68 25.37 3.73 0.00 galGal6_dna 1088 1221 (48221) CR1-X1_fAlb#LINE/CR1 923 1061 (2) m_b1s001i0 1

  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 11.26 6.90 0.00 galGal6_dna 1285 1313 (48129) (AAC)n#Simple_repeat 1 31 (0) m_b1s252i0 2

  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 30.45 2.98 8.12 galGal6_dna 1692 1859 (47583) C CR1-X1_fAlb#LINE/CR1 (9) 1054 895 m_b1s001i1 3

  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 27.34 5.26 1.27 galGal6_dna 1919 1994 (47448) (TAATA)n#Simple_repeat 1 79 (0) m_b1s252i1 4

  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 40.07 2.27 0.75 galGal6_dna 2693 2956 (46486) C ERVL-B4#LTR/ERVL (1055) 4659 4392 m_b1s001i2 5

  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 40.39 2.17 4.72 galGal6_dna 3117 3485 (45957) C TguERVL2_I-b_fAlb#LTR/ERVL (692) 1380 1021 m_b1s001i3 6

  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 14.55 0.00 0.00 galGal6_dna 5826 5878 (43564) (CTCT)n#Simple_repeat 1 53 (0) m_b1s252i2 7

  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 34.72 9.03 0.00 galGal6_dna 7490 7633 (41809) C HERVL40#LTR/ERVL (1545) 3985 3829 m_b1s001i4 8

  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 (1817) 4230 3913 m_b1s001i5 8

  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 25.64 5.36 0.00 galGal6_dna 8086 8141 (41301) (TAATA)n#Simple_repeat 1 59 (0) m_b1s252i3 9

  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 43.08 6.33 8.51 galGal6_dna 8840 9882 (39560) C ERVL#LTR/ERVL (1058) 4699 3678 m_b1s001i6 10

  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 42.84 6.70 4.87 galGal6_dna 9888 10633 (38809) C ERVL#LTR/ERVL (2711) 3046 2288 m_b1s001i7 10

  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 0.00 0.00 0.00 galGal6_dna 10867 10885 (38557) (C)n#Simple_repeat 1 19 (0) m_b1s252i4 11

  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 11.48 0.00 0.00 galGal6_dna 11028 11074 (38368) (GA)n#Simple_repeat 1 47 (0) m_b1s252i5 12

  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 35.16 15.38 2.27 galGal6_dna 11449 11838 (37604) C TguERVL2_I-b_fAlb#LTR/ERVL (4) 2068 1629 m_b1s001i8 10

  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 39.68 6.12 5.24 galGal6_dna 12578 14375 (35067) C HERVL18#LTR/ERVL (1162) 4885 3073 m_b1s001i9 13

  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 16.14 3.85 3.85 galGal6_dna 16205 16256 (33186) (ATA)n#Simple_repeat 1 52 (0) m_b1s252i6 14

  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 41.31 6.75 8.06 galGal6_dna 17058 18213 (31229) C HERVK14C#LTR/ERVK (2094) 5340 4199 m_b1s001i10 15

  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 17.11 0.00 0.00 galGal6_dna 20907 20939 (28503) (C)n#Simple_repeat 1 33 (0) m_b1s252i7 16

  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 20.83 4.55 0.00 galGal6_dna 20907 20950 (28492) (CCCCCT)n#Simple_repeat 1 46 (0) m_b1s252i8 17

  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 44.48 9.79 4.04 galGal6_dna 21468 22662 (26780) PABL_B-int#LTR/ERV1 2044 3304 (3818) m_b1s001i11 18

  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)


86 44.88 16.53 3.74 galGal6_dna 22667 23761 (25681) RLTR6-int#LTR/ERV1 3796 5025 (2753) m_b1s001i12 18

  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) m_b1s001i13 18

  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)


23 39.33 6.98 8.78 galGal6_dna 23742 24042 (25400) MURVY-int#LTR/ERV1 4896 5191 (2261) m_b1s001i14 18

  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) m_b1s001i15 18

  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 36.66 4.11 2.24 galGal6_dna 26285 26722 (22720) CR1-3_Croc#LINE/CR1 287 732 (2873) m_b1s001i16 19

