17 16.26 3.64 5.56 Tasmanian_Devil_Short_Consensus_IGS 178 232 (30902) (GGCGGT)n#Simple_repeat 1 54 (0) m_b1s252i0 1

  Tasmanian_Dev        178 GGCGTTGGC-GTGG-GGTGGTGGTGGTGGTGGNGTGGTGGCGGCGACGAT 225
                               v    -    -     i     i   - - i        i i  i 
  (GGCGGT)n#Sim          1 GGCGGTGGCGGTGGCGGTGGCGGTGGCGGT-G-GCGGTGGCGGTGGCGGT 48

  Tasmanian_Dev        226 GGTCGGT 232
                             -    
  (GGCGGT)n#Sim         49 GG-CGGT 54

Matrix = Unknown
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5)

18 13.17 4.35 2.13 Tasmanian_Devil_Short_Consensus_IGS 187 232 (30902) (GTG)n#Simple_repeat 1 47 (0) m_b1s252i1 1

  Tasmanian_Dev        187 GTGG-GGTGGTGGTGGTGGTGG-NGTGGTGGCGGCGACGATGGTCGGT 232
                               -                 -?       i  i ii i    -   
  (GTG)n#Simple          1 GTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGT-GGT 47

Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.07 (3 / 45), avg. gap size = 1.00 (3 / 3)


14 5.00 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 526 546 (30588) (TCGG)n#Simple_repeat 1 21 (0) m_b1s252i2 2

  Tasmanian_Dev        526 TCGGTCGGTCGGTCGATCGGT 546
                                          i     
  (TCGG)n#Simpl          1 TCGGTCGGTCGGTCGGTCGGT 21

Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)


14 12.53 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 1057 1082 (30052) (GCAG)n#Simple_repeat 1 26 (0) m_b1s252i3 3

  Tasmanian_Dev       1057 GCACGCAGGCAGGCAGGCAGACACGC 1082
                              v                i  v  
  (GCAG)n#Simpl          1 GCAGGCAGGCAGGCAGGCAGGCAGGC 26

Matrix = Unknown
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)


35 0.00 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 1322 1354 (30326) (TGCT)n#Simple_repeat 1 33 (0) c_b1s251i0 4

  Tasmanian_Dev       1322 TGCTTGCTTGCTTGCTTGCTTGCTTGCTTGCTT 1354
                                                            
  (TGCT)n#Simpl          1 TGCTTGCTTGCTTGCTTGCTTGCTTGCTTGCTT 33

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0)


16 0.00 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 2844 2860 (28306) (C)n#Simple_repeat 1 17 (0) m_b1s252i4 5

  Tasmanian_Dev       2844 CCCCCCCCCCCCCCCCC 2860
                                            
  (C)n#Simple_r          1 CCCCCCCCCCCCCCCCC 17

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0)


101 0.00 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 3248 3333 (28347) (TC)n#Simple_repeat 1 86 (0) c_b1s251i1 6

  Tasmanian_Dev       3248 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 3297
                                                                             
  (TC)n#Simple_          1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50

  Tasmanian_Dev       3298 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 3333
                                                               
  (TC)n#Simple_         51 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 86

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0)


54 0.00 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 3922 3967 (27713) (TC)n#Simple_repeat 1 46 (0) c_b1s251i2 7

  Tasmanian_Dev       3922 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 3967
                                                                         
  (TC)n#Simple_          1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 46

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0)


15 5.56 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 3968 3986 (27310) (C)n#Simple_repeat 1 19 (0) m_b1s252i5 8

  Tasmanian_Dev       3968 CCCCCCTCCCCCCCCCCCC 3986
                                 i            
  (C)n#Simple_r          1 CCCCCCCCCCCCCCCCCCC 19

Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0)


23 6.67 8.51 0.00 Tasmanian_Devil_Short_Consensus_IGS 7458 7504 (23792) (TCTCTG)n#Simple_repeat 1 51 (0) m_b1s252i6 9

  Tasmanian_Dev       7458 TCCCTGTCTCTG--TCTGTCTGTGTCTCTG--TCTGTCTGTGTCTCTGTC 7503
                             i         --       v        --       v          
  (TCTCTG)n#Sim          1 TCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTC 50

  Tasmanian_Dev       7504 T 7504
                            
  (TCTCTG)n#Sim         51 T 51

Matrix = Unknown
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.04 (2 / 46), avg. gap size = 2.00 (4 / 2)

29 9.55 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 7466 7510 (23786) (TCTG)n#Simple_repeat 1 45 (0) m_b1s252i7 9

  Tasmanian_Dev       7466 TCTGTCTGTCTGTGTCTCTGTCTGTCTGTGTCTCTGTCTGTCTGT 7510
                                        v v             v v             
  (TCTG)n#Simpl          1 TCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT 45

Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)


183 5.90 1.17 0.78 Tasmanian_Devil_Short_Consensus_IGS 7512 7767 (23913) (TC)n#Simple_repeat 1 257 (0) c_b1s251i3 10

  Tasmanian_Dev       7512 TCTCTGTCTGTCTGTCTCTGTCTGTCTGTCTGTCTCTCTCTCTCTCTCTC 7561
                                v   v   v     v   v   v   v                  
  (TC)n#Simple_          1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50

  Tasmanian_Dev       7562 TCTCTGTCTGTCTCTCTCTCTCTNCTCTCTCTCTGTCTCTCTCTCTNTCT 7611
                                v   v             -          v           ?   
  (TC)n#Simple_         51 TCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTCTCT 99

  Tasmanian_Dev       7612 NTCTCTCT-TNTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 7660
                           ?       - ?                                       
  (TC)n#Simple_        100 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 149

  Tasmanian_Dev       7661 CTCTCTCTCTGTCTCTCTCTCT-TCTCTGTCTCTCTCTCTCTCTC-CTCT 7708
                                     v           -     v                -    
  (TC)n#Simple_        150 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 199

