+ 68 25.4 3.7 0.0 galGal6_dna 1088 1221 (48269) + CR1-X1_fAlb LINE/CR1 923 1061 (2) 1
ANNOTATION EVIDENCE:
68 25.37 3.73 0.00 galGal6_dna 1088 1221 48221 + CR1-X1_fAlb LINE/CR1 923 1061 2
68 25.37 3.73 0.00 galGal6_dna 1088 1221 (48221) CR1-X1_fAlb#LINE/CR1 923 1061 (2) m_b1s001i0
galGal6_dna 1088 CTGA---AGTTCAAGAAGCATCTGGACAGTGCTTTCAGACATATAATCTG 1134
--- i i vi i i i i i i vii v
CR1-X1_fAlb#L 923 CTGACAGAGCTCAAGGAGGGTTTGGACAATGCTCTCGGGCACAGGGTGTG 972
galGal6_dna 1135 ATTTTTG--GGTGGTCCTGTCTAGAGTCAAGAGTTGGACTTGATGATCCT 1182
i i -- i v vvi i i i i i
CR1-X1_fAlb#L 973 ACTCTTGGGGATGGTGCTGGGCAGGGCCAGGAGCTGGACTCGATGATCCT 1022
galGal6_dna 1183 TATGGGTCCCTTCTAACTTGGGATATTCTATGATTCTAT 1221
i i ii v v iv
CR1-X1_fAlb#L 1023 TGTGGGTCCCTTCCAACTCAGCAGATTCTATGATTCTGA 1061
Matrix = HMM
Kimura (with divCpGMod) = 30.28
Transitions / transversions = 2.78 (25/9)
Gap_init rate = 0.02 (2 / 133), avg. gap size = 2.50 (5 / 2)
+ 12 11.3 6.9 0.0 galGal6_dna 1285 1313 (48177) + (AAC)n Simple_repeat 1 31 (0) 2
ANNOTATION EVIDENCE:
12 11.26 6.90 0.00 galGal6_dna 1285 1313 48129 + (AAC)n Simple_repeat 1 31 0
12 11.26 6.90 0.00 galGal6_dna 1285 1313 (48129) (AAC)n#Simple_repeat 1 31 (0) m_b1s252i0
galGal6_dna 1285 AAAAACAACAACAA-ACCCACAACAA-AACA 1313
v - v v -
(AAC)n#Simple 1 AACAACAACAACAACAACAACAACAACAACA 31
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.07 (2 / 28), avg. gap size = 1.00 (2 / 2)
+ 46 30.4 3.0 8.1 galGal6_dna 1692 1859 (47631) C CR1-X1_fAlb LINE/CR1 (9) 1054 895 3
ANNOTATION EVIDENCE:
46 30.45 2.98 8.12 galGal6_dna 1692 1859 47583 C CR1-X1_fAlb LINE/CR1 895 1054 9
46 30.45 2.98 8.12 galGal6_dna 1692 1859 (47583) C CR1-X1_fAlb#LINE/CR1 (9) 1054 895 m_b1s001i1
galGal6_dna 1692 CATAGAATAACCTGACTTGGAAGGGACCCACAAGGACCACTGAGAACTAC 1741
vvv v i ii vv vi
C CR1-X1_fAlb#L 1054 CATAGAATCTGCTGAGTTGGAAGGGACCCACAAGGATCATCGAGTCCAGC 1005
galGal6_dna 1742 TCCTAGCTTCACACAAGAC--TACCTAAAAATTAAACCATATGACTTAGA 1789
i iiii v iv -- v i i i i v v i v iv
C CR1-X1_fAlb#L 1004 TCCTGGCCCTGCCCAGCACCATCCCCAAGAGTCACACCCTGTGCCCGAGA 955
galGal6_dna 1790 GCATTTTCCAAACATTCAGCCTAGTTCCGTGACAAG---GGAGCAATGAA 1836
v vi --- v vv iv v iv--- v -------
C CR1-X1_fAlb#L 954 GCATTGTCCAAACCCTC---CTTGAGCTCTGTCAGCCTTGGTG------- 915
galGal6_dna 1837 ACCCAGAGACCCATGCCCTGGGG 1859
--- v v vv v
C CR1-X1_fAlb#L 914 ---CTGTGACCACTTCCCTGGGG 895
Matrix = HMM
Kimura (with divCpGMod) = 36.96
Transitions / transversions = 0.68 (19/28)
Gap_init rate = 0.09 (15 / 167), avg. gap size = 1.20 (18 / 15)
+ 15 27.3 5.3 1.3 galGal6_dna 1919 1994 (47496) + (TAATA)n Simple_repeat 1 79 (0) 4
ANNOTATION EVIDENCE:
15 27.34 5.26 1.27 galGal6_dna 1919 1994 47448 + (TAATA)n Simple_repeat 1 79 0
15 27.34 5.26 1.27 galGal6_dna 1919 1994 (47448) (TAATA)n#Simple_repeat 1 79 (0) m_b1s252i1
galGal6_dna 1919 TAATTTAGTA-AATAT-A-ATAGCAGAATATGAGATAATACAATATGATT 1965
v i - - - ii v i v i - v
(TAATA)n#Simp 1 TAATATAATATAATATAATATAATATAATATAATATAATATAATAT-AAT 49
galGal6_dna 1966 AGAATTGAAGCTAATA-AATAAAACAAAAT 1994
v vv vv - v i v
(TAATA)n#Simp 50 ATAATATAATATAATATAATATAATATAAT 79
Matrix = Unknown
Transitions / transversions = 0.55 (6/11)
Gap_init rate = 0.07 (5 / 75), avg. gap size = 1.00 (5 / 5)
+ 47 40.1 2.3 0.8 galGal6_dna 2693 2956 (46534) C ERVL-B4-int LTR/ERVL (1055) 4659 4392 5
ANNOTATION EVIDENCE:
47 40.07 2.27 0.75 galGal6_dna 2693 2956 46486 C ERVL-B4 LTR/ERVL 4392 4659 1055
47 40.07 2.27 0.75 galGal6_dna 2693 2956 (46486) C ERVL-B4#LTR/ERVL (1055) 4659 4392 m_b1s001i2
galGal6_dna 2693 GCTTCTCCCAGTGCTTAAATGTTCTGCCACCCATTA---CTTTCAACATA 2739
v vi iv vv v vi i viv---vi vi vv
C ERVL-B4#LTR/E 4659 CCTTGCCCCAGCCCTGCAAGGTATTGCCACCTAGCTGGCACTGTAACTGA 4610
galGal6_dna 2740 GTATTTAACAACCCATTGTATCATTCAATTTTACCAGAAGCTGGTGCATG 2789
v i v iv vi ii v ivvi vv vvv v
C ERVL-B4#LTR/E 4609 GTCTTCAAAAGGCCATTCCACTATTCTATCAAGCCAGCTGCTTCAGGATG 4560
galGal6_dna 2790 ATAGGGAATATGATAAATCCACTCAATGCCATGATCTTTGGCCCAAGTAT 2839
i i i i iv v v v v v v vvvvi
C ERVL-B4#LTR/E 4559 GTGGGGAACATGGTAAGACCAGTGAATTCCATGAGCATGGGCCCATTGCC 4510
galGal6_dna 2840 TTACAAGAGAATTTTTTAAATGAGTCCCATTATCTGATTCAATCCTTTCT 2889
vi vvvvvvvvi v v i i v v v vv v v v
C ERVL-B4#LTR/E 4509 ACACTTCTTTTGCTGTGAAGTGAGTTCCTTGATCAGAAGCAATGCTGTGT 4460
galGal6_dna 2890 GGAGTGCCATGTCACC--ATAGGACTTGTTTCTCAAGACCA-ATATGGTG 2936
i i viivi-- i i v-- iivi v -iv i
C ERVL-B4#LTR/E 4459 GGAATACCATGATGGTGGATAAGGCA--TTCTGTAAGTCCACGGATGGTA 4412
galGal6_dna 2937 TTTTGGGTGGTAGCATGGCT 2956
v v ii v v v
C ERVL-B4#LTR/E 4411 GTTTTGGCAGAAGCATTGCA 4392
Matrix = HMM
Kimura (with divCpGMod) = 56.62
Transitions / transversions = 0.57 (38/67)
Gap_init rate = 0.02 (5 / 263), avg. gap size = 1.60 (8 / 5)
+ 33 40.4 2.2 4.7 galGal6_dna 3117 3485 (46005) C TguERVL2_I-b_fAlb LTR/ERVL (692) 1380 1021 6
ANNOTATION EVIDENCE:
33 40.39 2.17 4.72 galGal6_dna 3117 3485 45957 C TguERVL2_I-b_fAlb LTR/ERVL 1021 1380 692
33 40.39 2.17 4.72 galGal6_dna 3117 3485 (45957) C TguERVL2_I-b_fAlb#LTR/ERVL (692) 1380 1021 m_b1s001i3
galGal6_dna 3117 AGTTTCCACCATATATCAGGTGTACTCCTCACTCTCTCAGGATCATGGTC 3166
v v i v vvvv i v v ii v i v
C TguERVL2_I-b_ 1380 AGATTCCACAACATCTGCCCTGTGCACCTGACCTTGTCAGGGTCATTGTC 1331
galGal6_dna 3167 TTGGTGTGGATTGCTAGGAACAAAATTAGGGTCATACAGAATTTCCACGT 3216
v v vv iiv vvv - i i vvvvv v ----- v --
C TguERVL2_I-b_ 1330 ATGCTGTCCACCCCTCCCAA-AGAGTACCTCTAATAC-----TGCCAC-- 1289
galGal6_dna 3217 CTGTTTCTTTCAAATACTGGATACCTTTTTCAACCGTATTCCACT---TT 3263
---- i iv i v ii vv v vi---
C TguERVL2_I-b_ 1288 ----TTCTCTCAGCTGCTGGATCCCTTCCTCAAGGGTCTTCCAGCGCATT 1243
galGal6_dna 3264 CTCATCTCAGG---CTTCAGATCGTCTTTGAAGGGATGCCTTTCCCTCAC 3310
vvvv viv --- v vviiv i vi iv vi i i
C TguERVL2_I-b_ 1242 CTATGGTGGTGCTCCTGCATTCTCTCTCTGTGGACAAACCTCTCTCTCAC 1193
galGal6_dna 3311 GGCTGCTAACACTCGTTCCCAGAGAGTGGCGGCTCCATCCAAACATCTAC 3360
iviiii v vii i i viiv vv vvv v-- vii
C TguERVL2_I-b_ 1192 ACTCATTAAAAGCTGCTCCCAGAGGGAAAGGGGGCCTGGCT--CCCTTAC 1145
galGal6_dna 3361 TAATCCCTCTGTCAGAAGCTGAGTCTCTGGCAATGCCTCCTAGTTGGCAG 3410
v v vvvi -v v iiv iv v vv i iv vv vv
C TguERVL2_I-b_ 1144 AAATACCTGATCCA-CACCTGAGTCCTGGGTCAAGGGTCCCAAATTCCTT 1096
galGal6_dna 3411 GCTTCGTTACCATCTAGAGAAATGCTACTGGCCCCAT--TGTACCAACAG 3458
i iv i vviv -- vv vi --v v ivvv
C TguERVL2_I-b_ 1095 GCCTCAGTACCATCCAGTTGTA--CACCTGTTCCCATAAGGTCCCAGACC 1048
galGal6_dna 3459 CGAAGCAACCAAGTGACAATAGTTTCA 3485
i vii v ii
C TguERVL2_I-b_ 1047 CGAAGTAACCAAGTTGTAAAAGCCTCA 1021
Matrix = HMM
Kimura (with divCpGMod) = 57.44
Transitions / transversions = 0.61 (54/88)
Gap_init rate = 0.05 (20 / 368), avg. gap size = 1.25 (25 / 20)
+ 29 14.6 0.0 0.0 galGal6_dna 5826 5878 (43612) + (CTCT)n Simple_repeat 1 53 (0) 7
ANNOTATION EVIDENCE:
29 14.55 0.00 0.00 galGal6_dna 5826 5878 43564 + (CTCT)n Simple_repeat 1 53 0
29 14.55 0.00 0.00 galGal6_dna 5826 5878 (43564) (CTCT)n#Simple_repeat 1 53 (0) m_b1s252i2
galGal6_dna 5826 CTCTCTCACTCTCTCTCTCTCTCCCTCTCTATCGCTCTTTCGCTCTCTCC 5875
v i v v i v i
(CTCT)n#Simpl 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50
galGal6_dna 5876 CTC 5878
(CTCT)n#Simpl 51 CTC 53
Matrix = Unknown
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 34 39.6 6.1 2.1 galGal6_dna 7490 7813 (41677) C HERVL40-int LTR/ERVL (1817) 4230 3829 8
ANNOTATION EVIDENCE:
34 34.72 9.03 0.00 galGal6_dna 7490 7633 41809 C HERVL40 LTR/ERVL 3829 3985 1545
34 34.72 9.03 0.00 galGal6_dna 7490 7633 (41809) C HERVL40#LTR/ERVL (1545) 3985 3829 m_b1s001i4
galGal6_dna 7490 AGAAAT-------------TTCTTAAGGAGGCCATTGGATCATTCTACAA 7526
------------- i i vv vi i v
C HERVL40#LTR/E 3985 AGAAATCTTTTTGAGTTAATTTTTGAGGAGGCCATTCCAATACTCAACAA 3936
galGal6_dna 7527 TGCCATTAGCTTGGGGGTAGTAGGGAGTGTGAAAGATCCAACAAATGCCT 7576
i vvv i v i i ii i i v i
C HERVL40#LTR/E 3935 TACCAGATGCCTGTGGATGGTAGGGAGCATGGAAGGTCCATCAAATACCT 3886
galGal6_dna 7577 TCCTGTCTAACCCATTCTTGTACTACCCCTAAGGTGAAATGGGAGCCATT 7626
vvivvii i v viivi iii iv i i v v vi
C HERVL40#LTR/E 3885 TGACTATCAGCCCATTGTTGAGTGGCTTTTGTGATAAAAGGTGCACCATT 3836
galGal6_dna 7627 GTCTCAT 7633
vv i
C HERVL40#LTR/E 3835 GTCAGAC 3829
Matrix = HMM
Kimura (with divCpGMod) = 48.12
Transitions / transversions = 1.27 (28/22)
Gap_init rate = 0.01 (1 / 143), avg. gap size = 13.00 (13 / 1)
29 43.46 3.77 3.77 galGal6_dna 7496 7813 41629 C HERVL18 LTR/ERVL 3913 4230 1817
29 43.46 3.77 3.77 galGal6_dna 7496 7813 (41629) C HERVL18#LTR/ERVL (1817) 4230 3913 m_b1s001i5
galGal6_dna 7496 TTCTTAAGGAGGCCATTGGATCATTCTACAATGCCATTAGCTTGGGGGTA 7545
v i v iv ii v iv i vi v v
C HERVL18#LTR/E 4230 TTCTTCAAGAGCCCATTATATCGCTCAATCATACCAGCAGCTTGTGGGTT 4181
galGal6_dna 7546 GTAGGGAGTGTGAAAGATCCAACAAATGCCTTCCTGTCTAACCCATTCTT 7595
i v viii i vvi vivv i ivi ivvi i v
C HERVL18#LTR/E 4180 ATATGGCACATGGAATCCCCACTTTATGTCCATCTGTTGTGCCCACTGTT 4131
galGal6_dna 7596 GTACTACCCCTAAGGTGAAATGGGAGCCATTGTCTCATTGGATGAAAT-T 7644
ivv iv vvi v vv vi i v vi vi ivvv-v
C HERVL18#LTR/E 4130 GTACCTGCTGTCCAGTGAAATGTGTTCCCCTATCACTCTCAATGGCCAGA 4081
galGal6_dna 7645 GGGTTTTGGAAGAATGCTAAACCATTTCTTTAGAGCTTTTACAGTGTTTT 7694
ivviviv -v v vi v iv v vi vi i iivv ii v--
C HERVL18#LTR/E 4080 GGGCGACCATA-CAGGGCACATAAGTGTTGCAGGGCCCGGATGGTGTG-- 4034
galGal6_dna 7695 CCCCTGTTGCTC-----------GAGGGAAGGATTCAGCTTGTAGTAGGC 7733
--- v -----------i v ------ vvii ii
C HERVL18#LTR/E 4033 ---CTGTTGGTCGGCCACCCTGCAAGGGTAGG------CGAACAACAGGC 3993
galGal6_dna 7734 CAGAGACTACTTCCACCCCTCCTAACACATACTATTTGCTTTCAGATTTA 7783
v v i i iv vv vii i i vvv vv ii vv i v
C HERVL18#LTR/E 3992 CTGTGGCCATGTCCACAGCTGTCAGCACATGCGTATACCCCTGCGACTTT 3943
galGal6_dna 7784 TGGAAGGGGCCAATGAAATCAATTTGCCAT 7813
v v iv v v i v i i
C HERVL18#LTR/E 3942 GGCAGCGGCCCAATGTAGTCTACTTGCCAC 3913
Matrix = HMM
Kimura (with divCpGMod) = 63.58
Transitions / transversions = 0.80 (59/74)
Gap_init rate = 0.04 (14 / 317), avg. gap size = 1.71 (24 / 14)
+ 13 25.6 5.4 0.0 galGal6_dna 8086 8141 (41349) + (TAATA)n Simple_repeat 1 59 (0) 9
ANNOTATION EVIDENCE:
13 25.64 5.36 0.00 galGal6_dna 8086 8141 41301 + (TAATA)n Simple_repeat 1 59 0
13 25.64 5.36 0.00 galGal6_dna 8086 8141 (41301) (TAATA)n#Simple_repeat 1 59 (0) m_b1s252i3
galGal6_dna 8086 TAATTTACTA-AATACAATAT--TGGAATGCAAGATAACACACTATAATA 8132
v v - i -- iv ii v i i v
(TAATA)n#Simp 1 TAATATAATATAATATAATATAATATAATATAATATAATATAATATAATA 50
galGal6_dna 8133 CAATATAAT 8141
i
(TAATA)n#Simp 51 TAATATAAT 59
Matrix = Unknown
Transitions / transversions = 1.40 (7/5)
Gap_init rate = 0.04 (2 / 55), avg. gap size = 1.50 (3 / 2)
+ 86 43.1 6.3 8.5 galGal6_dna 8840 9882 (39608) C ERVL-int LTR/ERVL (1058) 4699 3678 10
ANNOTATION EVIDENCE:
86 43.08 6.33 8.51 galGal6_dna 8840 9882 39560 C ERVL LTR/ERVL 3678 4699 1058
86 43.08 6.33 8.51 galGal6_dna 8840 9882 (39560) C ERVL#LTR/ERVL (1058) 4699 3678 m_b1s001i6
galGal6_dna 8840 TCCCAATTCTTAAATGTTCTACCACCCA-CTGC--TTTCAACATGGTCTT 8886
i iii vv v vi ii i - v--i vi vvi
C ERVL#LTR/ERVL 4699 CCCCAGCCCTGCAAGGTATTGTCACCTAGCTGGCACTGTAACTGAGTCTT 4650
galGal6_dna 8887 TAACAATCCATTGTATCATTTGATTATACCAGAAGCTGGTGCATGATAGG 8936
i v iv vi i iv i vi vv vvv v i i
C ERVL#LTR/ERVL 4649 CAAAAGGCCATTCCACCATTCTATCAAGCCAGCTGCTTCAGGATGGTGGG 4600
galGal6_dna 8937 GGATATGATAAATCCATTCAATGCCATGATCTCTGGCCGAA----GTATT 8982
i i i iv v v v v vivi v v----ii i
C ERVL#LTR/ERVL 4599 GAACATGGTAAGACCAGTGAATTCCATGAGCATGAGCCCATTGCCACACT 4550
galGal6_dna 8983 TCCAAGGGAATATTTCAAATGAGTCCCATTATCTGATTCAATTATTTCTG 9032
ivvv ----v v v i i v v v vv vv v v
C ERVL#LTR/ERVL 4549 TCTTTTG----CTGTGAAGTGAGTTCCTTGATCAGAAGCAATGCTGTGTG 4504
galGal6_dna 9033 GGGTGCCATGTCACCATAGAACTTGTTTCTTGAGACCTAAAATGGTGTTT 9082
ii i viiviiv v vvii iiv i v vvii iv
C ERVL#LTR/ERVL 4503 GAATACCATGATGGTGGATAAGGCATTCTGTAAGTCCATGGATGGTAGTT 4454
galGal6_dna 9083 TGGGCGGTAGCATGGGGTACTGCGATTTTTTCAAGCC-------ACCCAG 9125
v i v v vi i v v ------- i v------- i
C ERVL#LTR/ERVL 4453 TTGGCAGAAGCATTGCATGCAGGGA-------AGGCAAATCCATATCCAG 4411
galGal6_dna 9126 TG-----GTTGCTTCCCCCATGGTAAGCAGATAACGCTTACCGTTGCGAG 9170
v ----- ivv -----i v v v i vv v v iv
C ERVL#LTR/ERVL 4410 AGTAAGTGTCTATTCC-----AGTAAGGACAAAACACTGCCCCTTCCATG 4366
galGal6_dna 9171 ATCTTGGCAAGGTGATATAATCAACCTGCCAC------GCC--------T 9206
vvvi iiivvii i ------ i--------v
C ERVL#LTR/ERVL 4365 ATGGAAGTGGTCCAATGTAATCAACCTGCCACCAGGTAGCTGGCTGATCA 4316
galGal6_dna 9207 CCCCATATTTATACTTTTGCCATCGCCCTTCCTCCCAGAGAGGTTTCATC 9256
v------------------------------i iv vi v
C ERVL#LTR/ERVL 4315 CCCCAG------------------------------GGAATGGTGCCATA 4296
galGal6_dna 9257 -------CTCTTGGCTTGT--TTAATTATGGCACATGTTTCACAGTCATG 9297
------- vvv i v --i iv vv v -- vvi v vv
C ERVL#LTR/ERVL 4295 TCGGGGGCTCAGTGTTGGTCTCTGCTGCTGGCAGAT--TGGGCACTCAGC 4248
galGal6_dna 9298 AATAAACTGTGCAATAGCATCCATAGTTAAGTCCACCCCTCGGTCTCTAG 9347
i iivvvvv v viv v v i v ivvvv vi vi v viiv
C ERVL#LTR/ERVL 4247 AGTGGCAGTAGCCAGGTCAGCCTTGGTGAGTGGAAGTCCATGTTGCTGAG 4198
galGal6_dna 9348 CCCATTTATATGTTGCATCTCTTCCTTGATGGCCCGAGGCCTCATGGGCC 9397
vi vvi v i v viv vvvvvvi i
C ERVL#LTR/ERVL 4197 CCCATGCATAACCTCCATCCCTGCCACCATGGCCACTTTGTTCATGAGCC 4148
galGal6_dna 9398 AAT--------G-------AGCTAGAAATAATTCACCCTTGTTCTGACAG 9432
v -------- -------i i ii v i-------------------
C ERVL#LTR/ERVL 4147 CATTGGGCAATGACAGGGTGGCTGGGGAAAG------------------- 4117
galGal6_dna 9433 TCCAAGTCTATTTGAGTCACCTCAGTTCTTGCAGATTGATCTACCTGATG 9482
---- v ivi - vv v vvivv iviviiv i i v
C ERVL#LTR/ERVL 4116 ----AGGCTGACTG-GTATCCACAGAATAGGTCATCCTATCCACTTGATT 4072
galGal6_dna 9483 GTTATTTTTCTGATATTCAGCAGAACAACCCTTGGGCACATGAACATCTA 9532
i vvv i vv v v v - iv v i ----- i ii
C ERVL#LTR/ERVL 4071 ATTAAAATCCTCCTCTGCTG-AGGTCACCCTTTGG-----TGAGCATTCA 4028
galGal6_dna 9533 CATGGCGCACCTTTACAACCATATTCTTTATTCGGGCAGCAATGTCTTTC 9582
vi vvv ivvi i i iii ivv vi v v
C ERVL#LTR/ERVL 4027 CATGGGACACAAATATCTTCACATTTTTTGCCCATTCAGAGAGGTCTATC 3978
galGal6_dna 9583 CACAGTTCAGCAGCCCAATCAGGTTTACACCTTCGCTGCCAGTTATTTTG 9632
vvi vvivv vivvv iivv ivvvi v i i v v
C ERVL#LTR/ERVL 3977 CACATACCTCTTCCCCAAATTTCTTTGTCACCAATTTTCCAATCATGTTC 3928
galGal6_dna 9633 CTCCCACTGCTGTAACCATCTCCATAAGGCATTTGCCACCATCCATGAGT 9682
i vvv iv i ivvvi iv v i vii i
C ERVL#LTR/ERVL 3927 CTTCCAAGTCCCTGACCATCCAGCCAAACCATTGGCTACAGCCCATGAAT 3878
galGal6_dna 9683 CAGTATAAAGATAAAGCAATGGCCACCTCTCCCGTTCAGCAACATCTAAG 9732
v iviiv vvvv ii iviiv vi vi vi
C ERVL#LTR/ERVL 3877 CAGTATATAATCGCATATCTGGCCATTTCTCCTTCCAAGCAAAGTGCACA 3828
galGal6_dna 9733 GCCAGCTGGACAGCATTTACCTCTGCAAATTGGCTTGATTCTCCTTTG-- 9780
i v v v vivv vi vv i vvv ii ii--
C ERVL#LTR/ERVL 3827 ACCAGGTGCACTGCTCAAAGTTCTGCCCACTGGGAGGATTTCCCTTCACC 3778
galGal6_dna 9781 -----CCTTCAGTGGCCTCTGCAACTTCTC-ATGTGGGGCTCCAC-ACAG 9823
----- v iiv--------- i -iviv vi v-i v
C ERVL#LTR/ERVL 3777 ACTGTCCTTCAGGGATG---------TCCCAGAAAGGGGCTGTAGTGCTG 3737
galGal6_dna 9824 CAGCTTTCCATCTGTGATACTTCCCCACAATACGACACGATCCATCTGTG 9873
v ii v ivvvv v ii vvv ivvvv v i
C ERVL#LTR/ERVL 3736 CAGCTGTCCACTTTTGGGTGGTGCCTGCATATCATGCAGAACCATCTGTA 3687
galGal6_dna 9874 AACAGGGCA 9882
vi v
C ERVL#LTR/ERVL 3686 AACCAGGCC 3678
Matrix = HMM
Kimura (with divCpGMod) = 64.09
Transitions / transversions = 0.71 (171/240)
