i vv vv i ---
RTE1_ChrAsi#L 1448 AGACAAA---GCCAAATATTACAACGAAATGTGCAAAGATCTGGAGTCAG 1494
Crub_svsplocu 482838 AAAACAACAGAATAGGGAGGAC-----CAGAGATCTCTTCAAGAAAATTG 482882
-- i - i i ----- -v i - ----i
RTE1_ChrAsi#L 1495 AAAAC--CAAAA-AGGAAGAACACGCTCAG-CATTTCT-CAAG----CTG 1535
Crub_svsplocu 482883 GAGATA-TGAAGGGAACATTTCATGCAAAGATGGGCATGAT-AAAGGACC 482930
i iv - ii v - v vvv ivvv i v -i ii
RTE1_ChrAsi#L 1536 GGGGAACTGAAGAAAAAATT-CAAGCCTCGACTTTCGTTATTGAAGGATT 1584
Crub_svsplocu 482931 AAAATGGCAGAGACCTAACAGAGGCAGAAGAGATTAAGAAGAGATGGCAA 482980
vvvvv i vvvi i vv v iiv i i ii v i
RTE1_ChrAsi#L 1585 CTCTGGGCAAATTATTGAATGATGCAGAAAGCATCAAAAGAAGATGGAAG 1634
Crub_svsplocu 482981 AACTACACAGAAGAACTATACAAGAATGA---GCTTAACATCCCAGATAA 483027
i v ivv i v i v --- v i ii i -----
RTE1_ChrAsi#L 1635 GAATACACAGAGTCACTGTACCAAAAGGAAATGGTTGATGTTC-----AA 1679
Crub_svsplocu 483028 CCA---CAATGAGATAGTCAT-TGACCTCGAACCAGACATCCTAGAATGT 483073
i--- - i - - i vv i ivv v ii iviv
RTE1_ChrAsi#L 1680 CCGTTTCAA-GAGGTAG-CATATGATCAAGAGCCAATGATACTGAAGGAG 1727
Crub_svsplocu 483074 GAAGTAAAATGGGCCTTAAAAAATCTGAGCAACAACAAAGCTAGTGGAGG 483123
vv v v v i ii vi ivv v i vvvv iv
RTE1_ChrAsi#L 1728 GAAGTCCAAGGTGCATTGAAGGAATTGGCAAAGAACAAGGCACCAGGAAT 1777
Crub_svsplocu 483124 TGACAGTATTCCAGCTGAGCTATTCAAAATCTTAAAAGACAATG------ 483167
ii v -------- ivv -i vv v i ------
RTE1_ChrAsi#L 1778 TGATGGAAT--------AAAAATT-GAAATCTTTCAAGAAAGTGAGGCGG 1818
Crub_svsplocu 483168 CAGTAAAAGTGCTACACTCA-ATTTGCCAGCAAATTTAGAAAAC--TTAA 483214
v?ii i ii - -v ? iv i i --i v
RTE1_ChrAsi#L 1819 CACNGGAGGCACT-CACTCATCTNTGCCAAGAAATTTGGAAGACAACTAT 1867
Crub_svsplocu 483215 CAGTGGCCACAGGATTGGAAAAGATCAGTTTACATTCCAATTCCAAAGAA 483264
-- ivvv i v v vii v v i
RTE1_ChrAsi#L 1868 C--TGGCCGACTGATTGGAAGAGATCCGTATTTGTGCCCATTCCAAAGAG 1915
Crub_svsplocu 483265 AGGCAATGCCAA-AGAATGTTCAAACTATCGCACCATTGCACTCATTTCA 483313
ii i- -i ivv ii v v ?v vi v v v
RTE1_ChrAsi#L 1916 AGGTGAC-CCAACGGAATGCGGAAATCATCGGACAATNTCTTTGATATCC 1964
Crub_svsplocu 483314 CATGCTAGTAAAGTTATGCTTAAAATCCTACAAGCTAGACTCCA-GCAGT 483362
v v i v ii vv iivvv i v - -
RTE1_ChrAsi#L 1965 CATGCGAGTAAAGTTTTACTAAAGGTAATACAGAAACGGCTGCAAGCA-T 2013
Crub_svsplocu 483363 ATGTGGATCGAGAACTACCAGAAGTACAGGCAGGATTTCGAAGAGGCAGA 483412
ii v iv v i v i v iv v v
RTE1_ChrAsi#L 2014 ACATTGACAGAGAACTTCCAGAGGTTCAAGCCGGATTCAGAAGAGGCCGT 2063
Crub_svsplocu 483413 GGAACTAGAGATCAAATTGCCAACATACGCTGGATCATGGA-GAAAGCTA 483461
v i vvv ii ii v v v v- -
RTE1_ChrAsi#L 2064 GGAACGAGGGATATCATTGCTGATGTCCGATGGATCTTGGCTGAAAGC-A 2112
Crub_svsplocu 483462 GGGAGTTCCAGAAAAACATCTACTTCTGCTTCATTGACTATGCAAAAGCC 483511
i i v i ii i i v i i i i
RTE1_ChrAsi#L 2113 GAGAATACCAGAAAGATGTTTACCTGTGCTTTATTGACTACGCAAAGGCT 2162
Crub_svsplocu 483512 TTTGATTGTGTGGATCACAACAAATTGTGG-CAAGTTCTTAAAGAGATGG 483560
i ii ii i - vv ivii --- iv
RTE1_ChrAsi#L 2163 TTCGATTGTGTGGATCATGACAAGCTATGGACAACATTGCGAAG---TAT 2209
Crub_svsplocu 483561 GAGTA--CCAGACCATCTCATTTGT-CTCTTGAGAAACCTATATGCGGGT 483607
-- i v - i v - v i i i iii ii
RTE1_ChrAsi#L 2210 GAGTATTCCGGAACA-CTTAATTGTGCTCATGAGGAATCTGTACATGGAC 2258
Crub_svsplocu 483608 CAAGAAGCAACAGTGAGAACTGGACACGGAACCACTGATTGGTTCAAAAT 483657
i iiv vv v i i i v v i
RTE1_ChrAsi#L 2259 CAAGAGGCAGTTGTTCGAACAGAACATGGGAACACTGAATGGTTTAAAAT 2308
Crub_svsplocu 483658 TGGAAAAGGAGTCCGGCAAGGCTGTATACTGTCGCCCTGCCTATTTAACT 483707
iii v v i i i v v i v i i i i
RTE1_ChrAsi#L 2309 TAAGAAAGGTGTGCGACAGGGTTGTATTCTTTCACCATACTTATTCAACC 2358
Crub_svsplocu 483708 TATATGCAGAGCACATCATGAGAAAGGCAGGGCTAGATGAATCAAAAGTT 483757
i v v v vv i i v i v vv vv
RTE1_ChrAsi#L 2359 TGTATGCTGAGCAAATAATCCGAGAAGCTGGGTTATATGAAGAAAAACGT 2408
Crub_svsplocu 483758 GGAATTAAGATTGCCGGGAGAAATATCAAC-ACCTAAGATATGCAGATGA 483806
v i i vv i vvi i - iv
RTE1_ChrAsi#L 2409 GGCATCAGGATTGGAGGAAGACTCATTAACAACCTGCGATATGCAGATGA 2458
Crub_svsplocu 483807 TACCACTCTAATGGCAGAAAGTGAAGAGGAACTAAAGAGCCTCTTGATGC 483856
v ii iv v v vi iviii vi v
RTE1_ChrAsi#L 2459 TACAACCTTGCTTGCTGAAAGTGAAGAGGACTTAAAATATTTACTGATGA 2508
Crub_svsplocu 483857 GGGTAAAGAAGGAGAG--TGCAAAAGTTGGCTTGAAACTCAACATTAAGA 483904
i i v ii v v -- v iiv -- v v v ii v
RTE1_ChrAsi#L 2509 AGATCAAAGAGCACAGCCTTCGGTA--TGGATTGCATCTCAATGTAAAGA 2556
Crub_svsplocu 483905 AAACCAAAATCATGGCATCCGGCCCTCT---CA--ATTCCTGGCAAATAG 483949
v v vi vv i v vv --- -- i iv -----
RTE1_ChrAsi#L 2557 AAACAAAAATCCTCACCACTGGACCAATAAACAACATTCTTATCA----- 2601
Crub_svsplocu 483950 ATGGGGAAGAAATGGAGGTAGTGACAGATTTTATTTTTCTGGGCTCAAAG 483999
i i i i v i v v vi i i i v v vv
RTE1_ChrAsi#L 2602 ACGGAGAAAAGATTGAAGTTGTCAAGGACTTCATTCTTCTTGGATCAACT 2651
Crub_svsplocu 484000 ATCACCTCAGATGGGGACTGCAGCCAAGAAATTAAAAGACGC-TTGCTCC 484048
v v vv i iii v i i v i- -vi
RTE1_ChrAsi#L 2652 ATCAACACTCACGGAAGCAGCAGTCAAGAAATCAAACGACGTATTGC-AT 2700
Crub_svsplocu 484049 TGGGGAGGAAAGCTATGGCAAATCTAGAC------AGCATTCTAAAAAGC 484092
i --- v v iiv v --- ------ ivi vi i i
RTE1_ChrAsi#L 2701 TAG---GCAAATCTGCTGCACA---AGACCTTTTTAAAGTGTTGAAGAGC 2744
Crub_svsplocu 484093 AGAGACATCACCCTGCCAACAAAAATGCGTATAGTCCAGGCCATGGTTTT 484142
i ii v i vvi v ii iv iii i v
RTE1_ChrAsi#L 2745 AAAGATGTCAGCTTGAGGACTAAGGTGCGCCTGACCCAAGCCATGGTATT 2794
Crub_svsplocu 484143 CCCAGTTGCAATGTATGGCTGTGAAAGTTGGACCATAAGAAAGGCTGAGC 484192
ii i vi vvii vv i i vi i iv vv v
RTE1_ChrAsi#L 2795 TTCAATAACCTCATATGCATGCGAAAGCTGGACAGTGAATAAGGAAGACC 2844
Crub_svsplocu 484193 GCAAAAGAATTGAGGCCTTTGAACTATGGTGCTGGAGAAGACTCCTGCGA 484242
i i v ? ii i i v vi vi
RTE1_ChrAsi#L 2845 GTAGAAGAATTGATGCNTTTGAGTTATGGTGTTGGAGGAGAATATTGAAA 2894
Crub_svsplocu 484243 GTCCCTTGGACTGCAAGGCGTTCAAACCGGTCAGTCCTAGAAGAGATCAA 484292
v v i v iiv vv v v i v vi i ii vv
RTE1_ChrAsi#L 2895 GTGCCATGGGCTGCCAAAAGAACCAACAGATCTGTGTTGGAAGAAGTGCA 2944
Crub_svsplocu 484293 CCCCGACTGCTCTTTAGAAGGCCA-GAT-CCTGAAGTT-GAAACTCAAGT 484339
v v v i - i - -v ii v - vvv --
RTE1_ChrAsi#L 2945 GCCAGAGTGCTCCTT-GGAGGCCAGGATGGCCAAACTTCGTCTCTCA--T 2991
Crub_svsplocu 484340 ACTTTGGCCACCTAATGAGAAGGAAGGATTCACTGGAGAAGAGCCTAATG 484389
i v iv vi v i i vv v i iiiv v
RTE1_ChrAsi#L 2992 ACTTCGGACATATTGTCAGGAGGGACCAGTCGCTGGAGAAGGATATCATG 3041
Crub_svsplocu 484390 CTGGGAAAGATTGAGGGCAATAGAAGAAGGGGACGACAGAGAATGAGATG 484439
i v v i v iv v i i v vvvv ii
RTE1_ChrAsi#L 3042 TTTGGTAAGGTGGAGGGTCAGAGAAAAAGAGGAAGACCCCCAGCGAGATG 3091
Crub_svsplocu 484440 GCTGGATGGAGTCACTGAAGCAGTAGGTGTGAATTTAAATG-GACTCCA- 484487
v v iiii ------i i vvvi iii i ii - i vv -
RTE1_ChrAsi#L 3092 GATTGGCAAAGT------GGCAGCATCGATGGGCTCAAGCGTGGCAACAG 3135
Crub_svsplocu 484488 ----GAAGATGGTAGAGGA-CAGGAAGACCTGGAGGAACGTTGTCCATGG 484532
---- i v ivv - i v -iv vvv vvvi i v i
RTE1_ChrAsi#L 3136 TNGTGAGGTTGGCCCAGGATCGGGCAG-TGTTTCGTTCTGCTGTGCATAG 3184
Crub_svsplocu 484533 GGTCGCGATGGGTCGG-ACACGACT---TCGCAATTAACAACAACAACAA 484578
v i - - --- v vi
RTE1_ChrAsi#L 3185 GGTCGCTATGAGTCGGTAC-CGACTCGATGGCACCTAACAACAACAACAA 3233
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 42.01
Transitions / transversions = 1.06 (511/482)
Gap_init rate = 0.05 (156 / 3147), avg. gap size = 1.33 (207 / 156)
+ 355 30.8 6.8 4.6 Crub_svsplocus 484677 484972 (165028) C IAPEY5_I LTR/ERVK (1631) 1943 1642 283
ANNOTATION EVIDENCE:
355 30.82 6.76 4.64 Crub_svsplocus 484677 484972 165028 C IAPEY5_I LTR/ERVK 1642 1943 1631
355 30.82 6.76 4.64 Crub_svsplocus 484677 484972 (165028) C IAPEY5_I#LTR/ERVK (1631) 1943 1642 m_b9s001i27
Crub_svsplocu 484677 CAATTAACACGTTCCACGATAGCTTGACCC-GTGGAATTACAGAGAAGAC 484725
i v i i iv v i- - ii ii i
C IAPEY5_I#LTR/ 1943 CGATGAGCACGTTCCACAATGCCTTGTCCTTGTGGA-TTGTAAGGAAGGC 1895
Crub_svsplocu 484726 CA-TGAG-TA-AAAACAATATCTCAGGTTGTACAAAATTGTAAAAAGGCC 484772
- v - i-i v vv i-- v -i vi v-ii
C IAPEY5_I#LTR/ 1894 CAGTCAGATGTGAAACATTCACTT--GATG-GCAAAATTGTTGAAAC-TT 1849
Crub_svsplocu 484773 ACTGAAAAT-TAGGCTGGCCCATTGTCAGTTTTTAGGGAAGAGGGTTTAC 484821
i ii i- ? ? iivvvvi
C IAPEY5_I#LTR/ 1848 ATTAGAAACATANGCTGGCCCATTGTCAGTTTTTNGAATTTTAGGTTTAC 1799
Crub_svsplocu 484822 CC--AGGGCTGTA-ACGGCCAAAAAAAGATGAAAAATAATATGTGAAGCT 484868
-- vi vi -i vv i iiv iv v ---v v i i
C IAPEY5_I#LTR/ 1798 CCCAAGCACTCCATGCCTCTAGGCAGTGCTG---TATTACATGTGAGGCT 1752
Crub_svsplocu 484869 GTTTCCCCTCATAGAGGTGGGGGAAAT-TG-TTCCTAAATACCTATT--- 484913
v v vvi i v v i- - v i i vi vi---
C IAPEY5_I#LTR/ 1751 TTTTCACCTGTCAAAGGTGTGGCAAACATGATGCCTAGACAATTAGCAAN 1702
Crub_svsplocu 484914 -------TATGAATATACATTTCTAGGAAGCCAAAAAGAGAGAACATGGA 484956
------- i i vv i ------ v i ii i vi
C IAPEY5_I#LTR/ 1701 CGNCGCATGTAAATATTGATTTTT------CCCAAAGGAGGAAATATGCG 1658
Crub_svsplocu 484957 TAACGTCCATTTGTCA 484972
i i i
C IAPEY5_I#LTR/ 1657 TGACATCCATTTGCCA 1642
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 40.13
Transitions / transversions = 1.42 (51/36)
Gap_init rate = 0.08 (25 / 295), avg. gap size = 1.36 (34 / 25)
+ 16 16.2 6.2 6.2 Crub_svsplocus 486064 486127 (163873) + (TCT)n Simple_repeat 1 64 (0) 284
ANNOTATION EVIDENCE:
16 16.25 6.25 6.25 Crub_svsplocus 486064 486127 163873 + (TCT)n Simple_repeat 1 64 0
16 16.25 6.25 6.25 Crub_svsplocus 486064 486127 (163873) (TCT)n#Simple_repeat 1 64 (0) m_b9s252i19
Crub_svsplocu 486064 TCTTC-TCTACCTTCTTTCTCCCT-TTCTTC-TCTTCCTACTTCCCTCTT 486110
- -i - i i - - - v - i
(TCT)n#Simple 1 TCTTCTTCT-TCTTC-TTCTTCTTCTTCTTCTTCTT-CTTCTT-CTTCTT 46
Crub_svsplocu 486111 CTTCCTC-TCCTCTCCTT 486127
i - i i
(TCT)n#Simple 47 CTTCTTCTTCTTCTTCTT 64
Matrix = Unknown
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.13 (8 / 63), avg. gap size = 1.00 (8 / 8)
+ 33 25.7 4.1 5.3 Crub_svsplocus 486128 486230 (163770) + (TCCCTCT)n Simple_repeat 6 170 (0) 285
ANNOTATION EVIDENCE:
33 25.68 4.07 5.29 Crub_svsplocus 486059 486230 163770 + (TCCCTCT)n Simple_repeat 1 170 0
33 25.68 4.07 5.29 Crub_svsplocus 486059 486230 (163770) (TCCCTCT)n#Simple_repeat 1 170 (0) m_b9s252i18
Crub_svsplocu 486059 TCCACTCTTCTCTACCTTCTTTC-TCCCT-TTCTTCTCTTCCTACTTCCC 486106
- i -- ii - - -i iv
(TCCCTCT)n#Si 1 TCC-CTCTTCCCT--CTTCCCTCTTCCCTCTTC-CCTCTTCCCTCTTCCC 46
Crub_svsplocu 486107 TCTT-CTTCCTCTCCTC-TCCTTAACCACTCTGCTCCCCTTTCCTCTT-C 486153
- i i - - i vvi v v - i i -
(TCCCTCT)n#Si 47 TCTTCCCTCTTC-CCTCTTCCCTCTTCCCTCTTC-CCTCTTCCCTCTTCC 94
Crub_svsplocu 486154 CTC--CAACCTTCCTACTTCCTTCTCCCCTCCTTTACTCTTTTCTCTCTC 486201
-- vvi iv i i - iv ii ii
(TCCCTCT)n#Si 95 CTCTTCCCTCTTCCCTCTTCCCTCTTCCCT-CTTCCCTCTTCCCTCTTCC 143
Crub_svsplocu 486202 CTCTCGTTTCTTCCCTCTCATCCCTCTTC 486230
ivii --
(TCCCTCT)n#Si 144 CTCTTCCCTCTTCCCTCT--TCCCTCTTC 170
Matrix = Unknown
Transitions / transversions = 2.30 (23/10)
Gap_init rate = 0.09 (15 / 171), avg. gap size = 1.07 (16 / 15)
+ 15 16.4 5.9 0.0 Crub_svsplocus 486856 486889 (163111) + (CA)n Simple_repeat 1 36 (0) 286
ANNOTATION EVIDENCE:
15 16.41 5.88 0.00 Crub_svsplocus 486856 486889 163111 + (CA)n Simple_repeat 1 36 0
15 16.41 5.88 0.00 Crub_svsplocus 486856 486889 (163111) (CA)n#Simple_repeat 1 36 (0) m_b9s252i20
Crub_svsplocu 486856 CACACACACACATA-ACACA-AAACACAACCAGACA 486889
i - - v vv v
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACA 36
Matrix = Unknown
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2)
+ 225 15.2 16.9 0.0 Crub_svsplocus 488515 488573 (161427) + LTR13_v LTR/ERVK 583 651 (303) 287
ANNOTATION EVIDENCE:
225 15.25 16.95 0.00 Crub_svsplocus 488515 488573 161427 + LTR13_v LTR/ERVK 583 651 303
225 15.25 16.95 0.00 Crub_svsplocus 488515 488573 (161427) LTR13_v#LTR/ERVK 583 651 (303) m_b10s001i0
Crub_svsplocu 488515 AATAAAAGTACTTAATGG----GAAAATAAGAAATAGTGAT------TCT 488554
i i v ? v---- ? v? i i------ v
LTR13_v#LTR/E 583 AGTGAAAGTACTAAANGTCTTTGANAAGNAGAAATAATGACGTAAGCTGT 632
Crub_svsplocu 488555 CCCTCTCTCTCTTCTCTCT 488573
i
LTR13_v#LTR/E 633 CCCTCTCTCTCTCCTCTCT 651
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.14
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.03 (2 / 58), avg. gap size = 5.00 (10 / 2)
+ 31 0.0 0.0 0.0 Crub_svsplocus 488875 488903 (161097) + (TGTT)n Simple_repeat 1 29 (0) 288
ANNOTATION EVIDENCE:
31 0.00 0.00 0.00 Crub_svsplocus 488875 488903 161097 + (TGTT)n Simple_repeat 1 29 0
31 0.00 0.00 0.00 Crub_svsplocus 488875 488903 (161097) (TGTT)n#Simple_repeat 1 29 (0) c_b10s251i0
Crub_svsplocu 488875 TGTTTGTTTGTTTGTTTGTTTGTTTGTTT 488903
(TGTT)n#Simpl 1 TGTTTGTTTGTTTGTTTGTTTGTTTGTTT 29
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 371 14.8 7.1 1.2 Crub_svsplocus 489006 489102 (160898) C CR1-3_Croc LINE/CR1 (5) 3600 3517 289 *
ANNOTATION EVIDENCE:
371 13.92 6.25 1.19 Crub_svsplocus 489006 489085 160915 C CR1-3_Croc LINE/CR1 3517 3600 5
371 13.92 6.25 1.19 Crub_svsplocus 489006 489085 (160915) C CR1-3_Croc#LINE/CR1 (5) 3600 3517 m_b10s001i1
Crub_svsplocu 489006 AATAATATATAA-TAAAGTTGGAAGGGACCTT-GGAGGTCATCTAGTCCA 489053
v v v - ii i i-i
C CR1-3_Croc#LI 3600 AATCATAGAGAAGTAGGGCTGGAAGGGACCTCCAGAGGTCATCTAGTCCA 3551
Crub_svsplocu 489054 ACCCCCTG-CTCAGACAGGA--AACCCTATACCAA 489085
- v i -- v -
C CR1-3_Croc#LI 3550 ACCCCCTGCCTGAGGCAGGATCATCCCTAT-CCAA 3517
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.50
Transitions / transversions = 1.20 (6/5)
Gap_init rate = 0.06 (5 / 79), avg. gap size = 1.20 (6 / 5)
283 18.73 11.11 1.12 Crub_svsplocus 489022 489102 160898 C CR1-E5_fAlb LINE/CR1 216 304 23
283 18.73 11.11 1.12 Crub_svsplocus 489022 489102 (160898) C CR1-E5_fAlb#LINE/CR1 (23) 304 216 m_b10s001i2
Crub_svsplocu 489022 GTTGGAAGGGACCTTGGAGGTCATCTAG-TCCAA-CCCCCTGCT-CAGAC 489068
ii i - - i-ii i
C CR1-E5_fAlb#L 304 GTTGGAAGGGACCTTAAAGATCATCTAGTTCCAACCCCCCTGCCGTGGGC 255
Crub_svsplocu 489069 AGGAA-ACC-----CTATACCAACTTTATCAAATGCCTTA 489102
i - ----- v iv vv - ii
C CR1-E5_fAlb#L 254 AGGGACACCTTCCACTAGACCAGGTTGCTCAAA-GCCCCA 216
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.65
Transitions / transversions = 2.75 (11/4)
Gap_init rate = 0.07 (6 / 80), avg. gap size = 1.67 (10 / 6)
+ 2996 29.9 5.2 4.1 Crub_svsplocus 489085 490790 (159210) C L3 LINE/CR1 (1117) 2982 1259 290
ANNOTATION EVIDENCE:
2996 29.87 5.16 4.06 Crub_svsplocus 489085 490790 159210 C L3 LINE/CR1 1259 2982 1117
2996 29.87 5.16 4.06 Crub_svsplocus 489085 490790 (159210) C L3#LINE/CR1 (1117) 2982 1259 m_b10s001i3
Crub_svsplocu 489085 ACTTTATCAAATGCCTTACTGAAGTCCAAGTAAATTATATCCACAGCATT 489134
i i i ii v i ? i i i
C L3#LINE/CR1 2982 ACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTGTCTACGGCATT 2933
Crub_svsplocu 489135 CCTCTGGTCCACTAATTTTGTCACTTGGTCAAAGAATGCAATAAGATTTG 489184
i i i i i i v v iivi i v v i i --
C L3#LINE/CR1 2932 CCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGGAAATGAGGTT-- 2885
Crub_svsplocu 489185 TCTAGCTCTAGCATGATCTGTT-TTGACAAACCCATGTTGGCTTTTAGTA 489233
--- i - i ii - iiii i ii i
C L3#LINE/CR1 2884 ---AGTT-TGGCATGACTTGTTCTTAGTGAACCCATGCTGGCTCCTAGTG 2839
Crub_svsplocu 489234 ATGAC---TTTGTTCGCT----GCTT------CGT-TGTTTGATTATCTT 489269
v --- iv iv ---- i------ i - i v iv
C L3#LINE/CR1 2838 ATCACCGCTTCCTTTTCTAAGTGCTCACAAACCATCTGTTTAATAATCCG 2789
Crub_svsplocu 489270 TTCCAGAATCTTCCCAGGTATTGAGGTCAGGCTGATAGATCTGTAGTT-C 489318
i i v i v i v i v iv i -?
C L3#LINE/CR1 2788 TTCTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTTN 2739
Crub_svsplocu 489319 CTGGATCTATTCCTCCCCCCCCTTTTTTTTGAAGATGGGAACTACATCAG 489368
v i i iii iii ----- i i? i ? ? iv
C L3#LINE/CR1 2738 CAGAATCCATCTTTTTTCCC-----TTTTTAAAANTAGGNACNACATTTG 2694
Crub_svsplocu 489369 CTCTTTTCCAGTCCTCTGGTAGTTCCCCAGTGCTCCAGGACCTTTGAAAA 489418
i v i i i vi ii v v iv ii i v i
C L3#LINE/CR1 2693 CCCGTCTCCAGTCTTCTGGCACCTCTTCCGTTCTCCGTGATTTCTCAAAG 2644
Crub_svsplocu 489419 ATATAGTT-CAGTAGTTCTGAGATCACATCTGCCAGTTCTTTGAGAACCT 489467
- viv- ii i v v v v i
C L3#LINE/CR1 2643 AT-TACCGACAGCGGTTCCGCGATCACATCTGCAAGTTCTTTCAGTACCC 2595
Crub_svsplocu 489468 TGGAGTGTAATCTATATGGTCCTGGTGATCTGAACTCATCCATGCTGGAT 489517
ii iii v v v ii ii vivi v
C L3#LINE/CR1 2594 TGGGATGTAATTCGTCTGGGCCTGGAGACTTGAACTCATTTAAAGCGGCT 2545
Crub_svsplocu 489518 AAGTGCTCACTTACTATTTTCTTGCCCATCTTAA-CTTGTGTT---TCTA 489563
i v i i ii i ii- vvi --- v
C L3#LINE/CR1 2544 AGGTGCTCTCTTACTATCTCCTCACCTATCTTGGGCTTCAATTCCCTCTT 2495
Crub_svsplocu 489564 ATCTATTTTTTATGGTACTGTTTTTGATAAGTTGAACTGTTTCTTTTCCT 489613
v v v -i vv iv iiii ---i -- v iv i
C L3#LINE/CR1 2494 AACGATGTTT-GTTCTACCCTTTCCAGT---CTGAA--GATCATTCTCCT 2451
Crub_svsplocu 489614 TTGT-GTAAAGACAGATGCAAAAAAAAAAAAACAAATTAAATAGTTCTGT 489662
vi - vi i v v ii i------- i i i
C L3#LINE/CR1 2450 TGATAGAGAAGACGGAAGCAAAATAGGAG-------TTGAGTAGTTCTGC 2408
Crub_svsplocu 489663 TTTCTCCCTGTTGCTTGATA--------CCTTCTTCCCCCACTAATGGAC 489704
i iiii v -------- v v v vi ii i
C L3#LINE/CR1 2407 TTTCTCTCTGTCATCTGTTAACATTACGCCATCTGCCCCAAGCAGCGGGC 2358
Crub_svsplocu 489705 CAATAATTTCCTTCACTTTTTTTCTTGTTTTTTACATG---TTGAAAGAA 489751
vi v?i i --- ii - i iivv i--- --
C L3#LINE/CR1 2357 CTGTCNCTTTCTT---TTTCCTTCT-GCTCCGAACATAGCTTTGAAA--A 2314
Crub_svsplocu 489752 GC---TTTTTTGTTATTTTTGAC---TTTGATCACAAGCCTTAGTTCACT 489795
---? i ii ii --- vv i i i i
C L3#LINE/CR1 2313 GCCTTNTTTTTGTTGTCCTTAGCATTTTTTTTCGCAAGCCTCAGCTCATT 2264
Crub_svsplocu 489796 TTGAGCCTTAGCTTTCCTCAC-CTCATCTTGCAGGCTCAGACTAGTTGCT 489844
i i i i v - vv i iivi? v iv
C L3#LINE/CR1 2263 CTGGGCTTTAGCCTTCCTGACACTATTCTTACAGGCTTGTGNTACTCTCT 2214
Crub_svsplocu 489845 GATATTCTG-CTTTAGTTATGTGCCCCTCTTTCCA-CTTTTTATACTTGT 489892
----i i - i i i i - - i v v
C L3#LINE/CR1 2213 ----CTTTGTCCTTGGTTATATGTCC-TCTTTCCATCTTCTGATACATGT 2169
Crub_svsplocu 489893 CCTTTTTATCTTTCAATTTATCAGAGAGTTCTTTATGCAGCCATGCTGGT 489942
v vv i v ---i i ? i ? i i
C L3#LINE/CR1 2168 CCTTTTAAAATCTGA---CATCAGAGAATNCTCTATGNAGCCACGTTGGT 2122
Crub_svsplocu 489943 TTCTTTTGAGAGCTGTTATTTTTCTTCTTTATTGG--TATTGTGCTAGAC 489990
vviv vv viivi i i --i - - - i
C L3#LINE/CR1 2121 TTCTTAAATGCCCTCCCTCTTTTCTTCCTCATTGGATCATT-TG-TA-AT 2075
Crub_svsplocu 489991 TG-GGCTTTTATTATCTCATTTTTCAAAA-TTACCAAGCTTCTTGAGT-- 490036
-i --- i vv i v i i- v ?v i i--
C L3#LINE/CR1 2074 TGTAG---TCAGAATTTCATTTTTAAGAGCTTCCCANCCCTCTTGAGCCA 2028
Crub_svsplocu 490037 TGTTTCCCTTAGAGGATTCTCAT-CCATGGAATCCTTCCCAAGCCCTCTT 490085
v ii v --- ?v- v v ivvvii v
C L3#LINE/CR1 2027 TCTTTCTTTTTGAG---TCTCNGGCCATGGAATCATACCTCTTTTCTCTG 1981
Crub_svsplocu 490086 TATTTTTATTGAAATTAGCT----CTCTTAAAGTCCAAGACTCTAGTTTG 490131
v -- iv ---- v iiii -v vv v
C L3#LINE/CR1 1980 AATTTTT--TGAAATCTGCTTTTCCTCGTAAAGTCTGGAAC-ATATGTGG 1934
Crub_svsplocu 490132 ACTGTGTTCTAATGCTTGTGCTTCCATAA-TGTTA--AATTCCAATATTG 490178
---- i -- v v i v ii- i -- i i v vi
C L3#LINE/CR1 1933 ACT----TTTAA--CTTTTCCTTTCTTGGCTATTACGAACTCTAAGATGA 1890
Crub_svsplocu 490179 CATGATCACTTCCCCCCAAGGTTCCTGT-GGCTTCAAGACCTTCTATCAT 490227
i- i i i - i v vvi vi v i v
C L3#LINE/CR1 1889 CATGG-CACTTTCTCCCAAGGTTCCTATCGACTTCCACTTCACCAACCAG 1841
Crub_svsplocu 490228 TTTGTCTCTGTTAGTGAGGATTAGATCCAATATGGCCAATCCTCTAGTTC 490277
iv ii i v i ii ivi i viv i v v
C L3#LINE/CR1 1840 TTCTTCCTTGTTGGTCAGAATTAAGTCCAGAGTAGCAGTTCCCCTCGTTG 1791
Crub_svsplocu 490278 CCTTCTCTACTTTTTAGGAGACAAAGTTGTCTGCAAGTTTTGTCAAGAAT 490327
i i i i ii ii i v vivv
C L3#LINE/CR1 1790 CTTCCTCTACCTTCTGAGAGATGAAATTGTCAGCAAGGCAAGTCAAGAAT 1741
Crub_svsplocu 490328 CTGTTTGATCTTCCACTTGGTGCAGAGTTTGTCTCCCAGTTGATGTCAGG 490377
i i iv vi ii vvv ? i vv v i iv v
C L3#LINE/CR1 1740 TTATCAGATGCTCTGCTTTTAGCNGAATGAGACTTCCAGCAGATGTCCGG 1691
Crub_svsplocu 490378 GTAATTAAAATCCCCCATTACTATTGTCATGTGCTT-CCTACATACC--- 490423
i i i i i i -? --- - vii i ---
C L3#LINE/CR1 1690 ATAGTTGAAGTCCCCCATCACTACTG-NAT---CTTGCCTCTGTGCCAGT 1645
Crub_svsplocu 490424 TTAGTTAGCTG-ACTAGCAAAAAGATCATCTATTT--TCCCTTTGGTTGG 490470
v v v - ii -i iv i ? -- v i ii
C L3#LINE/CR1 1644 TTTGTAATCTGTATCAG-GAAAGCATCATCCATNTCCTCCATCTGGCCGG 1596
Crub_svsplocu 490471 ATGGCCTATAGTATACACCTATGGCAATGTCATTT---TTTCCCTCTTTT 490517
ii i i v i iii i i i --- i ii
C L3#LINE/CR1 1595 GCGGTCTGTAGTATACTCCCACAACGATATCACTTCTGTTTCTCTCTCCT 1546
Crub_svsplocu 490518 TCTAT--TGACCCAAGTGCATTCAAGACAGTTTTCATCATTGCTGTGCTC 490565
i -- v i vi v ?vvv i ii i v -- v - i
C L3#LINE/CR1 1545 TTTATCCTCACCCAAATGCTCTCCANCGCGCTTCTACCCT--CAG-GTTC 1499
Crub_svsplocu 490566 TT---TTTCTGTAGAGATGTAGTTAT-TTCTT-ATATAGAGAGCAGCTCC 490610
v --- iiiiv i -- - - i v v vi i
C L3#LINE/CR1 1498 GTGGATTTCCACGCAGGTGTA--TATCTTCTTGACATACAGTGCTACTCT 1451
Crub_svsplocu 490611 ACCT---CTTCTATTTGGTCTGCTTCTTTTAAAAAATTTAAATCCCTCTA 490657
? --- ? v i i i v vv ?v i i i
C L3#LINE/CR1 1450 NCCTCCCCTTCTANTAGATCTGTTTCTTTTGAACAAGGTNTACCCTTCCA 1401
Crub_svsplocu 490658 CCTGAGTGTTCCATTTGTGGG---------GCCATGTCTCCATAATGGCA 490698
i vvv i v ii i ---------i v vi i iv v
C L3#LINE/CR1 1400 TCGCCGTATTCCAGTCATGAGTCCCATCCCACCAAGTCTCGGTGATACCT 1351
Crub_svsplocu 490699 ACAATATCATATCTGCCCTCATTTATGT--GAATTTCTAGTTCACCCTGT 490746
ii v i i i ii -- i --i v ? ii ?
C L3#LINE/CR1 1350 ATGAGATCGTATTTACCTCC--TTGTGTTAAAATTTCAAGTTNACTTTNT 1303
Crub_svsplocu 490747 TTGCTCTTCATGCTCTATGCATTGGCGTACAGACATTTGAGTCC 490790
ii vii i i ii i i v
C L3#LINE/CR1 1302 TTATTACCCATACTCTGTGCATTGGTATATAGACATCTGAGGCC 1259
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.34
Transitions / transversions = 1.84 (317/172)
Gap_init rate = 0.06 (108 / 1705), avg. gap size = 1.46 (158 / 108)
+ 16 5.2 0.0 0.0 Crub_svsplocus 495229 495248 (154752) + (A)n Simple_repeat 1 20 (0) 291
ANNOTATION EVIDENCE:
16 5.20 0.00 0.00 Crub_svsplocus 495229 495248 154752 + (A)n Simple_repeat 1 20 0
16 5.20 0.00 0.00 Crub_svsplocus 495229 495248 (154752) (A)n#Simple_repeat 1 20 (0) m_b10s252i3
Crub_svsplocu 495229 AATAAAAAAAAAAAAAAAAA 495248
v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAA 20
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0)
+ 676 29.7 5.1 4.7 Crub_svsplocus 497406 497977 (152023) C MamGypsy2-I LTR/Gypsy (869) 3522 2942 292
ANNOTATION EVIDENCE:
533 29.72 5.07 4.70 Crub_svsplocus 497406 497977 152023 C Gypsy158-I_DR LTR/Gypsy 2949 3522 869
533 29.72 5.07 4.70 Crub_svsplocus 497406 497977 (152023) C Gypsy158-I_DR#LTR/Gypsy (869) 3522 2949 m_b10s001i4
Crub_svsplocu 497406 CATGCCTAATCATATTTGCCCTTAAGAAGGACTGAAACTTTGCAGAAGTA 497455
i i?i vvi ?vv? i v v?v ? i v? vvv
C Gypsy158-I_DR 3522 CGTGCTNGATGCCATTNCGNCTCATGAATNCCTNAAACTCTTNACTCGTA 3473
Crub_svsplocu 497456 AATTGAGCCCCATTGTCTGAGACTATAACATCTGGGAGCCCATGCATTGC 497505
vii ?iv i v iv iv v v ii --- ?
C Gypsy158-I_DR 3472 AAACAANTGCCATTGTCCGACACTACCATTTCAGGTAATCCATG---TNC 3426
Crub_svsplocu 497506 G---AAATGCTGTG-CAGAACCTGGATGGT---TCTGGCAGTAGTCATAG 497548
--- iv v- ?vv v ---? vi v? vv? ?
C Gypsy158-I_DR 3425 GCTAAAACTCTGTCTCAGNTACTCGATGGTAACNCGAGANGTAGAANTAN 3376
Crub_svsplocu 497549 TGGACATTGGAATGACCTCTAGCCACTTGGAGTGATTGTCCATAACAATG 497598
v v--- ?vvi ? i v vii iv v v
C Gypsy158-I_DR 3375 TCGAG---GGANACGCNTCCATCCACTTGGAGTGAGCATCCACCAGAATC 3329
Crub_svsplocu 497599 AAGAAGAATTGCCCTTGAAAGAGGCCAGCAAAATCAATATGAATCCTCGA 497648
ii v v vi i ?i i ? v i i i ivv
C Gypsy158-I_DR 3328 AGAAACATTTTTCCTTGGAANGGACCNGCATAGTCAATATGGATTCTTCT 3279
Crub_svsplocu 497649 CCAAGGGGCTTGTGTGGTCTCCCATCTCTGTA------CAGGAGCATGTG 497692
i v vi v?v? ?vvv ------ ?v - v
C Gypsy158-I_DR 3278 CCAGGGCGGCTGTGGNCNCTCCCANGGGTGTAATGGNGCNCGAGCA-GGG 3230
Crub_svsplocu 497693 GCATTTCTGGCCT--TGACTGCTGGCAAATGTGGCACCTGTGGACCTGGG 497740
i i vi -- vv ?i v ----- v -- v?vv
C Gypsy158-I_DR 3229 GCGTTCCTGCTCTCCTGACATCTGNTACATG-----CCTTT--ACCANTT 3187
Crub_svsplocu 497741 CCTCGATATCTTTAT-CATGCCCAGGCCACCAAAGGTAGCTGCGCGTGAG 497789
i v i ivi - -? i v v v ? iv i
C Gypsy158-I_DR 3186 CTTCCACATCCGCATCCAT-NCCGGGCCACCACACGTAGCTCCGNGCCAA 3138
Crub_svsplocu 497790 TGCCTTCATCCGGACTATTCCCAGATGTCCCTCATGCAGAGAATC----- 497834
iv i i v?i?i v ii i vv v ii i - vvi -----
C Gypsy158-I_DR 3137 CCCTTTCATTCTNGNCATGCCTGGGTGGGCATTGTGTA-ACTGTCTCGGT 3089
Crub_svsplocu 497835 AAGGATTCTAGCCCTCAGTGAGGTTGGGATTACTACCCTACTGCCCCACA 497884
v v ? iv v --- ? - i ? ? v vivi?
