+ 40 0.0 0.0 0.0 Rab3il1DNA 614 650 (36062) + (TGTA)n Simple_repeat 1 37 (0) 1
ANNOTATION EVIDENCE:
40 0.00 0.00 0.00 Rab3il1DNA 614 650 36062 + (TGTA)n Simple_repeat 1 37 0
40 0.00 0.00 0.00 Rab3il1DNA 614 650 (36062) (TGTA)n#Simple_repeat 1 37 (0) c_b1s251i0
Rab3il1DNA 614 TGTATGTATGTATGTATGTATGTATGTATGTATGTAT 650
(TGTA)n#Simpl 1 TGTATGTATGTATGTATGTATGTATGTATGTATGTAT 37
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)
+ 868 22.6 6.5 0.0 Rab3il1DNA 656 841 (35871) C B3 SINE/B2 (4) 212 14 2
ANNOTATION EVIDENCE:
868 22.58 6.53 0.00 Rab3il1DNA 656 841 31585 C B3 SINE/B2 14 212 4
868 22.58 6.53 0.00 Rab3il1DNA 656 841 (31585) C B3#SINE/B2 (4) 212 14 m_b1s501i0
Rab3il1DNA 656 TTTTGGTCTTATGTGTATAGGTGTT-------------TATCTGTATAAC 692
vi i i ------------- i ii v
C B3#SINE/B2 212 TTTTTATTTTATGTGTATGGGTGTTTTGCCTGCATGTATGTCTGTGCACC 163
Rab3il1DNA 693 ATATGCATGCCTGGTACCTGATGCAGCCAGAAGAGGGCACAGTATCCCTT 742
ii i i i vv vi iiv v i
C B3#SINE/B2 162 ACGTGCGTGCCTGGTGCCCGCGGAGGCCAGAAGAGGGCGTCGGATCCCCT 113
Rab3il1DNA 743 GAGACTTGAGTTTCAGATGGTTGTGAGTCAACATGTGGGTGCTGGAGATC 792
ii v v i i iv ii
C B3#SINE/B2 112 GGAACTGGAGTTACAGACGGTTGTGAGCCGCCATGTGGGTGCTGGGAATC 63
Rab3il1DNA 793 AAAGTCAGGTCCTCCGGAAGAAGAGCCATTGCTCTTAACTGGTGAGCCA 841
i vi i i iv v i v
C B3#SINE/B2 62 GAACCCGGGTCCTCTGGAAGAGCAGCCAGTGCTCTTAACCGCTGAGCCA 14
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 21.07
Transitions / transversions = 2.00 (28/14)
Gap_init rate = 0.01 (1 / 185), avg. gap size = 13.00 (13 / 1)
+ 30 15.8 3.0 3.0 Rab3il1DNA 1006 1072 (35640) + (CA)n Simple_repeat 1 67 (0) 3
ANNOTATION EVIDENCE:
30 15.78 2.99 2.99 Rab3il1DNA 1006 1072 31354 + (CA)n Simple_repeat 1 67 0
30 15.78 2.99 2.99 Rab3il1DNA 1006 1072 (31354) (CA)n#Simple_repeat 1 67 (0) m_b1s252i0
Rab3il1DNA 1006 CACGCACACACACTATACA-ACACACACACACACACACTGAGGC-CCCTG 1053
i - i - vv vi - v vv
(CA)n#Simple_ 1 CACACACACACAC-ACACACACACACACACACACACACACACACACACAC 49
Rab3il1DNA 1054 AGCACACACACACACACAC 1072
-
(CA)n#Simple_ 50 A-CACACACACACACACAC 67
Matrix = Unknown
Transitions / transversions = 0.50 (3/6)
Gap_init rate = 0.06 (4 / 66), avg. gap size = 1.00 (4 / 4)
+ 332 15.4 0.0 3.0 Rab3il1DNA 1081 1147 (35565) + MER5A1 DNA/hAT-Charlie 53 117 (49) 4
ANNOTATION EVIDENCE:
332 15.39 0.00 2.99 Rab3il1DNA 1081 1147 31279 + MER5A1 DNA/hAT-Charlie 53 117 49
332 15.39 0.00 2.99 Rab3il1DNA 1081 1147 (31279) MER5A1#DNA/hAT-Charlie 53 117 (49) m_b1s501i1
Rab3il1DNA 1081 AGATTGTTAGAGATGCAAGGATCTGAGGCTTCCACCCCAGACCTCCTCAG 1130
v i - i v -i v v i
MER5A1#DNA/hA 53 AGCTTGTTAGAAATGCA-GAATCTCAGGC-CCCACCCCAGACCTACTGAA 100
Rab3il1DNA 1131 TCATAATCTGCATTTCA 1147
v i
MER5A1#DNA/hA 101 TCAGAATCTGCATTTTA 117
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 17.29
Transitions / transversions = 1.00 (5/5)
Gap_init rate = 0.03 (2 / 66), avg. gap size = 1.00 (2 / 2)
+ 46 0.0 0.0 0.0 Rab3il1DNA 1179 1217 (35495) + (GT)n Simple_repeat 1 39 (0) 5
ANNOTATION EVIDENCE:
46 0.00 0.00 0.00 Rab3il1DNA 1179 1217 35495 + (GT)n Simple_repeat 1 39 0
46 0.00 0.00 0.00 Rab3il1DNA 1179 1217 (35495) (GT)n#Simple_repeat 1 39 (0) c_b1s251i1
Rab3il1DNA 1179 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 1217
(GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 39
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 523 24.0 6.2 2.4 Rab3il1DNA 1224 1347 (35365) C RSINE1 SINE/B4 (22) 143 15 6
ANNOTATION EVIDENCE:
523 23.97 6.20 2.42 Rab3il1DNA 1224 1347 31117 C RSINE1 SINE/B4 15 143 22
523 23.97 6.20 2.42 Rab3il1DNA 1224 1347 (31117) C RSINE1#SINE/B4 (22) 143 15 m_b1s501i2
Rab3il1DNA 1224 TACCACAGTACACATTCGGAGGTCAGAGGACAACTTTCAGGAGTTGGTTC 1273
i i ii i i vi v i i
C RSINE1#SINE/B 143 TGCCACGGCGCGCGTGTGGAGGTCAGAGGACAACTTGCGGGAGTCGGTTC 94
Rab3il1DNA 1274 TCTCCTTCCAGCTTGTGGGTCTCACGAATCAAACTA--------AGCCTT 1315
v v i iv i i v-------- v
C RSINE1#SINE/B 93 TCTCCTTCCACCATGTGGGTCCCGGGGATCGAACTCAGGTCGTCAGGCTT 44
Rab3il1DNA 1316 GACCGCAAGCACTGTTATCTACATCTGAGTCA 1347
i v i iv i ii--- i
C RSINE1#SINE/B 43 GGCGGCAAGCGCCTTTACCCG---CTGAGCCA 15
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 18.60
Transitions / transversions = 2.22 (20/9)
Gap_init rate = 0.03 (4 / 123), avg. gap size = 2.75 (11 / 4)
+ 742 21.1 9.8 0.0 Rab3il1DNA 1462 1627 (35085) C ID_B1 SINE/B4 (39) 185 2 7
ANNOTATION EVIDENCE:
742 21.08 9.78 0.00 Rab3il1DNA 1462 1627 30837 C ID_B1 SINE/B4 2 185 39
742 21.08 9.78 0.00 Rab3il1DNA 1462 1627 (30837) C ID_B1#SINE/B4 (39) 185 2 m_b1s501i3
Rab3il1DNA 1462 GGCCTTGAACCTGATGTGTATCTGAAGATGACCTTGAACCCCTAATTATC 1511
i ii v i v i i ii i iv
C ID_B1#SINE/B4 185 GGCCTCGAACTCGCTATGTAGCCGAGGATGACCTTGAACTTCTGATCCTC 136
Rab3il1DNA 1512 CTTTGCCCGTTTCCTAAGTGTTAAGATTGCAGGC-----CCAAC------ 1550
vivi iii ii i ii i ----- v ------
C ID_B1#SINE/B4 135 CTGCCTCCACCTCCCGAGTGCTGGGATTACAGGCGTGCGCCACCACGCCC 86
Rab3il1DNA 1551 ----TTATGCAGTGCTGGGGATTGAA-CCAAGGTTTCTTGCATGCCAGGC 1595
---- i i - i i v i
C ID_B1#SINE/B4 85 GGTTTTATGCGGTGCTGGGGATCGAACCCAGGGCTTCGTGCATGCTAGGC 36
Rab3il1DNA 1596 AAGCACTCTACCAACTGAGCGACA--CCCAGACC 1627
v -- v
C ID_B1#SINE/B4 35 AAGCACTCTACCAACTGAGCTACATCCCCAGCCC 2
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 20.79
Transitions / transversions = 2.89 (26/9)
Gap_init rate = 0.03 (5 / 165), avg. gap size = 3.60 (18 / 5)
+ 771 28.3 7.3 0.4 Rab3il1DNA 1703 1968 (34744) C L1M4 LINE/L1 (1103) 5043 4758 8
ANNOTATION EVIDENCE:
771 28.31 7.34 0.38 Rab3il1DNA 1703 1968 30496 C L1M4_orf2 LINE/L1 2649 2934 360
771 28.31 7.34 0.38 Rab3il1DNA 1703 1968 (30496) C L1M4_orf2#LINE/L1 (360) 2934 2649 m_b1s551i0
Rab3il1DNA 1703 TTCTGAGAATTTTATGATTTTTGCTGATACAGTTAAG-ATCTGATATATT 1751
i i ii v vv v i -v i vi
C L1M4_orf2#LIN 2934 TTCTAAGAGTTTTATAGTTTTAGCTCTTACATTTAGGTCTTTGATCCATT 2885
Rab3il1DNA 1752 TTGGATTCCTTTTTGTGGAGAGTGTGAGGTAAAGGTCCAAGGCCA--CTG 1799
ii vv iv vi ii vvi -- v
C L1M4_orf2#LIN 2884 TTGAGTTAATTTTTGTATATGGTGTGAGGTAGGGGTCCAACTTCATTCTT 2835
Rab3il1DNA 1800 AGACATATGGGTACCCAGCTGCCCATGTGCTGTTTGT------------- 1836
vvi i i i i i vv ii ii -------------
C L1M4_orf2#LIN 2834 TTGCATGTGGATATCCAGTTGTCCCAGCACCATTTGTTGAAAAGACTATT 2785
Rab3il1DNA 1837 -TTCCTTCATTGAATGGGTTTGGCATCATTGTTAAAGATCAATTTGTGAC 1885
- i ii ? vi i v ii i viiv i
C L1M4_orf2#LIN 2784 CTTTCCCCATTGAATNGTCTTGGCACCCTTGTCGAAAATCAATTGACCAT 2735
Rab3il1DNA 1886 AGATGTA----TCTATTTCTGGAGAGTCTGCTCAATTCCATTGACCTCTG 1931
i ---- i vvv vii v i v i
C L1M4_orf2#LIN 2734 AAATGTANGGGTTTATTTCTGGACTCTCAATTCTATTCCATTGATCTATA 2685
Rab3il1DNA 1932 TGTCTGTCCTGAGGCCAATACTACACTTGTTTTGATT 1968
i v v i i - i
C L1M4_orf2#LIN 2684 TGTCTATCCTTATGCCAGTACCACAC-TGTCTTGATT 2649
Matrix = 20p51g.matrix
Kimura (with divCpGMod) = 35.48
Transitions / transversions = 1.55 (45/29)
Gap_init rate = 0.02 (6 / 265), avg. gap size = 3.67 (22 / 6)
+ 522 25.5 2.1 5.4 Rab3il1DNA 2018 2166 (34546) C B4A SINE/B4 (4) 288 145 9
ANNOTATION EVIDENCE:
522 25.53 2.08 5.37 Rab3il1DNA 2018 2166 30298 C B4A SINE/B4 145 288 4
522 25.53 2.08 5.37 Rab3il1DNA 2018 2166 (30298) C B4A#SINE/B4 (4) 288 145 m_b1s501i4
Rab3il1DNA 2018 TATGTGTGCATTCATATTGAAGCCCTAGGTCAATGTCA-GTGTCTTCCTC 2066
i ii v i i v i vv i i i-
C B4A#SINE/B4 288 TGTGTGTGTGTGCGTGTGGAGGCCAGAGGTCGACGTCGGGTGTCTTCCTC 239
Rab3il1DNA 2067 AGTGGCTCT--ACTTCATTAATTGAGACAAGATCTCTTGCTGAACCCAGA 2114
?i v -- i i vv i i ii ii
C B4A#SINE/B4 238 NATCGCTCTCCACCTTATTTTTTGAGACAGGGTCTCTCACTGAACCTGGA 189
Rab3il1DNA 2115 GCTCACCAATTCTGCCTAGTCCTAGTCTAGCTTAGCCAGCTTGCCTCATA 2164
i v ------- v i - i vv i vi
C B4A#SINE/B4 188 GCTCACCGATTCGG-------CTAGGCTGGC-TGGCCAGCGAGCCCCAGG 147
Rab3il1DNA 2165 GA 2166
C B4A#SINE/B4 146 GA 145
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 26.24
Transitions / transversions = 1.92 (23/12)
Gap_init rate = 0.07 (10 / 148), avg. gap size = 1.10 (11 / 10)
+ 487 23.8 1.9 0.0 Rab3il1DNA 2268 2368 (34344) + RSINE1 SINE/B4 50 152 (13) 10
ANNOTATION EVIDENCE:
487 23.76 1.94 0.00 Rab3il1DNA 2268 2368 30096 + RSINE1 SINE/B4 50 152 13
487 23.76 1.94 0.00 Rab3il1DNA 2268 2368 (30096) RSINE1#SINE/B4 50 152 (13) m_b1s501i5
Rab3il1DNA 2268 GATGACCTCAATTCAATCCTCAGAATCCACA-AGTGGAAGGAGAGAAGTT 2316
i v i i i i i i -i viv
RSINE1#SINE/B 50 GACGACCTGAGTTCGATCCCCGGGACCCACATGGTGGAAGGAGAGAACCG 99
Rab3il1DNA 2317 ACTCCCACAATTTGTCCTCTGA-TTCTACATGTGCTCCATGGTACATGTG 2365
i v -i i i i v i i ii i
RSINE1#SINE/B 100 ACTCCCGCAAGTTGTCCTCTGACCTCCACACGCGCGCCGTGGCACGCGCG 149
Rab3il1DNA 2366 CAC 2368
RSINE1#SINE/B 150 CAC 152
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 15.66
Transitions / transversions = 3.80 (19/5)
Gap_init rate = 0.02 (2 / 100), avg. gap size = 1.00 (2 / 2)
+ 1173 25.4 4.0 9.7 Rab3il1DNA 2477 2878 (33834) C MTE2a LTR/ERVL-MaLR (1) 378 1 11
ANNOTATION EVIDENCE:
1173 25.35 3.97 9.70 Rab3il1DNA 2477 2878 30645 C MTE2a LTR/ERVL-MaLR 1 378 1
1173 25.35 3.97 9.70 Rab3il1DNA 2477 2878 (30645) C MTE2a#LTR/ERVL-MaLR (1) 378 1 c_b1s401i0
Rab3il1DNA 2477 GTTTTGG-TTCATTT-CTGATGCTGTGCTGAAACA-CCTGACAAGAGCCC 2523
i i - ? - v v i i - i vv
C MTE2a#LTR/ERV 378 GTCTTAGTTTCNTTTCCTGTTGCTGTGATAAAATACCCTGACAAAAGCAA 329
Rab3il1DNA 2524 TTCTGGGGAGGA--GGCCTTGTCTGACTTATGATTCCAGGTCACAGTATG 2571
i ivi i -- ii vv i i i iii i ---
C MTE2a#LTR/ERV 328 CTTAAGGGAGAAAGGGTTTATTTTGGCTCACAGTTCCAGGTTACAGT--- 282
Rab3il1DNA 2572 ACCTGGAATAAAACCCATCATTTCAGGGAAGTCAAGGCAGTCAGAATTTG 2621
-------------- v i i ivi ii
C MTE2a#LTR/ERV 281 --------------CCATCATTGCGGGGAAGTCAAGGCGGCAGGAGCTTG 246
Rab3il1DNA 2622 AAGCAGCCAGTCA-----TATCTATAGCCAGG-AGCAGAGAAAAAAAACG 2665
ii -----i i i i - i-------?