Gap_init rate = 0.10 (102 / 1042), avg. gap size = 1.50 (153 / 102)
+ 79 42.8 6.7 4.9 galGal6_dna 9888 10633 (38857) C ERVL-int LTR/ERVL (2711) 3046 2288 10
ANNOTATION EVIDENCE:
79 42.84 6.70 4.87 galGal6_dna 9888 10633 38809 C ERVL LTR/ERVL 2288 3046 2711
79 42.84 6.70 4.87 galGal6_dna 9888 10633 (38809) C ERVL#LTR/ERVL (2711) 3046 2288 m_b1s001i7
galGal6_dna 9888 TTTGGAACATGCATTCTCCAAAAGCCCACTACACCCAGAAAAGATTGTGT 9937
vv i ivvi v v vv vi vv iiv i
C ERVL#LTR/ERVL 3046 TGAGGAATATGTTGCCTCCAAAATCCAAAGAGGCCCACTAGGCATTGTGC 2997
galGal6_dna 9938 CTCTTA-TTAATGGGC--AGAGGCAT--GGCAGTGATTTTGTTGATCACA 9982
v- ii v vv-- i vv--v iii i -i ivv v
C ERVL#LTR/ERVL 2996 CTCTTTCTTGGTTGTAGGAGGGGCCAGATGCAACAACTT-ATCCTTCACC 2948
galGal6_dna 9983 TCCATTGAGATGGAATGACGTCAATCTTGCCACTTTATACCTAAGAACTG 10032
ivivv i ivvvii i vvvi vii vv iv ii i v
C ERVL#LTR/ERVL 2947 TTAGAAGGGATATCTCAACATGCCCCACACCACTGGACCCCTAGAAATTT 2898
galGal6_dna 10033 AATTACT-GGGCAGGTCCTTTCACTTTGCTTCGCTTAATAGCAAAACCA- 10080
v i ivv-vi v i i vv i iv v v v vv vv v v-
C ERVL#LTR/ERVL 2897 CACTGAGGTAGAAGGCCCCTGAATTTTAGTTGGATTTATTTCCCACCCTC 2848
galGal6_dna 10081 --GCATGCAGA-----------AGGATCTGGAGTATTTGCTG-TCCTTTC 10116
--i i i -----------viii i v i- i v
C ERVL#LTR/ERVL 2847 TGACATACAAATGTCTTACCAATAAGTCTAGAGTAGTTGCTACTTCTTGC 2798
galGal6_dna 10117 TCAAAAAACTTCCTTGCTGCGTTGTCCCAT-ACAATAATGTCATCAATGT 10165
vv i---------------- v - vv
C ERVL#LTR/ERVL 2797 TCACTAG----------------GTCCAATCAGCATAATGTCATCAATGT 2764
galGal6_dna 10166 ACTGTA--A-------GTGCTCAGGAGCACTGCCCTGTTCCAGTGCAGCT 10206
v v -- -------i vi vv ivivvivvv v v vv vviv
C ERVL#LTR/ERVL 2763 AATGGACCAGTGTGATATCTTGTGGAAGGGAAAGGTGATCAAGATCCCTG 2714
galGal6_dna 10207 TGGACCAACCCATGGCAAACGGTTGGGCTATGTTTTCACCCCTGGGGCAA 10256
iii i vii i v vi i ivvi vvv vi i i i
C ERVL#LTR/ERVL 2713 CAAACTAAATTATGACATAGAGCTGGAGAGTTGATATACCCCTGAGGTAG 2664
galGal6_dna 10257 ACAATTCTAGGTATACTGAATGCCCCTCCAGGTGAAAACATACTGCAGCC 10306
ivv v vv i vvv iiv v i v vv i
C ERVL#LTR/ERVL 2663 GACAGTGAAGGTATATTGCTGGCCTTGCCAGCTGAAAGCAAACTGCTTCT 2614
galGal6_dna 10307 TACATTCTGTGGTCAAAGGAATGGAGAAAACGGTGTTAGCAATGTCTGTG 10356
viiivv iv ivvv v i v ii v v vi vi i
C ERVL#LTR/ERVL 2613 GGTGGGCCTTATGGACAGGGATGGAGAAAAAGGCATTTGCCAGATCAATA 2564
galGal6_dna 10357 GTGGCATACCATTTGGC-----TTCTTTTGA----CTCCAGTTCATATTG 10397
iv vv iv -----v v v i ---- v ----i v
C ERVL#LTR/ERVL 2563 GCTGCATACCAGGTACCAGGGGATGTGTTAATTTGCTCAAG----CAATG 2518
galGal6_dna 10398 GAGTTCTAACATCTGGTACAGCAGCACTCAGTGCGGGTGTGACTTCATTC 10447
i ---viv vviv v vi viiiv vi v
C ERVL#LTR/ERVL 2517 AA---ACCACATCTGGTACAGCAGCTGCAATTGGAGTCACCACTTGGTTA 2471
galGal6_dna 10448 AGGCCACGGTAGTCTACTGTCAGCCTCCATTCCCCACTGGCTTTACGCAC 10497
vii i i i i vi vvvi iiv ii vi
C ERVL#LTR/ERVL 2470 AGCTTATGATAATCCACTGTCATTCTCCAAGATCCATCTGTCTTCTGCAC 2421
galGal6_dna 10498 TGGCCATATGGAGCTGTTAAAAGGCGAGTAAGTTTTGCTGATCACTCCTT 10547
v v i iivv v v vvvi vvviv v i i v
C ERVL#LTR/ERVL 2420 AGGCCAAATAGGAGAGTTAAATGGGGATGTGGTGGGAATCACCACCCCTG 2371
galGal6_dna 10548 GACTCTCT-AG---TTGACGA----ATCAACTTCTGAATGGGGAGCAAGG 10589
v iii ii- --- i i---- ii ii v ------------
C ERVL#LTR/ERVL 2370 CATCTTTCAAGTCCTTGATGGTGGCACTAATCTCTGCA------------ 2333
galGal6_dna 10590 AATCCCT--GTTGGTGCGGTACTGCTGTCTGTGCACCGTTTTTGTA 10633
- i --ivv i ii i v ivi vi ii iv
C ERVL#LTR/ERVL 2332 -ATTCCTCCAGGGATGTAGTATTGCTTTTGATTTACTATTTTCCTA 2288
Matrix = HMM
Kimura (with divCpGMod) = 64.73
Transitions / transversions = 0.85 (140/164)
Gap_init rate = 0.07 (54 / 745), avg. gap size = 1.61 (87 / 54)
+ 17 0.0 0.0 0.0 galGal6_dna 10867 10885 (38605) + (C)n Simple_repeat 1 19 (0) 11
ANNOTATION EVIDENCE:
17 0.00 0.00 0.00 galGal6_dna 10867 10885 38557 + (C)n Simple_repeat 1 19 0
17 0.00 0.00 0.00 galGal6_dna 10867 10885 (38557) (C)n#Simple_repeat 1 19 (0) m_b1s252i4
galGal6_dna 10867 CCCCCCCCCCCCCCCCCCC 10885
(C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCC 19
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0)
+ 31 11.5 0.0 0.0 galGal6_dna 11028 11074 (38416) + (GA)n Simple_repeat 1 47 (0) 12
ANNOTATION EVIDENCE:
31 11.48 0.00 0.00 galGal6_dna 11028 11074 38368 + (GA)n Simple_repeat 1 47 0
31 11.48 0.00 0.00 galGal6_dna 11028 11074 (38368) (GA)n#Simple_repeat 1 47 (0) m_b1s252i5
galGal6_dna 11028 GAGAGAGAGAGAAAGAGCGATAGAGAGAGAGAGAGAGAATGAGAGAG 11074
i v v iv
(GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 47
Matrix = Unknown
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 78 35.2 15.4 2.3 galGal6_dna 11449 11838 (37652) C ERVL-int LTR/ERVL (4) 2068 1629 10
ANNOTATION EVIDENCE:
78 35.16 15.38 2.27 galGal6_dna 11449 11838 37604 C TguERVL2_I-b_fAlb LTR/ERVL 1629 2068 4
78 35.16 15.38 2.27 galGal6_dna 11449 11838 (37604) C TguERVL2_I-b_fAlb#LTR/ERVL (4) 2068 1629 m_b1s001i8
galGal6_dna 11449 GACTTGAGGGCATTAGAGTGCACTGTGAACCAGTGTCCTCCAGTGCCTTA 11498
vii v i i i vv i iii ii
C TguERVL2_I-b_ 2068 GTTCTGATGGTATTAGGGTGCACTGTGAACCAGTATCAACTAACACTCTA 2019
galGal6_dna 11499 TATTTCTGTTGTTCTGATGTGTCCGGCCATCGAATCCACACAGTACAATA 11548
i v i i v i i vi v
C TguERVL2_I-b_ 2018 TGTTTCTGTGGCTCTGATGTGCCAGGCCATTGGATCCACACTATCCAATA 1969
galGal6_dna 11549 CAATCTATTATCCCTTTCCATCCCCCTGGCAGGGGGCAGGGCCCCTCTAT 11598
v vi i v- v v i vi i v
C TguERVL2_I-b_ 1968 GACCCTGTTATCCCA-TGCCTCTCCCTGGCTAGAGGCAGGGCCCCTCTAG 1920
galGal6_dna 11599 TTGTTAC--CTCTGTCATTCTTA----TGGCTATTGCCATGTCCTGCA-G 11641
iiv vii--i v v v i i---- ivv v ivvivv v -
C TguERVL2_I-b_ 1919 CCCTGGTTATTATTTCCTTCCTGGGCATACATAGTAGAGGTTCCTTCAAG 1870
galGal6_dna 11642 --CAACTG---GAGCAATAACCTTTTTGGAGAAG--TTCACCTTGGT--- 11681
--v v --- vi vivv i i v iv v-- v ---
C TguERVL2_I-b_ 1869 TGGATCTGACAGATTATCTTCCCTTCTGTAATATCCTGCACCTTGGTTAT 1820
galGal6_dna 11682 ------------------------------------------GATTA-AT 11688
------------------------------------------v v i-v
C TguERVL2_I-b_ 1819 GGGAGGTCGAGGCTACCTTCACTTTAGTAGAACTCCCTTGGTTAGTGCTT 1770
galGal6_dna 11689 CTGTCTTGTAATTCTTTTACCTGTGCTTGAAGTGCAGGAGTGGGTTTTTT 11738
iv iivv i vvivi i vvv vi i iii
C TguERVL2_I-b_ 1769 CCCTCCCTGAGTTGACGCACCCGTGCTGCCAGGACAGAAGTGGGTTTCCC 1720
galGal6_dna 11739 ATTCCACTTCTTCATATCTTCTTCATGGTCACATAGGTAACGCCAGAAGG 11788
i i iii i ii ii iv ivi v i v
C TguERVL2_I-b_ 1719 ATCCCATTTTCCCATGTCTTCCCCATGGTCACGCAGAAAGAACCACAGGT 1670
galGal6_dna 11789 CAAAATGTGACATAGTCTTACTGTTCTCACTTGCACAAGCTGGTGGACGT 11838
ivvi i---------iv v i v iv v v v
C TguERVL2_I-b_ 1669 CAGCTCGTGG---------GGTGTACCCTCTCTCCCCAGCTGGGGGACGT 1629
Matrix = HMM
Kimura (with divCpGMod) = 46.75
Transitions / transversions = 1.09 (70/64)
Gap_init rate = 0.05 (18 / 389), avg. gap size = 3.89 (70 / 18)
+ 237 39.7 6.1 5.2 galGal6_dna 12578 14375 (35115) C HERVL18-int LTR/ERVL (1162) 4885 3073 13
ANNOTATION EVIDENCE:
237 39.68 6.12 5.24 galGal6_dna 12578 14375 35067 C HERVL18 LTR/ERVL 3073 4885 1162
237 39.68 6.12 5.24 galGal6_dna 12578 14375 (35067) C HERVL18#LTR/ERVL (1162) 4885 3073 m_b1s001i9
galGal6_dna 12578 CTAGAAACTAAAAGACTCACAGAGAGTA-GTACAGATATT-TCAGGGGTA 12625
viiv v v ------ i i - i i i -v
C HERVL18#LTR/E 4885 CTACGGTCGAAATGAC------AAAGCAGGCACAGGTACTAACAGGGGTA 4842
galGal6_dna 12626 TCAGGAAGGGAAGGTCTGCCTTCCAGGGCAAGATACAGGCCATATTCCTA 12675
------------ii vvviii ivi i i vvi iii
C HERVL18#LTR/E 4841 ------------AATCACGTCCCTCAGGCAAAATACAGGCTAACCTTTCA 4804
galGal6_dna 12676 TCCTGGGTCAACACTTTGGCTTGCACTGGGGCATGCTCTGGCCACCTGTA 12725
iv vi v vii ivv vv vviv i v viv
C HERVL18#LTR/E 4803 TCCCTGGATAACAATGCAGCCACCAAGGGCTTCTGCCCTGGGCAATGGTA 4754
galGal6_dna 12726 CCACACCCATTGGACAGATATCTGTGG------------CTGTACAACTA 12763
ivi --- v vi ii ------------ i-- i
C HERVL18#LTR/E 4753 CCACACCTTCT---CAGCTCCCCATGGTTCCTTTGGGTCCTGTAT--CCA 4709
galGal6_dna 12764 TATCAGGCAGCAAAGT-ATGGGG----TCCTGATCTGCCATAGGGACATA 12808
-------iv - ii ---- v i vv i vi vv
C HERVL18#LTR/E 4708 T-------GCCAAAGTCACAGGGGAGCTCATAATAGGCCACACAGACAGT 4666
galGal6_dna 12809 ---------------ATGAGAGTCCCTTTAGCAATGAAAACCGGAGTGTT 12843
--------------- v i i i----------- v ivii
C HERVL18#LTR/E 4665 ACATATGTCCCCCGGAGGAGGGTTCCTTC-----------CCTGGCCATT 4627
galGal6_dna 12844 GACC-AC--AAAGTCAAT-----AGGCCATGTACTGATTAT---TGGAGG 12882
vv - i-- v i----- i i i v i---v v
C HERVL18#LTR/E 4626 CCCCTATGAACAGTCAACCATGGAGGCCATATATTAAATACCCAAGGAGT 4577
galGal6_dna 12883 GACTACCAAGCCTCCCACCTCCAATA--ATCTCCCC-CAAGGTGCAAGTA 12929
vvv i ------v v vi --vi - i v v vv
C HERVL18#LTR/E 4576 GACATGCAAGTC------ATACTGTAGGCCCTCCCCCCAGGGAGCTACGA 4533
galGal6_dna 12930 -GGCCACACCACT------TTGGTCCTACCTGCACCTTCGTAGGCCA--- 12969
- - i------vv vv --- v vvv vvv ---
C HERVL18#LTR/E 4532 TGGCCA-ACCACCTGCAGTGGGGGGCT---TGGAGGGTCCATGGCCAAAG 4487
galGal6_dna 12970 -------TTTTATTCTATGGGTACCTGGTTCTAGATTCTCAGGGGCAGGG 13012
------- i i i------- vi ii ivv viv v
C HERVL18#LTR/E 4486 CCAGGTTTTCTGTTCC-------CCTGCCTTCAGGGGCATTGGGGCAGGC 4444
galGal6_dna 13013 AGCAGAAGGTTAT-TTTCATTACCAAATTGGGGTCTTATCCGATTATCGG 13061
i iv i-v i iv v iiv- vv vvv i i vv
C HERVL18#LTR/E 4443 AACAACAGGTTACCATTCGTCCCCATACCT-GGTCGGAGGAGGTCATCCT 4395
galGal6_dna 13062 TGCTTGTAATTTGGATCCTAAGTGGG---GAGGCCCATGTTGTCTGTAGC 13108
v vvvv i v v iv vv --- v iv------ i
C HERVL18#LTR/E 4394 TGGTGTGTATCTGCAACTGAATGGGGGCAGCGGCCCGG------TGTAAC 4351
galGal6_dna 13109 ATTTTCAGGGCACC--GGCTCTGCTGTGT--C-TAGACCTTTCATTCAAG 13153
vvvi vv-- -- vv iiiv -- -vv i v
C HERVL18#LTR/E 4350 AAAGCCTC--CACCGGGGCTGGGCCACCTTTCCGTGGCCATTCATTCAAG 4303
galGal6_dna 13154 TCCTGCAGGGTTTCGTAGAGTCTCTTTGCCCACCCCTGCAGGGACTGAGA 13203
vii v viiivv vv i vvvvvi v i ii - i i
C HERVL18#LTR/E 4302 GTTTGGAGCACCAGGTCCAGCCTGGAACTCCAGCCCCGCAAAGAC-GGGG 4254
galGal6_dna 13204 GTCTGTCTT-C-AGGG-----CAGCCTTAAGAATACCATTATAGCGTTCA 13246
vv v v - - v ----- vi v ii vv v i
C HERVL18#LTR/E 4253 GAGTGACATGCAAGCGTAACCCATTCTTCAAGAGCCCATTATATCGCTCA 4204
galGal6_dna 13247 ATAAGTCCTGCCCCTGTCAGAATATATGGGAGGTAGAATCGCCATTCAAT 13296
v vv v vv vvii iv v vi i v i iv
C HERVL18#LTR/E 4203 ATCATACCAGCAGCTTGTGGGTTATATGGCACATGGAATCCCCACTTTAT 4154
galGal6_dna 13297 GCTGTTTTCGTCTGCCCAGCTTTGTATCATGGTGCCAGTGAAATGAGTCC 13346
iivv i vv v viv i vvvvvv v i
C HERVL18#LTR/E 4153 GTCCATCTGTTGTGCCCACTGTTGTACCTGCTGTCCAGTGAAATGTGTTC 4104
galGal6_dna 13347 CTTGGTCGCTCTCAATGACTTGAGGTGTCCTGTAGGCAGCCATCAACTTG 13396
iivi i i iv vvvv ii vivi vvvi v-
C HERVL18#LTR/E 4103 CCCTATCACTCTCAATGGCCAGAGGGCGACCATACAGGGCACATAAG-TG 4055
galGal6_dna 13397 GT-GAGTGCCTTGATGGTATATGCCTGGTTCGCT-CTCAGCACTGGATAG 13444
v -v v iv i iivvi iv i- i v -v i
C HERVL18#LTR/E 4054 TTGCAGGGCCCGGATGGTGTGCTGTTGGTCGGCCACCCTGCA-AGGGTAG 4006
galGal6_dna 13445 GTCTGCATTAGCCCACTTGCGTTATTGACGCAGGTCAGGACATATCTCTC 13494
ivvi vi v vv v vv i iv ivvv v iiv v v
C HERVL18#LTR/E 4005 GCGAACAACAGGCCTGTGGCCATGTCCACAGCTGTCAGCACATGCGTATA 3956
galGal6_dna 13495 CCCCTCAGACCGAGGGAGGGGCCCAGTGTAATCAACCTGCCAT-TGGTGG 13543
vv ivv v v i i v i i- vi
C HERVL18#LTR/E 3955 CCCCTGCGACTTTGGCAGCGGCCCAATGTAGTCTACTTGCCACCTGGTCA 3906
galGal6_dna 13544 AGAGGATTGTGTCCTCTAGCAAGATGGGCTGTTGTTTCAGGCAATTATAT 13593
i v ii-i i v v iv vv vvv viiviii ii iiv
C HERVL18#LTR/E 3905 AGGGCACC-CGCCCTATCGTCACTTGTTGTGTAACACTGGGCAGCTGCCT 3857
galGal6_dna 13594 CAGTCT----CATATTGGAGCACGTGTC--ACAGTCTCGGCATGCCTGGA 13637
vi i ----i iiiv i ii--i v iii i v vvv
C HERVL18#LTR/E 3856 CCATTTAGGGTATGCCTGAGCACATGCTGGGCATTTCTGACAAGCCTCCC 3807
galGal6_dna 13638 TGATATCAGATAGTTGTATGGGCAGTCCCCATGCTTTAGC-AGCTGCCCA 13686
vi i vvii vvv i v i v vvvi vi- v -iii
C HERVL18#LTR/E 3806 AAATGTCTTGCATGGGCAGGGACAGACCCCAACACTTATTGACCTG-TTG 3758
galGal6_dna 13687 CATTGTCTTTGGTCCAGCATGCCACAGCTTCTGATGTAACCAGCGGGTAT 13736
iivi vvvi v i v i iii i vvi ivv
C HERVL18#LTR/E 3757 CATCAGTTTACCCCCCGCATGTCCCAGTTTCCAGTGTAGCCACAAGGCCA 3708
galGal6_dna 13737 TGTTCTCA-GATGGTGAATTCTGAGTCCATCGAATTCGGGCCAGTGTGTC 13785
ii- - vv vvvv vviv i iiiv iv ii
C HERVL18#LTR/E 3707 CA-TCTCATGTAGGTGCCGACTCTAACCATCGGACCTTGGCCAAGGCATC 3659
galGal6_dna 13786 AGCTTCGTCATTTCCCAGTGACTGTAGGGGTTGGTGACCAGAAACATGGT 13835
v i i v vi v vvvvi ii ivvi i v v i
C HERVL18#LTR/E 3658 TGCCTCATCATTGCCAGGGGTGGCCAAAGGCATATGGCCTGACACATGAT 3609
galGal6_dna 13836 AGAAACGTATAGTCCTGTGTTTAACCACATTCCATACGTCTAACCACATA 13885
i v vv i viii v v v v iv i v vi i
C HERVL18#LTR/E 3608 AAATAGTTACATCTTTCTGATGACCCATTTCCCATAGGTCTTGCCACATG 3559
galGal6_dna 13886 TCTCTGCCCCAAATTGGTCGGGCGTGGATAGTCCATCCCTGGGTGGCCCA 13935
v iv v i vv ivi iviv vii vivvvi
C HERVL18#LTR/E 3558 GCTTGGCCCCAAATGGGCCGGTGGCCAACTAGCCAATTCTGTAACTTCCA 3509
galGal6_dna 13936 CTGCGGAATCCAAAGAGTGAGCCCCTGGTACACAGCCCAACTATCTGTGC 13985
vvvv vv v v i- v iv ii i v v i iv
C HERVL18#LTR/E 3508 GGTAGTTAACCACAA-GTTAAGCCTCGATAAACTGCCCAGCTATTGGTGC 3460
galGal6_dna 13986 AGATATTCA--GGACACTATCACCAGGTTCCTTGGTTATAACCAACCACA 14033
vvi -- ---- i ---- v v v
C HERVL18#LTR/E 3459 AGATTACCATAGG----TGTCACC----TCCTTGGTGATCACCATCCACA 3418
galGal6_dna 14034 TGGCTCACAGTTCTGCCCATTGGCTACTCTGACCATCCCCCCCTTCAAAC 14083
iv vv v i v iv ivvi
C HERVL18#LTR/E 3417 CTGCTCTGAGTTCAGCCCATTGGCTACTTTGTCCACACCTGGTTTCAAAC 3368
galGal6_dna 14084 CAGATTGTTTCAGGGAAGGGATGGTATGCTACTGCTCTCCACTTGCTCCG 14133
v v v vivvi v vv v v vv --v vv i
C HERVL18#LTR/E 3367 CATATGGTGTCAGTACTAGGCTGGACTGCAACAGCAGTCCA--GGCAGCA 3320
galGal6_dna 14134 GTTG--CCCTTGCTGGACCCATCCGTGTACCAGGCATCTTCTGGAATGGG 14181
v -- iv i i i v vi v v
C HERVL18#LTR/E 3319 GTAGCACCCCGGCTAGACCCATCTGTATACCATGCCCCATCAGGAATGGG 3270
galGal6_dna 14182 ATATTTCCCCTCCTGAACAG-----GACTCT-TCTCTGGTGGAGT----- 14220
iviv v i v vv ----- i v-vv i v v i-----
C HERVL18#LTR/E 3269 GGGATGCCCTTCCTTAAACGGTGAAGGCTCAGGGTCTAGGGGTGCCTCAG 3220
galGal6_dna 14221 GACCCATGTTTCTTTCGGTGCATTACTGT---GATATGTCACTGAGCCTG 14267
v v-i vivv ---v---v------- v iv ii
C HERVL18#LTR/E 3219 GCCCCATGG-CCTTATCTTGCATTA---GGACT-------ACAGGTCCCA 3181
galGal6_dna 14268 AGATCTTTTGAAGCTCTTCTTTCAGTGGTGATGAAGACAGACTACTCCTC 14317
i i v i v vii iv vvv v vv vv v
C HERVL18#LTR/E 3180 AGACCTCTTGCAACTCTGCTGCTAAGGGACTTGTACTCAGCGTACTCCGC 3131
galGal6_dna 14318 TGGCTGAGATAGGCAACCCATCATGCTACCATTTGTGCTTGGGACACCCC 14367
viiv ii iv iiv vvi vvi ii v v i
C HERVL18#LTR/E 3130 TGCTCCAAGTAGGCGCCCCACTTTGCTAAAGTGGATGTCTGTGCCATCCC 3081
galGal6_dna 14368 TGTCGTAG 14375
v vvi
C HERVL18#LTR/E 3080 AGTCCGGG 3073
Matrix = HMM
Kimura (with divCpGMod) = 55.53
Transitions / transversions = 0.75 (290/386)
Gap_init rate = 0.07 (131 / 1797), avg. gap size = 1.56 (205 / 131)
+ 18 16.1 3.9 3.9 galGal6_dna 16205 16256 (33234) + (ATA)n Simple_repeat 1 52 (0) 14
ANNOTATION EVIDENCE:
18 16.14 3.85 3.85 galGal6_dna 16205 16256 33186 + (ATA)n Simple_repeat 1 52 0
18 16.14 3.85 3.85 galGal6_dna 16205 16256 (33186) (ATA)n#Simple_repeat 1 52 (0) m_b1s252i6
galGal6_dna 16205 ATAA-AATAATAGCAGTAATTATAATAATAA-CATAATCATCATAACTCA 16252
- ii i v -v v v - -
(ATA)n#Simple 1 ATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAA-T-A 48
galGal6_dna 16253 ATAA 16256
(ATA)n#Simple 49 ATAA 52
Matrix = Unknown
Transitions / transversions = 0.75 (3/4)
Gap_init rate = 0.08 (4 / 51), avg. gap size = 1.00 (4 / 4)
+ 209 41.3 6.8 8.1 galGal6_dna 17058 18213 (31277) C HERVK14C-int LTR/ERVK (2094) 5340 4199 15