  Tasmanian_Dev       7709 CTNTCTCTCTCTCTCTCTCTCTCTCTCTGTCTCTCTCTCTGTCTCTCTCT 7758
                             ?                         v           v         
  (TC)n#Simple_        200 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 249

  Tasmanian_Dev       7759 NCTCTCTCT 7767
                           -        
  (TC)n#Simple_        250 -CTCTCTCT 257

Matrix = Unknown
Transitions / transversions = 0.00 (0/14)
Gap_init rate = 0.02 (5 / 255), avg. gap size = 1.00 (5 / 5)


987 30.11 4.15 3.99 Tasmanian_Devil_Short_Consensus_IGS 8275 8900 (22651) C L1ME3G_3end#LINE/L1 (294) 630 4 m_b1s551i0 11

  Tasmanian_Dev       8275 TGCTCATTTCACTCAGCATCAGTTCATGTAAGTCTCTCCAAGCCTCTCTG 8324
                               iv         i  vi vv  v  v ii   i    v i vv vii
C L1ME3G_3end#L        630 TGCTTTTTTCACTCAACAATATGTCTTGGAGATCTTTCCATGTCAGTACA 581

  Tasmanian_Dev       8325 TCTTCATCCCGCTGATCATTTCTTCCAGAACAATAATATTCCTTAACATT 8374
                            v vv   ivv  v  iv   i vv ? vvvv   i      v  ii  v
C L1ME3G_3end#L        580 TATAGATCTACCTCATTCTTTTTAACNGCTGCATAGTATTCCATAGTATG 531

  Tasmanian_Dev       8375 CATATACCACAATTTGCCCAAGCATTCTNCAATGGATGGGCATCCCTTCA 8424
                           v        i     iiii  v     i? v  v     i   ---  vi
C L1ME3G_3end#L        530 GATATACCATAATTTATTTAACCATTCCCCTATTGATGGACAT---TTAG 484

  Tasmanian_Dev       8425 GTT----TCAGTTTCTAGCTACTACAAACAGGGCTGCCACAAACATTTTG 8470
                              ----i  i   i v    i        iv     v ii     ii v
C L1ME3G_3end#L        483 GTTGTTTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACATCCTT 434

  Tasmanian_Dev       8471 GCACATACGGGTCCCTTTCCTTCT---TAATGTATTTCTTTGGGGTNGAA 8517
                            i    i ?--   i v v viv ---ii -        ? i  i ?  v
C L1ME3G_3end#L        433 GTACATGCN--TCCTTGTGCACATGTGCGA-GTATTTCTNTAGGATAGAT 387

  Tasmanian_Dev       8518 GCCCAGTAGGAGCACTGCTGGATCAAGGGTTATGCACAGTTTGATAACTT 8567
                           ?  ?  v  vi v i      i    i  v     i  v   i -- i  
C L1ME3G_3end#L        386 NCCNAGAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTTAA--ATTT 339

  Tasmanian_Dev       8568 TGGGGGCAGA-ATTGCTGA-TTGCTCTCCAGAATGATTGGATCCGGTCAC 8615
                            ii---i   - i   ii -    i     i  ? ii  v i viv i  
C L1ME3G_3end#L        338 TAA---TAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTAC 292

  Tasmanian_Dev       8616 GACTCCAGCAACAATGCATCAG--TGCCAGTTTTCCCTAAATCCCC-CCA 8662
                           ivii   v  i  i  i  v  -- i  v    i   - v i  i -   
C L1ME3G_3end#L        291 ACTCCCACCAGCAGTGTATGAGAGTACCCGTTTCCCC-ACACCCTCGCCA 243

  Tasmanian_Dev       8663 ACAGTCGTCATGATTTTTNTCCTGTCA--TCTTAGCCAATGTGACAGGGG 8710
                              v ? --  -   v i?v?  v i -- i  v      v   ii  v 
C L1ME3G_3end#L        242 ACACTNG--AT-ATTATCAANCTTTTAAATTTTTGCCAATCTGATGGGTG 196

  Tasmanian_Dev       8711 TGGAGTAGTATCTCAGAGTTCTCTTAATTTGCATTTCTCAGATCAACAGT 8760
                           vii i i        vv   v i              i v   i vi   
C L1ME3G_3end#L        195 AAAAATGGTATCTCATTGTTGTTTTAATTTGCATTTCCCTGATTACTAGT 146

  Tasmanian_Dev       8761 GA--TTTGGCACTCTTTCATATG---AGTGGAAAGAGGTTCGAGTTCACA 8805
                             --  vi   iii         --- v   vv ----  i vi  i- v
C L1ME3G_3end#L        145 GAGGTTGAGCATCTTTTCATATGTTTATTGGCCA----TTTGTATTT-CC 101

  Tasmanian_Dev       8806 TCCTCTGAAAAT----TGTTCATATCCTTTGACCCTTTGTCAAGTAGAGA 8851
                             i    vi   ----               v  v   v  v v i iv-
C L1ME3G_3end#L        100 TCTTCTGTGAATTGCCTGTTCATATCCTTTGCCCATTTTTCTATTGGGT- 52

  Tasmanian_Dev       8852 ATGGCTTGATTTCTTATAAA---GTAGTGAATTCTCTCTCTATTTTGGAA 8898
                           -  v   --        vi ---    -  i    i v v    i    v
C L1ME3G_3end#L         51 -TGTCTT--TTTCTTATTGATTTGTAG-GAGTTCTTTATATATTCTGGAT 6

  Tasmanian_Dev       8899 AT 8900
                             
C L1ME3G_3end#L          5 AT 4

Matrix = 20p49g.matrix
Kimura (with divCpGMod) = 39.67
Transitions / transversions = 1.18 (98/83)
Gap_init rate = 0.06 (36 / 625), avg. gap size = 1.42 (51 / 36)