C MTE2a#LTR/ERV 245 AAGCAGCTGGTCACATCGCATCCACAGTCAGGAAGCAGAGAG-------N 203
Rab3il1DNA 2666 GATGACCATGGCAACTGCTCCGCT--CTTTCTCAGCTCTTATGCAGTTCA 2713
-- - viv v -- -vi i i
C MTE2a#LTR/ERV 202 GATGA--AT-GCTGGTGCTCAGCTCGCTTTCTC-CTTCTTATACAGTCCA 157
Rab3il1DNA 2714 GATTCCAAACCCAGAAAATGAGAGCTCCCATTTTCAGCCTGGGTCTTCCC 2763
ivi v?i ii iviv v ivv i v?
C MTE2a#LTR/ERV 156 GGACCCCNGCCCAGGGAATGGTGCCGCCCACAGTTAGGNTGGGTCTTCCC 107
Rab3il1DNA 2764 ATATCAACTAATATAACCAAGAGA--CCCCCACAGGCATGGCCACGGATC 2811
i i ii i v -- i v ------
C MTE2a#LTR/ERV 106 ACATCAATTAACGTAATCAAGACAATCCCCCACAGACATGCCCA------ 63
Rab3il1DNA 2812 AACCTGACACTCTCTTCCCACGTGATTCAAGACTGTGTCAAGTTGGCAAT 2861
----- vi i vii v v i i
C MTE2a#LTR/ERV 62 -----GAGGCCCGTCTCCCAGGTGATTCTAGATTGTGTCAAGTTGACAAT 18
Rab3il1DNA 2862 TATAGCAAACCATTGCA 2878
v i v ii
C MTE2a#LTR/ERV 17 TAAAACTAACCATCACA 1
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 29.44
Transitions / transversions = 2.03 (59/29)
Gap_init rate = 0.12 (47 / 401), avg. gap size = 1.15 (54 / 47)
+ 302 27.9 8.6 9.4 Rab3il1DNA 2880 3112 (33600) C L1M4 LINE/L1 (1476) 4670 4427 8
ANNOTATION EVIDENCE:
302 27.90 8.59 9.38 Rab3il1DNA 2880 3112 29926 C L1M4_orf2 LINE/L1 2318 2561 733
302 27.90 8.59 9.38 Rab3il1DNA 2880 3112 (29926) C L1M4_orf2#LINE/L1 (733) 2561 2318 m_b1s551i1
Rab3il1DNA 2880 GGTGCCTTGACATTCCTTATGAATTTTAGGACCGTCTTGCC-ATTTCTG- 2927
v vvv v i iv i - -
C L1M4_orf2#LIN 2561 GGTCCCTTGCATTTCCATATGAATTTTAGGATCAGCTTGTCAATTTCTGC 2512
Rab3il1DNA 2928 AAGAATGCCAGTTGCGAGTGTGACA-GGCTGGTTTTGATTCCGTAGGACA 2976
i v ? i v v v i - v v iv v i iv
C L1M4_orf2#LIN 2511 AAAAAAGNCAGCTGGGATTTTGATAGGGATTGCGTTGAATCTGTAGATCA 2462
Rab3il1DNA 2977 CCCTATCGTGTGTATGGTATC------------ATTCTTCC------TGG 3008
vii ivv v i - vi ------------ v ------ i
C L1M4_orf2#LIN 2461 ATTTGGGGAGTAT-TGCCATCTTAACAATATTAAGTCTTCCGATCCATGA 2413
Rab3il1DNA 3009 ATGTGA---ATCTGTTCAATACCTTAGCTCTCTTTTAATTTCATTCTGCA 3055
ii i---i v i v vvi v ii v vi
C L1M4_orf2#LIN 2412 ACATGGGATGTCTTTCCATTTATTTAGGTCTTCTTTAATTTCTTTCAACA 2363
Rab3il1DNA 3056 A--GTTTGTAGTTTTCAGTGTGCAAGGTTTTTTGTTTGTTTGCTCGTTTG 3103
--v i --- i ---------- ii -
C L1M4_orf2#LIN 2362 ATGTTTTGTAGTTTTCAGTGTACAAG---TCTTG----------CACTT- 2327
Rab3il1DNA 3104 CTCTTGTTG 3112
i i
C L1M4_orf2#LIN 2326 CTTTTGTTA 2318
Matrix = 20p51g.matrix
Kimura (with divCpGMod) = 34.06
Transitions / transversions = 1.03 (30/29)
Gap_init rate = 0.09 (22 / 232), avg. gap size = 1.86 (41 / 22)
+ 613 22.3 3.5 1.4 Rab3il1DNA 3113 3253 (33459) C B1_Mur2 SINE/Alu (1) 148 5 12
ANNOTATION EVIDENCE:
613 22.31 3.48 1.42 Rab3il1DNA 3113 3253 33133 C B1_Mur2 SINE/Alu 5 148 1
613 22.31 3.48 1.42 Rab3il1DNA 3113 3253 (33133) C B1_Mur2#SINE/Alu (1) 148 5 c_b1s355i0
Rab3il1DNA 3113 TTGATTGTTTTAAGACAGAGTCTCTCTACATAAACCT-GCTATCCTCAAA 3161
vi v i i v ii iv - i vi
C B1_Mur2#SINE/ 148 TTTGTTTTTTTGAGACAGGGTCTCACTATGTAGCCCTGGCTGTCCTGGAA 99
Rab3il1DNA 3162 CTAGT----TAGATCAGGCTGGCGCCAAACCCACAGAGATCTTGCCTGCC 3207
v i---- i vi i i i-
C B1_Mur2#SINE/ 98 CTCGCTATGTAGACCAGGCTGGCCTCGAACTCACAGAGATCC-GCCTGCC 50
Rab3il1DNA 3208 TTTGCCTCCCAAGTGCTGGTTATTAAAGGCCTGAAGCTCCATGCTC 3253
i i v- v viv v i i
C B1_Mur2#SINE/ 49 TCTGCCTCCCGAGTGCTGGG-ATTAAAGGCGTGCGCCACCACGCCC 5
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 22.21
Transitions / transversions = 1.58 (19/12)
Gap_init rate = 0.03 (4 / 140), avg. gap size = 1.75 (7 / 4)
+ 302 27.9 8.6 9.4 Rab3il1DNA 3254 3300 (33412) C L1M4 LINE/L1 (1720) 4426 4390 8
ANNOTATION EVIDENCE:
302 27.90 8.59 9.38 Rab3il1DNA 3254 3300 29738 C L1M4_orf2 LINE/L1 2281 2317 977
302 27.90 8.59 9.38 Rab3il1DNA 3254 3300 (29738) C L1M4_orf2#LINE/L1 (977) 2317 2281 m_b1s551i1
Rab3il1DNA 3254 AATACAGTGTGTGCAAGTCTTATAGACCATCTTTGGTTAAAAATATC 3300
---v i vivi v v v---- -- i viv -
C L1M4_orf2#LIN 2317 AAT---TTATTCCTAAGTATTTTAT----TCTTT--TTGATGCTAT- 2281
Matrix = 20p51g.matrix
Kimura (with divCpGMod) = 34.06
Transitions / transversions = 0.62 (5/8)
Gap_init rate = 0.22 (10 / 46), avg. gap size = 1.00 (10 / 10)
+ 34 3.0 0.0 0.0 Rab3il1DNA 3301 3334 (33378) + (CT)n Simple_repeat 1 34 (0) 13
ANNOTATION EVIDENCE:
34 3.03 0.00 0.00 Rab3il1DNA 3301 3334 33378 + (CT)n Simple_repeat 1 34 0
34 3.03 0.00 0.00 Rab3il1DNA 3301 3334 (33378) (CT)n#Simple_repeat 1 34 (0) c_b1s251i2
Rab3il1DNA 3301 CTCTCTCTCTCTCTCTCCCTCTCTCTCTCTCTCT 3334
i
(CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 34
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0)
+ 302 27.9 8.6 9.4 Rab3il1DNA 3335 3404 (33308) C L1M4 LINE/L1 (1757) 4389 4322 8
ANNOTATION EVIDENCE:
302 27.90 8.59 9.38 Rab3il1DNA 3335 3404 29634 C L1M4_orf2 LINE/L1 2213 2280 1014
302 27.90 8.59 9.38 Rab3il1DNA 3335 3404 (29634) C L1M4_orf2#LINE/L1 (1014) 2280 2213 m_b1s551i1
Rab3il1DNA 3335 TGTGCTGCAACTAGAACTGTTTTCATTGACTTCACTTTTGGA--GTC--T 3380
----- i v i i - i i i i -- i--
C L1M4_orf2#LIN 2280 -----TGTAAATGGAATTGTTTTC-TTAATTTCATTTTCGGATTGTTCAT 2237
Rab3il1DNA 3381 TGATAGAAGATAGAAATGTAAGTG 3404
v viv ii v
C L1M4_orf2#LIN 2236 TGCTAGTGTATAGAAATACAATTG 2213
Matrix = 20p51g.matrix
Kimura (with divCpGMod) = 34.06
Transitions / transversions = 2.20 (11/5)
Gap_init rate = 0.12 (8 / 69), avg. gap size = 1.25 (10 / 8)
+ 282 20.8 8.0 0.2 Rab3il1DNA 3498 3517 (33195) C PB1D10 SINE/Alu (32) 117 41 14
ANNOTATION EVIDENCE:
259 25.67 3.90 1.33 Rab3il1DNA 3498 3572 29466 C B1F2 SINE/Alu 41 117 32
259 25.67 3.90 1.33 Rab3il1DNA 3498 3572 (29466) C B1F2#SINE/Alu (32) 117 41 m_b1s501i6
Rab3il1DNA 3498 AACCCTTGGTGTCATAAGACAAGGTATGTAGGCCAGGCTGGCCTTGAACT 3547
i v v v v iii vv v i i
C B1F2#SINE/Alu 117 AGCCCTGGCTGGCCTGGAACTCGCTATGTAGACCAGGCTGGCCTCGAACT 68
Rab3il1DNA 3548 TGT---GATCCTCTTCCCTTGTGCCACC 3572
i i--- i v i- v
C B1F2#SINE/Alu 67 CGCGGAGATCCTCCTGCCTC-TGCCTCC 41
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 26.17
Transitions / transversions = 1.11 (10/9)
Gap_init rate = 0.03 (2 / 74), avg. gap size = 2.00 (4 / 2)
282 19.67 8.96 0.00 Rab3il1DNA 3503 3563 29475 C PB1D10 SINE/Alu 49 115 2
282 19.67 8.96 0.00 Rab3il1DNA 3503 3563 (29475) C PB1D10#SINE/Alu (2) 115 49 m_b1s501i7
Rab3il1DNA 3503 TTGGTGTCATAAGACAAGG------TATGTAGGCCAGGCTGGCCTTGAAC 3546
v v iv i i ------ v i
C PB1D10#SINE/A 115 TTGTTTTTTTGAGACAGGGTCTCGCTATGTAGCCCAGGCTGGCCTCGAAC 66
Rab3il1DNA 3547 TTGTGATCCTCTTCCCT 3563
i i i v
C PB1D10#SINE/A 65 TCGCGATCCTCCTGCCT 49
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 17.09
Transitions / transversions = 1.40 (7/5)
Gap_init rate = 0.02 (1 / 60), avg. gap size = 6.00 (6 / 1)
+ 266 22.2 0.0 1.8 Rab3il1DNA 3518 3572 (33140) C 4.5SRNA scRNA (2) 92 39 15
ANNOTATION EVIDENCE:
266 22.22 0.00 1.82 Rab3il1DNA 3518 3572 29466 C 4.5SRNA scRNA 39 92 2
266 22.22 0.00 1.82 Rab3il1DNA 3518 3572 (29466) C 4.5SRNA#scRNA (2) 92 39 m_b1s501i8
Rab3il1DNA 3518 AAGGTATGTAGGCCAGGCTGGCCTTGAACTTGTGATCCTCTTCCCTTGTG 3567
ii i i i i ? ? i v i-
C 4.5SRNA#scRNA 92 AAAATGTGTAGACCAGGCTGGCCTCGAACTCGNGATCCNCCTGCCTC-TG 44
Rab3il1DNA 3568 CCACC 3572
v
C 4.5SRNA#scRNA 43 CCTCC 39
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 18.21
Transitions / transversions = 4.00 (8/2)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1)
+ 228 18.9 0.0 7.0 Rab3il1DNA 3522 3578 (33134) C ID_B1 SINE/B4 (53) 171 119 16 *
ANNOTATION EVIDENCE:
228 18.86 0.00 7.02 Rab3il1DNA 3522 3578 29460 C ID_B1 SINE/B4 119 171 53
228 18.86 0.00 7.02 Rab3il1DNA 3522 3578 (29460) C ID_B1#SINE/B4 (53) 171 119 m_b1s501i9
Rab3il1DNA 3522 TATGTAGGCCAGGCTGGCCTTGAACTTGTGATCCTCTTCCCTTGTGCCAC 3571
v v v i v i v ----
C ID_B1#SINE/B4 171 TATGTAGCCGAGGATGACCTTGAACTTCTGATCCTCCTGCCT----CCAC 126
Rab3il1DNA 3572 CACTCAA 3578
v i i
C ID_B1#SINE/B4 125 CTCCCGA 119
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 19.50
Transitions / transversions = 0.67 (4/6)
Gap_init rate = 0.07 (4 / 56), avg. gap size = 1.00 (4 / 4)
+ 293 27.9 9.0 9.0 Rab3il1DNA 3604 3632 (33080) C ORR1F LTR/ERVL-MaLR (1098) 865 745 17
ANNOTATION EVIDENCE:
293 27.93 9.02 9.02 Rab3il1DNA 3604 3725 29313 C ORR1A3-int LTR/ERVL-MaLR 744 865 1098
293 27.93 9.02 9.02 Rab3il1DNA 3604 3725 (29313) C ORR1A3-int#LTR/ERVL-MaLR (1098) 865 744 m_b1s501i10
Rab3il1DNA 3604 TTTTGCTTTCCTCCTCCCCCACCCCCTCA-----------TTAAAACAGG 3642
i i vv ii iv v -----------i ii ---
C ORR1A3-int#LT 865 TTCTGTTTTCCAACTCCTTCACTGCCTAAGCTTGGCTGTCCTGGAAC--- 819
Rab3il1DNA 3643 GTTTCTTTGTGTAGACCAGGCTGGCCTTAAACTCATAGATTCACCTGCCT 3692
- v i ------- i i i v iii v v
C ORR1A3-int#LT 818 -TTGCTCTGT-------AGACTGACCTTGAACTCAGAGATCTGCATGGCT 777
Rab3il1DNA 3693 CTGCTTCTCAAGTGCTGGGATTAAAGGTGTGCA 3725
ii iii i i i
C ORR1A3-int#LT 776 CTGTCTCCTGAATGCTGGGATTAAAGGCGTGTA 744
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 35.66
Transitions / transversions = 2.88 (23/8)
Gap_init rate = 0.10 (12 / 121), avg. gap size = 1.83 (22 / 12)
+ 539 17.4 2.1 0.0 Rab3il1DNA 3633 3724 (32988) C PB1D9 SINE/Alu (10) 110 17 18
ANNOTATION EVIDENCE:
539 17.39 2.12 0.00 Rab3il1DNA 3633 3724 29314 C PB1D9 SINE/Alu 17 110 10
539 17.39 2.12 0.00 Rab3il1DNA 3633 3724 (29314) C PB1D9#SINE/Alu (10) 110 17 m_b1s501i11
Rab3il1DNA 3633 TTAAAACAGGGTTTCTTTGTGTAGACCAGGCTGGCCTTAAACTCAT--AG 3680
i i i vi v v ii i--
C PB1D9#SINE/Al 110 TTGAGACAGGGTCTCACTGTGTAGCCCTGGCTGGCCTCGAACTCACAGAG 61
Rab3il1DNA 3681 ATTCACCTGCCTCTGCTTCTCAAGTGCTGGGATTAAAGGTGTGC 3724
i i i i i i
C PB1D9#SINE/Al 60 ATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGC 17
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 15.07
Transitions / transversions = 4.33 (13/3)
Gap_init rate = 0.01 (1 / 91), avg. gap size = 2.00 (2 / 1)
+ 1126 4.1 0.7 4.6 Rab3il1DNA 3735 3752 (32960) C B1_Mus2 SINE/Alu (0) 147 136 19
ANNOTATION EVIDENCE:
1126 4.11 0.68 4.58 Rab3il1DNA 3735 3752 32691 C B1_Mus2 SINE/Alu 136 147 0