C Gypsy158-I_DR 3088 ACGGCTNCCCGGCCT---TGNGG-TGGAATNACNACGCGGGCNCCCCACA 3043
Crub_svsplocu 497885 A-ATACAACCCTTATAAGTGGATAACTCA-TGCTTCCT-TCTCC--AG-- 497927
- i v v i----v i- - v v - i-- --
C Gypsy158-I_DR 3042 ACACACATCCGTC----CTGGAC-ACTCAGTTCATCCTGTCTCTTAAGGT 2998
Crub_svsplocu 497928 AAACTCTGAAAGTTAGGGCCAGTACAC-GTTTCTGGCCATCCTGTGAGCA 497976
v ii ? i i iv -- v - i iv v i
C Gypsy158-I_DR 2997 ATACTCCAANAGCTGGATCC--TCCACTGTCTTGGGCCATCCTCTAAGCA 2950
Crub_svsplocu 497977 C 497977
C Gypsy158-I_DR 2949 C 2949
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.46
Transitions / transversions = 0.80 (72/90)
Gap_init rate = 0.07 (40 / 571), avg. gap size = 1.40 (56 / 40)
676 33.76 4.17 3.73 Crub_svsplocus 497437 497916 152084 C MamGypsy2-I LTR/Gypsy 2942 3423 743
676 33.76 4.17 3.73 Crub_svsplocus 497437 497916 (152084) C MamGypsy2-I#LTR/Gypsy (743) 3423 2942 m_b10s001i5
Crub_svsplocu 497437 CTGAAACTTTGCAGAAGTAAATTGAGCCCCATTGTCTGAGACTATAACAT 497486
v ivi v i vv v v i v iii
C MamGypsy2-I#L 3423 CTTAAACTCAACTGAGGTAAATGCAGACCCATTGTCAGAAACGATAGTGT 3374
Crub_svsplocu 497487 CTGGGAGCCCATGCATTGCGAAATGCT-GTGCAGAACCTGGATGGTTCTG 497535
v ii i ii i vvi - i i ivv v vii
C MamGypsy2-I#L 3373 CTGGCAATCCGTGTGTTGCAAATAACTGGCGCAGAGCTGTGATTGTTGCA 3324
Crub_svsplocu 497536 GCAGTAGTCATAG-TGGACATTGGAATGACCTCTAGCCACTTGGAGTGAT 497584
vi ivv - - i i i vv i v i v viiv
C MamGypsy2-I#L 3323 GCAGAGGTTTGAGATGGA-ACTAGGAGCACTTCGAGCCATTTTGAGAAGG 3275
Crub_svsplocu 497585 TGTCCATAACAATGAAGAAGAATTGCCCTTGAAAGAGGCCAGCAAAATCA 497634
v i iv v vvi v i i vi v v
C MamGypsy2-I#L 3274 AGTCTACCACAATCAAGAAGTTCTTCCCCTGGAATGGTCCTGCAAAATCA 3225
Crub_svsplocu 497635 ATATGAATCCTCGACCAAGGGGCTTGTGTGGTCTCCCATCTCTGTACAGG 497684
i i i -- v - v --- i ii iv ii
C MamGypsy2-I#L 3224 ATATGGATTCTTGACCAA--GGCTTCT-TGGTCAC---TTTCCATGGAAA 3181
Crub_svsplocu 497685 AGCATGTGGCATTTCTGGCCTTGACTG------CTGGCAAATGTGGCACC 497728
i v v v vvi vi vvi i ------ vi ivi i
C MamGypsy2-I#L 3180 AGTAGGTGCCTTTGGCGGGTTATGCCGAGTAGCCTGGCATGTGCTACACT 3131
Crub_svsplocu 497729 TGTGGACCTGGGCC---TCGATATCTTTATCATGCCCAGGCCACCAAAGG 497775
iv vv ---i i --- i vvv vvi i vi
C MamGypsy2-I#L 3130 CCTTTAC---AGTCTTTTCAATATCAGAATCAATTCCAGGCCACCAGACA 3084
Crub_svsplocu 497776 TAGCTGCGCGTGAGTGCCTTCATCCGGACTATTCCCAGATGTCCCTCATG 497825
v vv iv i i v i v i v iv
C MamGypsy2-I#L 3083 TAGCTTCTAGCCAATGCTTTCATGCGAACAATTCCCGGATGTGCTGCATG 3034
Crub_svsplocu 497826 CAGAG-AATCAAG-------GATTCTAGCCCTCAGTGAGGTTGGGATTAC 497867
i v -iii ------- vviv i -------- i v
C MamGypsy2-I#L 3033 TAGTGTGGCCAAGATAACGTGATGACCGCCTTC--------TGGAATAAC 2992
Crub_svsplocu 497868 TACCCTACTGCCCCAC-AAATACAACCCTTATAAGTGGATAACTCATGCT 497916
v iv v i v i- vi v i ii ii i
C MamGypsy2-I#L 2991 AATGCGATTTCCCCATAAAAGGCATCCTTTATGGGCAGATAACTCATGTT 2942
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.88
Transitions / transversions = 1.11 (82/74)
Gap_init rate = 0.05 (25 / 479), avg. gap size = 1.52 (38 / 25)
+ 365 27.1 2.7 2.0 Crub_svsplocus 498235 498405 (151595) C MamGypsy2-I LTR/Gypsy (1776) 2655 2501 293
ANNOTATION EVIDENCE:
226 26.58 1.25 1.25 Crub_svsplocus 498235 498314 151686 C Gypsy156-I_DR LTR/Gypsy 4002 4081 2330
226 26.58 1.25 1.25 Crub_svsplocus 498235 498314 (151686) C Gypsy156-I_DR#LTR/Gypsy (2330) 4081 4002 m_b10s001i6
Crub_svsplocu 498235 TGTAGTGAACAACCCCAGAAGTGGCTTCTGGTCAGTGAAGACCGTGAAGT 498284
i i vviv vv i v v v v v v i v
C Gypsy156-I_DR 4081 TGTAGTAAGCACATACACTAGCGGGTTGTTGTCAGTTAATACAGTAAACT 4032
Crub_svsplocu 498285 GGTG-GCCATACAAAAAGTCATGAAACTTTT 498314
v- -i i i
C Gypsy156-I_DR 4031 T-TGCACCGTACAAAAAGTCATGAAATTTTT 4002
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.37
Transitions / transversions = 0.62 (8/13)
Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2)
365 27.51 3.92 2.58 Crub_svsplocus 498253 498405 151595 C Gypsy163-I_DR LTR/Gypsy 2501 2655 1776
365 27.51 3.92 2.58 Crub_svsplocus 498253 498405 (151595) C Gypsy163-I_DR#LTR/Gypsy (1776) 2655 2501 m_b10s001i7
Crub_svsplocu 498253 AAGTGGCTTCTGGTCAGTGAAGACCGTGAAGTGGTGGCCATACAAAAAGT 498302
i v iv vv i v vii v v iv v
C Gypsy163-I_DR 2655 AAGTGGCCTGTGGTCAGTGAGCAGAGTAAATTTACGTCCAAACAAGTACT 2606
Crub_svsplocu 498303 CATGAAAC--TTTTTATGCCCACCACAATGGTCAATGCTTTCCTATCTAT 498350
vi i -- ii v vi v i v ii vv v
C Gypsy163-I_DR 2605 GGTGGAACTTTTTTTACACCAAATACAATTGCCAAAGCTTCTCGTTCGAT 2556
Crub_svsplocu 498351 TTGTGTGTAATTGTGTTCTGCAGCAGAA---AGAGTCCTGGA-GTAATAG 498396
i -- ii - ? i--- v - i - i
C Gypsy163-I_DR 2555 TTGTGCGTAAT--TACTCT-CNGCAGAGTTTAGAGTCCTTGATGCAA-AA 2510
Crub_svsplocu 498397 GCCAGTGGT 498405
v v
C Gypsy163-I_DR 2509 GCGATTGGT 2501
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.88
Transitions / transversions = 0.95 (20/21)
Gap_init rate = 0.05 (7 / 152), avg. gap size = 1.43 (10 / 7)
+ 921 33.0 3.6 3.6 Crub_svsplocus 499210 499797 (150203) C MamGypsy2-I LTR/Gypsy (1812) 2354 1767 293
ANNOTATION EVIDENCE:
921 32.98 3.57 3.57 Crub_svsplocus 499210 499797 150203 C MamGypsy2-I LTR/Gypsy 1767 2354 1812
921 32.98 3.57 3.57 Crub_svsplocus 499210 499797 (150203) C MamGypsy2-I#LTR/Gypsy (1812) 2354 1767 m_b10s001i8
Crub_svsplocu 499210 TGCTCATTGAAATGAGCCAACACCGCATTTGATGACAACAATGCCTTAAC 499259
i i v vi i i v vv iv v v i ivv i
C MamGypsy2-I#L 2354 TGTTCATCGTAATGTACTAGCACAGACTCGGAAGTCAATAACTGCTTGAC 2305
Crub_svsplocu 499260 -TGCTGCAAAAC-TCCCCTTGTGGACACTTGTCCACTTCCATGGA--GCC 499305
- v i v i - i v iv i iv-- viv i --
C MamGypsy2-I#L 2304 ATTCCGGAAAGCGTCCTCATGCTGGCGA--GTCCAACGCCACGGAACGCC 2257
Crub_svsplocu 499306 TTCTTGTCCAAGAGCCAGTATAATGGCTCTGCCACTGAGGCCTTGTGGGG 499355
i i-- iv v ii iv i v v iv vv v v
C MamGypsy2-I#L 2256 TTTTC--CCAGTAGGCGATGAAGTGGCTCAGCAATGGTTGCCTTTTGTGG 2209
Crub_svsplocu 499356 GGAGGAGAGCGTGATAAAAATTAAGGAGTCCCAGGAAGGCCTGAAGCTCT 499405
i- i i i i i i i v i i
C MamGypsy2-I#L 2208 A-AGAAAAACATGGTAGAAATTGAGTAGCCCCAGGAAGGCTTGAAGCTCT 2160
Crub_svsplocu 499406 CCCTTCGTCTTGGGACTTGGTGCCTGCTGAATTGCTTTGAGCTTGGATTC 499455
iv i i v v v i v vv i vivv v ivv v
C MamGypsy2-I#L 2159 TGCTTTGTTTTTGGAGTAGGCGCGTCATGGATTGCACGTACCTTATCTTG 2110
Crub_svsplocu 499456 AGCAGGATGAATGCCTTCGGCATCTATACGAAACCCCAGGAA-----CTC 499500
ii i i vv i iv i iv v i i ----- v
C MamGypsy2-I#L 2109 AGTGGGGTGAATACCAGCAGCATTGATGCGGTAGCCTAAGAAGGTGACAC 2060
Crub_svsplocu 499501 TGTGGAAGTGACCCCAATTTTACATTTCTCCTGTTTGTGCTTCAG--CCC 499548
-- ---i i i - vii - i --v
C MamGypsy2-I#L 2059 TG--GAAGT---TCCGATTTCACATTTCTCCT-TTTTCAC-TCGGATACC 2017
Crub_svsplocu 499549 CGCTTCACAGAAATGTTGCAAGACAGCCCGGACCCTGTCAGTGAG---AC 499595
i v vi iv i v i i vv i i vi v v i --- i
C MamGypsy2-I#L 2016 TGATGTATCGAAACGATGTAGGACTTCCTGAAGTCTTTCCGCGAGTTCAT 1967
Crub_svsplocu 499596 TTTTGACTGATTCCCCAACTATGAGGACATCATTGAAATATGGGCATACA 499645
ii ivii i --- iv v i vvvi
C MamGypsy2-I#L 1966 CCTCTGTTGATCCC---ATGATCAGGACATCATCGAAATATGGTACCACA 1920
Crub_svsplocu 499646 CCCTGAATGTT-----GCAGAGTGTTTGCTCCATTACACTCTGAAAAATG 499690
iv vi ----- i ----- v vi v i v
C MamGypsy2-I#L 1919 CCTGGAATCCTAGAAAGCAGGGT-----CTCCATGAAGCACTGGAAAATT 1875
Crub_svsplocu 499691 TCCGGGGCTACATTAACCCTGAACTGTA-ACGTTTGCACTTTGAAGGCTC 499739
i v v vv ii i v -i i i- iv v i
C MamGypsy2-I#L 1874 CCAGGGGCAACAGAAATTCCGAACTGAAGGCGCTTA-ACTCGGAATGCCC 1826
Crub_svsplocu 499740 CCCTGTGAGTTACAATGGTTTGGGCCTCAGCCGTGGCATCTTCCACTG-C 499788
i vi v ii v v v v i vi v vi-
C MamGypsy2-I#L 1825 CTCGATGAGTGATGATTGTTTGGGCGTCTGCAGTAGCATCACCGACGATC 1776
Crub_svsplocu 499789 AGCTGTAGA 499797
v
C MamGypsy2-I#L 1775 AGCTGTTGA 1767
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.51
Transitions / transversions = 1.12 (99/88)
Gap_init rate = 0.05 (30 / 587), avg. gap size = 1.40 (42 / 30)
+ 252 28.4 0.0 0.0 Crub_svsplocus 503788 503854 (146146) + hAT-N78_DR DNA/hAT-Charlie 1 67 (252) 294
ANNOTATION EVIDENCE:
252 28.36 0.00 0.00 Crub_svsplocus 503788 503854 146146 + hAT-N78_DR DNA/hAT-Charlie 1 67 252
252 28.36 0.00 0.00 Crub_svsplocus 503788 503854 (146146) hAT-N78_DR#DNA/hAT-Charlie 1 67 (252) m_b10s001i9
Crub_svsplocu 503788 CAGGGCTTTTCAACCGGTGCTACGTATACCACTAGTTATATGCAACCACC 503837
v v i v v v i vi i iv vi
hAT-N78_DR#DN 1 CAGTGGTTCTCAAACTGTGGTACGTGTACCACTAGTGGTACGCAGGCTTC 50
Crub_svsplocu 503838 TGACTGGTGGTATGCGG 503854
ivv i i
hAT-N78_DR#DN 51 CTTCTAGTGGTACGCGG 67
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.51
Transitions / transversions = 0.90 (9/10)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0)
+ 21 0.0 0.0 0.0 Crub_svsplocus 504186 504208 (145792) + (TC)n Simple_repeat 1 23 (0) 295
ANNOTATION EVIDENCE:
21 0.00 0.00 0.00 Crub_svsplocus 504186 504208 145792 + (TC)n Simple_repeat 1 23 0
21 0.00 0.00 0.00 Crub_svsplocus 504186 504208 (145792) (TC)n#Simple_repeat 1 23 (0) m_b10s252i4
Crub_svsplocu 504186 TCTCTCTCTCTCTCTCTCTCTCT 504208
(TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCT 23
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 241 18.4 0.0 0.0 Crub_svsplocus 505219 505267 (144733) + RLTR12B LTR/ERVK 231 279 (277) 296 *
ANNOTATION EVIDENCE:
241 18.37 0.00 0.00 Crub_svsplocus 505219 505267 144733 + RLTR12B LTR/ERVK 231 279 277
241 18.37 0.00 0.00 Crub_svsplocus 505219 505267 (144733) RLTR12B#LTR/ERVK 231 279 (277) m_b10s001i10
Crub_svsplocu 505219 ACTTCCGATCCCTGATCGGAGAGAGAGTGAGAGAGAGAGAGGAAGAAAG 505267
? v viv i i i v i
RLTR12B#LTR/E 231 ACTTCCGNTCCCAGCCAGGGGAGGGGGGGAGAGAGAGAGAGGAAGAGAG 279
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.80
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 1550 18.3 0.1 0.7 Crub_svsplocus 505235 505960 (144040) C IMPB_01 Satellite (2147) 721 1 297
ANNOTATION EVIDENCE:
283 18.24 0.00 2.97 Crub_svsplocus 505235 505477 144523 C IMPB_01 Satellite 166 401 2147
283 18.24 0.00 2.97 Crub_svsplocus 505235 505477 (144523) C IMPB_01#Satellite (2147) 401 166 m_b10s001i11
Crub_svsplocu 505235 CGGAGAGAGAGTGAGAGAGAGAGAGGAAGAAAGAGAGGGAGAGAAAGAGA 505284
i v ii i i i
C IMPB_01#Satel 401 CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 352
Crub_svsplocu 505285 GAGGGAAAGAGAGGGAGAAAGATAGGGAGAAAGAAAGAGAGAGAGGGGGG 505334
i i i i v i i i i i i
C IMPB_01#Satel 351 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 302
Crub_svsplocu 505335 AAAAGAGAAAGAGGGAGAGAGAAAGAGAGAGGGAAAGAGGGAGAAAGATA 505384
i i i i i i i i i v
C IMPB_01#Satel 301 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 252
Crub_svsplocu 505385 GGGAGAAAGAAAGAGAAAGAAAGAGAGAGGGAAAAGAGAAAGAGGTAGAG 505434
i i i i i ----- i --
C IMPB_01#Satel 251 GAGAGAGAGAGAGAGAGAGAGAGAGAGAG-----AGAGAGAGAG--AGAG 209
Crub_svsplocu 505435 AGAGAGGAAGGAAGAGAAAGAGGGAGGGAGAGAGGAAGAGAGA 505477
ii ii i i i ii
C IMPB_01#Satel 208 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.31
Transitions / transversions = 13.33 (40/3)
Gap_init rate = 0.03 (7 / 242), avg. gap size = 1.00 (7 / 7)
311 19.50 0.00 1.27 Crub_svsplocus 505274 505512 144488 C IMPB_01 Satellite 165 400 2148
311 19.50 0.00 1.27 Crub_svsplocus 505274 505512 (144488) C IMPB_01#Satellite (2148) 400 165 m_b10s001i12
Crub_svsplocu 505274 AGAGAAAGAGAGAGGGAAAGAGAGGGAGAAAGATAGGGAGAAAGAAAGAG 505323
i i i i i v i i i
C IMPB_01#Satel 400 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 351
Crub_svsplocu 505324 AGAGAGGGGGGAAAAGAGAAAGAGGGAGAGAGAAAGAGAGAGGGAAAGAG 505373
i i ii i i i i i i
C IMPB_01#Satel 350 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 301
Crub_svsplocu 505374 GGAGAAAGATAGGGAGAAAGAAAGAGAAAGAAAGAGAGAGGGAAAAGAGA 505423
i i v i i i i i i i -
C IMPB_01#Satel 300 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGA 252
Crub_svsplocu 505424 AAGAGGTAGAGAGAGAGGAAGGAAGAGAAAGAGGGAGGGAGAGAGGAAGA 505473
i -- ii ii i i i ii
C IMPB_01#Satel 251 GAGAG--AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 204
Crub_svsplocu 505474 GAGAGAAAGACGGACAGAGAGGGAGAGAGAAATAGAGAT 505512
i vi v i i v
C IMPB_01#Satel 203 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAT 165
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.08
Transitions / transversions = 8.20 (41/5)
Gap_init rate = 0.01 (3 / 238), avg. gap size = 1.00 (3 / 3)
381 20.26 0.00 0.42 Crub_svsplocus 505338 505575 144425 C IMPB_01 Satellite 164 400 2148
381 20.26 0.00 0.42 Crub_svsplocus 505338 505575 (144425) C IMPB_01#Satellite (2148) 400 164 m_b10s001i13
Crub_svsplocu 505338 AGAGAAAGAGGGAGAGAGAAAGAGAGAGGGAAAGAGGGAGAAAGATAGGG 505387
i i i i i i i v i
C IMPB_01#Satel 400 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 351
Crub_svsplocu 505388 AGAAAGAAAGAGAAAGAAAGAGAGAGGGAAAAGAGAAAGAGGTAGAGAGA 505437
i i i i i i - i iv
C IMPB_01#Satel 350 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGA 302
Crub_svsplocu 505438 GAGGAAGGAAGAGAAAGAGGGAGGGAGAGAGGAAGAGAGAGAAAGACGGA 505487
ii ii i i i ii i vi
C IMPB_01#Satel 301 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 252
Crub_svsplocu 505488 CAGAGAGGGAGAGAGAAATAGAGATGAAGAGAGAGAAAGCGAGAGAGAAG 505537
v i i v vii i v ii
C IMPB_01#Satel 251 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 202
Crub_svsplocu 505538 GAAACAGAAAGAGAGAGGGAAAGAGAGGGAGAAAGATA 505575
i v i i i i i
C IMPB_01#Satel 201 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATA 164
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.95
Transitions / transversions = 5.00 (40/8)
Gap_init rate = 0.00 (1 / 237), avg. gap size = 1.00 (1 / 1)
331 21.16 0.00 0.41 Crub_svsplocus 505378 505619 144381 C IMPB_01 Satellite 166 406 2142
331 21.16 0.00 0.41 Crub_svsplocus 505378 505619 (144381) C IMPB_01#Satellite (2142) 406 166 m_b10s001i14
Crub_svsplocu 505378 AAAGATAGGGAGAAAGAAAGAGAAAGAAAGAGAGAGGGAAAAGAGAAAGA 505427
v?i i i i i i i i - i
C IMPB_01#Satel 406 AAACNCAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA-GAGAGAGA 358
Crub_svsplocu 505428 GGTAGAGAGAGAGGAAGGAAGAGAAAGAGGGAGGGAGAGAGGAAGAGAGA 505477
iv ii ii i i i ii
C IMPB_01#Satel 357 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 308
Crub_svsplocu 505478 GAAAGACGGACAGAGAGGGAGAGAGAAATAGAGATGAAGAGAGAGAAAGC 505527
i vi v i i v vii i v
C IMPB_01#Satel 307 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 258
Crub_svsplocu 505528 GAGAGAGAAGGAAACAGAAAGAGAGAGGGAAAGAGAGGGAGAAAGATAGG 505577
ii i v i i i i i v i
C IMPB_01#Satel 257 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 208
Crub_svsplocu 505578 GAGAAAGAGAAAGGGAGAAAGAGAAAGAGGGAGAGAGAGGGA 505619
i i i i i i i
C IMPB_01#Satel 207 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.46
Transitions / transversions = 4.67 (42/9)
Gap_init rate = 0.00 (1 / 241), avg. gap size = 1.00 (1 / 1)
256 19.04 1.94 2.33 Crub_svsplocus 505414 505671 144329 C IMPB_01 Satellite 166 422 2126
256 19.04 1.94 2.33 Crub_svsplocus 505414 505671 (144329) C IMPB_01#Satellite (2126) 422 166 m_b10s001i15
Crub_svsplocu 505414 GGAAAA-----GAGAAAGAGGTAGAGAGAGAGGAAGGAAGAGAAAGAGGG 505458
----- v i v?i ii ii i i
C IMPB_01#Satel 422 GGAAAACACTTGAGCAAAACNCAGAGAGAGAGAGAGAGAGAGAGAGAGAG 373
Crub_svsplocu 505459 AGGGAGAGAGGAAGAGAGAGAAAGACGGACAGAGAGGGAGAGAGAAATAG 505508
i ii i -- v i i v
C IMPB_01#Satel 372 AGAGAGAGAGAGAGAGAGAGAGAGA--GAGAGAGAGAGAGAGAGAGAGAG 325
Crub_svsplocu 505509 AGATGAAGAGAGAGAAAGCGAGAGAGAAGGAAACAGAAAGAGAGAGGGAA 505558
---- i v ii i v i i i
C IMPB_01#Satel 324 AGA----GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 279
Crub_svsplocu 505559 AGAGAGGGAGAAAGATAGGGAGAAAGAGAAAGGGAGAAAGAGAAAGAGGG 505608
i i v i i i i i i i
C IMPB_01#Satel 278 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 229
Crub_svsplocu 505609 AGAGAGAGGGAGGGAGGAAGAGAGAAAAAGAGGGAGAGGGAGGGAGAGAG 505658
i i ii i i i i i
C IMPB_01#Satel 228 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 179
Crub_svsplocu 505659 AAATAGAGAGAGA 505671
i v
C IMPB_01#Satel 178 AGAGAGAGAGAGA 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.23
Transitions / transversions = 5.00 (40/8)
Gap_init rate = 0.03 (7 / 257), avg. gap size = 1.57 (11 / 7)
354 20.78 0.00 0.00 Crub_svsplocus 505447 505677 144323 C IMPB_01 Satellite 168 398 2150
354 20.78 0.00 0.00 Crub_svsplocus 505447 505677 (144323) C IMPB_01#Satellite (2150) 398 168 m_b10s001i16
Crub_svsplocu 505447 AGAGAAAGAGGGAGGGAGAGAGGAAGAGAGAGAAAGACGGACAGAGAGGG 505496
i i i ii i vi v i
C IMPB_01#Satel 398 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 349
Crub_svsplocu 505497 AGAGAGAAATAGAGATGAAGAGAGAGAAAGCGAGAGAGAAGGAAACAGAA 505546
i v vii i v ii i v i
C IMPB_01#Satel 348 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 299
Crub_svsplocu 505547 AGAGAGAGGGAAAGAGAGGGAGAAAGATAGGGAGAAAGAGAAAGGGAGAA 505596
i i i i v i i i i i
C IMPB_01#Satel 298 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 249
Crub_svsplocu 505597 AGAGAAAGAGGGAGAGAGAGGGAGGGAGGAAGAGAGAAAAAGAGGGAGAG 505646
i i i i ii i i i
C IMPB_01#Satel 248 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 199
Crub_svsplocu 505647 GGAGGGAGAGAGAAATAGAGAGAGAAAAAAA 505677
i i i v i i i
C IMPB_01#Satel 198 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 168
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.77
Transitions / transversions = 5.00 (40/8)
Gap_init rate = 0.00 (0 / 230), avg. gap size = 0.0 (0 / 0)
351 19.52 0.00 1.22 Crub_svsplocus 505476 505724 144276 C IMPB_01 Satellite 166 411 2137
351 19.52 0.00 1.22 Crub_svsplocus 505476 505724 (144276) C IMPB_01#Satellite (2137) 411 166 m_b10s001i17
Crub_svsplocu 505476 GAGAAAGACGGACAGAGAGGGAGAGAGAAATAGAGATGAAGAGAGAGAAA 505525
v i ?-- i i v vii i
C IMPB_01#Satel 411 GAGCAAAACN--CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 364
Crub_svsplocu 505526 GCGAGAGAGAAGGAAACAGAAAGAGAGAGGGAAAGAGAGGGAGAAAGATA 505575
v ii i v i i i i i v
C IMPB_01#Satel 363 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 314
Crub_svsplocu 505576 GGGAGAAAGAGAAAGGGAGAAAGAGAAAGAGGGAGAGAGAGGGAGGGAGG 505625
i i i i i i i i i i
C IMPB_01#Satel 313 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 264
Crub_svsplocu 505626 AAGAGAGAAAAAGAGGGAGAGGGAGGGAGAGAGAAATAGAGAGAGAAAAA 505675
i i i i i i i v - i i
C IMPB_01#Satel 263 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-AGAG 215
Crub_svsplocu 505676 AAAGAGGGAGAGAGAAAGAGAGAGGGAAAGAGGGAGAAAGAAAGAGAGA 505724
i i i i i i i i
C IMPB_01#Satel 214 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.04
Transitions / transversions = 5.86 (41/7)
Gap_init rate = 0.01 (3 / 248), avg. gap size = 1.00 (3 / 3)
273 18.67 0.00 1.24 Crub_svsplocus 505539 505782 144218 C IMPB_01 Satellite 166 406 2142
273 18.67 0.00 1.24 Crub_svsplocus 505539 505782 (144218) C IMPB_01#Satellite (2142) 406 166 m_b10s001i18
Crub_svsplocu 505539 AAACAGAAAGAGAGAGGGAAAGAGAGGGAGAAAGATAGGGAGAAAGAGAA 505588
?v i i i i i v i i i
C IMPB_01#Satel 406 AAACNCAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 357
Crub_svsplocu 505589 AGGGAGAAAGAGAAAGAGGGAGAGAGAGGGAGGGAGGAAGAGAGAAAAAG 505638
i i i i i i ii i i
C IMPB_01#Satel 356 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 307
Crub_svsplocu 505639 AGGGAGAGGGAGGGAGAGAGAAATAGAGAGAGAAAAAAAAGAGGGAGAGA 505688
i i i i v --- i i i
C IMPB_01#Satel 306 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG---AGAGAGAGAGAGAGA 260
Crub_svsplocu 505689 GAAAGAGAGAGGGAAAGAGGGAGAAAGAAAGAGAGAGGGAGAAAGAGAAA 505738
i i i i i i i i i
C IMPB_01#Satel 259 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 210
Crub_svsplocu 505739 GAGGGAGAGAGAGAGGAAGGGAGAAAAAGAGGGAGGGAGAGAGA 505782
i ii i i i i i
C IMPB_01#Satel 209 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.14
Transitions / transversions = 14.00 (42/3)
Gap_init rate = 0.01 (3 / 243), avg. gap size = 1.00 (3 / 3)
314 17.79 0.00 0.42 Crub_svsplocus 505619 505855 144145 C IMPB_01 Satellite 165 400 2148
314 17.79 0.00 0.42 Crub_svsplocus 505619 505855 (144145) C IMPB_01#Satellite (2148) 400 165 m_b10s001i19
Crub_svsplocu 505619 AGGGAGGAAGAGAGAAAAAGAGGGAGAGGGAGGGAGAGAGAAATAGAGAG 505668
i ii i i i i i i v
C IMPB_01#Satel 400 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 351
Crub_svsplocu 505669 AGAAAAAAAAGAGGGAGAGAGAAAGAGAGAGGGAAAGAGGGAGAAAGAAA 505718
i i i - i i i i i i i
C IMPB_01#Satel 350 AGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 302
Crub_svsplocu 505719 GAGAGAGGGAGAAAGAGAAAGAGGGAGAGAGAGAGGAAGGGAGAAAAAGA 505768
i i i i ii i i i
C IMPB_01#Satel 301 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 252
Crub_svsplocu 505769 GGGAGGGAGAGAGAAAGAGAGGGAGAGAGTGGGGGAGAGAGAAAGAGAGA 505818
i i i i v i i i
C IMPB_01#Satel 251 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 202
Crub_svsplocu 505819 AAGAGGGAGAGAGAAAGAGGGAGAGAGAAAGAGAGAT 505855
i i i i i
C IMPB_01#Satel 201 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAT 165
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.77
Transitions / transversions = 20.00 (40/2)
Gap_init rate = 0.00 (1 / 236), avg. gap size = 1.00 (1 / 1)
1550 17.10 0.00 0.85 Crub_svsplocus 505683 505918 144082 C IMPB_01 Satellite 166 399 2149
1550 17.10 0.00 0.85 Crub_svsplocus 505683 505918 (144082) C IMPB_01#Satellite (2149) 399 166 m_b10s001i20
Crub_svsplocu 505683 GAGAGAGAAAGAGAGAGGGAAAGAGGGAGAAAGAAAGAGAGAGGGAGAAA 505732
i i i i i i i i
C IMPB_01#Satel 399 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 350
Crub_svsplocu 505733 GAGAAAGAGGGAGAGAGAGAGGAAGGGAGAAAAAGAGGGAGGGAGAGAGA 505782
i i ii i i i i i
C IMPB_01#Satel 349 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 300
Crub_svsplocu 505783 AAGAGAGGGAGAGAGTGGGGGAGAGAGAAAGAGAGAAAGAGGGAGAGAGA 505832
i i v i i i i i
C IMPB_01#Satel 299 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 250
Crub_svsplocu 505833 AAGAGGGAGAGAGAAAGAGAGATGAAGAGAGAGAAAGGGAGAGAGGGAGA 505882
i i i --i i i i
C IMPB_01#Satel 249 GAGAGAGAGAGAGAGAGAGAGA--GAGAGAGAGAGAGAGAGAGAGAGAGA 202
Crub_svsplocu 505883 GAGAAAGAGGGAAAGAGAGGAAGAAAGATAGGGAGA 505918
i i i ii i v i
C IMPB_01#Satel 201 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.70
Transitions / transversions = 19.00 (38/2)
Gap_init rate = 0.01 (2 / 235), avg. gap size = 1.00 (2 / 2)
331 17.95 0.00 0.00 Crub_svsplocus 505727 505960 144040 C IMPB_01 Satellite 166 399 2149
331 17.95 0.00 0.00 Crub_svsplocus 505727 505960 (144040) C IMPB_01#Satellite (2149) 399 166 m_b10s001i21
Crub_svsplocu 505727 GAGAAAGAGAAAGAGGGAGAGAGAGAGGAAGGGAGAAAAAGAGGGAGGGA 505776
i i i ii i i i i i
C IMPB_01#Satel 399 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 350
Crub_svsplocu 505777 GAGAGAAAGAGAGGGAGAGAGTGGGGGAGAGAGAAAGAGAGAAAGAGGGA 505826
i i v i i i i i
C IMPB_01#Satel 349 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 300
Crub_svsplocu 505827 GAGAGAAAGAGGGAGAGAGAAAGAGAGATGAAGAGAGAGAAAGGGAGAGA 505876
i i i vii i i
C IMPB_01#Satel 299 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 250
Crub_svsplocu 505877 GGGAGAGAGAAAGAGGGAAAGAGAGGAAGAAAGATAGGGAGAAAGAAAGA 505926
i i i i ii i v i i i
C IMPB_01#Satel 249 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 200
Crub_svsplocu 505927 GGGAGAGAGAAAGAGGGAGAGAGAAAGAAAGAGA 505960
i i i i i
C IMPB_01#Satel 199 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.89
Transitions / transversions = 13.00 (39/3)
Gap_init rate = 0.00 (0 / 233), avg. gap size = 0.0 (0 / 0)
+ 16 5.3 0.0 0.0 Crub_svsplocus 505962 505981 (144019) + (GA)n Simple_repeat 1 20 (0) 298
ANNOTATION EVIDENCE:
16 5.27 0.00 0.00 Crub_svsplocus 505962 505981 144019 + (GA)n Simple_repeat 1 20 0
16 5.27 0.00 0.00 Crub_svsplocus 505962 505981 (144019) (GA)n#Simple_repeat 1 20 (0) m_b10s252i5
Crub_svsplocu 505962 GAGAGAGAGGGAGAGAGAGA 505981
i
(GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGA 20
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0)
+ 13 19.3 2.2 4.5 Crub_svsplocus 509701 509745 (140255) + (AATAATA)n Simple_repeat 1 44 (0) 299
ANNOTATION EVIDENCE:
13 19.26 2.22 4.55 Crub_svsplocus 509701 509745 140255 + (AATAATA)n Simple_repeat 1 44 0
13 19.26 2.22 4.55 Crub_svsplocus 509701 509745 (140255) (AATAATA)n#Simple_repeat 1 44 (0) m_b10s252i7
Crub_svsplocu 509701 AATAATACACAATACACTATAATATGATAAATGAAT-AATAAAAAA 509745
v i v iv - i - - v
(AATAATA)n#Si 1 AATAATAAATAATAAATAATAA-ATAATAAAT-AATAAATAATAAA 44
Matrix = Unknown
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.07 (3 / 44), avg. gap size = 1.00 (3 / 3)
+ 12 21.0 4.8 6.5 Crub_svsplocus 509746 509760 (140240) + (AAT)n Simple_repeat 4 62 (0) 300
ANNOTATION EVIDENCE:
12 21.03 4.76 6.45 Crub_svsplocus 509698 509760 140240 + (AAT)n Simple_repeat 1 62 0
12 21.03 4.76 6.45 Crub_svsplocus 509698 509760 (140240) (AAT)n#Simple_repeat 1 62 (0) m_b10s252i6
Crub_svsplocu 509698 AACAATAATACACAATACACTATAAT-ATGATAAATGAATAATAA-AA-A 509744
i - i - iv - i - - - -
(AAT)n#Simple 1 AATAATAATA-ATAATA-ATAATAATAATAAT-AAT-AATAATAATAATA 46
Crub_svsplocu 509745 ACATTTGTAACAATAA 509760
i v vi i
(AAT)n#Simple 47 ATAATAATAATAATAA 62
Matrix = Unknown
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.11 (7 / 62), avg. gap size = 1.00 (7 / 7)
+ 12 23.8 3.9 1.9 Crub_svsplocus 513492 513542 (136458) + (TACTGC)n Simple_repeat 1 52 (0) 301
ANNOTATION EVIDENCE:
12 23.75 3.92 1.92 Crub_svsplocus 513492 513542 136458 + (TACTGC)n Simple_repeat 1 52 0
12 23.75 3.92 1.92 Crub_svsplocus 513492 513542 (136458) (TACTGC)n#Simple_repeat 1 52 (0) m_b10s252i8
Crub_svsplocu 513492 TAATGTTTCTGCTAGCTTTTAGTG--ACTTCTGCTGCTACTGCTATTGCT 513539
v i v - vi v -- v i i
(TACTGC)n#Sim 1 TACTGCTACTGCTA-CTGCTACTGCTACTGCTACTGCTACTGCTACTGCT 49
Crub_svsplocu 513540 CCT 513542
v
(TACTGC)n#Sim 50 ACT 52
Matrix = Unknown
Transitions / transversions = 0.67 (4/6)
Gap_init rate = 0.04 (2 / 50), avg. gap size = 1.50 (3 / 2)
+ 16 20.9 0.0 0.0 Crub_svsplocus 513926 513958 (136042) + A-rich Low_complexity 1 33 (0) 302
ANNOTATION EVIDENCE:
16 20.95 0.00 0.00 Crub_svsplocus 513926 513958 136042 + (A)n Simple_repeat 1 33 0
16 20.95 0.00 0.00 Crub_svsplocus 513926 513958 (136042) (A)n#Simple_repeat 1 33 (0) m_b10s252i9
Crub_svsplocu 513926 AAAAAAAAAACAATAAAACATAAAAGATAAAAA 513958
v v v v i v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 33
Matrix = Unknown
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 13 14.6 0.0 6.2 Crub_svsplocus 514470 514503 (135497) + (GTT)n Simple_repeat 1 32 (0) 303
ANNOTATION EVIDENCE:
13 14.60 0.00 6.25 Crub_svsplocus 514470 514503 135497 + (GTT)n Simple_repeat 1 32 0
13 14.60 0.00 6.25 Crub_svsplocus 514470 514503 (135497) (GTT)n#Simple_repeat 1 32 (0) m_b10s252i10
Crub_svsplocu 514470 GTTGTTGTTGTTAACTTGCTGTTGTTTTTCTTGT 514503
--v i v v
(GTT)n#Simple 1 GTTGTTGTTGTT--GTTGTTGTTGTTGTTGTTGT 32
Matrix = Unknown
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2)
+ 267 17.5 0.0 0.0 Crub_svsplocus 515321 515360 (134640) + AmnSINE2 SINE/tRNA-Deu 80 119 (239) 304
ANNOTATION EVIDENCE:
267 17.50 0.00 0.00 Crub_svsplocus 515321 515360 134640 + AmnSINE2 SINE/tRNA-Deu 80 119 239
267 17.50 0.00 0.00 Crub_svsplocus 515321 515360 (134640) AmnSINE2#SINE/tRNA-Deu 80 119 (239) m_b10s001i22
Crub_svsplocu 515321 CAAGGTTGACTCAGCCTTCCATCCTTTTGAGGTTGATAAA 515360
i i i i ii v
AmnSINE2#SINE 80 CAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAGATAAA 119
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.68
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 15 19.5 0.0 6.7 Crub_svsplocus 517548 517595 (132405) + A-rich Low_complexity 1 45 (0) 305
ANNOTATION EVIDENCE:
15 19.48 0.00 6.67 Crub_svsplocus 517548 517595 132405 + (AGAAAA)n Simple_repeat 1 45 0
15 19.48 0.00 6.67 Crub_svsplocus 517548 517595 (132405) (AGAAAA)n#Simple_repeat 1 45 (0) m_b10s252i11
Crub_svsplocu 517548 AGAGAAAGGAAATGAAAAGAGAAGCGGAGAGAAAGGAAAAGAAAAAGA 517595
i i v - --ii i i
(AGAAAA)n#Sim 1 AGAAAAAGAAAAAGAAAA-AGAA--AAAGAAAAAGAAAAAGAAAAAGA 45
Matrix = Unknown
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3)
16 17.40 0.00 4.88 Crub_svsplocus 517550 517592 132408 + (AGAAA)n Simple_repeat 1 41 0
16 17.40 0.00 4.88 Crub_svsplocus 517550 517592 (132408) (AGAAA)n#Simple_repeat 1 41 (0) m_b10s252i12
Crub_svsplocu 517550 AGAAAGGAAATGAAAAGAGAAGCGGAGAGAAAGGAAAAGAAAA 517592
i v - -v i i i
(AGAAA)n#Simp 1 AGAAAAGAAAAGAAAAGA-AA-AGAAAAGAAAAGAAAAGAAAA 41
Matrix = Unknown
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.05 (2 / 42), avg. gap size = 1.00 (2 / 2)
+ 14 24.9 3.0 4.5 Crub_svsplocus 518179 518245 (131755) + (TTCT)n Simple_repeat 1 66 (0) 306
ANNOTATION EVIDENCE:
14 24.91 2.99 4.55 Crub_svsplocus 518179 518245 131755 + (TTCT)n Simple_repeat 1 66 0
14 24.91 2.99 4.55 Crub_svsplocus 518179 518245 (131755) (TTCT)n#Simple_repeat 1 66 (0) m_b10s252i13
Crub_svsplocu 518179 TTATTTTTTATGTTTCTTT-GCTCTTGCTCTCCTTTCTTTCTTTTTTTCA 518227
v i - v -vi v - i i v
(TTCT)n#Simpl 1 TTCTTTCTT-TCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCT 48
Crub_svsplocu 518228 CTATTT-TATCTATTCCTT 518245
i v - v - i
(TTCT)n#Simpl 49 TTCTTTCTTTCT-TTCTTT 66
Matrix = Unknown
Transitions / transversions = 0.86 (6/7)
Gap_init rate = 0.08 (5 / 66), avg. gap size = 1.00 (5 / 5)
+ 15 27.6 0.0 0.0 Crub_svsplocus 518679 518717 (131283) + GA-rich Low_complexity 1 39 (0) 307
ANNOTATION EVIDENCE:
15 27.58 0.00 0.00 Crub_svsplocus 518679 518717 131283 + (AA)n Simple_repeat 1 39 0
15 27.58 0.00 0.00 Crub_svsplocus 518679 518717 (131283) (AA)n#Simple_repeat 1 39 (0) m_b10s252i14
Crub_svsplocu 518679 AAAAAAATCAATAAATTACAAAAAAAGAGAAAAAGAAAA 518717
vv v vv v i i i
(AA)n#Simple_ 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39
Matrix = Unknown
Transitions / transversions = 0.50 (3/6)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 381 21.4 5.6 0.0 Crub_svsplocus 519218 519306 (130694) + Plat_L3 LINE/CR1 3467 3560 (13) 308
ANNOTATION EVIDENCE:
381 21.35 5.62 0.00 Crub_svsplocus 519218 519306 130694 + Plat_L3 LINE/CR1 3467 3560 13
381 21.35 5.62 0.00 Crub_svsplocus 519218 519306 (130694) Plat_L3#LINE/CR1 3467 3560 (13) m_b10s001i23
Crub_svsplocu 519218 CAGCCATTTGTCTGAAACGGTATA--CGGTTTCCTTCCTGA--GCAGGGG 519263
? i ivii i v -- iv iv v i--
Plat_L3#LINE/ 3467 CANCCATCTGTCCTGGATGGTTTAGTCATTCACCTGCCTGGAGGCAGGGG 3516
Crub_svsplocu 519264 GTTGGACTAGATGACCTC-CAAGGTCCCTTCCAACTTTATTATT 519306
i i - i i i ?v
Plat_L3#LINE/ 3517 GCTGGACCAGATGACCTCTCGAGGTCCCTTCCAGCTCTANGATT 3560
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.03
Transitions / transversions = 2.17 (13/6)
Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.67 (5 / 3)
+ 913 31.7 3.3 3.5 Crub_svsplocus 522427 523305 (126695) + Gypsy72-I_DR LTR/Gypsy 1678 2341 (1927) 309
ANNOTATION EVIDENCE:
782 34.28 3.58 3.58 Crub_svsplocus 522427 523264 126736 + Gypsy138-I_DR LTR/Gypsy 3563 4400 7010
782 34.28 3.58 3.58 Crub_svsplocus 522427 523264 (126736) Gypsy138-I_DR#LTR/Gypsy 3563 4400 (7010) m_b10s001i24
Crub_svsplocu 522427 AGGAATATAGGGACCTTGCTGAAGTCTTCAGTGAGGAGAGGGCGAATGAG 522476
i i v i iiv i i vvvvi v v vvi
Gypsy138-I_DR 3563 AAGAATACATGGATCTCAGTGAAGTCTTTAGTAAGTCTCAGGCTACTTCA 3612
Crub_svsplocu 522477 CTTCCCCCCCACCGACCCACA-GACTGTATCATTGAATTCAAGCCTGGGG 522525
i v v i -i i - i vii i iivi i
Gypsy138-I_DR 3613 TTACCCCCGCATCG-TCCATATGATTGTTCTATTGAACTTGTACCTGGAG 3661
Crub_svsplocu 522526 CAAAACT--CCCGAAGCCCAGATTATACTCCATGAGCCCAAAGGAGAAGG 522573
iv i-- i i i-- i v v--i vvvvv i
Gypsy138-I_DR 3662 CAAGCCCACCTCGAGGT--AGATTGTACTCCCTC--TCCATTCCTGAAAG 3707
Crub_svsplocu 522574 AG--GAAATGGAAAGATTTATAAAAAAAAACCTGGAGAGAGGTTTCATTG 522621
i-- vv i i viv i vi iivi i v v v v
Gypsy138-I_DR 3708 AACTGCCATGGAGAAATACTTGAACGAGGCTCTAGACAGTGGATTCATTC 3757
Crub_svsplocu 522622 AGCC----AGCTAAGCCTAAAGTGGCTGCCCCGGTCCTTTTTAGAGAGAA 522667
iv ---- v v - iv vi v v i--- i ivvvvv
Gypsy138-I_DR 3758 GCCCTTCAACCTCA-CCTGCAGGAGCAGGCT---TCTTTTTTGTTTCCAA 3803
Crub_svsplocu 522668 GAAGGATGGCTCTTTACGTTTATGCGTGGATTATAGGGCCCTGAAT-ACA 522716
vvv i v viiv ii v i vii -
Gypsy138-I_DR 3804 GAAGGATGGGAGTCTTCGACCCTGTATTGATTATAGAGGTTTGAATCACA 3853
Crub_svsplocu 522717 --ATCAGTGAAAGCAACCTATACCCGCTGCCCCTCATGAAAGACA-TGCT 522763
-- i v -- - i vv ii i v --- -
Gypsy138-I_DR 3854 TCACCATT--AAG-AATCGTTACCCATTACCCCTAATGAA---CACTGCT 3897
Crub_svsplocu 522764 GTCACACCTATCGAAAGG-GAAA--ATTTTTTCTAAACTAGACTTAAGGG 522810
v ii- vv ii v i - vv -- i v v ii i i v ii
Gypsy138-I_DR 3898 TTTG-AGATACTGCAGGGCGCCACTATCTTTACGAAGTTGGACCTCAGAA 3946
Crub_svsplocu 522811 AACCTTACTATCGCGTGAGAATCAAGGAAGGGGACGAATGGAAGACCGCA 522860
vv i vv v i i i i v
Gypsy138-I_DR 3947 ATGCTTACCATCTGGTCAGGATCAAGGAAGGAGATGAGTGGAAGACCGCT 3996
Crub_svsplocu 522861 TTTAACTGCCCCATGGGGTGCTATCAATTCAAAGTCTTGCCATTTGG-AT 522909
vv ? ii vii v viv i vv v -v
Gypsy138-I_DR 3997 TTTAACACCCCNACAGGCCACTATGAATATCAGGTAATGCCCTTTGGCCT 4046
Crub_svsplocu 522910 TACAAGGGGGCCCTGCAGTCTT-TATGCAATTAATCAATGACGTTCTAAG 522958
ii -iv v v v -i v - v i i i v
Gypsy138-I_DR 4047 TGTAA-ATGCCCCAGCCGTCTTCCAGGC-ATTCATTAATGATGTCCTCAG 4094
Crub_svsplocu 522959 GGAGCACCTGTTTAAGGGG---GTCCTTGTTTACTTGGACGACATTCTTA 523005
---v v vi i--- ii i i v
Gypsy138-I_DR 4095 GGAG---ATGTTGAACAGATTTGTTTTCGTTTACTTGGATGACATACTTA 4141
Crub_svsplocu 523006 TCTTTACCGAAACAA--AAGAAGAACACGTCAAACTTGTCAGAGAGGTTT 523053
i v -- ii i-- v i i vv v v iv i
Gypsy138-I_DR 4142 TTTTTTC--AAGTAGCTATGAAGAGCATGTACAACATGTCCGGCAGGTTC 4189
Crub_svsplocu 523054 TAAAGAAGCTG-CGAGCCGCTCACCTATATGCCAAACTCTCAAAATGCGA 523102
vvvvv i -i v i vv - i vi ii i vvvi iv
Gypsy138-I_DR 4190 TCTCCCAGTTGTTGAGACACAGA-CTGTTCGTTAAGCTGGAGAAGAGCGA 4238
Crub_svsplocu 523103 ATTCCA-----CCAGGAAAGGATAGACTACCTAGGCT-ATCGCATATCCC 523146
----- --- vi v -i v i i i - v -- v
Gypsy138-I_DR 4239 ATTCCATGTCTCC---AAAGTGTCG-TTTCTTGGGTTCATAG--TATCCA 4282
Crub_svsplocu 523147 CACAGGGCATTGAAATGGACCCAGAGAAGGTCAGAGCAGTATTAGAATGG 523196
v iivi v v i i v iv i i ii i i v
Gypsy138-I_DR 4283 AATGTAGCCTTCAGATGGATCCTGGCAAGATTAAGGCAGTACTGGATTGG 4332
Crub_svsplocu 523197 GCACCACCCCGCACAAGAAAGCAACTACAAAGTTTCCTGGGCTTTGCAAA 523246
v v vi iv ivv iv iv v v ii v v
Gypsy138-I_DR 4333 CCACAACCATGTTCAGTTAAAGAGGTACAACGATTTTTGGGGTTTGCCAA 4382
Crub_svsplocu 523247 TTTTTACCGCCAATTCAT 523264
i vvi i
Gypsy138-I_DR 4383 TTTTTATCGGAGATTTAT 4400
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 45.78
Transitions / transversions = 1.01 (139/138)
Gap_init rate = 0.05 (46 / 837), avg. gap size = 1.30 (60 / 46)
913 33.05 3.41 3.24 Crub_svsplocus 522650 523265 126735 + Gypsy72-I_DR LTR/Gypsy 1678 2294 2003
913 33.05 3.41 3.24 Crub_svsplocus 522650 523265 (126735) Gypsy72-I_DR#LTR/Gypsy 1678 2294 (2003) m_b10s001i25
Crub_svsplocu 522650 GGTCCTTTTTAGAGA-GAAGAAGGATGGCTCTTTACGTTTATGCGTGGAT 522698
i i v v - i i i i iiiv i i i
Gypsy72-I_DR# 1678 GGTTCTTCTTTGTGAAGAAAAAGGATGGTTCTCTGCGCCCCTGCATAGAC 1727
Crub_svsplocu 522699 TATAGGGCCCTGAAT---ACAATCAGTGAAAGCAACCTATACCCGCTGCC 522745
v i vii --- i i v i --- i vi v i
Gypsy72-I_DR# 1728 TATCGAGGTTTGAATGACATAACCATTAAAA---ATCGGTACCCCCTACC 1774
Crub_svsplocu 522746 CCTCATGAAAGACAT--GCTGTCACACCTATCGAAAGGG--AAAATTTTT 522791
v i v---- v -- iv i- i v i v i -- i
Gypsy72-I_DR# 1775 GCTTATGT----CTTCGGCCTTCG-ATCTCTTGCAGGGGGCAAGATTTTT 1819
Crub_svsplocu 522792 TCTAAA-CTAGACTTAAGGGAACCTTACTATCGCGTGAGAATCAAGGAAG 522840
ivi -i i i v vi vv i v vv v v i i
Gypsy72-I_DR# 1820 CACAAAGTTGGACCTACGCAATGCTTACCATCTCGTCCGTATGAGGGAGG 1869
Crub_svsplocu 522841 GGGACGAATGGAAGACCGCATTTAACTGCCCCATGGGGTGCTATCAATTC 522890
v i vvv iv iii v v vi
Gypsy72-I_DR# 1870 GTGACGAATGGAAGACCGCATTCAACACGCCCACTGGGCATTTTGAATAT 1919
Crub_svsplocu 522891 AAAGTCTTGCCATTTGGATTACAAGGGGGC-CCTGCAGTCTTT-ATGCAA 522938
vvv i ii - vviiv - v - v -
Gypsy72-I_DR# 1920 CTTGTCCTGCCATTTGGGCT-CACCAATGCTCCAGCAGTCTTTCAGGC-A 1967
Crub_svsplocu 522939 TTAATCAATGACGTTCTAAGGGAGCACCTGTTTAAGGGG---GTCCTTGT 522985
i vi i i v vv i --- v v vvii--- ii
Gypsy72-I_DR# 1968 CTCGTCAACGATGTACTCCGAG---ACATGATTAATCAATTTGTTTTTGT 2014
Crub_svsplocu 522986 TTACTTGGACGACATTCTTATCTTTACCGAAACAAAAGAAGAACACGTCA 523035
i i i v ivvvi v viv i i v
Gypsy72-I_DR# 2015 TTATTTGGATGACATTCTTATTTTTTCTTCCGCCATGCAGGAACATGTCC 2064
Crub_svsplocu 523036 AACTTG-TCAGAGAGGTTTTAAAGAAGCTGCGAGCCGCTCACCTATATGC 523084
vi - i v - vi v ivi vi vviv v i i
Gypsy72-I_DR# 2065 AACACGTTCGGCGA-GTGCTACAACGGCTGCTGGAGAATCAGCTGTATGT 2113
Crub_svsplocu 523085 CAAACTCTCAAAATGCGAATTCCA---CCAGGAAAGGATAGACTACCTAG 523131
v ivivvvi i --- vv ---i vvv v i i
Gypsy72-I_DR# 2114 AAAGGCGGAGAAGTGCGAATTCCATGTCCAGTCA---GTTTCCTTCTTGG 2160
Crub_svsplocu 523132 GCTATCGCATATCCCCA---CAGGGCATTGAAATGGACCCAGAGAAGGTC 523178
vi --- viii ---v vv viv v v i
Gypsy72-I_DR# 2161 GACA---CATAATTTCAGTTGAGGGACTTCGCATGGACCCTGCGAAGGTT 2207
Crub_svsplocu 523179 AGAGCAGTATTAGAATGGGCACCACCCCGCACAAGAAAGCAACTACAAAG 523228
i v v iv v v i vi v vv vvii iv
Gypsy72-I_DR# 2208 AGGGCTGTCTCCGACTGGCCGCCACCCGACTCCCGAAAGGCGTTACAGCG 2257
Crub_svsplocu 523229 TTTCCTGGGCTTTGCAAATTTTTACCGCCAATTCATC 523265
v i v v i
Gypsy72-I_DR# 2258 GTTCCTGGGCTTCGCCAATTTTTACCGGCGATTCATC 2294
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.45
Transitions / transversions = 0.95 (96/101)
Gap_init rate = 0.05 (31 / 615), avg. gap size = 1.32 (41 / 31)
281 31.48 2.42 1.81 Crub_svsplocus 523141 523305 126695 + Gypsy164-I_DR LTR/Gypsy 1741 1906 1957
281 31.48 2.42 1.81 Crub_svsplocus 523141 523305 (126695) Gypsy164-I_DR#LTR/Gypsy 1741 1906 (1957) m_b10s001i26
Crub_svsplocu 523141 TATCCCCACAGGGCATTGAAATGGACCCAGAGAAGGTCAGAGCAGTATTA 523190
i v v vi vvi i v vv i v i vvi
Gypsy164-I_DR 1741 TGTCGCCAGAGGGAGTGCGAATGGATCCTGCCAAAGTGAAAGCAGTTGCA 1790
Crub_svsplocu 523191 GAATGGGCACCACCCCGCACAA--G-AAAGCAACTACAAAGTTTCCTGGG 523237
- v - iv i-- - i ii i- iv v i
Gypsy164-I_DR 1791 GA-TTGGC-CCACCCCAGACAGTCGCAAGGCGGCC-CAGCGATTTCTGGG 1837
Crub_svsplocu 523238 CTTTGCAAATTTTTACCGCCAATTCATCCCCTCATTTGCACAGATAGCCT 523287
v v v v ii i v vvv ivv i v ii
Gypsy164-I_DR 1838 GTTTGCCAATTTTTACAGACGGTTCATTCGCAATTTTAGTCAGGTTGCTC 1887
Crub_svsplocu 523288 TGCCCCTCACTAA-CTTAC 523305
i i v -
Gypsy164-I_DR 1888 TACCTCTGACTAATCTTAC 1906
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.21
Transitions / transversions = 0.89 (24/27)
Gap_init rate = 0.04 (6 / 164), avg. gap size = 1.17 (7 / 6)
284 24.44 3.70 6.06 Crub_svsplocus 523161 523295 126705 + Gypsy-223_DR-I LTR/Gypsy 2210 2341 1927
284 24.44 3.70 6.06 Crub_svsplocus 523161 523295 (126705) Gypsy-223_DR-I#LTR/Gypsy 2210 2341 (1927) m_b10s001i27
Crub_svsplocu 523161 ATGGACCCAGAGAAGG-TCAGAGCAGTATTAGAATGGGCACCACCCCGCA 523209
i - - v iv i v v -- iv
Gypsy-223_DR- 2210 ATGGATCCAGAGAAGGTTCAG-GCTGTGGTAAATTGGCCA--ACCCCAGA 2256
Crub_svsplocu 523210 ---CAAGAAAGCAACTACAAAGTTTCCTGGGCTTTGCAAATTTTTACCGC 523256
--- viv i -v i i v i i v v
Gypsy-223_DR- 2257 NTCCCGCAAGGC-CCTGCAGAGGTTTCTGGGCTTCGCCAATTTTTACCGG 2305
Crub_svsplocu 523257 CAATTCATCCCCTCATTTGCACAGATAGC-CTTGCCCCTC 523295
iv i i v -v --- vi - vi ?