383 32.52 5.03 5.17 Tasmanian_Devil_Short_Consensus_IGS 8818 9592 (21959) C L1M5_orf2#LINE/L1 (62) 3232 2459 m_b1s551i1 11

  Tasmanian_Dev       8818 TGTTCATATCCTTTGACCCTTTGTCAAGTAGA--GAATGGCTTGATTTCT 8865
                                 vi  i    v  v   v ?v v i i-- vv  v   --   ? 
C L1M5_orf2#LIN       3232 TGTTCAAGTCTTTTGCCCATTTTTNTATTGGGTTGTTTGTCTT--TTTNT 3185

  Tasmanian_Dev       8866 TATAAAGTAGT--GAATTCTCTCTCTATTTTGGAAATGAGGGCTTTATCA 8913
                              vi ? v  --  i    i v v    i    v i   vv    i   
C L1M5_orf2#LIN       3184 TATTGANTTGTAGGAGTTCTTTATATATTCTGGATACGAGTCCTTTGTCA 3135

  Tasmanian_Dev       8914 GA-ACCTTTAAT-TAAAAATCTTTTCCCAGTTTGTTGCTT-CCTTCTAAT 8960
                             - iv v ?v -i   v  i  i     ? i   v    -    i v  
C L1M5_orf2#LIN       3134 GATATATGTNTTGCAAATATTTTCTCCCANTCTGTGGCTTGCCTTTTCAT 3085

  Tasmanian_Dev       8961 CTTGTTGGCATTAGTTTTGTTCGGACAAAGGTTTTTTCATTCGATGTCAT 9010
                           i  v  ii iv ivi   vvv? ii  i i      vvv  i    ?vi 
C L1M5_orf2#LIN       3084 TTTCTTAACGGTGTCTTTTGANGAGCAGAAGTTTTTAATTTTGATGNAGT 3035

  Tasmanian_Dev       9011 CCAA-------ATTGTCTCTTTTGTTGTTCGATAATGATCTCTAGTTCTT 9053
                               -------   v i      i v   ? ----  v i i ivv  i 
C L1M5_orf2#LIN       3034 CCAATTTATCAATTTTTTCTTTTATGGTTNG----TGCTTTTTGTGTCCT 2989

  Tasmanian_Dev       9054 CTTTGGTCACAGATTTCTTCCTCCTCCACAAGTCTGAGAGTTGAAGTAGC 9103
                           v   i--- v i  i i v   v?i   - i   vvii  v -- v vv 
C L1M5_orf2#LIN       2988 GTTTA---AGAAATCTTTGCCTANCCCA-AGGTCACGAAGAT--ATTCTC 2945

  Tasmanian_Dev       9104 CAATGTTC----CTCGAATTTATTGATGATCTTGATCTTGACGCCTACAT 9149
                            v     i----  v   v  -- v  ii i  i?ii  v  iii  vi 
C L1M5_orf2#LIN       2944 CTATGTTTTCTTCTAGAAGTT--TTATAGTTTTANCTTTTACATTTAGGT 2897

  Tasmanian_Dev       9150 C-ATGGACCTATTTTTGATCTTTTCTTGGTATATGGTGTGAAGTCTGGGT 9198
                            -   - i i  i ?vi  ivv  i   - i          i  vv    
C L1M5_orf2#LIN       2896 CTATG-ATCCATCTNGAATTAATTTTTG-TGTATGGTGTGAGGTAGGGGT 2849

  Tasmanian_Dev       9199 CAATACCTGATTTCTGCCATACTAATTTCCAGTTTCCCCAGTAGTTTTGG 9248
                            i v?iiiiv   i v     ivi  v    i  vii    i viv  v 
C L1M5_orf2#LIN       2848 CGAGNTTCATTTTTTTCCATATGGATATCCAATTGTTCCAGCACCATTTG 2799

  Tasmanian_Dev       9249 TCAAATAATGAATTCTTTGCTCA--AAA----GTTGGGATCTTTGGGTTG 9292
                            ii  v ivvv  i    v i  --i  ----?    v i     -----
C L1M5_orf2#LIN       2798 TTGAAAAGACTATCCTTTCCCCACTGAATTGCNTTGGCACCTTTG----- 2754

  Tasmanian_Dev       9293 ATCAAACACTAGATTGCTATA---GTGCTTGACTATTTTGTCCTGTGAAC 9339
                           -     v ii i? v? i   ---   ivv v      i------  i  
C L1M5_orf2#LIN       2753 -TCAAAAATCAANTGNCCATATATGTGTGGGTCTATTTC------TGGAC 2711

  Tasmanian_Dev       9340 ---CTAAGCCATTCC-CTGATCAACTGATGTATTTCTTA-GCCAATACCA 9384
                           ---   vv ii    -i     v i vi v   i-    -          
C L1M5_orf2#LIN       2710 TCTCTATTCTGTTCCATTGATCTATTTGTCTATC-CTTACGCCAATACCA 2662

  Tasmanian_Dev       9385 AATGGTTTTATTGACTGTTGCTTTATAATATAATTTGAGATCAGGTACAG 9434
                           v iv  i  iv v     v           vivi    ?   ?    vv 
C L1M5_orf2#LIN       2661 CACTGTCTTGATTACTGTAGCTTTATAATAAGTCTTGANATCNGGTAGTG 2612

  Tasmanian_Dev       9435 CTAGGTCACCTTCA--TTTGAANTTTTTTTTTTCATTAATTCCTTGAA-A 9481
                           -  i  --   i  --    --? i  i       vv v vii   iv- 
C L1M5_orf2#LIN       2611 -TAAGT--CCTCCAACTTTG--TTCTTCTTTTTCAAGATTGTTTTGGCTA 2567

  Tasmanian_Dev       9482 TTCTCCACCTTTTGTTCTTCCATATGATTTTTCTGGTTATTTTTT---TT 9528
                               ?vii i    ivi        i v    vvii i vi  v ---  
C L1M5_orf2#LIN       2566 TTCTNGGTCCTTTGCATTTCCATATAAATTTTAGAATCAGCTTGTCAATT 2517