ANNOTATION EVIDENCE:
209 41.31 6.75 8.06 galGal6_dna 17058 18213 31229 C HERVK14C LTR/ERVK 4199 5340 2094
209 41.31 6.75 8.06 galGal6_dna 17058 18213 (31229) C HERVK14C#LTR/ERVK (2094) 5340 4199 m_b1s001i10
galGal6_dna 17058 GCACCTGTGGAAACACAAGCATAACCTCTCCCCCAAGTTATCAGTGGAAA 17107
v v vi v v v i v -----
C HERVK14C#LTR/ 5340 TCTCCTGGAGAAACACAAGCAAAACCTCTACCCCATGTTATTATT----- 5296
galGal6_dna 17108 CGGGACTTCCCATTGACCCCATT-------CCAGATTCTTTACTAGTACC 17150
------ v vv vv v v -------iiiivv v ----
C HERVK14C#LTR/ 5295 ------TTACCTATTTCCCAAGTTTTTGTTTTGACATCTTTCC----ACC 5256
galGal6_dna 17151 ATA---GTTTTTC--CATGAATATTCACTCTTTCCTCGTTAACTGAAATG 17195
v --- i -- viv i i i v i------ --- i
C HERVK14C#LTR/ 5255 AAACCTGTTTTCCTTCATGTGGATTTATTTTTTGCC------CTG---TA 5215
galGal6_dna 17196 AAATGAGGGCTG-TCAGCGGTCCTCCATCATCACACCCTCAATTTAAAAA 17244
---- - v v iiv v- v vv i ii---- vi v
C HERVK14C#LTR/ 5214 AAATG----CTGTTCTGCTGCTGTA-ATAATCTGATCTC----TAGACAA 5174
galGal6_dna 17245 GTTCAATACATATGTAGCTTTAGCAA--GCC---------TTTCTGTTGG 17283
v v v iv ivv ii -- --------- viv i vi
C HERVK14C#LTR/ 5173 GTTCAAAAAATTTAAAGTAATAATAAGAGCCAATTGTAGTTGCATATGAG 5124
galGal6_dna 17284 AAGTGCCTTCTTC----A-TTCCCTCT------TTTTGCTTAAGTAGCTT 17322
i ivvv v ----i- i i ------ i vv ii v
C HERVK14C#LTR/ 5123 GAGTAGAGTATTCTCTGGTTCCCCCCTTCTGTCTTTTGTTTTTGTAATTG 5074
galGal6_dna 17323 AGTTTTAAGGTTGCTATGGGTGCACTCAACTATGGCTTGTCCTGTGGGCA 17372
v v i v viv vi iv i v i -v i v
C HERVK14C#LTR/ 5073 AGATTTTAAGGTTTGATTAGCTCATTCAACAATGGCCTGTCC-TTGAGAA 5025
galGal6_dna 17373 -AGTATGGTATGTCCATGAGATGTTTAATTCCTCATGACTGTAAAAACTG 17421
-vi v v vi vi ivvi vivi vii v i ivv
C HERVK14C#LTR/ 5024 TTATAGGGGATTCCAGTATTGTGTTTAATATGCCATTGTTGAAAGAATGT 4975
galGal6_dna 17422 ---TAATACTT-TCTGGGATATATATCCCAGGCCATTATCTGTCTTAATA 17467
--- vi -v iv----v v ii v i v
C HERVK14C#LTR/ 4974 TTGTAAAGCTTTACTAC----AATAGCCTGGGCCATTATCAGTTTTAATT 4929
galGal6_dna 17468 GTTTTTAGTACCCCAAGAGTTACAAAGGCCAAGAGAAAATGTTTGCAGAT 17517
v v i v iv v v iivi ivvvi i v i vivi i
C HERVK14C#LTR/ 4928 TTTTGTGGAATGCCCATAACAGCAAAACAGGAAAGCAAATGTCTTTTAAC 4879
galGal6_dna 17518 ATTGCAAGCCTTTTCTCCAGCATGTGCTGTCGCTGCTATGGCTCCGGAAA 17567
vivv ivvii v iv vvvv v ivv iiivvivi
C HERVK14C#LTR/ 4878 ATGAGCAGTAGCCTCTCCTGTTTGGCAAGTAGCCCATACAAAATGAGAAA 4829
galGal6_dna 17568 AGGTATCCACTGACACATGGACATATTTAAGTCTTCCACATTCAGGGATG 17617
i i v vv vvv i i v vv v ii
C HERVK14C#LTR/ 4828 AAGTATCTACAGTAACATGGACATAAGAAAGTTTCCCAAATGAAGGTACA 4779
galGal6_dna 17618 TATTTGACATCTGTCTGCCATAATTCCAGAGCTGTTAGGCCTCGGGGATT 17667
ivv ii i v vv vvv v ii iv vi i
C HERVK14C#LTR/ 4778 TGAGTGACATCCATTTGCCAAAAAGCATTAGGTGCCAATCCTCTAGGGTT 4729
galGal6_dna 17668 AACCCCATGCAGTAGA----GAAGGTG--TCATTTGTTTGGCAATCAGGG 17711
i vv vv v ---- v v --v i----i vi
C HERVK14C#LTR/ 4728 AACTCCAGTCCCTTGATGTGGCAGTTGTAGCAC----CTGGCAAGTAGGG 4683
galGal6_dna 17712 CATGCTGCAATTATCTGCTGTGCCTGAGTTAAGCTAAGGCCATAAGACTT 17761
vvv vvv iv vvvi vv vv iv v v iv vvvi v
C HERVK14C#LTR/ 4682 CAATGTTGTACAATAGCTTTAGCCTGTTTCCAGGTAATGTGATATTTTTG 4633
galGal6_dna 17762 TTGCAGCACCTCAGTATTCTGGTGAAAAAAGGTATGTGACAGTTGAACCT 17811
vv iv iv v i vvvi ivv i vi vi vvv ii --
C HERVK14C#LTR/ 4632 TTTGAGTCCTGCTGCATTAACATGAGTTAAAGAGTGAAAATCTTGGGC-- 4585
galGal6_dna 17812 GTTCAAATGAATTGGGAAGAACAGTAACTCCAGATAACTGATCCACATAT 17861
---------- i v ivi iv--- iv iivi vi v iv
C HERVK14C#LTR/ 4584 ----------ATTAGTAAATGCAGTAGA---AACTAGTAAATCAGCTTGA 4548
galGal6_dna 17862 CTGTTT-CCTTCTACTAAAGGTCCT-GGCAAAGTGGTATCTGTTACAAAA 17909
iii v- i - -i i i- v i v i v i vi --
C HERVK14C#LTR/ 4547 TCATTAGCCCT-TA-CAAGGGTCCCAGGAAGATTAGTATGTGCTCTAA-- 4502
galGal6_dna 17910 TATGGTTCCTGT--------------TGGCAACTAACTAGAGA---CAAA 17942
iv vv i -------------- iiv vv ivvvv---i
C HERVK14C#LTR/ 4501 TATGAGTAATATAAAAAGGAAAATAGTGATCACGCACTGCCTTTTGTAAA 4452
galGal6_dna 17943 AAAATATACAGAACAAACAGTTGTTAATTAGAAATGTCTCT--TAGATAC 17990
iv v i vvv v v v iviv vi v i -- vi vi
C HERVK14C#LTR/ 4451 AAAGAAAATAGCTGATAGAGTTGTTCATCTATAAGATATTTAATTAAGGC 4402
galGal6_dna 17991 AATCCTTCTATTCT---AGTCACTATTCCTGTAATAC--AGGCTGAATCA 18035
i -- v viv--- vi----- v v vv -- i v
C HERVK14C#LTR/ 4401 AGT--TTCAATATATTGAGTGG-----CATGAACAACATAAGCAGAATCA 4359
galGal6_dna 18036 GCGATGATGTTAATTGGATTGGACCACTTTTGAAAAACTCTTACAACTGC 18085
vi ii i iv v vvvvvv v i vv v vvi i
C HERVK14C#LTR/ 4358 GAAACAATATTAACAGGCTGCTTAAAGTCTTCTAACACAGCTATAACTGC 4309
galGal6_dna 18086 AGCTAACTCTACAATTTGTG------GATAGCCCTTTATTGTCTGAATAT 18129
viv vi vv v ------i v i ------v i v
C HERVK14C#LTR/ 4308 CAGTAACTCAGCTCTTTGAGCTGATTAAAAGTC------AGTTTGAATAA 4265
galGal6_dna 18130 TTGACTTCCATCAGCCGGATGTGTCCTGCCAGTCAGTTAATGACCGACCT 18179
i v-iv iv vi i vvi i ivv ivv vi v i--------
C HERVK14C#LTR/ 4264 CTC-TGTCTTTAGGTCCTGTATAAGCTGCTTTTCCATTACTA-------- 4224
galGal6_dna 18180 GTTCTCCCTGACCCATCTGTGAATACAGTCAAGG 18213
--------- v v i v i vi
C HERVK14C#LTR/ 4223 ---------GAACCATCAGTAAAAACAGTTACAG 4199
Matrix = HMM
Kimura (with divCpGMod) = 60.27
Transitions / transversions = 0.69 (180/259)
Gap_init rate = 0.10 (114 / 1155), avg. gap size = 1.49 (170 / 114)
+ 19 17.1 0.0 0.0 galGal6_dna 20907 20939 (28551) + (C)n Simple_repeat 1 33 (0) 16
ANNOTATION EVIDENCE:
19 17.11 0.00 0.00 galGal6_dna 20907 20939 28503 + (C)n Simple_repeat 1 33 0
19 17.11 0.00 0.00 galGal6_dna 20907 20939 (28503) (C)n#Simple_repeat 1 33 (0) m_b1s252i7
galGal6_dna 20907 CCTCCACCCCCTCCCCCCCCCTCCCCCCGCCCC 20939
i v i i v
(C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 33
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)
+ 14 20.8 4.5 0.0 galGal6_dna 20940 20950 (28540) + (CCCCCT)n Simple_repeat 1 46 (0) 17
ANNOTATION EVIDENCE:
14 20.83 4.55 0.00 galGal6_dna 20907 20950 28492 + (CCCCCT)n Simple_repeat 1 46 0
14 20.83 4.55 0.00 galGal6_dna 20907 20950 (28492) (CCCCCT)n#Simple_repeat 1 46 (0) m_b1s252i8
galGal6_dna 20907 CCTCCACCCCCT-CCCC-CCCCCTCCCCCCGCCCCACACCGTTCCC 20950
i v - - iv v v v i
(CCCCCT)n#Sim 1 CCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCC 46
Matrix = Unknown
Transitions / transversions = 0.60 (3/5)
Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2)
+ 172 44.5 9.8 4.0 galGal6_dna 21468 22662 (26828) + PABL_B-int LTR/ERV1 2044 3304 (3818) 18
ANNOTATION EVIDENCE:
172 44.48 9.79 4.04 galGal6_dna 21468 22662 26780 + PABL_B-int LTR/ERV1 2044 3304 3818
172 44.48 9.79 4.04 galGal6_dna 21468 22662 (26780) PABL_B-int#LTR/ERV1 2044 3304 (3818) m_b1s001i11
galGal6_dna 21468 ATTTTCTGGTGGGTATGGGTGCCTCTTAC-----------CACCTGT--- 21503
i ii i v i iv iv i----------- vivv---
PABL_B-int#LT 2044 ACTTCTTAGTTGATACTGGTGCTACTTATTCAGTAGTTAACACACCAATG 2093
galGal6_dna 21504 -----AC------ATGATTTTGCAACAGTAGTAGGAGCTA-CTGCCCAAC 21541
----- ------ iivv i iv vvi i v i - v vvv vi
PABL_B-int#LT 2094 ACTGAACTTTCTGACACGTCTGTCAATATGGTTGGAGTTAGCAGGAAACT 2143
galGal6_dna 21542 ACGA--AAAAGCTTACCTTTTTGGGATCAATTACATATAGGCTGAGAAAA 21589
iv -- i vvv---- ii ivi i vv v i ii i v v
PABL_B-int#LT 2144 GAGATCAGAACAG----TTCCTACAACCCCTTTCATGTAAACTGGGCAAT 2189
galGal6_dna 21590 CAAGTAGGAATACATAAATTCTTGCACACACTAGGTTCTCCAAAACCATT 21639
v vv iv iv ivi i vi iiii i iv vi vv v
PABL_B-int#LT 2190 GATTTAATAACTCACTGATTCCTTTATGTGCCAGAATGCCCAATTCCTTT 2239
galGal6_dna 21640 ACTTTGGCAAGATTTATTAGAACAAATCAATGCAGAGATTAAATTCAA-- 21687
i vv ivi ii ii vivv v v vv ii vv v --
PABL_B-int#LT 2240 GCTGGGAAGAGACCTGCTATGTAAATTAAATGCTCAAGTTATCTTCTACC 2289
galGal6_dna 21688 ---TAAAACTGGAGCTAAGGGTCAAACAATATTAAGTG---ATTGAAAAT 21731
---vi viv ii v vv ---------i i v---viv v v
PABL_B-int#LT 2290 CTGAGAAACAACAATTATGTCTC---------CAGGTCCCTCCAGAACAA 2330
galGal6_dna 21732 ----TGTAAGT-CTGGC---TTTAATACAAACAGGGGAAAACAAT----- 21768
---- i iv - vi --- i i i v vv v i v------i-----
PABL_B-int#LT 2331 GGACTGCAGCTGCAAGCACTTCTGACAAACTCTGAGGC------CTCACG 2374
galGal6_dna 21769 -------------GTTGTACCCCCAGAAGTTACAGAAATCTTAAATAAGG 21805
-------------iiv v i ---------vi vi i
PABL_B-int#LT 2375 CCCTAAGGTAGAGACAGTTCCTC---------AGGAAATCTTTGACAAGG 2415
galGal6_dna 21806 TATGCTTAGGAGTGTGGGTATCAGGGATACCTGGTAGAGCCA-AAATGC- 21853
vivii i v i v ivvv v v ii v -v i-
PABL_B-int#LT 2416 TAAAACCAGAAGTTTGGGCATGAGACCAACCAGGGAAGGCAATTAATGTG 2465
galGal6_dna 21854 -AGCCCT---------------AAGCAAGAGCT-AGTCTGGTCAGAGTAA 21886
-iv vv--------------- i v i i i- ii ivi ii i-
PABL_B-int#LT 2466 AGTCCAGTAAAAATCAAACTTAAGGAAGGGGCCTAACCTATCCGAAA-AA 2514
galGal6_dna 21887 AGCAGTGCCCTTTGAGGATATGCAACTGTAGAAGG-ATAAAAGAAATAAT 21935
i i i i ii vi- v i iv - v ivvvi vv
PABL_B-int#LT 2515 AACAATACCCTTTAAAAAGG-GAAGCCTTAGAAGGAATACAGCCTGTCTT 2563
galGal6_dna 21936 AGA-TAACTTTTGGATTTTGGATTACTAATTGAATGTGAATCCAAATACA 21984
v-v i iv v v ii v v vvvvv v i vv i
PABL_B-int#LT 2564 AGTAAAATTTTTACAGTATGGGCTAATTAGACCTTGTCAGTCCCCATATA 2613
galGal6_dna 21985 GTACTCCAGTCTTGCC---GATGAAAAGTTGGATAGCAAGTGCTATAGTT 22031
i vi i --- vvi i iiiv ivvv vviv v v
PABL_B-int#LT 2614 ATACTCCTATCCTGCCTGAGTAAAGAAGCCACACTCAAATGAATATTGAT 2663
galGal6_dna 22032 TAGTACAAGATTTGAGGGCAAGTAATAGAACTGTTCAATGTATACACTCC 22081
v i i v ii i v vii v i v
PABL_B-int#LT 2664 TTGTGCAAGATTTAAGGGCAATTAATGAAATTGTTGAAGACATTCACCCA 2713
galGal6_dna 22082 GTGGTGGCAAATCCATACACTTTATTAACCAAGGTA--AGGAATGAGTAG 22129
iiv v v i v v vviv --v iivvvi ii
PABL_B-int#LT 2714 ACTGTGCCTAACCCATACACTATATTTACCTCACTACCTGGGGATTATGA 2763
galGal6_dna 22130 GTGGAGTTTAC-CTTCTGGATTTGAAGTATGCCTT-TTCTGCCTAGT-TT 22176
i -- v -v vi i i iv i - i v vvi-v
PABL_B-int#LT 2764 ATG--GTTTTCAGTGTTAGATTTAAAAGATGCTTTCTTTTGCATTCCAAT 2811
galGal6_dna 22177 GGCCAAAGGAAGCCTAAGGTTATTTGCCTTTGAATAGAAAATCCCTAATA 22226
viiv ii vivvi i i iv i v
PABL_B-int#LT 2812 GGATGCAGAGAGCCAGCTATTGTTTGCCTTTGAATGGAAAGACCCTGAGA 2861
galGal6_dna 22227 TGGGATGAGAAAGACCCAGTTAACCTGGACAGTGTTACC-CAGGGTTGTG 22275
ivi--viiv ivii vvvvi i v - i v v i
PABL_B-int#LT 2862 CTA--AAGCAAAATTTCAGTATTGTTGGACAGTGCTTCCTCAAGGGTTTA 2909
galGal6_dna 22276 AGAACAGCCCGATGATTTTTGAGAACTGGTCAACTCGTGAGCCTGAGATT 22325
i vvv i iv i i ------- v vv - ivi i
PABL_B-int#LT 2910 AAAACTCACCAACTATTTTTGGGGA-------AATATTG-GCTAAAGACT 2951
galGal6_dna 22326 TGGGT-TCCTGCAT-CCCACGGTGGAACTTTACGGCAGTTTAAAGATGCC 22373
ii v-v i v-ivv vii iii i vi i v ivi vi
PABL_B-int#LT 2952 TAAGAGACCTACAATTAGAAAATGGGGTTTTGCTACAATATGTGGATGAT 3001
galGal6_dna 22374 ACGGAAA-------------CAAAGAGGACTGTGTGCAATGGACTGTGAG 22410
vi vv -------------i iv i v ivv v vviv ii v v
PABL_B-int#LT 3002 TTGCTAATTGCCAGCCCCTCTAAGCAAGAGTGCCAGGATAACACCATTAT 3051
galGal6_dna 22411 TGTGCTGAATTTCTTTGTTTA-AATGATTATCAAGTTTCTCAACAGAAGG 22459
vi vi i v i v ivv -vi iv v i v vvivv i
PABL_B-int#LT 3052 AATTTTAAATTACCTGGCAGAATGTGGATATAAGGTATCAAGCAAAAAGG 3101
galGal6_dna 22460 CACAAATAACTCAACGGCAAGTGATGTATCTGGGATAGGAGGTTACAGCT 22509
v vviv iivvv vi ii i i vv-vvvi vv
PABL_B-int#LT 3102 CCCAAATATGCAAACAAACTGTGAAATACTTAGGGTTT-CTCCTACAGAA 3150
galGal6_dna 22510 -GGACTTTGAACCGTAAGGACTGCCAGGAAAGAAGCCATC--------TG 22550
- viiv i v i vviiv vv v i i v i--------
PABL_B-int#LT 3151 AGGAACCAGAGCCCTGACCGTGGAAAGGCAAAAGGCAATTGCCTCCATTG 3200
galGal6_dna 22551 CCAAACCCCTGAGCCACAAAGTGCCAAGGAACTCCATACATACTCAGGAA 22600
vi viv v viv i-------- v i viiviv vi i v
PABL_B-int#LT 3201 CCATGCCCACCACCAGAAG--------GCAGCTGTGGGGATTTTTAGGTA 3242
galGal6_dna 22601 TGACAGGATGGTGCCAACTGTGGATATACAGCTATGGGCTGCTGGTAAAG 22650
i v vv iiv v vivi ii v i iv i i i
PABL_B-int#LT 3243 TGGCTGGATTTTGCCGGATTTGGATTCCTAATTTTGGACTAATAGCAAAA 3292
galGal6_dna 22651 CCCCTTCATGAA 22662
i i
PABL_B-int#LT 3293 CCTCTTTATGAA 3304
Matrix = HMM
Kimura (with divCpGMod) = 68.99
Transitions / transversions = 0.95 (249/261)
Gap_init rate = 0.07 (83 / 1194), avg. gap size = 2.02 (168 / 83)
+ 154 41.2 14.6 2.9 galGal6_dna 22667 23761 (25729) + PABL_B-int LTR/ERV1 3541 5025 (2753) 18
ANNOTATION EVIDENCE:
86 44.88 16.53 3.74 galGal6_dna 22667 23761 25681 + RLTR6-int LTR/ERV1 3796 5025 2753
86 44.88 16.53 3.74 galGal6_dna 22667 23761 (25681) RLTR6-int#LTR/ERV1 3796 5025 (2753) m_b1s001i12
galGal6_dna 22667 GTAAGAGATGGCCAGAGTGGCTGAGGGCAGTGGTTGCACTAGTGCTCAAT 22716
vi ivi vivi v ii vi v i v iv vvvv
RLTR6-int#LTR 3796 CCAGTGGATGGCCCACATGTCTGAAAGCTATTGCTGCAGTAGCCCTGCTG 3845
galGal6_dna 22717 ATTCTAGAAGCCAGCAAATTTACG----AATAACAGTGTTAATATCTCAT 22762
i ivv v iii v v----i i --iv i i iv vv
RLTR6-int#LTR 3846 GTCAAAGATGCTGACAAATTGACTCTGGGACAACA--AATGACACATGTT 3893
galGal6_dna 22763 ACAGTGTCTACTGCATTGGAGGTAAAAGGGGGGCATTGGCTCTCA--CCC 22810
ii ivi vv v i i----------i i viivv -- v
RLTR6-int#LTR 3894 GTAGCCCCTCATGCCTTAGAA----------AGCATCGTTCGACAGCCCA 3933
galGal6_dna 22811 CCA-----AAGGTTCCTGAAATACCAGGCCATCCCAGT------------ 22843
v----- v v vvi- i v vviiv i v ------------
RLTR6-int#LTR 3934 CCTGACCGATGGATGAC-AAATGCCCGCATGACTCATTATCAGAGCCTGT 3982
galGal6_dna 22844 ----AGAGCAGGATGATGCAGAAATAATTGTA---ACTAATAATGTCAA- 22885
----ii ------ vvvv v ivv i ---v iv viv -
RLTR6-int#LTR 3983 TGCTGAA------TGAGCGTGTAACCTTTGCACCCCCTGCTATCCTCAAT 4026
galGal6_dna 22886 CCCAGCATCTTTCCTTAGAGGAACTCCTGAA---GAACCAGTATTTCATG 22932
vv ii v ivvvvv vvv v--- vv --- v v
RLTR6-int#LTR 4027 CCCAGCTACCCTGCTCCCTCTAACAGATGATTCCGTCCCAG---TACATC 4073
galGal6_dna 22933 ACTGCTTTGAAACAACTGCGGC---T-ATGGGCTGTTGCCAGTCGGACCT 22978
v iviv v ivvi v v---v-v vi---- viivvv
RLTR6-int#LTR 4074 AATGTACGGACATCCTTGCTGAAGAAACTGGGAC----CAGAAGTGACCT 4119
galGal6_dna 22979 GAAA-----GACGAACCCTTAGAAGATGCAGAAGACCC---TTGGTTTAA 23020
i----- v i viv------ v i vi ---i vi v
RLTR6-int#LTR 4120 GAAGGATCTGACCAGCCCTGGC------CTGGAGCTCCCAACTGGTACAC 4163
galGal6_dna 23021 TGATGGAAGCAGTTTTGTGAGACAAGGAAACCGTAAGGAAGGATA----- 23065
v v iv iv v v v v vv ivv-----
RLTR6-int#LTR 4164 GGATGGCAGCAGTTTCCTGGTAGAAGGTAAGCGAAAGGCTGGGGCAGCAG 4213
galGal6_dna 23066 TCCAGTAACTGCTACTGACAAGGTAATTGAAGCACAACCATTACCTGTGG 23115
v i iiiv viivvi vv vii vivv v i vi
RLTR6-int#LTR 4214 TGCGGTGGTGGACGGGAAACAGGTAATTTGGGCAAGCGCTTTGCCTGAAG 4263
galGal6_dna 23116 GGACTTTCCCTCAGAAGGCTGAAATAACTGCCTTGGCAAGAGCCT----- 23160
i v ivv i i v iv ii vi vi i-----
RLTR6-int#LTR 4264 GAACATCAGCCCAAAAGGCTGAACTAATAGCTCTCACACAAGCCCTTCGA 4313
galGal6_dna 23161 ------G-------------AAATATATGAACAGATGCTAATTATGTATT 23191
------i-------------v i v iv v iivi iv iv
RLTR6-int#LTR 4314 GAGGCTAAAGGTAAGATCATCAACATCTACACTGACAGCAGGTATGCTTT 4363
galGal6_dna 23192 TGGGATGCTACACACTCATTGTACTATCTGAAAAGAGCAAGGATTGCTCA 23241
vv iiviv iiii v vi i iv iiv vi ii i v
RLTR6-int#LTR 4364 TGCCACAGCCCATGTCCATGGGGCCATCTATAGGCAGAGAGGGCTACTGA 4413
galGal6_dna 23242 CA-CACAAGG-AAAAACAG------------------------------- 23258
- vv - i v-------------------------------
RLTR6-int#LTR 4414 CATCAGCAGGAAAAGACATTAAAAATAAAGAAGAAATTCTGGCCCTATTA 4463
galGal6_dna 23259 CATGATGTAAATCTACCAAAGAGCCTGGCTATTATATATTGTAAAGGACA 23308
v v vii v v v v ivv i i vi i ivvv
RLTR6-int#LTR 4464 GAGGCCATACATGTACCTAACAAGGTGGCCATCATCCACTGCCCTGGACA 4513
galGal6_dna 23309 TCAGAAAGGTAACACTGTACAGGAAACTGGAGATAAGATGGTGGTTCAGG 23358
i i vi viviv ivv vv vv vi iv i ii viivi
RLTR6-int#LTR 4514 CCAAAAAGGAGAAGACTTGGTGGCCAGGGGCAACCAAATGGCAGACTTAG 4563