Gypsy-223_DR- 2306 CGTTTTATTCGC-AATTT---CAGCCAGCTCGCGCNCCTC 2341
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.73
Transitions / transversions = 0.94 (15/16)
Gap_init rate = 0.08 (11 / 134), avg. gap size = 1.18 (13 / 11)
+ 369 32.0 3.2 2.8 Crub_svsplocus 523353 523809 (126191) + Gypsy69-I_DR LTR/Gypsy 2304 2741 (1504) 310
ANNOTATION EVIDENCE:
355 28.29 1.94 1.94 Crub_svsplocus 523353 523507 126493 + Gypsy39-I_DR LTR/Gypsy 4471 4625 424
355 28.29 1.94 1.94 Crub_svsplocus 523353 523507 (126493) Gypsy39-I_DR#LTR/Gypsy 4471 4625 (424) m_b10s001i28
Crub_svsplocu 523353 TGGACAATGGAGTGCCAAGCA-GCGTTTGAGAG-ACTAAAGAGACTTTTT 523400
v vi? i - - v i - i v- i v
Gypsy39-I_DR# 4471 TGGTCATCNGAATGCCA-GCATGCCTTTGAAAGTATTAAAGC-ACTTCTG 4518
Crub_svsplocu 523401 TCTGCCGAACCAGTACTAA-GGCACCCAGACATGGACAAGCCCTTCATAA 523449
v vv vv ii - -i i iv v v i i v
Gypsy39-I_DR# 4519 TGTGAAGCTCCAGTGTTAATGGC-TCCAAATTTCGAAAAGCCTTTTAAAA 4567
Crub_svsplocu 523450 TACAGGCAGATGCAAGTGATGTGGCAGTGGGGGCTGTGCTATTACAAGAA 523499
iv i v i v iv v v ii i i
Gypsy39-I_DR# 4568 TGGAGGTAGATGCAAGTGCTGTAGGAGCTGGCGCTGTCCTGCTGCAGGAA 4617
Crub_svsplocu 523500 AATGATGA 523507
i i v
Gypsy39-I_DR# 4618 GATAAGGA 4625
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 36.29
Transitions / transversions = 1.05 (22/21)
Gap_init rate = 0.04 (6 / 154), avg. gap size = 1.00 (6 / 6)
369 33.96 3.91 3.20 Crub_svsplocus 523375 523809 126191 + Gypsy69-I_DR LTR/Gypsy 2304 2741 1504
369 33.96 3.91 3.20 Crub_svsplocus 523375 523809 (126191) Gypsy69-I_DR#LTR/Gypsy 2304 2741 (1504) m_b10s001i29
Crub_svsplocu 523375 CGTTTGAGAGACTAAAGAGACTTTTTTCTGCCGAACCAGTACTAAGGCAC 523424
i v vvvvi iv ii ? v vi v i ii
Gypsy69-I_DR# 2304 CGTTTGAGAAACTTAAGACCAGCTTCACCACNGCACCCATTCTGAAACAC 2353
Crub_svsplocu 523425 CCAGACATGGACAAGCCCTTCATAATACAGGCAGATGCAAGTGA-TGTGG 523473
v vi? vvvi i vi ?v i ii ?vv? - i
Gypsy69-I_DR# 2354 CCCGACCCNGAGCTACCCTTCGTTGTNGAAGTGGATGCNTCNGACTATGG 2403
Crub_svsplocu 523474 CAGTGGGGGCTGTGCTATTACAAGAAAATGATGATGCAGT---ATTGCAA 523520
v - v ? i i vi?v i i i iv v--- i v v
Gypsy69-I_DR# 2404 CATTGGGG-CAGTNCTGTCACAACGNCACGGTAACCCAGGTAAACTCCAC 2452
Crub_svsplocu 523521 CCCTGTGCATATACATCCAAGAAACTCACGGAAACAGAACAGCGCTGGCC 523570
? v ? viv iviv v v i v viivi ivvv
Gypsy69-I_DR# 2453 CCNTGTGCTTNTTTTTCTCGCAAACTGACGGCAGCTGAAAGAAACTATGA 2502
Crub_svsplocu 523571 CGTATGGGAGAAGGAG--GCTT---ATGGGATACGTTGGGCATTACTCAC 523615
iv vi v i--i --- i--- v i-- i ivvviv
Gypsy69-I_DR# 2503 CGTGGGTAACAAGGAACTACTTTCNATGA---AGGC--GGCACTGGAAGA 2547
Crub_svsplocu 523616 ATGGCGACAGTTCCTGGAAGGCAACAAAATCC---CCTTCCAGGTGTGGA 523662
? v vv ? i viv i--- --- ? i vvvv
Gypsy69-I_DR# 2548 ATGGCGNCACTGGCTNGAGGGAGCCG---TCCATCCNTTCCAGATTATCA 2594
Crub_svsplocu 523663 CTGATCACAAAAATTTGGAAGCCCTGAAAACTTCCAGGAAACTCAATCCC 523712
v i ii ? ivviv v v v v ivi v i
Gypsy69-I_DR# 2595 CAGACCACAAAAACCTNGAGTATATCAAAAGTGCCCGACGACTAAACCCC 2644
Crub_svsplocu 523713 AAACAAGCCCGCTGGTCCCAGCATT-TTCACCAATTCCAATTTAAGCTCA 523761
i i i ? ii--i - vi? i v ---
Gypsy69-I_DR# 2645 AGACAGGCTCGNTGGTCTT--TATTCTTCACCCGNTTCAATTTTA---CA 2689
Crub_svsplocu 523762 AACATTTA----CCAGGAAGAAAGAACTTCCTGGCAGATGCACTATCTCG 523807
iv ii ---- v ?v ivivv v v
Gypsy69-I_DR# 2690 GTCACCTATCGCCCAGGCANCAAGAACCGTAAGGCAGATGCCCTCTCTCG 2739
Crub_svsplocu 523808 CA 523809
Gypsy69-I_DR# 2740 CA 2741
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.32
Transitions / transversions = 0.88 (67/76)
Gap_init rate = 0.05 (21 / 434), avg. gap size = 1.48 (31 / 21)
+ 231 26.4 0.0 0.0 Crub_svsplocus 524115 524167 (125833) + Gypsy69-I_DR LTR/Gypsy 3076 3128 (1190) 310
ANNOTATION EVIDENCE:
231 26.42 0.00 0.00 Crub_svsplocus 524115 524167 125833 + Gypsy97-I_DR LTR/Gypsy 3076 3128 1190
231 26.42 0.00 0.00 Crub_svsplocus 524115 524167 (125833) Gypsy97-I_DR#LTR/Gypsy 3076 3128 (1190) m_b10s001i30
Crub_svsplocu 524115 ACTTTACATTTAATTAAACGGCAATTTTGGTGGCCATCCATGAAAAAGGA 524164
v iv ii i i i v i iv vi
Gypsy97-I_DR# 3076 ACATTATTTTTGGTTAAACAGCGATTCTGGTGGCCAGCTATGGCACGGGA 3125
Crub_svsplocu 524165 CAT 524167
Gypsy97-I_DR# 3126 CAT 3128
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.02
Transitions / transversions = 1.80 (9/5)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 356 35.9 2.6 2.6 Crub_svsplocus 524312 524614 (125386) + Gypsy69-I_DR LTR/Gypsy 3280 3582 (742) 310
ANNOTATION EVIDENCE:
356 35.93 2.64 2.64 Crub_svsplocus 524312 524614 125386 + Gypsy-193_DR-I LTR/Gypsy 3280 3582 742
356 35.93 2.64 2.64 Crub_svsplocus 524312 524614 (125386) Gypsy-193_DR-I#LTR/Gypsy 3280 3582 (742) m_b10s001i31
Crub_svsplocu 524312 CAATGGGAATACTGTGGTCTGGACGGTCACGGACTTGTTTTCCAAACAGG 524361
i v i v i i vi v vii iv i v ivvv
Gypsy-193_DR- 3280 CAACGGCAACACGGTGATTTTAACCGTAGTGGACCGGTTCTCGAAGGCTG 3329
Crub_svsplocu 524362 TGCACTTTATCCCT-TGCCAAAAGATTCCCA-CTGCAAAAGCCTTAGCAA 524409
iv i ii - v -- v i- v v i vvvi ii
Gypsy-193_DR- 3330 CTCATTTCGTCCCTCTGCCCAAA--TTACCGTCAGCCAGAGAGACAGCGG 3377
Crub_svsplocu 524410 AACTTTTCATCCAACACAT-TTACAGATTGCATGGGGCACCCCAACG--C 524456
vvvi v iv v i - v iv - -- vi i --
Gypsy-193_DR- 3378 TTGCTGTCATTAATCACGTCTTTCGCATT-CATGG--CCTCCCGACGGAC 3424
Crub_svsplocu 524457 ATCATCTCTGACAGGGGGGTGCAATTTACGTCTGCATTTTGGAAGGAATT 524506
i vi i viv i iv iv i -
Gypsy-193_DR- 3425 GTGGTTTCTGACAGGGGGCCTCAGTTTATCTCTAAATTTTGGAGGGAA-T 3473
Crub_svsplocu 524507 TTTATC-CCTCTTAGGAACCACTCAGGGACTGACATCTAGCCACCACCCT 524555
i i -ii v i ii vv i v vv i i ivi i i
Gypsy-193_DR- 3474 TCTGTCGTTTATTGGGGGCCACTGTGAGTCTTTCGTCTGGCTTTCATCCC 3523
Crub_svsplocu 524556 CAAGGAAATGGGGGGGCTGAAAAAATGAACTCAGTA-CTTAAGCA-ATAT 524603
ii v i vvi i i i i iiv - v - i i- i -
Gypsy-193_DR- 3524 CAGAGTAACGGTCAGACCGAGAGAGCCAA-TCAGGATCTTGAGCGCACA- 3571
Crub_svsplocu 524604 TTAAGATGTTT 524614
iv
Gypsy-193_DR- 3572 TTGCGATGTTT 3582
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.39
Transitions / transversions = 1.36 (61/45)
Gap_init rate = 0.05 (15 / 302), avg. gap size = 1.07 (16 / 15)
+ 12 8.4 0.0 7.4 Crub_svsplocus 527263 527291 (122709) + (AATG)n Simple_repeat 1 27 (0) 311
ANNOTATION EVIDENCE:
12 8.44 0.00 7.41 Crub_svsplocus 527263 527291 122709 + (AATG)n Simple_repeat 1 27 0
12 8.44 0.00 7.41 Crub_svsplocus 527263 527291 (122709) (AATG)n#Simple_repeat 1 27 (0) m_b10s252i15
Crub_svsplocu 527263 AATGAAATAGAATGAGTGAATGAAAGAAT 527291
- - i v
(AATG)n#Simpl 1 AATG-AAT-GAATGAATGAATGAATGAAT 27
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2)
+ 225 15.2 16.9 0.0 Crub_svsplocus 527868 527926 (122074) + LTR13_v LTR/ERVK 583 651 (303) 312
ANNOTATION EVIDENCE:
225 15.25 16.95 0.00 Crub_svsplocus 527868 527926 122074 + LTR13_v LTR/ERVK 583 651 303
225 15.25 16.95 0.00 Crub_svsplocus 527868 527926 (122074) LTR13_v#LTR/ERVK 583 651 (303) m_b10s001i32
Crub_svsplocu 527868 AATAAAAGTACTTAATGG----GAAAATAAGAAATAGTGAT------TCT 527907
i i v ? v---- ? v? i i------ v
LTR13_v#LTR/E 583 AGTGAAAGTACTAAANGTCTTTGANAAGNAGAAATAATGACGTAAGCTGT 632
Crub_svsplocu 527908 CCCTCTCTCTCTTCTCTCT 527926
i
LTR13_v#LTR/E 633 CCCTCTCTCTCTCCTCTCT 651
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.14
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.03 (2 / 58), avg. gap size = 5.00 (10 / 2)
+ 371 14.8 7.1 1.2 Crub_svsplocus 528348 528444 (121556) C CR1-3_Croc LINE/CR1 (5) 3600 3517 313 *
ANNOTATION EVIDENCE:
371 13.92 6.25 1.19 Crub_svsplocus 528348 528427 121573 C CR1-3_Croc LINE/CR1 3517 3600 5
371 13.92 6.25 1.19 Crub_svsplocus 528348 528427 (121573) C CR1-3_Croc#LINE/CR1 (5) 3600 3517 m_b10s001i33
Crub_svsplocu 528348 AATAATATATAA-TAAAGTTGGAAGGGACCTT-GGAGGTCATCTAGTCCA 528395
v v v - ii i i-i
C CR1-3_Croc#LI 3600 AATCATAGAGAAGTAGGGCTGGAAGGGACCTCCAGAGGTCATCTAGTCCA 3551
Crub_svsplocu 528396 ACCCCCTG-CTCAGACAGGA--AACCCTATACCAA 528427
- v i -- v -
C CR1-3_Croc#LI 3550 ACCCCCTGCCTGAGGCAGGATCATCCCTAT-CCAA 3517
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.50
Transitions / transversions = 1.20 (6/5)
Gap_init rate = 0.06 (5 / 79), avg. gap size = 1.20 (6 / 5)
283 18.73 11.11 1.12 Crub_svsplocus 528364 528444 121556 C CR1-E5_fAlb LINE/CR1 216 304 23
283 18.73 11.11 1.12 Crub_svsplocus 528364 528444 (121556) C CR1-E5_fAlb#LINE/CR1 (23) 304 216 m_b10s001i34
Crub_svsplocu 528364 GTTGGAAGGGACCTTGGAGGTCATCTAG-TCCAA-CCCCCTGCT-CAGAC 528410
ii i - - i-ii i
C CR1-E5_fAlb#L 304 GTTGGAAGGGACCTTAAAGATCATCTAGTTCCAACCCCCCTGCCGTGGGC 255
Crub_svsplocu 528411 AGGAA-ACC-----CTATACCAACTTTATCAAATGCCTTA 528444
i - ----- v iv vv - ii
C CR1-E5_fAlb#L 254 AGGGACACCTTCCACTAGACCAGGTTGCTCAAA-GCCCCA 216
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 20.65
Transitions / transversions = 2.75 (11/4)
Gap_init rate = 0.07 (6 / 80), avg. gap size = 1.67 (10 / 6)
+ 2934 30.4 5.1 4.3 Crub_svsplocus 528427 530138 (119862) C L3 LINE/CR1 (1117) 2982 1259 314
ANNOTATION EVIDENCE:
2934 30.41 5.08 4.35 Crub_svsplocus 528427 530138 119862 C L3 LINE/CR1 1259 2982 1117
2934 30.41 5.08 4.35 Crub_svsplocus 528427 530138 (119862) C L3#LINE/CR1 (1117) 2982 1259 m_b10s001i35
Crub_svsplocu 528427 ACTTTATCAAATGCCTTACTGAGGTCCAAGTAAATTATATCCACAGCATT 528476
i i ii ii v i ? i i i
C L3#LINE/CR1 2982 ACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTGTCTACGGCATT 2933
Crub_svsplocu 528477 CCTCTGGTCCACTAATTTTGTCACTTGGTCAGAGAATGCAATAAGATTTG 528526
i i i i i i v v iivi i i v v i i --
C L3#LINE/CR1 2932 CCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGGAAATGAGGTT-- 2885
Crub_svsplocu 528527 TCTAGCTCTAGCATGATCTGTT-TTGACAAACCCATGTTGGCTTTTAGTA 528575
--- i - i ii - iiii i ii i
C L3#LINE/CR1 2884 ---AGTT-TGGCATGACTTGTTCTTAGTGAACCCATGCTGGCTCCTAGTG 2839
Crub_svsplocu 528576 ATGAC---TTTGTTCGCTA----CTT------CAT-TGTTTGATTATCTT 528611
v --- iv iv ---- i------ - i v iv
C L3#LINE/CR1 2838 ATCACCGCTTCCTTTTCTAAGTGCTCACAAACCATCTGTTTAATAATCCG 2789
Crub_svsplocu 528612 TTCCAGAATCTTCCCAGGTATTGAGGTCAGGCTGATAGATCTGTAGTT-C 528660
i i v i v i v i v iv i -?
C L3#LINE/CR1 2788 TTCTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTTN 2739
Crub_svsplocu 528661 CTGGATCTATTCCCCCCCCCCCTTTTTTTTTTTTTTTTTTGAAGATGGGA 528710
v i i i--------------- iii i i? i ?
C L3#LINE/CR1 2738 CAGAATCCATC---------------TTTTTTCCCTTTTTAAAANTAGGN 2704
Crub_svsplocu 528711 ACTACATCAGCTCTTTTCCAGTCCTCTGGTAGTTCCTCAGTGCTCCAGGA 528760
? iv i v i i i vi i v v iv
C L3#LINE/CR1 2703 ACNACATTTGCCCGTCTCCAGTCTTCTGGCACCTCTTCCGTTCTCCGTGA 2654
Crub_svsplocu 528761 CCTTTGAAAAATATAGTT-CAGTAGTTCTGAGATCACATCTGCCAGTTCT 528809
ii i v i - viv- ii i v v
C L3#LINE/CR1 2653 TTTCTCAAAGAT-TACCGACAGCGGTTCCGCGATCACATCTGCAAGTTCT 2605
Crub_svsplocu 528810 TTGAGAACCTTGGGGTGTAATCTATCTGGTCCTGGTGATCTGAACTCATC 528859
v v i i iii v v ii i
C L3#LINE/CR1 2604 TTCAGTACCCTGGGATGTAATTCGTCTGGGCCTGGAGACTTGAACTCATT 2555
Crub_svsplocu 528860 CATGCTGGATAAGTGCTCACTTACTATTTTCTTGCCCATCTTAA-CTTGT 528908
i vivi v i v i i ii i ii- vv
C L3#LINE/CR1 2554 TAAAGCGGCTAGGTGCTCTCTTACTATCTCCTCACCTATCTTGGGCTTCA 2505
Crub_svsplocu 528909 GTT---TCTAATCTATTTTTTATGGTACTGTTTTTGATAAGTTGAACTGT 528955
i --- v v v v -i vv iv iiii ---i -- v
C L3#LINE/CR1 2504 ATTCCCTCTTAACGATGTTT-GTTCTACCCTTTCCAGT---CTGAA--GA 2461
Crub_svsplocu 528956 TTCTTTTCCTTTGT-GTAAAGACAGATGCAAAAAAAATGAATTAAATAGT 529004
iv i vi - vi i v v i-- i i i
C L3#LINE/CR1 2460 TCATTCTCCTTGATAGAGAAGACGGAAGCAAAATAG--GAGTTGAGTAGT 2413
Crub_svsplocu 529005 TCTGTTTTCTCCCTGTTGCTTGATA--------CCTTCTTCCCCCACTAA 529046
i i iiii v -------- v v v vi i
C L3#LINE/CR1 2412 TCTGCTTTCTCTCTGTCATCTGTTAACATTACGCCATCTGCCCCAAGCAG 2363
Crub_svsplocu 529047 TGGACCAATAATTTCCTTCACTTTTTTATTGTTTTTTACATG---TTGAA 529093
i i vi v?i i --- ii vi i iivv i---
C L3#LINE/CR1 2362 CGGGCCTGTCNCTTTCTT---TTTCCTTCTGCTCCGAACATAGCTTTGAA 2316
Crub_svsplocu 529094 AGAAGC---TTTTTTGTTATTTTTGAC---TTTGGTCACAAGCCTTAGTT 529137
-- ---? i ii ii --- vv i i i
C L3#LINE/CR1 2315 A--AGCCTTNTTTTTGTTGTCCTTAGCATTTTTTTTCGCAAGCCTCAGCT 2268
Crub_svsplocu 529138 CACTTTGAGCCTTAGCTTTCCTCACCTCATCTTTGCAGGCTCAGACTAGT 529187
i i i i i v vii ii i iivi? v
C L3#LINE/CR1 2267 CATTCTGGGCTTTAGCCTTCCTGACACTATTCTTACAGGCTTGTGNTACT 2218
Crub_svsplocu 529188 TGCTGATATTCTG-CTTTAGTTATGTGCCCCTCTTTCCA-CTTTTTATAC 529235
iv ----i i - i i i i - - i v
C L3#LINE/CR1 2217 CTCT----CTTTGTCCTTGGTTATATGTCC-TCTTTCCATCTTCTGATAC 2173
Crub_svsplocu 529236 TTGTCCTTTTTATCTTTCAATTTATCAGTGAGTTCTTTATGCAGCCATGC 529285
v v vv i v ---i v i ? i ? i i
C L3#LINE/CR1 2172 ATGTCCTTTTAAAATCTGA---CATCAGAGAATNCTCTATGNAGCCACGT 2126
Crub_svsplocu 529286 TGGTTTCTTTTCAGAGCTGTTAATTTTCTTCTTTATTGG--TATTGTGCT 529333
vvvv vv viivv i i --i - -
C L3#LINE/CR1 2125 TGGTTTCTTAAATGCCCTCCCTCTTTTCTTCCTCATTGGATCATT-TG-T 2078
Crub_svsplocu 529334 AGACTG-GGCTTTTATTATCTCACTTTTCAAAATTACCCAAGCTTCTTGA 529382
- i -i --- i vv i i v i ii v ?v i
C L3#LINE/CR1 2077 A-ATTGTAG---TCAGAATTTCATTTTTAAGAGCTTCCCANCCCTCTTGA 2032
Crub_svsplocu 529383 GT--TGTTTCCCTTAGAAGATTCTCAT-CCATGGAATCCTTCCCAAGCCC 529429
i-- v ii v i--- ?v- v v iv--iii
C L3#LINE/CR1 2031 GCCATCTTTCTTTTTGAG---TCTCNGGCCATGGAATCATACCTC--TTT 1987
Crub_svsplocu 529430 TCTCTAATTTTATTGAAATTAGCT----CTCTTAAAGTCCAAGAC---TC 529472
i v v iv ---- v iiii --- v
C L3#LINE/CR1 1986 TCTCTGAATTTTTTGAAATCTGCTTTTCCTCGTAAAGTCTGGAACATATG 1937
Crub_svsplocu 529473 TAG---TTTGACTGTGTTCTATTGCTTGTGCTTCCATAATGTTAAATTCC 529519
i --- i --- iiv v - --- v i --- i i
C L3#LINE/CR1 1936 TGGACTTTTAACT---TTTCCTTTCTTG-GCT---ATTACG---AACTCT 1897
Crub_svsplocu 529520 AATATTGCATGATCACTTCCCCCCAAGGTTCCTGT-GGTTTCAACACCTT 529568
v vi i- i i i - ii v vi vi
C L3#LINE/CR1 1896 AAGATGACATGG-CACTTTCTCCCAAGGTTCCTATCGACTTCCACTTCAC 1848
Crub_svsplocu 529569 CTATCATTTTGTCTCTGTTAGTGAGGATTAGATCCAATATGGCCAATCCT 529618
v i v iv ii i v i ii ivi i viv i
C L3#LINE/CR1 1847 CAACCAGTTCTTCCTTGTTGGTCAGAATTAAGTCCAGAGTAGCAGTTCCC 1798
Crub_svsplocu 529619 CTAGTTCCCTTCTCTACTTTTTAGGAGACAAAGTTGTCTGCAAGTTTTGT 529668
v v i i i i ii ii i v vivv
C L3#LINE/CR1 1797 CTCGTTGCTTCCTCTACCTTCTGAGAGATGAAATTGTCAGCAAGGCAAGT 1748
Crub_svsplocu 529669 CAAGAATCTGTTTGATCTTCCACTTGGTGCAGAGTTTGTCTCCCAGTTGA 529718
i i iv vi ii vvv ? i vv v i iv
C L3#LINE/CR1 1747 CAAGAATTTATCAGATGCTCTGCTTTTAGCNGAATGAGACTTCCAGCAGA 1698
Crub_svsplocu 529719 TGTCAGGATAATTAAAGTCCCCCATTATTATTGTCATGTGCTT-CCTACA 529767
v i i i i i -? --- - vii
C L3#LINE/CR1 1697 TGTCCGGATAGTTGAAGTCCCCCATCACTACTG-NAT---CTTGCCTCTG 1652
Crub_svsplocu 529768 TACC---TTAGTTAGCTG-ACCAGCAAAAAGATCATCTATTTC--CCATT 529811
i --- v v v - i -i iv i ? -- i
C L3#LINE/CR1 1651 TGCCAGTTTTGTAATCTGTATCAG-GAAAGCATCATCCATNTCCTCCATC 1603
Crub_svsplocu 529812 TGGTTGGATAGCCTATAGTATACACCTATGGCAATGTCGTTT---TTTTC 529858
ii iii i i v i iii i i ii --- ii
C L3#LINE/CR1 1602 TGGCCGGGCGGTCTGTAGTATACTCCCACAACGATATCACTTCTGTTTCT 1553
Crub_svsplocu 529859 CTCTTTTTCTAT--TGACCCAAGGGCATTCAAGACAGTTTTCATCATTGC 529906
ii i -- v iv vi v ?vvv i ii i v --
C L3#LINE/CR1 1552 CTCTCCTTTTATCCTCACCCAAATGCTCTCCANCGCGCTTCTACCCT--C 1505
Crub_svsplocu 529907 TGTGCTCTT---TTTCTGTAGAGATGTAGTTAT-TTCTT-ATATAGAGAG 529951
v - i v --- iiiiv i -- - - i v v
C L3#LINE/CR1 1504 AG-GTTCGTGGATTTCCACGCAGGTGTA--TATCTTCTTGACATACAGTG 1458
Crub_svsplocu 529952 CAGCTCCACCT---CTTCTATTTGGTCTGCTTCTTTTAAATAATTTAAAT 529998
vi i? --- ? v i i i i vv ?v i
C L3#LINE/CR1 1457 CTACTCTNCCTCCCCTTCTANTAGATCTGTTTCTTTTGAACAAGGTNTAC 1408
Crub_svsplocu 529999 CCCTCTACCTGAGTGTTCCATTTGTGGG---------GCGATGTCTCCAT 530039
i i i vvv i v ii i ---------i v v vi
C L3#LINE/CR1 1407 CCTTCCATCGCCGTATTCCAGTCATGAGTCCCATCCCACCAAGTCTCGGT 1358
Crub_svsplocu 530040 GATGGCAACAATATCATATCGGCCCTCATTTACCTGAATTTCTAGTTCAC 530089
iv v ii v i ivi ii v v iiivi v ?
C L3#LINE/CR1 1357 GATACCTATGAGATCGTATTTACCTCCTTGTGTTAAAATTTCAAGTTNAC 1308
Crub_svsplocu 530090 CCTGTTTGCCCTTCATGCTCTATGCATTGGCGTACAGACATTTGAGTCC 530138
ii ? iiivii i i ii i i v
C L3#LINE/CR1 1307 TTTNTTTATTACCCATACTCTGTGCATTGGTATATAGACATCTGAGGCC 1259
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.26
Transitions / transversions = 1.90 (326/172)
Gap_init rate = 0.06 (110 / 1711), avg. gap size = 1.47 (162 / 110)
+ 13 29.9 0.0 0.0 Crub_svsplocus 530589 530637 (119363) + (AATTTGT)n Simple_repeat 1 49 (0) 315
ANNOTATION EVIDENCE:
13 29.94 0.00 0.00 Crub_svsplocus 530589 530637 119363 + (AATTTGT)n Simple_repeat 1 49 0
13 29.94 0.00 0.00 Crub_svsplocus 530589 530637 (119363) (AATTTGT)n#Simple_repeat 1 49 (0) m_b10s252i16
Crub_svsplocu 530589 AAATTGTCATTTCTGATTGGTGAGTTTAAATTTGTCTTTTCTAATTTGT 530637
v v v i v i v vv vv v
(AATTTGT)n#Si 1 AATTTGTAATTTGTAATTTGTAATTTGTAATTTGTAATTTGTAATTTGT 49
Matrix = Unknown
Transitions / transversions = 0.20 (2/10)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 14 25.4 1.9 1.9 Crub_svsplocus 535553 535605 (114395) + (GCCGCA)n Simple_repeat 1 53 (0) 316
ANNOTATION EVIDENCE:
14 25.36 1.89 1.89 Crub_svsplocus 535553 535605 114395 + (GCCGCA)n Simple_repeat 1 53 0
14 25.36 1.89 1.89 Crub_svsplocus 535553 535605 (114395) (GCCGCA)n#Simple_repeat 1 53 (0) m_b10s252i17
Crub_svsplocu 535553 GCCCCACCAGCAGCCGTAGCCTCCCCCGCAGCGGCAGGCCTC-GCCACAG 535601
v v v i v vv v - v - i
(GCCGCA)n#Sim 1 GCCGCAGCCGCAGCCGCAGCCGCAGCCGCAGCCGCA-GCCGCAGCCGCAG 49
Crub_svsplocu 535602 CTGC 535605
i
(GCCGCA)n#Sim 50 CCGC 53
Matrix = Unknown
Transitions / transversions = 0.38 (3/8)
Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2)
+ 452 33.1 4.9 4.4 Crub_svsplocus 538057 538714 (111286) + L2-13_DRe LINE/L2 363 1482 (1131) 317
ANNOTATION EVIDENCE:
283 36.44 3.23 3.41 Crub_svsplocus 538057 538644 111356 + L2-2_DRe LINE/L2 2611 3197 1041
283 36.44 3.23 3.41 Crub_svsplocus 538057 538644 (111356) L2-2_DRe#LINE/L2 2611 3197 (1041) m_b10s001i36
Crub_svsplocu 538057 TTTCCCGCAACCTTTAAAGGAAGCGGTGGTGAAGCCCCTCCTCAAGAAGC 538106
i i v? v - v i viv i vv v v v i
L2-2_DRe#LINE 2611 TTCCCCACTNCATTTAA-GCAGGCTAGGGTAACCCCACTGCTAAAGAAAC 2659
Crub_svsplocu 538107 CTTCCCTGGACC-CA-GCTGTTTTGAAGAACTTTCGTCCTGTCTCCAACC 538154
ivv -i - ii - - viv v v v vvv
L2-2_DRe#LINE 2660 CCAACCTGGACCATACGCTACTT-GAA-AACTACAGACCAGTATCCCTGC 2707
Crub_svsplocu 538155 TCCCCTTTGTGGGGAAGGTTGTAGAGAAGGTGGTGGCGTCC---CAACTC 538201
i v ii vv i v i i i --- i --- v
L2-2_DRe#LINE 2708 TTCCATTCATGGCCAAGATTCTGGAGAAAGTAGTG---TTCAATCAAGTC 2754
Crub_svsplocu 538202 TTGCGA--TCCTTGGATGAAACTAATTATCTGGACCCTTTTGAATCTGGT 538249
i - -- i ivvii - iviv vvivvvv i i
L2-2_DRe#LINE 2755 CTG-GACTTTCTTACTCAAAAC-AATCTCATGGACAACAAGCAATCCGGC 2802
Crub_svsplocu 538250 TTCAGGCCCGGCTACAGCACTGAGACTGCTTTGGTCGCACTGACCGATGA 538299
i i vvv i vvv ii v v iv viiv v
L2-2_DRe#LINE 2803 TTTAAGAAAGGCCACTCAACTGAGACTGCCCTGCTCTCGGTCGTGGAGGA 2852
Crub_svsplocu 538300 CCTCTGCCGAGCC----CGGGATACGGGTCAT---TCCTCTATCGTGGTG 538342
i v v vi i---- i iv viiii --- - iv v
L2-2_DRe#LINE 2853 TCTCAGACTGGCTAAAGCAGACTCTAAATCATCAGTCCTC-ATTTTGCTG 2901
Crub_svsplocu 538343 CTTCTTGACCTCTCAGCGGCTTTCGATACCATCGACCATGGTATCCTTCT 538392
------ i v v i i ii i iviv v
L2-2_DRe#LINE 2902 ------GACTTGTCAGCTGCTTTTGACACTGTCAACCACCAGATCCTGCT 2945
Crub_svsplocu 538393 GCAT-CGTCTCGGAGAGGTGGGGGTGGGTGGCACCGTATTGCGTTGGTTC 538441
iiv - - iivviv v v vv i vv i iv
L2-2_DRe#LINE 2946 ATCTACG-CTCGAGTCACTGGGCGTTGCGGGCACTGTTATACAATGGTTC 2994
Crub_svsplocu 538442 TCCTCCTACCTCTCTGACAGGTCGCAGTCAGTG----TTGGCGGGCGGAC 538487
vvv i -- v v ---- v -- v
L2-2_DRe#LINE 2995 AGATCTTACCTCTCTGACAGGT--CATTCAGGGTGTCTTGGAGG--GGAG 3040
Crub_svsplocu 538488 AGAGATCGACCCCTAGGCGCCTCGATCATGGGGTGCCTCAGGGCTCGGTC 538537
ivi v v ivvi ii vi ivv i i v i
L2-2_DRe#LINE 3041 AGGTGTCCAACCTACAGCATCTAAACACTGGGGTACCTCAAGGCTCTGTT 3090
Crub_svsplocu 538538 CTGTCCCCCCTCCTTTTTAACATTTACATGAAACCACTGGGTGAGATCAT 538587
vvvv v i i ivv i iivv i v i vvvii
L2-2_DRe#LINE 3091 CTTGGGCCACTTCTCTTCTCCATCTACACATCATCTCTAGGACCAGTCAT 3140
Crub_svsplocu 538588 TCATCGACACAGGGTGAGGTATCATCAGTACGCGGATGATACCCAATTGT 538637
i vv ii iv vvvv i iiiv i v ii i
L2-2_DRe#LINE 3141 CCAGAGACATGGATTCTCCTACCACTGCTATGCTGATGATACCCAGCTAT 3190
Crub_svsplocu 538638 ATATCTC 538644
iv
L2-2_DRe#LINE 3191 ACCTCTC 3197
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 49.71
Transitions / transversions = 0.90 (98/109)
Gap_init rate = 0.05 (28 / 587), avg. gap size = 1.39 (39 / 28)
394 35.19 2.47 1.63 Crub_svsplocus 538092 538455 111545 + AmnL2-1 LINE/L2 1116 1482 1131
394 35.19 2.47 1.63 Crub_svsplocus 538092 538455 (111545) AmnL2-1#LINE/L2 1116 1482 (1131) m_b10s001i37
Crub_svsplocu 538092 CCCTCCTCAAGAAGCCTTCCCTGGACCCAGCTGTTTTGAAGAACTTTCGT 538141
i i i i i v v viii i vvvv vi i
AmnL2-1#LINE/ 1116 CCCTTCTTAAAAAACCCTCCCTTGACCCCGACACTCTCTCTAACTACCGC 1165
Crub_svsplocu 538142 CCTGTCTCCAACCTCCCCTTTGTGGGGAAGGTTGTAGAGAAGGTGGTGGC 538191
i i i v vi v i vv v i i ivvi
AmnL2-1#LINE/ 1166 CCTATCTCTAACCTTCCCTTTCTCAGCAAAGTGCTTGAGAAAGTAGCCTT 1215
Crub_svsplocu 538192 GTCCCAACTCTTGCGATC--CTTGGATGAAACTAATTATC-TGGACCCTT 538238
v i v i- ii -- ivv iiv -- ? - v v?