  Tasmanian_Dev       9529 TCTAGATCATTAAAATAGTTTCTTGGAAGTCTGATTGGTATAGCACTAAA 9578
                               ------i    v iii vi   i v i       v  v   i i  
C L1M5_orf2#LIN       2516 TCTA------CAAAAAAACCTGCTGGGATTTTGATTGGGATTGCATTGAA 2473

  Tasmanian_Dev       9579 TAAATAAATAGATT 9592
                            vv   i  vi   
C L1M5_orf2#LIN       2472 TCTATAGATCAATT 2459

Matrix = 20p49g.matrix
Kimura (with divCpGMod) = 44.15
Transitions / transversions = 1.13 (127/112)
Gap_init rate = 0.07 (57 / 774), avg. gap size = 1.39 (79 / 57)


464 30.28 4.92 4.35 Tasmanian_Devil_Short_Consensus_IGS 9530 9895 (21656) L1MD1_3end#LINE/L1 266 633 (356) m_b1s551i2 12

  Tasmanian_Dev       9530 CTAGATCATTAAAATAGTTTCT--TGGAAGTCTGAT-TGGTATAGC-ACT 9575
                             i     i v v i -  v  --   i i v i v-     i   -   
  L1MD1_3end#LI        266 CTGGATCACTCATACA-TTGCTGGTGGGAATGTAAAATGGTACAGCCACT 314

  Tasmanian_Dev       9576 AAATAAATAAATAGATT---AGTTTATGCTCAAAAAGTTATCAAACTGTG 9622
                           v-- ii -   i  v  ---     ---  i     ii  ---   -i  
  L1MD1_3end#LI        315 C--TGGA-AAACAGTTTGGCAGTTT---CTTAAAAAACTA---AAC-ATG 354

  Tasmanian_Dev       9623 CA--TACCCTTTGATCCAGCAGTGTTACTACTGGG-ATTATATCCCAAGG 9669
                             --    v vi  i      i vvi   v     -   -       ii 
  L1MD1_3end#LI        355 CAACTACCATACGACCCAGCAATTGCACTCCTGGGCATT-TATCCCAGAG 403

  Tasmanian_Dev       9670 AGATTATAANAAGGG-----AAAGGGACCTGTATGTGCACGAATGTTTTT 9714
                            i  v v  ?vviv ----- v iii       ----           v 
  L1MD1_3end#LI        404 AAATGAAAACTTATGTTCACACAAAAACCTGTA----CACGAATGTTTAT 449

  Tasmanian_Dev       9715 -GCGRCCCTTTTTGTAGT-GCTAAAAACTGGAAACTGAATGGATGTCCAT 9762
                           -  i? ii v  i   i -  i             vivvii       v 
  L1MD1_3end#LI        450 AGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCAGATGTCCTT 499

  Tasmanian_Dev       9763 CAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGGAATAT 9812
                             iiv  v      i i  i   i       i  vv   ii        i
  L1MD1_3end#LI        500 CAACGGGTGAATGGTTAAACAAACTGTGGTACATCCATACCATGGAATAC 549

  Tasmanian_Dev       9813 TACTGTTCTGTAGAAATGACCAACAGGATGAT-TTCAGAAAGGCCTGGAG 9861
                               vvv vi  i   v  v i vvviv    -iv iv  vii      v
  L1MD1_3end#LI        550 TACTCAGCAATAAAAAGGAACGAACTATTGATACACGCAACAACCTGGAT 599

  Tasmanian_Dev       9862 AGACTTACACGAACTGATGCTGAGTGAAATGAGC 9895
                           ii ii v  vii v v             vi   
  L1MD1_3end#LI        600 GAATCTCCAGAGAATTATGCTGAGTGAAAAAAGC 633

Matrix = 20p49g.matrix
Kimura (with divCpGMod) = 37.61
Transitions / transversions = 1.26 (59/47)
Gap_init rate = 0.07 (26 / 365), avg. gap size = 1.31 (34 / 26)

488 29.92 3.42 3.42 Tasmanian_Devil_Short_Consensus_IGS 9552 9814 (21737) L1ME3E_3end#LINE/L1 288 550 (439) m_b1s551i3 12

  Tasmanian_Dev       9552 TGGAAGTCTGA-TTGGTATAGCACTAAATAAATAAATAGATTAGT-TTAT 9599
                              i   v i -      i --  i vv viiv   i iv  i i-    
  L1ME3E_3end#L        288 TGGGAGTGTAAATTGGTACA--ACCACTTTGGAAAACAATTTGGCATTAT 335

  Tasmanian_Dev       9600 GCTCAAAAAGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACT 9649
                           -  viv      i--  iv  i         vi  i      i vii   
  L1ME3E_3end#L        336 -CTAGTAAAGTTG--AAGATGCGCATACCCTACGACCCAGCAATTCCACT 382

  Tasmanian_Dev       9650 ACTGGGATTATATCCCAAGGAGATTATAANAAGGG-----AAAGGGACCT 9694
                           v  i  vv    i  i ii  i i v vi? v v -----v i i   --
  L1ME3E_3end#L        383 CCTAGGTATATACCCTAGAGAAACTCTTGCACGTGTGCACCAGGAGAC-- 430

  Tasmanian_Dev       9695 GTATGTGCACGAATGTTTTT-GCGRCCCTTTTTGTAGT-GCTAAAAACTG 9742
                           --    i  v       iv -  i? vi v      i -  v        
  L1ME3E_3end#L        431 --ATGTACAAGAATGTTCATAGCAGCATTGTTTGTAATAGCAAAAAACTG 478