galGal6_dna 23359 TGGCATAACAGGTAGTT-----GAACAAGGCTATAATTGCAGAAGGTAAA 23403
v i v i ----- iv v iiiv i v i i v
RLTR6-int#LTR 4564 TGGCAAAACAAGTTGCTCAAGGGGCCATGATCTTAACTGAAAAAGGTGAT 4613
galGal6_dna 23404 ---CTTAAAATTTCTGA--ACCTGAGTCAGAACCTGTAAAATATTTTAAA 23448
--- ii vii -- vv vi v v iv i vv v viv-
RLTR6-int#LTR 4614 CCGCCCAAAAGCCCTGAGGACGAGAGGTATAACATAAAAGAGCTATGGT- 4662
galGal6_dna 23449 GAGGATAGCAATCTAATT---AATGATTTAGAAGGGAAGAGAGCA--AGC 23493
-i ivi ii ivv i---v vv v i v v -- i
RLTR6-int#LTR 4663 -GGACCAGTGATCCCCTCCCATATTTTTTTGAAGGGAAAATAGAATTAAC 4711
galGal6_dna 23494 TGAC------------AGATGGGT-----ACATGCCCAGATGGACACACT 23526
vv ------------ i vv -----ivv i v vi vv v i
RLTR6-int#LTR 4712 TCCCAAAGAAGGAATAAAATTTGTGAAAGGACTACACCAATTCACCCACC 4761
galGal6_dna 23527 GTTGTGCCCTTTAGTATTCTATGGAAATTGGTT--------------CTA 23562
vvv v iiv----iv vvv ivv i i i --------------
RLTR6-int#LTR 4762 TGGGAGTTA----AAAAAATGATGAGACTAGTTAAAAATTCCCGATACTA 4807
galGal6_dna 23563 AGGGAGGATAAGAAAATGT----ACTGGGCAAACGGACATTACAAAG--- 23605
vvvv-----i vv v---- v viv --ii v i i v---
RLTR6-int#LTR 4808 AGTTCC-----AAACCTGAAGTCAGTGGCTCA--AAAGATTATAGACTCC 4850
galGal6_dna 23606 TACGATCCTAGTACCAGGAAC-----------AGGGTACAAGTGGGCCTG 23644
i i v vv i vvvv vi----------- vv - v ii
RLTR6-int#LTR 4851 TGCAAACCATGTGCATTCACTAATGCAACTAAAGCCTAC-AGAGAACCTG 4899
galGal6_dna 23645 TTGGGAA------AGGGAACCTTCCAGGGCAACAGTGACAAACTGATTTC 23688
vvii i------i ii v v ivvvi v iv iiv i i
RLTR6-int#LTR 4900 GAAAGAGACAACGGGGAGACCGTCCTGGAGTCTATTGGGAAGTAGACTTT 4949
galGal6_dna 23689 T-TGAAA--CTCCCAAGAAAAGGGGGGTATCGCTGTATGTTGGTACTAAC 23735
v- i--vvv i iviv vv viv i v i vi vii
RLTR6-int#LTR 4950 ACTGAAGTAAAACCAGGAAAGTATGGTAATAAGTATCTGTTAGTTTTTGT 4999
galGal6_dna 23736 TGATACCTTTTCGGGATGGCCAGAAG 23761
v i vi i
RLTR6-int#LTR 5000 AGATACCTTTTCAGGATGGGTAGAGG 5025
Matrix = HMM
Kimura (with divCpGMod) = 68.70
Transitions / transversions = 0.78 (207/266)
Gap_init rate = 0.07 (78 / 1094), avg. gap size = 2.91 (227 / 78)
154 38.68 13.30 2.35 galGal6_dna 22668 23321 26121 + PABL_B-int LTR/ERV1 3541 4264 2858
154 38.68 13.30 2.35 galGal6_dna 22668 23321 (26121) PABL_B-int#LTR/ERV1 3541 4264 (2858) m_b1s001i13
galGal6_dna 22668 TAAGAGATGGCCAGAGTGGCTGAGGGCAGTGGTTGC-ACTAGTGCTCAAT 22716
i i vvvv v v i - iv --iviiv
PABL_B-int#LT 3541 CAAGGGATGGCCCCCTTGCCTCAGGGCAGTGGCTGCCACCTG--TGTGCT 3588
galGal6_dna 22717 ATTCTAG-AAGCCAGCAAATTTACG-----------AATAACAGTGTTAA 22754
vi v - iiiv i v-----------v v vvi
PABL_B-int#LT 3589 TCTCAAGGAAGCTGAAAAGTTTACCTTGGGACAGCCTATCACAGTGTATG 3638
galGal6_dna 22755 TATCTCATACAGTGTCTACTGCATTGGAGGTAAAAGGGGGGCATTGGCTC 22804
ii i ivv ivi vi i ivv i i vi i v
PABL_B-int#LT 3639 TGCCCCACCAAGTGTTAGCTTTACTGGAACAAAAGGGAGGCTACTGGCTG 3688
galGal6_dna 22805 TCACCCCCAAAGGTTCCTGAAATACCAGGCCATCCCAGTAGAGCAGGATG 22854
v vv v-viv i vvvv i ivv ------ i
PABL_B-int#LT 3689 ACTGCA-GGCAGATTGGGCAAATATCAGGCCATCCTTCTA------GATA 3731
galGal6_dna 22855 ATGCAGAAATAATTGTAACTAATAATG------TCAACCCAGCATCTTTC 22898
iv i vi i viv ivvv vi viv------ v v vv i v
PABL_B-int#LT 3732 ACCCAAATGTGAACCTGCAAACCACCTCAACCTTAAACCCTGCCACCTTG 3781
galGal6_dna 22899 CTT--------AGAGGAACTCCTGAAGAACCAGTATTTCATGACTGCTTT 22940
--------v i i -- v vi --- i i v
PABL_B-int#LT 3782 CTTCCTCCCACTGGGGAGC--CAGAAGAACCTATA---CATAACTGTTTA 3826
galGal6_dna 22941 GAAACAACTGCGGCTATGGGCTGTTGCCAGTCGGACCTGAAAGACGAACC 22990
iv i vvvvvi vvii viv ii i i i v v
PABL_B-int#LT 3827 GAAATTATTGATCAAGTTTATTCCAGCCAACCAGACTTGAAGGACGCAGC 3876
galGal6_dna 22991 CTTAGAAGATGCAGAAGACCCTTGGTTTAATGATGGAAGCAGTTTTGTGA 23040
i vvv vi vvivvvv v i v i v v
PABL_B-int#LT 3877 CCTCCCATGTGCAGACTGGAAATTGTTCACTGATGGAAGCAGCTTGGTCA 3926
galGal6_dna 23041 GACAAGGAAACCGTAAGGAAGGATATCC---AGTAACTGCTACTGACAAG 23087
viv vi i vv v v vv i v ---i i iviiv v ---
PABL_B-int#LT 3927 CGGACAGGAAGAGAAATGCTGGGTATGCTGTGGTGACCTTCTCAG---AG 3973
galGal6_dna 23088 GTAATTGAAGCACAACCATTACCTGTGGGGACTTTCCCTCAGAAGGCTGA 23137
v i vi v v i ii i ivv v
PABL_B-int#LT 3974 GTAATAGAGGCAAGAACTTTGCCTGCAGGGACCTCAGCACAGAAGGCTGA 4023
galGal6_dna 23138 AATAACTGCCTTGGCAAGAGCCT------------------------GAA 23163
iv i i vi v ------------------------vv
PABL_B-int#LT 4024 GCTAATTGCCCTTACCAGAGCCTTACAACTGTCCCAAGGTAAGAGAGTCA 4073
galGal6_dna 23164 ATATATGAACAGATGCTAATTATGTATTTGGGATGCTACACACTCATTGT 23213
i v iv v v i v iv iiv i iv v ii v v
PABL_B-int#LT 4074 ACATTTACACTGATTCCAAGTATGCTTTCATGGTAGTCCATGCTCATGGG 4123
galGal6_dna 23214 ACTATCTGAAAAGAGCAAGGATTGCTCACAC------ACAAGGAAAAACA 23257
i i ivii ii v vi------ i i vvv
PABL_B-int#LT 4124 GCTATCTGGAAAGAAAGGGGGCTGCTAACTTCAGATAATAAAGAAATTAA 4173
galGal6_dna 23258 GCATGAT--GTAAAT-------CTACCAAAG--------AG-CC------ 23283
i v -- v -------i ii i --------i - ------
PABL_B-int#LT 4174 ACATGCTAAGGAAATTTTAGCATTATTAGAGGCAGTAAAGGCCCCACAGG 4223
galGal6_dna 23284 ---TGGCTATTATATATTGTAAAGGACATCAGAAAGGTAAC 23321
--- i v ii i ivvv v i vi i
PABL_B-int#LT 4224 AAGTAGCTATAATGCACTGCCCTGGCCATCAAAACAGTAAT 4264
Matrix = HMM
Kimura (with divCpGMod) = 55.05
Transitions / transversions = 0.87 (115/132)
Gap_init rate = 0.05 (31 / 653), avg. gap size = 3.35 (104 / 31)
+ 96 40.8 6.5 5.6 galGal6_dna 23742 24341 (25149) + PABL_B-int LTR/ERV1 4896 5475 (1647) 18 *
ANNOTATION EVIDENCE:
23 39.33 6.98 8.78 galGal6_dna 23742 24042 25400 + MURVY-int LTR/ERV1 4896 5191 2261
23 39.33 6.98 8.78 galGal6_dna 23742 24042 (25400) MURVY-int#LTR/ERV1 4896 5191 (2261) m_b1s001i14
galGal6_dna 23742 CTTTTCGGGATGGCCAGAAGTAGCAATCTCATCAGATTGA-GGCCCACAT 23790
vv i vv i---- i v vv ii viv- ii
MURVY-int#LTR 4896 CGGTTTGGGATCCCCAGG----GTAATATGCTTGGATAATGGGCCTGCAT 4941
galGal6_dna 23791 TTTTTTTGCCAAGGTGGTCCAACAAATAAGCACATTATTGGGAATTGATT 23840
--v v iivi iv v iv ivv i vii
MURVY-int#LTR 4942 TT--GTTGCCCAGGTAAGTCAGGAATTAGCCACACATTTGGGGAACAATT 4989
galGal6_dna 23841 GGCAATTGCACACACCTTATAGACCGCAGTCAAGCAGACAGGTGGAAAAA 23890
v i ii ivvvv i v vv vvviv i i ii
MURVY-int#LTR 4990 GGAAGTTATATTGTGCTTATAAACCCCAGAGATCAGTATAGGTAGAAGGA 5039
galGal6_dna 23891 ATGAAT---------------CACCTGATCAAATTACAGATAGTAAAACT 23925
i---------------vv i ii -- v vv i i i
MURVY-int#LTR 5040 ATGAACAGGACTCTAAAAGAAACCCTAACTAAATTA--GCTTTTGAGACC 5087
galGal6_dna 23926 TGGCCAAGAGGCTGGGATTCCCTGGCTGCAGGCACTGCCTTTGGCACTTC 23975
v vvvv i i vvv v---------- v i v ii i
MURVY-int#LTR 5088 AGTGGTAAAGACTGGGTGACCCTC----------CTTCCCTTTGTGCTCC 5127
galGal6_dna 23976 TGAGAATTCGGACTAAACCCCGAACCAAGGA-----AGGATTAAGCCCAT 24020
v iiii i vi v i-------- i-----v vv v vi v
MURVY-int#LTR 5128 TTAGGGCCCGAAACACACCT--------GGGTGTTTCGGCATTACTCCTT 5169
galGal6_dna 24021 ATGAGATTCTTTATGGGTGACC 24042
i vi v
MURVY-int#LTR 5170 ATGAAATTCTACATGGGGGACC 5191
Matrix = HMM
Kimura (with divCpGMod) = 56.54
Transitions / transversions = 0.89 (51/57)
Gap_init rate = 0.10 (29 / 300), avg. gap size = 1.62 (47 / 29)
96 42.25 5.91 2.43 galGal6_dna 23784 24341 25101 + PABL_B-int LTR/ERV1 4899 5475 1647
96 42.25 5.91 2.43 galGal6_dna 23784 24341 (25101) PABL_B-int#LTR/ERV1 4899 5475 (1647) m_b1s001i15
galGal6_dna 23784 CCCACATTTTTTTTGCCAAGGTGGTCCAACAAATAAGCACATTATTGGGA 23833
iv v -- ii i iiii i i ivv vi
PABL_B-int#LT 4899 CCTTCATTTATTT--CTGAAGTAACTCAGCAAGTAAGTCAAGCATTGGGA 4946
galGal6_dna 23834 ATTGATTGGCAATTGCACACACCTTATAGACCGCAGTCAAGCAGACAGGT 23883
vi v v i i iv i v iv i i v vii v iii
PABL_B-int#LT 4947 ATAAAATGGAAACTACATTCATCATGGAGACCACAATCTACTGGAAAAAC 4996
galGal6_dna 23884 GGAAAAAATGAATCACCTGATCAAATTACAGATAGTAAAACTTGGCCAAG 23933
v vivv v vv vvv v iv iv i i
PABL_B-int#LT 4997 TGAAAAAATGAATCACACCTTAAAAAAAATCATTGCCAAACTCTGTCAGG 5046
galGal6_dna 23934 AGGCTGGGATTCCCTGGCTGCAGGCACTGCCTTTGGCACTTCTGAGAATT 23983
ii ii v vvvv v vv i vvv v v v v vv ii v
PABL_B-int#LT 5047 AAACTAAGTTGAAATGGATTAAGGTACTTGGTATTGCCCTGCTCTGGGTA 5096
galGal6_dna 23984 CGGACTAAACCCCGAACCAAGGAAGGATTAAGCCCATATGAGATTCTTTA 24033
v iiivivv v viii vvvii v v i v
PABL_B-int#LT 5097 AGAGTAGCCCCCAGAAGTGGGCTTAAATTAAGCCCTTTTGAAATTATTTA 5146
galGal6_dna 24034 TGGGTGACCTTATACTGTA---CAA---AAGGAAATCTCTGTGCCGGTGG 24077
v i v i v iv--- vi---vi vv iivvv vv i
PABL_B-int#LT 5147 TGGGAGACCCTTTGCAGCTAACCCGTCTCGGGTTACTGAAGTGCCTCTAG 5196
galGal6_dna 24078 AGGATGAAGTG---TTGAGTGAATATAT-GGTCAGCTTGGCAAAACAATT 24123
vii iv i---v v ivi v i -iv vi v vv vv
PABL_B-int#LT 5197 ATAGTGAGTTAGCTATTAAGAATTATGTTACTCACTTAGGACAAACTCTT 5246
galGal6_dna 24124 AAAGAAAATTGAGAAAATGGTATTCGCTGC---CAGG-GCACGAGG---C 24166
vvvv-- viv -----i i v --- - i viv ---
PABL_B-int#LT 5247 AACCTT--TTGCATAA-----GTTTGCTTCTAACAGGAGCGCTGTGAACC 5289
galGal6_dna 24167 CTAGATGGTCCAGTGCATGATGCATT---ACCAGGCGACTGTGTCTATGT 24213
v - i--- iv viv iv v ---i v iviv vi- i
PABL_B-int#LT 5290 CTACA-GA---AGCCCTCCACCCTTTCCAGCCAGGAGATAAAGTGC-TGC 5334
galGal6_dna 24214 TAAATCCCT-------------CTCAGATTCACCTTTGGAACCAAGGTGG 24250
vi v -------------ii iiv vvi ivvivv ii
PABL_B-int#LT 5335 TAAAGTCATGGAAGGAAACAGGTCCAGACCAACAACTACCGGAAAAATGG 5384
galGal6_dna 24251 GAAGGACCCTACCATGTACTTCTGACCACCCACACAGCAGCGAAAGTAGA 24300
i i i iv v i v i v v i v i v
PABL_B-int#LT 5385 AAAGGGCCTTATGAGGTGCTGCTGACCACTCACTCATCAGTGAAACTGGC 5434
galGal6_dna 24301 AGGATGGACACCGTGGATACATCATACCCGCCTGAAGAAAG 24341
vvvv vi v v i ii vv i i v
PABL_B-int#LT 5435 AGGCATTAAGCCTTGGATCCATCACACTTGAGTAAAAAAAT 5475
Matrix = HMM
Kimura (with divCpGMod) = 61.35
Transitions / transversions = 0.80 (102/128)
Gap_init rate = 0.04 (23 / 557), avg. gap size = 2.04 (47 / 23)
+ 120 36.7 4.1 2.2 galGal6_dna 26285 26722 (22768) + CR1-J3_fAlb LINE/CR1 287 732 (2873) 19
ANNOTATION EVIDENCE:
120 36.66 4.11 2.24 galGal6_dna 26285 26722 22720 + CR1-3_Croc LINE/CR1 287 732 2873
120 36.66 4.11 2.24 galGal6_dna 26285 26722 (22720) CR1-3_Croc#LINE/CR1 287 732 (2873) m_b1s001i16
galGal6_dna 26285 GTTGGAAGACATTGTGTG-GCAGGTAAGCATGACCTAATTGCCATTACGG 26333
i viiiv iv - v iiv vi i i v i i
CR1-3_Croc#LI 287 GCTGGAAGCTGCAGCCTGTGAAAAGAACTATGATCTGATTGGCATCACAG 336
galGal6_dna 26334 AAACATGGTGGGACCACTCCCATGACTGGAGTGCTGCAATGGATGGCTAC 26383
i v vi ii i iiivv v v i
CR1-3_Croc#LI 337 AGACCTGGTGGGACAGCTCTTATGACTGGAATGTCAACATTGAGGGTTAC 386
galGal6_dna 26384 AAATTCTTCAGGAAGGATAGGCAAGGAAGGAGGGGCGGTGGCGTGGCTCT 26433
vvi v iv i vvv i i ii i i v ii
CR1-3_Croc#LI 387 ACTCTGTTTTGGAAGGACAGGGTTGGGAGAAAAGGTGGTGGTGTTGCCTT 436
galGal6_dna 26434 CTATGTTAGAGAGTGCT-TTGATGTTACTGAGCTTA--TGGCTGGGGATG 26480
v i i i vvvv -ivvv v ivi i i --v vv ii i
CR1-3_Croc#LI 437 GTATGTCAAAAACACATACACTTGTTCCCTGGTTCAGGAGGAAGAAGATA 486
galGal6_dna 26481 ATAAGGTTGAATCCCTATGGGTAAAGAACAAGG--GAAGG--GCTGACAA 26526
ii i iv v v v i vv i -- i -- v vvvv
CR1-3_Croc#LI 487 GCAAAGCAGAATGCATTTGGGTGAAGATGAAAGGTGAAAGATGCAGCACC 536
galGal6_dna 26527 GACATCCTGGTGAGCATCTGTTATAGACCGCCAAACCAGGATGAAGAGAC 26576
i vv i v i i i i i v i ii
CR1-3_Croc#LI 537 GATATAATGGTGGGGATTTATTATAGGCCACCAAATCAGGAAGAGGAGGT 586
galGal6_dna 26577 AGATAAGGTGTTCTGCGAGCAGCTGGCAG----------AAGCTGCGTGA 26616
i i iii v i v i i---------- ii v
CR1-3_Croc#LI 587 GGATGAGGCACTCTTCAAGCAGGTGACAAATCTATCCAAAAGCTATGGGA 636
galGal6_dna 26617 TCGGCAGCCCTTGTCCTCATGGGGGACTTCAACTTCCCTGACATATGCTT 26666
---------- v v v i i i v v v
CR1-3_Croc#LI 637 ----------TGGTACTGATGGGAGACTTCAATTTTCCGGACATCTGCTG 676
galGal6_dna 26667 GGAATACAACATAATGCAGAAGAAGCAGTCTAGGAGGTTTCTGGAATGTA 26716
i iv iii iivv iv v ivv v vvi i iivv i
CR1-3_Croc#LI 677 GAAGAACAATGCAGCCAAACATAAAATGTCAAGCCAGTTCCTAACTTGTG 726
galGal6_dna 26717 TGGAGG 26722
CR1-3_Croc#LI 727 TGGAGG 732
Matrix = HMM
Kimura (with divCpGMod) = 52.11
Transitions / transversions = 1.24 (87/70)
Gap_init rate = 0.04 (16 / 437), avg. gap size = 1.75 (28 / 16)
+ 806 24.1 0.3 1.2 galGal6_dna 26727 28441 (21049) + CR1-J3_fAlb LINE/CR1 2 2978 (627) 19
ANNOTATION EVIDENCE:
638 35.98 1.19 1.69 galGal6_dna 26727 28329 21113 + CR1-3_Croc LINE/CR1 1384 2978 627
638 35.98 1.19 1.69 galGal6_dna 26727 28329 (21113) CR1-3_Croc#LINE/CR1 1384 2978 (627) m_b1s001i17
galGal6_dna 26727 AAAAGGCAGAGGTTCTCAATGCCTTCTTTACGTCTGTCTTTAAAAGTCAG 26776
i v v iiv v i v v i v ivv i
CR1-3_Croc#LI 1384 AGAAGGCAGAGCTACTCAACAGCTACTTTGCCTCAGTCTTCACAAAAAAA 1433
galGal6_dna 26777 ----------ACCAGTTATC--CTCAGGGTACTCTGCTCTCTGACATGGT 26814
----------i vi i --v v i vv i ------ i v v
CR1-3_Croc#LI 1434 TTAAGCTGCAGCCAGACACCTAATAAGGATTATTTG------GATAAGGA 1477
galGal6_dna 26815 AGTCTCGGCTGGGGAGCAGACTAAACCCCCCACGATTCAGGAGGAAACAG 26864
---------- i ii i iv--vviiv vvvii i i i
CR1-3_Croc#LI 1478 AG----------GGGGCAAGCTGAGG--GATGAGATAACAAAAGAGACGG 1515
galGal6_dna 26865 TCAGAGACC----GACTACTCTAAATGGACAGCCACAAGTCCATGGGACC 26910
v ---- iviv i i i----v viii i
CR1-3_Croc#LI 1516 TCAGAGAGCTTTTGATGGGTCTGAATGAAT----TCAAGTCAGCAGGGCC 1561
galGal6_dna 26911 AGATGAGGATTCACCCAAGAGTGCTGAGGGAACTGGCGGAGGTGATAGCC 26960
v i-v i v i i i i v vv v
CR1-3_Croc#LI 1562 TGATGAA-CTTCATCCCAGGGTACTGAAGGAACTGGCAGAGGAGATCTCG 1610
galGal6_dna 26961 GAGCTGTTTTCCATCATCTATCAGCGCTCCTTGTTGACAGGTGAGGTCCC 27010
iv vv v v vivv viv v v vv ii iv v
CR1-3_Croc#LI 1611 GAGCCCTTGGCAATGATCTTCATGAAGTCGTGGGAGATGGGCCAGGTACC 1660
galGal6_dna 27011 AGAAGACTGGAGTTTTGCCAATGTGACTCCCATCTACAAGAAGGGCTGCA 27060
i ivvvv ii iiiv v vi i i viv
CR1-3_Croc#LI 1661 AGAGGACTGGAAAAGGGCCAACATAGTGCCCCTCTTTAAAAAAGGCAAAA 1710
galGal6_dna 27061 GGGAGGATCCGGGGAACTACAGGCCTGTTTGCCTGACCTCAGTGCCAGGG 27110
i i i iv v v i i v
CR1-3_Croc#LI 1711 AGGAGGACCCGGGGAACTACAGACTGGTTAGCCTCACCTCAATACCTGGG 1760
galGal6_dna 27111 AAGGTTATGGAGCAGATTGTCTTGAGGGAGATCACGCG---GCACGTGCA 27157
v vv v --- i i i ii ivi --- iv v
CR1-3_Croc#LI 1761 AAGTTACTGGAGCATA---TCCTAAGGAAGGCCATTTGCAAGCATCTGGA 1807
galGal6_dna 27158 GGACAACCGGGGGATCAGGCCTAGCCAGCATGGGTTCAAGAAGGGCAGGT 27207
vi vv vv vivvi i i v iii ii
CR1-3_Croc#LI 1808 GGAGGAAAGGCTGATCACAAGCAGCCAGCATGGATTTATGAAAAACAAAT 1857
galGal6_dna 27208 CCTGCTTGACCAACCTGATCTCCTTCTATGATCTAGTGACCCGTCTGGTG 27257
v iivi v i v ivv i ivv iv
CR1-3_Croc#LI 1858 CATGTCAAACAAACTTGATCTCCTTCTTTGACAAAGTAACTACTTGGGTG 1907
galGal6_dna 27258 GATGAGGGAAAGGCTGTTGATGTAGTCTACCTAGACTTCAGCAAAGCCTT 27307
i i v v i v i i i i
CR1-3_Croc#LI 1908 GATGAAGGGAATGCTGTGGATATAGTGTATCTGGACTTCAGCAAGGCTTT 1957
galGal6_dna 27308 TGACACTGTCTCCCACAGTATTCTCCTGCAGAAGCTGGCAGTCCGTGGCT 27357
vv i v iiiiv v iv v ii viivvi vi
CR1-3_Croc#LI 1958 TGACAAGGTCCCACATGACCTTCTCATAAACAAATTGGAGAAATGTGGGC 2007
galGal6_dna 27358 TGGACAGATACACTCTTGGCTGGGTAAGGAACTGGCTCAAGGGCAGGGCC 27407
i vvi v vi v i iiv vi vivivv
CR1-3_Croc#LI 2008 TGGACAAAACTACTATAAGGTGGATAGATAACTGGCTCAATAGCCACAAG 2057
galGal6_dna 27408 CAGAGAGTGGTGGTGAATGGAGTTAAATCCAGCTGGCAACCAGTCACGAG 27457
i i ii vi v ivii vi viiv ivvi ivi
CR1-3_Croc#LI 2058 CAAAGGGTAATTATTAATGGGTCCATGTCAGAATGGCAGGAGGTTTTGAG 2107
galGal6_dna 27458 TGGTGTTCCCCAGGGGTCGGTGCTGGGGCCTGTCCTGTTTAATATCTGTA 27507
v i v v v v v v i ii v v
CR1-3_Croc#LI 2108 TGGAGTCCCACAGGGGTCTGTCCTGGGCCCAGTGCTGTTCAACGTGTTTA 2157
galGal6_dna 27508 TTGATGACCTGGATGAGGGCATTGAGTGGACCCTCAGTAAGTTTGCAGAT 27557
i ii vv v iv vvi i v i
CR1-3_Croc#LI 2158 TTAATGATTTGGATGCTGGCATAGAAAGCTTCTTGAGCAAGTTTGCAGAT 2207
galGal6_dna 27558 GACACCAAGCTGGCTGGAAGTGTTGATCTGCCTGAGGGTAGCGAGGCCCT 27607