1126 4.11 0.68 4.58 Rab3il1DNA 3735 3752 (32691) C B1_Mus2#SINE/Alu (0) 147 136 c_b1s355i1
Rab3il1DNA 3735 TTTTGTTTGCTTGCTTGC 3752
-- v ----
C B1_Mus2#SINE/ 147 TTTTGTTT--TTTC---- 136
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 2.93
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.35 (6 / 17), avg. gap size = 1.00 (6 / 6)
+ 26 0.0 0.0 0.0 Rab3il1DNA 3753 3777 (32935) + (T)n Simple_repeat 1 25 (0) 20
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 Rab3il1DNA 3753 3777 32935 + (T)n Simple_repeat 1 25 0
26 0.00 0.00 0.00 Rab3il1DNA 3753 3777 (32935) (T)n#Simple_repeat 1 25 (0) c_b1s251i3
Rab3il1DNA 3753 TTTTTTTTTTTTTTTTTTTTTTTTT 3777
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)
+ 1126 4.1 0.7 4.6 Rab3il1DNA 3778 3911 (32801) C B1_Mus2 SINE/Alu (12) 135 1 19
ANNOTATION EVIDENCE:
1126 4.11 0.68 4.58 Rab3il1DNA 3778 3911 32532 C B1_Mus2 SINE/Alu 1 135 12
1126 4.11 0.68 4.58 Rab3il1DNA 3778 3911 (32532) C B1_Mus2#SINE/Alu (12) 135 1 c_b1s355i1
Rab3il1DNA 3778 GAGACAGGGTTTCTCT-TTTAGCTCTGGCTGTCCTGGAACTCACTCTGTA 3826
- v i
C B1_Mus2#SINE/ 135 GAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTA 86
Rab3il1DNA 3827 GACCAGGCTGGCCTCGAACTCAGAAATCCGACTGCCTCTGCCTCCCGAGT 3876
v
C B1_Mus2#SINE/ 85 GACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCGAGT 36
Rab3il1DNA 3877 GCTGGGATTAAAGGCGTGCACCACCACGCCCAGCT 3911
i i
C B1_Mus2#SINE/ 35 GCTGGGATTAAAGGCGTGCGCCACCACGCCCGGCT 1
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 2.93
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.01 (1 / 133), avg. gap size = 1.00 (1 / 1)
+ 1161 6.2 0.0 4.0 Rab3il1DNA 3977 4127 (32585) C B1_Mus1 SINE/Alu (3) 145 1 21
ANNOTATION EVIDENCE:
1161 6.21 0.00 3.97 Rab3il1DNA 3977 4127 32316 C B1_Mus1 SINE/Alu 1 145 3
1161 6.21 0.00 3.97 Rab3il1DNA 3977 4127 (32316) C B1_Mus1#SINE/Alu (3) 145 1 c_b1s355i2
Rab3il1DNA 3977 TGTTTTTTTCCCCCCAAGACAGGGTTTCTCTGTATATCTCTGGCTGTCCT 4026
------ i i v i
C B1_Mus1#SINE/ 145 TGTTTTTT------CGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCT 102
Rab3il1DNA 4027 GGAACTCACTTTGTAGACCAGGCTGGCCTTGAACTCAGAAATCCACCTGC 4076
i i i
C B1_Mus1#SINE/ 101 GGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGC 52
Rab3il1DNA 4077 CTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACTACCGCCCAGC 4126
i i
C B1_Mus1#SINE/ 51 CTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACCACCGCCCGGC 2
Rab3il1DNA 4127 T 4127
C B1_Mus1#SINE/ 1 T 1
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 3.85
Transitions / transversions = 8.00 (8/1)
Gap_init rate = 0.04 (6 / 150), avg. gap size = 1.00 (6 / 6)
+ 270 28.1 0.0 0.0 Rab3il1DNA 4178 4234 (32478) C ID4_v SINE/ID (25) 58 2 22
ANNOTATION EVIDENCE:
270 28.07 0.00 0.00 Rab3il1DNA 4178 4234 29130 C ID4_v SINE/ID 2 58 25
270 28.07 0.00 0.00 Rab3il1DNA 4178 4234 (29130) C ID4_v#SINE/ID (25) 58 2 m_b1s501i12
Rab3il1DNA 4178 CCTAAGGTCTTCCAAATGCCAAGCAGACATTCTATCACTGAGCTACATCT 4227
i i i iv iv i i ii i i i
C ID4_v#SINE/ID 58 CCCAGGGCCTCGCGCATGCTAGGCAAGCACTCTACCACTGAGCTACATCC 9
Rab3il1DNA 4228 CCAGTTC 4234
ii
C ID4_v#SINE/ID 8 CCAGCCC 2
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 32.92
Transitions / transversions = 7.00 (14/2)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)
+ 409 31.6 5.5 0.0 Rab3il1DNA 4251 4386 (32326) C B1F2 SINE/Alu (2) 147 4 23
ANNOTATION EVIDENCE:
409 31.62 5.55 0.00 Rab3il1DNA 4251 4386 32057 C B1F2 SINE/Alu 4 147 2
409 31.62 5.55 0.00 Rab3il1DNA 4251 4386 (32057) C B1F2#SINE/Alu (2) 147 4 c_b1s355i3
Rab3il1DNA 4251 TTGGTATTTTGAAATAGAGCCGCTGTATGTA-TATGGGTTGGCCTGGGAC 4299
v v i i i i v vv -iviv i i
C B1F2#SINE/Alu 147 TTGTTTTTTTGAGACAGGGTCTCACTATGTAGCCCTGGCTGGCCTGGAAC 98
Rab3il1DNA 4300 CTGCTATATAGCCCA----GGTCTAGAACTTGCAG---TCTTCTCTCACC 4342
ii i v ---- i v i i --- i iiv vi
C B1F2#SINE/Alu 97 TCGCTATGTAGACCAGGCTGGCCTCGAACTCGCGGAGATCCTCCTGCCTC 48
Rab3il1DNA 4343 TGCATTCCAAATGCTAGGAGTCTAGGCATGCAACACCATGCCTG 4386
v i i i i v vi i iiv i i
C B1F2#SINE/Alu 47 TGCCTCCCGAGTGCTGGGATTACAGGCGTGTGCCACCACGCCCG 4
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 34.28
Transitions / transversions = 1.87 (28/15)
Gap_init rate = 0.02 (3 / 135), avg. gap size = 2.67 (8 / 3)
+ 536 21.1 6.3 1.5 Rab3il1DNA 4476 4610 (32102) C ORR1F LTR/ERVL-MaLR (735) 774 633 17
ANNOTATION EVIDENCE:
536 21.05 6.34 1.48 Rab3il1DNA 4476 4610 28889 C ORR1B1-int LTR/ERVL-MaLR 633 774 735
536 21.05 6.34 1.48 Rab3il1DNA 4476 4610 (28889) C ORR1B1-int#LTR/ERVL-MaLR (735) 774 633 m_b1s501i13
Rab3il1DNA 4476 CCTTTACTGTCT----TTATCTTTTACTTATTTCTGACTATGTAGA---- 4517
i i ---- iv v -- i ivvv vi v ----
C ORR1B1-int#LT 774 CCTTCACTGCCTAAGCTTGGCTGT--CCTGGAACTCGCTCTGTAGACCAG 727
Rab3il1DNA 4518 GCTGGCCTGGAGCTCAGAGATCCACCTGCCTTGGACTCCTGAGTGCTGAG 4567
v i i iv v i
C ORR1B1-int#LT 726 GCTGGCCTTGAACTCAGAGATCCGCCTGCCTCTGCCTCCTGAGTGCTGGG 677
Rab3il1DNA 4568 ATCAAAGGCATGCACCACCACCCCTGG-CTTAAGTTCATCTTTA 4610
i i i v - i i iv
C ORR1B1-int#LT 676 ATTAAAGGCGTGTACCACCACGCCTGGNCCTAAGCTTTTCTTTA 633
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 22.12
Transitions / transversions = 1.33 (16/12)
Gap_init rate = 0.04 (5 / 134), avg. gap size = 2.20 (11 / 5)
+ 15 12.2 0.0 0.0 Rab3il1DNA 4661 4687 (32025) + (AAAT)n Simple_repeat 1 27 (0) 24
ANNOTATION EVIDENCE:
15 12.16 0.00 0.00 Rab3il1DNA 4661 4687 28812 + (AAAT)n Simple_repeat 1 27 0
15 12.16 0.00 0.00 Rab3il1DNA 4661 4687 (28812) (AAAT)n#Simple_repeat 1 27 (0) m_b1s252i1
Rab3il1DNA 4661 AAAAAAATAAGTAAATGAATAAATAAA 4687
v i i
(AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAA 27
Matrix = Unknown
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0)
+ 318 18.6 2.8 2.8 Rab3il1DNA 4703 4774 (31938) C ORR1F LTR/ERVL-MaLR (319) 72 1 17
ANNOTATION EVIDENCE:
318 18.58 2.78 2.78 Rab3il1DNA 4703 4774 28725 C ORR1F LTR/ERVL-MaLR 1 72 319
318 18.58 2.78 2.78 Rab3il1DNA 4703 4774 (28725) C ORR1F#LTR/ERVL-MaLR (319) 72 1 m_b1s501i14
Rab3il1DNA 4703 TGACGCTA--AGCTAGGGCCCATTCCTTGAACACATGAGCCTTTGGGTGG 4750
ii i -- i v vv v i --
C ORR1F#LTR/ERV 72 TAGCGCCACGAGCTGGGGACCAAGCCTTTAACACATGGGCCTTTGG--GG 25
Rab3il1DNA 4751 ACACATCAGAGCCAAACTACAGCA 4774
iv v i
C ORR1F#LTR/ERV 24 ACATTTCAGATCCAAACTATAGCA 1
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 21.52
Transitions / transversions = 1.17 (7/6)
Gap_init rate = 0.04 (3 / 71), avg. gap size = 1.33 (4 / 3)
+ 409 28.6 3.6 7.0 Rab3il1DNA 4856 4998 (31714) + B4 SINE/B4 3 140 (152) 25
ANNOTATION EVIDENCE:
409 28.57 3.63 6.99 Rab3il1DNA 4856 4998 28501 + B4 SINE/B4 3 140 152
409 28.57 3.63 6.99 Rab3il1DNA 4856 4998 (28501) B4#SINE/B4 3 140 (152) m_b1s501i15
Rab3il1DNA 4856 GGTTGGGAAGACGACTCAGTCAGTGAAGCACTTGCCTTGCAAGTGGAAGA 4905
i i i i i i ii ? iivi i
B4#SINE/B4 3 GGCTGGGGAGATGGCTCAGTCGGTAAAGTGCTTGCCNTGCAAGCATGAGG 52
Rab3il1DNA 4906 ACTTGAGCTGGATCCCCAGAAGCAATCCTAGAACACATTAGGGAGCAAGC 4955
i i v v ---------- i v iii vi v
B4#SINE/B4 53 ACCTGAGTTCGATCCCCAGAACC----------CACGTAAAAAAGCCGGG 92
Rab3il1DNA 4956 AGTGGTGA---GCACTTGTCTTCCCACTGGTTGGT--GCAGAACCAGG 4998
v i--- i vv vi v v v-- iv
B4#SINE/B4 93 CGTGGTGGCGCGCGCTTGTAATCCCAGCGCTGGGGAGGCAGAGACAGG 140
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 30.38
Transitions / transversions = 1.64 (23/14)
Gap_init rate = 0.08 (12 / 142), avg. gap size = 1.25 (15 / 12)
+ 771 20.0 6.0 0.0 Rab3il1DNA 5180 5319 (31393) + RSINE1 SINE/B4 1 149 (16) 26
ANNOTATION EVIDENCE:
771 20.00 6.04 0.00 Rab3il1DNA 5180 5319 31124 + RSINE1 SINE/B4 1 149 16
771 20.00 6.04 0.00 Rab3il1DNA 5180 5319 (31124) RSINE1#SINE/B4 1 149 (16) c_b1s355i4
Rab3il1DNA 5180 CAGGGCTGGCAAGATGGCTCAGTGGGTAAAGGCACTTTCTGCCAAGCCTG 5229
i i i i i v i
RSINE1#SINE/B 1 CGGGGCCGGCGAGATGGCTCAGCGGGTAAAGGCGCTTGCCGCCAAGCCTG 50
Rab3il1DNA 5230 ATGACGTGAGTTAAATTCCTGGGACCCACATGG--AAAAGAAAGAACCAA 5277
i v vi i i --i i i i
RSINE1#SINE/B 51 ACGACCTGAGTTCGATCCCCGGGACCCACATGGTGGAAGGAGAGAACCGA 100
Rab3il1DNA 5278 CTCCCATATGTTGTCCTC------CCATATGTGT-CCATGGCACACATG 5319
ii v ------ i i i i- i i ii
RSINE1#SINE/B 101 CTCCCGCAAGTTGTCCTCTGACCTCCACACGCGCGCCGTGGCACGCGCG 149
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 9.01
Transitions / transversions = 6.00 (24/4)
Gap_init rate = 0.02 (3 / 139), avg. gap size = 3.00 (9 / 3)
+ 978 14.4 0.0 2.0 Rab3il1DNA 5366 5514 (31198) C B1_Mus2 SINE/Alu (1) 146 1 27
ANNOTATION EVIDENCE:
978 14.38 0.00 2.01 Rab3il1DNA 5366 5514 30929 C B1_Mus2 SINE/Alu 1 146 1
978 14.38 0.00 2.01 Rab3il1DNA 5366 5514 (30929) C B1_Mus2#SINE/Alu (1) 146 1 c_b1s355i5
Rab3il1DNA 5366 TTTGTTTTATTTTCAAGGCAGAGTTTCTCTGTGTAACCCTGGCTGTCCTG 5415
--- i i i i
C B1_Mus2#SINE/ 146 TTTGTT---TTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTG 100
Rab3il1DNA 5416 GAACTCCCTCTGTAAACCAGGCTAGCCTCAAAATTAAAGATCCGCCTGCC 5465
v i i i v i i i
C B1_Mus2#SINE/ 99 GAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCC 50
Rab3il1DNA 5466 TCTGCCTCCAGAGTGCTGGGATTAAAGATCTGCGCCACTGCTCCCAGTT 5514
v iiv ii v i i
C B1_Mus2#SINE/ 49 TCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCGCCACCACGCCCGGCT 1
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 13.19
Transitions / transversions = 3.20 (16/5)
Gap_init rate = 0.02 (3 / 148), avg. gap size = 1.00 (3 / 3)
+ 534 22.4 2.7 0.0 Rab3il1DNA 5670 5776 (30936) + ID_B1 SINE/B4 115 224 (0) 28
ANNOTATION EVIDENCE:
534 22.43 2.72 0.00 Rab3il1DNA 5670 5776 28010 + ID_B1 SINE/B4 115 224 0
534 22.43 2.72 0.00 Rab3il1DNA 5670 5776 (28010) ID_B1#SINE/B4 115 224 (0) m_b1s501i16
Rab3il1DNA 5670 GCACTTGGGAGGTAAAAGCAGGAAGTTTAGGAATCCAAGGTC---TTTGG 5716
i ii i i v i i i i ---i i
ID_B1#SINE/B4 115 GCACTCGGGAGGTGGAGGCAGGAGGATCAGAAGTTCAAGGTCATCCTCGG 164
Rab3il1DNA 5717 CTCCATAGTGAATTTGAGGTCAGCATGGGCTACATGAGAGCTCATCTCAA 5766