  Tasmanian_Dev       9743 GAAACTGAATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGT 9792
                                vivviii         iiiv         v i             
  L1ME3E_3end#L        479 GAAACAACCCAAATGTCCATCGACAGGAGAATGGATAAATAAATTGTGGT 528

  Tasmanian_Dev       9793 ATATGAATATTATGGAATATTA 9814
                               vv   iv        i  
  L1ME3E_3end#L        529 ATATTCATACAATGGAATACTA 550

Matrix = 20p49g.matrix
Kimura (with divCpGMod) = 37.65
Transitions / transversions = 1.38 (44/32)
Gap_init rate = 0.05 (14 / 262), avg. gap size = 1.29 (18 / 14)

493 28.97 4.46 4.46 Tasmanian_Devil_Short_Consensus_IGS 9584 9919 (21632) L1ME1_3end#LINE/L1 320 655 (271) m_b1s551i4 12

  Tasmanian_Dev       9584 AAATAGATT---AGTTTATGCTCAAAAAGTTATCAAAC-TGTGCATACCC 9629
                              i  v  ---     ---  i ?       ---   - iii v    v
  L1ME1_3end#LI        320 AAACAGTTTGGCAGTTT---CTTANAAAGTTA---AACATACACTTACCA 363

  Tasmanian_Dev       9630 TTTGATCCAGCAGTGTTACTACTGGG-ATTATATCCCAAGGAGATTATAA 9678
                            v   i      i vii   v  i  -   -  i  v ii  i  v v  
  L1ME1_3end#LI        364 TATGACCCAGCAATTCCACTCCTAGGTATT-TACCCAAGAGAAATGAAAA 412

  Tasmanian_Dev       9679 NAAGGG-----AAAGGGACCTGTATGTGCACGAATGTTTTT-GCGRCCCT 9722
                           ? viv ----- v ii   i    ----          iv -  i? ii 
  L1ME1_3end#LI        413 CATATGTCCACACAAAGACTTGTA----CACGAATGTTCATAGCAGCTTT 458

  Tasmanian_Dev       9723 TTTTGTAGT-GCTAAAAACTGGAAACTGAATGGATGTCCATCAGTTGGAG 9771
                           v  i   i -  i             vivviii          ii?  v 
  L1ME1_3end#LI        459 ATTCGTAATAGCCAAAAACTGGAAACAACCCAAATGTCCATCAACNGGTG 508

  Tasmanian_Dev       9772 AATGGCTGAATAAATTGTGGTATATGAATATTATGGAATATTACTGTTCT 9821
                                v i  i              vv   iv        i    vvv v
  L1ME1_3end#LI        509 AATGGATAAACAAATTGTGGTATATCCATACAATGGAATACTACTCAGCA 558

  Tasmanian_Dev       9822 GTAGAAATGACCAACAGGATGAT-TTCAGAAAGGCCTGGA-GAGACTTAC 9869
                           i  i   v  v i vvviv    -iv iv  vii v    -  iv  i v
  L1ME1_3end#LI        559 ATAAAAAGGAACGAACTACTGATACACGCAACAACATGGATGAATCTCAA 608

  Tasmanian_Dev       9870 ACGAACTGATGCTGAGTGAAATGAGCAGGAC-CAGGAGATCATTATATAC 9918
                            v?v i -             vi   vi   -  ii  --- ?  i    
  L1ME1_3end#LI        609 AANCATT-ATGCTGAGTGAAAGAAGCCAGACACAAAAG---ANTACATAC 654

  Tasmanian_Dev       9919 T 9919
                            
  L1ME1_3end#LI        655 T 655

Matrix = 20p49g.matrix
Kimura (with divCpGMod) = 36.74
Transitions / transversions = 1.21 (51/42)
Gap_init rate = 0.07 (24 / 335), avg. gap size = 1.25 (30 / 24)

625 31.38 2.71 1.68 Tasmanian_Devil_Short_Consensus_IGS 9605 9899 (21652) L1ME4c_3end#LINE/L1 342 639 (191) m_b1s551i5 12

  Tasmanian_Dev       9605 AAAAGTTATCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGG 9654
                             i  ii  v   v   v            i    i i vii   v    
  L1ME4c_3end#L        342 AAGAGCCATAAAAATGTTCATACCCTTTGACCCAGTAATTCCACTTCTGG 391

  Tasmanian_Dev       9655 GATTATATCCCAAGGAGATTAT----AANAAGGGAAAGGGACCTGTATGT 9700
                             v v     i     i  v  ----  ?    i   i ---  i    i
  L1ME4c_3end#L        392 GAATTTATCCTAAGGAAATAATTCAAAAGAAGGAAAAAG---CTATATGC 438

  Tasmanian_Dev       9701 GCACGAATGTTT-TTGCGRCCCTTTTTGTAGT-GCTAAAAACTGGAAACT 9748
                           i ivii     i-    i? vi v   i  i -  v     i       v
  L1ME4c_3end#L        439 ACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAAACA 488

  Tasmanian_Dev       9749 GAATGGATGTCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGA 9798
                           ivv ii       v  i v  i      i i i      i     i  v?
  L1ME4c_3end#L        489 ACCTAAATGTCCAACAATAGGGGAATGGTTAAGTAAATTATGGTACATCN 538

  Tasmanian_Dev       9799 ATATTATGGAATATTACTGT--TCTGTAGAAATGACCAACAGGATGATTT 9846
                            iviv           -  i--i vv  i      iv vi v  v  i v
  L1ME4c_3end#L        539 ACTCGATGGAATATTA-TGCAGCCATTAAAAATGATAATTATGAAGACTA 587

  Tasmanian_Dev       9847 CAGAAAGGCCTGGAGAGACTTACACGAACTGATGCTGAGTGAAATGAGCA 9896
                           iiv ivii v    - i iv vi i  vv i   i i       vi    
  L1ME4c_3end#L        588 TGTAGCAACATGGA-AAATGTTTATGATATAATGTTAAGTGAAAAAAGCA 636