iv i vvi i v vi iviiiiv i i viiv vv
CR1-3_Croc#LI 2208 GACATGAAACTGGGAAGGATTGTGAACACATTGGAGGATGGGAGTGCAAT 2257
galGal6_dna 27608 ACAGAGGGATCTGGATAGGTTGGATAGCTGGGCTGAAGCCAATGGGATGG 27657
v i v i i v ii i ii i
CR1-3_Croc#LI 2258 TCAGAAGGATCTTGACAGATTGGAAAGCTGGGCTAGAGCTAACAGGATGA 2307
galGal6_dna 27658 GATTCAACAAGACCAAATGCCGGGTCCTGCACTTTGGCCACAATAACCCC 27707
ii iivviv vi v i i i vv v i vv
CR1-3_Croc#LI 2308 AGTTCAATGCTGACAAATGCAAGGTGCTACACCTCGGGAAGAATAATCAA 2357
galGal6_dna 27708 AGGCAACGCTACAGGCTTGGGGCAGAGTGGCTGGAAGACTGTGTAGAGGA 27757
ii vviv iiv v v vvivv v i v iiiviv
CR1-3_Croc#LI 2358 AAACACAAATACAAAATGGGTGACACCTGGCTGGATGGCAGCACTATGGA 2407
galGal6_dna 27758 AATGGACCTGGGGGGTGCTGATTGACGCTAGACTGAACATGAGCCAGCAG 27807
i v ii -i vi i v ivvi v i i v
CR1-3_Croc#LI 2408 GAAGGATTTGGG-AGTCTTGGTAGATCACAGACTCAATATGAGTCTGCAG 2456
galGal6_dna 27808 TGTGCCCAGGTGGCCAAGAAGGCCAATGGCATCCTGGCTTGTATCAGAAA 27857
vivvi iv vv i v vvi ii vv i iv i
CR1-3_Croc#LI 2457 TGTGATGCAGCTGCACAAAAGGCAAATGCGGTTTTGGGATGCATCAATAG 2506
galGal6_dna 27858 TAGTGTGGTCAGCAGGAACAGGGAAGTAATTGTCCCCCTGTACTCAGCAC 27907
v ii vivvv i vvv i i v v i v i
CR1-3_Croc#LI 2507 AAGCATTAGGTGCAAGACATGGGAGGTGATAGTGCCTCTCTACTCGGCAC 2556
galGal6_dna 27908 TGGTGAGGCCGCACCTCAAGTACTGTGTCCAGTTTTGGGCCCCTCACTGT 27957
v v i vi v i i v i v
CR1-3_Croc#LI 2557 TGGTTAGGCCTCATCTGGAGTACTGTGTGCAGTTCTGGGCTCCACATTTT 2606
galGal6_dna 27958 AAGAAAGACATCAAGGCCCTGGAGCGTGTCCAGAGAAGGGCAACAAAGCT 28007
i i i vi ivvi i v v ivi v
CR1-3_Croc#LI 2607 AAAAAGGACGTGGAGAAGTTAGAGAGGGTCCAGAGGTAGGCAACAAAGAT 2656
galGal6_dna 28008 GGTAAGGGGTCTGGAGCACAGGCCTTACGAGGAGCAGCTGAAGGAGCTGG 28057
i i ii ivi i i v i vi i
CR1-3_Croc#LI 2657 GATAAAGGGCTTGGAAGGCAAGTCATATGAGGAGAGGCTGAAGGAGCTAG 2706
galGal6_dna 28058 GATTGTTCGGTCTAGAGAAGAGGAGGCTCAGGGGAGACCTTATTGCTCTC 28107
vv i ii ivi i v vi v i i v v v vv
CR1-3_Croc#LI 2707 GCATGTTCAGCTTGTGGAAAAGGTGCTTAAGAGGGGACATGATAGCAGTC 2756
galGal6_dna 28108 TATAACTACCTGAAAGGAGGTTGTAGTGAGCTGGGGGTCGGCCTCTTCTC 28157
vi v i i vv iii iv ivv iivvvi i
CR1-3_Croc#LI 2757 TTCAAATACTTGAAGGGCTGCCATAAAGAAGAGGGAAAGCACCTTTTCTC 2806
galGal6_dna 28158 TCGTGTGACTAGTGATAGGACTAGAAGGAATGGCTTCAAGCTGCGCCGTG 28207
v ivi viiviiv ivv i vv v i iv ivi
CR1-3_Croc#LI 2807 TCTTGCTGCAGAGAGGAGGATGTGGACCAATGGCTTGAAGTTGCAGCAAA 2856
galGal6_dna 28208 GTAGTTTCAGGCTGGACGTTAGGAAATACTACTTCTCTGAAAGGGTGGTC 28257
v i ii ii i v v v vv iiii v
CR1-3_Croc#LI 2857 GTAGGTTTAGATTGGATATCAGGAAAAACTTCTTCACTGTTAGAACAGTG 2906
galGal6_dna 28258 AGGCACTGGAATGGGCTGTCCAGAGAGGTGGTGGAGTCACCGAGCCTGGT 28307
v i i i i i i v v v ivvv v
CR1-3_Croc#LI 2907 AGGCAGTGGAATAGACTGCCTAGGGAAGTTGTGGACTCTCCATCACTGGA 2956
galGal6_dna 28308 GGTGTTCAAAGAGCATTTGGAT 28329
ii viv i
CR1-3_Croc#LI 2957 GGTGTTCAAGAAGAGGTTGGAC 2978
Matrix = HMM
Kimura (with divCpGMod) = 49.51
Transitions / transversions = 1.08 (294/273)
Gap_init rate = 0.02 (31 / 1602), avg. gap size = 1.48 (46 / 31)
791 24.45 0.36 1.56 galGal6_dna 27340 28440 21002 + CR1-K4_fAlb LINE/CR1 3 1090 1
791 24.45 0.36 1.56 galGal6_dna 27340 28440 (21002) CR1-K4_fAlb#LINE/CR1 3 1090 (1) m_b1s001i18
galGal6_dna 27340 AGCTGGCAGTCCGTGGCTTGGACAGATACACTCTTGGCTGGGTAAGGAAC 27389
ii i ivi i v v v vi
CR1-K4_fAlb#L 3 AATTGGCAGTCCATGGCTTGGACAGGAGCACTCCTTGCTGGGTTATGACT 52
galGal6_dna 27390 TGGCTCAAGGGCAGGGCCCAGAGAGTGGTGGTGAATGGAGTTAAATCCAG 27439
v ivv vvi v v v v i vv v
CR1-K4_fAlb#L 53 AGGCCGTATCACCGGGCCCAGTGTGTTGTGGTGAATGGAGCTCCATCCTG 102
galGal6_dna 27440 -CTGGCAACCAGTCACGAGTG-GTGTTCCCCAGGGGTCGGTGCTGGGGCC 27487
- i iiv ii v v- i vi v i v i v
CR1-K4_fAlb#L 103 GCTAGTGCCTGGTCACCAGTTCGTGTCCATCCGGAGTCTGTGTTGGGGAC 152
galGal6_dna 27488 TGTCCTGTTTAATATCTGTATTGATGACCTGGATGAGGGCATTGAGTGGA 27537
v i v i v v iivi iv i ivvv
CR1-K4_fAlb#L 153 TGTGCTGTCTAATTTTTTTAGTGGCTGCCTGGATGAGGAGATCGAGCCTT 202
galGal6_dna 27538 CCCTCAGTAAGTTTGCAGATGACACCAAGCTGGCTGGAAGTGTTGATCTG 27587
ii i vi v viv i
CR1-K4_fAlb#L 203 CTTTCAGTAAGTTTGTAGATGACAATAAGCTGGCAGTGTGTGTCGATCTG 252
galGal6_dna 27588 CCTGAGGGTAGCGAGGCCCTACAGAGGGATCTGGATAGGTTGGATAGCTG 27637
iv i vii i i i i vv i v
CR1-K4_fAlb#L 253 CTGGAAGGTAGGAGGGCTCTGCAGAGAGACCTGGAATGGCTGGATAGATG 302
galGal6_dna 27638 GGCTGAAGCCAATGGGATGGGATTCAACAAGACCAAATGCCGGGTCCTGC 27687
v iv ii ii i i v i i
CR1-K4_fAlb#L 303 GGCAGAGTCCAATAAGATGAAATTTAATAAGTCCAAGTGCCGAGTCCTGC 352
galGal6_dna 27688 ACTTTGGCCACAATAACCCCAGGCAACGCTACAGGCTTGGGGCAGAGTGG 27737
i vv vv ii i v i v
CR1-K4_fAlb#L 353 ATTTTGTGCACAATAACCCCCTGCAGTGTTACAGGCTGGGGACAGTGTGG 402
galGal6_dna 27738 CTGGAAGACTGTGTAG-AGGAAATGGACCTGGGGGGTGCTGATTGACGCT 27786
vii- ivi -vi v - i ivi
CR1-K4_fAlb#L 403 CTGGACAG-TGCCCAGGCAGAAAGGGACCTGGG-GGTGCTGGTTGACAGC 450
galGal6_dna 27787 AGACTGAACATGAGCCAGCAGTGTGCCCAGGTGGCCAAGAAGGCCAATGG 27836
v
CR1-K4_fAlb#L 451 CGACTGAACATGAGCCAGCAGTGTGCCCAGGTGGCCAAGAAGGCCAATGG 500
galGal6_dna 27837 CATCCTGGCTTGTATCAGAAATAGTGTGGTCAGCAGGAACAGGGAAGTAA 27886
-i i i i i i i v
CR1-K4_fAlb#L 501 C-CCCTGGCCTGTATCAGGAACAGTGTGGCCAGCAGGAGCAGGGAGGTCA 549
galGal6_dna 27887 TTGTCCCCCTGTACTCAGCACTGGTGAGGCCGCACCTCAAGTACTGTGTC 27936
v i i i i i
CR1-K4_fAlb#L 550 TTCTTCCCCTGTACTCAGCACTGGTGAGGCCACACCCCGAGTGCTGTGTC 599
galGal6_dna 27937 CAGTTTTGGGCCCCTCACTGTAAGAAAGACATCAAGGCCCTGGAGCGTGT 27986
i v v i i ii iiv i
CR1-K4_fAlb#L 600 CAGTTCTGGGCCCCTCAGTTTAGGAAGGACATTGAGATGCTGGAGCATGT 649
galGal6_dna 27987 CCAGAGAAGGGCAACAAAGCTGGTAAGGGGTCTGGAGCACAGGCCTTACG 28036
i - i i i i i i i ii
CR1-K4_fAlb#L 650 CCAGAGGAGG-CAGCAAGGCTGGTGAGGGGCCTGGAACACAAGCCCTGTG 698
galGal6_dna 28037 AGGAGCAGCTGAAGGAGCTGGGATTGTTCGGTCTAGAGAAGAGGAGGCTC 28086
iii i iv i i i i i
CR1-K4_fAlb#L 699 AGGAATGGCTGAGGGAGCTGGGGGTGTTCAGCCTGGAGAAAAGGAGACTC 748
galGal6_dna 28087 AGGGGAGACCTTATTGCTCTCTATAACTACCTGAAAGGAGGTTGTAGTGA 28136
v i ii i v v i v
CR1-K4_fAlb#L 749 AGGGGTGACCTTGTCACTCTCTACAACTCCCTGAAAGGTGGCTGTAGTCA 798
galGal6_dna 28137 GCTGGGGGTCGGCCTCTTCTCTCGTGTGACTAGTGATAGGACTAGAAGGA 28186
v i i iii iv iii v i i i i iv
CR1-K4_fAlb#L 799 GGTGGGGGTTGGTCTCTTCCTCCAGGCAGCAAGTGACAGAACCAGAGGAC 848
galGal6_dna 28187 ATGGCTTCAAGCTGCGCCGTGGTAGTTTCAGGCTGGACGTTAGGAAATAC 28236
ii ii i ii iv v v vi i ii v
CR1-K4_fAlb#L 849 ACAGTCTTAAGCTGTACCAAGGGAGGTATAGGTTGGATATTAGGAAAAAC 898
galGal6_dna 28237 TACTTCTCTGAAAGGGTGGTCAGGCACTGGAATGGGCTGTCCAGAGAGGT 28286
ivi iv v i i i i i v i i
CR1-K4_fAlb#L 899 CTTTTTACAGAAAGAGTGATTAAGTACTGGAATGGTCTGCCCAGGGAGGT 948
galGal6_dna 28287 GGTGGAGTCACCGAGCCTGGTGGTGTTCAAAGAGCATTTGGATGTTGTGT 28336
ivv vv i i iviv v iii
CR1-K4_fAlb#L 949 GGTGGAGTCACCATCCCTGGATGTGTTTAAAAAAAGGTTGGATGTGGCAC 998
galGal6_dna 28337 TGAGGGACATGGTTTAGCGAGAACCATTGGTGAAGGGCGAACGAAT-GGT 28385
vi v v ivii------------i v iv iv v -
CR1-K4_fAlb#L 999 TCGGTGCCATGGTTTAGTTGA------------GGTGTTAGGGCATGGGT 1036
galGal6_dna 28386 TGGACTGGATGATCCTGCGGGTCTTTTCCAACCGTAGCGATTCTATGATT 28435
v i vi vv -i i
CR1-K4_fAlb#L 1037 TGGACTCGATGATCTTGAAGGTCTTTTCCAACCTAA-TGATTCTGTGATT 1085
galGal6_dna 28436 CTATG 28440
i i
CR1-K4_fAlb#L 1086 CTGTA 1090
Matrix = HMM
Kimura (with divCpGMod) = 29.70
Transitions / transversions = 1.68 (166/99)
Gap_init rate = 0.02 (21 / 1100), avg. gap size = 1.00 (21 / 21)
806 20.88 0.00 0.82 galGal6_dna 27457 28441 21001 + CR1-J3_fAlb LINE/CR1 2 978 1
806 20.88 0.00 0.82 galGal6_dna 27457 28441 (21001) CR1-J3_fAlb#LINE/CR1 2 978 (1) m_b1s001i19
galGal6_dna 27457 GTGGTGTTCCCCAGGGGTCGGTGCTGGGGCCTGTCCTGTTTAATATCTGT 27506
v i ii i v v
CR1-J3_fAlb#L 2 GTGGTGTTCCCCAGGGCTCAGTATTGGGGTCAGTCCTGTTTAATATCTTT 51
galGal6_dna 27507 ATTGATGACCTGGATGAGGGCATTGAGTGGACCCTCAGTAAGTTTGCAGA 27556
i i v v v i ii
CR1-J3_fAlb#L 52 ATCGATGATCTGGATGAGGGGATTGAGTGCAGCCTCAGTAAATTTGTGGA 101
galGal6_dna 27557 TGACACCAAGCTGGCTGGAAGTGTTGATCTGCCTGAGGGTAGCGAGGCCC 27606
i v i i iv vi i
CR1-J3_fAlb#L 102 TGACACCAAGTTGGGTGGGAGTGCTGATCTGCTGGAGGGTAGGAAGGCTC 151
galGal6_dna 27607 TACAGAGGGATCTGGATAGGTTGGATAGCTGGGCTGAAGCCAATGGGATG 27656
i i i i v i iiv v
CR1-J3_fAlb#L 152 TGCAGAGGGACCTGGACAGGCTGGATAGATGGGCTGAGGCCAGCTGTATG 201
galGal6_dna 27657 GGATTCAACAAGACCAAATGCCGGGTCCTGCACTTTGGCCACAATAACCC 27706
i i i ii i i i
CR1-J3_fAlb#L 202 AGGTTCAACAAGGCCAGGTGCTGGGTCCTGCACTTTGGCCACAACAGCCC 251
galGal6_dna 27707 CAGGCAACGCTACAGGCTTGGGGCAGAGTGGCTGGAAGACTGTGTAGAGG 27756
vv ii v i iii v ivii v
CR1-J3_fAlb#L 252 CCTGCAGTGCTACAGGCTGGGGACAGAGTGGCTGGAGAGCGGCCCGGCGG 301
galGal6_dna 27757 AAATGGACCTGGGGGGTGCTGATTGACGCTAGACTGAACATGAGCCAGCA 27806
v -i i vivi -
CR1-J3_fAlb#L 302 AAAAGGACCTGG-AGGTGCTGGTTGAGAGCAGACTGAACATGAGCCAGC- 349
galGal6_dna 27807 GTGTGCCCAGGTGGCCAAGAAGGCCAATGGCATCCTGGCTTGTATCAGAA 27856
i i v
CR1-J3_fAlb#L 350 GTGTGCCCAGGTGGCCAAGAAGGCCAATGGCATCCTGGCCTGTGTCAGCA 399
galGal6_dna 27857 ATAGTGTGGTCAGCAGGAACAGGGAAGTAATTGTCCCCCTGTACTCAGCA 27906
i v v i v i i
CR1-J3_fAlb#L 400 ATAGTGTGGCCAGCAGGATCAGGGCAGTGATTCTTCCCCTGTACTCGGCA 449
galGal6_dna 27907 CTGGTGAGGCCGCACCTCAAGTACTGTGTCCAGTTTTGGGCCCCTCACTG 27956
i ii v i vi i v v
CR1-J3_fAlb#L 450 CTGGTGAGGCCACACCTTGAGTTCTGTGTCCAGTTCTGTACCTCTCAATT 499
galGal6_dna 27957 TAAGAAAGACATCAAGGCCCTGGAGCGTGTCCAGAGAAGGGCAACAAAGC 28006
i i i iii iv i i
CR1-J3_fAlb#L 500 CAGGAAGGACACTGAGGTGCTGGAGTGTGTCCAGAGAAGGGCAACAGAGC 549
galGal6_dna 28007 TGGTAAGGGGTCTGGAGCACAGGCCTTACGAGGAGCAGCTGAAGGAGCTG 28056
i i i i i ii i
CR1-J3_fAlb#L 550 TGGTGAAGGGTCTGGAGCACAAGTCCTGTGAGGAGCAGCTGAGGGAGCTG 599
galGal6_dna 28057 GGATTGTTCGGTCTAGAGAAGAGGAGGCTCAGGGGAGACCTTATTGCTCT 28106
i ii i i i ii
CR1-J3_fAlb#L 600 GGGTTGTTTAGCCTGGAGAAAAGGAGGCTCAGGGGAGACCTTATCACTCT 649
galGal6_dna 28107 CTATAACTACCTGAAAGGAGGTTGTAGTGAGCTGGGGGTCGGCCTCTTCT 28156
i i iv v i i
CR1-J3_fAlb#L 650 CTACAACTGCCTGAAAGGAGGTTGTAGCCAGGTGGGGGTTGGTCTCTTCT 699
galGal6_dna 28157 CTCGTGTGACTAGTGATAGGACTAGAAGGAATGGCTTCAAGCTGCGCCGT 28206
i iv ii i i v i iv i ii i i iv
CR1-J3_fAlb#L 700 CCCAGGCAACCAGTGACAGGACAAGAGGACATAGTCTTAAGCTGCACCAA 749
galGal6_dna 28207 GGTAGTTTCAGGCTGGACGTTAGGAAATACTACTTCTCTGAAAGGGTGGT 28256
v v i i i iv i v v v ii
CR1-J3_fAlb#L 750 GGGAGGTTCAGGTTGGACATCAGGAAGAATTTCTTCACAGAAAGGGTAAT 799
galGal6_dna 28257 CAGGCACTGGAATGGGCTGTCCAGAGAGGTGGTGGAGTCACCGAGCCTGG 28306
i ii i i i i i vv
CR1-J3_fAlb#L 800 TAGATATTGGAATGGGCTGCCCAGGGAAGTGATGGAGTCACCGTCCCTGG 849
galGal6_dna 28307 TGGTGTTCAAAGAGCATTTGGATGTTGTGTTGAGGGACATGGTTTAGCGA 28356
vi ii iiivi v v iii v v v i ivi
CR1-J3_fAlb#L 850 AAGTGTTCAAGAAATGACTGTATGTGGCACTCAGTGCCATGGTCTAGTTG 899
galGal6_dna 28357 GAACCATTGGTGAAGGGCGAACGAATGGTTGGACTGGATGATCCTGCGGG 28406
iv i-iv vv ii-----vi v vi iiivi
CR1-J3_fAlb#L 900 ACAT-GGTGGTGTTGGGCAG-----AAGGTGGACTTAATGATCTCAGAGG 943
galGal6_dna 28407 TCTTTTCCAACCGTAGCGATTCTATGATTCTATGA 28441
vv ii i i
CR1-J3_fAlb#L 944 TCTTTTCCAACCTAAATGATTCTGTGATTCTGTGA 978
Matrix = HMM
Kimura (with divCpGMod) = 24.81
Transitions / transversions = 2.29 (142/62)
Gap_init rate = 0.01 (8 / 984), avg. gap size = 1.00 (8 / 8)
+ 31 37.9 1.8 7.4 galGal6_dna 29224 29394 (20096) + TguERVL2_I-b_fAlb LTR/ERVL 1592 1753 (319) 20
ANNOTATION EVIDENCE:
31 37.90 1.75 7.41 galGal6_dna 29224 29394 20048 + TguERVL2_I-b_fAlb LTR/ERVL 1592 1753 319
31 37.90 1.75 7.41 galGal6_dna 29224 29394 (20048) TguERVL2_I-b_fAlb#LTR/ERVL 1592 1753 (319) m_b1s001i20
galGal6_dna 29224 CACCTGTATCATCAAAAATCCCAGCTATTAAAGGCAAATGCTTTCCTGCT 29273
v iiv viv v iv vivvi i v v i iiii v
TguERVL2_I-b_ 1592 CACCAGTGCAAGTCACAGGCCCCAAAGTTAGAGCCCAACGTCCCCCAGCT 1641
galGal6_dna 29274 CAAGCAA---GGAACAACAGAAGGACTGCATCGCGTATTGCCTTGTGGTG 29320
vii vi --- v v vv v ii ------------v i v
TguERVL2_I-b_ 1642 GGGGAGAGAGGGTACACCCCACGAGCTG------------ACCTGTGGTT 1679
galGal6_dna 29321 TTACCTCCGTGATCATGGAGAAGACATGAGGAAGTGGCATGATCAAGCTA 29370
i vi v i i i i i v ivv v i
TguERVL2_I-b_ 1680 CTTTCTGCGTGACCATGGGGAAGACATGGGAAAATGGGATGGGAAACCCA 1729
galGal6_dna 29371 CTCCTGTACTGCGAGCATGGGTGA 29394
i v vv i v
TguERVL2_I-b_ 1730 CTTCTGTCCTGGCAGCACGGGTGC 1753
Matrix = HMM
Kimura (with divCpGMod) = 50.87
Transitions / transversions = 0.94 (29/31)
Gap_init rate = 0.08 (13 / 170), avg. gap size = 1.15 (15 / 13)
+ 58 28.2 2.0 0.0 galGal6_dna 29452 29600 (19890) + TguERVL2_I-b_fAlb LTR/ERVL 1919 2070 (2) 20
ANNOTATION EVIDENCE:
58 28.19 2.01 0.00 galGal6_dna 29452 29600 19842 + TguERVL2_I-b_fAlb LTR/ERVL 1919 2070 2
58 28.19 2.01 0.00 galGal6_dna 29452 29600 (19842) TguERVL2_I-b_fAlb#LTR/ERVL 1919 2070 (2) m_b1s001i21
galGal6_dna 29452 AACAGAGGGGCCCTGCCCTCAGTCGGAGGGAAAA-AGTGA--TAATAGTT 29498
ivi iii i i i i iiv-v v --vv vi i
TguERVL2_I-b_ 1919 GCTAGAGGGGCCCTGCCTCTAGCCAGGGAGAGGCATGGGATAACAGGGTC 1968
galGal6_dna 29499 TATTGGGCTGTGTGGATTCGATGGCCTGGCACATCAGAACCACAGAAATA 29548
iiv i i i i
TguERVL2_I-b_ 1969 TATTGGATAGTGTGGATCCAATGGCCTGGCACATCAGAGCCACAGAAACA 2018
galGal6_dna 29549 TAAGGCACTGGTGGATACCGGTGCACAGTGCACTCTAATGCCCTCGAATC 29598
ii iii i v i v i i v ii v
TguERVL2_I-b_ 2019 TAGAGTGTTAGTTGATACTGGTTCACAGTGCACCCTAATACCATCAGAAC 2068
galGal6_dna 29599 AT 29600
TguERVL2_I-b_ 2069 AT 2070
Matrix = HMM
Kimura (with divCpGMod) = 37.40
Transitions / transversions = 2.50 (30/12)
Gap_init rate = 0.01 (2 / 148), avg. gap size = 1.50 (3 / 2)
+ 303 24.5 3.9 1.9 galGal6_dna 30025 30481 (19009) + CR1-K4_fAlb LINE/CR1 624 1089 (2) 21
ANNOTATION EVIDENCE:
303 24.54 3.94 1.93 galGal6_dna 30025 30481 18961 + CR1-K4_fAlb LINE/CR1 624 1089 2
303 24.54 3.94 1.93 galGal6_dna 30025 30481 (18961) CR1-K4_fAlb#LINE/CR1 624 1089 (2) m_b1s001i22
galGal6_dna 30025 AAAGACATTGAGGCTCTGGAACGTGTCCAGAGAAGGGCAACAAAGCTGGT 30074
i iiv i i i - i i
CR1-K4_fAlb#L 624 AAGGACATTGAGATGCTGGAGCATGTCCAGAGGAGG-CAGCAAGGCTGGT 672
galGal6_dna 30075 AAGGGGTCTGGAGCACAGGCCTTATGAGGAGTGGCTGAAGGAACTGGGAT 30124
i i i i i i i i i iv
CR1-K4_fAlb#L 673 GAGGGGCCTGGAACACAAGCCCTGTGAGGAATGGCTGAGGGAGCTGGGGG 722
galGal6_dna 30125 TGTTCAGTCTAGAGAAGAGGAGGCTCAGGGGAGACCTTATTGCTCTCTAT 30174
i i i i v i ii i
CR1-K4_fAlb#L 723 TGTTCAGCCTGGAGAAAAGGAGACTCAGGGGTGACCTTGTCACTCTCTAC 772
galGal6_dna 30175 AACTACCTGAAAGGAGGTTGTAGTGAGCTGGGGTTTAGCCTCTTCTCTCG 30224
v v i v v v i i iii i
CR1-K4_fAlb#L 773 AACTCCCTGAAAGGTGGCTGTAGTCAGGTGGGGGTTGGTCTCTTCCTCCA 822
galGal6_dna 30225 GGTGACTAGTGATAGGACTAGAGGGAATGGCTTCAAGTTGCATTATGGAA 30274
iii v i i i iv ii ii i i i ii v i
CR1-K4_fAlb#L 823 GGCAGCAAGTGACAGAACCAGAGGACACAGTCTTAAGCTGTACCAAGGGA 872
galGal6_dna 30275 GGTTCAGGCTGGACGTTAGGAAATAG-TACTTCCTGAAAGGGTGGTCAGG 30323
vi i ii v v- vi v v i i i i
CR1-K4_fAlb#L 873 GGTATAGGTTGGATATTAGGAAAAACCTTTTTACAGAAAGAGTGATTAAG 922
galGal6_dna 30324 ATCTGGAATGGGGTGCCCAGGGAGGTGGTGGAGTCACC----------GT 30363
vv vv ----------
CR1-K4_fAlb#L 923 TACTGGAATGGTCTGCCCAGGGAGGTGGTGGAGTCACCATCCCTGGATGT 972
galGal6_dna 30364 GTTTAAAGAACATTTGGATGTT-------GTGTTGAGGTTTAGTGAGAAC 30406
i viv v------- iiiv vii---
CR1-K4_fAlb#L 973 GTTTAAAAAAAGGTTGGATGTGGCACTCGGTGCCATGGTTTAGTTGA--- 1019
galGal6_dna 30407 TATTGGTGATGGGTGGATAATTGGACTGGGTGATCCTGTGGGTCTTTTCC 30456
---- v i vvivvii v i i vi
CR1-K4_fAlb#L 1020 ----GGTGTTAGGGCATGGGTTGGACTCGATGATCTTGAAGGTCTTTTCC 1065
galGal6_dna 30457 AACCTTGATGATTCTATGATTCTAT 30481
vi- i i
CR1-K4_fAlb#L 1066 AACCTAA-TGATTCTGTGATTCTGT 1089
Matrix = HMM
Kimura (with divCpGMod) = 30.94