v i i i i v v iii
ID_B1#SINE/B4 165 CTACATAGCGAGTTCGAGGCCAGCCTGGGCTACATGAGACCCTGTCTCAA 214
Rab3il1DNA 5767 AACAAAAGAA 5776
v i
ID_B1#SINE/B4 215 AAAAAAAAAA 224
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 22.82
Transitions / transversions = 3.80 (19/5)
Gap_init rate = 0.01 (1 / 106), avg. gap size = 3.00 (3 / 1)
+ 44 2.4 0.0 0.0 Rab3il1DNA 5946 5987 (30725) + (GT)n Simple_repeat 1 42 (0) 29
ANNOTATION EVIDENCE:
44 2.44 0.00 0.00 Rab3il1DNA 5946 5987 30725 + (GT)n Simple_repeat 1 42 0
44 2.44 0.00 0.00 Rab3il1DNA 5946 5987 (30725) (GT)n#Simple_repeat 1 42 (0) c_b1s251i4
Rab3il1DNA 5946 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGT 5987
i
(GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 42
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0)
+ 258 33.5 13.1 1.6 Rab3il1DNA 6052 6233 (30479) C HAL1 LINE/L1 (2021) 486 281 30
ANNOTATION EVIDENCE:
258 33.52 13.11 1.65 Rab3il1DNA 6052 6233 27594 C HAL1 LINE/L1 281 486 2021
258 33.52 13.11 1.65 Rab3il1DNA 6052 6233 (27594) C HAL1#LINE/L1 (2021) 486 281 m_b1s551i2
Rab3il1DNA 6052 TCCAAAGAACCTTCAATTTACCATCTCCAGAGAGT-AATTTCTAGTTTTA 6100
i v iiiv v i - ii i i v
C HAL1#LINE/L1 486 TCCAGAGACCCTCTGTTTTACCCTCTCCAGAGAATAAACCTCCAGTCTTC 437
Rab3il1DNA 6101 GGTAGGATTCAGAAAGGTG-AACTGCCTGGTGGTACGAT-------GGGA 6142
v iv iv vi ii v - iii i-- i i-------
C HAL1#LINE/L1 436 TGCCGGGGTGGGGGAGGGGCAGTCGCCTGGC--TGCGACGGAGTGGGGGA 389
Rab3il1DNA 6143 ACAGACCCAGGGATGCAATTGCTTCCCAGTTTG-TTTGGAACCAGT---- 6187
ivi i ii i vi i ii iviv -i vv i ----
C HAL1#LINE/L1 388 GGGGATCTGGGGGTCTAACTGCTTCTTAAACAGACTTTCAACCAATCCTC 339
Rab3il1DNA 6188 ----------GCTCTACGCTTTACTGCCAATG-CAGAGGT--CTGCTACT 6224
---------- i i - i iv v v- -- v i i
C HAL1#LINE/L1 338 CCTGTTTTTAGCCCCAC-CTTCACCCCCACTTCCAGAGGTACCTGGTGCC 290
Rab3il1DNA 6225 GCCAAATCC 6233
v
C HAL1#LINE/L1 289 GCCAATTCC 281
Matrix = 20p51g.matrix
Kimura (with divCpGMod) = 43.91
Transitions / transversions = 2.00 (40/20)
Gap_init rate = 0.06 (11 / 181), avg. gap size = 2.73 (30 / 11)
+ 1041 28.6 8.8 5.7 Rab3il1DNA 6391 6843 (29869) C Lx8 LINE/L1 (0) 7473 7006 31
ANNOTATION EVIDENCE:
1041 28.57 8.76 5.74 Rab3il1DNA 6391 6843 26984 C Lx8_3end LINE/L1 1420 1887 0
1041 28.57 8.76 5.74 Rab3il1DNA 6391 6843 (26984) C Lx8_3end#LINE/L1 (0) 1887 1420 m_b1s551i3
Rab3il1DNA 6391 TTTTTATTTTTT--AAATTTT-TACATGTATATGATATATAATATATATC 6437
i --i i- ii i vv i---
C Lx8_3end#LINE 1887 TTTTTATTCTTTGAGAATTTCATACATGTATACAATGTATTTTG---ATC 1841
Rab3il1DNA 6438 ATGTATATAACGAATTTCAGCCCGTTTCACCTCATTCACCTCTTTC---A 6484
i------------ v i i v i - v iii ---
C Lx8_3end#LINE 1840 ATA------------TTCATCCCATTCCTCCCC-TTCAACTCCCCCCAGA 1804
Rab3il1DNA 6485 TGCCCCTCCTCTCTTCTTCTCAGCAAGTTGCTATG----CAACTTCCATG 6530
- i vv ? i i -v v --i ---- v - ?
C Lx8_3end#LINE 1803 T-CCCCCCAACTNTCCCTCTC-CCAACTT--CATGTCTTCTACTT-CNTG 1759
Rab3il1DNA 6531 TCTTCTTTTTTATGTGTGACCCACTGTGTATAGTTCGGGTTGCTTGCACG 6580
i - i-i i v vi i v v i ii i i
C Lx8_3end#LINE 1758 TCCTCTTTTTT-TA-ATAACCCACTGAGTCCAATTAGTGCTGCCCGTATG 1711
Rab3il1DNA 6581 AGCACTGGTGGGCAGTTATTTACTGGACTAAGAGCTACTTATCAGTGCCT 6630
v iv v vi ii ii vi v i v i i ? v i
C Lx8_3end#LINE 1710 CGCATGGGTGTGGGGCCATCCACTGGAGCATGGGCAACCTACCAGNGGCC 1661
Rab3il1DNA 6631 ACACTACTGAAGAAAATCATTTCCTTCTCCCCCAGCAAGTCTCAGCTGCC 6680
iv i iiivi iii iviv i
C Lx8_3end#LINE 1660 ACACCCCTAAAGAAAACTGACTCTCCCTCCCCCAGCAGCCATCAACTGCC 1611
Rab3il1DNA 6681 AGTAGCCCAGCAGGGACAGGTGGGACCTCATAAGTACTTCCACCGTCCAA 6730
i i vv ?v vi i i i iv i v i v
C Lx8_3end#LINE 1610 AATAGCTCCTCAGNTAGGGGTGGGGCCTCGTGAGCCCCTCCCCCATCCAT 1561
Rab3il1DNA 6731 GATGAAGTGTTGAAGGGCCTGCTCCTG----GGT---------------- 6760
v i i vv i v i ---- ----------------
C Lx8_3end#LINE 1560 GCTGGAATGTTGACTGGCTTGATCTTGTGCAGGTCTTGTGCAGGCAACCA 1511
Rab3il1DNA 6761 -----------AGTTGATGGGCACAACAACCGTGTCATGTCCAGAAGACA 6799
----------- v i ii ii ?
C Lx8_3end#LINE 1510 CAGCTGCTGTGAGTTCATGAGTGCAACGGCCNTGTCATGTCCAGAAGACA 1461
Rab3il1DNA 6800 GAGGTTCACATCACTCCTCCCTCGCTCCCCCTGGCCCTTACATT 6843
v v v --- vi i i i ?
C Lx8_3end#LINE 1460 GCGTTTCACAGCACTCCTCCC---CATCCTCCGGCTCTTACANT 1420
Matrix = 20p51g.matrix
Kimura (with divCpGMod) = 34.04
Transitions / transversions = 1.76 (74/42)
Gap_init rate = 0.07 (33 / 452), avg. gap size = 2.03 (67 / 33)
+ 399 27.4 8.9 0.0 Rab3il1DNA 7384 7496 (29216) C PB1 SINE/Alu (3) 124 1 32
ANNOTATION EVIDENCE:
399 27.43 8.87 0.00 Rab3il1DNA 7384 7496 28988 C PB1 SINE/Alu 1 124 3
399 27.43 8.87 0.00 Rab3il1DNA 7384 7496 (28988) C PB1#SINE/Alu (3) 124 1 c_b1s355i6
Rab3il1DNA 7384 TTTGTTT--GTATAGAGTCACATTATGTTGCCCAAGCTGCTCTTCAA-TG 7430
--iv i i v ii i vi iv - v
C PB1#SINE/Alu 124 TTTGTTTTGAGACAGGGTCTCGCTATGTTGCCCAGGCTGGCCTCGAACTC 75
Rab3il1DNA 7431 CTGGACTTAAGTCATCCTCTTGTCTCA--------AGTAGTTGGAATCAC 7472
i v i i -------- i i ii
C PB1#SINE/Alu 74 CTGGACTCAAGTGATCCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTAC 25
Rab3il1DNA 7473 AGATGAACCCTCCCATGCCTGGCT 7496
ii vi v iv ii i
C PB1#SINE/Alu 24 AGGCGTGCGCCACCGCGCCCGGCT 1
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 27.71
Transitions / transversions = 2.44 (22/9)
Gap_init rate = 0.03 (3 / 112), avg. gap size = 3.67 (11 / 3)
+ 350 31.3 6.7 3.2 Rab3il1DNA 7558 7605 (29107) C ORR1F LTR/ERVL-MaLR (672) 837 674 17
ANNOTATION EVIDENCE:
350 31.32 6.66 3.19 Rab3il1DNA 7558 7745 26194 C ORR1B1-int LTR/ERVL-MaLR 643 837 672
350 31.32 6.66 3.19 Rab3il1DNA 7558 7745 (26194) C ORR1B1-int#LTR/ERVL-MaLR (672) 837 643 m_b1s501i17
Rab3il1DNA 7558 GGAGCAGAAAT---GCCCCCGTGTCTAAATGCACCT--AGGAGTCTTCCT 7602
i v i i--- vi ii v i i -- vv - i
C ORR1B1-int#LT 837 GGGGCTGGAACATGGCCCCCTCGTTCAATTACATCTTCACCAG-CTTTCT 789
Rab3il1DNA 7603 GGGTTTTGA--GACTATTTTA-TG---AAGCTCGGGCTGACCTTAGGCTC 7646
- v i -- vi vi i - --- i- v viii
C ORR1B1-int#LT 788 -GTTTTCGATGGTTTCCTTCACTGCCTAAGCTT-GGCTGTCCTGGAACTC 741
Rab3il1DNA 7647 ACTATA-AGCCAAAGCTAATCTTGAAGACCTCC-TGATCTTCCTGCCGCT 7694
i v i- v v i iii --- v-v iv v
C ORR1B1-int#LT 740 GCTCTGTAGACCAGGCTGGCCTTGAA---CTCAGAGATCCGCCTGCCTCT 694
Rab3il1DNA 7695 ACCTCCCAAGTGCTGGGATTACAGGACTACTTCACCGTACTTGGCCCTTA 7744
i ii v vv iivi iii i ? v
C ORR1B1-int#LT 693 GCCTCCTGAGTGCTGGGATTAAAGGCGTGTACCACCACGCCTGGNCCTAA 644
Rab3il1DNA 7745 G 7745
C ORR1B1-int#LT 643 G 643
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 36.53
Transitions / transversions = 1.55 (34/22)
Gap_init rate = 0.07 (13 / 187), avg. gap size = 1.46 (19 / 13)
+ 551 26.1 2.3 2.3 Rab3il1DNA 7606 7738 (28974) C ID_B1 SINE/B4 (8) 216 84 33
ANNOTATION EVIDENCE:
551 26.15 2.26 2.26 Rab3il1DNA 7606 7738 26201 C ID_B1 SINE/B4 84 216 8
551 26.15 2.26 2.26 Rab3il1DNA 7606 7738 (26201) C ID_B1#SINE/B4 (8) 216 84 m_b1s501i18
Rab3il1DNA 7606 TTTTGAGACTA--TTTTATGAAGCTCGGGCTGACCTTAGGCTCACTATA- 7652
vi-- i i v i i i iiii i i-
C ID_B1#SINE/B4 216 TTTTGAGACAGGGTCTCATGTAGCCCAGGCTGGCCTCGAACTCGCTATGT 167
Rab3il1DNA 7653 AGCCAAAGCTAATCTTGAAGACCTCCTGATCTTCCTGCCGCTACCTCCCA 7702
i i v i i --- i i v i i
C ID_B1#SINE/B4 166 AGCCGAGGATGACCTTGAA---CTTCTGATCCTCCTGCCTCCACCTCCCG 120
Rab3il1DNA 7703 AGTGCTGGGATTACAGGACTACTTCACCGTACTTGG 7738
vv i vi iii ii
C ID_B1#SINE/B4 119 AGTGCTGGGATTACAGGCGTGCGCCACCACGCCCGG 84
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 27.00
Transitions / transversions = 3.86 (27/7)
Gap_init rate = 0.04 (5 / 132), avg. gap size = 1.20 (6 / 5)
+ 23 15.1 0.0 2.2 Rab3il1DNA 8443 8489 (28223) + (AATG)n Simple_repeat 1 46 (0) 34
ANNOTATION EVIDENCE:
23 15.11 0.00 2.17 Rab3il1DNA 8443 8489 25450 + (AATG)n Simple_repeat 1 46 0
23 15.11 0.00 2.17 Rab3il1DNA 8443 8489 (25450) (AATG)n#Simple_repeat 1 46 (0) m_b1s252i2
Rab3il1DNA 8443 AATAGAATGAATGAATGAGTGGATAAATGGATGGATGAAGGAATGAA 8489
- i i i i i v
(AATG)n#Simpl 1 AAT-GAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAA 46
Matrix = Unknown
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.02 (1 / 46), avg. gap size = 1.00 (1 / 1)
+ 395 24.2 1.1 0.0 Rab3il1DNA 8771 8861 (27851) + PB1D7 SINE/Alu 29 120 (0) 35
ANNOTATION EVIDENCE:
395 24.18 1.09 0.00 Rab3il1DNA 8771 8861 25078 + PB1D7 SINE/Alu 29 120 0
395 24.18 1.09 0.00 Rab3il1DNA 8771 8861 (25078) PB1D7#SINE/Alu 29 120 (0) m_b1s501i19
Rab3il1DNA 8771 TTTCAGTGCTTGGGAGCCAGAGTCAGGAGTGTTGCCCTGAGGTCCAGGCC 8820
ii ii i v v v vi i v v v
PB1D7#SINE/Al 29 TCCCAGCACTCGGGAGGCTGAGGCAGGAGGATCGCCGTGAGTTCGAGGCC 78
Rab3il1DNA 8821 AGCC-AGGTTTCATAGTGAGACCCTGTTACAGAAAAACAAGA 8861
-i i v v iv i i
PB1D7#SINE/Al 79 AGCCTGGGCTACAGAGTGAGACCCTGTCTCAAAAAAACAAAA 120
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 26.53
Transitions / transversions = 1.20 (12/10)
Gap_init rate = 0.01 (1 / 90), avg. gap size = 1.00 (1 / 1)
+ 528 24.8 0.8 4.4 Rab3il1DNA 8867 9001 (27711) + RSINE1 SINE/B4 3 132 (33) 36
ANNOTATION EVIDENCE:
528 24.80 0.77 4.44 Rab3il1DNA 8867 9001 24938 + RSINE1 SINE/B4 3 132 33
528 24.80 0.77 4.44 Rab3il1DNA 8867 9001 (24938) RSINE1#SINE/B4 3 132 (33) m_b1s501i20
Rab3il1DNA 8867 GGGTGGATGAGATGGCTTGGTGGGTTAAGGGTGCTTGCTGATAAGCCTGA 8916
iv ii ii i - i i i vi
RSINE1#SINE/B 3 GGGCCGGCGAGATGGCTCAGCGGGT-AAAGGCGCTTGCCGCCAAGCCTGA 51
Rab3il1DNA 8917 CAACCTTAGTTCAATCCCTGGGGCCCTCA-GGTGGAAGAGGAGAGCCGAG 8965
i v i i i v - ii i v
RSINE1#SINE/B 52 CGACCTGAGTTCGATCCCCGGGACCCACATGGTGGAAGGAGAGAACCGAC 101
Rab3il1DNA 8966 TTTTGCAAGTAGTTCTGACACATGGCCTCTGCATGC 9001
iii v i -----v i ii i
RSINE1#SINE/B 102 TCCCGCAAGTTGTCCT-----CTGACCTCCACACGC 132
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 21.88
Transitions / transversions = 3.57 (25/7)
Gap_init rate = 0.05 (7 / 134), avg. gap size = 1.00 (7 / 7)
+ 542 25.0 13.7 1.8 Rab3il1DNA 9044 9210 (27502) + ID_B1 SINE/B4 29 218 (6) 37
ANNOTATION EVIDENCE:
542 25.00 13.69 1.80 Rab3il1DNA 9044 9210 24729 + ID_B1 SINE/B4 29 218 6