AmnL2-1#LINE/ 1216 CTCTCATCTCTC-CAGTCACCTCTCACACAAC--ANTATCCTTGACCGNT 1262
Crub_svsplocu 538239 TTGAATCTGGTTTCAGGCCCGGCTACAGCACTGAGACTGCTTTGGTC--- 538285
v i v iv vi i i i v i i i vv ---
AmnL2-1#LINE/ 1263 TTCAGTCTGGGTTTCGCTCTGGCCATAGCACGGAAACCGCTCTCCTCCGT 1312
Crub_svsplocu 538286 GCACTGACCGATGACCTCTGCCGAGCCCGGGATACGGGTCATTCCTCTAT 538335
i v v --- iv vvv ivvv iv? iiv i iv
AmnL2-1#LINE/ 1313 GTAGTTA---ATGACCTCCTCCTTTCTGCTGATGANGGCTCTTTCTCCTT 1359
Crub_svsplocu 538336 CGTGGTGCTTCTTGACCTCTCAGCGGCTTTCGATACCATCGACCATGGTA 538385
v vi v i vvv i i i ii v vvi
AmnL2-1#LINE/ 1360 CCTCATTCTCCTTGACCTCAGTGCAGCCTTCGACACTGTGGACCATTCCA 1409
Crub_svsplocu 538386 TCCTTCTGCATCGTCT-CGGAG--AGGTGGGGGTGGGTGGCACCGTATTG 538432
i v i i - i? -- v ii v vvv iv v vi
AmnL2-1#LINE/ 1410 TCCTCCTGGACCGCCTCCANAGCTATGCAGGCGTCTCTGGTTCCCTCCTG 1459
Crub_svsplocu 538433 CGTTGGTTCTCCTCCTACCTCTC 538455
ivv iv v
AmnL2-1#LINE/ 1460 TCATGGTTCCGCTCCTACCTATC 1482
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 48.01
Transitions / transversions = 0.97 (62/64)
Gap_init rate = 0.03 (11 / 363), avg. gap size = 1.36 (15 / 11)
452 32.57 5.30 4.69 Crub_svsplocus 538133 538641 111359 + L2-13_DRe LINE/L2 363 874 1000
452 32.57 5.30 4.69 Crub_svsplocus 538133 538641 (111359) L2-13_DRe#LINE/L2 363 874 (1000) m_b10s001i38
Crub_svsplocu 538133 AACTTTCGTCCTGTCTCCAACCTCCCCTTTGTGGGGAAGGTTGTAGAGAA 538182
v v ii v ii v v vv i iv v ivi
L2-13_DRe#LIN 363 AACTATCGACCCATCTCAAATTTACCATTTGTGGCTAAAGTCCTTGAACG 412
Crub_svsplocu 538183 GGTGGTGGCGTCCCAACTCTTGCGATC--CTTGGATGAAACTAAT-TATC 538229
v i vv i-iii -- v- v vi v - i
L2-13_DRe#LIN 413 TGTGGTGGTGAGCCAACTCC-ATAATCATCTTC-ATGCAAACACTCTATT 460
Crub_svsplocu 538230 TGGACCCTTTTGAATCTGGTTTCAGGCCCGGCTACAGCACTGAGACTGCT 538279
iivvv i- i iv ? ii i i i
L2-13_DRe#LIN 461 TGAGAAATTTC-AGTCTGGTTTCAGAGCNGGTCACAGTACTGAAACTGCC 509
Crub_svsplocu 538280 TT------GGTCGCACTGACCGATGACCT--------CTGCCGAGCCCGG 538315
i ------ i ------i i -------- v vvvi
L2-13_DRe#LIN 510 CTAGTTAGGGTCGTA------AACGACCTTCTTCTAACTGCAGATAGTGG 553
Crub_svsplocu 538316 GATACGGGTCATTCCTCTATCGTGGTGCTTCTT-GACCTCTCAGCGGCTT 538364
iivi v v ----- ---- v - i v ? v
L2-13_DRe#LIN 554 GGCCTGTGGCATTC-----TCGT----CTTATTAGATCTCACNGCTGCTT 594
Crub_svsplocu 538365 TCGATACCATCGACCATGGTATCCTTCTGCATCGTCTCGGAGAGGTGGG- 538413
i i vvii ii v v v iv v i - i i-
L2-13_DRe#LIN 595 TTGACACCATATGTCACAGTATACTGCTGGACAGGCTCAG-GAAGTGGAT 643
Crub_svsplocu 538414 -GG--TGGGTGGCACCGTATTGCGTTGGTTCTCCTCCTACCTCTCTGACA 538460
- -- vv i v v vv i ivi i i v v
L2-13_DRe#LIN 644 TGGTTTGTCTGGTACAGTAATTAGCTGGTTTGTCTCTTATCTCGCTGACC 693
Crub_svsplocu 538461 GGTCGCAGTCAG--TGTTGGCGGGCGGACAGAGATC---GACCCCTAGGC 538505
v v iv -- --i i vv v --- ivi --v
L2-13_DRe#LIN 694 GCTCTCAGTTTGTCTGTT--TGGGTGCTCATAGATCTCGGACTGTT--CC 739
Crub_svsplocu 538506 GCCTCGATCATGGGGTGCCTCAGGGCTCGGTCCTGTCCCCCCTCCTTTTT 538555
iiv - v v v v v vvvi v v v
L2-13_DRe#LIN 740 GTTGC-ATCAGGGTGTTCCTCAGGGGTCTGTCCTTGGTCCACTGCTGTTT 788
Crub_svsplocu 538556 AACATTTACATGAAACCACTGGGTGAGATCATTCATCGACACAGGGTGAG 538605
ii i vvi v v iv i vvi vi i ii vv i
L2-13_DRe#LIN 789 AGTATTTATATGTTGCCTCTTGGCCAGATTATGAGTAAATATGGCTTGGG 838
Crub_svsplocu 538606 GTATCATCAGTACGCGGATGATACCCAATTGTATAT 538641
i iiiv v i i v v i
L2-13_DRe#LIN 839 GTACCACTGCTACGCTGATGACACTCAAATCTATGT 874
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.82
Transitions / transversions = 0.95 (77/81)
Gap_init rate = 0.07 (34 / 508), avg. gap size = 1.50 (51 / 34)
232 33.81 4.24 4.94 Crub_svsplocus 538267 538714 111286 + L2-33_DRe LINE/L2 102 546 902
232 33.81 4.24 4.94 Crub_svsplocus 538267 538714 (111286) L2-33_DRe#LINE/L2 102 546 (902) m_b10s001i39
Crub_svsplocu 538267 CACTGAGACTGCTTTGGTCGCACTGACCGATGACCTCTGCCGA--GCCCG 538314
vi iv vv ------ v i v -- --
L2-33_DRe#LIN 102 CACTGAGACTGCACTACTGTCACTGA------AGCCCTGCGGATTGCC-- 143
Crub_svsplocu 538315 GGATACGGGTCAT---TCCTCTATCGTGGTGCTTCTTGACCTCTCAGCGG 538361
-i vi i iv --- v ? iv v vi v v v v v
L2-33_DRe#LIN 144 -AAAGCAGGTTCTAAATCATCNATTCTGCTTTTACTGGACCTGTCTGCTG 192
Crub_svsplocu 538362 CTTTCGATACCATCGACCATGGTATCCTTCTG--CATCGTCTCGGAGAGG 538409
i vi vi i viv i v -- i v vvvi --
L2-33_DRe#LIN 193 CTTTTGATACGGTGAATCATCAGATTCTACTGTCCACCCTCTCCTCAA-- 240
Crub_svsplocu 538410 TGGGGGTGGGTGGCACCGTATTGCGTTGGTTCTCCTCCTACCTCTCTGAC 538459
vi viv v viii vi i vvvv i v i i
L2-33_DRe#LIN 241 TGGGCATCACTGGAACCCCGCTCTGCTGGTTGGAGTCTTACCTCACCGGC 290
Crub_svsplocu 538460 AGGTCGCAGTCAGTGTTGGCGGGCGGACAGAGATCGACCCCTAGGCGCCT 538509
i -- v v v v v iiv i -- i v- i v v
L2-33_DRe#LIN 291 AGAT--CATTCAGGGTTGCCTGGAGAGGAGAGGT--ATCCA-AAGCTCAT 335
Crub_svsplocu 538510 C----GATCA-TGGGGTGCCTCAGGG--CTCGGTCCTGTCCCCCCTCCTT 538552
---- i - i -- ? v i vi i iv
L2-33_DRe#LIN 336 CAGCTGGTCACTGGGGTACCTCAGGGATCTNGTTCTTGGTCCCCTTCTAT 385
Crub_svsplocu 538553 TTTAACATTTACATGAAACCACTGGGTGAGATCATTCATCGACACAGGGT 538602
-vi iv v i vivv i viv ii vv
L2-33_DRe#LIN 386 TTT-CTATTTACACCACATCACTGGGAACCATCATCCAATCACATGGTTT 434
Crub_svsplocu 538603 GAGGTATCATCAGTACGCGGATGATACCCAATTGTATATCTC----CACC 538648
vvvv iiv i v i v ii v v i ---- i
L2-33_DRe#LIN 435 CTCTTATCATTGTTATGCCGATGACACACAGCTCTATCTTTCATTTCATC 484
Crub_svsplocu 538649 CCG-TGTCCTTTCAGTGAAGCAGTCGACATGATGTGCCAGTGCCTGGAAG 538697
v - v --- ii -- i ii vv v v vv v i
L2-33_DRe#LIN 485 CAGATGACC---CAACG--GTAGCTGCAAGGATCTCGCACTGCCTGGAGG 529
Crub_svsplocu 538698 ATGTGAGGGTCTGGATG 538714
i vvv ii
L2-33_DRe#LIN 530 ATATCTCGGCTTGGATG 546
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.29
Transitions / transversions = 0.80 (64/80)
Gap_init rate = 0.07 (30 / 447), avg. gap size = 1.37 (41 / 30)
+ 237 26.0 0.0 0.0 Crub_svsplocus 538835 538884 (111116) + L2-36_DRe LINE/L2 1007 1056 (723) 318
ANNOTATION EVIDENCE:
237 26.00 0.00 0.00 Crub_svsplocus 538835 538884 111116 + L2-36_DRe LINE/L2 1007 1056 723
237 26.00 0.00 0.00 Crub_svsplocus 538835 538884 (111116) L2-36_DRe#LINE/L2 1007 1056 (723) m_b10s001i40
Crub_svsplocu 538835 GCAGGCACGCAACTTGGGTGTCCTCCTGGACTCACAGCTAAATTTGGAAC 538884
ii i ii v i v v i i i i
L2-36_DRe#LIN 1007 GCAGGTGCGTAATCTTGGTGTTCTCCTGGACTCCCAGCTTAGTCTGAAGC 1056
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 34.01
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 612 27.6 2.2 2.2 Crub_svsplocus 538964 539215 (110785) + X24_LINE LINE/L2 1 209 (105) 319
ANNOTATION EVIDENCE:
255 35.96 2.56 2.56 Crub_svsplocus 538964 539197 110803 + L2-42_DRe LINE/L2 2924 3157 412
255 35.96 2.56 2.56 Crub_svsplocus 538964 539197 (110803) L2-42_DRe#LINE/L2 2924 3157 (412) m_b10s001i41
Crub_svsplocu 538964 GGTCACTCATGCCCTTGTCACCTCAAGACTGGATTACTGTAATGCGCTCT 539013
iv ii i v vv v i i i i v vi v
L2-42_DRe#LIN 2924 GGTCATACATGCTTTTATCACGTCCCGCCTAGACTATTGCAATTCCTTAT 2973
Crub_svsplocu 539014 ACATGGGACTACCCTTGAAGAGCGTTCGGA-GGCTGCAGTTGGTTCAGAA 539062
ii v v - ii vvvv i v v - i i
L2-42_DRe#LIN 2974 ATGTTGGTCT-CCCTCAATCCTCATTGGCACGGTTGCAGTTGGTTCAAAA 3022
Crub_svsplocu 539063 TGCAGCCTCGAGAGCAATTGTGGGCGCGCCAAGGTACCCCCACATGTCAC 539112
i vv v vivv viii i vvv iii iv i i v
L2-42_DRe#LIN 3023 TGCGGCAGCTAGACTTTTAACAGGCACCAAAAAACATGCTCATATCTCAC 3072
Crub_svsplocu 539113 C-----TATCCTCCACGAGCTGCACTGGCTTCCTGTGGGTCTCCAGACGC 539157
----- v v ----- v i vii i ivii iv
L2-42_DRe#LIN 3073 CAGTTTTAGCATCC-----CTTCATTGGCTTCCTGTTAATTTTAGAATTC 3117
Crub_svsplocu 539158 AATTCAAGGTGTTGGTTATCACCTTTAAAGCCCTTCATGG 539197
i i v iv iiii v vv
L2-42_DRe#LIN 3118 AGTTCAAGATTTTACTTATTGTTTTTAAAGCACTGAATGG 3157
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 49.33
Transitions / transversions = 1.10 (43/39)
Gap_init rate = 0.03 (8 / 233), avg. gap size = 1.50 (12 / 8)
283 29.94 4.02 4.02 Crub_svsplocus 538970 539143 110857 + L2-8_DR LINE/L2 2976 3149 441
283 29.94 4.02 4.02 Crub_svsplocus 538970 539143 (110857) L2-8_DR#LINE/L2 2976 3149 (441) m_b10s001i42
Crub_svsplocu 538970 TCATGCCCTTGTCACCTCAAGACTGGATTACTGTAATGCGC-TCTACATG 539018
ii v i v v iv v iv - viv
L2-8_DR#LINE/ 2976 TCATGCTTTGGTTACATCACGGATTGATTACTGTAACTCGCTTCTCTCTG 3025
Crub_svsplocu 539019 GGACTACCCT--TGAAGAGCGTTCGGAGGCTGCAGTTGGTTCAGAATGCA 539066
v i -- -- i v i - iv i i i v
L2-8_DR#LINE/ 3026 GCATT--CCTGATAAACAAC-TTCATAGACTACAGTTGATTCAGAATTCA 3072
Crub_svsplocu 539067 GCCTCGAGAGCAATTGTGGGCGCGCCAAGGTACCCC----CACATGTCAC 539112
vv v iii i iivv v ---- ii ---- iv v
L2-8_DR#LINE/ 3073 GCGGCTAGGATAGTTACCTGCTCGC----GTACTTCTGATCACATAACTC 3118
Crub_svsplocu 539113 CTATCCTCCACGAGCTGCACTGGCTTCCTGT 539143
v i iviv v i
L2-8_DR#LINE/ 3119 CAATTCTCTTTCACCTGCACTGGCTCCCTGT 3149
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.83
Transitions / transversions = 1.08 (26/24)
Gap_init rate = 0.06 (10 / 173), avg. gap size = 1.40 (14 / 10)
612 26.83 1.91 1.91 Crub_svsplocus 539007 539215 110785 + X24_LINE LINE/L2 1 209 105
612 26.83 1.91 1.91 Crub_svsplocus 539007 539215 (110785) X24_LINE#LINE/L2 1 209 (105) m_b10s001i43
Crub_svsplocu 539007 GCGCTCTACATGGGACTACCCTTGAAGAGCGTTCGGAGGCTGCAGTTGGT 539056
i ?? vv i i v iii i v i
X24_LINE#LINE 1 GTGCTCNNCTGGGGGCTGCCCTTGAAGACCACCCGGAAGCTTCAGCTGGT 50
Crub_svsplocu 539057 TCAGAATGCAGC--CTCGAGAGC--AATTGTGGGCGCGCCAAGGTACCCC 539102
v -- vvv -- ?v v?v vv ? vi ---
X24_LINE#LINE 51 GCAGAATGCAGCGGCTCGTCTGCTGAANGGTGTNAGCCACANGGAGC--- 97
Crub_svsplocu 539103 CACATGTCACCTATCCTCCACGAGCTGCACTGGCTTCCTGTGGGTCTCCA 539152
- vv i v i iiv v ?i vv ii i
X24_LINE#LINE 98 -ACATTACACCTGTGCTCCGCAGTCTGCACTGGCTACCNATTTGCTTCCG 146
Crub_svsplocu 539153 GACGCAATTCAAGGTGTTGGTTATCACCTTTAAAGCCCTTCATGGCATAG 539202
iii ii v v i v vi iv i
X24_LINE#LINE 147 AGTGCAATTCAAGGTGTTGACTTTAATCTATAAAGCCCTATATGGTTTGG 196
Crub_svsplocu 539203 GGCCAGGTTACTT 539215
v v i
X24_LINE#LINE 197 GCCCTGGTTACCT 209
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.30
Transitions / transversions = 0.96 (27/28)
Gap_init rate = 0.03 (6 / 208), avg. gap size = 1.33 (8 / 6)
+ 19 0.0 0.0 0.0 Crub_svsplocus 539582 539605 (110395) + (AAAT)n Simple_repeat 1 24 (0) 320
ANNOTATION EVIDENCE:
19 0.00 0.00 0.00 Crub_svsplocus 539582 539605 110395 + (AAAT)n Simple_repeat 1 24 0
19 0.00 0.00 0.00 Crub_svsplocus 539582 539605 (110395) (AAAT)n#Simple_repeat 1 24 (0) m_b10s252i18
Crub_svsplocu 539582 AAATAAATAAATAAATAAATAAAT 539605
(AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAAT 24
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 696 32.6 4.2 3.8 Crub_svsplocus 539672 540241 (109759) C MamGypsy2-I LTR/Gypsy (743) 3423 2946 321
ANNOTATION EVIDENCE:
448 35.15 4.16 3.78 Crub_svsplocus 539672 540224 109776 C Gypsy-175_DR-I LTR/Gypsy 1515 2069 894
448 35.15 4.16 3.78 Crub_svsplocus 539672 540224 (109776) C Gypsy-175_DR-I#LTR/Gypsy (894) 2069 1515 m_b10s001i44
Crub_svsplocu 539672 TTGGTGTTATAACCATGCGTTCCACTTGGCTGTTAGAGTCCGGGGGGAAA 539721
i ivv i ivi ii v v v i v i
C Gypsy-175_DR- 2069 TTGATGTCTGAACCATGCGTTCCGCCAAGCCATTCGTGGCTGGGTGAAAA 2020
Crub_svsplocu 539722 GGAACCGAAGTG-GCATGCCTAATCATATTTGCCTTTAAGAAG-GACTGA 539769
vi?v - i - ii iv i - ivv iv i i- v i
C Gypsy-175_DR- 2019 GGTGNAGA-GCGTGTGTGTGTGA-CACCGTTAGCTTTGAGAAATGTCTGG 1972
Crub_svsplocu 539770 AACTCTGCAGAAGTAAATTGAGCCCCATTGTCTGAGACTATAACATCTGG 539819
vv vi i i i v vv i vvvi i vv v
C Gypsy-175_DR- 1971 AACTCGTCCAAGGTGAACTTAGGACCATTATCGCTAACCAGCACTTCTGG 1922
Crub_svsplocu 539820 GAGCCCATGTGTTGCAAAATGCTGTGC--AAAACCTGGATGGTTCTGGCA 539867
i v -i vi v iv v -- iv i i ii v
C Gypsy-175_DR- 1921 AAGGCCATG-ATGACTAAATAATGTCCTCAGCACTTGAATGGTCTTTGCA 1873
Crub_svsplocu 539868 GTAGTCATAGTGGA---CACTGGAATGACCTCTAGCCACTTGCAGTGACT 539914
vv --- v --- iiiv vvv i vi vv vi
C Gypsy-175_DR- 1872 GATGT---AGTTGAATCCATCACACACACTTCGGGCCACTTTGAGTGAGC 1826
Crub_svsplocu 539915 GTCCACAACAATGAAGAAGAATTGCCCCTTAAAGGGGCCAGCAAAATCAA 539964
i i v? i i iiv viv i i v i v i v
C Gypsy-175_DR- 1825 ATCTACTNCGACGAGACACGTTTGTCCCTCAAATGGACCAGCATAGTCTA 1776
Crub_svsplocu 539965 TATGAATCCTCGACCAAGGGG-CTTGTGTGGTC--TCCCATCTATGTACA 540011
i v v vivi i - i--- i -- i vvvi vi
C Gypsy-175_DR- 1775 CATGCATACGTTGCCAAGGAGACTC---TGGCCATTTCCAGGGGTGTAAG 1729
Crub_svsplocu 540012 GGAGCATGT---GGCATTTCTGGCCTTGACTGCTGGCAAATGTGGCACCT 540058
v v --- iii i i v --- i iivv i vi
C Gypsy-175_DR- 1728 GGAGAAGGTCCAGGTGCTTTTAGCGTT---TGTTGGCAGGACTGACAGTT 1682
Crub_svsplocu 540059 GTG-GAC--CTGGGCCTCGATATCTT---TATCGAGCCCAGGCCACCAAA 540102
v- -- ---i v --- --- i i vv v i
C Gypsy-175_DR- 1681 GTTTGACAACTG---TTCTA---CTTGAGTGTCAATGCCTGGCCACCAGA 1638
Crub_svsplocu 540103 GGTAGCTGCGTGTGAGTGCCTTCATTGGGACTATTCCCAGATGTCCCTCA 540152
vi i vv i ii v v v v iv ii ivi
C Gypsy-175_DR- 1637 CATAACGCCGCGCAACTGCCTTCATTCGCACGACACCTGGATGTCCTGTA 1588
Crub_svsplocu 540153 TGCAGAGAATCA---AGGATTCTAGCCCTCAGTGAGGTTGGGATTACTAC 540199
--- i?v --- v ii i vi v i vvi vv i v
C Gypsy-175_DR- 1587 T---GAANTTCAGGCAGCACCCTGGATCGCAATTTAGGAGGAATAACTAC 1541
Crub_svsplocu 540200 CCTACTGCCCCACA-AATACAACCCT 540224
v v - v i i
C Gypsy-175_DR- 1540 CCTCCTTCCCCACATAAGACAGCCTT 1515
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 46.68
Transitions / transversions = 1.05 (96/91)
Gap_init rate = 0.06 (33 / 552), avg. gap size = 1.33 (44 / 33)
696 32.09 4.20 3.77 Crub_svsplocus 539766 540241 109759 C MamGypsy2-I LTR/Gypsy 2946 3423 743
696 32.09 4.20 3.77 Crub_svsplocus 539766 540241 (109759) C MamGypsy2-I#LTR/Gypsy (743) 3423 2946 m_b10s001i45
Crub_svsplocu 539766 CTGAAACTCTGCAGAAGTAAATTGAGCCCCATTGTCTGAGACTATAACAT 539815
v vi v i vv v v i v iii
C MamGypsy2-I#L 3423 CTTAAACTCAACTGAGGTAAATGCAGACCCATTGTCAGAAACGATAGTGT 3374
Crub_svsplocu 539816 CTGGGAGCCCATGTGTTGCAAAATGCT-GTGCAAAACCTGGATGGTTCTG 539864
v ii i vvi - i i i ivv v vii
C MamGypsy2-I#L 3373 CTGGCAATCCGTGTGTTGCAAATAACTGGCGCAGAGCTGTGATTGTTGCA 3324
Crub_svsplocu 539865 GCAGTAGTCATAG-TGGACACTGGAATGACCTCTAGCCACTTGCAGTGAC 539913
vi ivv - - i i vv i v i vv viiv
C MamGypsy2-I#L 3323 GCAGAGGTTTGAGATGGA-ACTAGGAGCACTTCGAGCCATTTTGAGAAGG 3275
Crub_svsplocu 539914 TGTCCACAACAATGAAGAAGAATTGCCCCTTAAAGGGGCCAGCAAAATCA 539963
v i v v vvi v vi v v v
C MamGypsy2-I#L 3274 AGTCTACCACAATCAAGAAGTTCTTCCCCTGGAATGGTCCTGCAAAATCA 3225
Crub_svsplocu 539964 ATATGAATCCTCGACCAAGGGGCTTGTGTGGTCTCCCATCTATGTA---- 540009
i i i -- v - v ii- i v ----
C MamGypsy2-I#L 3224 ATATGGATTCTTGACCAA--GGCTTCT-TGGTCACTT-TCCATGGAAAAG 3179
Crub_svsplocu 540010 CAGGAGCATGTGGCATTTCTGGCCTTGACTG--CTGGCAAATGTGGCACC 540057
i v v v ivv ivv -- v i-- vi ivi i
C MamGypsy2-I#L 3178 TAGGTGCCTTTGGCGGGTTATGCC--GAGTAGCCTGGCATGTGCTACACT 3131
Crub_svsplocu 540058 TGTGGACCTGGGCC---TCGATATCTTTATCGAGCCCAGGCCACCAAAGG 540104
iv vv ---i i --- i vvv i vi i vi
C MamGypsy2-I#L 3130 CCTTTAC---AGTCTTTTCAATATCAGAATCAATTCCAGGCCACCAGACA 3084
Crub_svsplocu 540105 TAGCTGCGTGTGAGTGCCTTCATTGGGACTATTCCCAGATGTCCCTCATG 540154
v vv iv i i vv i v i v iv
C MamGypsy2-I#L 3083 TAGCTTCTAGCCAATGCTTTCATGCGAACAATTCCCGGATGTGCTGCATG 3034
Crub_svsplocu 540155 CAGAG-AATCAAG-------GATTCTAGCCCTCAGTGAGGTTGGGATTAC 540196
i v -iii ------- vviv i -------- i v
C MamGypsy2-I#L 3033 TAGTGTGGCCAAGATAACGTGATGACCGCCTTC--------TGGAATAAC 2992
Crub_svsplocu 540197 TACCCTACTGCCCCAC-AAATACAACCCTTATAAGTGGATAACTCA 540241
v iv v i v i- vi v i ii ii
C MamGypsy2-I#L 2991 AATGCGATTTCCCCATAAAAGGCATCCTTTATGGGCAGATAACTCA 2946
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.92
Transitions / transversions = 0.93 (71/76)
Gap_init rate = 0.05 (26 / 475), avg. gap size = 1.46 (38 / 26)
+ 554 7.0 0.0 0.0 Crub_svsplocus 540374 540444 (109556) C URR1A DNA/hAT-Charlie (0) 226 156 322
ANNOTATION EVIDENCE:
554 7.04 0.00 0.00 Crub_svsplocus 540374 540444 109556 C URR1A DNA/hAT-Charlie 156 226 0
554 7.04 0.00 0.00 Crub_svsplocus 540374 540444 (109556) C URR1A#DNA/hAT-Charlie (0) 226 156 m_b10s001i46
Crub_svsplocu 540374 CAGTGGTTCTCAACCTTTCTAATGCCGCGACCCCATAATACAGTTCCCCA 540423
i i iv i
C URR1A#DNA/hAT 226 CAGTGGTTCTCAACCTTCCTAATGCTGCGACCCTTTAATACAGTTCCTCA 177
Crub_svsplocu 540424 TGTTGTGGTGACCCCCAACCA 540444
C URR1A#DNA/hAT 176 TGTTGTGGTGACCCCCAACCA 156
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.49
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 425 14.5 0.0 0.0 Crub_svsplocus 540510 540578 (109422) C URR1A DNA/hAT-Charlie (157) 69 1 322
ANNOTATION EVIDENCE:
425 14.49 0.00 0.00 Crub_svsplocus 540510 540578 109422 C URR1B DNA/hAT-Charlie 1 69 156
425 14.49 0.00 0.00 Crub_svsplocus 540510 540578 (109422) C URR1B#DNA/hAT-Charlie (156) 69 1 m_b10s001i47
Crub_svsplocu 540510 TTTGGCGACCCCCGTGAAATGGTTGTTCGACCCCAAATGTGGTCCCGACC 540559
v i v i v v v v
C URR1B#DNA/hAT 69 TTAGGCGACCCCTGTGAAAGGGTCGTTCGACCCCCAAAGGGGTCGCGACC 20
Crub_svsplocu 540560 CACAGGTTGAGAACAACTG 540578
vi
C URR1B#DNA/hAT 19 CACAGGTTGAGAACCGCTG 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 12.99
Transitions / transversions = 0.43 (3/7)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
+ 395 25.7 2.7 1.6 Crub_svsplocus 540777 540939 (109061) C MamGypsy2-I LTR/Gypsy (1776) 2655 2508 323
ANNOTATION EVIDENCE:
245 25.32 1.25 1.25 Crub_svsplocus 540777 540856 109144 C Gypsy156-I_DR LTR/Gypsy 4002 4081 2330
245 25.32 1.25 1.25 Crub_svsplocus 540777 540856 (109144) C Gypsy156-I_DR#LTR/Gypsy (2330) 4081 4002 m_b10s001i48
Crub_svsplocu 540777 TGTAGTGAACAACCCCAGAAGTGGCTTGTGGTCAGTGAAGACTGTGAAGT 540826
i i vviv vv i v v v v v i v
C Gypsy156-I_DR 4081 TGTAGTAAGCACATACACTAGCGGGTTGTTGTCAGTTAATACAGTAAACT 4032
Crub_svsplocu 540827 GGTG-GCCATACAAAAAGTCATGAAACTTTT 540856
v- -i i i
C Gypsy156-I_DR 4031 T-TGCACCGTACAAAAAGTCATGAAATTTTT 4002
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 27.52
Transitions / transversions = 0.67 (8/12)
Gap_init rate = 0.03 (2 / 79), avg. gap size = 1.00 (2 / 2)
395 26.05 4.14 2.03 Crub_svsplocus 540795 540939 109061 C Gypsy163-I_DR LTR/Gypsy 2508 2655 1776
395 26.05 4.14 2.03 Crub_svsplocus 540795 540939 (109061) C Gypsy163-I_DR#LTR/Gypsy (1776) 2655 2508 m_b10s001i49
Crub_svsplocu 540795 AAGTGGCTTGTGGTCAGTGAAGACTGTGAAGTGGTGGCCATACAAAAAGT 540844
i iv vv i v vii v v iv v
C Gypsy163-I_DR 2655 AAGTGGCCTGTGGTCAGTGAGCAGAGTAAATTTACGTCCAAACAAGTACT 2606
Crub_svsplocu 540845 CATGAAACTTTTT--ATGCCCACCACAATAGTCAATGATTTCCTATCTAT 540892
vi i -- ii v vi v i v v ii vv v
C Gypsy163-I_DR 2605 GGTGGAACTTTTTTTACACCAAATACAATTGCCAAAGCTTCTCGTTCGAT 2556
Crub_svsplocu 540893 TTGTGCGTAATTGCGTTCTGCAGCAGAA---AGAGTCCTGGA-GTAATAG 540938
i -- - ? i--- v - i v
C Gypsy163-I_DR 2555 TTGTGCGTAATTAC--TCT-CNGCAGAGTTTAGAGTCCTTGATGCAAAAG 2509
Crub_svsplocu 540939 C 540939
C Gypsy163-I_DR 2508 C 2508
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 31.46
Transitions / transversions = 0.85 (17/20)
Gap_init rate = 0.04 (6 / 144), avg. gap size = 1.50 (9 / 6)
+ 13 20.3 2.8 0.0 Crub_svsplocus 541352 541387 (108613) + (CTCAC)n Simple_repeat 1 37 (0) 324
ANNOTATION EVIDENCE:
13 20.27 2.78 0.00 Crub_svsplocus 541352 541387 108613 + (CTCAC)n Simple_repeat 1 37 0
13 20.27 2.78 0.00 Crub_svsplocus 541352 541387 (108613) (CTCAC)n#Simple_repeat 1 37 (0) m_b11s252i0
Crub_svsplocu 541352 CTC-CCCCACCTTGCCTCGCCTTACCTCACTTCACCT 541387
- i ii i i i
(CTCAC)n#Simp 1 CTCACCTCACCTCACCTCACCTCACCTCACCTCACCT 37
Matrix = Unknown
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1)
+ 554 7.0 0.0 0.0 Crub_svsplocus 541661 541731 (108269) C URR1A DNA/hAT-Charlie (0) 226 156 325
ANNOTATION EVIDENCE:
554 7.04 0.00 0.00 Crub_svsplocus 541661 541731 108269 C URR1A DNA/hAT-Charlie 156 226 0
554 7.04 0.00 0.00 Crub_svsplocus 541661 541731 (108269) C URR1A#DNA/hAT-Charlie (0) 226 156 m_b11s001i6
Crub_svsplocu 541661 CAGTGGTTCTCAACCTTTCTAATGCCGCGACCCCATAATACAGTTCCCCA 541710
i i iv i
C URR1A#DNA/hAT 226 CAGTGGTTCTCAACCTTCCTAATGCTGCGACCCTTTAATACAGTTCCTCA 177
Crub_svsplocu 541711 TGTTGTGGTGACCCCCAACCA 541731
C URR1A#DNA/hAT 176 TGTTGTGGTGACCCCCAACCA 156
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.49
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)
+ 259 15.1 0.0 16.0 Crub_svsplocus 541785 541797 (108203) + CYRA11_Mm Satellite/Y-chromosome 317 386 (226) 326
ANNOTATION EVIDENCE:
259 15.05 0.00 16.00 Crub_svsplocus 541785 541871 108129 + CYRA11_Mm Satellite/Y-chromosome 317 391 226
259 15.05 0.00 16.00 Crub_svsplocus 541785 541871 (108129) CYRA11_Mm#Satellite/Y-chromosome 317 391 (226) m_b11s001i7
Crub_svsplocu 541785 GCGGACAGACTTGTTTGGCGACCCCCGTGAAATGGTTGTTCGACCCCAAA 541834
i i v i--- ?-- ----- v -
CYRA11_Mm#Sat 317 GCAGATAGTCTTA---GGCGACCCCCGTGAAAN--TTGT-----CACAA- 355
Crub_svsplocu 541835 TGGGGTCCCGACACACAGGTTGAGAACCACTGGGCTA 541871
- v v v v v i
CYRA11_Mm#Sat 356 -GGGCTCGCGACCCACAGGTTGAGAACCACAGTGCCA 391
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.57
Transitions / transversions = 0.57 (4/7)
Gap_init rate = 0.14 (12 / 86), avg. gap size = 1.00 (12 / 12)
+ 446 13.0 0.0 0.0 Crub_svsplocus 541798 541866 (108134) C URR1A DNA/hAT-Charlie (157) 69 1 325
ANNOTATION EVIDENCE:
446 13.04 0.00 0.00 Crub_svsplocus 541798 541866 108134 C URR1B DNA/hAT-Charlie 1 69 156
446 13.04 0.00 0.00 Crub_svsplocus 541798 541866 (108134) C URR1B#DNA/hAT-Charlie (156) 69 1 m_b11s001i8
Crub_svsplocu 541798 TTTGGCGACCCCCGTGAAATGGTTGTTCGACCCCAAATGGGGTCCCGACA 541847
v i v i v v v v
C URR1B#DNA/hAT 69 TTAGGCGACCCCTGTGAAAGGGTCGTTCGACCCCCAAAGGGGTCGCGACC 20
Crub_svsplocu 541848 CACAGGTTGAGAACCACTG 541866
i
C URR1B#DNA/hAT 19 CACAGGTTGAGAACCGCTG 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 11.27
Transitions / transversions = 0.50 (3/6)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
+ 1251 34.7 3.0 3.1 Crub_svsplocus 541959 542816 (107184) C MamGypsy2-I LTR/Gypsy (1812) 2354 1498 323
ANNOTATION EVIDENCE:
1251 34.66 3.03 3.15 Crub_svsplocus 541959 542816 107184 C MamGypsy2-I LTR/Gypsy 1498 2354 1812
1251 34.66 3.03 3.15 Crub_svsplocus 541959 542816 (107184) C MamGypsy2-I#LTR/Gypsy (1812) 2354 1498 m_b11s001i9
Crub_svsplocu 541959 TGCTCATTGAAATGAGCCAACACCGCATTTGATGACAACAATGCCTTAAC 542008
i i v vi i i v vv iv v v i ivv i
C MamGypsy2-I#L 2354 TGTTCATCGTAATGTACTAGCACAGACTCGGAAGTCAATAACTGCTTGAC 2305
Crub_svsplocu 542009 -TGCTGCAGAAC-TTCTCTTGTGGACACTCGTCCACTTCCATGGA--GCC 542054
- v i v i i - i v iv i iv-- viv i --
C MamGypsy2-I#L 2304 ATTCCGGAAAGCGTCCTCATGCTGGCGA--GTCCAACGCCACGGAACGCC 2257
Crub_svsplocu 542055 TTCTTGTCCAAGAGCCAGTATAATGGCTCTGCCACTGTGGCCTTGTGGGT 542104
i i-- iv v ii iv i v v iv v v v -
C MamGypsy2-I#L 2256 TTTTC--CCAGTAGGCGATGAAGTGGCTCAGCAATGGTTGCCTTTTGTG- 2210
Crub_svsplocu 542105 GGAGGAGAGTGTGATAAAAGTTAAGGAGTCCCAGGAAGGCCTGAAGCTCT 542154
i i i iii i i i i v i i
C MamGypsy2-I#L 2209 GAAGAAAAACATGGTAGAAATTGAGTAGCCCCAGGAAGGCTTGAAGCTCT 2160
Crub_svsplocu 542155 CCCTTCGTCTTGGGACTTGGTGCCTGCTGAATTGCTTTGAGCTTGGATTC 542204
iv i i v v v i v vv i vivv v ivv v
C MamGypsy2-I#L 2159 TGCTTTGTTTTTGGAGTAGGCGCGTCATGGATTGCACGTACCTTATCTTG 2110
Crub_svsplocu 542205 AGCAGGATGAATGCCTTTGGCATCTATACGAAACTCCAGGAA-----CTC 542249
ii i i vvii iv i iv vi i i ----- v
C MamGypsy2-I#L 2109 AGTGGGGTGAATACCAGCAGCATTGATGCGGTAGCCTAAGAAGGTGACAC 2060
Crub_svsplocu 542250 TGTGGAAGTGACCCCAATTTTACATTTCTCCTGTTTGTGCTTCAG--CCC 542297
-- ---i i i - vii - i --v
C MamGypsy2-I#L 2059 TG--GAAGT---TCCGATTTCACATTTCTCCT-TTTTCAC-TCGGATACC 2017
Crub_svsplocu 542298 CGCTTCACAGAAATGTTGCAATATGGCCCGGAGCCTGTCAGTGAG---AC 542344
i v vi iv i v i iv ivv i i i v v i --- i
C MamGypsy2-I#L 2016 TGATGTATCGAAACGATGTAGGACTTCCTGAAGTCTTTCCGCGAGTTCAT 1967
Crub_svsplocu 542345 TTTTGACTGATTCCCCAGCTATGAGGACATCATTGAATTATGGGCATACA 542394
ii ivii -- -iv v i v vvvi
C MamGypsy2-I#L 1966 CCTCTGTTGAT--CCCA-TGATCAGGACATCATCGAAATATGGTACCACA 1920
Crub_svsplocu 542395 CCCTGAATGTT-----GCAGAGTGTTCGCTCCATTACACTCTGAAAAATG 542439
iv vi ----- i ----- v vi v i v
C MamGypsy2-I#L 1919 CCTGGAATCCTAGAAAGCAGGGT-----CTCCATGAAGCACTGGAAAATT 1875
Crub_svsplocu 542440 CCCAGGGCTACATTAACCCTGAACTGTAACCGTTGCACTTTGAAGGCTCC 542489
vi v vv ii i v iv i vv iv v i
C MamGypsy2-I#L 1874 CCAGGGGCAACAGAAATTCCGAACTGAAGGCGCTTAACTCGGAATGCCCC 1825
Crub_svsplocu 542490 CCTGTGAGTTACAATGGTTTGGGCCTCAGCCGTGGCATCTTCCACCGGCA 542539
i vi v ii v v v v i vi v viv
C MamGypsy2-I#L 1824 TCGATGAGTGATGATTGTTTGGGCGTCTGCAGTAGCATCACCGACGATCA 1775
Crub_svsplocu 542540 GCTGCGGATAGGCCTGGGCCAAATCTAATTTGGCAAAAATGAGACCT--- 542586
iv i i v ii v i v ----- ---
C MamGypsy2-I#L 1774 GCTGTTGATAAGCTTGGGCAAGGTCAAGTTTTGCAA-----AGACCTTTT 1730
Crub_svsplocu 542587 -CCCTGTAGAGATGCCAAAATG-TGGCTGACTACAAGCACCGGACAGGAG 542634
- v i iii iiv iiv - ii i i i i v i
C MamGypsy2-I#L 1729 CCCCAGCAAGAACAGCAAGGAGTTGATTGACTGCAGGCACTGGATATGGG 1680
Crub_svsplocu 542635 TGCTGCTGGAGAGCTTTGTTTAGCATGCATTTATAGCCGGCACAAATGCG 542684
vi v i i i vvi i i i vv vv v
C MamGypsy2-I#L 1679 TGCTGCTTAAGTGCCTTATTCACAGTGCACTTGTAGTCTCCACAAAGTCT 1630
Crub_svsplocu 542685 GACTTCTCCGTTGGCCTTAAGTGGCATGACAATTGGAGTTTCCCA-TGGA 542733
v i iv i i v v iv ivvi vi vv -i i
C MamGypsy2-I#L 1629 CACCTTACCATTAGGCTTTAGTACCGGCGCAATTGGTATAGCCCACCGGG 1580
Crub_svsplocu 542734 T-TGCTATCCACTGGCTCTAAGATGCCTTGCTGCAATAGCTTGTCCAGTT 542782
- - i -v i v i iii i vv v v vv v i
C MamGypsy2-I#L 1579 TATG-TGT-AACTGGTTCGAGGGCACCTTGTTTGATTAGATGCTCAAGCT 1532
Crub_svsplocu 542783 CTGAATTGATTCTCTGCTTTAGGGCAAAAGGCAC 542816
vvv ii? i i v i i i
C MamGypsy2-I#L 1531 CTTCTTCANTTTTTTTCCTTAGAGCAAAAGGTAC 1498
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 43.64
Transitions / transversions = 1.20 (157/131)
Gap_init rate = 0.05 (39 / 857), avg. gap size = 1.36 (53 / 39)
+ 20 0.0 0.0 3.6 Crub_svsplocus 546623 546651 (103349) + (TTAT)n Simple_repeat 1 28 (0) 327
ANNOTATION EVIDENCE:
20 0.00 0.00 3.57 Crub_svsplocus 546623 546651 103349 + (TTAT)n Simple_repeat 1 28 0
20 0.00 0.00 3.57 Crub_svsplocus 546623 546651 (103349) (TTAT)n#Simple_repeat 1 28 (0) m_b11s252i1
Crub_svsplocu 546623 TTATTTATTTTATTTATTTATTTATTTAT 546651
-
(TTAT)n#Simpl 1 TTATTTA-TTTATTTATTTATTTATTTAT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1)
+ 259 26.9 0.0 0.0 Crub_svsplocus 546738 546804 (103196) + hAT-N78_DR DNA/hAT-Charlie 1 67 (252) 328
ANNOTATION EVIDENCE:
259 26.87 0.00 0.00 Crub_svsplocus 546738 546804 103196 + hAT-N78_DR DNA/hAT-Charlie 1 67 252
259 26.87 0.00 0.00 Crub_svsplocus 546738 546804 (103196) hAT-N78_DR#DNA/hAT-Charlie 1 67 (252) m_b11s001i10
Crub_svsplocu 546738 CAGGGCTTTTCAACCGGTGCTACGTGTACCACTAGTTATATGCAACCACC 546787
v v i v v v vi i iv vi
hAT-N78_DR#DN 1 CAGTGGTTCTCAAACTGTGGTACGTGTACCACTAGTGGTACGCAGGCTTC 50
Crub_svsplocu 546788 TGGCTGGTGGTATGCGG 546804
ivv i i
hAT-N78_DR#DN 51 CTTCTAGTGGTACGCGG 67
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.21
Transitions / transversions = 0.80 (8/10)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0)
+ 79 0.0 0.0 0.0 Crub_svsplocus 547138 547204 (102796) + (TC)n Simple_repeat 1 67 (0) 329
ANNOTATION EVIDENCE:
79 0.00 0.00 0.00 Crub_svsplocus 547138 547204 102796 + (TC)n Simple_repeat 1 67 0
79 0.00 0.00 0.00 Crub_svsplocus 547138 547204 (102796) (TC)n#Simple_repeat 1 67 (0) c_b11s251i0
Crub_svsplocu 547138 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 547187
(TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50
Crub_svsplocu 547188 TCTCTCTCTCTCTCTCT 547204
(TC)n#Simple_ 51 TCTCTCTCTCTCTCTCT 67
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0)
+ 1325 19.4 0.1 0.7 Crub_svsplocus 548239 548897 (101103) C IMPB_01 Satellite (2153) 654 1 330
ANNOTATION EVIDENCE:
1325 18.30 0.00 4.78 Crub_svsplocus 548239 548479 101521 C IMPB_01 Satellite 166 395 2153
1325 18.30 0.00 4.78 Crub_svsplocus 548239 548479 (101521) C IMPB_01#Satellite (2153) 395 166 m_b11s001i11
Crub_svsplocu 548239 GAGAGAGAGTGAGAGAGAGGGAGGAAGAAAGAGAGGGAGAGAAAGAGAGA 548288
v i ii i i i
C IMPB_01#Satel 395 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 346
Crub_svsplocu 548289 GGGAAAGAGAGGGAGAAAGATAGGGAGAATGAAAGAGAGAGAAAGAGAGA 548338
i i i i v i iv i i
C IMPB_01#Satel 345 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 296
Crub_svsplocu 548339 GGGAAAAGAGAAAGAGGGAGAGAGAGAGGAAGGAAGAGAAAGAGGGAGGG 548388
--- i i i ii ii i i i
C IMPB_01#Satel 295 G---AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 249
Crub_svsplocu 548389 AGAGAGGAAGAAAGAGAAAGACGGACAGAGAGGGAGAGAGAAATAGAGAT 548438
ii i i -- v i i v -
C IMPB_01#Satel 248 AGAGAGAGAGAGAGAGAGAGA--GAGAGAGAGAGAGAGAGAGAGAGAGA- 202
Crub_svsplocu 548439 GAAGAGAGAGAATGCAAGAGAGAAGGAAACAGAAAGAGAGA 548479
-i ----i ii i v i
C IMPB_01#Satel 201 -GAGAGAGAGA----GAGAGAGAGAGAGAGAGAGAGAGAGA 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 22.05
Transitions / transversions = 6.00 (36/6)
Gap_init rate = 0.05 (11 / 240), avg. gap size = 1.00 (11 / 11)
247 21.28 0.00 1.70 Crub_svsplocus 548345 548583 101417 C IMPB_01 Satellite 166 400 2148
247 21.28 0.00 1.70 Crub_svsplocus 548345 548583 (101417) C IMPB_01#Satellite (2148) 400 166 m_b11s001i12
Crub_svsplocu 548345 AGAGAAAGAGGGAGAGAGAGAGGAAGGAAGAGAAAGAGGGAGGGAGAGAG 548394
i i ii ii i i i
C IMPB_01#Satel 400 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 351
Crub_svsplocu 548395 GAAGAAAGAGAAAGACGGACAGAGAGGGAGAGAGAAATAGAGATGAAGAG 548444
ii i i vi v i i v vii
C IMPB_01#Satel 350 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 301
Crub_svsplocu 548445 AGAGAATGCAAGAGAGAAGGAAACAGAAAGAGAGAGGGAAAGAGAGGGAG 548494
----i ii i v i i i i
C IMPB_01#Satel 300 AGAGA----GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 255
Crub_svsplocu 548495 AAAGATAGGGAGAAAGAGAAAGGGAGAAAGAGAAAGAGGGAGAGAGAAGG 548544
i v i i i i i i i ii
C IMPB_01#Satel 254 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 205
Crub_svsplocu 548545 AGGGAGGAAGAGAGAAAAAGAGGGAGAGGGAGGGAGAGA 548583
i ii i i i i i
C IMPB_01#Satel 204 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.85
Transitions / transversions = 7.33 (44/6)
Gap_init rate = 0.02 (4 / 238), avg. gap size = 1.00 (4 / 4)
229 21.29 0.00 2.55 Crub_svsplocus 548369 548609 101391 C IMPB_01 Satellite 166 400 2148
229 21.29 0.00 2.55 Crub_svsplocus 548369 548609 (101391) C IMPB_01#Satellite (2148) 400 166 m_b11s001i13
Crub_svsplocu 548369 AGGAAGAGAAAGAGGGAGGGAGAGAGGAAGAAAGAGAAAGACGGACAGAG 548418
ii i i i ii i i vi v
C IMPB_01#Satel 400 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 351
Crub_svsplocu 548419 AGGGAGAGAGAAATAGAGATGAAGAGAGAGAATGCAAGAGAGAAGGAAAC 548468
i i v vii ------ ii i v
C IMPB_01#Satel 350 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAG------AGAGAGAGAGAGAG 307
Crub_svsplocu 548469 AGAAAGAGAGAGGGAAAGAGAGGGAGAAAGATAGGGAGAAAGAGAAAGGG 548518
i i i i i v i i i i
C IMPB_01#Satel 306 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 257
Crub_svsplocu 548519 AGAAAGAGAAAGAGGGAGAGAGAAGGAGGGAGGAAGAGAGAAAAAGAGGG 548568
i i i ii i ii i i i
C IMPB_01#Satel 256 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 207
Crub_svsplocu 548569 AGAGGGAGGGAGAGAAAAAGAGGGAGAGGGAGGGAGAGAGA 548609
i i i i i i i
C IMPB_01#Satel 206 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.85
Transitions / transversions = 7.33 (44/6)
Gap_init rate = 0.03 (6 / 240), avg. gap size = 1.00 (6 / 6)
341 21.94 0.00 0.00 Crub_svsplocus 548397 548633 101367 C IMPB_01 Satellite 164 400 2148
341 21.94 0.00 0.00 Crub_svsplocus 548397 548633 (101367) C IMPB_01#Satellite (2148) 400 164 m_b11s001i14
Crub_svsplocu 548397 AGAAAGAGAAAGACGGACAGAGAGGGAGAGAGAAATAGAGATGAAGAGAG 548446
i i vi v i i v vii
C IMPB_01#Satel 400 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 351
Crub_svsplocu 548447 AGAATGCAAGAGAGAAGGAAACAGAAAGAGAGAGGGAAAGAGAGGGAGAA 548496
iv vi ii i v i i i i i
C IMPB_01#Satel 350 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 301
Crub_svsplocu 548497 AGATAGGGAGAAAGAGAAAGGGAGAAAGAGAAAGAGGGAGAGAGAAGGAG 548546
v i i i i i i i ii
C IMPB_01#Satel 300 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 251
Crub_svsplocu 548547 GGAGGAAGAGAGAAAAAGAGGGAGAGGGAGGGAGAGAAAAAGAGGGAGAG 548596
i ii i i i i i i i i
C IMPB_01#Satel 250 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 201
Crub_svsplocu 548597 GGAGGGAGAGAGAAAGAGAGGGAGAAAGAAAGAGGTA 548633
i i i i i i i
C IMPB_01#Satel 200 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATA 164
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 27.71
Transitions / transversions = 5.50 (44/8)
Gap_init rate = 0.00 (0 / 236), avg. gap size = 0.0 (0 / 0)
261 21.55 0.00 0.00 Crub_svsplocus 548441 548672 101328 C IMPB_01 Satellite 167 398 2150
261 21.55 0.00 0.00 Crub_svsplocus 548441 548672 (101328) C IMPB_01#Satellite (2150) 398 167 m_b11s001i15