Transitions / transversions = 2.24 (76/34)
Gap_init rate = 0.03 (12 / 456), avg. gap size = 2.25 (27 / 12)
+ 13 19.1 0.0 5.3 galGal6_dna 31654 31693 (17797) + A-rich Low_complexity 1 38 (0) 22
ANNOTATION EVIDENCE:
13 19.05 0.00 5.26 galGal6_dna 31654 31693 17749 + (GAAAAG)n Simple_repeat 1 38 0
13 19.05 0.00 5.26 galGal6_dna 31654 31693 (17749) (GAAAAG)n#Simple_repeat 1 38 (0) m_b1s252i9
galGal6_dna 31654 GAAATGGGAAGGGAAAAGCGAAAAGGGTAGGGAAACAGGA 31693
v i i - iv i -
(GAAAAG)n#Sim 1 GAAAAGGAAAAGGAAAAG-GAAAAGGAAAAGGAAA-AGGA 38
Matrix = Unknown
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2)
+ 19 31.8 2.5 1.2 galGal6_dna 32179 32258 (17232) + (AT)n Simple_repeat 1 81 (0) 23
ANNOTATION EVIDENCE:
19 31.77 2.50 1.23 galGal6_dna 32179 32258 17184 + (AT)n Simple_repeat 1 81 0
19 31.77 2.50 1.23 galGal6_dna 32179 32258 (17184) (AT)n#Simple_repeat 1 81 (0) m_b1s252i11
galGal6_dna 32179 ATGTATATATATATATATGTATAAAAACA-AGCAATA-ATTAAAATGCAC 32226
i i v v i - vvv - vv v ii -
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATA- 49
galGal6_dna 32227 TACACACACATCTATATACATATATATACATA 32258
i i i i v i i
(AT)n#Simple_ 50 TATATATATATATATATATATATATATATATA 81
Matrix = Unknown
Transitions / transversions = 1.22 (11/9)
Gap_init rate = 0.04 (3 / 79), avg. gap size = 1.00 (3 / 3)
+ 76 39.3 6.8 7.3 galGal6_dna 32576 33636 (15854) C ERVL-int LTR/ERVL (1674) 4083 2355 24
ANNOTATION EVIDENCE:
30 44.50 1.94 3.45 galGal6_dna 32576 32987 16455 C ERVL LTR/ERVL 3678 4083 1674
30 44.50 1.94 3.45 galGal6_dna 32576 32987 (16455) C ERVL#LTR/ERVL (1674) 4083 3678 m_b1s001i23
galGal6_dna 32576 ATCTACCTGATGGTTGTTTTGTTCTTCTTCAGTAGCCCGATTCTTGGGCA 32625
i i vi ivvv vi i v v vi i -- ii v --
C ERVL#LTR/ERVL 4083 ATCCACTTGATTATTAAAATCCTCCTCTGCTGAGGTC--ACCCTTTGG-- 4038
galGal6_dna 32626 CATGAGCATCTACGTGACGCACCTTTACAACCATATTCTTTATTCGGGCA 32675
-- ii i ivi vvv ivvi i i iii ivv
C ERVL#LTR/ERVL 4037 --TGAGCATTCACATGGGACACAAATATCTTCACATTTTTTGCCCATTCA 3990
galGal6_dna 32676 GCAATGTCTTTCCGCAGTTCAGCAGACCAAATAGGTTTACCCTTGCTTTG 32725
vi v v i vvi vvivvv vvv ii viiiv v
C ERVL#LTR/ERVL 3989 GAGAGGTCTATCCACATACCTCTTCCCCAAATTTCTTTGTCACCAATTTT 3940
galGal6_dna 32726 TCTGTTATTCTGCTCCCACTGCTGTAACCATCTCCATAAGGCATTTACCA 32775
i vi i vi v i vvv iv i ivvvi iv vi i
C ERVL#LTR/ERVL 3939 CCAATCATGTTCCTTCCAAGTCCCTGACCATCCAGCCAAACCATTGGCTA 3890
galGal6_dna 32776 CCATCCATGAGTCAGTATAAAGATAAAGCACTGGCCACCCCTCCCGTTCA 32825
vii i v iviiv vvv iii iviiv
C ERVL#LTR/ERVL 3889 CAGCCCATGAATCAGTATATAATCGCATATCTGGCCATTTCTCCTTCCAA 3840
galGal6_dna 32826 GCAACATCTAAGGCCAGCTGGACAGCATTTACCTCTGCAAATTGGCTTGA 32875
vi vi vii v v v vivv vi vv i vvv
C ERVL#LTR/ERVL 3839 GCAAAGTGCACAACCAGGTGCACTGCTCAAAGTTCTGCCCACTGGGAGGA 3790
galGal6_dna 32876 TTCTCCTTTG-------CCTTCAGTGGCCTCTGCAACTTCTCGTGTGGGG 32918
ii ii------- v iiv-------- i iv viv
C ERVL#LTR/ERVL 3789 TTTCCCTTCACCACTGTCCTTCAGGGATG--------TCCCAGAAAGGGG 3748
galGal6_dna 32919 CTCCAC-ACAGCAGCTTTCCGTCTGTGATACTTCCCCACAATACGACACG 32967
vi v-i v v iii v ivvvv v ii vvv ivvvv
C ERVL#LTR/ERVL 3747 CTGTAGTGCTGCAGCTGTCCACTTTTGGGTGGTGCCTGCATATCATGCAG 3698
galGal6_dna 32968 ATCCATCTGTGAACAGGGCA 32987
v i vi v
C ERVL#LTR/ERVL 3697 AACCATCTGTAAACCAGGCC 3678
Matrix = HMM
Kimura (with divCpGMod) = 68.22
Transitions / transversions = 0.88 (83/94)
Gap_init rate = 0.04 (16 / 411), avg. gap size = 1.38 (22 / 16)
51 36.94 9.02 9.02 galGal6_dna 32905 33636 15806 C MERVL LTR/ERVL 2355 3086 2399
51 36.94 9.02 9.02 galGal6_dna 32905 33636 (15806) C MERVL#LTR/ERVL (2399) 3086 2355 m_b1s001i24
galGal6_dna 32905 CTTCTCGTGTG--GGGCTCCACACA------GCAGCTTTCCGTCT---GT 32943
v v--i i ------ vv ---v
C MERVL#LTR/ERV 3086 CTTCTCCTGTTCCAGGCCCCACACAAAGCTAGCAGCTTTCCGAGTCACTT 3037
galGal6_dna 32944 GATA-CTTCCCCACAATACGACACGATCCATCTGTGAACAGGGCATATAG 32992
i -v vvv vv i vv --- ------------------
C MERVL#LTR/ERV 3036 GGTAAATAGGCCTAAGTAACACAC---CCA------------------AG 3008
galGal6_dna 32993 TTTGGAACATGCATTCTCCAAAAGCCCACTACACCCAGAAAAGATTGTGT 33042
vv i ii ivv i v v v v vv vi i
C MERVL#LTR/ERV 3007 TGAGGGATGTGTTGTCTCCAGAATCCAAATAGACCCACTAAACGTTGTGC 2958
galGal6_dna 33043 CTTTTTCTTATTAATGGGCAGAGACATG-GCAGTGATTTTGTCGATCACA 33091
i i iv vi i vi i v v - i i i- i vv v
C MERVL#LTR/ERV 2957 TTCTTTCTTGGTTGTAGGAGGGGCCAGGTGCAATAAC-TTATCTTTCACC 2909
galGal6_dna 33092 TCCGCTGGGATGTGACAACGCCCATCTTGCCACTTTATACCTTGGAACTG 33141
iv vv i i vv vi iiv vi vii vv iv vi i -
C MERVL#LTR/ERV 2908 TTAGAAGGAATATCTCTGCATGCCCCACACCACTGGACTCCTAAGAATT- 2860
galGal6_dna 33142 AATCTCCTG-GGCA---GGTCCCTTCACTTTGCTTCGCTTAATAGCAAAA 33187
-- v- - i --- i vv i v v v v vv vv v
C MERVL#LTR/ERV 2859 --TCA-CTGAGGTAGATGGTCCTTGAATTTTGGTTGGATTTATTTCCCAT 2813
galGal6_dna 33188 CCAGCACTAAGAACCATCTGGATTAT-----------------TTGCTCT 33220
---v i v vv v vi i----------------- --
C MERVL#LTR/ERV 2812 CC---TCTGATACGCATATGTGTTACCAATGAGTCCAAAGTGGTTGCT-- 2768
galGal6_dna 33221 CCTTTCTCAAAAACATCCTCTGCTGTATCGCCCCACGCAACA--GTATCA 33268
------------ v -- vvv i vi vv i --i i
C MERVL#LTR/ERV 2767 ------------ACTTC--CTGCTCACTTGGTCCAATCAGCATAATGTCA 2732
galGal6_dna 33269 TCAGTGTATTGCAGGTGCTCAGGAGCACTTTCCTGTTATAGTGCAGGTTG 33318
i i v -----------v v v vv i v ivv v i iv
C MERVL#LTR/ERV 2731 TCAATATAGTGCA-----------CCAATGTGATATTTTGTGGAAGATCC 2693
galGal6_dna 33319 AA----TCAA---CC-------------CGTGGCAAATGGTTGGGCTGTG 33348
---- --- -------------ii i v v iv ivv v
C MERVL#LTR/ERV 2692 AAACGATCAAGATCCCTTCTAACTAAATTATGACACAGGGCAGGAGAGTT 2643
galGal6_dna 33349 TTTCCACCCCTGGGGCAAACGGTTCCAAGTATACTGAACGCCCCTCCAGG 33398
vv vi i i i vvvv vv i vvv iiv iv
C MERVL#LTR/ERV 2642 AATATATCCTTGAGGCAAAACTGTGAAGGTATACTGTTGGCCTTGCCAAC 2593
galGal6_dna 33399 TAAAGGCAAATAGCTGCCTGCATTC--TGTGGCCAGAGGAATGAAAAAGA 33446
i i v v iv iiv -- i v -- v ivi i
C MERVL#LTR/ERV 2592 TGAAAGCAAATTGCTTCTGGTGGTCCTTATGGACA--GGTACTGAGAAGA 2545
galGal6_dna 33447 AGGCATTAGCAATGACAGTGGTGGCATACCACTTA------GCTGCTTTT 33490
v v viv i i iv vv i------ v iv v
C MERVL#LTR/ERV 2544 AGGCATTTGCCAGATCAATAGCCGCATACCAGGTGCCAGGAGATGTGTTA 2495
galGal6_dna 33491 GACTGCAATTCAT--ATTGGAGTTCTAGCATGTCTGGTACAGCAGCACTC 33538
ivi --- v-- vi i --v --- ii vviv
C MERVL#LTR/ERV 2494 ATTTGC---TCAAGTAACGAA--ACT---ACATCTGGTACAGCAGCTGCA 2453
galGal6_dna 33539 AGTGGGGGTGTGACTTCATTCAGGCCATGGTAGTCTACTGTCAGCCTCCA 33588
v i v iiv i v i viivi i i v vi
C MERVL#LTR/ERV 2452 ATTGGAGTTACTACCTGATTTAGTTTTCGATAATCAACTGTCATTCTCCA 2403
galGal6_dna 33589 TTCTTCACAGGCTTTGCGCACTGGCCATATGGGGCTGTTAAAAGGTGA 33636
vv i ivv i vi v i ivv v v
C MERVL#LTR/ERV 2402 TGATCCATCTGTTTTCTGCACTGGCCAGATAGGAGAGTTAAACGGAGA 2355
Matrix = HMM
Kimura (with divCpGMod) = 50.30
Transitions / transversions = 0.72 (103/143)
Gap_init rate = 0.11 (81 / 731), avg. gap size = 1.63 (132 / 81)
76 42.69 5.43 3.98 galGal6_dna 32993 33636 15806 C ERVL LTR/ERVL 2394 3046 2711
76 42.69 5.43 3.98 galGal6_dna 32993 33636 (15806) C ERVL#LTR/ERVL (2711) 3046 2394 m_b1s001i25
galGal6_dna 32993 TTTGGAACATGCATTCTCCAAAAGCCCACTACACCCAGAAAAGATTGTGT 33042
vv i ivvi v v vv vi vv iiv i
C ERVL#LTR/ERVL 3046 TGAGGAATATGTTGCCTCCAAAATCCAAAGAGGCCCACTAGGCATTGTGC 2997
galGal6_dna 33043 CTTTTTCTTATTAATGGGCAGAGACAT-GGCAGTGATTTTGTCGATCACA 33091
i iv vi i vi i v v-v iii i- i vv v
C ERVL#LTR/ERVL 2996 CTCTTTCTTGGTTGTAGGAGGGGCCAGATGCAACAAC-TTATCCTTCACC 2948
galGal6_dna 33092 TCCGCTGGGATGTGACAACGCCCATCTTGCCACTTTATACCTTGGAACTG 33141
iv vv i vv iiv vi vii vv iv v i i v
C ERVL#LTR/ERVL 2947 TTAGAAGGGATATCTCAACATGCCCCACACCACTGGACCCCTAGAAATTT 2898
galGal6_dna 33142 AATCTCCTGGGCAGGTCCCTTCACTTTGCTTCGCTTAATAGCAAAACCA- 33190
v iivvvvvi v i vv i iv v v v vv vv v v-
C ERVL#LTR/ERVL 2897 CACTGAGGTAGAAGGCCCCTGAATTTTAGTTGGATTTATTTCCCACCCTC 2848
galGal6_dna 33191 --GC-------------ACTAAGAACCATCTGGATTATTTGCTC-TCCTT 33224
--i ------------- i v v-- i v v v- i
C ERVL#LTR/ERVL 2847 TGACATACAAATGTCTTACCAATAAG--TCTAGAGTAGTTGCTACTTCTT 2800
galGal6_dna 33225 TCTCAAAAACATCCTCTGCTGTATCGCCCCACGCAACA--GTATCATCAG 33272
v vv i-----------------vi vv i --i i i
C ERVL#LTR/ERVL 2799 GCTCACTAG-----------------GTCCAATCAGCATAATGTCATCAA 2767
galGal6_dna 33273 TGTATTGCAGGTGCTCAGGAGCACTTTCCTGTTATAGTGCAGGT------ 33316
v v v------vi v iiv v i viv v v i v------
C ERVL#LTR/ERVL 2766 TGTAATGGAC------CAGTGTGATATCTTGTGGAAGGGAAAGGTGATCA 2723
galGal6_dna 33317 ---------TGAATCAACCCGTGGCAAATGGTTGGGCTGTGTTTCCACCC 33357
---------ii ii viii i v vi i ivv vvv vi
C ERVL#LTR/ERVL 2722 AGATCCCTGCAAACTAAATTATGACATAGAGCTGGAGAGTTGATATACCC 2673
galGal6_dna 33358 CTGGGGCAAACGGTTCCAAGTATACTGAACGCCCCTCCAGGTAAAGGCAA 33407
i i iivviv vv i i vvv iiv v i i
C ERVL#LTR/ERVL 2672 CTGAGGTAGGACAGTGAAGGTATATTGCTGGCCTTGCCAGCTGAAAGCAA 2623
galGal6_dna 33408 ATAGCTGCCTGCATTCTGTGGCCAGAGGAATGAAAAAGAAGGCATTAGCA 33457
iv v iv iivv iv ivvv v i i i i v v
C ERVL#LTR/ERVL 2622 ACTGCTTCTGGTGGGCCTTATGGACAGGGATGGAGAAAAAGGCATTTGCC 2573
galGal6_dna 33458 ATGACAGTGGTGGCATACCACTTAGCTGCTTTTGACTGCAATTCATATTG 33507
viv i i iv vv v v vvvv vv vv v vv vvv
C ERVL#LTR/ERVL 2572 AGATCAATAGCTGCATACCAGGTACCAGGGGATGTGTTAATTTGCTCAAG 2523
galGal6_dna 33508 GAGTTCTAGCATGTCTGGTACAGCAGCACTCAGTGGGGGTGTGACTTCAT 33557
v i vvv v ii vviv v i viiiv vi
C ERVL#LTR/ERVL 2522 CAATGAAACCACATCTGGTACAGCAGCTGCAATTGGAGTCACCACTTGGT 2473
galGal6_dna 33558 TCAGGCCATGGTAGTCTACTGTCAGCCTCCATTCTTCACAGGCTTTGCGC 33607
v vii i i i vi vvv i ivv ii vi
C ERVL#LTR/ERVL 2472 TAAGCTTATGATAATCCACTGTCATTCTCCAAGATCCATCTGTCTTCTGC 2423
galGal6_dna 33608 ACTGGCCATATGGGGCTGTTAAAAGGTGA 33636
v v i ivv v v
C ERVL#LTR/ERVL 2422 ACAGGCCAAATAGGAGAGTTAAATGGGGA 2394
Matrix = HMM
Kimura (with divCpGMod) = 63.67
Transitions / transversions = 0.70 (109/155)
Gap_init rate = 0.05 (34 / 643), avg. gap size = 1.79 (61 / 34)
+ 23 3.7 0.0 0.0 galGal6_dna 34191 34218 (15272) + (CT)n Simple_repeat 1 28 (0) 25
ANNOTATION EVIDENCE:
23 3.67 0.00 0.00 galGal6_dna 34191 34218 15224 + (CT)n Simple_repeat 1 28 0
23 3.67 0.00 0.00 galGal6_dna 34191 34218 (15224) (CT)n#Simple_repeat 1 28 (0) m_b1s252i12
galGal6_dna 34191 CTCTCTCACTCTCTCTCTCTCTCTCTCT 34218
v
(CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCT 28
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0)
+ 18 20.3 2.1 2.1 galGal6_dna 35325 35372 (14118) + GA-rich Low_complexity 1 48 (0) 26
ANNOTATION EVIDENCE:
18 20.33 2.08 2.08 galGal6_dna 35325 35372 14070 + (AGA)n Simple_repeat 1 48 0
18 20.33 2.08 2.08 galGal6_dna 35325 35372 (14070) (AGA)n#Simple_repeat 1 48 (0) m_b1s252i13
galGal6_dna 35325 AGAACGAA-AAAAAGAAGAAGAAGAAGTGGAGGAGGAGGTAGAGGAAGA 35372
- - i vi i i i v i
(AGA)n#Simple 1 AGAA-GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 48
Matrix = Unknown
Transitions / transversions = 3.00 (6/2)
Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2)
+ 31 11.0 0.0 0.0 galGal6_dna 35774 35822 (13668) + (CT)n Simple_repeat 1 49 (0) 27
ANNOTATION EVIDENCE:
31 10.99 0.00 0.00 galGal6_dna 35774 35822 13668 + (CT)n Simple_repeat 1 49 0
31 10.99 0.00 0.00 galGal6_dna 35774 35822 (13668) (CT)n#Simple_repeat 1 49 (0) c_b1s251i0
galGal6_dna 35774 CTCTCTCACTCTCTCTCTCTCTCTCTCTATCGCTCTTTCACTCTCTCTC 35822
v v v i v
(CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 49
Matrix = Unknown
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)
+ 27 40.1 7.0 6.6 galGal6_dna 36037 36306 (13184) + HERVL18-int LTR/ERVL 1034 1304 (768) 28
ANNOTATION EVIDENCE:
27 40.07 7.04 6.64 galGal6_dna 36037 36306 13184 + TguERVL2_I-b_fAlb LTR/ERVL 1034 1304 768
27 40.07 7.04 6.64 galGal6_dna 36037 36306 (13184) TguERVL2_I-b_fAlb#LTR/ERVL 1034 1304 (768) m_b1s001i26
galGal6_dna 36037 ACCTGGTTGCTTTGCTGTTGGGA--TGGTGGGGCCAGTAGCTTCTCTCTC 36084
i i i vvvi -- vi iv vv ---- vivv
TguERVL2_I-b_ 1034 ACTTGGTTACTTCGGGTCTGGGACCTTATGGGAACAGGTG----TACAAC 1079
galGal6_dna 36085 TAGATGGTAACAAAGCCCGCCAACTAGGAGTCATTGCCAGAGACAAATCT 36134
i vii i vv vv vi i vi v vi vii vv vv
TguERVL2_I-b_ 1080 TGGATGGTACTGAGGCAAGGAATTTGGGACCCTTGACCCAGGACTCAGGT 1129
galGal6_dna 36135 ATTGACAGGGGAATTAGTAGATGTTTGGATGG--------AGCTGCAACC 36176
i-----------vvv vi i i v v --------vv ivivv
TguERVL2_I-b_ 1130 G-----------TGGATCAGGTATTTGTAAGGGAGCCAGGCCCCCTTTCC 1168
galGal6_dna 36177 CTCTGGGACCGAATATTAATAGCTGTGAGAGAAAGGTATCCCTACAAAGA 36226
v iiv v iiv i v vi i i
TguERVL2_I-b_ 1169 CTCTGGGAGCAGCTTTTAATGAGTGTGAGAGAGAGGTTTGTCCACAGAGA 1218
galGal6_dna 36227 TATTCTGCAG---------CCTGCAATGAAAATGTGGGATACAATTGAGA 36267
v vvv --------- v iv v---vv i v vv i
TguERVL2_I-b_ 1219 GAGAATGCAGGAGCACCACCATAGAATGC---GCTGGAAGACCCTTGAGG 1265
galGal6_dna 36268 AAGGTATCCAGTATTTGAGGGAAATAGCCCTGGTGGAAA 36306
v i vi i i i vv iv i ii
TguERVL2_I-b_ 1266 AAGGGATCCAGCAGCTGAGAGAAGTGGCAGTATTAGAGG 1304
Matrix = HMM
Kimura (with divCpGMod) = 56.96
Transitions / transversions = 0.74 (43/58)
Gap_init rate = 0.08 (21 / 269), avg. gap size = 1.76 (37 / 21)
+ 55 29.3 0.0 1.3 galGal6_dna 36773 36931 (12559) + HERVL18-int LTR/ERVL 1914 2070 (2) 28
ANNOTATION EVIDENCE:
55 29.30 0.00 1.27 galGal6_dna 36773 36931 12559 + TguERVL2_I-b_fAlb LTR/ERVL 1914 2070 2
55 29.30 0.00 1.27 galGal6_dna 36773 36931 (12559) TguERVL2_I-b_fAlb#LTR/ERVL 1914 2070 (2) m_b1s001i27
galGal6_dna 36773 TAATGAATAGAGGGGCCCTGCCCTAAGTCAGGGTGGAGGGAAAGGAATAA 36822
iv v iv iiv i v i-- v v i
TguERVL2_I-b_ 1914 CCAGGGCTAGAGGGGCCCTGCCTCTAGCCAGGGAGA--GGCATGGGATAA 1961
galGal6_dna 36823 TAGAGTGTAATGGACTGTGTGGATTTGATGGCCTGGCATATCAGAACCAC 36872
i i v v iv iii i i
TguERVL2_I-b_ 1962 CAGGGTCTATTGGATAGTGTGGATCCAATGGCCTGGCACATCAGAGCCAC 2011
galGal6_dna 36873 TGAAATATAAGGCACTGGTGGACTCCGGTGCACAGTGCCCTCTAATGCCC 36922
v i ii iii i v iv i v v i i v
TguERVL2_I-b_ 2012 AGAAACATAGAGTGTTAGTTGATACTGGTTCACAGTGCACCCTAATACCA 2061
galGal6_dna 36923 TCGAGTCAT 36931
iiiv
TguERVL2_I-b_ 2062 TCAGAACAT 2070
Matrix = HMM
Kimura (with divCpGMod) = 38.58
Transitions / transversions = 1.71 (29/17)
Gap_init rate = 0.01 (2 / 158), avg. gap size = 1.00 (2 / 2)
+ 72 34.2 4.7 4.7 galGal6_dna 37350 37671 (11819) + HERVL18-int LTR/ERVL 2009 2330 (3717) 28
ANNOTATION EVIDENCE:
72 34.20 4.66 4.66 galGal6_dna 37350 37671 11819 + HERVL18 LTR/ERVL 2009 2330 3717
72 34.20 4.66 4.66 galGal6_dna 37350 37671 (11819) HERVL18#LTR/ERVL 2009 2330 (3717) m_b1s001i28
galGal6_dna 37350 GAACGCACTCACCTTTTAACAGCCCCATATGGCCAGTGCGTAAAGCC-AG 37398
v v vvv i vi ivvi vi vv - -ii
HERVL18#LTR/E 2009 GCACCCACAGCCCCTACAATTCTCCAGTATGGCCAGTCAG-AAAGCCTGA 2057
galGal6_dna 37399 TGGAGAATGGAGGCTGATGGTAGACTACCGTGGCCTGAATGAAGTCACAC 37448
ivv v v i i i i v iv i v
HERVL18#LTR/E 2058 TGGAACTTGGCGGATGACGGTGGATTATCGGGAACTGAATAAAGTAACAC 2107
galGal6_dna 37449 CCGCACTGAGTGCTGCTGTTCCAGATATGTTAGAACTCCAATTTGAATTG 37498
v vi vi v v vv vv i ------- --
HERVL18#LTR/E 2108 CCCCTTTGCATGCAGCTGTACCATCTATCATGG-------ATTTGA--TG 2148
galGal6_dna 37499 GA------GTCAAAAGCAGCCAACTGGTATGCTACCACT--------GAC 37534
------ v vi ----- v iiv --------
HERVL18#LTR/E 2149 GACCGCTTGACAATGG-----AACTGGGACAGTACCACTATGTGGTGGAC 2193
galGal6_dna 37535 ATGGCTAATGCCTTCTTTTCCATTCCTCTGGCAACAGAATGCAGGCCGCA 37584
v i v i vviv v vv iv vi vvi
HERVL18#LTR/E 2194 TTGGCCAATGCATTCTTCTCCATTGACATTGCTCCAGAGAGCCAGGAACA 2243