  Tasmanian_Dev       9897 GGA 9899
                            i 
  L1ME4c_3end#L        637 GAA 639

Matrix = 20p49g.matrix
Kimura (with divCpGMod) = 41.61
Transitions / transversions = 1.60 (56/35)
Gap_init rate = 0.03 (9 / 294), avg. gap size = 1.44 (13 / 9)

631 24.50 2.48 0.98 Tasmanian_Devil_Short_Consensus_IGS 9613 9814 (21737) L1ME3G_3end#LINE/L1 343 547 (377) m_b1s551i6 12

  Tasmanian_Dev       9613 TCAAACTGTGCATACCCTTTGATCCAGCAGTGTTACTACTGGGATTATAT 9662
                            i   v  i             i      i vii   v  ?  ?v v   
  L1ME3G_3end#L        343 TTAAAATGCGCATACCCTTTGACCCAGCAATTCCACTTCTNGGNATCTAT 392

  Tasmanian_Dev       9663 CCCAAGGAGAT--TATAANAAGGGAA-AGGGACCTGTATGTGCACGAATG 9709
                             i ?i  i  -- vvv ? v v v - i   ?-- i    i  v i   
  L1ME3G_3end#L        393 CCTANAGAAATACTCGCACATGTGCACAAGGAN--GCATGTACAAGGATG 440

  Tasmanian_Dev       9710 TTT-TTGCGRCCCTTTTTGTAGT-GCTAAAAACTGGAAACTGAATGGATG 9757
                             i-    i? vi v      i -  v     i       vivv ii   
  L1ME3G_3end#L        441 TTCATTGCAGCATTGTTTGTAATAGCGAAAAATTGGAAACAACCTAAATG 490

  Tasmanian_Dev       9758 TCCATCAGTTGGAGAATGGCTGAATAAATTGTGGTATATGAATATTATGG 9807
                                  i v  i      i i        i        vv   i     
  L1ME3G_3end#L        491 TCCATCAATAGGGGAATGGTTAAATAAATTATGGTATATCCATACTATGG 540

  Tasmanian_Dev       9808 AATATTA 9814
                               i  
  L1ME3G_3end#L        541 AATACTA 547

Matrix = 20p49g.matrix
Kimura (with divCpGMod) = 30.62
Transitions / transversions = 1.33 (28/21)
Gap_init rate = 0.03 (6 / 201), avg. gap size = 1.17 (7 / 6)


17 15.79 0.00 6.67 Tasmanian_Devil_Short_Consensus_IGS 10336 10383 (21168) (TAAA)n#Simple_repeat 1 45 (0) m_b1s252i8 13

  Tasmanian_Dev      10336 TAAATAAAGGCTATTAAATAAAATTAAAAAATAAATAAATAAATAGAT 10383
                                   -vvv  -    -    v  v                 i  
  (TAAA)n#Simpl          1 TAAATAAA-TAAAT-AAAT-AAATAAATAAATAAATAAATAAATAAAT 45

Matrix = Unknown
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.06 (3 / 47), avg. gap size = 1.00 (3 / 3)


19 7.25 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 10539 10569 (20982) (T)n#Simple_repeat 1 31 (0) m_b1s252i9 14

  Tasmanian_Dev      10539 TTTGTTTTYCYTTTTTTTTTTTTTTTTTTTT 10569
                              v    ?i?                    
  (T)n#Simple_r          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31

Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)


28 3.33 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 10707 10737 (20943) (T)n#Simple_repeat 1 31 (0) c_b1s251i4 15

  Tasmanian_Dev      10707 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTT 10737
                               i                          
  (T)n#Simple_r          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31

Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0)


28 11.63 1.61 5.00 Tasmanian_Devil_Short_Consensus_IGS 11787 11848 (19733) (AAAT)n#Simple_repeat 1 60 (0) m_b1s252i10 16

  Tasmanian_Dev      11787 AAATAAATAAATCAATAAA-AAAACAATAAATTAATAAAATAAAATAAAA 11835
                                       v      -   vv       v   -    -       v
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAAT-AAAT-AAATAAAT 48

  Tasmanian_Dev      11836 AAAAAAATTAAAT 11848
                              v   -     
  (AAAT)n#Simpl         49 AAATAAA-TAAAT 60

Matrix = Unknown
Transitions / transversions = 0.00 (0/6)
Gap_init rate = 0.07 (4 / 61), avg. gap size = 1.00 (4 / 4)


31 10.85 8.57 0.00 Tasmanian_Devil_Short_Consensus_IGS 12351 12420 (19161) (TAAAA)n#Simple_repeat 1 76 (0) m_b1s252i11 17

  Tasmanian_Dev      12351 TAAAAT-AAAT-AAAT-CAATAAAA-AAAAAAAAAAACAAT-AAAT-TAA 12394
                                 -    -    -v       -    v    v v   -    -v  
  (TAAAA)n#Simp          1 TAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA 50

  Tasmanian_Dev      12395 TAAAATAAAATAAAAAAAAATTAAAT 12420
                                          v     v    
  (TAAAA)n#Simp         51 TAAAATAAAATAAAATAAAATAAAAT 76

Matrix = Unknown
Transitions / transversions = 0.00 (0/7)
Gap_init rate = 0.09 (6 / 69), avg. gap size = 1.00 (6 / 6)

30 22.55 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 12352 12414 (19167) (A)n#Simple_repeat 1 63 (0) m_b1s252i12 17

  Tasmanian_Dev      12352 AAAATAAATAAATCAATAAAAAAAAAAAAAAACAATAAATTAATAAAATA 12401
                               v   v   vv  v               v  v   vv  v    v 
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50

  Tasmanian_Dev      12402 AAATAAAAAAAAA 12414
                              v         
  (A)n#Simple_r         51 AAAAAAAAAAAAA 63

Matrix = Unknown
Transitions / transversions = 0.00 (0/12)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)