Crub_svsplocu 548441 AGAGAGAGAATGCAAGAGAGAAGGAAACAGAAAGAGAGAGGGAAAGAGAG 548490
iv vi ii i v i i i
C IMPB_01#Satel 398 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 349
Crub_svsplocu 548491 GGAGAAAGATAGGGAGAAAGAGAAAGGGAGAAAGAGAAAGAGGGAGAGAG 548540
i i v i i i i i i i
C IMPB_01#Satel 348 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 299
Crub_svsplocu 548541 AAGGAGGGAGGAAGAGAGAAAAAGAGGGAGAGGGAGGGAGAGAAAAAGAG 548590
ii i ii i i i i i i i
C IMPB_01#Satel 298 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 249
Crub_svsplocu 548591 GGAGAGGGAGGGAGAGAGAAAGAGAGGGAGAAAGAAAGAGGTAGAAAGAG 548640
i i i i i i i iv i
C IMPB_01#Satel 248 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 199
Crub_svsplocu 548641 AAGGAGAGAGAGAGGAAGGGAGAGAAAGAGGG 548672
ii ii i i i
C IMPB_01#Satel 198 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 167
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 27.44
Transitions / transversions = 9.00 (45/5)
Gap_init rate = 0.00 (0 / 231), avg. gap size = 0.0 (0 / 0)
233 19.92 0.00 2.12 Crub_svsplocus 548468 548708 101292 C IMPB_01 Satellite 166 401 2147
233 19.92 0.00 2.12 Crub_svsplocus 548468 548708 (101292) C IMPB_01#Satellite (2147) 401 166 m_b11s001i16
Crub_svsplocu 548468 CAGAAAGAGAGAGGGAAAGAGAGGGAGAAAGATAGGGAGAAAGAGAAAGG 548517
i i i i i v i i i i
C IMPB_01#Satel 401 CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 352
Crub_svsplocu 548518 GAGAAAGAGAAAGAGGGAGAGAGAAGGAGGGAGGAAGAGAGAAAAAGAGG 548567
i i i ii i ii i i i
C IMPB_01#Satel 351 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 302
Crub_svsplocu 548568 GAGAGGGAGGGAGAGAAAAAGAGGGAGAGGGAGGGAGAGAGAAAGAGAGG 548617
i i i i i i i i i
C IMPB_01#Satel 301 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 252
Crub_svsplocu 548618 GAGAAAGAAAGAGGTAGAAAGAGAAGGAGAGAGAGAGGAAGGGAGAGAAA 548667
i i iv i ii ii i i
C IMPB_01#Satel 251 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 202
Crub_svsplocu 548668 GAGGGGGGAGAGAAAAAGAGGGAGAAAGAGAAAGAGGGAGA 548708
----- i i i i i i
C IMPB_01#Satel 201 GA-----GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 166
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.13
Transitions / transversions = 22.50 (45/2)
Gap_init rate = 0.02 (5 / 240), avg. gap size = 1.00 (5 / 5)
276 19.48 0.43 0.00 Crub_svsplocus 548553 548783 101217 C IMPB_01 Satellite 167 398 2150
276 19.48 0.43 0.00 Crub_svsplocus 548553 548783 (101217) C IMPB_01#Satellite (2150) 398 167 m_b11s001i17
Crub_svsplocu 548553 AGAGAGAAAAAGAGGGAGAGGGAGGGAGAGAAAAAGAGGGAGAGGGAGGG 548602
i i i i i i i i i i
C IMPB_01#Satel 398 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 349
Crub_svsplocu 548603 AGAGAGAAAGAGAGGGAGAAAGAAAGAGGTAGAAAGAGAAGGAGAGAGAG 548652
i i i i iv i ii
C IMPB_01#Satel 348 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 299
Crub_svsplocu 548653 AGGAAGGGAGAGAAAGAGGGGG-GAGAGAAAAAGAGGGAGAAAGAGAAAG 548701
ii i i i i - i i i i i
C IMPB_01#Satel 298 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 249
Crub_svsplocu 548702 AGGGAGAGAGAAAGAGAGGCAGAGAGAAATAGAGATGAAGAGAGAGAAAG 548751
i i iv i v vii i
C IMPB_01#Satel 248 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 199
Crub_svsplocu 548752 GGAGAGAGGGAGAGAGAAAGAGGGAAAGAGAG 548783
i i i i i
C IMPB_01#Satel 198 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 167
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.17
Transitions / transversions = 10.25 (41/4)
Gap_init rate = 0.00 (1 / 230), avg. gap size = 1.00 (1 / 1)
344 19.41 0.00 0.42 Crub_svsplocus 548603 548840 101160 C IMPB_01 Satellite 164 400 2148
344 19.41 0.00 0.42 Crub_svsplocus 548603 548840 (101160) C IMPB_01#Satellite (2148) 400 164 m_b11s001i18
Crub_svsplocu 548603 AGAGAGAAAGAGAGGGAGAAAGAAAGAGGTAGAAAGAGAAGGAGAGAGAG 548652
i i i i iv i ii
C IMPB_01#Satel 400 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 351
Crub_svsplocu 548653 AGGAAGGGAGAGAAAGAGGGGGGAGAGAAAAAGAGGGAGAAAGAGAAAGA 548702
ii i i i i - i i i i i
C IMPB_01#Satel 350 AGAGAGAGAGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGA 302
Crub_svsplocu 548703 GGGAGAGAGAAAGAGAGGCAGAGAGAAATAGAGATGAAGAGAGAGAAAGG 548752
i i iv i v vii i i
C IMPB_01#Satel 301 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 252
Crub_svsplocu 548753 GAGAGAGGGAGAGAGAAAGAGGGAAAGAGAGGAAGAAAGATAGGGAGAAA 548802
i i i i ii i v i i
C IMPB_01#Satel 251 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 202
Crub_svsplocu 548803 GAAAGAGGGAGAGAGAAAGAGGGAGAGAGAGAGAAATA 548840
i i i i i
C IMPB_01#Satel 201 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATA 164
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.95
Transitions / transversions = 8.20 (41/5)
Gap_init rate = 0.00 (1 / 237), avg. gap size = 1.00 (1 / 1)
417 17.79 0.00 0.42 Crub_svsplocus 548661 548897 101103 C IMPB_01 Satellite 165 400 2148
417 17.79 0.00 0.42 Crub_svsplocus 548661 548897 (101103) C IMPB_01#Satellite (2148) 400 165 m_b11s001i19
Crub_svsplocu 548661 AGAGAAAGAGGGGGGAGAGAAAAAGAGGGAGAAAGAGAAAGAGGGAGAGA 548710
i i i - i i i i i i
C IMPB_01#Satel 400 AGAGAGAGAGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 352
Crub_svsplocu 548711 GAAAGAGAGGCAGAGAGAAATAGAGATGAAGAGAGAGAAAGGGAGAGAGG 548760
i iv i v vii i i i
C IMPB_01#Satel 351 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 302
Crub_svsplocu 548761 GAGAGAGAAAGAGGGAAAGAGAGGAAGAAAGATAGGGAGAAAGAAAGAGG 548810
i i i ii i v i i i i
C IMPB_01#Satel 301 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 252
Crub_svsplocu 548811 GAGAGAGAAAGAGGGAGAGAGAGAGAAATAGAAGGAGAGAGAGGGAGAGA 548860
i i i v ii i
C IMPB_01#Satel 251 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 202
Crub_svsplocu 548861 GAAATAGAGAGAGAGAGAGAAAGAGGGAGAGAGAGAT 548897
i v i i
C IMPB_01#Satel 201 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAT 165
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.37
Transitions / transversions = 6.00 (36/6)
Gap_init rate = 0.00 (1 / 236), avg. gap size = 1.00 (1 / 1)
+ 3736 31.3 1.6 0.5 Crub_svsplocus 550475 551702 (98298) + L3 LINE/CR1 2840 4080 (19) 331
ANNOTATION EVIDENCE:
3736 31.26 1.55 0.48 Crub_svsplocus 550475 551702 98298 + L3 LINE/CR1 2840 4080 19
3736 31.26 1.55 0.48 Crub_svsplocus 550475 551702 (98298) L3#LINE/CR1 2840 4080 (19) m_b11s001i20
Crub_svsplocu 550475 ACTAAAAGCCAACATGGGTTTGTCAAAAACAGATCATGCCAGACAAACCT 550524
ii i iiii i ii i v
L3#LINE/CR1 2840 ACTAGGAGCCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTAACCT 2889
Crub_svsplocu 550525 TATTGCATTCTTTGACCAAGTGACAAAATTAGTGGATCAGAGGAATGCTG 550574
i v v i ivii v v i i i i i i
L3#LINE/CR1 2890 CATTTCCTTTTTTGATAGGGTTACTAGACTGGTAGATCAGGGGAATGCCG 2939
Crub_svsplocu 550575 TGGATATAATTTACTTGGACTTCAGTAAGGCATTTGATAAAGTAGATCAC 550624
i i ? i v ii i i i vvv i
L3#LINE/CR1 2940 TAGACANAGTGTATCTGGATTTCAGCAAGGCATTTGACAAAGTCTCTCAT 2989
Crub_svsplocu 550625 AACCTACTACTCAATAAGATG--------TGGGTTAGACAGTATCACCAT 550666
i iv v vv vi i -------- i i iii vi vi
L3#LINE/CR1 2990 GATATCCTTGTGGACAAGATGGAGAAATATGGGCTGGATGATAGTACAGT 3039
Crub_svsplocu 550667 CAGATGGATTTGTAGCTGGCTGACCGGCTGCATTCAGCATGTGCTCCTCA 550716
i i i i v i i i ii iv v i vv i
L3#LINE/CR1 3040 TAGGTGGATTCGTAGCTGGTTGAACGACCGTACCCAAAAGGTGTTGATTA 3089
Crub_svsplocu 550717 ATGGAACTGCATCTACATGGAGGGAAGTGTATAGTGAGGTGCCCCAGGGC 550766
v viii v v i v v iv v
L3#LINE/CR1 3090 ATGGATCGATGTCAACCTGGAGGGAGGTCTCTAGTGGCGTGCCACAGGGC 3139
Crub_svsplocu 550767 TCTGTTCTGGGCCCAGTGCTCTTCAACATCTTCATCAACGATTTGGACGA 550816
i v v v v i i i i i
L3#LINE/CR1 3140 TCTGTCCTTGGCCCTGTCCTGTTCAACATTTTTATCAATGACTTGGATGA 3189
Crub_svsplocu 550817 GGGTACAGATTGGGGA-ACTCATCAAATTTGCGGATGACACCAAGCTGGC 550865
i ii i --i v -i i i v v
L3#LINE/CR1 3190 AGACATAGA--AGGCATGCTTATCAAATTTGCAGATGACACAAAGCTGGG 3237
Crub_svsplocu 550866 CGGAATAGCCAACACTCCAGAAGACAGGCTTAAGATACAGGAGGACCTGG 550915
v i i i v?ii v iv i v ii ? i v
L3#LINE/CR1 3238 AGGGATAGCTAATACGNTGGATGACAGAATCAAGATTCAAAANGATCTCG 3287
Crub_svsplocu 550916 ACAGACTTGAACACTGGGCGCTATCTAACAAAATGAAATTTAATGGTGAA 550965
i v iv vvv v i i ii v v
L3#LINE/CR1 3288 ACAGGCTGGAACGATGGGCCGAAACCAACAAGATGAAATTTAACAGGGAT 3337
Crub_svsplocu 550966 AAAAGTAAGGTTCTACATT-AGGCAAGAAAAACCAAATGTACAGGTATAG 551014
v i i i - ivvi i v i i i
L3#LINE/CR1 3338 AAATGTAAAGTCCTGCATTTAGGTTCAAAAAATCAACTGCACAAGTACAG 3387
Crub_svsplocu 551015 TATAGGG-GTACCTTGCTCAATAGTAGTAACTGTGAGAGGGATCTCGAAG 551063
v i i - v i v i ii i vvvi i ii i v ii
L3#LINE/CR1 3388 GATGGAGAGGATCTGGCTTAGCAGCAGTTCACGTGAAAAAGACCTAGGGG 3437
Crub_svsplocu 551064 TCCTAGTGGACAATCACTTAAATATGAGTCAGCAGTGTGCTGCAGCTGCC 551113
ii v viiv vi v i i v ii
L3#LINE/CR1 3438 TTTTAGTTGACCGCAAGCTCAATATGAGCCAACAGTGTGATGTGGCTGCC 3487
Crub_svsplocu 551114 AAAAAAGCCAACACAGTGCTGGGCTGCATTAACAGAGGGATAGAATCAAG 551163
i ii i vi i i i v vi v
L3#LINE/CR1 3488 AAAAAAGCTAATGCAATCTTAGGCTGCATTAATAGAAGTATAGTGTCCAG 3537
Crub_svsplocu 551164 ATCATGTGAAGTATTCATACCACTTTACAATGCCTTGGTAAGGCCACACT 551213
? v v i v vi v i v vv vi v i ii
L3#LINE/CR1 3538 ANCAAGGGAGGTAATAGTCCCGCTGTACTCTGCGCTGGTCAGACCACATC 3587
Crub_svsplocu 551214 TGGAAAGCTGCATCCAGTTTTGGTCACCGCAATGTAAAAAAGATGTTGAG 551263
ivii i i i v i i v v i ii ii v
L3#LINE/CR1 3588 TGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGAC 3637
Crub_svsplocu 551264 ACTCTAGAAAGAATATAGAGAAGAGCAACAAAGATGATTAGGAGACTGGA 551313
vv i iv vi vi i i v i i v i i v
L3#LINE/CR1 3638 AAACTGGAGCGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGGA 3687
Crub_svsplocu 551314 GGCTAAAACATATAAGGAAAGGTTGCTAGAATTGGGTACGTATGGTTTAA 551363
ii i viv i v vvi i v i v i ii ii
L3#LINE/CR1 3688 AACCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTGG 3737
Crub_svsplocu 551364 CGAAGAGAAGGACAAGTGGGGACATGATAGCAGTGTTCCAATATCTCAGG 551413
v iviv v i v v v i v i
L3#LINE/CR1 3738 AGAAGAGAAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAAG 3787
Crub_svsplocu 551414 GGCTGCCACAAAGAAGATGGAGTCAAGCTATTCTCCCAAGTGCCTGAAGG 551463
i iivi v v vi vi vivvi iv v i
L3#LINE/CR1 3788 GGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGGG 3837
Crub_svsplocu 551464 CAGGACAAGAAGCAACAGATGGAAACTAATCAAGGAGAGAAG----CAGC 551509
i v i v ii i ii -- i - v ---- i
L3#LINE/CR1 3838 CAGAACTAGGACCAATGGGTGGAAGTTA--CAGGGAG-GCAGATTTCGGC 3884
Crub_svsplocu 551510 CTAGAACTAAGGAGAAACTTCCTGACAGTTAGAATAATTAACCAATGGAA 551559
ii iv - ii i i i i iivi iv vv
L3#LINE/CR1 3885 TCAATA-TAAGGAAGAACTTTCTAACAATCAGAGCTGTCCAAAAATGGAA 3933
Crub_svsplocu 551560 CAACCTGCCTCCAGAAGCGGTGAATGCTCCAACACTGGAAGTTTTTAAAA 551609
iiiv v? i ii iiv i iv i v i iv
L3#LINE/CR1 3934 TGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAGGTGTTCAAGC 3983
Crub_svsplocu 551610 AGAGACCGGATAGCCATTTGTCCAAAATGATGT---AGGGTTTCCTGCCT 551656
i i ii i viii v --- v v
L3#LINE/CR1 3984 AGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGGATTCCTGCAT 4033
Crub_svsplocu 551657 -GAGCAGGGGGTTGGAAACGATGACCACCAAGGTCCTTTCTAACTTT 551702
- iiii i vvv v i i i i
L3#LINE/CR1 4034 CGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTCCAACTCT 4080
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.49
Transitions / transversions = 1.69 (240/142)
Gap_init rate = 0.01 (13 / 1227), avg. gap size = 1.92 (25 / 13)
+ 19 4.0 0.0 0.0 Crub_svsplocus 551703 551728 (98272) + (ATT)n Simple_repeat 1 26 (0) 332
ANNOTATION EVIDENCE:
19 4.00 0.00 0.00 Crub_svsplocus 551703 551728 98272 + (ATT)n Simple_repeat 1 26 0
19 4.00 0.00 0.00 Crub_svsplocus 551703 551728 (98272) (ATT)n#Simple_repeat 1 26 (0) m_b11s252i2
Crub_svsplocu 551703 ATTATTATTATTATTATTACTATTAT 551728
i
(ATT)n#Simple 1 ATTATTATTATTATTATTATTATTAT 26
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
+ 14 16.8 9.7 4.0 Crub_svsplocus 552009 552080 (97920) + (TTTCTA)n Simple_repeat 1 76 (0) 333
ANNOTATION EVIDENCE:
14 16.83 9.72 3.95 Crub_svsplocus 552009 552080 97920 + (TTTCTA)n Simple_repeat 1 76 0
14 16.83 9.72 3.95 Crub_svsplocus 552009 552080 (97920) (TTTCTA)n#Simple_repeat 1 76 (0) m_b11s252i3
Crub_svsplocu 552009 TTTCTATTTCTATTTGTAGGTC--TTTGTATTT-TGTTATCT-TCTCCAG 552054
v vv -- v - i - - i i v
(TTTCTA)n#Sim 1 TTTCTATTTCTATTTCTATTTCTATTTCTATTTCTATT-TCTATTTCTAT 49
Crub_svsplocu 552055 TTC--TTTCT-CTTCTATTCTGCTATCTC 552080
-- -i - - i
(TTTCTA)n#Sim 50 TTCTATTTCTATTTCTATT-T-CTATTTC 76
Matrix = Unknown
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.11 (8 / 71), avg. gap size = 1.25 (10 / 8)
+ 152 0.0 0.0 0.0 Crub_svsplocus 552274 552404 (97596) + (TAT)n Simple_repeat 1 131 (0) 334
ANNOTATION EVIDENCE:
152 0.00 0.00 0.00 Crub_svsplocus 552274 552404 97596 + (TAT)n Simple_repeat 1 131 0
152 0.00 0.00 0.00 Crub_svsplocus 552274 552404 (97596) (TAT)n#Simple_repeat 1 131 (0) c_b11s251i1
Crub_svsplocu 552274 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTA 552323
(TAT)n#Simple 1 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTA 50
Crub_svsplocu 552324 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATT 552373
(TAT)n#Simple 51 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATT 100
Crub_svsplocu 552374 ATTATTATTATTATTATTATTATTATTATTA 552404
(TAT)n#Simple 101 ATTATTATTATTATTATTATTATTATTATTA 131
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 130), avg. gap size = 0.0 (0 / 0)
+ 3083 31.0 5.1 1.4 Crub_svsplocus 556085 557281 (92719) + L3 LINE/CR1 2840 4080 (19) 335
ANNOTATION EVIDENCE:
3083 31.00 5.10 1.37 Crub_svsplocus 556085 557281 92719 + L3 LINE/CR1 2840 4080 19
3083 31.00 5.10 1.37 Crub_svsplocus 556085 557281 (92719) L3#LINE/CR1 2840 4080 (19) m_b11s001i21
Crub_svsplocu 556085 ACTAAAAGCCAACATGGGTTTATCAAAAACAGATCATGCCAGACAAACCT 556134
ii i i ii i ii i v
L3#LINE/CR1 2840 ACTAGGAGCCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTAACCT 2889
Crub_svsplocu 556135 TATTGCATTCTTCGACCAAGTGACAAAATTAGTGGATCAGAGGAATGCTG 556184
i v v i i ivii v v i i i i i i
L3#LINE/CR1 2890 CATTTCCTTTTTTGATAGGGTTACTAGACTGGTAGATCAGGGGAATGCCG 2939
Crub_svsplocu 556185 TGGATATAATTTACATGGACTTCAGTAAGGCATTTGATAAAGTAGATCAC 556234
i i ? i v iv i i i vvv i
L3#LINE/CR1 2940 TAGACANAGTGTATCTGGATTTCAGCAAGGCATTTGACAAAGTCTCTCAT 2989
Crub_svsplocu 556235 AACCTACTACTCAATAAGATG--------TGGGTTAGACAGTATCACCAC 556276
i iv v vv vi i -------- i i iii vi vii
L3#LINE/CR1 2990 GATATCCTTGTGGACAAGATGGAGAAATATGGGCTGGATGATAGTACAGT 3039
Crub_svsplocu 556277 CAGATGGATTTGTAGCTAGCTGACCAGCCGTACTCAGCATGTGGTCCTCA 556326
i i i i i v ii i iv v v vv i
L3#LINE/CR1 3040 TAGGTGGATTCGTAGCTGGTTGAACGACCGTACCCAAAAGGTGTTGATTA 3089
Crub_svsplocu 556327 ATGGAACTGCATGT--ACATGGTGGGAAGTGTGTAGTAGGATGCCCCAAG 556374
v - - -- v v i v v i vi v i
L3#LINE/CR1 3090 ATGGATC-G-ATGTCAACCTGGAGGGAGGTCTCTAGTGGCGTGCCACAGG 3137
Crub_svsplocu 556375 GCTCC-------------------TCAACATCTTCATCAATGATTTGGAC 556405
i------------------- i i i i
L3#LINE/CR1 3138 GCTCTGTCCTTGGCCCTGTCCTGTTCAACATTTTTATCAATGACTTGGAT 3187
Crub_svsplocu 556406 TAGGGGATAGATGGGGAACTCCATCAAATTTGCGGGTGACACCAAGCTGG 556455
v i iv v vivi i- i i v
L3#LINE/CR1 3188 GAAGACATAGAAGGCATGCTT-ATCAAATTTGCAGATGACACAAAGCTGG 3236
Crub_svsplocu 556456 CCGGAATAGCCAACACTC-------------CAAAATACAGGAGGACGTG 556492
vv i i i v?------------- i v ii ? iv v
L3#LINE/CR1 3237 GAGGGATAGCTAATACGNTGGATGACAGAATCAAGATTCAAAANGATCTC 3286
Crub_svsplocu 556493 GACAGACTTGAACACTGGGCGCTATCTAACAAAATGAAATTCAATGGTGA 556542
i v iv vvv v i i i ii v
L3#LINE/CR1 3287 GACAGGCTGGAACGATGGGCCGAAACCAACAAGATGAAATTTAACAGGGA 3336
Crub_svsplocu 556543 AAAAAGTAAGGTTCTACATTTAGGCAAGAAAAACCAAAACTACAGGTATA 556592
v v i i i ivvi i vvvi i i
L3#LINE/CR1 3337 TAAATGTAAAGTCCTGCATTTAGGTTCAAAAAATCAACTGCACAAGTACA 3386
Crub_svsplocu 556593 GTATAGGG-TTATCTTGCTCAATAGTAATAACTGTGAGAGGGATCTTGGA 556641
v i i -vv v i ii i i vvvi i ii i v i
L3#LINE/CR1 3387 GGATGGAGAGGATCTGGCTTAGCAGCAGTTCACGTGAAAAAGACCTAGGG 3436
Crub_svsplocu 556642 GTCCTAGTGGACAATCATTTAAATATGAGCCAGCAGTGTGCTGCAGCTGT 556691
ii v viiv vi v i v ii i
L3#LINE/CR1 3437 GTTTTAGTTGACCGCAAGCTCAATATGAGCCAACAGTGTGATGTGGCTGC 3486
Crub_svsplocu 556692 CAAAAAAGCCAACACAATACTAGGCTGCATTAACAGAGGGATAAAATCAA 556741
i ii vi i i v ivi v
L3#LINE/CR1 3487 CAAAAAAGCTAATGCAATCTTAGGCTGCATTAATAGAAGTATAGTGTCCA 3536
Crub_svsplocu 556742 GATCACG---TGTATTAATACCACTTTACAGTGCCTTGGTAAAGCCACAC 556788
? v ---v v i v i v vv vi v ii i
L3#LINE/CR1 3537 GANCAAGGGAGGTAATAGTCCCGCTGTACTCTGCGCTGGTCAGACCACAT 3586
Crub_svsplocu 556789 TTGGAAAACTGCATCCAGTTTTGGTCACCACGATGTAAAAAAGATGTTGA 556838
i iv i i i i v i iv v i ii ii
L3#LINE/CR1 3587 CTGGAGTATTGCGTTCAGTTCTGGGCGCCACATTTTAAGAGGGACATTGA 3636
Crub_svsplocu 556839 GAATCTAGAAAGAGTACAGAGAAGCGCAACAAAGATGATTAGAGGTCTGG 556888
v v i iv v v i v i v i i v ii
L3#LINE/CR1 3637 CAAACTGGAGCGCGTCCAGAGGAGAGCGACCAGGATGGTGAAGGGTCTGG 3686
Crub_svsplocu 556889 AGGCTAAAACATATAAGGAACT------GGAATTGGGTATGTCTAATTTA 556932
ii i viv i v------ i v i iii i
L3#LINE/CR1 3687 AAACCATGTCATATGAGGAACGGTTGAAGGAACTGGGGATGTTTAGCCTG 3736
Crub_svsplocu 556933 ATGAAGAGAAGGATGAAGGGGGACATGATAGCAGTGTTCCAATATCTCAG 556982
iv iv v ii i v v v i v i
L3#LINE/CR1 3737 GAGAAGAGAAGACTTAGAGGAGACATGATAGCTGTCTTCAAATATTTGAA 3786
Crub_svsplocu 556983 GGACTGACCCAAAGAAGAGGGAGTCAAGCTGTTCTCCAAAGTGCCTGAAG 557032
i v viivi v vi vi i viivi iv v i
L3#LINE/CR1 3787 GGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTGGCTCCAGAGG 3836
Crub_svsplocu 557033 GCAGGACAAGAAGCAACAGATGGAAACTAATCAAGGAGAGAAG----CAG 557078
i v i v ii i ii -- i - v ---- i
L3#LINE/CR1 3837 GCAGAACTAGGACCAATGGGTGGAAGTTA--CAGGGAG-GCAGATTTCGG 3883
Crub_svsplocu 557079 CCTAGAACTAAGG-AGAACTTTACATAGAATAATTAGAATTAGAATAATT 557127
ii iv - - vi---- i i ii ------i i
L3#LINE/CR1 3884 CTCAATA-TAAGGAAGAACTTTCT----AACAATCAGAGCT------GTC 3922
Crub_svsplocu 557128 AACCAATGGAACAACCTGCCTCCAGAAGCCGTGAATGCTCCAACAATGTA 557177
v vv iiiv v? i iv iiv i iv v v
L3#LINE/CR1 3923 CAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGA 3972
Crub_svsplocu 557178 GGTTTTTAAGAAGAGACCGGATAGCCATTTGTCCAAAATGATGT---AGG 557224
v i v i i ii i viii v ---
L3#LINE/CR1 3973 GGTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGG 4022
Crub_svsplocu 557225 GTTTCCTGCCT-GAGCAGGGGGTTGGAAACGATGACCACCAAGGTCCTTT 557273
v v - iiii i vvv v i i
L3#LINE/CR1 4023 GATTCCTGCATCGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTT 4072
Crub_svsplocu 557274 CTAACTTT 557281
i i
L3#LINE/CR1 4073 CCAACTCT 4080
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.83
Transitions / transversions = 1.58 (224/142)
Gap_init rate = 0.02 (28 / 1196), avg. gap size = 2.79 (78 / 28)
+ 17 17.8 0.0 0.0 Crub_svsplocus 557283 557326 (92674) + (TTGATG)n Simple_repeat 1 44 (0) 336
ANNOTATION EVIDENCE:
15 27.08 0.00 0.00 Crub_svsplocus 557283 557326 92674 + (TTG)n Simple_repeat 1 44 0
15 27.08 0.00 0.00 Crub_svsplocus 557283 557326 (92674) (TTG)n#Simple_repeat 1 44 (0) m_b11s252i4
Crub_svsplocu 557283 TTATTATTGTTGTTGTTGTTGATGACGATGATGATGATGATGTT 557326
i i v vi v v v v v
(TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTT 44
Matrix = Unknown
Transitions / transversions = 0.43 (3/7)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
17 17.81 0.00 0.00 Crub_svsplocus 557289 557326 92674 + (TTGATG)n Simple_repeat 1 38 0
17 17.81 0.00 0.00 Crub_svsplocus 557289 557326 (92674) (TTGATG)n#Simple_repeat 1 38 (0) m_b11s252i5
Crub_svsplocu 557289 TTGTTGTTGTTGTTGATGACGATGATGATGATGATGTT 557326
v v vi v v
(TTGATG)n#Sim 1 TTGATGTTGATGTTGATGTTGATGTTGATGTTGATGTT 38
Matrix = Unknown
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 30 0.0 0.0 0.0 Crub_svsplocus 557609 557644 (92356) + (TTG)n Simple_repeat 1 36 (0) 337
ANNOTATION EVIDENCE:
30 0.00 0.00 0.00 Crub_svsplocus 557609 557644 92356 + (TTG)n Simple_repeat 1 36 0
30 0.00 0.00 0.00 Crub_svsplocus 557609 557644 (92356) (TTG)n#Simple_repeat 1 36 (0) m_b11s252i6
Crub_svsplocu 557609 TTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTG 557644
(TTG)n#Simple 1 TTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTG 36
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
+ 71 0.0 0.0 0.0 Crub_svsplocus 557645 557707 (92293) + (TTA)n Simple_repeat 1 63 (0) 338
ANNOTATION EVIDENCE:
71 0.00 0.00 0.00 Crub_svsplocus 557645 557707 92293 + (TTA)n Simple_repeat 1 63 0
71 0.00 0.00 0.00 Crub_svsplocus 557645 557707 (92293) (TTA)n#Simple_repeat 1 63 (0) c_b11s251i2
Crub_svsplocu 557645 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATT 557694
(TTA)n#Simple 1 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATT 50
Crub_svsplocu 557695 ATTATTATTATTA 557707
(TTA)n#Simple 51 ATTATTATTATTA 63
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 19 19.8 4.8 6.0 Crub_svsplocus 560678 560761 (89239) + (ATATT)n Simple_repeat 1 83 (0) 339
ANNOTATION EVIDENCE:
19 19.77 4.76 6.02 Crub_svsplocus 560678 560761 89239 + (ATATT)n Simple_repeat 1 83 0
19 19.77 4.76 6.02 Crub_svsplocus 560678 560761 (89239) (ATATT)n#Simple_repeat 1 83 (0) m_b11s252i7
Crub_svsplocu 560678 ATA-TATATCATTTTTTCTTATCAGCTTCTGTTATTTTCATA-AAAGTCA 560725
- i v v v - -- v i v - -v vi i
(ATATT)n#Simp 1 ATATTATATTATATTATATTAT-A--TTATATTATATT-ATATTATATTA 46
Crub_svsplocu 560726 TCTTATATTATA--ATATTATATTATATTATTTTCATA 560761
v -- v -
(ATATT)n#Simp 47 TATTATATTATATTATATTATATTATATTATATT-ATA 83
Matrix = Unknown
Transitions / transversions = 0.44 (4/9)
Gap_init rate = 0.10 (8 / 83), avg. gap size = 1.12 (9 / 8)
+ 232 12.2 0.0 12.1 Crub_svsplocus 563407 563426 (86574) C hAT-N53_DR DNA/hAT-Ac (2982) 2837 2784 340
ANNOTATION EVIDENCE:
232 12.25 0.00 12.07 Crub_svsplocus 563407 563467 86533 C hAT-N53_DR DNA/hAT-Ac 2784 2837 2982
232 12.25 0.00 12.07 Crub_svsplocus 563407 563467 (86533) C hAT-N53_DR#DNA/hAT-Ac (2982) 2837 2784 m_b11s001i22
Crub_svsplocu 563407 AATTCTGATGCCCTTTCTCAAAAGTGTATGTTCGTGTGTGTGTGTGTGTG 563456
---- --- vv i i vi
C hAT-N53_DR#DN 2837 AATTCTGA----CTT---CAACTGTATGTGTGTGTGTGTGTGTGTGTGTG 2795
Crub_svsplocu 563457 TGTGTGTGTGT 563467
C hAT-N53_DR#DN 2794 TGTGTGTGTGT 2784
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.50
Transitions / transversions = 1.00 (3/3)
Gap_init rate = 0.12 (7 / 60), avg. gap size = 1.00 (7 / 7)
+ 270 14.0 1.6 3.0 Crub_svsplocus 563427 563467 (86533) + RLTR20A4 LTR/ERVK 452 489 (96) 341
ANNOTATION EVIDENCE:
264 22.54 1.41 0.00 Crub_svsplocus 563427 563467 86533 + RLTR20C2_MM LTR/ERVK 359 399 98
264 22.54 1.41 0.00 Crub_svsplocus 563427 563467 (86533) RLTR20C2_MM#LTR/ERVK 359 399 (98) m_b11s001i23
Crub_svsplocu 563427 AAAGTGTATGTTCGTGTGTGTGTGTGTGTGTGTGTGTGTGT 563467
v i vi
RLTR20C2_MM#L 359 AATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 399
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.98
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0)
270 13.34 1.61 3.28 Crub_svsplocus 563430 563467 86533 + RLTR20A4 LTR/ERVK 452 489 96
270 13.34 1.61 3.28 Crub_svsplocus 563430 563467 (86533) RLTR20A4#LTR/ERVK 452 489 (96) m_b11s001i24
Crub_svsplocu 563430 GTGTATGTTCGTGTGTGTGTGTGTGTGTGTGTGTGTGT 563467
i vi
RLTR20A4#LTR/ 452 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 489
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.34
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 73 0.0 0.0 0.0 Crub_svsplocus 563468 563529 (86471) + (GA)n Simple_repeat 1 62 (0) 342
ANNOTATION EVIDENCE:
73 0.00 0.00 0.00 Crub_svsplocus 563468 563529 86471 + (GA)n Simple_repeat 1 62 0
73 0.00 0.00 0.00 Crub_svsplocus 563468 563529 (86471) (GA)n#Simple_repeat 1 62 (0) c_b11s251i3
Crub_svsplocu 563468 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 563517
(GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50
Crub_svsplocu 563518 GAGAGAGAGAGA 563529
(GA)n#Simple_ 51 GAGAGAGAGAGA 62
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0)
+ 270 15.2 1.6 2.6 Crub_svsplocus 563533 563558 (86442) + RLTR20A4 LTR/ERVK 490 511 (74) 341
ANNOTATION EVIDENCE:
264 22.54 1.41 0.00 Crub_svsplocus 563530 563558 86442 + RLTR20C2_MM LTR/ERVK 400 429 68
264 22.54 1.41 0.00 Crub_svsplocus 563530 563558 (86442) RLTR20C2_MM#LTR/ERVK 400 429 (68) m_b11s001i23
Crub_svsplocu 563530 TATTAATCATTTA-AAATTCACAGGTAGTT 563558
i ivv ii-ii i v i i
RLTR20C2_MM#L 400 TGTCTTTCATTCGCGGATCCAAAGATAGCT 429
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.98
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1)
270 13.34 1.61 3.28 Crub_svsplocus 563530 563552 86448 + RLTR20A4 LTR/ERVK 490 511 74
270 13.34 1.61 3.28 Crub_svsplocus 563530 563552 (86448) RLTR20A4#LTR/ERVK 490 511 (74) m_b11s001i24
Crub_svsplocu 563530 TATTAATCATTT-AAAATTCACAG 563552
i -- i- i i v
RLTR20A4#LTR/ 490 TGTT--TCATTCGAGAATCCAGAG 511
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.34
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.14 (3 / 22), avg. gap size = 1.00 (3 / 3)
+ 13 8.5 4.0 0.0 Crub_svsplocus 564124 564148 (85852) + (ATA)n Simple_repeat 1 26 (0) 343
ANNOTATION EVIDENCE:
13 8.48 4.00 0.00 Crub_svsplocus 564124 564148 85852 + (ATA)n Simple_repeat 1 26 0
13 8.48 4.00 0.00 Crub_svsplocus 564124 564148 (85852) (ATA)n#Simple_repeat 1 26 (0) m_b11s252i8
Crub_svsplocu 564124 ATAATAATAATAAGAATAACAA-AAT 564148
v i -
(ATA)n#Simple 1 ATAATAATAATAATAATAATAATAAT 26
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1)
+ 336 34.0 2.7 3.0 Crub_svsplocus 565983 566439 (83561) C Gypsy39-I_DR LTR/Gypsy (5863) 5547 5174 344
ANNOTATION EVIDENCE:
300 35.41 1.72 3.04 Crub_svsplocus 565983 566215 83785 C Gypsy-129_DR-I LTR/Gypsy 3286 3515 810
300 35.41 1.72 3.04 Crub_svsplocus 565983 566215 (83785) C Gypsy-129_DR-I#LTR/Gypsy (810) 3515 3286 m_b11s001i25
Crub_svsplocu 565983 CTTGAGGGTGGTGGCTAGATGTCAATCCCTG-AGAGGGATAAAAATTCCT 566031
i i i -- i vi - ii i-i vv ii v- i
C Gypsy-129_DR- 3515 CCTGAGGATAG--GCTGGCCGT-AGCCCCTATGGACTGGCAAAAAG-CTT 3470
Crub_svsplocu 566032 TCCAAAATGCAGACGTAAATTGCACTCCCCTATCAGAGATGATGCGTTGG 566081
v i vvi v v viv i vi v ii iv
C Gypsy-129_DR- 3469 GCCAGAATCGGGAGGAAAATTGAGGTCCTCGGTCTGAGACAATGTCTTGG 3420
Crub_svsplocu 566082 GGTGCCCCGTGCAATCTGTAAATGTGCTGGATGAAAAGTCTTGCTAAGGC 566131
viiv iviv v v v v i v vv iv iiiv ivvv
C Gypsy-129_DR- 3419 GGAATGCCAAAGACTCGGAACACGTGATTTATGGTAAGCTCGGCTGTCTC 3370
Crub_svsplocu 566132 CTTTGCAGTGGGAATCTTTTGGCAAGGG-ATAAA--GTGCACCTGTTTGG 566178
i v -v v - i -- v --
C Gypsy-129_DR- 3369 TTTGGCAGTGGGAA-GTTTGGGCAAGGGAATGAATCGTGCAGC--TTTGG 3323
Crub_svsplocu 566179 AAAACAAGTCCGTGACTGTCCAGATAACAGTATTCCC 566215
ivi iii i ii v i iii
C Gypsy-129_DR- 3322 AAAATCGGTCCACAATTACCAAAATAGTGGTATTCCC 3286
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 45.96
Transitions / transversions = 1.22 (44/36)
Gap_init rate = 0.04 (10 / 232), avg. gap size = 1.10 (11 / 10)
336 35.45 3.48 3.48 Crub_svsplocus 566024 566397 83603 C Gypsy138-I_DR LTR/Gypsy 5174 5547 5863
336 35.45 3.48 3.48 Crub_svsplocus 566024 566397 (83603) C Gypsy138-I_DR#LTR/Gypsy (5863) 5547 5174 m_b11s001i26
Crub_svsplocu 566024 AAATTCCTTCCAAAATGCAGACGTAAATTGCACTCCCCTATCAGAGATGA 566073
v i ivii i i iivi v i iv
C Gypsy138-I_DR 5547 AAATGCCTTCCAGAACCTGGACGTGAACTGTGGCCCCCGATCGGAGACCA 5498
Crub_svsplocu 566074 TGCGTTGGGGTGCCCCGTGCAATCTGTAAATGTGCTGGATGAAAAGTCTT 566123
ivi v vivv i v vi iv v ii v v i iii
C Gypsy138-I_DR 5497 TGTCCTGCGGAAAGCCATGGATCCTAAACACATTCTGCATGAGAAGCTCT 5448
Crub_svsplocu 566124 GCTAAGGCCT---TTGCAGT-GGGAATCTTTTGGCAA-GGGATAAAGTGC 566168
--- i --- v v - i -- v - vv ii -
C Gypsy138-I_DR 5447 GCT---GTCTGACTAGCTGTTGGGAGT--TTGGGCAAAGGGAGTAGATG- 5404
Crub_svsplocu 566169 ACCTGT-TTGGAAAACAAGTCCGTGACTGTCCAGATAACAGTATTCCCAT 566217
v i- i ivv iiv iii vii i v v v
C Gypsy138-I_DR 5403 ACATGCCTTAGAAAATCTGTCCACCACCACCAGAATGACTGTATTACCTT 5354
Crub_svsplocu 566218 TGCTTTCTGGCAATTCCACTATAAAATCCATGGCTATTTCCCTCCAGGGG 566267
vvi i ivi iiiv ii i vv v v v v v i
C Gypsy138-I_DR 5353 TGGACTCTGGTAGGCCTGTAACGAAGTCCAATGATATATGCGTCCATGGA 5304
Crub_svsplocu 566268 -GCTGAGGGACTTGCCACTGGTTGTAACAGTCCT---GG-CGATTTCCCT 566312
- i v v - v v v v i i v --- - iv --
C Gypsy138-I_DR 5303 TGTTTAGGTA-TAGGCAGTGGGTGCAGCAGGCCTTGAGGTCGGGTTC--T 5257
Crub_svsplocu 566313 TGCAACCTCTTTGCTG-ATGCACAGGTTGGGCAGCTGGCAACATAACTTT 566361
v---i i i v-i iiiv i ivii - v v
C Gypsy138-I_DR 5256 TGG---TTCCTTGTTTTGTGCACAAACAGAGCAAGCAGCAACA-AAGTTG 5211
Crub_svsplocu 566362 CT-ATGTCCTTTTTTATTGATGGCCACCAAAATTGCC 566397
v- ii i vi v vv v
C Gypsy138-I_DR 5210 CGGACATCCTTCTGCAGTCTTGGCCACCAAAATTTCC 5174
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 48.11
Transitions / transversions = 1.13 (68/60)
Gap_init rate = 0.06 (22 / 373), avg. gap size = 1.18 (26 / 22)
256 29.91 3.33 2.48 Crub_svsplocus 566320 566439 83561 C Gypsy89-I_DR LTR/Gypsy 3104 3224 1144
256 29.91 3.33 2.48 Crub_svsplocus 566320 566439 (83561) C Gypsy89-I_DR#LTR/Gypsy (1144) 3224 3104 m_b11s001i27
Crub_svsplocu 566320 TCTTTGCT--GATGCACAGGTTGGGCAGCTGGCAACATAACT-TTCTATG 566366
-- - v i i v - - vi ii
C Gypsy89-I_DR# 3224 TCTTTGCTCTGA-GCACAGGTGGGGCAACTAGAAACA-AACTCTTGCACA 3177
Crub_svsplocu 566367 TCCTTTTTTATTGATGGCCACCAAAATTGCCGTTTAATTAAGTGTAAAGT 566416
i ivi iiv i i v vivv i - v iv v
C Gypsy89-I_DR# 3176 TCTTTTCGCATCATTGGCCACCAGAACTTCCTCAAAATCAA-TTTGTAGG 3128
Crub_svsplocu 566417 TTTTACAAAT-CCAAAATGCCCTG 566439
i iiv - iii i
C Gypsy89-I_DR# 3127 TTCTGTTAATACCAGGGTGTCCTG 3104
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.20
Transitions / transversions = 1.69 (22/13)
Gap_init rate = 0.05 (6 / 119), avg. gap size = 1.17 (7 / 6)
+ 344 31.8 3.7 2.9 Crub_svsplocus 566722 567176 (82824) C Gypsy39-I_DR LTR/Gypsy (424) 4625 4471 344
ANNOTATION EVIDENCE:
340 33.24 4.62 3.42 Crub_svsplocus 566722 567154 82846 C Gypsy69-I_DR LTR/Gypsy 2304 2741 1504
340 33.24 4.62 3.42 Crub_svsplocus 566722 567154 (82846) C Gypsy69-I_DR#LTR/Gypsy (1504) 2741 2304 m_b11s001i28
Crub_svsplocu 566722 TGCGAGATAGTGCATCTGCCAGGAAGTTCTTTTTTCCTGG----TAAATG 566767
v v vvivi v? v ---- ii
C Gypsy69-I_DR# 2741 TGCGAGAGAGGGCATCTGCCTTACGGTTCTTGNTGCCTGGGCGATAGGTG 2692
Crub_svsplocu 566768 TTTGAGCTTAAATTGGAATTGGTGAA-AATGCTGGGACCAGCGGGCTTGT 566816
vi --- v i ?iv - i--ii ? i i
C Gypsy69-I_DR# 2691 ACTG---TAAAATTGAANCGGGTGAAGAATA--AAGACCANCGAGCCTGT 2647
Crub_svsplocu 566817 TTGGGATTGAGGAAT--GGAAGTTTTCAGGGCTTCCAAATTTTTGTGATC 566864
i i v vvi -- v v v vivvi ? ii i
C Gypsy69-I_DR# 2646 CTGGGGTTTAGTCGTCGGGCACTTTTGATATACTCNAGGTTTTTGTGGTC 2597
Crub_svsplocu 566865 AGTCCAT-ACCTGGAAGG---GGATTTTGTTGCCTTCCAGGAACTGTCGC 566910
v -v - i ? --- ---i viv i ? vv v ?
C Gypsy69-I_DR# 2596 TGT-GATAATCTGGAANGGATGGA---CGGCTCCCTCNAGCCAGTGNCGC 2551
Crub_svsplocu 566911 CACGTGAGTAATGCCCAACGTATCCCAT---AAGC--CTCCTTCTCCCAT 566955
ivivvvi i --i v ---i --- i--i v iv vi
C Gypsy69-I_DR# 2550 CATTCTTCCAGTGCC--GCCT---TCATNGAAAGTAGTTCCTTGTTACCC 2506
Crub_svsplocu 566956 ACGGGCCAGCGCTGTTCTGTTTCCGTGAGTTTCTTGGATGTATATGCACA 567005
vvvi iviiv v i v v vivi viv ? v
C Gypsy69-I_DR# 2505 ACGTCATAGTTTCTTTCAGCTGCCGTCAGTTTGCGAGAAAAANAAGCACA 2456
Crub_svsplocu 567006 GGGTTGCAAT---ACTGCATCATCATTTTCTTGTAATAGTACAGCCCCCA 567052
? v v i ---v vi i i i v?iv i i ? v -
C Gypsy69-I_DR# 2455 NGGGTGGAGTTTACCTGGGTTACCGTGNCGTTGTGACAGNACTG-CCCCA 2407
Crub_svsplocu 567053 CTGCCACA-TCACTTGCATCTGCCTGTATTATGAAGGGTTTGTCCATGTC 567101
v i - ?vv? ii i v? iv i vvv ?iv
C Gypsy69-I_DR# 2406 ATGCCATAGTCNGANGCATCCACTTCNACAACGAAGGGTAGCTCNGGGTC 2357
Crub_svsplocu 567102 TGGGTGCCTTAGTACTGGTTCGGCAGAAAAAAGTCTCTTTAGTCTCTCAA 567151
v ii i v iv v ? ii vi ivvvv v i
C Gypsy69-I_DR# 2356 GGGGTGTTTCAGAATGGGTGCNGTGGTGAAGCTGGTCTTAAGTTTCTCAA 2307
Crub_svsplocu 567152 ACG 567154
C Gypsy69-I_DR# 2306 ACG 2304
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.99
Transitions / transversions = 0.90 (66/73)
Gap_init rate = 0.06 (24 / 432), avg. gap size = 1.46 (35 / 24)
344 28.95 1.94 1.94 Crub_svsplocus 567022 567176 82824 C Gypsy39-I_DR LTR/Gypsy 4471 4625 424
344 28.95 1.94 1.94 Crub_svsplocus 567022 567176 (82824) C Gypsy39-I_DR#LTR/Gypsy (424) 4625 4471 m_b11s001i29
Crub_svsplocu 567022 TCATCATTTTCTTGTAATAGTACAGCCCCCACTGCCACATCACTTGCATC 567071
v i i i i ii v v vi v i v
C Gypsy39-I_DR# 4625 TCCTTATCTTCCTGCAGCAGGACAGCGCCAGCTCCTACAGCACTTGCATC 4576
Crub_svsplocu 567072 TGCCTGTATTATGAAGGGTTTGTCCATGTCTGGGTGCC-TTAGTACTGGT 567120
i vi v i i i v v vi i i- - ii v
C Gypsy39-I_DR# 4575 TACCTCCATTTTAAAAGGCTTTTCGAAATTTGGA-GCCATTAACACTGGA 4527
Crub_svsplocu 567121 TCGGCAGAAAAAAGTCTCTTTAGT-CTCTCAAACGC-TGCTTGGCACTCC 567168
v vv v v i -v i - i v - - i ?