542 25.00 13.69 1.80 Rab3il1DNA 9044 9210 (24729) ID_B1#SINE/B4 29 218 (6) m_b1s501i21
Rab3il1DNA 9044 AGGGCTCACCCAACATCCATGAATCCCTAAATTAAATTCTCAGCAC-ACA 9092
v ii i i v i v iii vi i i -i
ID_B1#SINE/B4 29 AGTGCTTGCCTAGCATGCACGAAGCCCTGGGTTCGATCCCCAGCACCGCA 78
Rab3il1DNA 9093 CAAA-CTGGATTTGGTGGCACGTGCCTGCTGCGACCCCAGCACT------ 9135
i - i iiv i ii i---i i ------
ID_B1#SINE/B4 79 TAAAACCGGGCGTGGTGGCGCACGCCTGT---AATCCCAGCACTCGGGAG 125
Rab3il1DNA 9136 ------GCAGGAA---------TTCAAGGTCATCCTCAACTACCTAGCTA 9170
------ i--------- ii v v
ID_B1#SINE/B4 126 GTGGAGGCAGGAGGATCAGAAGTTCAAGGTCATCCTCGGCTACATAGCGA 175
Rab3il1DNA 9171 GTTGGAGGCTAGCCTAGGCTCCGTAAGACT---TCTTTAAAAA 9210
v i i v i i i--- iv
ID_B1#SINE/B4 176 GTTCGAGGCCAGCCTGGGCTACATGAGACCCTGTCTCAAAAAA 218
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 24.88
Transitions / transversions = 3.10 (31/10)
Gap_init rate = 0.05 (9 / 166), avg. gap size = 3.22 (29 / 9)
+ 244 31.0 1.4 0.0 Rab3il1DNA 9362 9432 (27280) C ID2 SINE/ID (11) 72 1 38
ANNOTATION EVIDENCE:
244 30.99 1.39 0.00 Rab3il1DNA 9362 9432 24507 C ID2 SINE/ID 1 72 11
244 30.99 1.39 0.00 Rab3il1DNA 9362 9432 (24507) C ID2#SINE/ID (11) 72 1 m_b1s501i22
Rab3il1DNA 9362 TGTAAAAGAT-GAAACCTGGGTCTTATGCTTGCTAGGCAGGTGCTATGCC 9410
ivi i - v v i iii i i v i
C ID2#SINE/ID 72 TGCTGAGGATCGAACCCAGGGCCTCGCGCTTGCTAGGCAAGCGCTCTACC 23
Rab3il1DNA 9411 ACAGGCCTAAGCCCCTAGACCC 9432
v iv vii i v
C ID2#SINE/ID 22 ACTGAGCTACATCCCCAGCCCC 1
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 34.33
Transitions / transversions = 1.75 (14/8)
Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1)
+ 907 19.6 0.7 0.0 Rab3il1DNA 9455 9602 (27110) + B1_Mur3 SINE/Alu 1 149 (0) 39
ANNOTATION EVIDENCE:
907 19.59 0.68 0.00 Rab3il1DNA 9455 9602 26882 + B1_Mur3 SINE/Alu 1 149 0
907 19.59 0.68 0.00 Rab3il1DNA 9455 9602 (26882) B1_Mur3#SINE/Alu 1 149 (0) c_b1s355i7
Rab3il1DNA 9455 AGTCAGGTGTGATGGTACACACCTTTAATCCCAGCATTAAGGAGGCAGAG 9504
i i i i ii i i vi
B1_Mur3#SINE/ 1 AGCCGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCGGGAGGCAGAG 50
Rab3il1DNA 9505 GTGTGTGGATATCTGTGAGTTTGAGGCCAGTTTAATCCATAGAGTGAGTT 9554
iiv i v i ii ii i i i
B1_Mur3#SINE/ 51 GCAGGCGGATCTCTGTGAGTTCGAGGCCAGCCTGGTCTACAGAGCGAGTT 100
Rab3il1DNA 9555 CTAGGATAGCTAGGGCTACATAGAGAAACCCTGTCTTGAAAAA-CAAAA 9602
i i i i ii -
B1_Mur3#SINE/ 101 CCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCAAAAAAACAAAA 149
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 16.97
Transitions / transversions = 8.67 (26/3)
Gap_init rate = 0.01 (1 / 147), avg. gap size = 1.00 (1 / 1)
+ 1201 5.5 0.7 0.0 Rab3il1DNA 9606 9751 (26961) + B1_Mus1 SINE/Alu 1 147 (1) 40
ANNOTATION EVIDENCE:
1201 5.48 0.68 0.00 Rab3il1DNA 9606 9751 26733 + B1_Mus1 SINE/Alu 1 147 1
1201 5.48 0.68 0.00 Rab3il1DNA 9606 9751 (26733) B1_Mus1#SINE/Alu 1 147 (1) c_b1s355i8
Rab3il1DNA 9606 AGCCGGGCAGTGGTGGCTCACACCTTTAATCCCAGCACTTGGGAGGCAGA 9655
i v i
B1_Mus1#SINE/ 1 AGCCGGGCGGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGA 50
Rab3il1DNA 9656 GGCAGGCGAATTTCTGAGTTGGAGGCCAGCCTGGTCTACAGAGTGAGTTC 9705
i v
B1_Mus1#SINE/ 51 GGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTC 100
Rab3il1DNA 9706 CAGGACAGTCAAGACTACACAGAGAAACCCTGTCTC-AAAAAACAAA 9751
i i i -
B1_Mus1#SINE/ 101 CAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCGAAAAAACAAA 147
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 4.39
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.01 (1 / 145), avg. gap size = 1.00 (1 / 1)
+ 28 18.9 1.5 1.5 Rab3il1DNA 9753 9820 (26892) + A-rich Low_complexity 1 68 (0) 41
ANNOTATION EVIDENCE:
28 18.86 1.47 1.47 Rab3il1DNA 9753 9820 24411 + (AAACAA)n Simple_repeat 1 68 0
28 18.86 1.47 1.47 Rab3il1DNA 9753 9820 (24411) (AAACAA)n#Simple_repeat 1 68 (0) m_b1s252i3
Rab3il1DNA 9753 AAACAAACAAACAAACAAAAACAAAAAAAGAAAAGAAAAACAAAAA-TAA 9801
v v v v - v -v
(AAACAA)n#Sim 1 AAACAAAAACAAAAACAAAAACAAAAACA-AAAACAAAAACAAAAACAAA 49
Rab3il1DNA 9802 AATAAAAATAGGAACAGAA 9820
i i ii i
(AAACAA)n#Sim 50 AACAAAAACAAAAACAAAA 68
Matrix = Unknown
Transitions / transversions = 0.83 (5/6)
Gap_init rate = 0.03 (2 / 67), avg. gap size = 1.00 (2 / 2)
29 20.06 0.00 0.00 Rab3il1DNA 9753 9809 24422 + (A)n Simple_repeat 1 57 0
29 20.06 0.00 0.00 Rab3il1DNA 9753 9809 (24422) (A)n#Simple_repeat 1 57 (0) m_b1s252i4
Rab3il1DNA 9753 AAACAAACAAACAAACAAAAACAAAAAAAGAAAAGAAAAACAAAAATAAA 9802
v v v v v i i v v
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50
Rab3il1DNA 9803 ATAAAAA 9809
v
(A)n#Simple_r 51 AAAAAAA 57
Matrix = Unknown
Transitions / transversions = 0.25 (2/8)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)
+ 1260 11.9 10.7 0.0 Rab3il1DNA 10213 10413 (26299) + URR1A DNA/hAT-Charlie 2 226 (0) 42
ANNOTATION EVIDENCE:
1260 11.94 10.67 0.00 Rab3il1DNA 10213 10413 24476 + URR1A DNA/hAT-Charlie 2 226 0
1260 11.94 10.67 0.00 Rab3il1DNA 10213 10413 (24476) URR1A#DNA/hAT-Charlie 2 226 (0) c_b1s401i1
Rab3il1DNA 10213 AGCAGTTCTCAATCTGTGGGTTGAGACCCC-------------------- 10242
i i i v --------------------
URR1A#DNA/hAT 2 AGCGGTTCTCAACCTGTGGGTCGCGACCCCTTTGGGGGTCGAACGACCCT 51
Rab3il1DNA 10243 ---ACAGAGGTAGACTATCAGATATCCTGTATAGCAGATATTTACATTAT 10289
--- i v vv i v i
URR1A#DNA/hAT 52 TTCACAGGGGTCGCATATCAGATATCCTGCATATCAGATATTTACATTAC 101
Rab3il1DNA 10290 GACTCATTATAGTAGCAAAATTATAGTTATAAAGTAGCAATGAAA-TAAT 10338
i v i i i i -
URR1A#DNA/hAT 102 GATTCATAACAGTAGCAAAATTACAGTTATGAAGTAGCAACGAAAATAAT 151
Rab3il1DNA 10339 TTTATGGTTGGGGGTCACCCCACCATGAGGAACTGTATTAAAGTGTCACA 10388
v v v i
URR1A#DNA/hAT 152 TTTATGGTTGGGGGTCACCACAACATGAGGAACTGTATTAAAGGGTCGCA 201
Rab3il1DNA 10389 GCATTAGGAACTTGGAGAACCACTG 10413
vv v
URR1A#DNA/hAT 202 GCATTAGGAAGGTTGAGAACCACTG 226
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 10.39
Transitions / transversions = 1.00 (12/12)
Gap_init rate = 0.01 (3 / 200), avg. gap size = 8.00 (24 / 3)
+ 1550 6.2 0.0 2.5 Rab3il1DNA 10480 10678 (26034) + B2_Mm2 SINE/B2 2 195 (0) 43
ANNOTATION EVIDENCE:
1550 6.19 0.00 2.51 Rab3il1DNA 10480 10678 25806 + B2_Mm2 SINE/B2 2 195 0
1550 6.19 0.00 2.51 Rab3il1DNA 10480 10678 (25806) B2_Mm2#SINE/B2 2 195 (0) c_b1s355i9
Rab3il1DNA 10480 GGGCTGGAGAGATGGCTCAGCGGTTGAGAGCACTGATTGTTCTCCCAGAG 10529
i i i i
B2_Mm2#SINE/B 2 GGGCTGGAGAGATGGCTCAGCGGTTAAGAGCACTGACTGCTCTTCCAGAG 51
Rab3il1DNA 10530 GTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCGCA 10579
v i i
B2_Mm2#SINE/B 52 GTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGTA 101
Rab3il1DNA 10580 ATGAGATCTGATGCCTGCCCTCTTCTGGTGTGTCTGGAGACAGCTACAGT 10629
i ---- i
B2_Mm2#SINE/B 102 ATGGGATCTGATGCC----CTCTTCTGGTGTGTCTGAAGACAGCTACAGT 147
Rab3il1DNA 10630 GTGCTCACATACATAAAATAAATAAATGATTCTTTAAAAAAAAAAAAAA 10678
i - i v
B2_Mm2#SINE/B 148 GTACTCACATACATAAA-TAAATAAATAAATCTTTAAAAAAAAAAAAAA 195
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 6.54
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.03 (5 / 198), avg. gap size = 1.00 (5 / 5)
+ 180 30.2 0.0 0.0 Rab3il1DNA 11987 12029 (24683) + MIR3 SINE/MIR 110 152 (56) 44
ANNOTATION EVIDENCE:
180 30.23 0.00 0.00 Rab3il1DNA 11987 12029 22600 + MIR3 SINE/MIR 110 152 56
180 30.23 0.00 0.00 Rab3il1DNA 11987 12029 (22600) MIR3#SINE/MIR 110 152 (56) m_b1s601i0
Rab3il1DNA 11987 CTCTTCAAGCCTCAGTTTCCTGATTTGCAAGAGACCAGGGTTG 12029
iiii v i i i vivvi
MIR3#SINE/MIR 110 CTCTCTGGGCCTCAGTTTCCTCATCTGTAAAATGAGGGGGTTG 152
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 40.98
Transitions / transversions = 2.25 (9/4)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)
+ 59 0.0 0.0 0.0 Rab3il1DNA 12098 12147 (24565) + (GT)n Simple_repeat 1 50 (0) 45
ANNOTATION EVIDENCE:
59 0.00 0.00 0.00 Rab3il1DNA 12098 12147 24565 + (GT)n Simple_repeat 1 50 0
59 0.00 0.00 0.00 Rab3il1DNA 12098 12147 (24565) (GT)n#Simple_repeat 1 50 (0) c_b1s251i5
Rab3il1DNA 12098 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 12147
(GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)
+ 379 13.6 9.6 0.0 Rab3il1DNA 12650 12715 (23997) C MIRc SINE/MIR (114) 154 82 46
ANNOTATION EVIDENCE:
379 13.64 9.59 0.00 Rab3il1DNA 12650 12715 21963 C MIRc SINE/MIR 82 154 114
379 13.64 9.59 0.00 Rab3il1DNA 12650 12715 (21963) C MIRc#SINE/MIR (114) 154 82 m_b1s601i1
Rab3il1DNA 12650 ATAGTTCCTATTTTATAGATGAGG-------GCCCCAGAGAGGTTAAGTG 12692
vi i i i ------- v i
C MIRc#SINE/MIR 154 ATTATCCCCATTTTACAGATGAGGAAACTGAGGCTCAGAGAGGTTAAGTG 105
Rab3il1DNA 12693 ACTTGTCCAAGGTCACACAGCCA 12715
i i
C MIRc#SINE/MIR 104 ACTTGCCCAAGGTCACACAGCTA 82
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 15.44
Transitions / transversions = 3.50 (7/2)
Gap_init rate = 0.02 (1 / 65), avg. gap size = 7.00 (7 / 1)
+ 218 28.6 6.0 4.5 Rab3il1DNA 12776 12841 (23871) + ID4_v SINE/ID 2 68 (15) 47
ANNOTATION EVIDENCE:
218 28.57 5.97 4.55 Rab3il1DNA 12776 12841 21837 + ID4_v SINE/ID 2 68 15
218 28.57 5.97 4.55 Rab3il1DNA 12776 12841 (21837) ID4_v#SINE/ID 2 68 (15) m_b1s501i23
Rab3il1DNA 12776 GAATTGGGTGTGTGGTGACTCAGTAGT----TATCTATCTTGCATACACA 12821
iii vi i --- i ---- iii ii v i i i
ID4_v#SINE/ID 2 GGGCTGGGGATGTAG---CTCAGTGGTAGAGTGCTTGCCTAGCATGCGCG 48
Rab3il1DNA 12822 AGGCTCTGGCTTCAATCCCC 12841
i v
ID4_v#SINE/ID 49 AGGCCCTGGGTTCAATCCCC 68
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 33.93
Transitions / transversions = 5.00 (15/3)
Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.75 (7 / 4)
+ 217 18.2 0.0 2.2 Rab3il1DNA 12964 13008 (23704) C MIR1_Amn SINE/MIR (81) 149 106 48
ANNOTATION EVIDENCE:
217 18.18 0.00 2.22 Rab3il1DNA 12964 13008 21670 C MIR1_Amn SINE/MIR 106 149 81
217 18.18 0.00 2.22 Rab3il1DNA 12964 13008 (21670) C MIR1_Amn#SINE/MIR (81) 149 106 m_b1s601i2
Rab3il1DNA 12964 CCATTTTATGGTTGGGGAAACTGAGGCACAGAATGGCTGAAGTGA 13008
ii v i ? iv - ?