  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)


638 35.98 1.19 1.69 galGal6_dna 26727 28329 (21113) CR1-3_Croc#LINE/CR1 1384 2978 (627) m_b1s001i17 19

  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) m_b1s001i18 19

  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) m_b1s001i19 19

  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 37.90 1.75 7.41 galGal6_dna 29224 29394 (20048) TguERVL2_I-b_fAlb#LTR/ERVL 1592 1753 (319) m_b1s001i20 20

  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 28.19 2.01 0.00 galGal6_dna 29452 29600 (19842) TguERVL2_I-b_fAlb#LTR/ERVL 1919 2070 (2) m_b1s001i21 20

  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 24.54 3.94 1.93 galGal6_dna 30025 30481 (18961) CR1-K4_fAlb#LINE/CR1 624 1089 (2) m_b1s001i22 21

  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 19.05 0.00 5.26 galGal6_dna 31654 31693 (17749) (GAAAAG)n#Simple_repeat 1 38 (0) m_b1s252i9 22

  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 31.77 2.50 1.23 galGal6_dna 32179 32258 (17184) (AT)n#Simple_repeat 1 81 (0) m_b1s252i11 23

  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)


30 44.50 1.94 3.45 galGal6_dna 32576 32987 (16455) C ERVL#LTR/ERVL (1674) 4083 3678 m_b1s001i23 24

  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 (2399) 3086 2355 m_b1s001i24 24

  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 (2711) 3046 2394 m_b1s001i25 24

  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 3.67 0.00 0.00 galGal6_dna 34191 34218 (15224) (CT)n#Simple_repeat 1 28 (0) m_b1s252i12 25

  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 20.33 2.08 2.08 galGal6_dna 35325 35372 (14070) (AGA)n#Simple_repeat 1 48 (0) m_b1s252i13 26

  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 10.99 0.00 0.00 galGal6_dna 35774 35822 (13668) (CT)n#Simple_repeat 1 49 (0) c_b1s251i0 27

  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 40.07 7.04 6.64 galGal6_dna 36037 36306 (13184) TguERVL2_I-b_fAlb#LTR/ERVL 1034 1304 (768) m_b1s001i26 28

  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 29.30 0.00 1.27 galGal6_dna 36773 36931 (12559) TguERVL2_I-b_fAlb#LTR/ERVL 1914 2070 (2) m_b1s001i27 28

  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 34.20 4.66 4.66 galGal6_dna 37350 37671 (11819) HERVL18#LTR/ERVL 2009 2330 (3717) m_b1s001i28 28

  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 19.30 0.77 3.98 galGal6_dna 37737 37995 (11495) C CR1-E4_fAlb#LINE/CR1 (0) 430 180 m_b1s001i29 29

  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)


57 42.38 5.97 6.80 galGal6_dna 38927 39964 (9526) C HERVL66#LTR/ERVL (1991) 2338 1309 m_b1s001i30 30

  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 (1674) 4083 3659 m_b1s001i31 30

  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 (1722) 3992 3597 m_b1s001i32 30

  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 4.35 0.00 0.00 galGal6_dna 40779 40802 (8688) (T)n#Simple_repeat 1 24 (0) m_b1s252i14 31

  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 15.80 2.70 2.70 galGal6_dna 40938 40974 (8516) (AATGGG)n#Simple_repeat 1 37 (0) m_b1s252i15 32

  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 41.80 12.49 16.33 galGal6_dna 44154 45274 (4216) TguERVL2_I-b_fAlb#LTR/ERVL 984 2067 (5) m_b1s001i33 33

  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 36.45 2.84 6.47 galGal6_dna 45650 46001 (3489) HERVL18#LTR/ERVL 1975 2314 (3733) m_b1s001i34 33

  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)


67 42.13 2.07 2.71 galGal6_dna 46076 46558 (2932) ERVL-E#LTR/ERVL 2766 3245 (2422) m_b1s001i35 33

  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) m_b1s001i36 33

  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) m_b1s001i37 33

  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 42.93 6.77 9.02 galGal6_dna 46860 47878 (1612) ERVL#LTR/ERVL 3659 4656 (1101) m_b1s001i38 33

  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)