22 15.79 7.58 1.43 Tasmanian_Devil_Short_Consensus_IGS 12919 12984 (18597) (TAAAT)n#Simple_repeat 1 70 (0) m_b1s252i13 18

  Tasmanian_Dev      12919 TAAAATAAA-TAAA-TCAATAAAAAAAACAATAAATT-AATAAAATAAAA 12965
                               v    -    - v   v   vv  - v      -   v    v   
  (TAAAT)n#Simp          1 TAAATTAAATTAAATTAAATTAAATTAA-ATTAAATTAAATTAAATTAAA 49

  Tasmanian_Dev      12966 TAAAATTAAA--AAATTAAAT 12984
                            v        --         
  (TAAAT)n#Simp         50 TTAAATTAAATTAAATTAAAT 70

Matrix = Unknown
Transitions / transversions = 0.00 (0/9)
Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.20 (6 / 5)

27 18.48 1.56 1.56 Tasmanian_Devil_Short_Consensus_IGS 12921 12984 (18597) (AAAT)n#Simple_repeat 1 64 (0) m_b1s252i14 18

  Tasmanian_Dev      12921 AAATAAATAAATCAATAAAAAAAACAATAAATTAATAAAATAAA-ATAAA 12969
                                       v      v   vv       v   -       - v v 
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAAT-AAATAAATAAATA 49

  Tasmanian_Dev      12970 ATTAAAAAATTAAAT 12984
                            v    v  v     
  (AAAT)n#Simpl         50 AATAAATAAATAAAT 64

Matrix = Unknown
Transitions / transversions = 0.00 (0/10)
Gap_init rate = 0.03 (2 / 63), avg. gap size = 1.00 (2 / 2)


17 17.81 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 13476 13514 (18067) (AAAT)n#Simple_repeat 1 39 (0) m_b1s252i15 19

  Tasmanian_Dev      13476 AAATAAATAAATCAATNAAAAAAACAATAAATCGATAAA 13514
                                       v   ?  v   vv       vi     
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAA 39

Matrix = Unknown
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)


25 40.86 0.55 1.68 Tasmanian_Devil_Short_Consensus_IGS 13989 14169 (17412) (CTCT)n#Simple_repeat 1 179 (0) m_b1s252i16 20

  Tasmanian_Dev      13989 CTATCTCTCTGTCTCTCTCTGCCTCCATTTCTCTCTCAACCCCTCTCKCA 14038
                             v       v         vi   iv i        vvi i     ? v
  (CTCT)n#Simpl          1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50

  Tasmanian_Dev      14039 CCCCCCCTTGCTCTCTCCCTCGTTCCCGTCCATGCTTTTCCCCTTCCTCT 14088
                            i i i  iv       i   vi  i -  iv -  i ii i  ii    
  (CTCT)n#Simpl         51 CTCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCT-CTCTCTCTCTCTCTCT 98

  Tasmanian_Dev      14089 CTC-CTCTATCCCTACCTCCCTTACTCTTCCTTGTTYCCTCCCTGGCTGC 14137
                              -    v  i  vi   i  iv    ii  ivi ?i   i  vv  - 
  (CTCT)n#Simpl         99 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-C 147

  Tasmanian_Dev      14138 ACCCTTGCTCCCTCCCTCCCTCTGTCTCTCTC 14169
                           v i  iv   i   i   i    v        
  (CTCT)n#Simpl        148 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 179

Matrix = Unknown
Transitions / transversions = 1.79 (34/19)
Gap_init rate = 0.02 (4 / 180), avg. gap size = 1.00 (4 / 4)

16 29.30 2.83 4.81 Tasmanian_Devil_Short_Consensus_IGS 14080 14185 (17396) (CCTT)n#Simple_repeat 1 104 (0) m_b1s252i17 20

  Tasmanian_Dev      14080 CCTTCC-TCTCTCCTCTATCCCTACCTCCCTTACTCTTCCTTGTTYCCTC 14128
                                 -  ii    iiv i   v   i    - -       vi ?   i
  (CCTT)n#Simpl          1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT-C-CTTCCTTCCTTCCTT 48

  Tasmanian_Dev      14129 CCTGGC-TGCACCCTTGC-TCCCTCCCTCCCTCTGTCTCTCTCCTTCCCT 14176
                              vv - v vi    v -   i   i   i  iv  -  -     -   
  (CCTT)n#Simpl         49 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CT-TCCTT-CCT 95

  Tasmanian_Dev      14177 TCCTTCATT 14185
                                 v  
  (CCTT)n#Simpl         96 TCCTTCCTT 104

Matrix = Unknown
Transitions / transversions = 1.30 (13/10)
Gap_init rate = 0.08 (8 / 105), avg. gap size = 1.00 (8 / 8)


49 29.92 2.09 6.81 Tasmanian_Devil_Short_Consensus_IGS 15045 15474 (16107) (CTTC)n#Simple_repeat 1 411 (0) m_b1s252i18 21

  Tasmanian_Dev      15045 CTTTCTATCTCTCCCTTCCTCCCTTGCTGTTCCTT-GTTCTCTCCCTTGC 15093
                              i  -  -  i       i    - -v      -v   -  i    v 
  (CTTC)n#Simpl          1 CTTCCT-TC-CTTCCTTCCTTCCTT-C-CTTCCTTCCTTC-CTTCCTTCC 45

  Tasmanian_Dev      15094 TACCTCCCTCGCTCCCTCCCTCCCMCCCATCGCT-CTACSCCTCCCTCCG 15142
                            v   i   iv  i   i   i  ?i  v  vi -  v - i   i   v
  (CTTC)n#Simpl         46 TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTC-CTTCCTTCCT 94

  Tasmanian_Dev      15143 TCTGTCTCTTCTTTCCTTCC-TCCTTGGCTCCCCCCGTCCCTCCGTTCCC 15191
                             iv  -    i        -     vvi   ii  v   i   -    i
  (CTTC)n#Simpl         95 TCCTTC-CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC-TTCCT 142