C Gypsy39-I_DR# 4526 GCTTCACACAGAAGT-GCTTTAATACTTTCAAAGGCATGC-TGGCATTCN 4479
Crub_svsplocu 567169 ATTGTCCA 567176
iv v
C Gypsy39-I_DR# 4478 GATGACCA 4471
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.47
Transitions / transversions = 1.10 (23/21)
Gap_init rate = 0.04 (6 / 154), avg. gap size = 1.00 (6 / 6)
+ 895 32.5 3.2 3.3 Crub_svsplocus 567224 568102 (81898) C Gypsy72-I_DR LTR/Gypsy (1978) 2317 1678 345
ANNOTATION EVIDENCE:
256 32.10 2.42 1.81 Crub_svsplocus 567224 567388 82612 C Gypsy164-I_DR LTR/Gypsy 1741 1906 1957
256 32.10 2.42 1.81 Crub_svsplocus 567224 567388 (82612) C Gypsy164-I_DR#LTR/Gypsy (1957) 1906 1741 m_b11s001i30
Crub_svsplocu 567224 GTAAG-TTCGTGAGGGGCAAGGCTATCTGTGCAAATGAGGGGATGAATTG 567272
- v v i i ii v i vvi vvv v i ii
C Gypsy164-I_DR 1906 GTAAGATTAGTCAGAGGTAGAGCAACCTGACTAAAATTGCGAATGAACCG 1857
Crub_svsplocu 567273 GCGGTAAAAATTTGCAAAGCCCAGGAAACTTTGTAGTTGCTTT-C--TTG 567319
v v v v i v vi -i ii i - --i
C Gypsy164-I_DR 1856 TCTGTAAAAATTGGCAAACCCCAGAAATCGCTG-GGCCGCCTTGCGACTG 1808
Crub_svsplocu 567320 TGCGGGGTGGTGCCCATTCTAATACTGCTCTGACCTTCTCTGGGTCCATT 567369
vi - v - ivv i v i vv v i
C Gypsy164-I_DR 1807 TCTGGGGTGG-GCCAA-TCTGCAACTGCTTTCACTTTGGCAGGATCCATT 1760
Crub_svsplocu 567370 TCAATGCCCTGTGGGGATA 567388
ivv iv v v i
C Gypsy164-I_DR 1759 CGCACTCCCTCTGGCGACA 1741
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 39.22
Transitions / transversions = 0.86 (24/28)
Gap_init rate = 0.04 (6 / 164), avg. gap size = 1.17 (7 / 6)
362 26.97 2.05 3.47 Crub_svsplocus 567234 567379 82621 C Gypsy70-I_DR LTR/Gypsy 2174 2317 1978
362 26.97 2.05 3.47 Crub_svsplocus 567234 567379 (82621) C Gypsy70-I_DR#LTR/Gypsy (1978) 2317 2174 m_b11s001i31
Crub_svsplocu 567234 GAGGGGCAAGGCTATCTG--TGCAAATGAGGGGATGAATTGGCGGTAAAA 567281
v-- i -- i iv v i-- vi v vi i
C Gypsy70-I_DR# 2317 GAGGGGCC--GCTACCTGGCTGTAGTTGCGA--ATGAAACGCCTATAGAA 2272
Crub_svsplocu 567282 ATTTGCAAAGCCCAGGAAACTTTGTAGTTGCTTT-CTTGTGCGGGGTGGT 567330
i i viv -v - v v vi vivi
C Gypsy70-I_DR# 2271 ATTCGCAAAGCCCAAGAATTGTTGTAG-AGCTTTGCGTGAGCCAGGAACC 2223
Crub_svsplocu 567331 GCCCATTCTAATACTGCTCTGACCTTCTCTGGGTCCATTTCAATGCCCT 567379
v v vi v v v i i iv
C Gypsy70-I_DR# 2222 GGCCAGTCGGAGACAGCTCTTACCTTTTCTGGATCCATTCGAATGCCCT 2174
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.54
Transitions / transversions = 0.81 (17/21)
Gap_init rate = 0.05 (7 / 145), avg. gap size = 1.14 (8 / 7)
895 33.22 3.41 3.24 Crub_svsplocus 567264 567879 82121 C Gypsy72-I_DR LTR/Gypsy 1678 2294 2003
895 33.22 3.41 3.24 Crub_svsplocus 567264 567879 (82121) C Gypsy72-I_DR#LTR/Gypsy (2003) 2294 1678 m_b11s001i32
Crub_svsplocu 567264 GATGAATTGGCGGTAAAAATTTGCAAAGCCCAGGAAACTTTGTAGTTGCT 567313
i v v i v vi iivv
C Gypsy72-I_DR# 2294 GATGAATCGCCGGTAAAAATTGGCGAAGCCCAGGAACCGCTGTAACGCCT 2245
Crub_svsplocu 567314 TTCTTGTGCGGGGTGGTGCCCATTCTAATACTGCTCTGACCTTCTCTGGG 567363
vv v iv i v v vi v v i i v v
C Gypsy72-I_DR# 2244 TTCGGGAGTCGGGTGGCGGCCAGTCGGAGACAGCCCTAACCTTCGCAGGG 2195
Crub_svsplocu 567364 TCCATTTCAATGCCCTG---TGGGGATATGCGATAGCCTAGGTAGTCTAT 567410
viv vv v--- iiiv --- iv i i v vvv i
C Gypsy72-I_DR# 2194 TCCATGCGAAGTCCCTCAACTGAAATTATG---TGTCCCAAGAAGGAAAC 2148
Crub_svsplocu 567411 CCTTTCCTGG---TGGAATTCGCATTTTGAGAGTTTGGCATATAGGTGAG 567457
--- vv --- i ivvvivi vi i v v
C Gypsy72-I_DR# 2147 ---TGACTGGACATGGAATTCGCACTTCTCCGCCTTTACATACAGCTGAT 2101
Crub_svsplocu 567458 CGGCTCGCAGCTTCTTTAAAAC-CGCTCTGACAAGTTTGACGTGTTCTTC 567506
ivv iv ivi v iv - - vi iv v i i v
C Gypsy72-I_DR# 2100 TCTCCAGCAGCCGTTGTAGCACTCGC-CGAACGTGTTGGACATGTTCCTG 2052
Crub_svsplocu 567507 TTTTGTTTCGGTAAAGATAAGAATGTCGTCCAAGTAAACAAGGAC---CC 567553
iv v ivvvi v i i i ii ---ii
C Gypsy72-I_DR# 2051 CATGGCGGAAGAAAAAATAAGAATGTCATCCAAATAAACAAAAACAAATT 2002
Crub_svsplocu 567554 CCTTAAACAGGTGTTCCCTTAGAATGTCATTGATTAGTTGCAT-AAAGAC 567602
vv v v --- i vv v ii i iv - v -
C Gypsy72-I_DR# 2001 GATTAATCATGT---CTCGGAGTACATCGTTGACGAGT-GCCTGAAAGAC 1956
Crub_svsplocu 567603 TGCAGG-GCCCCCTTGTAATCCAAATGGCAAGACTTTGAATTGATAGCAC 567651
v - viivv - ii i vvviv v v iii
C Gypsy72-I_DR# 1955 TGCTGGAGCATTGGTG-AGCCCAAATGGCAGGACAAGATATTCAAAATGC 1907
Crub_svsplocu 567652 CCCATGGGGCAGTTAAATGCAGTCTTCCATTCGTCCCCTTCCTTGATTCT 567701
vi vvv i i v i i v v v
C Gypsy72-I_DR# 1906 CCAGTGGGCGTGTTGAATGCGGTCTTCCATTCGTCACCCTCCCTCATACG 1857
Crub_svsplocu 567702 CACTCGATAGTAAGCTTCCCTTAAGTCTAG-TTTAGAAAAAATTTT--CC 567748
v vv i v iv v i i i- ivi i --
C Gypsy72-I_DR# 1856 GACGAGATGGTAAGCATTGCGTAGGTCCAACTTTGTGAAAAATCTTGCCC 1807
Crub_svsplocu 567749 CTTTCGATAGGTGTGACAGC--ATGTCTTTCATGAGGGGCAGTGGGTATA 567796
i v i v i -i vi -- v ----v i v i v iv
C Gypsy72-I_DR# 1806 CCTGCAAGAGAT-CGAAGGCCGAAG----ACATAAGCGGTAGGGGGTACC 1762
Crub_svsplocu 567797 GGTTGCTTTCACTGATTGT---ATTCAGGGCCCTATAATCCACGCATAAA 567843
i --- i v i i --- iiv i v i i i viii
C Gypsy72-I_DR# 1761 GAT---TTTTAATGGTTATGTCATTCAAACCTCGATAGTCTATGCAGGGG 1715
Crub_svsplocu 567844 CGTAAAGAGCCATCCTTCTTC-TCTCTAAAAAGGACC 567879
i i i i - v v i i
C Gypsy72-I_DR# 1714 CGCAGAGAACCATCCTTTTTCTTCACAAAGAAGAACC 1678
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.76
Transitions / transversions = 0.96 (97/101)
Gap_init rate = 0.05 (31 / 615), avg. gap size = 1.32 (41 / 31)
771 34.73 3.46 3.46 Crub_svsplocus 567265 568102 81898 C Gypsy138-I_DR LTR/Gypsy 3563 4400 7010
771 34.73 3.46 3.46 Crub_svsplocus 567265 568102 (81898) C Gypsy138-I_DR#LTR/Gypsy (7010) 4400 3563 m_b11s001i33
Crub_svsplocu 567265 ATGAATTGGCGGTAAAAATTTGCAAAGCCCAGGAAACTTTGTAGTTGCTT 567314
i ivv i v v ii v v vi vi
C Gypsy138-I_DR 4400 ATAAATCTCCGATAAAAATTGGCAAACCCCAAAAATCGTTGTACCTCTTT 4351
Crub_svsplocu 567315 TCTTGTGCGGGGTGGTGCCCATTCTAATACTGCTCTGACCTTCTCTGGGT 567364
vvi vi iv v v v i i ii i i vi v i
C Gypsy138-I_DR 4350 AACTGAACATGGTTGTGGCCAATCCAGTACTGCCTTAATCTTGCCAGGAT 4301
Crub_svsplocu 567365 CCATTTCAATGCCCTGTGGGGATATGCGAT-AGCCTAGGTAGTCTATCCT 567413
i v v ivii vv -- v - i i i v i- v iv
C Gypsy138-I_DR 4300 CCATCTGAAGGCTACATTTGGATA--CTATGAACCCAAGAAA-CGACACT 4254
Crub_svsplocu 567414 TTCCTGG-----TGGAATTCGCATTTTGAGAGTTTGGCATATAGGTGAGC 567458
--- ----- vi ivvv i ii iv i - vv i
C Gypsy138-I_DR 4253 TT---GGAGACATGGAATTCGCTCTTCTCCAGCTTAACGAACAG-TCTGT 4208
Crub_svsplocu 567459 GGCTCG-CAGCTTCTTTAAAACCGCTCTGACAAGTTTGACGTGTTCTTCT 567507
v i- i vvvvv i vvi v v vv i i v
C Gypsy138-I_DR 4207 GTCTCAACAACTGGGAGAGAACCTGCCGGACATGTTGTACATGCTCTTCA 4158
Crub_svsplocu 567508 T--TTGTTTCGGTAAAGATAAGAATGTCGTCCAAGTAAACAAGGAC---C 567552
--i ii -- v i v i i ii ---i
C Gypsy138-I_DR 4157 TAGCTACTT--GAAAAAATAAGTATGTCATCCAAGTAAACGAAAACAAAT 4110
Crub_svsplocu 567553 CCCTTAAACAGGTGTTCCCTTAGAATGTCATTGATTAGTTGCATA-AAGA 567601
iv v v---i v i ii i v i - v i-
C Gypsy138-I_DR 4109 CTGTTCAACAT---CTCCCTGAGGACATCATTAATGAAT-GCCTGGAAGA 4064
Crub_svsplocu 567602 CTGCAGGGCCCCCTTGTAAT-CCAAATGGCAAGACTTTGAATTGATAGCA 567650
v v v vi- ii v- v vv i viv v ii
C Gypsy138-I_DR 4063 CGGCTGGGGCAT-TTACAAGGCCAAAGGGCATTACCTGATATTCATAGTG 4015
Crub_svsplocu 567651 CCCCATGGGGCAGTTAAATGCAGTCTTCCATTCGTCCCCTTCCTTGATTC 567700
v ii ? vv v i i i i i
C Gypsy138-I_DR 4014 GCCTGTNGGGGTGTTAAAAGCGGTCTTCCACTCATCTCCTTCCTTGATCC 3965
Crub_svsplocu 567701 TCACTCGATAGTAAGCTTCCCTTAAGTCTAGTTTAGAAAAAAT--TTTC- 567747
v iv i v ii v i i ii v v i -- vv -
C Gypsy138-I_DR 3964 TGACCAGATGGTAAGCATTTCTGAGGTCCAACTTCGTAAAGATAGTGGCG 3915
Crub_svsplocu 567748 CCTTTCGATAGGTGTGACAGCA-TGTCTTTCATGAGGGGCAGTGGGTATA 567796
i v ii vv -ii v - --- v i i vv
C Gypsy138-I_DR 3914 CCCTGCAGTATCT-CAAAAGCAGTG---TTCATTAGGGGTAATGGGTAAC 3869
Crub_svsplocu 567797 GGTTGCTTTCACTGAT--TGT-ATTCAGGGCCCTATAATCCACGCATAAA 567843
i - -- v i -- - iiv i v ii viiv
C Gypsy138-I_DR 3868 GATT-CTT--AATGGTGATGTGATTCAAACCTCTATAATCAATACAGGGT 3822
Crub_svsplocu 567844 CGTAAAGAGCCATCCTTCTTCTCTCTAAAAAGGACCGGGGCAGCCACTTT 567893
v i vvv vvvvvi i ---i v v iv vi
C Gypsy138-I_DR 3821 CGAAGACTCCCATCCTTCTTGGAAACAAAAAAGA---AGCCTGCTCCTGC 3775
Crub_svsplocu 567894 AGGCTTGGCT---GGCTCAATGAAACCTCTCTCCAGGTTTTTTTTTATAA 567940
ivv i --- viv v v v i ivii iv i viv
C Gypsy138-I_DR 3774 AGGTGAGGTTGAAGGGCGAATGAATCCACTGTCTAGAGCCTCGTTCAAGT 3725
Crub_svsplocu 567941 ATCTTTCCATTTC--CTCCTTCTCCTTTGGGCTCATGGAGTATAATCTGG 567988
i i vv --i i vvvvv i--v v i --
C Gypsy138-I_DR 3724 ATTTCTCCATGGCAGTTCTTTCAGGAATGGA--GAGGGAGTACAATCT-- 3679
Crub_svsplocu 567989 GCTTCGGG--AGTTTTGCCCCAGGCTTGAATTCAATGGTACAGTC-TGTG 568035
i i i --i vi i ivii i i v i - i
C Gypsy138-I_DR 3678 ACCTCGAGGTGGGCTTGCTCCAGGTACAAGTTCAATAGAACAATCATATG 3629
Crub_svsplocu 568036 GGTCGGTGGGGGGGAAGCTCATTCGCCCTCTCCTCACTGAAGACTTCAGC 568085
i- i v v iivv v v ivvvv i i vi
C Gypsy138-I_DR 3628 GA-CGATGCGGGGGTAATGAAGTAGCCTGAGACTTACTAAAGACTTCACT 3580
Crub_svsplocu 568086 AAGGTCCCTATATTCCT 568102
i i v i i
C Gypsy138-I_DR 3579 GAGATCCATGTATTCTT 3563
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 46.52
Transitions / transversions = 1.05 (144/137)
Gap_init rate = 0.05 (45 / 837), avg. gap size = 1.29 (58 / 45)
+ 14 11.2 0.0 6.5 Crub_svsplocus 570829 570861 (79139) + (GTT)n Simple_repeat 1 31 (0) 346
ANNOTATION EVIDENCE:
14 11.19 0.00 6.45 Crub_svsplocus 570829 570861 79139 + (GTT)n Simple_repeat 1 31 0
14 11.19 0.00 6.45 Crub_svsplocus 570829 570861 (79139) (GTT)n#Simple_repeat 1 31 (0) m_b11s252i9
Crub_svsplocu 570829 GTTGTTGTTGTTAACTTGTTGTTGTTTTTCTTG 570861
--v v v
(GTT)n#Simple 1 GTTGTTGTTGTT--GTTGTTGTTGTTGTTGTTG 31
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2)
+ 32 0.0 0.0 0.0 Crub_svsplocus 571661 571690 (78310) + (ATC)n Simple_repeat 1 30 (0) 347
ANNOTATION EVIDENCE:
32 0.00 0.00 0.00 Crub_svsplocus 571661 571690 78310 + (ATC)n Simple_repeat 1 30 0
32 0.00 0.00 0.00 Crub_svsplocus 571661 571690 (78310) (ATC)n#Simple_repeat 1 30 (0) c_b11s251i4
Crub_svsplocu 571661 ATCATCATCATCATCATCATCATCATCATC 571690
(ATC)n#Simple 1 ATCATCATCATCATCATCATCATCATCATC 30
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)
+ 1667 31.4 1.5 0.5 Crub_svsplocus 571691 572279 (77721) C L3 LINE/CR1 (47) 4052 3458 348
ANNOTATION EVIDENCE:
1667 31.40 1.53 0.50 Crub_svsplocus 571691 572279 77721 C L3 LINE/CR1 3458 4052 47
1667 31.40 1.53 0.50 Crub_svsplocus 571691 572279 (77721) C L3#LINE/CR1 (47) 4052 3458 m_b11s001i34
Crub_svsplocu 571691 TAGTCCAACCCCCTGCTC-AGGCAGGAAACCCT---ATACCATTTCAGAC 571736
i iiii - v v --- i v ii v
C L3#LINE/CR1 4052 TAGTCCAACCTCCCATCCGATGCAGGAATCCCTTCTACAACATCCCTGAC 4003
Crub_svsplocu 571737 AAACGGCTGTCCAGCCTCTTCTTAAAAACTTCCAGGGTTGGAGCATTCGC 571786
ii iii v i v i v vi i vii i
C L3#LINE/CR1 4002 AAGTGGTCATCCAGCCTCTGCTTGAACACCTCCAGTGACGGGGAGCTCAC 3953
Crub_svsplocu 571787 CGCTTCTGGAGGCAGGTTGTTCCACTGGTTAATTGTTCTAACTGTCAGAA 571836
ii i ?v viii i vv vi iv i i i i
C L3#LINE/CR1 3952 TACCTCNCGAGGCAGCCCATTCCATTTTTGGACAGCTCTGATTGTTAGAA 3903
Crub_svsplocu 571837 AGTTTCTCCTTAGTTCCAGGTTGCTTCT--CTCCTTGATTAGTTTCCATC 571884
ii vv iv vivivv -- i -- ii i
C L3#LINE/CR1 3902 AGTTCTTCCTTATATTGAGCCGAAATCTGCCTCCCTG--TAACTTCCACC 3855
Crub_svsplocu 571885 TGTTGCTTCTTGCCCTGCCTTCAGGTGCTTTGGAGAATAGCTTGACTCCC 571934
ii v i v ii i v v iviiv iv iv v
C L3#LINE/CR1 3854 CATTGGTCCTAGTTCTGCCCTCTGGAGCCACACAGAATAAGTCTAATCCC 3805
Crub_svsplocu 571935 TCTTCTTTGTGGCAGCCCCTGAGATATTGGAACACTGCTATCATGTC-CC 571983
ivii i i v i v v v -
C L3#LINE/CR1 3804 TCTTCCACATGACAGCCCTTCAAATATTTGAAGACAGCTATCATGTCTCC 3755
Crub_svsplocu 571984 TCCACGTCCTTCTCTTCGTTAAACTAGACATACCCAATTCCAGCAACTGT 572033
i v - vii ii i v i vv i
C L3#LINE/CR1 3754 TCTAAGT-CTTCTCTTCTCCAGGCTAAACATCCCCAGTTCCTTCAACCGT 3706
Crub_svsplocu 572034 TCCTTATATGTTTTAGCCTCCAGTCCCCTAATCATCTTTGTTGCTCTTCT 572083
i viv i ii v i v i i v i i
C L3#LINE/CR1 3705 TCCTCATATGACATGGTTTCCAGACCCTTCACCATCCTGGTCGCTCTCCT 3656
Crub_svsplocu 572084 CTATACTCTTTCTAGAGTCTCCACATCTTTTTTACATCGTGGTGATCAAA 572133
iv v vi i vv v v ii ii i v vi i vi i
C L3#LINE/CR1 3655 CTGGACGCGCTCCAGTTTGTCAATGTCCCTCTTAAAATGTGGCGCCCAGA 3606
Crub_svsplocu 572134 ACTGGATGCAGTATTCCAAGTGTGGCCTTTCCAAAGCATTGTAAAGTAGT 572183
i i i i ii i vv iv vv v ii v
C L3#LINE/CR1 3605 ACTGAACGCAATACTCCAGATGTGGTCTGACCAGCGCAGAGTACAGCGGG 3556
Crub_svsplocu 572184 ATTAATACTTCACGTGATCTTAATTCTATCC--CTGTTAATTCAGCCTAG 572231
i v i v v ? vi iv v -- i v i
C L3#LINE/CR1 3555 ACTATTACCTCCCTTGNTCTGGACACTATACTTCTATTAATGCAGCCTAA 3506
Crub_svsplocu 572232 CACTGTGTTGGCTTTTTTGGCAGCTGCAGCACACTGCTGGCTCATATT 572279
v i ii i ii v i
C L3#LINE/CR1 3505 GATTGCATTAGCTTTTTTGGCAGCCACATCACACTGTTGGCTCATATT 3458
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.25
Transitions / transversions = 1.56 (112/72)
Gap_init rate = 0.01 (8 / 588), avg. gap size = 1.50 (12 / 8)
+ 267 17.5 0.0 0.0 Crub_svsplocus 572352 572391 (77609) + AmnSINE2 SINE/tRNA-Deu 80 119 (239) 349
ANNOTATION EVIDENCE:
267 17.50 0.00 0.00 Crub_svsplocus 572352 572391 77609 + AmnSINE2 SINE/tRNA-Deu 80 119 239
267 17.50 0.00 0.00 Crub_svsplocus 572352 572391 (77609) AmnSINE2#SINE/tRNA-Deu 80 119 (239) m_b11s001i35
Crub_svsplocu 572352 CAAGGTTGACTCAGCCTTCCATCCTTTTGAGGTTGATAAA 572391
i i i i ii v
AmnSINE2#SINE 80 CAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAGATAAA 119
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.68
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 17 12.9 2.1 6.5 Crub_svsplocus 575021 575068 (74932) + A-rich Low_complexity 1 46 (0) 350
ANNOTATION EVIDENCE:
17 12.95 2.08 6.52 Crub_svsplocus 575021 575068 74932 + (AAATCTA)n Simple_repeat 1 46 0
17 12.95 2.08 6.52 Crub_svsplocus 575021 575068 (74932) (AAATCTA)n#Simple_repeat 1 46 (0) m_b11s252i10
Crub_svsplocu 575021 AAATATAAAACCTGAAATTTAAAA-CTCAAATCTGAATAAATCTAAAAT 575068
v i i i - v -- -
(AAATCTA)n#Si 1 AAATCTAAAATCTAAAATCTAAAATCTAAAATCT--A-AAATCTAAAAT 46
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.09 (4 / 47), avg. gap size = 1.00 (4 / 4)
+ 11 22.8 0.0 5.1 Crub_svsplocus 575814 575854 (74146) + A-rich Low_complexity 1 39 (0) 351
ANNOTATION EVIDENCE:
11 22.76 0.00 5.13 Crub_svsplocus 575814 575854 74146 + (AGAAAA)n Simple_repeat 1 39 0
11 22.76 0.00 5.13 Crub_svsplocus 575814 575854 (74146) (AGAAAA)n#Simple_repeat 1 39 (0) m_b11s252i11
Crub_svsplocu 575814 AGAGAAAGGAAATGATAAGAGAAGGGAGAGAAAGAAAAAGA 575854
i i v - i -ii i
(AGAAAA)n#Sim 1 AGAAAAAGAAAAAGA-AAAAGAA-AAAGAAAAAGAAAAAGA 39
Matrix = Unknown
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.05 (2 / 40), avg. gap size = 1.00 (2 / 2)
+ 15 18.2 2.1 4.3 Crub_svsplocus 576435 576481 (73519) + (TTCT)n Simple_repeat 1 46 (0) 352
ANNOTATION EVIDENCE:
15 18.25 2.13 4.35 Crub_svsplocus 576435 576481 73519 + (TTCT)n Simple_repeat 1 46 0
15 18.25 2.13 4.35 Crub_svsplocus 576435 576481 (73519) (TTCT)n#Simple_repeat 1 46 (0) m_b11s252i12
Crub_svsplocu 576435 TTGTTTTTTATGTTTCTTT-GCTCTTGCTCTCCTTTCTTTCTTTCTTT 576481
v i - v -vi v - i
(TTCT)n#Simpl 1 TTCTTTCTT-TCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTT 46
Matrix = Unknown
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.07 (3 / 46), avg. gap size = 1.00 (3 / 3)
+ 16 0.0 0.0 0.0 Crub_svsplocus 579552 579569 (70431) + (A)n Simple_repeat 1 18 (0) 353
ANNOTATION EVIDENCE:
16 0.00 0.00 0.00 Crub_svsplocus 579552 579569 70431 + (A)n Simple_repeat 1 18 0
16 0.00 0.00 0.00 Crub_svsplocus 579552 579569 (70431) (A)n#Simple_repeat 1 18 (0) m_b11s252i13
Crub_svsplocu 579552 AAAAAAAAAAAAAAAAAA 579569
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAA 18
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0)
+ 323 34.2 2.5 2.5 Crub_svsplocus 582785 583105 (66895) + Gypsy-115-I_DR LTR/Gypsy 3247 3567 (761) 354
ANNOTATION EVIDENCE:
276 38.61 1.56 1.56 Crub_svsplocus 582785 583105 66895 + Gypsy88-I_DR LTR/Gypsy 3247 3567 761
276 38.61 1.56 1.56 Crub_svsplocus 582785 583105 (66895) Gypsy88-I_DR#LTR/Gypsy 3247 3567 (761) m_b11s001i36
Crub_svsplocu 582785 ATAGCCATGGATTTTATAGTGGAATTACCAGAAAGCAATGGGAATACTGT 582834
v i viii i i v vvv vv v v i i iii
Gypsy88-I_DR# 3247 ATATCCATGGACTTTATCACAGGACTTCCTTCATCCCAGGGAAACACCAC 3296
Crub_svsplocu 582835 TGTCTGGACGGTCACGGACTTGTTTTCCAAACAAGTGCAC--TTTAT-CC 582881
i v viiivi ii vvi --iv v-- i -
Gypsy88-I_DR# 3297 TATATTAGTCATCGTGGACAGATTTTCCAAA--GCTGCAAGATTCATTCC 3344
Crub_svsplocu 582882 CTTGCCAAAAGATTCCCATTGCAAAAGCCTTAGCGAAACTTTTCGTCCAG 582931
i i v v- i i v vvvi vi i vv i v v
Gypsy88-I_DR# 3345 CCTGTCCAAAC-TCCCCACTGCTAAAGAGACAGCTGAATTAGTCATCAAC 3393
Crub_svsplocu 582932 CATATTTATAGATTGCATGGAGCACCCCAATGCATCATCTCTGATAGGGG 582981
i v v v v viv viiv vivi i ii v i
Gypsy88-I_DR# 3394 CATGTGTTTCGAGTCTTTGGTATTCCCCTGGACGTTGTCTCTGATCGAGG 3443
Crub_svsplocu 582982 AGTGCAATTTACATCTGCATTTTGGAAGGAATTTTTATCCCTCT-TCAGG 583030
viv iv v iiv i v i v-i i vv i- vi
Gypsy88-I_DR# 3444 ACCTCAATTCTCCTCCAGATTCTGGCAAGC-CTTTTGTCAATCCATAGGG 3492
Crub_svsplocu 583031 ACCACTCAGGAACTGACATCTAGCCATCACCCTCAGTCGAATGGTCAATC 583080
i vv iiv iv v vi iivi v v
Gypsy88-I_DR# 3493 GCCACTGCGAGTCTATCTTCAGGTTTCCACCCTGAGTCGAATGGTCAAAC 3542
Crub_svsplocu 583081 GGAAAAATCGAAGTCAGTA-CTTGAG 583105
v i i iiv - v -
Gypsy88-I_DR# 3543 TGAGAGACTTAA-TCAGGACCTTGAG 3567
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 54.13
Transitions / transversions = 1.00 (61/61)
Gap_init rate = 0.03 (9 / 320), avg. gap size = 1.11 (10 / 9)
323 31.42 3.05 3.05 Crub_svsplocus 582820 583016 66984 + Gypsy-115-I_DR LTR/Gypsy 3276 3472 849
323 31.42 3.05 3.05 Crub_svsplocus 582820 583016 (66984) Gypsy-115-I_DR#LTR/Gypsy 3276 3472 (849) m_b11s001i37
Crub_svsplocu 582820 CAATGGGAATACTGTTGTCTGGACGGTCACGGACTTGTTTTCCAAA-CAA 582868
i v vi i v v vii iv v - v
Gypsy-115-I_D 3276 CAACGGGAATACGGTGATTTTGACCGTAGTGGACCGGTTTTCGAAAGCCA 3325
Crub_svsplocu 582869 GTGCACTTTATCCCT-TGCCAAAAGATTCCCATT-GCAAAAGCCTTAGCG 582916
v - - v -- v i- v i vvvi
Gypsy-115-I_D 3326 CT-CACTTTATCCCTCTGCCCAA--ATTACCATCAGCCAGAGAGACAGCG 3372
Crub_svsplocu 582917 AAACTTTTCGTCCAGCATATTTATAG-ATTGCATGGAGCACCCCAATGCA 582965
ivvvi v i iv v i i v v - - -- vi i i v
Gypsy-115-I_D 3373 GCTGCTGTCATTGACCATGTCTTTCGTATT-CATG--GCCTCCCGACGGA 3419
Crub_svsplocu 582966 --TCATCTCTGATAGGGGAGTGCAATTTACATCTGCATTTTGGAAGGAAT 583013
-- vi i i iviv i i iv iv ii i
Gypsy-115-I_D 3420 TGTGGTTTCTGACAGGGGGCCTCAGTTCATCTCTAAATTTTGGAGAGAGT 3469
Crub_svsplocu 583014 TTT 583016
Gypsy-115-I_D 3470 TTT 3472
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.84
Transitions / transversions = 1.00 (30/30)
Gap_init rate = 0.06 (11 / 196), avg. gap size = 1.09 (12 / 11)
279 36.36 2.48 2.48 Crub_svsplocus 582824 583105 66895 + Gypsy-129_DR-I LTR/Gypsy 3286 3567 758
279 36.36 2.48 2.48 Crub_svsplocus 582824 583105 (66895) Gypsy-129_DR-I#LTR/Gypsy 3286 3567 (758) m_b11s001i38
Crub_svsplocu 582824 GGGAATACTGTTGTCTGGACGGTCACGGACTTGTTTTCCAAACAAGTGCA 582873
iii i i v iiii iii ivi -- iv
Gypsy-129_DR- 3286 GGGAATACCACTATTTTGGTAATTGTGGACCGATTTTCCAA--AGCTGCA 3333
Crub_svsplocu 582874 C--TTTA-TCCCTTGCCAAAAGATTCCCATTGCAAAAGCCTTAGCGAAAC 582920
-- i - v -v i v vvvi vi i
Gypsy-129_DR- 3334 CGATTCATTCCCTTGCCCAAA-CTTCCCACTGCCAAAGAGACAGCCGAGC 3382
Crub_svsplocu 582921 TTTTCGTCCAGCATATTTATAGATTGCATGGAGCACCCCAATGCATCATC 582970
vi i vv v ii v viv v viv viiv vi ii
Gypsy-129_DR- 3383 TTACCATAAATCACGTGTTCCGAGTCTTTGGCATTCCCCAAGACATTGTC 3432
Crub_svsplocu 582971 TCTGATAGGGGAGTGCAATTTACATCTGCATTTTGGAAGGAATTTTTATC 583020
v iv i viv v v ivv i v i -v ii
Gypsy-129_DR- 3433 TCAGACCGAGGACCTCAATTTTCCTCCCGATTCTGGCAAG-CTTTTTGCC 3481
Crub_svsplocu 583021 CCTCT-TCAGGACCAC--TCAGGAACTGACATCTAGCCATCACCCTCAGT 583067
vv i- vi i i --i --v iv v vi iiv vv
Gypsy-129_DR- 3482 AGTCCATAGGGGCTACGGCCAG--CCTATCCTCAGGTTTTCACCCAGAGT 3529
Crub_svsplocu 583068 CGAATGGTCAATCGGAAAAATCGAAGTCAGTA-CTTGAG 583105
v v v i iiv - iv -
Gypsy-129_DR- 3530 CCAATGGTCAAACCGAAAGACTCAA-TCAAGACCTTGAG 3567
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 48.74
Transitions / transversions = 1.08 (52/48)
Gap_init rate = 0.04 (12 / 281), avg. gap size = 1.17 (14 / 12)
+ 19 6.4 2.9 2.9 Crub_svsplocus 584499 584533 (65467) + (CCTC)n Simple_repeat 1 35 (0) 355
ANNOTATION EVIDENCE:
19 6.44 2.86 2.86 Crub_svsplocus 584499 584533 65467 + (CCTC)n Simple_repeat 1 35 0
19 6.44 2.86 2.86 Crub_svsplocus 584499 584533 (65467) (CCTC)n#Simple_repeat 1 35 (0) m_b11s252i14
Crub_svsplocu 584499 CCT-CCTCCACCCCCTCCCTCCCTCTCTCCCTCCCT 584533
- - i i
(CCTC)n#Simpl 1 CCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCTCCCT 35
Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2)
+ 7507 29.9 2.3 2.4 Crub_svsplocus 587930 590753 (59247) C L3 LINE/CR1 (19) 4080 1259 356
ANNOTATION EVIDENCE:
7507 29.86 2.34 2.41 Crub_svsplocus 587930 590753 59247 C L3 LINE/CR1 1259 4080 19
7507 29.86 2.34 2.41 Crub_svsplocus 587930 590753 (59247) C L3#LINE/CR1 (19) 4080 1259 m_b11s001i39
Crub_svsplocu 587930 AAAGTTGGAAGGGACCTTGGAGGTCATCTAGTCCAACCCCCTGCTC-AGG 587978
i i i iiii - v
C L3#LINE/CR1 4080 AGAGTTGGAAGGGACCTTAGAGGTCATCTAGTCCAACCTCCCATCCGATG 4031
Crub_svsplocu 587979 CAGGAAACC---CTACACAATTTCGGACAAATGGCTGTCCAGTCTCTTCT 588025
v --- vv ii v i iii i v
C L3#LINE/CR1 4030 CAGGAATCCCTTCTACAACATCCCTGACAAGTGGTCATCCAGCCTCTGCT 3981
Crub_svsplocu 588026 TAAAAACTTCCAGTGTTGGAGCATTTACTGCTTCTGGAGGCAGGCTGTTC 588075
i v i vi i vii i i i ?v v ii
C L3#LINE/CR1 3980 TGAACACCTCCAGTGACGGGGAGCTCACTACCTCNCGAGGCAGCCCATTC 3931
Crub_svsplocu 588076 CACTGATTAATTGTTCTCACTGTCAGGAAGTTTCTCCTTAGTTCTAGGTT 588125
i vv vi iv i v i i i ii - vi ii ii
C L3#LINE/CR1 3930 CATTTTTGGACAGCTCTGATTGTTAGAAAGTTCTTCCTTA-TATTGAGCC 3882
Crub_svsplocu 588126 G---CTTCTCTCCTTGATTAGTTTCCACCCGTTGCTTCTTGTTCTGCCTT 588172
---ii vi i -- ii i v i v i
C L3#LINE/CR1 3881 GAAATCTGCCTCCCTG--TAACTTCCACCCATTGGTCCTAGTTCTGCCCT 3834
Crub_svsplocu 588173 CAGGTGCTTTGGAAAAT-AGCTTAATTCCCTCTTCTATATGGCAGCCCCT 588221
v v iviiv i - ii - i i i i
C L3#LINE/CR1 3833 CTGGAGCCACACAGAATAAGTCTAA-TCCCTCTTCCACATGACAGCCCTT 3785
Crub_svsplocu 588222 GAGATATCGGAATACTGCTATCATGTCCCCCCTTGTCCTTCTCTTCGTTA 588271
v i iv v v i i vivi vii
C L3#LINE/CR1 3784 CAAATATTTGAAGACAGCTATCATGTCTCCTCTAAGTCTTCTCTTCTCCA 3735
Crub_svsplocu 588272 AACTAGACATACCCAATTCTAGCAACCGTTCCTTATATGTTTTAGCCTCC 588321
ii i v i ivv i viv i ii
C L3#LINE/CR1 3734 GGCTAAACATCCCCAGTTCCTTCAACCGTTCCTCATATGACATGGTTTCC 3685
Crub_svsplocu 588322 AGTCCCCTAATTATCTTTGTTGCTCTTCTCTGTACTCTTTCTAGAGTCTC 588371
v i v ii i v i i v v vi i vv v
C L3#LINE/CR1 3684 AGACCCTTCACCATCCTGGTCGCTCTCCTCTGGACGCGCTCCAGTTTGTC 3635
Crub_svsplocu 588372 AACATCTTTTTTACATCATGGTGACCAAAACTGGATGCAGTATTCCAAGT 588421
ii ii i v vii i v i i i i i ii
C L3#LINE/CR1 3634 AATGTCCCTCTTAAAATGTGGCGCCCAGAACTGAACGCAATACTCCAGAT 3585
Crub_svsplocu 588422 GTGGCCTTACCAAGGCATTGAAGAGTGGTATTAATACTTCACGTGATCTT 588471
i v iv vv v v i v i v i v v ? v
C L3#LINE/CR1 3584 GTGGTCTGACCAGCGCAGAGTACAGCGGGACTATTACCTCCCTTGNTCTG 3535
Crub_svsplocu 588472 GATTCTATCCCTCTGTTAATGCAGCCTAGCACTGTGTTGGCCTTTTTGGC 588521
iv v i i iv i ii i i
C L3#LINE/CR1 3534 GACACTATACTTCTATTAATGCAGCCTAAGATTGCATTAGCTTTTTTGGC 3485
Crub_svsplocu 588522 AGCTGCAGCACACTGCTGGCTCATATTTAGGTGATTGTCTACTAGGACTC 588571
ii v i v v viiv v ii i
C L3#LINE/CR1 3484 AGCCACATCACACTGTTGGCTCATATTGAGCTTGCGGTCAACTAAAACCC 3435
Crub_svsplocu 588572 CGAGGTCCCTCTCACAGTTACTACTATTGAGCATGGTGCCACCTATGCTG 588621
v ii i ivvv i ii i vv i v ivi i v
C L3#LINE/CR1 3434 CTAGGTCTTTTTCACGTGAACTGCTGCTAAGCCAGATCCTCTCCATCCTG 3385
Crub_svsplocu 588622 TACTTGTGCATTTGGTTTTTCTTACCTAAATGTAGAATCTTGCTTTTTTC 588671
v i ivv i i ii i v v
C L3#LINE/CR1 3384 TACTTGTGCAGTTGATTTTTTGAACCTAAATGCAGGACTTTACATTTATC 3335
Crub_svsplocu 588672 ACCATTGAATTTCATTTTGTTAGTTAATGCCCAGTGTTCAAGTCTGTCCA 588721
v ii i i i vvv vi v i v
C L3#LINE/CR1 3334 CCTGTTAAATTTCATCTTGTTGGTTTCGGCCCATCGTTCCAGCCTGTCGA 3285
Crub_svsplocu 588722 GATCCTTCTGTATCTTAAGCCTGTCTTCTGGAGTGTTGGCTATTCCTGCC 588771
? i v i vi v ii?v i i i v
C L3#LINE/CR1 3284 GATCNTTTTGAATCTTGATTCTGTCATCCANCGTATTAGCTATCCCTCCC 3235
Crub_svsplocu 588772 AGCTTGGTGTCGTCTTCAAATTTGATGAGTTCCCCATCTATCCCTTCATC 588821
v i v i iviv v vi
C L3#LINE/CR1 3234 AGCTTTGTGTCATCTGCAAATTTGATAAGCATGCCTTCTATGTCTTCATC 3185
Crub_svsplocu 588822 CAAATCGTTGATGAAGATGTTGAAAAGCACTGGGCCCAGAATAAAGCCCT 588871
i i i i v v v v i i i
C L3#LINE/CR1 3184 CAAGTCATTGATAAAAATGTTGAACAGGACAGGGCCAAGGACAGAGCCCT 3135
Crub_svsplocu 588872 GGGGCACCCCACTACACACTTCCCTCCATATAGATGCAGTTCCACTGAGG 588921
v v v v i vi v iiiv v i i vv
C L3#LINE/CR1 3134 GTGGCACGCCACTAGAGACCTCCCTCCAGGTTGACATCGATCCATTAATC 3085
Crub_svsplocu 588922 ACCACTCGCTGAGTACGGCCGGTCAGCCAGCTACGGATCCATCTGGTGGT 588971
v iivi i i v i i i iiiv
C L3#LINE/CR1 3084 AACACCTTTTGGGTACGGTCGTTCAACCAGCTACGAATCCACCTAACTGT 3035
Crub_svsplocu 588972 GATTCTGTCTACCCCACATTTTTCTATCTTATCAAGTAGTAGGTTGTGAT 589021
iv viii i v i i i i v vv v vi ii v
C L3#LINE/CR1 3034 ACTATCATCCAGCCCATATTTCTCCATCTTGTCCACAAGGATATCATGAG 2985
Crub_svsplocu 589022 CTACTTTATCAAATGCCTTACTGAAGTCCAAGTAAATTATGTCCACAGCG 589071
vv i i i ii v i ? i i i
C L3#LINE/CR1 2984 AGACTTTGTCAAATGCCTTGCTGAAATCCAGATACACTNTGTCTACGGCA 2935
Crub_svsplocu 589072 TTCCCCTGATCCACTAATTTTGTCACTTGGTCAAAGAATGCAATAAGATT 589121
i i i i v v iivi i v v i i
C L3#LINE/CR1 2934 TTCCCCTGATCTACCAGTCTAGTAACCCTATCAAAAAAGGAAATGAGGTT 2885
Crub_svsplocu 589122 TGTCTGGCATGATCTATTTTTGACAAACCCATGTTGGCTTTTAGTAATGA 589171
v i ii i i iiii i ii i v
C L3#LINE/CR1 2884 AGTTTGGCATGACTTGTTCTTAGTGAACCCATGCTGGCTCCTAGTGATCA 2835
Crub_svsplocu 589172 ---CTTTGTTTGCCTCTAGGTGTTCGTTGATTCAT-TGTTTGATTATCTT 589217
--- iv --- i i i-ii vi - i v iv
C L3#LINE/CR1 2834 CCGCTTCCTTT---TCTAAGTGCTCA-CAAACCATCTGTTTAATAATCCG 2789
Crub_svsplocu 589218 TTCCAGGATCTTCCCAGGTATTGAGGTCAGGCTGATAGGTCTGTAATTTC 589267
i i i v i v i v i v iv i ?
C L3#LINE/CR1 2788 TTCTAGAATTTTGCCGGGGATCGACGTCAAGCTTACCGGTCTGTAGTTTN 2739
Crub_svsplocu 589268 CTGAGTCCATTTTTTTCCCTTTTTTGAGGATTGGAACTACATCAGCTCTT 589317
v i i i i i ii? v ? ? iv i v
C L3#LINE/CR1 2738 CAGAATCCATCTTTTTTCCCTTTTTAAAANTAGGNACNACATTTGCCCGT 2689
Crub_svsplocu 589318 TTCCAGTCCTCTGGTAGTTCCCCTGTGTTCCAGGATCTTTGAAA-ACTAT 589366
i i i vi ii i vi iv i i v - i i
C L3#LINE/CR1 2688 CTCCAGTCTTCTGGCACCTCTTCCGTTCTCCGTGATTTCTCAAAGATTAC 2639
Crub_svsplocu 589367 AGTTCAGTGGTTCCGATATCATATCTGCCAGTTCCTTGAGAACTCTGGGG 589416
v -v i vv i v i v v i i
C L3#LINE/CR1 2638 CG-ACAGCGGTTCCGCGATCACATCTGCAAGTTCTTTCAGTACCCTGGGA 2590
Crub_svsplocu 589417 TGTAATCCATCTGGTCCTGGCGATTTGAACTCCTCTAGGCTGAACAGGTG 589466
i i v v i v i iivi ivi
C L3#LINE/CR1 2589 TGTAATTCGTCTGGGCCTGGAGACTTGAACTCATTTAAAGCGGCTAGGTG 2540
Crub_svsplocu 589467 CTCACTTACCATTTTCTTGCCTATCTT-AACTTGTGTTTCTATTT----- 589510
v i i i ii -ii vvi i ivi -----
C L3#LINE/CR1 2539 CTCTCTTACTATCTCCTCACCTATCTTGGGCTTCAATTCCCTCTTAACGA 2490
Crub_svsplocu 589511 TGTTTTTTATGGCACTATTTTTGATAGGTTGGTCTG----TTTTTTCCCT 589556
v ------ iii vvi ----- ---- iv ii
C L3#LINE/CR1 2489 TGTTTGTT------CTACCCTTTCCA-----GTCTGAAGATCATTCTCCT 2451
Crub_svsplocu 589557 TTGT-GTAAAGACAGATGCAAAAAACGAGTTAAATAGTTCTGCTTTCTCC 589605
vi - vi i v v v i i i
C L3#LINE/CR1 2450 TGATAGAGAAGACGGAAGCAAAATAGGAGTTGAGTAGTTCTGCTTTCTCT 2401
Crub_svsplocu 589606 ATGTTGCTTGTCACCTGCTTGCCACTTCCACCCACTAATGGACCAATCAT 589655
v iiii i v vvivi ii v v v vi ii i vi ?i
C L3#LINE/CR1 2400 CTGTCATCTGTTAACATTACGCCATCTGCCCCAAGCAGCGGGCCTGTCNC 2351
Crub_svsplocu 589656 TTCCTTCACTTTTTTCTTGTTTTTTACATG---TTGAAAGAAGCTTTTTT 589702
i --- ii ii i iivv i--- -- i ?
C L3#LINE/CR1 2350 TTTCTT---TTTCCTTCTGCTCCGAACATAGCTTTGAA--AAGCCTTNTT 2306
Crub_svsplocu 589703 TTTGTTATTTTTAAC---TTTGGTCGCAAGCCTTAGTTCATTTTGAGCCT 589749
i ii i --- vv i i i i i
C L3#LINE/CR1 2305 TTTGTTGTCCTTAGCATTTTTTTTCGCAAGCCTCAGCTCATTCTGGGCTT 2256
Crub_svsplocu 589750 TAGCTTTCCTCATTTCATCTTTGCAGGCTCGGGCTATTTGCTGATATTCT 589799
i v ivii ii i i v ? i iv ----i i
C L3#LINE/CR1 2255 TAGCCTTCCTGACACTATTCTTACAGGCTTGTGNTACTCTCT----CTTT 2210
Crub_svsplocu 589800 G-ACTTAGTTATGTTCCCCTCTTTCCA-CTTTTTATACTTATCCTTTTTA 589847
-v i i- vi - i v v i v
C L3#LINE/CR1 2209 GTCCTTGGTTATA-TGTCCTCTTTCCATCTTCTGATACATGTCCTTTTAA 2161
Crub_svsplocu 589848 TCTTTCAATTTG---TCAGAGAGTTCTTTATGCAGCCATGCTGGTTTTTT 589894
------ i --- i ? i ? i i i
C L3#LINE/CR1 2160 ------AATCTGACATCAGAGAATNCTCTATGNAGCCACGTTGGTTTCTT 2117
Crub_svsplocu 589895 TTGAGAGCTGTTGTTTTTCCTCTTTGTTGG--TA-TTGTACTAGACTGTG 589941
vviv vv viivi i i ii --i - ---- i i
C L3#LINE/CR1 2116 AAATGCCCTCCCTCTTTTCTTCCTCATTGGATCATTTGTA----ATTGTA 2071
Crub_svsplocu 589942 CTTTTATTATCTCATTTTTCAAAATTTCCCAAGCTTCTTGAGTTGT-TTT 589990
--v i vv i v i ii ?v i iii -
C L3#LINE/CR1 2070 --GTCAGAATTTCATTTTTAAGAGCTTCCCANCCCTCTTGAGCCATCTTT 2023
Crub_svsplocu 589991 CCCCTTGAGGATTCTCA-TCCATGGAATCCTTCCCAAGCCCTCTCTAAGT 590039
iii --- ?-v v v i--viii i i
C L3#LINE/CR1 2022 CTTTTTGAG---TCTCNGGCCATGGAATCATACCT--CTTTTCTCTGAAT 1978
Crub_svsplocu 590040 TTATTGAAAATAGCT----CTCTTGAAGTCCAAGAC---TCTAG---TTT 590079
v viv ---- v i iiii --- v i ---
C L3#LINE/CR1 1977 TTTTTGAAATCTGCTTTTCCTCGTAAAGTCTGGAACATATGTGGACTTTT 1928
Crub_svsplocu 590080 GACTGTGTTCTATTGCTTGTGCTTCTATAATGTTGAATTCTAATATTACA 590129
i --- iiv v - vi ------i i v v
C L3#LINE/CR1 1927 AACT---TTTCCTTTCTTG-GCTATTA------CGAACTCTAAGATGACA 1888
Crub_svsplocu 590130 TGATCATTTCCTCCCAGGGTTCCTAT-GGCTTCAACACCTTCTATCATTT 590178
i- i i i - i v vi vi v i v
C L3#LINE/CR1 1887 TGG-CACTTTCTCCCAAGGTTCCTATCGACTTCCACTTCACCAACCAGTT 1839
Crub_svsplocu 590179 CATCTCTGTTAGTGAGAATTAGATCCAAAATGGCTAATCCCCTAGTTTCC 590228
v ii i v ii i i i viv v v i
C L3#LINE/CR1 1838 CTTCCTTGTTGGTCAGAATTAAGTCCAGAGTAGCAGTTCCCCTCGTTGCT 1789
Crub_svsplocu 590229 TTCTCTACTTTTGGGGAGACAAAGCTGTCTGCTAAGTTTGCCAGGAACCT 590278
i i iv i ii ii v v i ivv i i ii
C L3#LINE/CR1 1788 TCCTCTACCTTCTGAGAGATGAAATTGTCAGCAAGGCAAGTCAAGAATTT 1739
Crub_svsplocu 590279 GTTTGATCTTCCACTTGATGTGGAGTTTGTCTCCCGGTTGATGTCAGGGT 590328
i iv vi ii vvv i? i vv v i i iv v i
C L3#LINE/CR1 1738 ATCAGATGCTCTGCTTTTAGCNGAATGAGACTTCCAGCAGATGTCCGGAT 1689
Crub_svsplocu 590329 AGTTAAAGTCCCCCATTACTATTGTGATGTGCTTCC-TACATACTTTAGT 590377
i i i ?iviv i i- i -i v v
C L3#LINE/CR1 1688 AGTTGAAGTCCCCCATCACTACTGNATCTTGCCTCTGTGC-CAGTTTTGT 1640
Crub_svsplocu 590378 TAGCTGACTAGCA-AAAAGT-TCATCTATTTCCTCTGTTTGGTTGGGTGG 590425
v v -- v -i i- i ? ii i ii i
C L3#LINE/CR1 1639 AATCTG--TATCAGGAAAGCATCATCCATNTCCTCCATCTGGCCGGGCGG 1592
Crub_svsplocu 590426 TCTGTAGTATACACCTATGGCAATGTCATCCC-----CCCCCTTTTTTTA 590470
v i iii i i iii ----- i i ii
C L3#LINE/CR1 1591 TCTGTAGTATACTCCCACAACGATATCACTTCTGTTTCTCTCTCCTTTTA 1542
Crub_svsplocu 590471 TATTGACCCAAATGCATTCAAGACAGTTTTTATTATT--GTT-GTACTCT 590517
vi v vi v ?vvv i i iiv i-- - i---v
C L3#LINE/CR1 1541 TCCTCACCCAAATGCTCTCCANCGCGCTTCTACCCTCAGGTTCGTG---G 1495
Crub_svsplocu 590518 ATTTCTGTGGAGATGTAGTTATTTTTTATATAGAGAGCAACTCCACCTCC 590567
iii v i vv v i v i v v v i?
C L3#LINE/CR1 1494 ATTTCCACGCAGGTGTATATCTTCTTGACATACAGTGCTACTCTNCCTCC 1445
Crub_svsplocu 590568 TCTTTTATTTGGTCTGTTTCTTTTAAATAATTTAAATCCCTCTAGCTGTG 590617
i i ? v i i i vv ?v i i i v vvi
C L3#LINE/CR1 1444 CCTTCTANTAGATCTGTTTCTTTTGAACAAGGTNTACCCTTCCATCGCCG 1395
Crub_svsplocu 590618 TATTCCATGTGTGGGTTTCATCCCACCATGTTTCCGTAATGGCAACAATA 590667
vvii i ii v i v i iv v ii v
C L3#LINE/CR1 1394 TATTCCAGTCATGAGTCCCATCCCACCAAGTCTCGGTGATACCTATGAGA 1345
Crub_svsplocu 590668 TCGTATCTGCCCTC----ATTAACCTGAATTTCTAGTTCACCCTGTTTGC 590713
i i ii ----i ---- v ? ii ? ii
C L3#LINE/CR1 1344 TCGTATTTACCTCCTTGTGTTAA----AATTTCAAGTTNACTTTNTTTAT 1299
Crub_svsplocu 590714 TGTTCATACTCTGTGCATTGGTGTATAAACATTTGAGTCC 590753
iii i i i v
C L3#LINE/CR1 1298 TACCCATACTCTGTGCATTGGTATATAGACATCTGAGGCC 1259
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.36
Transitions / transversions = 1.79 (528/295)
Gap_init rate = 0.04 (99 / 2823), avg. gap size = 1.35 (134 / 99)
+ 4857 30.5 1.3 2.7 Crub_svsplocus 592658 594466 (55534) + L3 LINE/CR1 2163 3921 (178) 357
ANNOTATION EVIDENCE:
4857 30.48 1.29 2.67 Crub_svsplocus 592658 594440 55560 + L3 LINE/CR1 2163 3921 178
4857 30.48 1.29 2.67 Crub_svsplocus 592658 594440 (55560) L3#LINE/CR1 2163 3921 (178) m_b11s001i40
Crub_svsplocu 592658 AAAAGGACAAGTAT-AGAAAGTGGAAAGAGTGGCACATAACTAAGT-CAG 592705
v - ii - i i i v- i
L3#LINE/CR1 2163 AAAAGGACATGTATCAGAAGATGGAAAGAG-GACATATAACCAAGGACAA 2211
Crub_svsplocu 592706 AATATCAGCAAATAGCCCGAGCCTGCAAAAATGAAGTGAAGAAAGCTAAG 592755
i---- vi i ? v i i i iiv v i i i
L3#LINE/CR1 2212 AG----AGAGAGTANCACAAGCCTGTAAGAATAGTGTCAGGAAGGCTAAA 2257
Crub_svsplocu 592756 GCTCAAAATGAACTAAGGCTTGCGACCAAA---GTCAAAAATAACAAAAA 592802
i i i i vv --- ii ii i
L3#LINE/CR1 2258 GCCCAGAATGAGCTGAGGCTTGCGAAAAAAAATGCTAAGGACAACAAAAA 2307
Crub_svsplocu 592803 --AGTTTCTTTCAA---CATGTAAAAAACAAGAAAAAAGTGAAGGAAATG 592847
-- vi - ---i vvii i ii ii --- i i?