galGal6_dna 37585 ATTTGCCTTCAACTGGAGGGGCGTTCAGTATACTTGGAACTGTTTGCCCC 37634
i vv iii vvvv i iv vv vvvvv iv
HERVL18#LTR/E 2244 GTTTGCCTTCACATGGGAAGGGCGACAATGGACTTTCACAGTGTTGCTGC 2293
galGal6_dna 37635 AGGGGTGGAAACACAGCCCAATCATTTGCCACGGGTT 37671
v ivivi i v i v i i vi
HERVL18#LTR/E 2294 AGGGCTATGTGCATAGCCCCACCATATGTCATGGTCT 2330
Matrix = HMM
Kimura (with divCpGMod) = 45.20
Transitions / transversions = 0.64 (41/64)
Gap_init rate = 0.06 (18 / 321), avg. gap size = 1.67 (30 / 18)
+ 190 19.3 0.8 4.0 galGal6_dna 37737 37995 (11495) C CR1-E4_fAlb LINE/CR1 (0) 430 180 29
ANNOTATION EVIDENCE:
190 19.30 0.77 3.98 galGal6_dna 37737 37995 11495 C CR1-E4_fAlb LINE/CR1 180 430 0
190 19.30 0.77 3.98 galGal6_dna 37737 37995 (11495) C CR1-E4_fAlb#LINE/CR1 (0) 430 180 m_b1s001i29
galGal6_dna 37737 CAGAATCACAGAAGTGCCTGGGTTGGAAGGGACCTCAAGGATCATGAATC 37786
vv ii i i vv vi
C CR1-E4_fAlb#L 430 CAGAATCACAGAATGGTTTGGGTTGGAAGGGACCTTAAAGATCATCTAAT 381
galGal6_dna 37787 TCTAATCCCCCTGCC--GGGCAGGGCCACCAACCTCCGCATTTACTAGAC 37834
i i - -- v ---------v ii
C CR1-E4_fAlb#L 380 TCCAACCCC-CTGCCATGGGCAGGGACACC---------TTCCACTAGAC 341
galGal6_dna 37835 CAGGTTACCCAGAGCCCCATCCAACCTGGCCTTGAACACCTACAGGGACG 37884
i i i i v i
C CR1-E4_fAlb#L 340 CAGGTTGCTCAGAGCCCCATCCAGCCTGGCCTTGAACACTTCCAGGGATG 291
galGal6_dna 37885 GGGCATCCACAACCTCTCTGGGCAGCCCGTTCCAGCACCTCACCACTCTC 37934
i i i i ii i
C CR1-E4_fAlb#L 290 GGGCATCCACAGCTTCTCTGGGCAACCTGTTCCAGTGCCTCACCACCCTC 241
galGal6_dna 37935 CTGGTAAAGAACTTCCCCCTAACATCCAACCTAAATCTTACCTCTTTAAA 37984
vii i ii i i i i vv v i
C CR1-E4_fAlb#L 240 ACAGTAAAGAATTTCTTCCTAATATCTAATCTAAACCTACCCTCTTTCAG 191
galGal6_dna 37985 CTTTAAACCTG 37995
i v i vv
C CR1-E4_fAlb#L 190 TTTAAAGCCAT 180
Matrix = HMM
Kimura (with divCpGMod) = 22.88
Transitions / transversions = 2.20 (33/15)
Gap_init rate = 0.04 (11 / 258), avg. gap size = 1.09 (12 / 11)
+ 60 41.7 3.6 4.3 galGal6_dna 38927 39964 (9526) C ERVL-B4-int LTR/ERVL (1674) 4083 3597 30
ANNOTATION EVIDENCE:
57 42.38 5.97 6.80 galGal6_dna 38927 39964 9526 C HERVL66 LTR/ERVL 1309 2338 1991
57 42.38 5.97 6.80 galGal6_dna 38927 39964 (9526) C HERVL66#LTR/ERVL (1991) 2338 1309 m_b1s001i30
galGal6_dna 38927 GCTTTCAACATGGTTTTTAACAACCCGTTGTATTGTTCAATTTTACCAGA 38976
i i vvvv v i i i vvv iv i vv v
C HERVL66#LTR/E 2338 ACCTTCAACTGTTTGTTCAATAACCCATTCATTCTTTCAGTTAAACCAGC 2289
galGal6_dna 38977 AGCTGGTGCGTTATAGGGGATATGATAAATCCACTCAATGCCATGATCTT 39026
v iv iiv vii i i iv i vv vvv
C HERVL66#LTR/E 2288 TGCCTGCAGGTGGCAAGGAATATGGAAAATCCATTCAATGCCATCTTGGG 2239
galGal6_dna 39027 TGGCCCAAGTATTTACAAGGGAATTTTTGAAATGAGTCCCATTATCTGAT 39076
iv vv i v v ivvvv ii i vv i i i -
C HERVL66#LTR/E 2238 CTGCAAAGGTTTGTACAGCCTCACCTTTGAAATGGGAGCCACTGTCCG-T 2190
galGal6_dna 39077 TCGACTCTCTCTGGGGTAAC-ATGTCGCCAGAGAACTTGT--TTCTCGAG 39123
i v i v v vvv - ---vvi v i v v--v i iv
C HERVL66#LTR/E 2189 TTGAATTTGTATGGGCACACCAT---CATATAGAATTAGGATATTTCATG 2143
galGal6_dna 39124 GCCTAATATGGTGTTTCGGCCGGTAGCATGGGGTACTGCGTATGTTTCAG 39173
vii -- vvvviv v vi vvvvv ii v i v vi
C HERVL66#LTR/E 2142 TTTTAATA--GTGTTAATTTGGTTAGCATTAGCATAAGCACAGGCTACTA 2095
galGal6_dna 39174 GCCACCC--AGTGGTTGCTTCCACCATGGTAAGCACATAACGATT---AC 39218
vvi -- ii v ii v --i----v i vvv ---
C HERVL66#LTR/E 2094 GGAGCCCTAAGCAGGTGTCTACA--G----CAGTACATATATATTGGCAC 2051
galGal6_dna 39219 CATTGCGAGATCTTGGCAAGGT---GATATAATCAACCTGCCACGCCT-- 39263
v v-- vvv v---i i v ii v viii --
C HERVL66#LTR/E 2050 CCTTT--AGAAAGTGGCAAGGGACAAATATAGTCCATTTGACAAATTTGT 2003
galGal6_dna 39264 CCCCATATTTAT-------ACTTCTG--CCATCGCCCTTCCTCCCAGAGA 39304
ivii v -------ivv v -- v --------vv
C HERVL66#LTR/E 2002 CCTGGCATTTTTCCCCGGTGAATGTGCCCCATAGCCCT--------CTGA 1961
galGal6_dna 39305 GGTTTCATCCTCTTAGCTTG---TTTAATT-ATGGCACATGTTTCAGACA 39350
v--- -----i i --- i -v ii iv v v-ii
C HERVL66#LTR/E 1960 GGA---A-----CTGGCTTGGTTTTTAACTGTTGGCATGTAGTGCAT-TG 1920
galGal6_dna 39351 TGAACAACTTGTGCA-ATAGCGTCCA-----------CTCCCT-----CG 39383
v vv v vii- iv i v-----------v ----- i
C HERVL66#LTR/E 1919 GGATAAAATTGTCTGAACCGCATCCTGGGGTAACGATATCCCTCTTTACA 1870
galGal6_dna 39384 GTCTCTAGCGCATTTATATGTTGCATCTCTTCCTTGACGACCCGAAGTTT 39433
v i i ivv -----v v v v viv v ii v vv vvvv
C HERVL66#LTR/E 1869 CTCCCCAAGCCAT-----GGTTCCCTGTACGCCTAGGTGTCCGCACTGGT 1825
galGal6_dna 39434 CATGGGCCCACCGAGCTAGAAATAATTCACCCTTGTTCTTC-AAGTCCAA 39482
v vi ii v iv vvi-i iii vi ivv v -ivi i
C HERVL66#LTR/E 1824 GATGCACCCATTGCGTGATCG-CAGCCCAATCCACTTCATCCGCATTCAA 1776
galGal6_dna 39483 GTCTATTTGAGTCACCTCAATTTTGGCAGCTCGATCTACCTGATGGTTGT 39532
i iivvvvi viivvv vvv i i v i iv
C HERVL66#LTR/E 1775 GTTTGCAGTTATGGTGGAAATTTTGGCCTGTTGATCTGCCTGCTGATTAA 1726
galGal6_dna 39533 TTTGTTCTTCTTCAGTAGCCCGATTCTTGGGCACGTGAGCATCTACATGG 39582
v v iiv vvv v iv v ------ iii i v
C HERVL66#LTR/E 1725 ATAGTCTGTCAAGAGAAAGCAGA------GATGCATGAGCATCAACATGG 1682
galGal6_dna 39583 CGCACCTTTACAACCATATTCTTTATTCGGGCAGCAATGTCTTTCCACAG 39632
viv vv v i ivi v v vi iiv iivvvi i i vvi
C HERVL66#LTR/E 1681 AAAACAGTGATAATGGTAGTGTGCACCAGGATTCAGATATCTTCCCAGTA 1632
galGal6_dna 39633 TTCAGCAGCCCAAACAGGTTTGCCCCTCCTTTGCCAGTTATTTTGCTCCC 39682
vvvivv vvv iii ivv vi v i i i v
C HERVL66#LTR/E 1631 TTGTTTTCCCCAAACCTCTTTATTCCCAATTAACCATTTGTTTCGTTGCC 1582
galGal6_dna 39683 ACTGCTGTAACCACCCCCATAAGGCATTTGCCACCATCCATGAGTCAGTA 39732
i vv i v vvivvvv iiv i iiv v ii
C HERVL66#LTR/E 1581 ATTGGGGCATCCAGGTAGTAAGACCATTTGCTACTGACCAAGAGTTGGTA 1532
galGal6_dna 39733 TAAAG---ATAAAGCGT--TGGCCACCTCTCCCGTTCAGCAACATCTAAG 39777
v i--- i v vi-- v -- i ------ i v vi
C HERVL66#LTR/E 1531 TACAAGTGACAAATCCCTCTGGCCTCCTC--CTG------AATAGCTCGG 1490
galGal6_dna 39778 GCCAGTTGGATAGCCTTTACCTCTGTGAACTGACTTGATTCTCCTTTACC 39827
i------ ii ivi vi v iv i i vvvii v ii v
C HERVL66#LTR/E 1489 A------GGACGGCTACTAGTTCAGCCAGCTGGCTGCTCCCACCCCTTCC 1446
galGal6_dna 39828 TTCAGTGGCCTCTGCAACTTGTCGTGT-------GGGGCTCCACACAGCA 39870
vii ------- v vv ii -------i ii vi vi vi
C HERVL66#LTR/E 1445 TTCATCAG-------AAATGCTTATGTTTTTAACAGGATTATAAGCCACA 1403
galGal6_dna 39871 GCTTTCCATCTGCAATGCTTCCCCACATTACG---ACATGATCCATCTGT 39917
i --- vi vv vv v iii---ivvv v
C HERVL66#LTR/E 1402 GCCTTCCA---GCATCGGGTCCCACCAATGTATTTGGTGGATCCATCAGT 1356
galGal6_dna 39918 GAACAGGGCATATTTCTTTTCATTTTCTGG---TAGTTCATTGTATGGTT 39964
i vii i vv v--- --- v iv v i
C HERVL66#LTR/E 1355 AAACCAAGCATGTTTCTGATCC---TCTGGGCTTAGTTCTTTAAAGGATT 1309
Matrix = HMM
Kimura (with divCpGMod) = 61.24
Transitions / transversions = 0.78 (180/230)
Gap_init rate = 0.09 (89 / 1037), avg. gap size = 1.48 (132 / 89)
58 41.74 1.86 3.29 galGal6_dna 39516 39946 9544 C ERVL LTR/ERVL 3659 4083 1674
58 41.74 1.86 3.29 galGal6_dna 39516 39946 (9544) C ERVL#LTR/ERVL (1674) 4083 3659 m_b1s001i31
galGal6_dna 39516 ATCTACCTGATGGTTGTTTTGTTCTTCTTCAGTAGCCCGATTCTTGGGCA 39565
i i vi ivvv vi i v v vi i -- ii v ---
C ERVL#LTR/ERVL 4083 ATCCACTTGATTATTAAAATCCTCCTCTGCTGAGGTC--ACCCTTTG--- 4039
galGal6_dna 39566 CGTGAGCATCTACATGGCGCACCTTTACAACCATATTCTTTATTCGGGCA 39615
- ii vi vvv ivvi i i iii ivv
C ERVL#LTR/ERVL 4038 -GTGAGCATTCACATGGGACACAAATATCTTCACATTTTTTGCCCATTCA 3990
galGal6_dna 39616 GCAATGTCTTTCCACAGTTCAGCAGCCCAAACAGGTTTGCCCCTCCTTTG 39665
vi v v vvi vvivv ivvv i v ivv v
C ERVL#LTR/ERVL 3989 GAGAGGTCTATCCACATACCTCTTCCCCAAATTTCTTTGTCACCAATTTT 3940
galGal6_dna 39666 CCAGTTATTTTGCTCCCACTGCTGTAACCACCCCCATAAGGCATTTGCCA 39715
i i v v i vvv iv i i vvvi iv v i
C ERVL#LTR/ERVL 3939 CCAATCATGTTCCTTCCAAGTCCCTGACCATCCAGCCAAACCATTGGCTA 3890
galGal6_dna 39716 CCATCCATGAGTCAGTATAAAGATAAAGCGTTGGCCACCTCTCCCGTTCA 39765
vii i v iviiv vvvi ii iviiv
C ERVL#LTR/ERVL 3889 CAGCCCATGAATCAGTATATAATCGCATATCTGGCCATTTCTCCTTCCAA 3840
galGal6_dna 39766 GCAACATCTAAGGCCAGTTGGATAGCCTTTACCTCTGTGAACTGACTTGA 39815
vi vi vii v v iv iivv vi ivv ivvv
C ERVL#LTR/ERVL 3839 GCAAAGTGCACAACCAGGTGCACTGCTCAAAGTTCTGCCCACTGGGAGGA 3790
galGal6_dna 39816 TTCTCCTTTAC-------CTTCAGTGGCCTCTGCAACTTGTCGTGTGGGG 39858
ii i ------- v iiv i- ------- viv
C ERVL#LTR/ERVL 3789 TTTCCCTTCACCACTGTCCTTCAGGGATGTCC-CA-------GAAAGGGG 3748
galGal6_dna 39859 CTCCAC-ACAGCAGCTTTCCATCTGCAATGCTTCCCCACATTACGACATG 39907
vi v-i v v ii viiivvvv v ii vv ivvvv
C ERVL#LTR/ERVL 3747 CTGTAGTGCTGCAGCTGTCCACTTTTGGGTGGTGCCTGCATATCATGCAG 3698
galGal6_dna 39908 ATCCATCTGTGAACAGGGCATATTTCTTTTCATTTTCTG 39946
v i vi vi vv i v ii
C ERVL#LTR/ERVL 3697 AACCATCTGTAAACCAGGCCCAAGTCTTCTCTTCCTCTG 3659
Matrix = HMM
Kimura (with divCpGMod) = 61.43
Transitions / transversions = 0.87 (81/93)
Gap_init rate = 0.04 (16 / 430), avg. gap size = 1.38 (22 / 16)
60 40.94 2.53 2.53 galGal6_dna 39567 39962 9528 C ERVL-B4 LTR/ERVL 3597 3992 1722
60 40.94 2.53 2.53 galGal6_dna 39567 39962 (9528) C ERVL-B4#LTR/ERVL (1722) 3992 3597 m_b1s001i32
galGal6_dna 39567 GTGAGCATCTACATGGCGCACCTTTACAACCATATTCTTTATTCGGGCAG 39616
ii vi vvv ivvi i i iii ivv
C ERVL-B4#LTR/E 3992 GTGAGCATTCACATGGGACACAAATATCTTCACATTTTTTGCCCATTCAG 3943
galGal6_dna 39617 CAATGTCTTTCCACAGTTCAGCAGCCCAAACAGGTTTGCCCCTCCTTTGC 39666
vi v v vvi vvivv ivvvi i v ivv v
C ERVL-B4#LTR/E 3942 AGAGGTCTATCCACATACCTCTTCCCCAAATTTCCTTGTCACCAATTTTC 3893
galGal6_dna 39667 CAGTTATTTTGCTCCCACTGCTGTAACCACCCCCATAAGGCATTTGCCAC 39716
i i v v i vvv iv i i vvvi iv v
C ERVL-B4#LTR/E 3892 CAATCATGTTCCTTCCAAGTCCCTGACCATCCAGCCAAACCATTGGCCAC 3843
galGal6_dna 39717 CATCCATGAGTCAGTATAAAGATAAAGCGTTGGCCACCTCTCCCGTTCAG 39766
vii i v ivi v vvvi ii iviiv
C ERVL-B4#LTR/E 3842 AGCCCATGAATCAGTATATAATCACACATCTGGCCATTTCTCCTTCCAAG 3793
galGal6_dna 39767 CAACATCTAAGGCCAGTTGGATAGCCTTTACCTCTGTGAACTGACTTGAT 39816
vi vv vii v v iv iivv vi ivv ivvv
C ERVL-B4#LTR/E 3792 CAAAGTGAACAACCAGGTGCACTGCTCAAAGTTCTGCCCACTGGGAGGAT 3743
galGal6_dna 39817 TCTCCTTTAC-------CTTCAGTGGCCTC--TGCAACTTGTCGTGTGGG 39857
ii i ------- v iiv --v v ----------
C ERVL-B4#LTR/E 3742 TTCCCTTCACCACTGTCCTTCAGGGATGTCCCAGAAA----------GGG 3703
galGal6_dna 39858 GCTCCA-CACAGCAGCTTTCCATCTGCAATGCTTCCCCACATTACGACAT 39906
vi -ii v v ii v ivvvv v ii vv ivvvv
C ERVL-B4#LTR/E 3702 GCTGTAGTGCTGCAGCTGTCCACTTTCAGGTGGTGCCTGCATATCATGCA 3653
galGal6_dna 39907 GATCCATCTGTGAACAGGGCATATTTCTTTTCATTTTCTGGTAGTTCATT 39956
v i vi vi vv i v ii vi ii v i
C ERVL-B4#LTR/E 3652 GAACCATCTGTAAACCAGGCCCAAGTCTTCTCTTCCTCTGTCAACTGATC 3603
galGal6_dna 39957 GTATGG 39962
i v
C ERVL-B4#LTR/E 3602 ATAGGG 3597
Matrix = HMM
Kimura (with divCpGMod) = 59.96
Transitions / transversions = 0.82 (71/87)
Gap_init rate = 0.03 (13 / 395), avg. gap size = 1.54 (20 / 13)
+ 20 4.3 0.0 0.0 galGal6_dna 40779 40802 (8688) + (T)n Simple_repeat 1 24 (0) 31
ANNOTATION EVIDENCE:
20 4.35 0.00 0.00 galGal6_dna 40779 40802 8688 + (T)n Simple_repeat 1 24 0
20 4.35 0.00 0.00 galGal6_dna 40779 40802 (8688) (T)n#Simple_repeat 1 24 (0) m_b1s252i14
galGal6_dna 40779 TTTTTTTTTTTTTTTTTCTTTTTT 40802
i
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 13 15.8 2.7 2.7 galGal6_dna 40938 40974 (8516) + G-rich Low_complexity 1 37 (0) 32
ANNOTATION EVIDENCE:
13 15.80 2.70 2.70 galGal6_dna 40938 40974 8516 + (AATGGG)n Simple_repeat 1 37 0
13 15.80 2.70 2.70 galGal6_dna 40938 40974 (8516) (AATGGG)n#Simple_repeat 1 37 (0) m_b1s252i15
galGal6_dna 40938 AATGGGAAGGGAAAAGGGAATGGGGTAT-GGAACGGGA 40974
v i v - v - i
(AATGGG)n#Sim 1 AATGGGAATGGGAATGGGAAT-GGGAATGGGAATGGGA 37
Matrix = Unknown
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2)
+ 108 41.8 12.5 16.3 galGal6_dna 44154 45274 (4216) + TguERVL2_I-b_fAlb LTR/ERVL 984 2067 (5) 33
ANNOTATION EVIDENCE:
108 41.80 12.49 16.33 galGal6_dna 44154 45274 4216 + TguERVL2_I-b_fAlb LTR/ERVL 984 2067 5
108 41.80 12.49 16.33 galGal6_dna 44154 45274 (4216) TguERVL2_I-b_fAlb#LTR/ERVL 984 2067 (5) m_b1s001i33
galGal6_dna 44154 TCCGTGGTCTGAGAAAGGACTTCACACGCCACCCCAATGAGCCTATTGTC 44203
ii v i v iii i viivvv vi v v iiv
TguERVL2_I-b_ 984 TCCGTAATCTGCGAAAAGACATTGTATGATGGGGCTGTGAGGCTTTTACA 1033
galGal6_dna 44204 ACCTGGTTACTTCGATGCTGGGACAGTGGGGCCAATCGTGTGTGGCTAGA 44253
i ivv vv iv vv vvv iiii i
TguERVL2_I-b_ 1034 ACTTGGTTACTTCGGGTCTGGGACCTTATGGGAACAGGTGTACAACTGGA 1083
galGal6_dna 44254 TAACAGAGAAGCTCGTCAGCTCGGTGGCATTGCTAGGGACTCAGCCATTG 44303
iii vv i vv vv vi v vvv v vi ivi vii-
TguERVL2_I-b_ 1084 TGGTACTGAGGCAAGGAATTTGGGACCCTTGACCCAGGACTCAGGTG-TG 1132
galGal6_dna 44304 GCAGACGAATTAGCACATGCCAGAACCAGGCCT--TCCCCCTCTGGAAGC 44351
vvv v v v i viv---- i i-- ii i
TguERVL2_I-b_ 1133 GATCAGGTATTTGTAAGG----GAGCCAGGCCCCCTTTCCCTCTGGGAGC 1178
galGal6_dna 44352 GGATGTTGTTAGCCGTGAGAGAAAAACACCCCTTTAAAGATGATCTCATG 44401
i v v iv iivi i iiivivi ivi i v---------
TguERVL2_I-b_ 1179 AGCTTTTAATGAGTGTGAGAGAGAGGTTTGTCCACAGAGAG--------- 1219
galGal6_dna 44402 CCTGAG--------------------AAAAGGAAATGGACTGATATGGAA 44431
-----i-------------------- i v viv vviviv v i
TguERVL2_I-b_ 1220 -----AGAATGCAGGAGCACCACCATAGAATGCGCTGGAAGACCCTTGAG 1264
galGal6_dna 44432 AAAGGCATCCGTTATTTGAGAGAATGCGCC--ATGG-----------TGG 44468
i v ivi vi vvv v-- vi-----------
TguERVL2_I-b_ 1265 GAAGGGATCCAGCAGCTGAGAGAAGTGGCAGTATTAGAGGTACTCTTTGG 1314
galGal6_dna 44469 AAATGATATACAGCCCTGATTTCATCCCTGACGAGCCAGACCAAGAGCAT 44518
i iv i iv -v ivvi---------------------------
TguERVL2_I-b_ 1315 GAGGGGTGGACAGC-ATGACAAT--------------------------- 1336
galGal6_dna 44519 GATCCTGAGAGAGTCTGGTGTACACCAAATATGTGGTGCACATTCACTAA 44568
i v ii v i vviv v v v vvi ------
TguERVL2_I-b_ 1337 GACCCTGACAAGGTCAGGTGCACAGGGCAGATGTTGTGGAATCT------ 1380
galGal6_dna 44569 GACTGC-ACCAGAAAGGTATGCCAGTACATTTGCAGCACTGTATGGCAGA 44617
---v - v vviii vi vi i i iivv vv i i vv vvv
TguERVL2_I-b_ 1381 ---GGCAAACCTGGGGCCATCTCAATATACCACCTTCATTGCAATGATTA 1427
galGal6_dna 44618 GGGGAAAGAAGACCCCTTATAG-------ATGATTTGGTTAATAGACTCC 44660
iv v--v vi v iv v -------i vv v v ii i ii v
TguERVL2_I-b_ 1428 ATGC--TGATAACCACCAAGAGACAGTGGGTTCTGTTGCCAACAAGCTCA 1475
galGal6_dna 44661 AAGACTTTGAGTTGCATTTAAAT---CCTCTACGAGCTTGTGTTTCAGCC 44707
i i i vvvvvvv v --- ivv i ii ii i v i
TguERVL2_I-b_ 1476 GAAATTTTGAGAGTGTGATCAATGGCCTAATGCAGGCTCATGTCTCTGCT 1525
galGal6_dna 44708 ATCACAAGGATAGTTGA----------AAAGCTAGACAGAATAGAGAGCA 44747
i viiv i vvv iv ---------- ----------------------
TguERVL2_I-b_ 1526 GTGGTCAAGAGCCTCCAAGAGGAGATAA---------------------- 1553
galGal6_dna 44748 AACAAGAAGATATAATAGACAAACTGTCTATCATACGTGATGCTGATGGA 44797
-------------------------------------------- v
TguERVL2_I-b_ 1554 --------------------------------------------GAGGGA 1559
galGal6_dna 44798 T---CCATGGTGGATGAGGACCACAATTCCCAAAACCCTCCACTGGAAGA 44844
v---vvivi vi ------------------------i vv
TguERVL2_I-b_ 1560 GGTGGGGGAGGAGATGAGGA------------------------AGATCA 1585
galGal6_dna 44845 GCTGATCAACTTGGTGTCCTCCCGACCTACATCATTCAACATCTCAGATA 44894
ivv v v vvv iivviiv v i ---------- vvv vv i vv
TguERVL2_I-b_ 1586 GTGCAGCACCAGTGCAAGTCACAGGC----------CCCAAAGTTAGAGC 1625
galGal6_dna 44895 TCATCAAAAGGGGACGTCGTCCTGCTAGAGGAAATGATAACGGTAAGACT 44944
i v i---------- vi v i i ii iv ------ vv v i
TguERVL2_I-b_ 1626 CCAACG----------TCCCCCAGCTGGGGAGAGAG------GGTACACC 1659
galGal6_dna 44945 ATAATACGTCTTGCCTTGTGGCGTTACCTGCGTGACCATGGAGAAGATAC 44994
v---i vvi v i ivi vi i i i