C MIR1_Amn#SINE 149 CCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGG-TNAAGTGA 106
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 16.10
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1)
+ 640 25.3 3.2 11.2 Rab3il1DNA 14949 15153 (21559) C B3A SINE/B2 (8) 190 3 49
ANNOTATION EVIDENCE:
640 25.28 3.19 11.22 Rab3il1DNA 14949 15153 19983 C B3A SINE/B2 3 190 8
640 25.28 3.19 11.22 Rab3il1DNA 14949 15153 (19983) C B3A#SINE/B2 (8) 190 3 c_b1s401i2
Rab3il1DNA 14949 TACTTTATTACGTGTGTATGTTCATTTGTGGATTTCTACACACTCATGCA 14998
i ii i ------ ------ii iiiiv?i i
C B3A#SINE/B2 190 TATTTTATTGTGTGTGTGTG------TGTG------CGCGTGTGNGTGCG 153
Rab3il1DNA 14999 GGTGCCCACAGAGGCCAAAAGAGGGAAGAAGAGGGCATAGGATTCCCCTG 15048
i i ---------- i v -
C B3A#SINE/B2 152 GGTGCCCGCGGAGGCC----------AGAAGAGGGCGTCGGA-TCCCCTG 114
Rab3il1DNA 15049 TAGCTGGAGTCAGA----GTTTTGAATTGCCTGATATGGGTGCTGGGAAC 15094
v i v ---- v iii i ii
C B3A#SINE/B2 113 GAGCTGGAGTTACAGGCGGTTGTGAGCCGCCCGACGTGGGTGCTGGGAAC 64
Rab3il1DNA 15095 CACACGTGGGTCCTCTGTAAGTGCAATGCATACCCTTTCTGGCTGAGCCA 15144
iv vi i v iiiviii i vviv
C B3A#SINE/B2 63 CGAACTCGGGTCCTCTGCAAGAGCAGCAAGCGCTCTTAACCGCTGAGCCA 14
Rab3il1DNA 15145 --TCTCCAGCC 15153
--
C B3A#SINE/B2 13 TCTCTCCAGCC 3
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 21.99
Transitions / transversions = 2.75 (33/12)
Gap_init rate = 0.12 (25 / 204), avg. gap size = 1.16 (29 / 25)
+ 18 0.0 3.9 0.0 Rab3il1DNA 15166 15191 (21521) + (TGTGT)n Simple_repeat 1 27 (0) 50
ANNOTATION EVIDENCE:
18 0.00 3.85 0.00 Rab3il1DNA 15166 15191 19691 + (TGTGT)n Simple_repeat 1 27 0
18 0.00 3.85 0.00 Rab3il1DNA 15166 15191 (19691) (TGTGT)n#Simple_repeat 1 27 (0) m_b1s252i5
Rab3il1DNA 15166 TGTGTTGTGTTGTGTTGTGTTGT-TTG 15191
-
(TGTGT)n#Simp 1 TGTGTTGTGTTGTGTTGTGTTGTGTTG 27
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1)
+ 953 13.6 0.0 3.3 Rab3il1DNA 15239 15390 (21322) C B1_Mm SINE/Alu (0) 147 1 51
ANNOTATION EVIDENCE:
953 13.61 0.00 3.29 Rab3il1DNA 15239 15390 21143 C B1_Mm SINE/Alu 1 147 0
953 13.61 0.00 3.29 Rab3il1DNA 15239 15390 (21143) C B1_Mm#SINE/Alu (0) 147 1 c_b1s355i10
Rab3il1DNA 15239 TTTTGGCTTTTTGAGACAGAGTTTTTCTGTGTAACAGTCCTAGCTGTCCT 15288
vi i i i --- i i i
C B1_Mm#SINE/Al 147 TTTTGTTTTTTCGAGACAGGGTTTCTCTGT---ATAGCCCTGGCTGTCCT 101
Rab3il1DNA 15289 GGAACTCACATTGTAGAGCAGGCTGGCCTTGAACTCAGAGATCTTGCCTG 15338
v v i i -i
C B1_Mm#SINE/Al 100 GGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATC-CGCCTG 52
Rab3il1DNA 15339 TCTTTGCCTCCAGAATGCTGGGATTAAAGGTGTGTGCCACCACACCCTGG 15388
i i v i i i i -
C B1_Mm#SINE/Al 51 CCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCGCCACCACGCCC-GG 3
Rab3il1DNA 15389 CT 15390
C B1_Mm#SINE/Al 2 CT 1
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 10.80
Transitions / transversions = 4.00 (16/4)
Gap_init rate = 0.03 (5 / 151), avg. gap size = 1.00 (5 / 5)
+ 508 25.3 12.1 3.7 Rab3il1DNA 17920 18108 (18604) C B4A SINE/B4 (84) 208 2 52
ANNOTATION EVIDENCE:
508 25.28 12.08 3.70 Rab3il1DNA 17920 18108 16925 C B4A SINE/B4 2 208 84
508 25.28 12.08 3.70 Rab3il1DNA 17920 18108 (16925) C B4A#SINE/B4 (84) 208 2 m_b1s501i24
Rab3il1DNA 17920 GGTCTCTCACTGAACCTGGAACTTGTTGA----GCCAAGCTGG-TGGCGA 17964
i iiii ---- i i - v
C B4A#SINE/B4 208 GGTCTCTCACTGAACCTGGAGCTCACCGATTCGGCTAGGCTGGCTGGCCA 159
Rab3il1DNA 17965 GTATATGCCAGTGATTCTCACGGTGCTGTGTCC-CCT-CGCAGTGCTGAG 18012
iiviiv v i ------ v - - v i i
C B4A#SINE/B4 158 GCGAGCCCCAGGGATCCTC------CTGTCTCCGCCTCCCCAGCGCTGGG 115
Rab3il1DNA 18013 CTTGCTGGTGCA---TATGATGACC--------AC------ACT-GGGAT 18044
v i v i i---iiiv i v -------- ------i -
C B4A#SINE/B4 114 ATTACAGGCGCGCGCCGCCACGCCCGGCTTTTTACGTGGGTGCTGGGGAT 65
Rab3il1DNA 18045 CTGAACTTGGGTCCTCAGGCTTACACAGAGAGCCTTCTTACCCACTGAGC 18094
i ii v i i i vi vi - ?
C B4A#SINE/B4 64 CCGAACTCAGGTCCTCATGCTTGCGCGGCAAGCACT-TTACCNACTGAGC 16
Rab3il1DNA 18095 CGTCTTCCCAGCCC 18108
i i
C B4A#SINE/B4 15 CATCTCCCCAGCCC 2
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 23.44
Transitions / transversions = 2.46 (32/13)
Gap_init rate = 0.08 (15 / 188), avg. gap size = 2.13 (32 / 15)
+ 719 25.0 9.2 0.0 Rab3il1DNA 18482 18669 (18043) C ID_B1 SINE/B4 (15) 209 3 53
ANNOTATION EVIDENCE:
719 25.00 9.18 0.00 Rab3il1DNA 18482 18669 17864 C ID_B1 SINE/B4 3 209 15
719 25.00 9.18 0.00 Rab3il1DNA 18482 18669 (17864) C ID_B1#SINE/B4 (15) 209 3 c_b1s355i11
Rab3il1DNA 18482 ACAGGGTCTCATGTAGCCTAGGTTGGCCTCAAACTCCCCATTTAGCCAAG 18531
i i i v i v i
C ID_B1#SINE/B4 209 ACAGGGTCTCATGTAGCCCAGGCTGGCCTCGAACTCGCTATGTAGCCGAG 160
Rab3il1DNA 18532 GATGA-------------GTCCCTCT--CTCCATCTCCCAAGTACTGGCA 18566
-------------i ii -- i i i v
C ID_B1#SINE/B4 159 GATGACCTTGAACTTCTGATCCTCCTGCCTCCACCTCCCGAGTGCTGGGA 110
Rab3il1DNA 18567 CGACAGGCATGTGCCACAATGCCTGG-CTTAGG-AGTGCTGAGAATGGAA 18614
iv i i v i i -i v -i i i v
C ID_B1#SINE/B4 109 TTACAGGCGTGCGCCACCACGCCCGGTTTTATGCGGTGCTGGGGATCGAA 60
Rab3il1DNA 18615 TCTAGAGCTTTGTGC--TCTGCGCAAGGACTCGGGCAGCGGGGCTGTGTA 18662
i i i i --v iv v viv i v i iii v
C ID_B1#SINE/B4 59 CCCAGGGCTTCGTGCATGCTAGGCAAGCACTCTACCAACTGAGCTACATC 10
Rab3il1DNA 18663 ACCAACC 18669
v i
C ID_B1#SINE/B4 9 CCCAGCC 3
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 24.67
Transitions / transversions = 2.13 (32/15)
Gap_init rate = 0.03 (5 / 187), avg. gap size = 3.80 (19 / 5)
+ 1685 4.2 0.0 0.0 Rab3il1DNA 18744 18936 (17776) C B2_Mm1a SINE/B2 (0) 193 1 54
ANNOTATION EVIDENCE:
1685 4.15 0.00 0.00 Rab3il1DNA 18744 18936 17597 C B2_Mm1a SINE/B2 1 193 0
1685 4.15 0.00 0.00 Rab3il1DNA 18744 18936 (17597) C B2_Mm1a#SINE/B2 (0) 193 1 c_b1s355i12
Rab3il1DNA 18744 TTTTTTTTTTTTTTAAAGATTTATTTATTTATTATATGTAAGTACACTGT 18793
C B2_Mm1a#SINE/ 193 TTTTTTTTTTTTTTAAAGATTTATTTATTTATTATATGTAAGTACACTGT 144
Rab3il1DNA 18794 AGCTATCTTCAGACACTCCAGAAGAGGGAGTCAGATCTCATTACAGATGG 18843
i i i
C B2_Mm1a#SINE/ 143 AGCTGTCTTCAGACACTCCAGAAGAGGGAGTCAGATCTCGTTACGGATGG 94
Rab3il1DNA 18844 TTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCTTCAGAAG 18893
i i
C B2_Mm1a#SINE/ 93 TTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCCGGACCTTCGGAAG 44
Rab3il1DNA 18894 AGCAGTCGGGTGCTCTTAACCACTAAGCCATCTCGCCAGCCCC 18936
v i i
C B2_Mm1a#SINE/ 43 AGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCC 1
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 2.32
Transitions / transversions = 7.00 (7/1)
Gap_init rate = 0.00 (0 / 192), avg. gap size = 0.0 (0 / 0)
+ 37 0.0 0.0 0.0 Rab3il1DNA 18971 19002 (17710) + (GT)n Simple_repeat 1 32 (0) 55
ANNOTATION EVIDENCE:
37 0.00 0.00 0.00 Rab3il1DNA 18971 19002 17710 + (GT)n Simple_repeat 1 32 0
37 0.00 0.00 0.00 Rab3il1DNA 18971 19002 (17710) (GT)n#Simple_repeat 1 32 (0) c_b1s251i6
Rab3il1DNA 18971 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 19002
(GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 32
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 555 29.7 0.0 3.3 Rab3il1DNA 19019 19171 (17541) C RSINE1 SINE/B4 (15) 150 3 56
ANNOTATION EVIDENCE:
555 29.73 0.00 3.27 Rab3il1DNA 19019 19171 17393 C RSINE1 SINE/B4 3 150 15
555 29.73 0.00 3.27 Rab3il1DNA 19019 19171 (17393) C RSINE1#SINE/B4 (15) 150 3 c_b1s355i13
Rab3il1DNA 19019 GCACATGTGTCATCACACACATGTTGAAGTCAGAGGACAACTTTGTGCAG 19068
i ii i ivi i i i v i vvv v
C RSINE1#SINE/B 150 GCGCGCGTGCCACGGCGCGCGTGTGGAGGTCAGAGGACAACTTGCGGGAG 101
Rab3il1DNA 19069 TTGGTACTCTCCTACTACTTTTTATGTGGGTTTTAGGGATCAAAATGAGG 19118
i v v i i---- iiii i v v
C RSINE1#SINE/B 100 TCGGTTCTCTCCTTCCACC----ATGTGGGTCCCGGGGATCGAACTCAGG 55
Rab3il1DNA 19119 CCCCCGAGCTTATACAGCAAACCCCTTTCCTCGCTTAGCCATCTCACTGG 19168
i vi ii i-i i i v v i v i i
C RSINE1#SINE/B 54 TCGTCAGGCTTG-GCGGCAAGCGCCTTTACCCGCTGAGCCATCTCGCCGG 6
Rab3il1DNA 19169 TCC 19171
i
C RSINE1#SINE/B 5 CCC 3
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 26.06
Transitions / transversions = 2.14 (30/14)
Gap_init rate = 0.03 (5 / 152), avg. gap size = 1.00 (5 / 5)
+ 14 5.0 0.0 0.0 Rab3il1DNA 19266 19286 (17426) + (CAGA)n Simple_repeat 1 21 (0) 57
ANNOTATION EVIDENCE:
14 5.00 0.00 0.00 Rab3il1DNA 19266 19286 16309 + (CAGA)n Simple_repeat 1 21 0
14 5.00 0.00 0.00 Rab3il1DNA 19266 19286 (16309) (CAGA)n#Simple_repeat 1 21 (0) m_b1s252i6
Rab3il1DNA 19266 CAAACAGACAGACAGACAGAC 19286
i
(CAGA)n#Simpl 1 CAGACAGACAGACAGACAGAC 21
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
+ 24 0.0 0.0 0.0 Rab3il1DNA 20066 20091 (16621) + (GT)n Simple_repeat 1 26 (0) 58
ANNOTATION EVIDENCE:
24 0.00 0.00 0.00 Rab3il1DNA 20066 20091 15541 + (GT)n Simple_repeat 1 26 3
24 0.00 0.00 0.00 Rab3il1DNA 20066 20091 (15541) (GT)n#Simple_repeat 1 26 (3) m_b1s252i7
Rab3il1DNA 20066 GTGTGTGTGTGTGTGTGTGTGTGTGT 20091
(GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGT 26
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)
+ 44 0.0 0.0 0.0 Rab3il1DNA 20092 20129 (16583) + (GA)n Simple_repeat 1 38 (0) 59
ANNOTATION EVIDENCE:
44 0.00 0.00 0.00 Rab3il1DNA 20092 20129 16583 + (GA)n Simple_repeat 1 38 0
44 0.00 0.00 0.00 Rab3il1DNA 20092 20129 (16583) (GA)n#Simple_repeat 1 38 (0) c_b1s251i7
Rab3il1DNA 20092 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 20129
(GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 38
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 17 10.7 0.0 11.1 Rab3il1DNA 20675 20724 (15988) + (CCCATT)n Simple_repeat 1 45 (0) 60
ANNOTATION EVIDENCE:
17 10.66 0.00 11.11 Rab3il1DNA 20675 20724 14908 + (CCCATT)n Simple_repeat 1 45 0
17 10.66 0.00 11.11 Rab3il1DNA 20675 20724 (14908) (CCCATT)n#Simple_repeat 1 45 (0) m_b1s252i8
Rab3il1DNA 20675 CCCCTTCCCACTTCCTCATTCCCATCCCACAATTCTCATTCACCTTTCCC 20724
v - - i - - i - v
(CCCATT)n#Sim 1 CCCATTCCCA-TTCC-CATTCCCATTCC-C-ATTCCCATTC-CCATTCCC 45
Matrix = Unknown
Transitions / transversions = 1.00 (2/2)
Gap_init rate = 0.10 (5 / 49), avg. gap size = 1.00 (5 / 5)
+ 291 33.6 5.8 2.2 Rab3il1DNA 22706 22839 (13873) + MIR1_Amn SINE/MIR 40 178 (52) 61
ANNOTATION EVIDENCE:
291 33.59 5.76 2.24 Rab3il1DNA 22706 22839 12793 + MIR1_Amn SINE/MIR 40 178 52
291 33.59 5.76 2.24 Rab3il1DNA 22706 22839 (12793) MIR1_Amn#SINE/MIR 40 178 (52) m_b1s601i3
Rab3il1DNA 22706 GGGGCT--GAAGACCTGGCTGCCTGTCTCCACACTACCCCTGACCAGTTA 22753
i -- i v v ?v? i vi v i v ?i ? i i
MIR1_Amn#SINE 40 GGGACTCGGGAGACCTGGGTTCNANTCCCGGCTCTGCCACTNGCCNGCTG 89
Rab3il1DNA 22754 TGGGAACTCCATGG--AAGTCCCCTCCTCTCTCTGGGCTT--GCACCCCT 22799
? v v --- -- v i ?vi ? i -- ivi ii
MIR1_Amn#SINE 90 NGTGACCT---TGGGCAAGTCACTTNACCTCTCTGNGCCTCAGTTTCCTC 136
Rab3il1DNA 22800 ATCTGTAGTATGGGGGAAAGACTAC--AATTACTGTGTAAAG 22839
iv iv viv -- vi v v
MIR1_Amn#SINE 137 ATCTGTAAAATGGGGATAATGATACTGACCTCCTTTGTAAAG 178
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 38.61
Transitions / transversions = 1.06 (19/18)
Gap_init rate = 0.05 (7 / 133), avg. gap size = 1.57 (11 / 7)
+ 19 0.0 7.7 0.0 Rab3il1DNA 22841 22866 (13846) + (AT)n Simple_repeat 1 28 (0) 62
ANNOTATION EVIDENCE:
19 0.00 7.69 0.00 Rab3il1DNA 22841 22866 12766 + (AT)n Simple_repeat 1 28 0
19 0.00 7.69 0.00 Rab3il1DNA 22841 22866 (12766) (AT)n#Simple_repeat 1 28 (0) m_b1s252i9
Rab3il1DNA 22841 ATATATATATAT-TATATATATA-ATAT 22866
- -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATAT 28
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2)
+ 440 29.4 12.8 3.5 Rab3il1DNA 22876 23044 (13668) + B3A SINE/B2 1 187 (11) 63
ANNOTATION EVIDENCE:
440 29.45 12.83 3.55 Rab3il1DNA 22876 23044 13557 + B3A SINE/B2 1 187 11
440 29.45 12.83 3.55 Rab3il1DNA 22876 23044 (13557) B3A#SINE/B2 1 187 (11) c_b1s355i14
Rab3il1DNA 22876 GGGGAGGGAGAGCACGCTCAGTCATTAAGAGCACTTACTGCTCTATCAGA 22925
vv vvv ivi i i vv
B3A#SINE/B2 1 GGGGCTGGAGAGATGGCTCAGCGGTTAAGAGCGCTTGCTGCTCTTGCAGA 50
Rab3il1DNA 22926 GGACCCAAGTTC-----CCAGCACCCAC-----------------TGCTT 22953
i ----- -----------------i i
B3A#SINE/B2 51 GGACCCGAGTTCGGTTCCCAGCACCCACGTCGGGCGGCTCACAACCGCCT 100
Rab3il1DNA 22954 GATGCTCTACCACCAGGGGATCTAATACTTACTTCTGGTCCCTATGAGTA 23003
vvi i v v ii ii iiv i i iii i i
B3A#SINE/B2 101 GTAACTCCAGCTCCAGGGGATCCGACGCCCTCTTCTGGCCTCCGCGGGCA 150
Rab3il1DNA 23004 CC-GTGGAAAGACACATATGTGTGTACATGAGTACA-AATAAA 23044
- i------ ? i i i iii iivii -
B3A#SINE/B2 151 CCCGC------ACNCACACGCGCACACACACACACACAATAAA 187
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 28.57
Transitions / transversions = 2.36 (33/14)
Gap_init rate = 0.06 (10 / 168), avg. gap size = 3.00 (30 / 10)
+ 50 0.0 0.0 0.0 Rab3il1DNA 23049 23091 (13621) + (AC)n Simple_repeat 1 43 (0) 64
ANNOTATION EVIDENCE:
50 0.00 0.00 0.00 Rab3il1DNA 23049 23091 13621 + (AC)n Simple_repeat 1 43 0
50 0.00 0.00 0.00 Rab3il1DNA 23049 23091 (13621) (AC)n#Simple_repeat 1 43 (0) c_b1s251i8
Rab3il1DNA 23049 ACACACACACACACACACACACACACACACACACACACACACA 23091
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACA 43
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)
+ 668 27.3 15.4 5.1 Rab3il1DNA 23111 23365 (13347) + B4 SINE/B4 5 290 (2) 65
ANNOTATION EVIDENCE:
668 27.27 15.38 5.10 Rab3il1DNA 23111 23365 12731 + B4 SINE/B4 5 290 2
668 27.27 15.38 5.10 Rab3il1DNA 23111 23365 (12731) B4#SINE/B4 5 290 (2) c_b1s401i3
Rab3il1DNA 23111 CTGGGGAGCTAGCTTAGTTGATAAAGTGCTTGCTATGCATGCATGAAGAC 23160
v i i i i i? v i
B4#SINE/B4 5 CTGGGGAGATGGCTCAGTCGGTAAAGTGCTTGCCNTGCAAGCATGAGGAC 54
Rab3il1DNA 23161 CTAAGTTTGAGCCC----------------------GGCACGGTGGCACA 23188
i i v ---------------------- ii i i
B4#SINE/B4 55 CTGAGTTCGATCCCCAGAACCCACGTAAAAAAGCCGGGCGTGGTGGCGCG 104
Rab3il1DNA 23189 CTCTTGTCATCACAGTCGGGGGGGGGGGGGGAGGGACAAGAAAATCCCTT 23238
v v v i---- vv i v i i vii v
B4#SINE/B4 105 CGCTTGTAATCCCAGC----GCTGGGGAGGCAGAGACAGGCGGATCCCTG 150
Rab3il1DNA 23239 AGGCTCCTTATCCATGCAACGGAAGCAAATCGGCCAACCCCAGATCCCAG 23288
i vi iv vv i vv iv v v v i i i--
B4#SINE/B4 151 GGGCTCGCTGGCCAGCCAGCCTAGCCTACTCGGCGAGCTCCAGG--CCAG 198
Rab3il1DNA 23289 TAAGAGACCTTGTGATAATTTCAAAGAAGCA-----------GCCT---- 23323
i i ------i i - ----------- ----
B4#SINE/B4 199 TGAGAGACCCTGT------CTCAAAAAA-CAAGGTGGACGGCGCCTGAGG 241
Rab3il1DNA 23324 -------CCCAAGCTTGGCCTCCAACCTCCACATCCATGTGCGTAGACA 23365
------- i v ? iii iv i ii ii v
B4#SINE/B4 242 AACGACACCCGAGGTTGNCCTCTGGCCTCCACACGCACGCACACACACA 290
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 27.76
Transitions / transversions = 1.67 (40/24)
Gap_init rate = 0.07 (17 / 254), avg. gap size = 3.35 (57 / 17)
+ 180 21.9 0.0 0.0 Rab3il1DNA 24733 24764 (11948) C MIRc SINE/MIR (119) 149 118 66
ANNOTATION EVIDENCE:
180 21.88 0.00 0.00 Rab3il1DNA 24733 24764 11332 C MIRc SINE/MIR 118 149 119
180 21.88 0.00 0.00 Rab3il1DNA 24733 24764 (11332) C MIRc#SINE/MIR (119) 149 118 m_b1s601i4
Rab3il1DNA 24733 CTCTATTTTACAGACGGGCAGACTGAGGCTTA 24764
i i i i v i i
C MIRc#SINE/MIR 149 CCCCATTTTACAGATGAGGAAACTGAGGCTCA 118
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 27.68
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 1240 4.3 0.0 0.0 Rab3il1DNA 25229 25369 (11343) + B1_Mm SINE/Alu 3 143 (4) 67
ANNOTATION EVIDENCE:
1240 4.26 0.00 0.00 Rab3il1DNA 25229 25369 11274 + B1_Mm SINE/Alu 3 143 4
1240 4.26 0.00 0.00 Rab3il1DNA 25229 25369 (11274) B1_Mm#SINE/Alu 3 143 (4) c_b1s355i15
Rab3il1DNA 25229 CTGGGCGTGGTGGTGCACACCTTTAATCCCAGCACTTGGGAGGCAGAGGC 25278
i i i i
B1_Mm#SINE/Al 3 CCGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCGGGAGGCAGAGGC 52
Rab3il1DNA 25279 AGGCAGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAG 25328
i
B1_Mm#SINE/Al 53 AGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAG 102
Rab3il1DNA 25329 GACAGCCAGGGCTATACAGAGAAACCTTGTCTCGAAAAAAC 25369
i
B1_Mm#SINE/Al 103 GACAGCCAGGGCTATACAGAGAAACCCTGTCTCGAAAAAAC 143
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 1.08
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.00 (0 / 140), avg. gap size = 0.0 (0 / 0)
+ 48 0.0 0.0 0.0 Rab3il1DNA 25371 25414 (11298) + (AACAA)n Simple_repeat 1 44 (0) 68
ANNOTATION EVIDENCE:
48 0.00 0.00 0.00 Rab3il1DNA 25371 25414 11298 + (AACAA)n Simple_repeat 1 44 0
48 0.00 0.00 0.00 Rab3il1DNA 25371 25414 (11298) (AACAA)n#Simple_repeat 1 44 (0) c_b1s251i9
Rab3il1DNA 25371 AACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACA 25414
(AACAA)n#Simp 1 AACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACA 44
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
+ 204 27.8 8.9 0.0 Rab3il1DNA 26421 26520 (10192) + MIRc SINE/MIR 78 199 (69) 69
ANNOTATION EVIDENCE:
200 31.75 3.07 0.00 Rab3il1DNA 26421 26483 9796 + MIR3 SINE/MIR 78 142 66
200 31.75 3.07 0.00 Rab3il1DNA 26421 26483 (9796) MIR3#SINE/MIR 78 142 (66) m_b1s601i5
Rab3il1DNA 26421 CTCACAATGTGACCTGAGGCAGGTCATGTCTCCTGTC--AGCCTTGGGTG 26468
?i vi vi i iv v v --i ii v v
MIR3#SINE/MIR 78 CTNGCTGTGTGACCTTGGGCAAGTCACTTCACCTCTCTGGGCCTCAGTTT 127
Rab3il1DNA 26469 CCCTATCTCTAGAAT 26483
ii v i
MIR3#SINE/MIR 128 CCTCATCTGTAAAAT 142
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 40.53
Transitions / transversions = 1.38 (11/8)
Gap_init rate = 0.02 (1 / 62), avg. gap size = 2.00 (2 / 1)
196 29.03 14.68 0.00 Rab3il1DNA 26428 26520 9759 + MIRb SINE/MIR 91 199 69
196 29.03 14.68 0.00 Rab3il1DNA 26428 26520 (9759) MIRb#SINE/MIR 91 199 (69) m_b1s601i7
Rab3il1DNA 26428 TGTGACCTGAGGCAGGTCATGTCTCCTGTC--AGCCTTGGGTGCCCTATC 26475
vi i i iv vv v -- ii v v ii
MIRb#SINE/MIR 91 TGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATC 140
Rab3il1DNA 26476 TCTAGAATAG--ATAAT----CTTA------GAGGTTGTTCCAAGGGT-- 26511
v i i -- ---- i ------ii vii i --
MIRb#SINE/MIR 141 TGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTA 190
Rab3il1DNA 26512 AAGGAGACA 26520
v i
MIRb#SINE/MIR 191 AATGAGATA 199
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 38.09
Transitions / transversions = 1.70 (17/10)
Gap_init rate = 0.05 (5 / 92), avg. gap size = 3.20 (16 / 5)
204 26.98 5.97 0.00 Rab3il1DNA 26428 26490 9789 + MIRc SINE/MIR 88 154 114
204 26.98 5.97 0.00 Rab3il1DNA 26428 26490 (9789) MIRc#SINE/MIR 88 154 (114) m_b1s601i6
Rab3il1DNA 26428 TGTGACCTGAGGCAGGTCATGTCTCCTGTC--AGCCTTGGGTGCCCTATC 26475
vi i iv vv v -- ii v v ii
MIRc#SINE/MIR 88 TGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATC 137
Rab3il1DNA 26476 TCTAGAATAG--ATAAT 26490
v i i --
MIRc#SINE/MIR 138 TGTAAAATGGGGATAAT 154
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 33.94