L3#LINE/CR1 2308 NAAGGCT-TTTCAAAGCTATGTTCGGAGCAGAAGGAAA---AAGAAAGNG 2353
Crub_svsplocu 592848 ATTGGTCCATTAGTGGGGGAAAGTGGCAAGAAGGTGACAAGCAACAGGGA 592897
iv i ii iv v v ii ivi v v i iiii i
L3#LINE/CR1 2354 ACAGGCCCGCTGCTTGGGGCAGATGGCGTAATGTTAACAGATGACAGAGA 2403
Crub_svsplocu 592898 GAAAGCAAAATTATTTAACTCATTTTTTGCATCTGACTTTAC-ACAAAGG 592946
i i i i v v v i v iv - iv
L3#LINE/CR1 2404 GAAAGCAGAACTACTCAACTCCTATTTTGCTTCCGTCTTCTCTATCAAGG 2453
Crub_svsplocu 592947 GAAAAAACAGACCAACCTACCAAAAATAGTGCCATAAAAAAC---AGAAT 592993
--- i i- i vv vv iii vi ivv i v v --- ii v
L3#LINE/CR1 2454 ---AGAAT-GATCTTCAGACTGGAAAGGGTAGAACAAACATCGTTAAGAG 2499
Crub_svsplocu 592994 AGAAATGCAAGTTAAGATAGGCAAGAAAATGGTAAGTGAGCACCTGTCCA 593043
i v v ivii ii i i i v iv i
L3#LINE/CR1 2500 GGAATTGAAGCCCAAGATAGGTGAGGAGATAGTAAGAGAGCACCTAGCCG 2549
Crub_svsplocu 593044 GCCTAAATGAGTTCAAATCACCAGGACCAGATGGATTACACCCCAGGGTT 593093
vii i v v i i i v
L3#LINE/CR1 2550 CTTTAAATGAGTTCAAGTCTCCAGGCCCAGACGAATTACATCCCAGGGTA 2599
Crub_svsplocu 593094 CTCAAGGAACTGGCAGATGTGGTCTCAGAACCATTG-AACTATATTTTTC 593142
v i v i v i ii -viv - i v
L3#LINE/CR1 2600 CTGAAAGAACTTGCAGATGTGATCGCGGAACCGCTGTCGGTA-ATCTTTG 2648
Crub_svsplocu 593143 AAGGATCCTGGAGCACTGGGGAACTACCGGAGGACTTGAATAGAGCTGAT 593192
iii vi v v ii iv i i i v ivv i vi
L3#LINE/CR1 2649 AGAAATCACGGAGAACGGAAGAGGTGCCAGAAGACTGGAGACGGGCAAAT 2698
Crub_svsplocu 593193 GTAGTTCCCATCTTCAAAAAAGGAAAAAAAATGGACTCAGGAAATTACAG 593242
? ? i ?i i i i i v ? i
L3#LINE/CR1 2699 GTNGTNCCTANTTTTAAAAAGGGAAAAAAGATGGATTCTGNAAACTACAG 2748
Crub_svsplocu 593243 ACCTATCAGCCTGACCTCAATACCCGGGAAGATCCTGGAAAAGATACTCA 593292
vi v i v i v v i i i vi vv i
L3#LINE/CR1 2749 ACCGGTAAGCTTGACGTCGATCCCCGGCAAAATTCTAGAACGGATTATTA 2798
Crub_svsplocu 593293 AACA-ATGAATCAGCGAACACCTAGAGGCAAACAAAG---TCATTACTAA 593338
- iv i- i i i --- vi --- v i i
L3#LINE/CR1 2799 AACAGATGGTTT-GTGAGCACTTAGA---AAAGGAAGCGGTGATCACTAG 2844
Crub_svsplocu 593339 AAGCCAACATGGGTTTGTCAAAAACAGATCATGCCAGACAAACTTTATTG 593388
i i iiii i ii i v i i v
L3#LINE/CR1 2845 GAGCCAGCATGGGTTCACTAAGAACAAGTCATGCCAAACTAACCTCATTT 2894
Crub_svsplocu 593389 CATTCTTTGACCAAGTGACAAAATTAGTGGATCAGAGGAATGCTGTGGAT 593438
v i ivii v v i i i i i i i i
L3#LINE/CR1 2895 CCTTTTTTGATAGGGTTACTAGACTGGTAGATCAGGGGAATGCCGTAGAC 2944
Crub_svsplocu 593439 ATAATTTACTTGGACTTCAGTAAGGCATTTGATAAAATAGATCACAACCT 593488
? i v ii i i i i ------------
L3#LINE/CR1 2945 ANAGTGTATCTGGATTTCAGCAAGGCATTTGACAAAGT------------ 2982
Crub_svsplocu 593489 ACTACTTGATAAGATATCACAACCTATTACTTGATAAGATAGAAAAATGT 593538
- - i- -- ---- i i v---- i i i i
L3#LINE/CR1 2983 -CT-CTC-AT--GATATC----CTTGTG----GACAAGATGGAGAAATAT 3019
Crub_svsplocu 593539 GGGTTAGACAGCATCACCACCACATGGATCCGTAACTGGCTGATCGGCCA 593588
i i iiii vi viii vi i i i v i i
L3#LINE/CR1 3020 GGGCTGGATGATAGTACAGTTAGGTGGATTCGTAGCTGGTTGAACGACCG 3069
Crub_svsplocu 593589 TACTCAGCATGTGGTCCTCAATGGAACCACATCTACATGTAGGGAAGTGT 593638
i iv v v vv i v v ii v v v i v
L3#LINE/CR1 3070 TACCCAAAAGGTGTTGATTAATGGATCGATGTCAACCTGGAGGGAGGTCT 3119
Crub_svsplocu 593639 GTAGTGGGGTGCCCCAGGGCTCTATTCTGGGCCCAGTGCTTTTCAACATC 593688
v v v i i v v v v i
L3#LINE/CR1 3120 CTAGTGGCGTGCCACAGGGCTCTGTCCTTGGCCCTGTCCTGTTCAACATT 3169
Crub_svsplocu 593689 TTCATCAATGATTTGGACGCGGGGATAGATGCTGAAATCATTAAATTTGC 593738
i i i vi iv v viiviv i i
L3#LINE/CR1 3170 TTTATCAATGACTTGGATGAAGACATAGAAGGCATGCTTATCAAATTTGC 3219
Crub_svsplocu 593739 AGATGACACCAAGTTGGCAGGAATAGCCAACACTCCAGAAGACAGGCTTA 593788
v i v i i i v?ii v iv i
L3#LINE/CR1 3220 AGATGACACAAAGCTGGGAGGGATAGCTAATACGNTGGATGACAGAATCA 3269
Crub_svsplocu 593789 AGATATAGAAGGATCTGGACAGACTTGAACACTGGGCGCTATCTAACAAA 593838
vi i ? v i v iv vvv v i i
L3#LINE/CR1 3270 AGATTCAAAANGATCTCGACAGGCTGGAACGATGGGCCGAAACCAACAAG 3319
Crub_svsplocu 593839 ATGAAATTCAATGGTGAAAAAAGGAAGGTTCTACATTTAGGCAAGAAAAA 593888
i ii v v v v i i i ivvi
L3#LINE/CR1 3320 ATGAAATTTAACAGGGATAAATGTAAAGTCCTGCATTTAGGTTCAAAAAA 3369
Crub_svsplocu 593889 CCAAATGCACAAGTACAGCATAGGTAGCACCATGCTCAATAGTAGTAACT 593938
i v v i iv v i vv i ii i vvvi
L3#LINE/CR1 3370 TCAACTGCACAAGTACAGGATGGAGAGGATCTGGCTTAGCAGCAGTTCAC 3419
Crub_svsplocu 593939 GTGAGAGGGACCTCAGAGTCCTAGTGGACAATCACTTAAATATGAGCCAG 593988
i ii vi i ii v viiv vi v i
L3#LINE/CR1 3420 GTGAAAAAGACCTAGGGGTTTTAGTTGACCGCAAGCTCAATATGAGCCAA 3469
Crub_svsplocu 593989 CAGTGTGCTGCAGCTGCCCAAAAGACCAACACAGTGCTAGGCTGCATTAA 594038
v ii v ii i ii i vi
L3#LINE/CR1 3470 CAGTGTGATGTGGCTGCCAAAAAAGCTAATGCAATCTTAGGCTGCATTAA 3519
Crub_svsplocu 594039 CAGAGGGATAGAATCAAGATCACATGAAGTATTAATACCACTTAACAATG 594088
i i v vi v ? viv i v i v i vv vv
L3#LINE/CR1 3520 TAGAAGTATAGTGTCCAGANCAAGGGAGGTAATAGTCCCGCTGTACTCTG 3569
Crub_svsplocu 594089 CCTTGGTAAGGTCACACTTGGAATACTGCATCCAGTTTTGGTCACCACAA 594138
vi v ii ii i i i i i v i v
L3#LINE/CR1 3570 CGCTGGTCAGACCACATCTGGAGTATTGCGTTCAGTTCTGGGCGCCACAT 3619
Crub_svsplocu 594139 TGTAAAAAAGATGCTGAGACTCTAGAAAGAGTACAGAGAAGAGCAACAAA 594188
v i ii iii v vv i iv v v i i v i
L3#LINE/CR1 3620 TTTAAGAGGGACATTGACAAACTGGAGCGCGTCCAGAGGAGAGCGACCAG 3669
Crub_svsplocu 594189 GATGATTAGGGGACTGAAGGCTAAAACATATAAGGAAAGGTTGCTGGAAT 594238
i v i v i ii i viv i v vv i
L3#LINE/CR1 3670 GATGGTGAAGGGTCTGGAAACCATGTCATATGAGGAACGGTTGAAGGAAC 3719
Crub_svsplocu 594239 TGGGTATGTCTAGTTTAATGAAGAGAAGGACGAGGGGGGATATGATAGCA 594288
v i ii iiv iviv i i i v
L3#LINE/CR1 3720 TGGGGATGTTTAGCCTGGAGAAGAGAAGACTTAGAGGAGACATGATAGCT 3769
Crub_svsplocu 594289 GTGTTCCAGTATCTCAGGGGCTGCCACAAAGAAGAGGGAGTCAAGCTATT 594338
v v i i v i i iivi v vi vi
L3#LINE/CR1 3770 GTCTTCAAATATTTGAAGGGCTGTCATGTGGAAGAGGGATTAGACTTATT 3819
Crub_svsplocu 594339 TTCCAAAGCGCCTGAAGGCAGGACAAGAAGCAATGAATGGAAACTAATCA 594388
i viivi v v i i v i v ii ii --
L3#LINE/CR1 3820 CTGTGTGGCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTA--CA 3867
Crub_svsplocu 594389 AGGAGAGAAG----CAACCTAGAACTAAGGAGAAACTTCCTGACAGTTAG 594434
i - v ---- ii ii iv - ii i i i i
L3#LINE/CR1 3868 GGGAG-GCAGATTTCGGCTCAATA-TAAGGAAGAACTTTCTAACAATCAG 3915
Crub_svsplocu 594435 TGTTAT 594440
v i i
L3#LINE/CR1 3916 AGCTGT 3921
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.85
Transitions / transversions = 1.74 (336/193)
Gap_init rate = 0.03 (58 / 1782), avg. gap size = 1.21 (70 / 58)
296 33.22 1.29 3.98 Crub_svsplocus 594235 594466 55534 + CR1-E4_fAlb LINE/CR1 44 269 161
296 33.22 1.29 3.98 Crub_svsplocus 594235 594466 (55534) CR1-E4_fAlb#LINE/CR1 44 269 (161) m_b11s001i41
Crub_svsplocu 594235 GAATTGGGTATGTCTAGTTTAATGAAGAGAAGGACGAGGGGGGATATGAT 594284
ii ?v ii ii iiv vi?v ? iv ?
CR1-E4_fAlb#L 44 GAGCTGGGNTTGTTCAGCCTGGAGAAGAGAAGGCTNCGGGGNGACCTNAT 93
Crub_svsplocu 594285 AGCAGTGTTCCAGTATCTCAGGGGCTGCCACAAAGAAGAGGGAGTCAAGC 594334
v i iv i iv i vvv i ii ?v vviii
CR1-E4_fAlb#L 94 TGCGGCCTTCCAGTACCCGAAGGGAGCCTACAAGAAAGNTGGAGAGGGAC 143
Crub_svsplocu 594335 TATTTTCCAAAGCGCCTGAA--GGCAGGACAAGAAGCAATGAATGGAAAC 594382
? v -- v v v -- i ii v iv vv
CR1-E4_fAlb#L 144 TNTTTAC--AAGGGCATGTAGTGACAGGACAAGGGGGAATGGCTTCAAAC 191
Crub_svsplocu 594383 TAATCAAGGAGAGAAGCAACCTAGA-ACTAAGGAGAAACTTCCTGACAGT 594431
i vvi iv ivvi ivi - i i i - i v v
CR1-E4_fAlb#L 192 TGAAAGAGGGTAGGTTTAGATTAGATATTAGGAAGAAA-TTCTTTACTGT 240
Crub_svsplocu 594432 TAGTGTTATGTCCTGGGCCGGCAGGCACAGGCTGC 594466
v v vi ----i --i v i
CR1-E4_fAlb#L 241 GAGGGTGGTG----AGGC--ACTGGCACAGGTTGC 269
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.94
Transitions / transversions = 1.18 (40/34)
Gap_init rate = 0.05 (11 / 231), avg. gap size = 1.09 (12 / 11)
+ 1844 36.2 1.6 1.6 Crub_svsplocus 596227 597519 (52481) + MamGypsy2-I LTR/Gypsy 1456 2748 (1418) 358
ANNOTATION EVIDENCE:
1844 36.24 1.62 1.62 Crub_svsplocus 596227 597519 52481 + MamGypsy2-I LTR/Gypsy 1456 2748 1418
1844 36.24 1.62 1.62 Crub_svsplocus 596227 597519 (52481) MamGypsy2-I#LTR/Gypsy 1456 2748 (1418) m_b12s001i2
Crub_svsplocu 596227 CTAGACCCAGCCATAGCCCCCATTAGAATCAAGCCAAGCAGGGTGCCCTT 596276
i i v v v vivv v iv v v iv i i
MamGypsy2-I#L 1456 CTGGATCCAGCCATTGCACCAATTCACTTGAAAGCTAGAAATGTACCTTT 1505
Crub_svsplocu 596277 TGCCTTAAAGGGTAAAATAGATGCAGAGCTGGATAAACTGATTCAGCAGG 596326
ii i iiv ?v v v v vv v i iv i i
MamGypsy2-I#L 1506 TGCTCTAAGGAAAAAAANTGAAGAAGAGCTTGAGCATCTAATCAAACAAG 1555
Crub_svsplocu 596327 GTATCTTAGAGCCTGTGG-ACAGTAGTCCATGGGAAACGCCCATAGTTAT 596375
ii i v i v vi- - vi vi vv ii --- i ii
MamGypsy2-I#L 1556 GTGCCCTCGAACCAGTTACACA-TACCCGGTGGGCTATACC---AATTGC 1601
Crub_svsplocu 596376 GCC---ACTGAAGGCCAATGGTGAAGTCCGATTCTGTGCGGACTACAAGT 596422
--- i v i i i vv i i vi
MamGypsy2-I#L 1602 GCCGGTACTAAAGCCTAATGGTAAGGTGAGACTTTGTGGAGACTACAAGT 1651
Crub_svsplocu 596423 GCACACTTAACAAAGTGCTGCAGCAGCATTTGTACCCAGTACCAGTGGTC 596472
vv v i i ii vv iiii i i v ii
MamGypsy2-I#L 1652 GCACTGTGAATAAGGCACTTAAGCAGCACCCATATCCAGTGCCTGCAGTC 1701
Crub_svsplocu 596473 AGTCACATTCTAGCCTCCCTCAAGGGGGGGGGGCAGATCTTTGCTAAGCT 596522
i vv i v ivii i--- vv iiv i v i
MamGypsy2-I#L 1702 AATCAACTCCTTGCTGTTCTT---GCTGGGGAAAAGGTCTTTGCAAAACT 1748
Crub_svsplocu 596523 TGACCT-GCTCAGGCCTATCAACAATTGCCAGTTGATGAGGCAATGGCTG 596571
- i i i ii viv i i v v iv v
MamGypsy2-I#L 1749 TGACCTTGCCCAAGCTTATCAACAGCTGATCGTCGGTGATGCTACTGCAG 1798
Crub_svsplocu 596572 AGGCCCAAACTATAGTGACTCACAGGGGGGCATTCAAGGTAAAAAGATTG 596621
v v vi v iv i vii v iv vi v
MamGypsy2-I#L 1799 ACGCCCAAACAATCATCACTCATCGAGGGGCATTCCGAGTTAAGCGCCTT 1848
Crub_svsplocu 596622 CAATTTGGAGTAAACGTAGCCCCTGGCATCTTCCAGAGTGTAATGGAGCG 596671
i i i vvvi v v i v iv v --
MamGypsy2-I#L 1849 CAGTTCGGAATTTCTGTTGCCCCTGGAATTTTCCAGTGCTTCATGGAG-- 1896
Crub_svsplocu 596672 AAC---GCTCCAAAATATCCCTGGCGTTTGCCCATACTTTGACGATATCC 596718
- --- iivv iv i v i vvvv i i i i
MamGypsy2-I#L 1897 -ACCCTGCTTTCTAGGATTCCAGGTGTGGTACCATATTTCGATGATGTCC 1945
Crub_svsplocu 596719 TCATCGCTGGGGATT--CAGCTGACAATTTAGCCGAAAGGCTGAGAGCCA 596766
v ii-- i-- vv ii vi v v i vvii vvi
MamGypsy2-I#L 1946 TGATCAT--GGGATCAACAGAGGATGAACTCGCGGAAAGACTTCAGGAAG 1993
Crub_svsplocu 596767 TTTTGCTACGTTTCTGCCAAGTGAGG---CTGAAGCTTAAGCAAGACAAG 596813
ii i vv - vi vi v --- i i-- v iv i v i
MamGypsy2-I#L 1994 TCCTACATCGTTTC-GATACATCAGGTATCCGAG--TGAAAAAGGAGAAA 2040
Crub_svsplocu 596814 TGCAAGATTGGGGTTACCTCCACGG--AGTTTCT-AGGATTCCGCATTGA 596860
ii i i i--- i vv -- vi - v v ii
MamGypsy2-I#L 2041 TGTGAAATCGGA---ACTTCCAGTGTCACCTTCTTAGGCTACCGCATCAA 2087
Crub_svsplocu 596861 TGCTCAGGACATCCACCCTGCTGAATCCAAGCTGCAAGCAATTCAGCAGG 596910
vvv ii i ii v vvi v i iv i vv v
MamGypsy2-I#L 2088 TGCTGCTGGTATTCACCCCACTCAAGATAAGGTACGTGCAATCCATGACG 2137
Crub_svsplocu 596911 CCCCAAGTCCCAAATCCAAGC--GAACTTCAGACCTTTCTGGGACTGCTA 596958
v v v v v v -- i ii i i i v
MamGypsy2-I#L 2138 CGCCTACTCCAAAAACAAAGCAAGAGCTTCAAGCCTTCCTGGGGCTACTC 2187
Crub_svsplocu 596959 AATTTTTACCACTCATTCCTTCCTCACAAGGCTGCAGTGGCTAAGCCGTT 597008
i iviv i v v vi vi v i ii
MamGypsy2-I#L 2188 AATTTCTACCATGTTTTTCTTCCACAAAAGGCAACCATTGCTGAGCCACT 2237
Crub_svsplocu 597009 ACACCAGCTCTTGGACAAACAGGCCCCTTGGCAGTGGACACAACCACATG 597058
v i iv vi iv viv ii v iv v iv vi
MamGypsy2-I#L 2238 TCATCGCCTACTGGGAAAAGGCGTTCCGTGGCGTTGGACTCGCCAGCATG 2287
Crub_svsplocu 597059 AAAAGAGCTTCAAAGAGGTCAAGGCCTTGCTCTCTTCAAATGCGATCCTC 597108
ii vivi viii v vvv ii vv vi vv vi v v
MamGypsy2-I#L 2288 AGGACGCTTTCCGGAATGTCAAGCAGTTATTGACTTCCGAGTCTGTGCTA 2337
Crub_svsplocu 597109 GCGCACTTCAATGAGAACTTGCCAGTGTGCATCGCCTGTGATGCATCCCC 597158
ii i v i iv ivvi v viv ii vv i v v
MamGypsy2-I#L 2338 GTACATTACGATGAACATAAACCACTGTTTCTTACCACTGACGCTTCACC 2387
Crub_svsplocu 597159 TTATGGGATTGGGGCTGTGTTAAGTCACTTGAAGGCTGATGGAACGCAAG 597208
i vii i i v i vvi v v v v vv i
MamGypsy2-I#L 2388 TTACGGTGCTGGAGCTGTGCTTAGCCACAAAATGCCAGATGGCACTGAGG 2437
Crub_svsplocu 597209 TCCCAATAGCATACTACTCTAGAACCCTATCATCAGCTGAATGCAATTAT 597258
iv v v v vv i vi v i v i
MamGypsy2-I#L 2438 CACCAATTGCTTACTACTCAAGAACAATGTCATCTACAGAACGGAACTAT 2487
Crub_svsplocu 597259 GCACAGATAGATAGGGAAGCCTTAGCCATAGTGGCTGGCATAAAGAAGTT 597308
i i v i ii i v ii vi v v vi v
MamGypsy2-I#L 2488 ACACAAATTGACAAAGAAGCCCTTGCTGTTATCGCGGGAGTCAAGAAGTT 2537
Crub_svsplocu 597309 CCATGATTTTGTATATGGACGCCACTTCACAGTCTTTACAGACCATAAGC 597358
ii i viv v i v ivv i i i v v i i
MamGypsy2-I#L 2538 CCACAACTACCTCTACGGCCGTGCCTTTACAATTTGTACTGATCACAAGC 2587
Crub_svsplocu 597359 CACTGCTGGGGTTGTTCACAACGAACAAACAAAC-CCCACACATAATATC 597407
v viv ii v iv v v i i i vv - vi - v i
MamGypsy2-I#L 2588 CTCTTTGGGGACTCTTTTCTAAGGATAAGCCTACGCCCTTA-ATTATGTC 2636
Crub_svsplocu 597408 CCCATAAAGGCTGAGGTGGTCTATCTTCCTGTCTGCATATGACCATACAC 597457
v iiv v v v v vv v i v vvv v i ii i
MamGypsy2-I#L 2637 ACCACGTATGCAGCGCTGGAGTCTTTTGCTCAGTGCTTATGACTACGCGC 2686
Crub_svsplocu 597458 TGGTTCACAAGCCAGGCAAAGAAATGGGTC--ATGCAGATGGTCTCAGCA 597505
v ii v v i v --i -- v vi v v
MamGypsy2-I#L 2687 TTGTCTACAAGCCTGGAAGAGCAAT--ATCGAATGCTGATGCCCTGAGCC 2734
Crub_svsplocu 597506 GGTTGCCATTACAG 597519
vi i i
MamGypsy2-I#L 2735 GTCTGCCACTGCAG 2748
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 47.20
Transitions / transversions = 1.00 (231/230)
Gap_init rate = 0.02 (32 / 1292), avg. gap size = 1.31 (42 / 32)
+ 601 31.8 4.0 3.6 Crub_svsplocus 597727 598278 (51722) + MamGypsy2-I LTR/Gypsy 3024 3577 (814) 358
ANNOTATION EVIDENCE:
601 31.77 3.99 3.61 Crub_svsplocus 597727 598278 51722 + Gypsy158-I_DR LTR/Gypsy 3024 3577 814
601 31.77 3.99 3.61 Crub_svsplocus 597727 598278 (51722) Gypsy158-I_DR#LTR/Gypsy 3024 3577 (814) m_b12s001i3
Crub_svsplocu 597727 GTTCAAG--GGGTATGTCCTATGGGATAGCCGGGTAGTAATCCCAACCTC 597774
i i -- i i vi i i?iv v ? ? i - ?
Gypsy158-I_DR 3024 GTCCAGGACGGATGTGTGTTGTGGGGNGCCCGCGTNGTNATTCCA-CCNC 3072
Crub_svsplocu 597775 ATTGAGGACTAGA----GTCCTG---CAGTCTCTGCATGAGGGACATTTA 597817
--- v vi ?---- v i --- --- i ii v vv iii
Gypsy158-I_DR 3073 A---AGGCCGGGNAGCCGTACCGAGACAGT---TACACAATGCCCACCCA 3116
Crub_svsplocu 597818 AGAATAGTCTGGATGAAGGCATTAGCGCACAGCCATCTTTGGTGGCCTGG 597867
i v i?i?v i i vi i ? iv i iv v i
Gypsy158-I_DR 3117 GGCATGNCNAGAATGAAAGGGTTGGCNCGGAGCTACGTGTGGTGGCCCGG 3166
Crub_svsplocu 597868 GCTCAACAAAGACGTCGAGGCCCAGGTCCACGGGTGCACTGTTTGTCAAC 597917
?v vi iivi i v i vv?v vv v vi i ?iivv iv
Gypsy158-I_DR 3167 NATGGATGCGGATGTGGAAGAANTGGTAAAGGCATGTANCAGATGTCAGG 3216
Crub_svsplocu 597918 AGTCAAGGCCGGAGATGCCCC-----AGGCCCCAGTTCATAGGTGGGAGG 597962
----i v - i -----i? ? v v ivv? ?
Gypsy158-I_DR 3217 AG----AGCAGGA-ACGCCCCTGCTCGNGCNCCATTACACCCNTGGGAGN 3261
Crub_svsplocu 597963 AGACTCATACCCCATGGTGAAGAGTCCATATCAACTACGCTGGGCCCTTT 598012
i?v v vv v v v i ii i ? v ? i
Gypsy158-I_DR 3262 GNCCACAGCCGCCCTGGAGAAGAATCCATATTGACTATGCNGGTCCNTTC 3311
Crub_svsplocu 598013 CAGGGGCAATTCTTCTTAATTCTCGTAGACAGCCATTCCAAGTGGCTAGA 598062
i iv v v ii i v i iivi i v i
Gypsy158-I_DR 3312 CAAGGAAAAATGTTTCTGATTCTGGTGGATGCTCACTCCAAGTGGATGGA 3361
Crub_svsplocu 598063 GGTCACGCCTGTCTCCTCCACTACCACTGCTAGG---ACCATCCAAGT-G 598108
? --- i? vi vv?i ? v i ?v v ?--- - i -?
Gypsy158-I_DR 3362 NG---CGTNTCCCTCGANTANTTCTACNTCTCGNGTTACCAT-CGAGTAN 3407
Crub_svsplocu 598109 CTGAGAGGAATCTTCACCGCACATGGACTTCCAGATGTCCTTGTCTCCAA 598158
vii vi i v ? i v v vi vv v v vi
Gypsy158-I_DR 3408 CTGAGACAGAGTTTTAGCGNACATGGATTACCTGAAATGGTAGTGTCGGA 3457
Crub_svsplocu 598159 CAATGGGCCCCAATTCACATCATTT--GAGTTCAAGGCGTTCCTCCAAGC 598206
vv?iiiv i i-- v ?-- i? ?i v --i ?
Gypsy158-I_DR 3458 CAATGGCANTTGTTTTACG--AGTNAAGAGTTTNAGGNATTCAT--GAGN 3503
Crub_svsplocu 598207 CAACATG--ATCTGGCATGCCACATCTGCACTGTTCCATCTAGCTTCCAA 598254
i?v -- ?i i iv ?v v i? v i ?
Gypsy158-I_DR 3504 CGNAATGGCATCNAGCACGTGACNACAGCACCNTACCATCCANCTTCCAA 3553
Crub_svsplocu 598255 TGGCCAGACTGAACGAATGGTGCA 598278
i ?iv i v iiv
Gypsy158-I_DR 3554 CGGNTTGGCAGAACGAGCTGTGCA 3577
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 42.32
Transitions / transversions = 1.17 (91/78)
Gap_init rate = 0.05 (28 / 551), avg. gap size = 1.50 (42 / 28)
+ 12 23.4 1.6 8.3 Crub_svsplocus 599017 599080 (50920) + (GCCAG)n Simple_repeat 1 60 (0) 359
ANNOTATION EVIDENCE:
12 23.39 1.56 8.33 Crub_svsplocus 599017 599080 50920 + (GCCAG)n Simple_repeat 1 60 0
12 23.39 1.56 8.33 Crub_svsplocus 599017 599080 (50920) (GCCAG)n#Simple_repeat 1 60 (0) m_b12s252i0
Crub_svsplocu 599017 GCCTGG-CAGGCGAGCTGGCAGGCCAGGCACACACACCGGCCATGAGAAG 599065
v - v -- v - vi - v - ivv
(GCCAG)n#Simp 1 GCCAGGCCAGGCCAG--GCCAGGCCAGGC-CAGGC-CAGGCCA-GGCCAG 45
Crub_svsplocu 599066 ATCAGGCCAGGCCAG 599080
ii
(GCCAG)n#Simp 46 GCCAGGCCAGGCCAG 60
Matrix = Unknown
Transitions / transversions = 0.57 (4/7)
Gap_init rate = 0.10 (6 / 63), avg. gap size = 1.00 (6 / 6)
+ 601 23.2 6.4 0.8 Crub_svsplocus 599553 599737 (50263) + L3 LINE/CR1 3907 4080 (19) 360
ANNOTATION EVIDENCE:
601 27.81 2.94 0.57 Crub_svsplocus 599553 599722 50278 + L3 LINE/CR1 3907 4080 19
601 27.81 2.94 0.57 Crub_svsplocus 599553 599722 (50278) L3#LINE/CR1 3907 4080 (19) m_b12s001i4
Crub_svsplocu 599553 AACAGTTAGAACAATTAACCAGTGAAACAACCTGCCTCCAGAAGTGGTGA 599602
i i i vi iv vv i i iiiv v? i i
L3#LINE/CR1 3907 AACAATCAGAGCTGTCCAAAAATGGAATGGGCTGCCTCGNGAGGTAGTGA 3956
Crub_svsplocu 599603 ATGCTCCAACACTGGAAGTTTTTTAAGAAGAGACTGGATGGCCATATGTC 599652
iiv i iv i v i- v i i iv
L3#LINE/CR1 3957 GCTCCCCGTCACTGGAGGTGTTC-AAGCAGAGGCTGGATGACCACTTGTC 4005
Crub_svsplocu 599653 TGAAATGGTATAG---GGTTTCCTGCCT-GACCAGGGGGTTG-ACCAGAT 599697
v ii v i --- v v - ivii i - i
L3#LINE/CR1 4006 AGGGATGTTGTAGAAGGGATTCCTGCATCGGATGGGAGGTTGGACTAGAT 4055
Crub_svsplocu 599698 GACCTCCAAGGTCCCTTCCAACTTT 599722
i i
L3#LINE/CR1 4056 GACCTCTAAGGTCCCTTCCAACTCT 4080
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 35.50
Transitions / transversions = 1.94 (31/16)
Gap_init rate = 0.02 (4 / 169), avg. gap size = 1.50 (6 / 4)
326 18.17 10.11 1.03 Crub_svsplocus 599649 599737 50263 + CR1-3_Croc LINE/CR1 3504 3600 5
326 18.17 10.11 1.03 Crub_svsplocus 599649 599737 (50263) CR1-3_Croc#LINE/CR1 3504 3600 (5) m_b12s001i5
Crub_svsplocu 599649 TGTCTGAAATGGT----ATAGGGTT--TCCTGCCTGAC-CAGGGGGTTG- 599690
v ii ---- v -- v v- -
CR1-3_Croc#LI 3504 TGTATGGGATGGTTTGGATAGGGATGATCCTGCCTCAGGCAGGGGGTTGG 3553
Crub_svsplocu 599691 ACCAGATGACCTCCA-AGGTCCCTTCCAACTTTATTACTATTATTATT 599737
i ii- i ii i v -i v
CR1-3_Croc#LI 3554 ACTAGATGACCTCTGGAGGTCCCTTCCAGCCCTACTTCT-CTATGATT 3600
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.18
Transitions / transversions = 1.67 (10/6)
Gap_init rate = 0.07 (6 / 88), avg. gap size = 1.67 (10 / 6)
+ 176 5.6 1.0 0.0 Crub_svsplocus 599958 600165 (49835) + (TAT)n Simple_repeat 1 210 (0) 361
ANNOTATION EVIDENCE:
176 5.59 0.96 0.00 Crub_svsplocus 599958 600165 49835 + (TAT)n Simple_repeat 1 210 0
176 5.59 0.96 0.00 Crub_svsplocus 599958 600165 (49835) (TAT)n#Simple_repeat 1 210 (0) c_b12s251i0
Crub_svsplocu 599958 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTA 600007
(TAT)n#Simple 1 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTA 50
Crub_svsplocu 600008 TTATTATTATTATTATTATTATTATTATTATTACTATTATTACTATTATT 600057
i i
(TAT)n#Simple 51 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATT 100
Crub_svsplocu 600058 ATTACTATTATTATTGTT-TTGTTGTT-TTGTTGTTGTTGTTGTTATTAT 600105
i i - i i - i i i i i
(TAT)n#Simple 101 ATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAT 150
Crub_svsplocu 600106 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTA 600155
(TAT)n#Simple 151 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTA 200
Crub_svsplocu 600156 TTATTATTAT 600165
(TAT)n#Simple 201 TTATTATTAT 210
Matrix = Unknown
Transitions / transversions = 1.00 (11/0)
Gap_init rate = 0.01 (2 / 207), avg. gap size = 1.00 (2 / 2)
+ 462 31.7 6.3 5.6 Crub_svsplocus 600585 601201 (48799) + L2-1_DR LINE/L2 3071 3480 (1505) 362
ANNOTATION EVIDENCE:
375 34.12 4.56 4.05 Crub_svsplocus 600585 601198 48802 + L2-2_DRe LINE/L2 2581 3197 1041
375 34.12 4.56 4.05 Crub_svsplocus 600585 601198 (48802) L2-2_DRe#LINE/L2 2581 3197 (1041) m_b12s001i6
Crub_svsplocu 600585 ATAATCAATACCTCT-TTGATGGAGGGGTCTTTCCCGCAACCTTTGAAGG 600633
i i v - ivvv vv v i i v? v i --
L2-2_DRe#LINE 2581 ATAATTAACACATCTCTTGACTCTGGTTTATTCCCCACTNCATTTAA--G 2628
Crub_svsplocu 600634 CAG-CGGTGGTGAGGCCCCTCCTCAAGAAGCCTTCCCTGGACC-CA-GCT 600680
- viv i vv v v v i ivv -i -
L2-2_DRe#LINE 2629 CAGGCTAGGGTAACCCCACTGCTAAAGAAACCCAACCTGGACCATACGCT 2678
Crub_svsplocu 600681 GTTTTGAAGAACTTTCGTCCTGTCTCCAACCTCCCCTTTGTGGGGAAGGT 600730
ii - - viv v v v vvv i v ii vv i
L2-2_DRe#LINE 2679 ACTT-GAA-AACTACAGACCAGTATCCCTGCTTCCATTCATGGCCAAGAT 2726
Crub_svsplocu 600731 TGTAGAGAAGGTGGTGGCGTCC---CAACTCTTGCAATC-CTTGGATGAA 600776
v i i i --- i --- v i v v i- ivvii
L2-2_DRe#LINE 2727 TCTGGAGAAAGTAGTG---TTCAATCAAGTCCTGGACTTTCTTACTCAAA 2773
Crub_svsplocu 600777 ACAAATTATC-TGGACCCTTTTCAATCTGGCTTCAGGCCCGGCTACAGCA 600825
-- v - vvivvv i i i vvv i vvv
L2-2_DRe#LINE 2774 ACAA--TCTCATGGACAACAAGCAATCCGGCTTTAAGAAAGGCCACTCAA 2821
Crub_svsplocu 600826 CTGAAGCTGCTTTGGTCGCACTGACCGATGACCTC----TGGCGAGCCCG 600871
ii ii v v iv viiv v i ---- v ivv i
L2-2_DRe#LINE 2822 CTGAGACTGCCCTGCTCTCGGTCGTGGAGGATCTCAGACTGGCTAAAGCA 2871
Crub_svsplocu 600872 GGATAGGGGTCAT---TCCTCTATCTTGGTGCTTCTTGACCTCTCAGCGG 600918
iv vviii --- - i v ------ i v v
L2-2_DRe#LINE 2872 GACTCTAAATCATCAGTCCTC-ATTTTGCTG------GACTTGTCAGCTG 2914
Crub_svsplocu 600919 CTTTCGATACCATCGACCATGGTATCCT----TTTGCG-TCGTCTCAGAG 600963
i i ii i iviv ---- i i - vv v--
L2-2_DRe#LINE 2915 CTTTTGACACTGTCAACCACCAGATCCTGCTATCTACGCTCGAGTCAC-- 2962
Crub_svsplocu 600964 AGGTAGGGGTGGGCGGCACCGTATTGCGGTGGTTCTCCTCCTACTTCTCT 601013
--- i v v vv i vv i ii vvv i i
L2-2_DRe#LINE 2963 ---TGGGCGTTGCGGGCACTGTTATACAATGGTTCAGATCTTACCTCTCT 3009
Crub_svsplocu 601014 GACAGGTCG--CAGTTGGTG--TTGGCGGGCGGACAGAGATCAACCCCTA 601059
i-- -- -- v vi -i v vi ivi
L2-2_DRe#LINE 3010 GACAGGTCATTCAG--GGTGTCTTGGAGGGGAGA-GGTGTCCAACCTACA 3056
Crub_svsplocu 601060 GGCACCTCGATTATGGGGTGCCTCAGGGCTC-GGTCTT--GTCCCTTCTT 601106
- i vi ivv i i - v -- i v i
L2-2_DRe#LINE 3057 -GCATCTAAACACTGGGGTACCTCAAGGCTCTGTTCTTGGGCCACTTCTC 3105
Crub_svsplocu 601107 TTTAACATCTACATGAAGCCGCTGGGTGAGATCATTCGGCAACACGGGGT 601156
ivv iivvii v i vvvii i i vi i iv
L2-2_DRe#LINE 3106 TTCTCCATCTACACATCATCTCTAGGACCAGTCATCCAGAGACATGGATT 3155
Crub_svsplocu 601157 GAGGTATCATCAGTATGCGGATGATACCCAATAATATATCTC 601198
vvvv i iiiv v iiv iv
L2-2_DRe#LINE 3156 CTCCTACCACTGCTATGCTGATGATACCCAGCTATACCTCTC 3197
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 45.33
Transitions / transversions = 0.93 (97/104)
Gap_init rate = 0.07 (40 / 613), avg. gap size = 1.32 (53 / 40)
438 34.73 2.75 1.91 Crub_svsplocus 600649 601012 48988 + AmnL2-1 LINE/L2 1116 1482 1131
438 34.73 2.75 1.91 Crub_svsplocus 600649 601012 (48988) AmnL2-1#LINE/L2 1116 1482 (1131) m_b12s001i7
Crub_svsplocu 600649 CCCTCCTCAAGAAGCCTTCCCTGGACCCAGCTGTTTTGAAGAACTTTCGT 600698
i i i i i v v viii i vvvv vi i
AmnL2-1#LINE/ 1116 CCCTTCTTAAAAAACCCTCCCTTGACCCCGACACTCTCTCTAACTACCGC 1165
Crub_svsplocu 600699 CCTGTCTCCAACCTCCCCTTTGTGGGGAAGGTTGTAGAGAAGGTGGTGGC 600748
i i i v vi v i vv v i i ivvi
AmnL2-1#LINE/ 1166 CCTATCTCTAACCTTCCCTTTCTCAGCAAAGTGCTTGAGAAAGTAGCCTT 1215
Crub_svsplocu 600749 GTCCCAACTCTTGCAATC--CTTGGATGAAACAA-ATTATC-TGGACCCT 600794
v i v i- i -- i--- v v - ? - v v?