TguERVL2_I-b_ 1660 C---CACGAGCTGACCTGTGGTTCTTTCTGCGTGACCATGGGGAAGACAT 1706
galGal6_dna 44995 GAAGAAGTGGCATAAGAAACCCACTTCGGCACTCCAAGCACGGATAA--- 45041
iii i v ii v iv vvv i iv---
TguERVL2_I-b_ 1707 GGGAAAATGGGATGGGAAACCCACTTCTGTCCTGGCAGCACGGGTGCGTC 1756
galGal6_dna 45042 -------------AAGAATT---------------A-------CAAGGCA 45056
------------- v i --------------- -------v i
TguERVL2_I-b_ 1757 AACTCAGGGAGGGAAGCACTAACCAAGGGAGTTCTACTAAAGTGAAGGTA 1806
galGal6_dna 45057 GAT--------CAACCACCAAGGTGAAG--TCCTCCAAAAGGG----TGA 45092
vi-------- v iv v -- vi v i ---- i
TguERVL2_I-b_ 1807 GCCTCGACCTCCCATAACCAAGGTGCAGGATATTACAGAAGGGAAGATAA 1856
galGal6_dna 45093 TCGCTC---------------------CAGT--TGCTGC---GGACAACC 45116
vv ---------------------i v --vvv --- viivv
TguERVL2_I-b_ 1857 TCTGTCAGATCCACTTGAAGGAACCTCTACTATGTATGCCCAGGAAGGAA 1906
galGal6_dna 45117 AAGGTAACA---AGTAGGGGGGCCCTGCCCCCAGCCAGGAGGGGGAAAGG 45163
vii v---iv i i i ii i v v
TguERVL2_I-b_ 1907 ATAATAACCAGGGCTAGAGGGGCCCTGCCTCTAGCCAGGGAGAGGCATGG 1956
galGal6_dna 45164 GATAATAGAGTGTATTGGACTGTGTGGATTAGATGGCCTGGTACATCAAA 45213
i i v iv ivi i i
TguERVL2_I-b_ 1957 GATAACAGGGTCTATTGGATAGTGTGGATCCAATGGCCTGGCACATCAGA 2006
galGal6_dna 45214 ACCACAGAAATTTAAGGCACTTGTAGACACTGGTGCACAGTGTTCGCTAA 45263
i iv ii iii v v i v iv v
TguERVL2_I-b_ 2007 GCCACAGAAACATAGAGTGTTAGTTGATACTGGTTCACAGTGCACCCTAA 2056
galGal6_dna 45264 TGCCCTCGAGT 45274
i v iiiv
TguERVL2_I-b_ 2057 TACCATCAGAA 2067
Matrix = HMM
Kimura (with divCpGMod) = 61.26
Transitions / transversions = 0.91 (187/205)
Gap_init rate = 0.18 (197 / 1120), avg. gap size = 1.61 (317 / 197)
+ 59 36.5 2.8 6.5 galGal6_dna 45650 46001 (3489) + TguERVL2_I-b_fAlb LTR/ERVL 1975 2314 (3733) 33
ANNOTATION EVIDENCE:
59 36.45 2.84 6.47 galGal6_dna 45650 46001 3489 + HERVL18 LTR/ERVL 1975 2314 3733
59 36.45 2.84 6.47 galGal6_dna 45650 46001 (3489) HERVL18#LTR/ERVL 1975 2314 (3733) m_b1s001i34
galGal6_dna 45650 ATTCAGAAGTTGATTCATCAACTAGAGAGTCAGGGAGTGATCAGCAAAAC 45699
v i---------vi ivv iv vvii ---
HERVL18#LTR/E 1975 ATTAAGAAGTTGG---------AGGAGGTGCAGATAGTGCGTGGC---AC 2012
galGal6_dna 45700 TCACTCCCCTTTCAACAGCCCCATATGGCCAGTGCGTAAAGCC-AGTGGA 45748
i vv i v ivvi vi vv - -ii
HERVL18#LTR/E 2013 CCACAGCCCCTACAATTCTCCAGTATGGCCAGTCAG-AAAGCCTGATGGA 2061
galGal6_dna 45749 GAATGGAGGCTGACGGTAGACTACCGTGACCTGCATGGAGTCACACCCCC 45798
ivv v v i i i v v v ii v
HERVL18#LTR/E 2062 ACTTGGCGGATGACGGTGGATTATCGGGAACTGAATAAAGTAACACCCCC 2111
galGal6_dna 45799 ACTGAGTGCTGCTGTGCCGCACATGTTAGAACTCCAATATGAACTGG-AG 45847
vi vi v i iivi vv i vi ----v i i v-v
HERVL18#LTR/E 2112 TTTGCATGCAGCTGTACCATCTATCATGGATTT----GATGGACCGCTTG 2157
galGal6_dna 45848 TCAAAAGCAGCCAAGTGGTATGCCACCACT--------GACACTGCTAAT 45889
v vi ----- v v iivi -------- viv i
HERVL18#LTR/E 2158 ACAATGG-----AACTGGGACAGTACCACTATGTGGTGGACTTGGCCAAT 2202
galGal6_dna 45890 GCTTTCTTTTCCATTCCATTGGCCACGGAATGCAGGCCACAGTTTGCTTT 45939
v i vvvv v iv i iv vi vv i
HERVL18#LTR/E 2203 GCATTCTTCTCCATTGACATTGCTCCAGAGAGCCAGGAACAGTTTGCCTT 2252
galGal6_dna 45940 CACCTGGAGGGGTGTTCAGTAAACTTGGAATCGTTTGCCCCAGGGGTGGA 45989
v iii vvvv i ii vv vvvvv iv v ivi
HERVL18#LTR/E 2253 CACATGGGAAGGGCGACAATGGACTTTCACAGTGTTGCTGCAGGGCTATG 2302
galGal6_dna 45990 AACACAGCCCAA 46001
vi i v
HERVL18#LTR/E 2303 TGCATAGCCCCA 2314
Matrix = HMM
Kimura (with divCpGMod) = 49.54
Transitions / transversions = 0.76 (52/68)
Gap_init rate = 0.07 (25 / 351), avg. gap size = 1.28 (32 / 25)
+ 69 42.2 2.0 2.7 galGal6_dna 46076 46649 (2841) + TguERVL2_I-b_fAlb LTR/ERVL 2766 3438 (2319) 33
ANNOTATION EVIDENCE:
67 42.13 2.07 2.71 galGal6_dna 46076 46558 2932 + ERVL-E LTR/ERVL 2766 3245 2422
67 42.13 2.07 2.71 galGal6_dna 46076 46558 (2932) ERVL-E#LTR/ERVL 2766 3245 (2422) m_b1s001i35
galGal6_dna 46076 AAAGTGAAAGGACCTGCACAAGAGATTCAGTTCCTAGGTATAAAGTGGCA 46125
i vv i i vvvvvvii vv i vi vv iv
ERVL-E#LTR/ER 2766 AAAATTCAGGGGCCTGCCACCTCAGTGAAGTTTCTAGGGGTCCAGTGGTC 2815
galGal6_dna 46126 AGATGGACGTCGTCACATCCCAACGGACGTGGTGGACAAAATCACTGCC- 46174
v iv v i i vv i vv vi v ivi i- ii v-
ERVL-E#LTR/ER 2816 TGGGGCATGTTGAGATATCCCTTCCAAGGTGAAAGACAAG-TTGCTGCAT 2864
galGal6_dna 46175 ATGTCTCTGCCCACTAATAAGAAAGAGGCACAGTCTTTTCTGGGCGTAGT 46224
v vv v iv i i v i vi vv v vv
ERVL-E#LTR/ER 2865 CTTGCACCTCCTACCACTAAGAAAGAGGCACAATGCTTGGTGGGCCTCTT 2914
galGal6_dna 46225 GGGCTTTTGGAGAATGCATGTTCCAAACTAGAGCCTCATTGTAAGCCCCC 46274
v v ivvi i v v i v i iv vv vv vv v v
ERVL-E#LTR/ER 2915 TGGATTTTGGAGGCAACATATACCACATTTGGGTATGCTACTCTGACCCA 2964
galGal6_dna 46275 TTTATCAAGTGACGCGGAAGAATG---ATTTTAAGTGGGGTCCTGAACAG 46321
iii i viii iv ---i i i v i i
ERVL-E#LTR/ER 2965 TTTACTGAGTAACCTAAAAGGCTGCCAGTTTTGAGTGGGGCCCAGAGCAA 3014
galGal6_dna 46322 CAGCAGGCTTTTGAGCAGATTAAGCAGGAGATAGCCCGTGCCGTGGCCCT 46371
v v i vv i iv vvv vii ivvvvv iv v v
ERVL-E#LTR/ER 3015 GAGAAGGCTCTGCAGCAGGTCCAGGCTGCAGTGCAAGCTGCTCTGCCACT 3064
galGal6_dna 46372 GGGGCCAGTACGGACGGAACAGGATGTAAAGAACATCCTCTATACTGCTG 46421
v - i- vv i - vi v i--- v iv viivv
ERVL-E#LTR/ER 3065 TGGGCCA-TAT-GACCCAGCA-GATCCAATGG---TGCTTGAAGTGTCTG 3108
galGal6_dna 46422 CTGGAGAGAAAGGTCCCACCTGGAGTTTGATGCAAAGAGCCTCAGGAGAG 46471
iv v v ii i v iiiv ii vvv ivvv vvi i
ERVL-E#LTR/ER 3109 TGGCAGATAGGGATGCTGTATGGAGCCTTTGGCAAGCCCCAATAGGAGAA 3158
galGal6_dna 46472 ACCTGAGGCCGACCCCTGGGATTCTGGAGTCGGGCC------TACAGGGG 46515
v viiivi v ii i i ivii i------ vi-----
ERVL-E#LTR/ER 3159 TCACAGTACAGACCTTTAGGATTTTGGAGCAAAGCTATGCCATCT----- 3203
galGal6_dna 46516 GTCTGAAGAGCACTACACTCCAACTGAAAAGGAGATCTTAGCT 46558
- v vv iv vvi i iv v ii i
ERVL-E#LTR/ER 3204 -TCTGCAGATAACTATTCTCCTTTTGAGAAACAGCTTCTGGCT 3245
Matrix = HMM
Kimura (with divCpGMod) = 62.67
Transitions / transversions = 0.80 (88/110)
Gap_init rate = 0.03 (16 / 482), avg. gap size = 1.44 (23 / 16)
61 42.66 1.40 2.47 galGal6_dna 46078 46649 2841 + HERVL LTR/ERVL 2834 3399 2255
61 42.66 1.40 2.47 galGal6_dna 46078 46649 (2841) HERVL#LTR/ERVL 2834 3399 (2255) m_b1s001i36
galGal6_dna 46078 AGTGAAAGGACCTGCACAAGAGATTCAGTTCCTAGGTATAAAGTGGCAAG 46127
i vv i v vvvvvvii vv i i vi vv iiv
HERVL#LTR/ERV 2834 AATTCAGGGACCTTCTACCTCAGTAAAATTTCTAGGGGTCCAGTGGTGTG 2883
galGal6_dna 46128 ATGGACGTCGTCACATCCCAACGGACGTGGTGGACAAAATCACTGCC-AT 46176
iv vvi vv i i vv vi v iv i i- ii v-v
HERVL#LTR/ERV 2884 GGGCCTGTCGAGATATTCCTTCTAAGGTGAAGGATAAG-TTGCTGCATTT 2932
galGal6_dna 46177 GTCTCTGCCCACTAATAAGAAAGAGGCACAGTCTTTTCTGGGCGTAGTGG 46226
v i iv i v vi i vii vv v v v
HERVL#LTR/ERV 2933 GGCCCCTCCTACAACCAAGAAAGAGGCACAATGCCTAGTGGGCCTATTTG 2982
galGal6_dna 46227 GCTTTTGGAGAATGCATGTTCCAAACTAGAGCCTCATTGTAAGCCCCCTT 46276
v ivvi ii vv i v i iv vv vv vv v v
HERVL#LTR/ERV 2983 GATTTTGGAGGCAACACATTCCTCATTTGGGTGTGTTACTCTGGCCCATT 3032
galGal6_dna 46277 TATCAAGTGACGCGGAAGAATG---ATTTTAAGTGGGGTCCTGAACAGCA 46323
i v i iv ---i i v v
HERVL#LTR/ERV 3033 TATCGAGTGACCCGAAAGGCTGCCAGTTTTGAGTGGGGTCCAGAACAGGA 3082
galGal6_dna 46324 GCAGGCTTTTGAGCAGATTAAGCAG---GAGATAGCCCGTGCCGTGGCCC 46370
v i vv i i iv vvv--- v vv --- iv v v
HERVL#LTR/ERV 3083 GAAGGCTCTGCAACAGGTCCAGGCTGCTGTGCAAGC---TGCTCTGCCAC 3129
galGal6_dna 46371 TGGGGCCAGTACGGACGGAACAGGATGTAAAGAACATCCTCTATACTGCT 46420
v vvv-- vv i - vi v i--- v iv viivv v
HERVL#LTR/ERV 3130 TTGGGCCATAT--GACCCAGCAG-ATCCAATGG---TGCTTGAGGTGTCA 3173
galGal6_dna 46421 GCTGGAGAGAAAGGTCCCACCTGGAGTTTGATGCAAAGAGCCTCAGGAGA 46470
iv v v ii i v iiii ii vvv iivvv vi v
HERVL#LTR/ERV 3174 GTGGCAGATAGGGATGCTGTTTGGAGCCTTTGGCAGGCCCCCATAGGTGA 3223
galGal6_dna 46471 GACCTGAGGCCGACCCCTGGGATTCTGGAGTCGGGCCTACAGGGGGTCTG 46520
iv viiiv vv i i i i ivi ivvvvivvv
HERVL#LTR/ERV 3224 ATCACAGTGGAGGCCTCTAGGATTTTGGAGCAAGGCCCTGCCATCTTCTG 3273
galGal6_dna 46521 AAGAGCACTACACTCCAACTGAAAAGGAGATCTTAGCTGCATATGAGGGG 46570
v vv v vvi i iiv v i i--- i v vv
HERVL#LTR/ERV 3274 CAGATAACTACTCTCCTTTTGAGAGACAGCTCTTGGCC---TGTTACTGG 3320
galGal6_dna 46571 GTTCAAGCTGCTTCTGAAGTAGTTGG-TACTGAAACGCAGCTCCATCTAG 46619
i ivi iv vvv vvv- i- iv ivvvv iv vviv iv
HERVL#LTR/ERV 3321 GCTTTGGTGGAAACTGAACGT-TTGACTATGGGTCATCAAGTCACCATGT 3369
galGal6_dna 46620 CACCTCGATTGCCAGTGTTGAACTGGATGT 46649
v vi i vi vv i i
HERVL#LTR/ERV 3370 GACCTGAACTGCCTATCATGAACTGGGTGC 3399
Matrix = HMM
Kimura (with divCpGMod) = 63.02
Transitions / transversions = 0.68 (96/142)
Gap_init rate = 0.03 (18 / 571), avg. gap size = 1.22 (22 / 18)
69 43.04 3.74 4.83 galGal6_dna 46169 46649 2841 + ERVL LTR/ERVL 2963 3438 2319
69 43.04 3.74 4.83 galGal6_dna 46169 46649 (2841) ERVL#LTR/ERVL 2963 3438 (2319) m_b1s001i37
galGal6_dna 46169 ACTGCC-ATGTCTCTGCCCACTAATAAGAAAGAGGCACAGTCTTTTCTGG 46217
ii v-v v i iv i v vi i vii vv
ERVL#LTR/ERVL 2963 GTTGCATCTGGCCCCTCCTACAACCAAGAAAGAGGCACAATGCCTAGTGG 3012
galGal6_dna 46218 GCGTAGTGGGCTTTTGGAGAATGCATGTTCCAAACTAGAGCCTCATTGTA 46267
v vv v v ivvi i vv i v i iv vv vv v
ERVL#LTR/ERVL 3013 GCCTCTTTGGATTTTGGAGGCAACATATTCCTCATTTGGGTGTGTTACTC 3062
galGal6_dna 46268 AGCCCCCTTTATCAAGTGACGCGGAAGAA---TGATTTTAAGTGGGGTCC 46314
v v v iii vi i iiv--- ii i i
ERVL#LTR/ERVL 3063 TGGCCCATTTACTGAGTGACCTGAAAAGCTGCTAGTTTTGAGTGGGGCCC 3112
galGal6_dna 46315 TGAACAGCAGCAGGCTTTTGAGCAGATTAAGCAGGAG---ATAGCCCGTG 46361
v v v i vv i i iv vvv vv---vv ---
ERVL#LTR/ERVL 3113 AGAACAGGAGAAGGCTCTGCAACAGGTCCAGGCTGCTGTGCAAGC---TG 3159
galGal6_dna 46362 CCGTGGCCCTGGGGCCAGTACGGACGGAACAGGATGTAAAGAACATCCTC 46411
iv v v v ------------ i v v--v v v --
ERVL#LTR/ERVL 3160 CTCTGCCACTTGGGCC------------ATATGATC--CAGCAGATCC-- 3193
galGal6_dna 46412 TATACTG----------CTGCTGGAGAGAAAGGTCCCACCTGGAGTTTGA 46451
v iv ---------- v iv v v ii i v iiii ii vv
ERVL#LTR/ERVL 3194 AATGGTGCTTGAAGTGTCAGTGGCAGATAGGGATGCTGTTTGGAGCCTTT 3243
galGal6_dna 46452 TGCAAAGAGCCTCAGGAGAGACCTGAGGCCGACCCCTGGGATTCTGGAGT 46501
v iivvv ivi v iviviiiv v i ii i i i
ERVL#LTR/ERVL 3244 GGCAGGCCCCTATAGGTGAATTACAGCGCAGGCCTTTAGGATTTTGGAGC 3293
galGal6_dna 46502 CGGGCCTACAGGGGGTCTGAAGAGCACTACACTCCAACTGAAAAGGAGAT 46551
vi ivvvvivvi v vv v vvi i iiv v
ERVL#LTR/ERVL 3294 AAGGCCCTGCCATCATCTGCAGATAACTACTCTCCTTTTGAGAGACAGCT 3343
galGal6_dna 46552 CTTAGCTGCATATGAGGGGGTTCAAGCTGCTTCTGAAGTAGTTGGTACTG 46601
i ivvv i---v iiiv iv vvv -i v iivv
ERVL#LTR/ERVL 3344 CTTGGCCTGCTAC---TGGGCCTTAGTAGAGACTGAA-CACTTGACCATG 3389
galGal6_dna 46602 AAACGCAGCTCCATCTAG-CACCTCGATTGCCAGTGTTGAACTGGATGT 46649
iiv i vivvii i vv -v viii vi vv i
ERVL#LTR/ERVL 3390 GGCCACCAAGTTACCATGTGACCTGAGCTGCCCATCATGAACTGGGTGT 3438
Matrix = HMM
Kimura (with divCpGMod) = 64.83
Transitions / transversions = 0.81 (88/109)
Gap_init rate = 0.06 (28 / 480), avg. gap size = 1.46 (41 / 28)
+ 100 42.9 6.8 9.0 galGal6_dna 46860 47878 (1612) + TguERVL2_I-b_fAlb LTR/ERVL 3659 4656 (1101) 33
ANNOTATION EVIDENCE:
100 42.93 6.77 9.02 galGal6_dna 46860 47878 1612 + ERVL LTR/ERVL 3659 4656 1101
100 42.93 6.77 9.02 galGal6_dna 46860 47878 (1612) ERVL#LTR/ERVL 3659 4656 (1101) m_b1s001i38
galGal6_dna 46860 CAGAAAATGAAAAGAAATATGCCCTGTTCACAGATGGATCATGTCGTAAT 46909
ii v i vv iv iv i v vvvvi vv
ERVL#LTR/ERVL 3659 CAGAGGAAGAGAAGACTTGGGCCTGGTTTACAGATGGTTCTGCATGATAT 3708
galGal6_dna 46910 GTGGGGAAGCATTGCAGATGGAAAGCTGCTGT-GTGGAGCCCCACACGAC 46958
ii v vvvviiiv ii v v i-v iv viv ---
ERVL#LTR/ERVL 3709 GCAGGCACCACCCAAAAGTGGACAGCTGCAGCACTACAGCCCCTTTC--- 3755
galGal6_dna 46959 AAGTTGCAGAGGCCACTGAAG-------GTAAAGGAGAATCAAGTCAGTT 47001
---- -i vii v ------- i ii vvvi v
ERVL#LTR/ERVL 3756 ----TG-GGACATCCCTGAAGGACAGTGGTGAAGGGAAATCCTCCCAGTG 3800
galGal6_dna 47002 CACAGAGGTAAAGGCTATCCAACTGGCCTTAGATGTTGCTGAACGGGAGA 47051
vi iv vvii vi v v iiv iv iv viivi
ERVL#LTR/ERVL 3801 GGCAGAACTTTGAGCAGTGCACCTGGTTGTGCACTTTGCTTGGAAGGAGA 3850
galGal6_dna 47052 GGTGGCCAACGCTTTATCTTTATACTGACTCATGGATGGTGGCAAATGCC 47101
ii ivvv viivi v i iiv i v vi
ERVL#LTR/ERVL 3851 AATGGCCAGATATGCGATTATATACTGATTCATGGGCTGTAGCCAATGGT 3900
galGal6_dna 47102 TTATGGGGGTGGTTACAGCAGTGGGAGCAAAATAACTGGCAAAGGAGGGG 47151
ivvv i i vi vvv i v v i i v vvi v i
ERVL#LTR/ERVL 3901 TTGGCTGGATGGTCAGGGACTTGGAAGGAACATGATTGGAAAATTGGTGA 3950
galGal6_dna 47152 CAAACCTGTTTGGGCTGCTGAACTGTGGAAAGACATTGCTGCCCGAATAA 47201
vvvi vvivv ivv v v iv vvi iii
ERVL#LTR/ERVL 3951 CAAAGAAATTTGGGGAAGAGGTATGTGGATAGACCTCTCTGAATGGGCAA 4000
galGal6_dna 47202 AGAATATGGTTGTAAAGGTGCGCCATGTAGATGCTCACGTGCCCAAGAAT 47251
i i ivvi vvv iv ii ---- v ii
ERVL#LTR/ERVL 4001 AAAATGTGAAGATATTTGTGTCCCATGTGAATGCTCAC----CAAAGGGT 4046
galGal6_dna 47252 CGGGCTACTGAAGAAGAACAAAACAACCATCAGGTAGATCGAGCTGCCAA 47301
-- i iv v v i iv vvvi iv i i v iiivi v
ERVL#LTR/ERVL 4047 --GACCTCAGCAGAGGAGGATTTTAATAATCAAGTGGATAGGATGACCTA 4094
galGal6_dna 47302 AATTGAGGTGACTCAAATAGACTTGGACTTGAAGAACAAGGGTGAATTAT 47351
vvi v vv - ivi v -----------------------i v
ERVL#LTR/ERVL 4095 TTCTGTGGATAC-CAGTCAGCCT-----------------------CTTT 4120
galGal6_dna 47352 TTCTAG--------------CTCGGTGGGCCCATGAAACTTCGGGTCATC 47387
ii i -------------- i ii i vvvvvv i v
ERVL#LTR/ERVL 4121 CCCCAGCCACCCTGTCATTGCCCAATGGGCTCATGAACAAAGTGGCCATG 4170
galGal6_dna 47388 AAGGAAGAGATGCAACATATAAATGCGCTAGAGACCGAGG---------- 47427
iv v i v ivv iv v viiv v iv ----------
ERVL#LTR/ERVL 4171 GTGGCAGGGATGGAGGTTATGCATGGGCTCAGCAACATGGACTTCCACTC 4220
galGal6_dna 47428 -----GGTGGACTTAACTATGGACACTAT----TGCACAAGCTGTTCATG 47468
----- iv i ii iv v ii---- v v iiviii
ERVL#LTR/ERVL 4221 ACCAAGGCTGACCTGGCTACTGCCACTGCTGAGTGCCCAATCTGCCAGCA 4270
galGal6_dna 47469 TCTGAAACGTGCCATAATTAAACAAGCCAAGAGGATGAAACCTCTCTGGG 47518
v v i ---- vv i i ---- vvviiv iv vi i---
ERVL#LTR/ERVL 4271 GCAGAGAC----CAACACTGA----GCCCCCGATATGGCACCATTCC--- 4309
galGal6_dna 47519 AGGAAGGGCGATGGCAGAAGTATAAATA---------------------T 47547
---------------------------v---------------------
ERVL#LTR/ERVL 4310 ---------------------------CTGGGGTGATCAGCCAGCTACCT 4332
galGal6_dna 47548 GGGGAGGCGTGGCAGGTTGATTATATCACCTTGCCAAGATCTCGCAATGG 47597
------- i iivviii ivvv vi v v
ERVL#LTR/ERVL 4333 G-------GTGGCAGGTTGATTACATTGGACCACTTCCATCATGGAAGGG 4375
galGal6_dna 47598 TAAGCGTTATGTGCTTACCATGGTGGAAGCAAC-----CACTGGGT--GG 47640
vv i v v ----- vvi ----- v i --
ERVL#LTR/ERVL 4376 GCAGTGTTTTGTCCTTAC-----TGGAATAGACACTTACTCTGGATATGG 4420
galGal6_dna 47641 CCTGAAACATACGCAGTACCCCATGCTACCGGCCGAAACACCATATTAGG 47690
vi v--i v v v v i iv v v i v vi vi vivv
ERVL#LTR/ERVL 4421 ATTT--GCCTTCCCTGCATGCAATGCTTCTGCCAAAACTACCATCCATGG 4468
galGal6_dna 47691 CCTCGAGAAACAAGTTCTCTGGCGACATGGTACCCCAGAGAGAGTCGAAT 47740
v iivii iivv v iiv iv ii v v vi i vv
ERVL#LTR/ERVL 4469 ACTTACAGAATGCCTTATCCACCATCATGGTATTCCACACAGCATTGCTT 4518
galGal6_dna 47741 CAGATAATGGGACTCATTTCAAAAACTCTCTTATAAATACATGGGCCAAA 47790
v v v i i v ivvvvvvvvi ivivvv iv v
ERVL#LTR/ERVL 4519 CTGATCAAGGAACTCACTTCACAGCAAAAGAAGTGTGGCAATGGGCTCAT 4568
galGal6_dna 47791 GATCATGGCATTGAGTGGATTTATCGTATCCCCTATCACGCACCAGCTTC 47840
v v v v vi i i i i i i iv vvv vv
ERVL#LTR/ERVL 4569 GCTCATGGAATTCACTGGTCTTACCATGTTCCCCACCATCCTGAAGCAGC 4618
galGal6_dna 47841 TGGTAATATTAAACGATACAACGGGTTGTTAAAAACTA 47878
ivvv vi i i iv i vi v i i v
ERVL#LTR/ERVL 4619 TGGCTTGATAGAATGGTGGAATGGCCTTTTGAAGACTC 4656
Matrix = HMM
Kimura (with divCpGMod) = 63.97
Transitions / transversions = 0.83 (180/218)
Gap_init rate = 0.10 (99 / 1018), avg. gap size = 1.61 (159 / 99)