Transitions / transversions = 1.12 (9/8)
Gap_init rate = 0.03 (2 / 62), avg. gap size = 2.00 (4 / 2)
+ 1511 7.8 0.0 0.0 Rab3il1DNA 27154 27345 (9367) C B2_Mm2 SINE/B2 (2) 193 2 70
ANNOTATION EVIDENCE:
1511 7.81 0.00 0.00 Rab3il1DNA 27154 27345 9341 C B2_Mm2 SINE/B2 2 193 2
1511 7.81 0.00 0.00 Rab3il1DNA 27154 27345 (9341) C B2_Mm2#SINE/B2 (2) 193 2 c_b1s355i16
Rab3il1DNA 27154 TTTTTGTTTTTTTAAGATTTATTTATTTATTTTTATGTGTGAATACACTG 27203
v v v i i i
C B2_Mm2#SINE/B 193 TTTTTTTTTTTTAAAGATTTATTTATTTATTTATGTATGTGAGTACACTG 144
Rab3il1DNA 27204 TTGCTGACTTCAGAAACACCAGAAGAGGGCATCAGATCCCGTTACAGATG 27253
v v v i
C B2_Mm2#SINE/B 143 TAGCTGTCTTCAGACACACCAGAAGAGGGCATCAGATCCCATTACAGATG 94
Rab3il1DNA 27254 GTTGTGAGCCACCATGTGGTTGCTGAGAATTGAACTCAGGACCTCTGGAA 27303
i
C B2_Mm2#SINE/B 93 GTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAA 44
Rab3il1DNA 27304 GAGCAGTCAGTGCTCTTAGCCGCTGAGCCATTTCACTAGCCC 27345
i i v i
C B2_Mm2#SINE/B 43 GAGCAGTCAGTGCTCTTAACCGCTGAGCCATCTCTCCAGCCC 2
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 8.27
Transitions / transversions = 1.14 (8/7)
Gap_init rate = 0.00 (0 / 191), avg. gap size = 0.0 (0 / 0)
+ 17 14.8 5.1 0.0 Rab3il1DNA 27748 27786 (8926) + (CTGT)n Simple_repeat 1 41 (0) 71
ANNOTATION EVIDENCE:
17 14.81 5.13 0.00 Rab3il1DNA 27748 27786 8684 + (CTGT)n Simple_repeat 1 41 0
17 14.81 5.13 0.00 Rab3il1DNA 27748 27786 (8684) (CTGT)n#Simple_repeat 1 41 (0) m_b1s252i10
Rab3il1DNA 27748 CTGTCTGTC--TCTGTTTGTCTGTTTGTCTATCCATCTGTC 27786
-- i i i ii
(CTGT)n#Simpl 1 CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTC 41
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.03 (1 / 38), avg. gap size = 2.00 (2 / 1)
+ 1105 20.8 3.1 0.5 Rab3il1DNA 29029 29245 (7467) + ID_B1 SINE/B4 1 223 (1) 72
ANNOTATION EVIDENCE:
1105 20.84 3.14 0.46 Rab3il1DNA 29029 29245 7441 + ID_B1 SINE/B4 1 223 1
1105 20.84 3.14 0.46 Rab3il1DNA 29029 29245 (7441) ID_B1#SINE/B4 1 223 (1) c_b1s355i17
Rab3il1DNA 29029 GGGTCTGGGGGATATAGTTCAGT----AAAGTCCTTGACTAGCATGCACA 29074
v - i i ---- i v v i
ID_B1#SINE/B4 1 GGGGCTGGGG-ATGTAGCTCAGTTGGTAGAGTGCTTGCCTAGCATGCACG 49
Rab3il1DNA 29075 AAACCATGAATCTG-TCCCCAGCACCATGTAAAACCAAGTATGGTGGCAT 29123
i v ii ii - iii ii ii ii
ID_B1#SINE/B4 50 AAGCCCTGGGTTCGATCCCCAGCACCGCATAAAACCGGGCGTGGTGGCGC 99
Rab3il1DNA 29124 ACACCTGTGATCC-AGGACTTGGGAGGTCGAGGCAGGGAGGTCAGAAGTT 29172
i i - v i v ii i
ID_B1#SINE/B4 100 ACGCCTGTAATCCCAGCACTCGGGAGGTGGAGGCAGGAGGATCAGAAGTT 149
Rab3il1DNA 29173 GAAGGTCATTCTTGGTTACATAGCAAATTCAAGAAAAGCCTGGCCTACAT 29222
v i i i i i i ivv v
ID_B1#SINE/B4 150 CAAGGTCATCCTCGGCTACATAGCGAGTTCGAGGCCAGCCTGGGCTACAT 199
Rab3il1DNA 29223 AAAACCCTG-CTTAAAAAAATAAA 29245
i i - i v
ID_B1#SINE/B4 200 GAGACCCTGTCTCAAAAAAAAAAA 223
Matrix = 18p51g.matrix
Kimura (with divCpGMod) = 18.64
Transitions / transversions = 3.09 (34/11)
Gap_init rate = 0.02 (5 / 216), avg. gap size = 1.60 (8 / 5)
+ 12 9.7 0.0 0.0 Rab3il1DNA 30566 30587 (6125) + (GCCT)n Simple_repeat 1 22 (0) 73
ANNOTATION EVIDENCE:
12 9.71 0.00 0.00 Rab3il1DNA 30566 30587 6099 + (GCCT)n Simple_repeat 1 22 0
12 9.71 0.00 0.00 Rab3il1DNA 30566 30587 (6099) (GCCT)n#Simple_repeat 1 22 (0) m_b1s252i11
Rab3il1DNA 30566 GCCTTCCTGCCTGCCTGTCTGC 30587
v i
(GCCT)n#Simpl 1 GCCTGCCTGCCTGCCTGCCTGC 22
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)
+ 13 25.0 0.0 0.0 Rab3il1DNA 33119 33156 (3556) + (AGCAAGG)n Simple_repeat 1 38 (0) 74
ANNOTATION EVIDENCE:
13 25.00 0.00 0.00 Rab3il1DNA 33119 33156 3530 + (AGCAAGG)n Simple_repeat 1 38 0
13 25.00 0.00 0.00 Rab3il1DNA 33119 33156 (3530) (AGCAAGG)n#Simple_repeat 1 38 (0) m_b1s252i12
Rab3il1DNA 33119 AGAAAGCACCAAAGACCAAGGTGCTCGGAGCAAGGAGC 33156
v v v i v v vv
(AGCAAGG)n#Si 1 AGCAAGGAGCAAGGAGCAAGGAGCAAGGAGCAAGGAGC 38
Matrix = Unknown
Transitions / transversions = 0.14 (1/7)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 416 18.8 1.2 5.6 Rab3il1DNA 35127 35216 (1496) + BC1_Mm scRNA 1 86 (66) 75
ANNOTATION EVIDENCE:
416 18.83 1.16 5.56 Rab3il1DNA 35127 35216 1470 + BC1_Mm SINE/ID 1 86 66
416 18.83 1.16 5.56 Rab3il1DNA 35127 35216 (1470) BC1_Mm#SINE/ID 1 86 (66) m_b1s501i25
Rab3il1DNA 35127 GAGGTTGGGTTTATTTACCTCAGTGGTAGAG-GCTTGCCTAGCAAGTACA 35175
i --v ? v - ? ii
BC1_Mm#SINE/I 1 GGGGTTGGG--GATNTAGCTCAGTGGTAGAGCGCTTGCCTAGCANGCGCA 48
Rab3il1DNA 35176 AGGCCCTAGCTGGTTCAGTCTCCTGCTCCAGGAAAAAAAAA 35216
i --- i ii v ? ii i
BC1_Mm#SINE/I 49 AGGCCCTGG---GTTCGGTCCTCAGCNCTGGAAAAAAAAAA 86
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 15.24
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.07 (6 / 89), avg. gap size = 1.00 (6 / 6)
+ 28 0.0 0.0 0.0 Rab3il1DNA 35279 35305 (1407) + (GTTG)n Simple_repeat 1 27 (0) 76
ANNOTATION EVIDENCE:
28 0.00 0.00 0.00 Rab3il1DNA 35279 35305 1407 + (GTTG)n Simple_repeat 1 27 0
28 0.00 0.00 0.00 Rab3il1DNA 35279 35305 (1407) (GTTG)n#Simple_repeat 1 27 (0) c_b1s251i10
Rab3il1DNA 35279 GTTGGTTGGTTGGTTGGTTGGTTGGTT 35305
(GTTG)n#Simpl 1 GTTGGTTGGTTGGTTGGTTGGTTGGTT 27
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0)
+ 12 15.8 0.0 3.5 Rab3il1DNA 35879 35908 (804) + (TCAT)n Simple_repeat 1 29 (0) 77
ANNOTATION EVIDENCE:
12 15.81 0.00 3.45 Rab3il1DNA 35879 35908 804 + (TCAT)n Simple_repeat 1 29 0
12 15.81 0.00 3.45 Rab3il1DNA 35879 35908 (804) (TCAT)n#Simple_repeat 1 29 (0) m_b1s252i13
Rab3il1DNA 35879 TCATTCACTCATTCATACAATGCATGCATT 35908
i v - v v
(TCAT)n#Simpl 1 TCATTCATTCATTCATTC-ATTCATTCATT 29
Matrix = Unknown
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1)
+ 457 33.0 8.8 8.2 Rab3il1DNA 35929 36209 (503) C B4 SINE/B4 (0) 292 10 78
ANNOTATION EVIDENCE:
457 32.95 8.84 8.19 Rab3il1DNA 35929 36209 503 C B4 SINE/B4 10 292 0
457 32.95 8.84 8.19 Rab3il1DNA 35929 36209 (503) C B4#SINE/B4 (0) 292 10 m_b1s501i26
Rab3il1DNA 35929 TGTGTGAATGCACATGTGCCATGGTTCACAAGGCAGAAGACAA-CTCTTA 35977
vi ii i i -ii ----- i v i ? - vvi
C B4#SINE/B4 292 TGTGTGTGTGTGCGTGCG-TGTGG-----AGGCCAGAGGNCAACCTCGGG 249
Rab3il1DNA 35978 TATTGT--CTTGGTCCTCATCTTCCCCCTTGTTTGAGGAAGTCTCTCTCA 36025
i i -- ii v vi i iv iiv v iv vv
C B4#SINE/B4 248 TGTCGTTCCTCAGGCGCCGTCCACCTTGTTTTTTGAGACAGGGTCTCTCA 199
Rab3il1DNA 36026 TTGACCCTTGAAGC-------ATAGGTCAGGCT------------AGCTT 36056
i i -- i -------i ii ------------ ii
C B4#SINE/B4 198 CTGGCC--TGGAGCTCGCCGAGTAGGCTAGGCTGGCTGGCCAGCGAGCCC 151
Rab3il1DNA 36057 CTGGGAACTGTGCCATCTCTGCCTCCCACCTTCCCACTAGGAGCATAGGG 36106
v v i i- ii -------------v iiv
C B4#SINE/B4 150 CAGGGATCCGC-CTGTCTCTGCCTCCC-------------CAGCGCTGGG 115
Rab3il1DNA 36107 ATTACAGGCATGGACTACCGGATCAAGCTTTATAAGAT---TTCTGCAGT 36153
i ii vi i ivii vi v v vi --- vi v
C B4#SINE/B4 114 ATTACAAGCGCGCGCCACCACGCCCGGCTTTTTTACGTGGGTTCTGGGGA 65
Rab3il1DNA 36154 TCTGGACTCAGGTCATCAGACTTTCACAGGAGGTGCTTTACCCACGAAGC 36203
- i v vi v ?i v i ii v vi
C B4#SINE/B4 64 TC-GAACTCAGGTCCTCATGCTTGCANGGCAAGCACTTTACCGACTGAGC 16
Rab3il1DNA 36204 AATCTC 36209
v
C B4#SINE/B4 15 CATCTC 10
Matrix = 25p51g.matrix
Kimura (with divCpGMod) = 36.19
Transitions / transversions = 1.68 (52/31)
Gap_init rate = 0.10 (28 / 280), avg. gap size = 1.71 (48 / 28)
+ 1218 26.6 5.4 0.9 Rab3il1DNA 36228 36652 (60) C L1MB2 LINE/L1 (16) 6155 5711 79
ANNOTATION EVIDENCE:
1218 26.60 5.40 0.94 Rab3il1DNA 36228 36652 60 C L1MB2_3end LINE/L1 458 902 16
1218 26.60 5.40 0.94 Rab3il1DNA 36228 36652 (60) C L1MB2_3end#LINE/L1 (16) 902 458 m_b1s551i4
Rab3il1DNA 36228 AAAAAATA-AAAACCTAACATGTA--ATCTTACACATTTTAAAGTGTAGA 36274
? i - v v v v -- vv v v
C L1MB2_3end#LI 902 AAAANACACATAACATAAAATTTACCATCTTAACCATTTTTAAGTGTACA 853
Rab3il1DNA 36275 ATTATACTTGTGCTAGGCACATTCATACTGCCATGAAACCAAGCTACAAA 36324
i -i v v i i i i i i iii v i v v i
C L1MB2_3end#LI 852 GTT-CAGTAGTGTTAAGTATATTCACATTGTTGTGCAACCGATCTCCAGA 804
Rab3il1DNA 36325 CATTTTGCATCTTGCAAAAC--AAACACTATGCCCATTG---ACTAATTC 36369
vv v -- v i i--- vi i
C L1MB2_3end#LI 803 ACTTTTTCATCTTGCAAAACTGAAACTCTATACCCATTAAACAACAACTC 754
Rab3il1DNA 36370 CCTATTT-CTCCTGCCCCTAGACTGTGGACATCAGCATTCCACCTTCTGC 36418
i - i v i v iv vv i v i i i
C L1MB2_3end#LI 753 CCCATTTCCCCCTCCCCCCAGCCCCTGGCAACCACCATTCTACTTTCTGT 704
Rab3il1DNA 36419 CTCCGTGAATCTGATTCCTCTAGAGATTTGCTGTAAATGGAAGCA-GCA- 36466
ii i i v v ii vv i i v -i -
C L1MB2_3end#LI 703 CTCTATGAATTTGACTACTCTAGATACCTCATATAAGTGGAATCATACAG 654
Rab3il1DNA 36467 TACTCATCTTCTAGTGACTGGCTTGTTTCACTTAATGCAATG---TCAAT 36513
i ii i v i iiii --- v
C L1MB2_3end#LI 653 TATTTGTCTTTTTGTGACTGGCTTATTTCACTTAGCATAATGTCCTCAAG 604
Rab3il1DNA 36514 ATCCATCCATGTTGTA--AGATGACAGGATTTCC-----TTTTAAGACTT 36556
i i -- vi ? i ----- i v
C L1MB2_3end#LI 603 GTTCATCCATGTTGTAGCATGTGNCAGAATTTCCTTCCTTTTTAAGGCTG 554
Rab3il1DNA 36557 GGTAATATTCTGATGTATGTGTAACAGCCCACTGTGTTTATCCATTAAT- 36605
ii iiv i - i v v i v v -
C L1MB2_3end#LI 553 AATAATATTCCATTGTATGTAT-ATACCACATTTTGTTTATCCATTCATC 505
Rab3il1DNA 36606 --TGGAGACACACACGGGTTACTGGTACCTGTTAATGTATATGCAAATA 36652
-- v viv vi i vvi v iii- - ii
C L1MB2_3end#LI 504 CGTCGATGGACACTTGGGTTGCTTCCACCTCTTGGC-TAT-TGTGAATA 458
Matrix = 20p51g.matrix
Kimura (with divCpGMod) = 32.71
Transitions / transversions = 1.44 (65/45)
Gap_init rate = 0.04 (16 / 424), avg. gap size = 1.75 (28 / 16)