AmnL2-1#LINE/ 1216 CTCTCATCTCTC-CAGTCACCTC---TCACACAACANTATCCTTGACCGN 1261
Crub_svsplocu 600795 TTTCAATCTGGCTTCAGGCCCGGCTACAGCACTGAAGCTGCTTTGGTC-- 600842
i v iv vi i i i v i i i vv --
AmnL2-1#LINE/ 1262 TTTCAGTCTGGGTTTCGCTCTGGCCATAGCACGGAAACCGCTCTCCTCCG 1311
Crub_svsplocu 600843 -GCACTGACCGATGACCTCTGGCGAGCCCGGGATAGGGGTCATTCCTCTA 600891
- i v v --- ivv vvv ivvv ii? iiv i iv
AmnL2-1#LINE/ 1312 TGTAGTTA---ATGACCTCCTCCTTTCTGCTGATGANGGCTCTTTCTCCT 1358
Crub_svsplocu 600892 TCTTGGTGCTTCTTGACCTCTCAGCGGCTTTCGATACCATCGACCATGGT 600941
i vi v i vvv i i i ii v vvi
AmnL2-1#LINE/ 1359 TCCTCATTCTCCTTGACCTCAGTGCAGCCTTCGACACTGTGGACCATTCC 1408
Crub_svsplocu 600942 ATCCTTTTGCGTCGTCT-CAGAG--AGGTAGGGGTGGGCGGCACCGTATT 600988
ii vii i - ? -- v i v vvvi iv v vi
AmnL2-1#LINE/ 1409 ATCCTCCTGGACCGCCTCCANAGCTATGCAGGCGTCTCTGGTTCCCTCCT 1458
Crub_svsplocu 600989 GCGGTGGTTCTCCTCCTACTTCTC 601012
ivi iv i v
AmnL2-1#LINE/ 1459 GTCATGGTTCCGCTCCTACCTATC 1482
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 47.33
Transitions / transversions = 1.07 (64/60)
Gap_init rate = 0.04 (14 / 363), avg. gap size = 1.21 (17 / 14)
462 30.43 7.13 6.34 Crub_svsplocus 600795 601201 48799 + L2-1_DR LINE/L2 3071 3480 1505
462 30.43 7.13 6.34 Crub_svsplocus 600795 601201 (48799) L2-1_DR#LINE/L2 3071 3480 (1505) m_b12s001i8
Crub_svsplocu 600795 TTTCAATCTGGCTTCAGGCCCGGCTACAGCACTGAAGCTGCTTTGGTCGC 600844
i v i v ivi i i v i i i i viv
L2-1_DR#LINE/ 3071 TTTCAGTCAGGTTTCAGGGCTCACCACAGTACAGAAACCGCCTTAGTGAA 3120
Crub_svsplocu 600845 ACTGACCGATGACCT--------CTGGCGAGCCCGGGATAGGGGTCATTC 600886
v i i i ii -------- vi -- ---- vv i ii
L2-1_DR#LINE/ 3121 AATAACCAACGATTTACTCTTAGCTGCTGA--CCG----AGGGTGCGTCT 3164
Crub_svsplocu 600887 CTCTATCTTGGTGCTTCTTGACCTCTCAG--CGGCTTTCGATACCATCGA 600934
v -- i vi v i -- i -- v i i
L2-1_DR#LINE/ 3165 CGCTAT--TAGTTTTACTCGA--TCTTAGTGCGGCATTTGATACCATTGA 3210
Crub_svsplocu 600935 CCATGGTATCCTTTTGCGTCGTCTCAGAG-----AGGT----AGGGGTGG 600975
iii iv ivi - i i ----- ---- iii
L2-1_DR#LINE/ 3211 CCACAATATCCTCATAAATCG-CTTAAAGTCTACAGGTGTCCAGGGACAG 3259
Crub_svsplocu 600976 GCGGCACCGTATTGCGGTGGTTCTCCTCCTACTTCTCTGACAGGTCGCAG 601025
v--------i i ii ivvv v vv v v vv
L2-1_DR#LINE/ 3260 GCT--------CTACAATGGTTTAAGTCATACTTAACTGACCGCTACCAG 3301
Crub_svsplocu 601026 TTGGTG----TTGGCGGGCGGAC---AGAGATCAACCCCTAGGCACCTCG 601068
v ---- iii i i v --- v ii ?i -- ----- vi
L2-1_DR#LINE/ 3302 TTTGTGAATATTAATGGACAGCCTTCACAAGTCNGCCC--AG-----TAA 3344
Crub_svsplocu 601069 ATTATGGGGTGCCTCAGGGCTCGGTCTT-GTCCCTT--CTTTTTAACATC 601115
v i v i i - v -- v vv i
L2-1_DR#LINE/ 3345 AGTATGGGGTGCCTCAAGGATCAGTTTTAGGCCCTTTACTGTTTACAATT 3394
Crub_svsplocu 601116 TACATGAAGCCGCTGGGTGAGATCATTCGGCAACACGGGGTGAGGTATCA 601165
vvi v v v i v ivi i i v v v
L2-1_DR#LINE/ 3395 TACATGCTACCTCTGGGAGACATTATTAGAAGACATGGGATCAGCTTTCA 3444
Crub_svsplocu 601166 TCAGTATGCGGATGATACCCAATAATATATCTCAAC 601201
iiiv i i v i
L2-1_DR#LINE/ 3445 CTGCTATGCAGATGATACTCAATTATATATTTCAAC 3480
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 38.51
Transitions / transversions = 1.37 (67/49)
Gap_init rate = 0.08 (34 / 406), avg. gap size = 1.62 (55 / 34)
+ 227 28.0 0.0 0.0 Crub_svsplocus 601385 601434 (48566) + L2-36_DRe LINE/L2 1007 1056 (723) 363
ANNOTATION EVIDENCE:
227 28.00 0.00 0.00 Crub_svsplocus 601385 601434 48566 + L2-36_DRe LINE/L2 1007 1056 723
227 28.00 0.00 0.00 Crub_svsplocus 601385 601434 (48566) L2-36_DRe#LINE/L2 1007 1056 (723) m_b12s001i9
Crub_svsplocu 601385 GTAGGCACGCAACTTGGGTGTCCTCCTGGACTCACAGCTAAATTTGGAAC 601434
i ii i ii v i v v i i i i
L2-36_DRe#LIN 1007 GCAGGTGCGTAATCTTGGTGTTCTCCTGGACTCCCAGCTTAGTCTGAAGC 1056
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.85
Transitions / transversions = 3.67 (11/3)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 587 27.1 3.4 3.4 Crub_svsplocus 601526 601777 (48223) + X24_LINE LINE/L2 1 209 (105) 364
ANNOTATION EVIDENCE:
256 33.63 3.42 3.42 Crub_svsplocus 601526 601759 48241 + L2-42_DRe LINE/L2 2924 3157 412
256 33.63 3.42 3.42 Crub_svsplocus 601526 601759 (48241) L2-42_DRe#LINE/L2 2924 3157 (412) m_b12s001i10
Crub_svsplocu 601526 GGTTACTCATGCCCTTGTCACCTCAAGACTGGACTACTGTAATGCGCTCT 601575
i iv ii i v vv v i i i v vi v
L2-42_DRe#LIN 2924 GGTCATACATGCTTTTATCACGTCCCGCCTAGACTATTGCAATTCCTTAT 2973
Crub_svsplocu 601576 ACATGGGGCTACCCTTGAAGAGCGTTCGGA-GGCTGCAGTTGGTTCAGAA 601624
ii v v - ii vvvv i v v - i i
L2-42_DRe#LIN 2974 ATGTTGGTCT-CCCTCAATCCTCATTGGCACGGTTGCAGTTGGTTCAAAA 3022
Crub_svsplocu 601625 TGCAGCCGCGAAAGCGATTGTGGGTGCACCAAGGCACA--CCCACGTGTC 601672
i v v i - vv ivvi - iiv -- i ii v
L2-42_DRe#LIN 3023 TGCGGCAGCTAGA-CTTTTAACAG-GCACCAAAAAACATGCTCATATCTC 3070
Crub_svsplocu 601673 ACC-----TATCCTCCGCGAGCTGCACTGGCTTCCTGTGGGTCTCCTGAC 601717
----- v v ----- v i vii i ivvi i
L2-42_DRe#LIN 3071 ACCAGTTTTAGCATCC-----CTTCATTGGCTTCCTGTTAATTTTAGAAT 3115
Crub_svsplocu 601718 GCAATTCAAGGTGTTGGTTGTCACCTTTAAAGCCCTTCATGG 601759
v i i v iv i iiii v vv
L2-42_DRe#LIN 3116 TCAGTTCAAGATTTTACTTATTGTTTTTAAAGCACTGAATGG 3157
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 44.78
Transitions / transversions = 1.11 (40/36)
Gap_init rate = 0.05 (11 / 233), avg. gap size = 1.45 (16 / 11)
587 25.74 3.35 3.35 Crub_svsplocus 601569 601777 48223 + X24_LINE LINE/L2 1 209 105
587 25.74 3.35 3.35 Crub_svsplocus 601569 601777 (48223) X24_LINE#LINE/L2 1 209 (105) m_b12s001i11
Crub_svsplocu 601569 GCGCTCTACATGGGGCTACCCTTGAAGAGCGTTCGGAGGCTGCAGTTGGT 601618
i ?? vv i v iii i v i
X24_LINE#LINE 1 GTGCTCNNCTGGGGGCTGCCCTTGAAGACCACCCGGAAGCTTCAGCTGGT 50
Crub_svsplocu 601619 TCAGAATGCAGCCGCGAAAGCGATTGT----GGGTGCACCAAGGCACAC- 601663
v v ----v vi i----? ---i? v ?-
X24_LINE#LINE 51 GCAGAATGCAGCGGC----TCGTCTGCTGAANGGTG---TNAGCCACANG 93
Crub_svsplocu 601664 --CCACGTGTCACCTATCCTCCGCGAGCTGCACTGGCTTCCTGTGGGTCT 601711
--v i vv i v iiv v ?i vv ii
X24_LINE#LINE 94 GAGCACATTACACCTGTGCTCCGCAGTCTGCACTGGCTACCNATTTGCTT 143
Crub_svsplocu 601712 CCTGACGCAATTCAAGGTGTTGGTTGTCACCTTTAAAGCCCTTCATGGCT 601761
viii ii v v i v vi i
X24_LINE#LINE 144 CCGAGTGCAATTCAAGGTGTTGACTTTAATCTATAAAGCCCTATATGGTT 193
Crub_svsplocu 601762 TAGGACCAAGTTACTT 601777
i v vi i
X24_LINE#LINE 194 TGGGCCCTGGTTACCT 209
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 33.25
Transitions / transversions = 1.17 (28/24)
Gap_init rate = 0.05 (10 / 208), avg. gap size = 1.40 (14 / 10)
+ 18 11.4 2.5 2.5 Crub_svsplocus 602134 602179 (47821) + A-rich Low_complexity 1 46 (0) 365
ANNOTATION EVIDENCE:
18 11.44 2.50 2.50 Crub_svsplocus 602134 602173 47827 + (ATAAATA)n Simple_repeat 1 40 0
18 11.44 2.50 2.50 Crub_svsplocus 602134 602173 (47827) (ATAAATA)n#Simple_repeat 1 40 (0) m_b12s252i1
Crub_svsplocu 602134 ATAAAT-TTTACTAATAAATAATAAATAAATAAATTATAAA 602173
-v v v - v
(ATAAATA)n#Si 1 ATAAATAATAAATAATAAATAATAAAT-AATAAATAATAAA 40
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2)
17 12.96 2.94 0.00 Crub_svsplocus 602146 602179 47821 + (AATA)n Simple_repeat 1 35 0
17 12.96 2.94 0.00 Crub_svsplocus 602146 602179 (47821) (AATA)n#Simple_repeat 1 35 (0) m_b12s252i2
Crub_svsplocu 602146 AATAAAT-AATAAATAAATAAATTATAAAATCAAT 602179
- v vv v
(AATA)n#Simpl 1 AATAAATAAATAAATAAATAAATAAATAAATAAAT 35
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.03 (1 / 33), avg. gap size = 1.00 (1 / 1)
+ 13 14.8 0.0 6.2 Crub_svsplocus 603480 603513 (46487) + (GTT)n Simple_repeat 1 32 (0) 366
ANNOTATION EVIDENCE:
13 14.79 0.00 6.25 Crub_svsplocus 603480 603513 46487 + (GTT)n Simple_repeat 1 32 0
13 14.79 0.00 6.25 Crub_svsplocus 603480 603513 (46487) (GTT)n#Simple_repeat 1 32 (0) m_b12s252i3
Crub_svsplocu 603480 GTTGTTGTTGTTAACTTCTTGTTGTTTTTCTTGT 603513
--v v v v
(GTT)n#Simple 1 GTTGTTGTTGTT--GTTGTTGTTGTTGTTGTTGT 32
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.06 (2 / 33), avg. gap size = 1.00 (2 / 2)
+ 267 17.5 0.0 0.0 Crub_svsplocus 604304 604343 (45657) + AmnSINE2 SINE/tRNA-Deu 80 119 (239) 367
ANNOTATION EVIDENCE:
267 17.50 0.00 0.00 Crub_svsplocus 604304 604343 45657 + AmnSINE2 SINE/tRNA-Deu 80 119 239
267 17.50 0.00 0.00 Crub_svsplocus 604304 604343 (45657) AmnSINE2#SINE/tRNA-Deu 80 119 (239) m_b12s001i12
Crub_svsplocu 604304 CAAGGTTGACTCAGCCTTCCATCCTTTTGAGGTTGATAAA 604343
i i i i ii v
AmnSINE2#SINE 80 CAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAGATAAA 119
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.68
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0)
+ 14 11.8 2.3 7.3 Crub_svsplocus 607040 607082 (42918) + A-rich Low_complexity 1 41 (0) 368
ANNOTATION EVIDENCE:
14 11.76 2.33 7.32 Crub_svsplocus 607040 607082 42918 + (TAAAATC)n Simple_repeat 1 41 0
14 11.76 2.33 7.32 Crub_svsplocus 607040 607082 (42918) (TAAAATC)n#Simple_repeat 1 41 (0) m_b12s252i4
Crub_svsplocu 607040 TAAAACCTGAAATTTAAAA-CTCAAATCTGAATAAATCTAAAAT 607082
i i i - v -- -
(TAAAATC)n#Si 1 TAAAATCTAAAATCTAAAATCTAAAATCT--A-AAATCTAAAAT 41
Matrix = Unknown
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4)
+ 399 32.5 0.5 0.5 Crub_svsplocus 608434 608631 (41369) + L1-109_DR LINE/L1 3675 3872 (1428) 369
ANNOTATION EVIDENCE:
399 32.49 0.51 0.51 Crub_svsplocus 608434 608631 41369 + L1-109_DR LINE/L1 3675 3872 1428
399 32.49 0.51 0.51 Crub_svsplocus 608434 608631 (41369) L1-109_DR#LINE/L1 3675 3872 (1428) m_b12s001i13
Crub_svsplocu 608434 AACTATATGGCATTAGTCCAACAA-ATAAAGAAAGATTTGGAAAAGTGGG 608482
vvv v - i - v iiv i ii i i ii
L1-109_DR#LIN 3675 AACTATAGTTCCTTA-TTCAACAATATCAGACAGGACCTAGAGAGATGGG 3723
Crub_svsplocu 608483 GGAGGCTACAACTATTGCTTTTATGTAGGATTGCAACTATCAAAATGAAT 608532
vivi iv v iv viv v i i
L1-109_DR#LIN 3724 GCGCACTATTACTCTCTCTGCAAGGTAGGATTGCGATTATCAAAATGAAT 3773
Crub_svsplocu 608533 ATCCTACCCAAATTACTATACTTATTTCTGACAATTCCCATATCATTAGA 608582
i i i i i v vi viv ii iv v vii v
L1-109_DR#LIN 3774 GTTCTACCTAGACTTCTATTTTTATTTACCATGATTCCTCTTTCTCCACA 3823
Crub_svsplocu 608583 TAAGAAATTTTTTTGAGAACTTAATAAAATTATTACAAAATATGTTTGG 608631
vi vi v v vvv v v v i
L1-109_DR#LIN 3824 TAAGACGTTTTTTAAAGAAATAAATTCCATTATAACTAAATTTATTTGG 3872
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 40.62
Transitions / transversions = 1.00 (32/32)
Gap_init rate = 0.01 (2 / 197), avg. gap size = 1.00 (2 / 2)
+ 694 29.1 1.6 1.6 Crub_svsplocus 609692 609957 (40043) C X24_LINE LINE/L2 (93) 221 1 370
ANNOTATION EVIDENCE:
694 27.98 1.36 1.36 Crub_svsplocus 609692 609912 40088 C X24_LINE LINE/L2 1 221 93
694 27.98 1.36 1.36 Crub_svsplocus 609692 609912 (40088) C X24_LINE#LINE/L2 (93) 221 1 m_b12s001i14
Crub_svsplocu 609692 AGGCGGTCTTGCAAATAGCCTGGCCCTGAGCCATATAGCGCTTTAAAGGT 609741
i ivv ii i v v ii i v v i
C X24_LINE#LINE 221 AGGCGATCTCTAAGGTAACCAGGGCCCAAACCATATAGGGCTTTATAGAT 172
Crub_svsplocu 609742 AATAACCAACACCTTGAATTGGACCCGGAGACCAATAGGCAATCAGTGCA 609791
v v ii v i ii v ? i ii
C X24_LINE#LINE 171 TAAAGTCAACACCTTGAATTGCACTCGGAAGCAAATNGGTAGCCAGTGCA 122
Crub_svsplocu 609792 GCTCGCGGAGGATAGGTGTAATGTGG---GTGTACCGAGGAACACCCGCT 609838
vii v i v---? iv v?--- ?vii
C X24_LINE#LINE 121 GACTGCGGAGCACAGGTGTAATGTGCTCCNTGTGGCTN---ACACCNTTC 75
Crub_svsplocu 609839 ATCACTCGCGCGGCTGCATTCTGGACCAACTGTAGTCTGCAAATACTTTA 609888
v vv v v v i v ii v iii iv i v
C X24_LINE#LINE 74 AGCAGACGAGCCGCTGCATTCTGCACCAGCTGAAGCTTCCGGGTGGTCTT 25
Crub_svsplocu 609889 CAAGGGTAGCCCCATGTAGAGCGC 609912
i vv ?? i
C X24_LINE#LINE 24 CAAGGGCAGCCCCCAGNNGAGCAC 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 36.21
Transitions / transversions = 1.18 (33/28)
Gap_init rate = 0.02 (4 / 220), avg. gap size = 1.50 (6 / 4)
349 34.78 2.54 2.54 Crub_svsplocus 609722 609957 40043 C L2-43_DR LINE/L2 1812 2047 368
349 34.78 2.54 2.54 Crub_svsplocus 609722 609957 (40043) C L2-43_DR#LINE/L2 (368) 2047 1812 m_b12s001i15
Crub_svsplocu 609722 CCATATAG-CGCTTTAAAGGTAATAACCAACACCTTGAATTGGACCCGGA 609770
v - i v ivv v- ii v i v i v
C L2-43_DR#LINE 2047 CCATTTAGACACTTAAAAACAAATAAA-AGTAACTTAAAATGGATCCTGA 1999
Crub_svsplocu 609771 GACCAATAGGCAATCAGTGCAGCTCGCGGAGGATA-----GGTGTAATGT 609815
i ivv ii ii v -----i i ----- v i
C L2-43_DR#LINE 1998 AATGCACGGGCAGCCAGTGAAG-----AGAAGATAAAATCGGGGTGATGT 1954
Crub_svsplocu 609816 GGGTGTACCGAGGAACACCCGCTATCACTCGCGCGGCTGCATTCTGGACC 609865
vvi iiviv viii v i vv vv i i i
C L2-43_DR#LINE 1953 GCTCGTATTTGCGTGTGCCAGTTAAAAGACGTGCAGCTGCATTCTGAACC 1904
Crub_svsplocu 609866 AACTGTAGTCTGCAAATACTTTACAAGGGTAGCCCCATGTAGAGCGCATT 609915
ii i viv i vvvv viivvi v v vi i v
C L2-43_DR#LINE 1903 AGTTGCAGTCGAGAGATAGAAGACTGACTCACCCCAAAATAAAGGGCATT 1854
Crub_svsplocu 609916 GCAGTAGTCCAAGCGTGAGGTGACAAGGGCATGAGTGACTGT 609957
i v v i ii ii v
C L2-43_DR#LINE 1853 ACAGTAGTCCAAGCGGGAGGTTATAAAAGCATGGATTACTGT 1812
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 46.10
Transitions / transversions = 1.11 (42/38)
Gap_init rate = 0.03 (8 / 235), avg. gap size = 1.50 (12 / 8)
373 29.51 0.00 0.00 Crub_svsplocus 609833 609954 40046 C L2-6_DRe LINE/L2 1679 1800 541
373 29.51 0.00 0.00 Crub_svsplocus 609833 609954 (40046) C L2-6_DRe#LINE/L2 (541) 1800 1679 m_b12s001i16
Crub_svsplocu 609833 CCCGCTATCACTCGCGCGGCTGCATTCTGGACCAACTGTAGTCTGCAAAT 609882
i i i v vv i i viv i v
C L2-6_DRe#LINE 1800 CCTGTTATTAATCTGGCGGCTGCATTTTGGACCAACTGTAGCCGAGAGAG 1751
Crub_svsplocu 609883 ACTTTACAAGGGTAGCCCCATGTAGAGCGCATTGCAGTAGTCCAAGCGTG 609932
vv v vii v v v iv vi i v v
C L2-6_DRe#LINE 1750 TGTTGACTGAGGTAGACCAATGTACAAAGAGTTGCAGTAGTCTAACCGAG 1701
Crub_svsplocu 609933 AGGTGACAAGGGCATGAGTGAC 609954
v iv ii i v
C L2-6_DRe#LINE 1700 AGGAGATTAAAGCATGGGTTAC 1679
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 37.71
Transitions / transversions = 0.80 (16/20)
Gap_init rate = 0.00 (0 / 121), avg. gap size = 0.0 (0 / 0)
+ 424 30.0 5.9 3.9 Crub_svsplocus 610278 610689 (39311) C L2-5_DRe LINE/L2 (1534) 693 279 371
ANNOTATION EVIDENCE:
424 31.60 6.40 4.10 Crub_svsplocus 610278 610683 39317 C L2-5_DRe LINE/L2 279 693 1534
424 31.60 6.40 4.10 Crub_svsplocus 610278 610683 (39317) C L2-5_DRe#LINE/L2 (1534) 693 279 m_b12s001i17
Crub_svsplocu 610278 GGGAAGAGATATACAGCTGGGTATCGTCAGCATACTGATGAAACCTCACC 610327
i i v i v i viii i v v i
C L2-5_DRe#LINE 693 GAGAGGAGATATAAAGTTGTGTATCATCAGCATAACAGTGGAAGCTAACT 644
Crub_svsplocu 610328 CCGTGCTGTCTGATGATCTCACCCAGCGGCTTCATGTA-AATGTTAAATA 610376
i i v i i v i i ivv i - i v vi
C L2-5_DRe#LINE 643 CCATGTTTTTTAATGATATCGCCTAGCGGTAGCATATATAGTGTGAAAAG 594
Crub_svsplocu 610377 GGAGGGGGGGAGGACCGACCCCTGCGGCACCCCGCATTCAAGGGGCCTCG 610426
vi ivvi i i v i i i i v ---- vi i --
C L2-5_DRe#LINE 593 TAAGGGACCAAGAACTGAGCCTTGTGGTACCCCACAGT----GTACTT-- 550
Crub_svsplocu 610427 GGGTTGACCTCT-----GCCCCTCCA----CCAGTACCGATTGTGACCGG 610467
--- i v ----- i i ---- iii vi vv v v
C L2-5_DRe#LINE 549 ---TTGATCTGTATGATGCCTCTTCATTAACTGATACAAATTGATAACGT 503
Crub_svsplocu 610468 CCAAAGAGGTAGGA---GAACCACCGTAAAACAGTGCCTCCCACTCCCAC 610514
i i v i i --- vvvi vi v viv iv v
C L2-5_DRe#LINE 502 TCAGATAGATAAGACCTGAACCAGGCCAATGCAGTTCCTGTAATACCAAC 453
Crub_svsplocu 610515 CC---CTCCAAGTC-GTCGCAAAAGGATACCATGATCGATGGTATCAAAA 610560
vi---i i i -i i- ii i ii v v
C L2-5_DRe#LINE 452 ATAATTTTCAAGCCTATCA-AGGAGAATATTATGATCGATTGTATCAAAT 404
Crub_svsplocu 610561 GCCGCTGAGAGGTCAAGTAGCACCAAGACAGAGGAAT--AACC-CGTCTC 610607
v vvv v i i i -- i -- - -v
C L2-5_DRe#LINE 403 GCAGCACTGAGGTCCAATAACACTAAG--AGAGAAATGCAACCACG-ATC 357
Crub_svsplocu 610608 GGGC--CCGCCAGAGATCATCCATCAGTGCGACCAAAGCAGTTTCTGTGC 610655
i -- v vvi i iii v v viv vv iv v
C L2-5_DRe#LINE 356 GGACGACAGGAGGAGGTCATTTGTAACTCTTAGGAGTGCTGTTTCTGTGC 307
Crub_svsplocu 610656 --TGAA--GCTGGGCCTGAAGCCAGATTGAAA 610683
-- -- ---- i v
C L2-5_DRe#LINE 306 TATGAAATGCT----CTAAATCCAGATTGAAA 279
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 41.69
Transitions / transversions = 1.28 (69/54)
Gap_init rate = 0.07 (28 / 405), avg. gap size = 1.54 (43 / 28)
230 18.37 2.00 2.00 Crub_svsplocus 610640 610689 39311 C L2-49_DR LINE/L2 1349 1398 1490
230 18.37 2.00 2.00 Crub_svsplocus 610640 610689 (39311) C L2-49_DR#LINE/L2 (1490) 1398 1349 m_b12s001i18
Crub_svsplocu 610640 AAAGCAGTTTCTGTGCTG-AAGCTGGGCCTGAAGCCAGATTGAAAAGGGT 610688
i i v v i-i i - i v
C L2-49_DR#LINE 1398 AGAGCGGATTCAGTGCTATGAGCCGG-CCTAAAGCCAGATTGAAAAGGCT 1350
Crub_svsplocu 610689 C 610689
C L2-49_DR#LINE 1349 C 1349
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 16.51
Transitions / transversions = 2.00 (6/3)
Gap_init rate = 0.04 (2 / 49), avg. gap size = 1.00 (2 / 2)
+ 474 10.1 0.0 0.0 Crub_svsplocus 610695 610763 (39237) + URR1B DNA/hAT-Charlie 1 69 (156) 372
ANNOTATION EVIDENCE:
474 10.14 0.00 0.00 Crub_svsplocus 610695 610763 39237 + URR1B DNA/hAT-Charlie 1 69 156
474 10.14 0.00 0.00 Crub_svsplocus 610695 610763 (39237) URR1B#DNA/hAT-Charlie 1 69 (156) m_b12s001i19
Crub_svsplocu 610695 CAGTGGTTCTCAACCTGTGGGTCGGGACCCCATTTGGGGTCGAACGACCA 610744
i v v v v
URR1B#DNA/hAT 1 CAGCGGTTCTCAACCTGTGGGTCGCGACCCCTTTGGGGGTCGAACGACCC 50
Crub_svsplocu 610745 TTTCACGGGGGTCGCCAAA 610763
i v
URR1B#DNA/hAT 51 TTTCACAGGGGTCGCCTAA 69
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.42
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
+ 256 9.1 0.0 0.0 Crub_svsplocus 611020 611052 (38948) + URR1B DNA/hAT-Charlie 193 225 (0) 373
ANNOTATION EVIDENCE:
256 9.09 0.00 0.00 Crub_svsplocus 611020 611052 38948 + URR1B DNA/hAT-Charlie 193 225 0
256 9.09 0.00 0.00 Crub_svsplocus 611020 611052 (38948) URR1B#DNA/hAT-Charlie 193 225 (0) m_b12s001i20
Crub_svsplocu 611020 GGGTCGCGGCATTAAAAAGGTTGAGAACCACTG 611052
i ii
URR1B#DNA/hAT 193 GGGTCGCAGCATTAGGAAGGTTGAGAACCACTG 225
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.03
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 252 36.4 0.0 0.0 Crub_svsplocus 611069 611102 (38898) C L2-16_DRe LINE/Rex-Babar (1505) 2784 2731 374
ANNOTATION EVIDENCE:
252 36.42 0.00 0.00 Crub_svsplocus 611069 611219 38781 C L2-16_DRe LINE/Rex-Babar 2634 2784 1505
252 36.42 0.00 0.00 Crub_svsplocus 611069 611219 (38781) C L2-16_DRe#LINE/Rex-Babar (1505) 2784 2634 m_b12s001i21
Crub_svsplocu 611069 TCATCCAGAGACCGTCGGAGCTAGAGCGCCACCACTCTCTCTACAACCTT 611118
i i i ii viv iv ivi v i i v i
C L2-16_DRe#LIN 2784 TCATCTAAAAATTGATTGAGCTGTAGCAATACAACTTTTTCTAAAATCTT 2735
Crub_svsplocu 611119 CCCCAAAAAGGGGAGATTGGAGACTGGACGGAAGTTATTTAAATTAGCCG 611168
v iv v vi v i i i v v v i viv iv
C L2-16_DRe#LIN 2734 ACTAAAAAATGTAACATTAGAAATTGGTCTGTAATTATTTAAAACTGTGG 2685
Crub_svsplocu 611169 GGTCCAGGGTAGGCTTCTTGAGAAGGGGCCTCACAACCGCTTCTTTCAAG 611218
i iiv v vi i v i v i i v v i v i
C L2-16_DRe#LIN 2684 AGTCCAAATTTGTTTTTTTTAAAAGTGGCTTTACCACAGCTTTTTTAAAA 2635
Crub_svsplocu 611219 G 611219
C L2-16_DRe#LIN 2634 G 2634
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 51.44
Transitions / transversions = 1.20 (30/25)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 278 20.7 0.0 0.0 Crub_svsplocus 611103 611160 (38840) C L2-42_DRe LINE/L2 (1430) 2139 2082 375
ANNOTATION EVIDENCE:
278 20.69 0.00 0.00 Crub_svsplocus 611103 611160 38840 C L2-42_DRe LINE/L2 2082 2139 1430
278 20.69 0.00 0.00 Crub_svsplocus 611103 611160 (38840) C L2-42_DRe#LINE/L2 (1430) 2139 2082 m_b12s001i22
Crub_svsplocu 611103 CTCTCTCTACAACCTTCCCCAAAAAGGGGAGATTGGAGACTGGACGGAAG 611152
i v ivv v v i v i iv
C L2-42_DRe#LIN 2139 CTCTTTCTAGAACCTTTGACATAAATGGAAGTTTAGAGATAGGACGGAAG 2090
Crub_svsplocu 611153 TTATTTAA 611160
C L2-42_DRe#LIN 2089 TTATTTAA 2082
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.25
Transitions / transversions = 0.71 (5/7)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
+ 252 36.4 0.0 0.0 Crub_svsplocus 611161 611219 (38781) C L2-16_DRe LINE/Rex-Babar (1505) 2730 2634 374
ANNOTATION EVIDENCE:
252 36.42 0.00 0.00 Crub_svsplocus 611069 611219 38781 C L2-16_DRe LINE/Rex-Babar 2634 2784 1505
252 36.42 0.00 0.00 Crub_svsplocus 611069 611219 (38781) C L2-16_DRe#LINE/Rex-Babar (1505) 2784 2634 m_b12s001i21
Crub_svsplocu 611069 TCATCCAGAGACCGTCGGAGCTAGAGCGCCACCACTCTCTCTACAACCTT 611118
i i i ii viv iv ivi v i i v i
C L2-16_DRe#LIN 2784 TCATCTAAAAATTGATTGAGCTGTAGCAATACAACTTTTTCTAAAATCTT 2735
Crub_svsplocu 611119 CCCCAAAAAGGGGAGATTGGAGACTGGACGGAAGTTATTTAAATTAGCCG 611168
v iv v vi v i i i v v v i viv iv
C L2-16_DRe#LIN 2734 ACTAAAAAATGTAACATTAGAAATTGGTCTGTAATTATTTAAAACTGTGG 2685
Crub_svsplocu 611169 GGTCCAGGGTAGGCTTCTTGAGAAGGGGCCTCACAACCGCTTCTTTCAAG 611218
i iiv v vi i v i v i i v v i v i
C L2-16_DRe#LIN 2684 AGTCCAAATTTGTTTTTTTTAAAAGTGGCTTTACCACAGCTTTTTTAAAA 2635
Crub_svsplocu 611219 G 611219
C L2-16_DRe#LIN 2634 G 2634
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 51.44
Transitions / transversions = 1.20 (30/25)
Gap_init rate = 0.00 (0 / 150), avg. gap size = 0.0 (0 / 0)
+ 15 25.3 4.3 2.9 Crub_svsplocus 612311 612379 (37621) + (TTCT)n Simple_repeat 1 70 (0) 376
ANNOTATION EVIDENCE:
15 25.27 4.35 2.86 Crub_svsplocus 612311 612379 37621 + (TTCT)n Simple_repeat 1 70 0
15 25.27 4.35 2.86 Crub_svsplocus 612311 612379 (37621) (TTCT)n#Simple_repeat 1 70 (0) m_b12s252i5
Crub_svsplocu 612311 TTATTT-TTTGTTTCTTT-GCTCTTGCTCTCCTTTCTTTTTTTCTCTCAC 612358
v - v -vi v - i i i vi
(TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCT-TTCTTTCTTTCTTTCTTTCTT 49
Crub_svsplocu 612359 TGTTT-TATCTATCTATTCCTT 612379
v - v v - i
(TTCT)n#Simpl 50 TCTTTCTTTCTTTCT-TTCTTT 70
Matrix = Unknown
Transitions / transversions = 0.75 (6/8)
Gap_init rate = 0.07 (5 / 68), avg. gap size = 1.00 (5 / 5)
+ 12 16.3 2.8 2.8 Crub_svsplocus 613273 613308 (36692) + A-rich Low_complexity 1 36 (0) 377
ANNOTATION EVIDENCE:
12 16.31 2.78 2.78 Crub_svsplocus 613273 613308 36692 + (ATAGAAA)n Simple_repeat 1 36 0
12 16.31 2.78 2.78 Crub_svsplocus 613273 613308 (36692) (ATAGAAA)n#Simple_repeat 1 36 (0) m_b12s252i6
Crub_svsplocu 613273 ATAAAAACTA-CAAATAGAAAAATAGAAAAGAAAAAA 613308
i v -v - v i
(ATAGAAA)n#Si 1 ATAGAAAATAGAAAATAG-AAAATAGAAAATAGAAAA 36
Matrix = Unknown
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2)
+ 25 7.8 6.9 3.3 Crub_svsplocus 613520 613577 (36423) + (TCCC)n Simple_repeat 1 60 (0) 378
ANNOTATION EVIDENCE:
25 7.85 6.90 3.33 Crub_svsplocus 613520 613577 36423 + (TCCC)n Simple_repeat 1 60 0
25 7.85 6.90 3.33 Crub_svsplocus 613520 613577 (36423) (TCCC)n#Simple_repeat 1 60 (0) m_b12s252i7
Crub_svsplocu 613520 TCTCTCCCTCCCT--CTCCCTCCCCTTCCCTCCCT-CTTTCC-CCCTCCC 613565
i -- - - - i i -
(TCCC)n#Simpl 1 TCCCTCCCTCCCTCCCTCCCT-CCC-TCCCTCCCTCCCTCCCTCCCTCCC 48
Crub_svsplocu 613566 TCCCTCCCTGCC 613577
v
(TCCC)n#Simpl 49 TCCCTCCCTCCC 60
Matrix = Unknown
Transitions / transversions = 3.00 (3/1)
Gap_init rate = 0.09 (5 / 57), avg. gap size = 1.20 (6 / 5)
+ 269 22.6 3.2 0.0 Crub_svsplocus 614688 614749 (35251) C Chaplin1B_DR DNA/hAT-Charlie (846) 64 1 379
ANNOTATION EVIDENCE:
269 22.58 3.23 0.00 Crub_svsplocus 614688 614749 35251 C Chaplin1B_DR DNA/hAT-Charlie 1 64 846
269 22.58 3.23 0.00 Crub_svsplocus 614688 614749 (35251) C Chaplin1B_DR#DNA/hAT-Charlie (846) 64 1 m_b12s001i23
Crub_svsplocu 614688 GGAGCCACAATAGAAGAATGAAAGAACCGCATGCAGCTT--GAGTCGCGG 614735
vi v viiv i i i-- i
C Chaplin1B_DR# 64 GGAGCCACAAGGGCAGCGCTAAAGAGCCGCATGCGGCTCTAGAGCCGCGG 15
Crub_svsplocu 614736 GCTGCCGACCCGTG 614749
i i v
C Chaplin1B_DR# 14 GTTGCTGACCCCTG 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 23.16
Transitions / transversions = 1.80 (9/5)
Gap_init rate = 0.02 (1 / 61), avg. gap size = 2.00 (2 / 1)
+ 16 0.0 0.0 0.0 Crub_svsplocus 616486 616502 (33498) + (A)n Simple_repeat 1 17 (0) 380
ANNOTATION EVIDENCE:
16 0.00 0.00 0.00 Crub_svsplocus 616486 616502 33498 + (A)n Simple_repeat 1 17 0
16 0.00 0.00 0.00 Crub_svsplocus 616486 616502 (33498) (A)n#Simple_repeat 1 17 (0) m_b12s252i8
Crub_svsplocu 616486 AAAAAAAAAAAAAAAAA 616502
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0)
+ 17 12.7 0.0 0.0 Crub_svsplocus 617032 617057 (32943) + (A)n Simple_repeat 1 26 (0) 381
ANNOTATION EVIDENCE:
17 12.69 0.00 0.00 Crub_svsplocus 617032 617057 32943 + (A)n Simple_repeat 1 26 0
17 12.69 0.00 0.00 Crub_svsplocus 617032 617057 (32943) (A)n#Simple_repeat 1 26 (0) m_b12s252i9
Crub_svsplocu 617032 AAAAATAAAAAAAAAACAAAAACAAA 617057
v v v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 26
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
+ 16 0.0 0.0 0.0 Crub_svsplocus 617343 617359 (32641) + (A)n Simple_repeat 1 17 (0) 382
ANNOTATION EVIDENCE:
16 0.00 0.00 0.00 Crub_svsplocus 617343 617359 32641 + (A)n Simple_repeat 1 17 0
16 0.00 0.00 0.00 Crub_svsplocus 617343 617359 (32641) (A)n#Simple_repeat 1 17 (0) m_b12s252i10
Crub_svsplocu 617343 AAAAAAAAAAAAAAAAA 617359
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0)
+ 24 6.5 0.0 0.0 Crub_svsplocus 620518 620549 (29451) + (TC)n Simple_repeat 1 32 (0) 383
ANNOTATION EVIDENCE:
24 6.54 0.00 0.00 Crub_svsplocus 620518 620549 29451 + (TC)n Simple_repeat 1 32 0
24 6.54 0.00 0.00 Crub_svsplocus 620518 620549 (29451) (TC)n#Simple_repeat 1 32 (0) m_b12s252i11
Crub_svsplocu 620518 TCTCTTTCTCTCTCTCTCTCTCTCTCTCTGTC 620549
i v
(TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 32
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 12 13.2 2.7 5.6 Crub_svsplocus 622912 622948 (27052) + (GGATAG)n Simple_repeat 1 36 (0) 384
ANNOTATION EVIDENCE:
12 13.17 2.70 5.56 Crub_svsplocus 622912 622948 27052 + (GGATAG)n Simple_repeat 1 36 0
12 13.17 2.70 5.56 Crub_svsplocus 622912 622948 (27052) (GGATAG)n#Simple_repeat 1 36 (0) m_b12s252i12
Crub_svsplocu 622912 GGAT-GGGAAAGGGATAGGGAATCATGGGCAGGGATAG 622948
- v - - v ii
(GGATAG)n#Sim 1 GGATAGGGATAGGGATAGGG-AT-AGGGATAGGGATAG 36
Matrix = Unknown
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3)
+ 540 34.7 5.0 2.0 Crub_svsplocus 626974 627270 (22730) + L3 LINE/CR1 3780 4085 (14) 385
ANNOTATION EVIDENCE:
540 34.69 5.05 1.96 Crub_svsplocus 626974 627270 22730 + L3 LINE/CR1 3780 4085 14
540 34.69 5.05 1.96 Crub_svsplocus 626974 627270 (22730) L3#LINE/CR1 3780 4085 (14) m_b12s001i24
Crub_svsplocu 626974 ATCTGAACAGGGATTGCCACAAGGAAGAGGGAGTCAAGCTATTCTCCAAA 627023
i --- ii i iiv v vi vi viivi
L3#LINE/CR1 3780 ATTTGAA---GGGCTGTCATGTGGAAGAGGGATTAGACTTATTCTGTGTG 3826
Crub_svsplocu 627024 GCACCTGAAGGCAAGAAAAGAAGCAATGGATGGAAACTAATCAAGGGGAG 627073
v v i ii vv i v i ii -- i i iv
L3#LINE/CR1 3827 GCTCCAGAGGGCAGAACTAGGACCAATGGGTGGAAGTTA--CAGGGAGGC 3874
Crub_svsplocu 627074 AAG---CAACCTAGAACTGAGGAGAAATTTCTTGACA----GAATAGTTA 627116
ii--- ii ii iv - i ii i ii i ---- iiv iv
L3#LINE/CR1 3875 AGATTTCGGCTCAATA-TAAGGAAGAACTTTCTAACAATCAGAGCTGTCC 3923
Crub_svsplocu 627117 ATCAGTGGAACAATTTGCCTCCAGAAAATTTGGGTGCTCCAACACCGGAG 627166
vv i iiivi v? iivvv i iv i iv i
L3#LINE/CR1 3924 AAAAATGGAATGGGCTGCCTCGNGAGGTAGTGAGCTCCCCGTCACTGGAG 3973
Crub_svsplocu 627167 GT-TTTAAG---AGACTGAACAGCCATTTGTCTGAACTGATATAG---GA 627209
- i --- i i iii i v iiv v i --- i
L3#LINE/CR1 3974 GTGTTCAAGCAGAGGCTGGATGACCACTTGTCAGGGATGTTGTAGAAGGG 4023
Crub_svsplocu 627210 TTTCCTGCCT-GAGCAGGGGGTTGGACTAGATGATCTCCACGGTCCCTTC 627258
v v - iiii i i i v
L3#LINE/CR1 4024 ATTCCTGCATCGGATGGGAGGTTGGACTAGATGACCTCTAAGGTCCCTTC 4073
Crub_svsplocu 627259 CAACTTTATGAT 627270
i iv
L3#LINE/CR1 4074 CAACTCTGAGAT 4085
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 49.06
Transitions / transversions = 2.26 (70/31)
Gap_init rate = 0.04 (12 / 296), avg. gap size = 1.75 (21 / 12)
+ 28 0.0 0.0 0.0 Crub_svsplocus 632405 632431 (17569) + (GAGG)n Simple_repeat 1 27 (0) 386
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 Crub_svsplocus 632405 632431 17569 + (GAGG)n Simple_repeat 1 27 0
28 0.00 0.00 0.00 Crub_svsplocus 632405 632431 (17569) (GAGG)n#Simple_repeat 1 27 (0) c_b12s251i1
Crub_svsplocu 632405 GAGGGAGGGAGGGAGGGAGGGAGGGAG 632431
(GAGG)n#Simpl 1 GAGGGAGGGAGGGAGGGAGGGAGGGAG 27
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0)
+ 14 20.4 8.4 2.7 Crub_svsplocus 632679 632749 (17251) + (ATGTAT)n Simple_repeat 1 75 (0) 387
ANNOTATION EVIDENCE:
14 20.35 8.45 2.67 Crub_svsplocus 632679 632749 17251 + (ATGTAT)n Simple_repeat 1 75 0
14 20.35 8.45 2.67 Crub_svsplocus 632679 632749 (17251) (ATGTAT)n#Simple_repeat 1 75 (0) m_b12s252i13
Crub_svsplocu 632679 ATGCATATGTACATGCATATATAATATGTATA-G-CTAGGT-TTTGATTA 632725
i i i i - - -v v - v vv
(ATGTAT)n#Sim 1 ATGTATATGTATATGTATATGT-ATATGTATATGTATATGTATATGTATA 49
Crub_svsplocu 632726 T-TAT-TGTA-ATAGTTAATGTACATG 632749
- - - - vv i
(ATGTAT)n#Sim 50 TGTATATGTATAT-GTATATGTATATG 75
Matrix = Unknown
Transitions / transversions = 0.71 (5/7)
Gap_init rate = 0.11 (8 / 70), avg. gap size = 1.00 (8 / 8)
+ 33 0.0 0.0 0.0 Crub_svsplocus 632803 632830 (17170) + (GT)n Simple_repeat 1 28 (0) 388
ANNOTATION EVIDENCE:
33 0.00 0.00 0.00 Crub_svsplocus 632803 632830 17170 + (GT)n Simple_repeat 1 28 0
33 0.00 0.00 0.00 Crub_svsplocus 632803 632830 (17170) (GT)n#Simple_repeat 1 28 (0) c_b12s251i2
Crub_svsplocu 632803 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 632830
(GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 26 0.0 0.0 0.0 Crub_svsplocus 632861 632885 (17115) + (TGGA)n Simple_repeat 1 25 (0) 389
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 Crub_svsplocus 632861 632885 17115 + (TGGA)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 Crub_svsplocus 632861 632885 (17115) (TGGA)n#Simple_repeat 1 25 (0) c_b12s251i3
Crub_svsplocu 632861 TGGATGGATGGATGGATGGATGGAT 632885
(TGGA)n#Simpl 1 TGGATGGATGGATGGATGGATGGAT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 363 20.0 1.1 1.1 Crub_svsplocus 632990 633080 (16920) + HAT1_DR DNA/hAT-Ac 419 509 (2783) 390
ANNOTATION EVIDENCE:
363 20.00 1.10 1.10 Crub_svsplocus 632990 633080 16920 + HAT1_DR DNA/hAT-Ac 419 509 2783
363 20.00 1.10 1.10 Crub_svsplocus 632990 633080 (16920) HAT1_DR#DNA/hAT-Ac 419 509 (2783) m_b12s001i25
Crub_svsplocu 632990 TGGGATGGATGAATGGATGGCTGGATAGATAGATAGACAGACAGAGACAG 633039
i i ii i i v i v v v
HAT1_DR#DNA/h 419 TAGGATAGATAGATAGATAGATAGATAGATAGATAGACAGACAGATAGAT 468
Crub_svsplocu 633040 AGAATGGATAGATAGAT-GATGGATAGACAGACAGATAGACA 633080
- i i i- ii i i
HAT1_DR#DNA/h 469 AG-ATAGATAGACAGACAGACAGACAGACAGACAGATAGATA 509
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 24.30
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.02 (2 / 90), avg. gap size = 1.00 (2 / 2)
+ 329 20.6 3.9 0.9 Crub_svsplocus 632993 633095 (16905) + Kolobok-2_DR DNA/Kolobok-T2 3253 3358 (3342) 391 *
ANNOTATION EVIDENCE:
329 20.58 3.88 0.94 Crub_svsplocus 632993 633095 16905 + Kolobok-2_DR DNA/Kolobok-T2 3253 3358 3342
329 20.58 3.88 0.94 Crub_svsplocus 632993 633095 (16905) Kolobok-2_DR#DNA/Kolobok-T2 3253 3358 (3342) m_b12s001i26
Crub_svsplocu 632993 GATGGATGAATGGATGGCTGGATAGATAGATAGACAGACAGAGACAGAGA 633042
i ii i i vii ? i ? i v v v ?
Kolobok-2_DR# 3253 GATAGATAGATAGATAGACAGATAGATAGATANATANATACATACATANA 3302
Crub_svsplocu 633043 ---ATGGATAGATAGAT-GATGGATAGACAGACAGATAGACATCACGCAC 633088
--- i? ? - i i i vi i
Kolobok-2_DR# 3303 TANATANATANATAGATAGATAGATAGATAGACAGATAGATATAGCACAC 3352
Crub_svsplocu 633089 ACGATAC 633095
- v
Kolobok-2_DR# 3353 -CGCTAC 3358
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 26.49
Transitions / transversions = 2.50 (15/6)
Gap_init rate = 0.03 (3 / 102), avg. gap size = 1.67 (5 / 3)
+ 464 13.2 0.0 0.0 Crub_svsplocus 633112 633189 (16811) + URR1B DNA/hAT-Charlie 1 144 (166) 392
ANNOTATION EVIDENCE:
264 25.68 0.00 0.00 Crub_svsplocus 633112 633185 16815 + hAT-N8b_Testu DNA/hAT-Charlie 71 144 166
264 25.68 0.00 0.00 Crub_svsplocus 633112 633185 (16815) hAT-N8b_Testu#DNA/hAT-Charlie 71 144 (166) m_b12s001i27
Crub_svsplocu 633112 CATATACACCAGTGGTTCTCAACCTGTGGGTTGGGACCCCATTTGGGGTC 633161
v v i v v i v vvvv
hAT-N8b_Testu 71 CATCTAGATCAGTGTTTCTCAACCTGGGGGTCGCGACCCCCAGGGGGGTC 120
Crub_svsplocu 633162 GAACGACCATTTCACGGGGGTCGC 633185
viv viv i v
hAT-N8b_Testu 121 GCGGGACGGGTTTAGGGGGGTCGC 144
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 28.01
Transitions / transversions = 0.36 (5/14)
Gap_init rate = 0.00 (0 / 73), avg. gap size = 0.0 (0 / 0)
464 11.59 0.00 0.00 Crub_svsplocus 633121 633189 16811 + URR1B DNA/hAT-Charlie 1 69 156
464 11.59 0.00 0.00 Crub_svsplocus 633121 633189 (16811) URR1B#DNA/hAT-Charlie 1 69 (156) m_b12s001i28
Crub_svsplocu 633121 CAGTGGTTCTCAACCTGTGGGTTGGGACCCCATTTGGGGTCGAACGACCA 633170
i i v v v v
URR1B#DNA/hAT 1 CAGCGGTTCTCAACCTGTGGGTCGCGACCCCTTTGGGGGTCGAACGACCC 50
Crub_svsplocu 633171 TTTCACGGGGGTCGCCAAA 633189
i v
URR1B#DNA/hAT 51 TTTCACAGGGGTCGCCTAA 69
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.59
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 68), avg. gap size = 0.0 (0 / 0)
+ 18 4.2 0.0 0.0 Crub_svsplocus 634328 634352 (15648) + (GGA)n Simple_repeat 1 25 (0) 393
ANNOTATION EVIDENCE:
18 4.17 0.00 0.00 Crub_svsplocus 634328 634352 15648 + (GGA)n Simple_repeat 1 25 0
18 4.17 0.00 0.00 Crub_svsplocus 634328 634352 (15648) (GGA)n#Simple_repeat 1 25 (0) m_b12s252i14
Crub_svsplocu 634328 GGAGGAGGAGGAGGAGGAGGAGAAG 634352
i
(GGA)n#Simple 1 GGAGGAGGAGGAGGAGGAGGAGGAG 25
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 15 25.5 0.0 0.0 Crub_svsplocus 636832 636868 (13132) + (TT)n Simple_repeat 1 37 (0) 394
ANNOTATION EVIDENCE:
15 25.52 0.00 0.00 Crub_svsplocus 636832 636868 13132 + (TT)n Simple_repeat 1 37 0
15 25.52 0.00 0.00 Crub_svsplocus 636832 636868 (13132) (TT)n#Simple_repeat 1 37 (0) m_b12s252i16
Crub_svsplocu 636832 TTTTTTATTTTGTCTTGTGTTCTGTCTTTTTTTTTTT 636868
v v i v v i v i
(TT)n#Simple_ 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37
Matrix = Unknown
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 42 0.0 0.0 0.0 Crub_svsplocus 637829 637864 (12136) + (GT)n Simple_repeat 1 36 (0) 395
ANNOTATION EVIDENCE:
42 0.00 0.00 0.00 Crub_svsplocus 637829 637864 12136 + (GT)n Simple_repeat 1 36 0
42 0.00 0.00 0.00 Crub_svsplocus 637829 637864 (12136) (GT)n#Simple_repeat 1 36 (0) c_b12s251i4
Crub_svsplocu 637829 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 637864
(GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 36
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0)
+ 58 33.2 0.5 1.9 Crub_svsplocus 640532 640744 (9256) + (CCCT)n Simple_repeat 1 210 (0) 396
ANNOTATION EVIDENCE:
58 33.19 0.47 1.90 Crub_svsplocus 640532 640744 9256 + (CCCT)n Simple_repeat 1 210 0
58 33.19 0.47 1.90 Crub_svsplocus 640532 640744 (9256) (CCCT)n#Simple_repeat 1 210 (0) m_b12s252i17
Crub_svsplocu 640532 CCTTCCTTCCCTCCCTCTCTCCCTCCCATTGTCCCTTCTTTCCTTCCTTT 640581
i i i viiv i i i i ii
(CCCT)n#Simpl 1 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 50
Crub_svsplocu 640582 CTTCCTTCC-CTCTCTCTTTGTCTCTTCCTCCTTCTCTCCCTTCCTTCCA 640630
i i - i i iiv i i i i i i v
(CCCT)n#Simpl 51 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 100
Crub_svsplocu 640631 TTGTCCCTCCCTCATTGTCCTTCCCTTCCTTCCTTCCCTCCCTCCCTTCC 640680
iiv --iv i - i i -
(CCCT)n#Simpl 101 CCCTCCCTCCCTC--CCTCCCTCCC-TCCCTCCCTCCCTCCCTCCC-TCC 146
Crub_svsplocu 640681 TTCCATTGTTCCTTCCCTCCTTCCTTCCCTCTCCCTCTTTGTCCCTTCCT 640730
i v ivi i i i i i i iiv i
(CCCT)n#Simpl 147 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 196
Crub_svsplocu 640731 TCCTCCCCCCCTCC 640744
i i
(CCCT)n#Simpl 197 CCCTCCCTCCCTCC 210
Matrix = Unknown
Transitions / transversions = 4.78 (43/9)
Gap_init rate = 0.02 (5 / 212), avg. gap size = 1.00 (5 / 5)
+ 13 8.5 4.0 0.0 Crub_svsplocus 641390 641414 (8586) + (AGCA)n Simple_repeat 1 26 (0) 397
ANNOTATION EVIDENCE:
13 8.53 4.00 0.00 Crub_svsplocus 641390 641414 8586 + (AGCA)n Simple_repeat 1 26 0
13 8.53 4.00 0.00 Crub_svsplocus 641390 641414 (8586) (AGCA)n#Simple_repeat 1 26 (0) m_b12s252i18
Crub_svsplocu 641390 AGAAAGCAAGC-AGAAAGCAAGCAAG 641414
v - v
(AGCA)n#Simpl 1 AGCAAGCAAGCAAGCAAGCAAGCAAG 26
Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.04 (1 / 24), avg. gap size = 1.00 (1 / 1)
+ 12 24.3 0.0 2.5 Crub_svsplocus 641783 641823 (8177) + (TTCCCC)n Simple_repeat 1 40 (0) 398
ANNOTATION EVIDENCE:
12 24.33 0.00 2.50 Crub_svsplocus 641783 641823 8177 + (TTCCCC)n Simple_repeat 1 40 0
12 24.33 0.00 2.50 Crub_svsplocus 641783 641823 (8177) (TTCCCC)n#Simple_repeat 1 40 (0) m_b12s252i19
Crub_svsplocu 641783 TTCCTCTCTCCCAATCCCCTTCCTCTTCTTCACCCCCTTCC 641823
i - vv i ii vi
(TTCCCC)n#Sim 1 TTCCCCT-TCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCC 40
Matrix = Unknown
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.03 (1 / 40), avg. gap size = 1.00 (1 / 1)
+ 267 25.4 0.0 0.0 Crub_svsplocus 642401 642467 (7533) C DNA8-4_DR DNA/hAT-Charlie (2328) 67 1 399
ANNOTATION EVIDENCE:
267 25.37 0.00 0.00 Crub_svsplocus 642401 642467 7533 C DNA8-4_DR DNA/hAT-Charlie 1 67 2328
267 25.37 0.00 0.00 Crub_svsplocus 642401 642467 (7533) C DNA8-4_DR#DNA/hAT-Charlie (2328) 67 1 m_b12s001i29
Crub_svsplocu 642401 CCGCATACCACCAGTCAGGTGGTCGCGTACCACCAGCGGTACGCGTACCA 642450
i i vvi iv vi i i
C DNA8-4_DR#DNA 67 CCGCGTACCACTAGGAGGAAGCCCGCGTACCACTAGTGGTACGCGTACCA 18
Crub_svsplocu 642451 CCAGTTGAAAAGCTCTG 642467
viv i v v
C DNA8-4_DR#DNA 17 CAGTTTGAGAACCACTG 1
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 29.23
Transitions / transversions = 1.12 (9/8)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0)