  Tasmanian_Dev      15192 TCCTCSGTCCCTTCCATCCCYTCCTTCGTT-CTTTCTYGC-CCCCTCCTT 15239
                               i?v i      - i  ?      v  -   i  ?v -i  i     
  (CTTC)n#Simpl        143 TCCTTCCTTCCTTCC-TTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT 191

  Tasmanian_Dev      15240 CCTTCKCTCCCGCTTCCCTTAYCTCCYTCCCTCTCCYTAATCCACCTCC- 15288
                                ?i   iv i i    -?  i ? i   -   ? vv i - i   -
  (CTTC)n#Simpl        192 CCTTCCTTCCTTCCTTCCTT-CCTTCCTTCCT-TCCTTCCTTC-CTTCCT 238

  Tasmanian_Dev      15289 CCCTCCATTTCTCTCTCACCCCCTCNNCNCCCCTCYNCTCTCCCCCCYTT 15338
                           i   i v  i  ii  iv ii   -?? ?i  i  --  -   ii  -  
  (CTTC)n#Simpl        239 TCCTTCCTTCCTTCCTTCCTTCCT-TCCTTCCTTC--CT-TCCTTCC-TT 283

  Tasmanian_Dev      15339 CCCTTCC-HCCTTCCTCCCTCCTCTCTCCCTCTCTCCWTCCCTCTTTCCT 15387
                           -      -?       i   i -  -   i  ii   ?   i  i     
  (CTTC)n#Simpl        284 -CCTTCCTTCCTTCCTTCCTTC-CT-TCCTTCCTTCCTTCCTTCCTTCCT 330

  Tasmanian_Dev      15388 TCCCTTCC-TCCTTGCTCTTCCTT-GTTCCCTCCYTGGCTCCMCCTGCTC 15435
                            -      -     - -       -v    i   - vv  i - i v  i
  (CTTC)n#Simpl        331 T-CCTTCCTTCCTT-C-CTTCCTTCCTTCCTTCC-TTCCTTC-CTTCCTT 375

  Tasmanian_Dev      15436 CCTCCCCTCCCTCTGTCTCTCTCCTTCCCTTCCTTCATT 15474
                              i  i   i  iv  -  -     -         v  
  (CTTC)n#Simpl        376 CCTTCCTTCCTTCCTTC-CT-TCCTT-CCTTCCTTCCTT 411

Matrix = Unknown
Transitions / transversions = 2.26 (61/27)
Gap_init rate = 0.09 (37 / 429), avg. gap size = 1.00 (37 / 37)


83 28.18 2.01 2.83 Tasmanian_Devil_Short_Consensus_IGS 16278 16775 (14806) (CTCC)n#Simple_repeat 1 494 (0) m_b1s252i19 22

  Tasmanian_Dev      16278 CTCCCTCATTTCCTCCCTTGCTCCCTGGCTACCTCCYT-TGTCCCT-CCT 16325
                                  vi i       iv      vv  v     ? -iv     -   
  (CTCC)n#Simpl          1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 50

  Tasmanian_Dev      16326 CCTNTCTCTCCCTCYAYCCCCTCCBYTTCCTTGCTCTCTCCCTTCCYCCC 16375
                             -?  i       -v?i      -? i   iv   i      i  ?   
  (CTCC)n#Simpl         51 CC-CTCCCTCCCTC-CCTCCCTCC-CTCCCTCCCTCCCTCCCTCCCTCCC 97

  Tasmanian_Dev      16376 CTCCTYCCCCCCTCCTYCCATCCCTCTCCCYCCCCCCCCCTTCGTCYCTT 16425
                           ii   ?  i      i?  v      i i ? i   i    i v  ?  i
  (CTCC)n#Simpl         98 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 147

  Tasmanian_Dev      16426 CCTTCCYTCCTTCCTCGGCTCCCCCCCTTCMCTCCYCCCYGYTCCYCCCN 16475
                              i  ?i   i    -v     i   -  ?    - i -v?   - i ?
  (CTCC)n#Simpl        148 CCTCCCTCCCTCCCTC-CCTCCCTCCC-TCCCTCC-CTC-CCTCC-CTCC 192

  Tasmanian_Dev      16476 CTGGCTCCCCYYCGCTCCTTTCACYCTCCC-CCCT-GCTTCCTCCTCYTK 16523
                             vv     i?? v -   ii v ?     -    -v  i     - - ?
  (CTCC)n#Simpl        193 CTCCCTCCCTCCCTC-CCTCCCTCCCTCCCTCCCTCCCTCCCTCC-C-TC 239

  Tasmanian_Dev      16524 CCTCCTTCCCTCCCCCTATCTCT-CYTCCSACCCCYCCTCNC-NCATVCC 16571
                                i        i iv  i  - ?   ?v   i?    ? -? v ?  
  (CTCC)n#Simpl        240 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 289

  Tasmanian_Dev      16572 -GCCTCCCTCCCTTACTCCACCTTTCCCTGCNTNATTNCAMCCCT-CTTY 16619
                           -v           iv    vi ii     v ? ?vi ? v?    - i ?
  (CTCC)n#Simpl        290 TCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC 339

  Tasmanian_Dev      16620 TCTCCCTCCCTTGCTCTCTCCCTTCCTCCTTYCC-CCCTTCCTCTCTCCC 16668
                           i          iv   i      i     i ?  -    i    i     
  (CTCC)n#Simpl        340 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 389

  Tasmanian_Dev      16669 TCTMTCCCTACCTCTATCTTTCCTTCCCTYCCCTCCC-CTTGCTCTTCCT 16717
                             i?     v    iv  ii   i     -       - iiv i  i   
  (CTCC)n#Simpl        390 TCCCTCCCTCCCTCCCTCCCTCCCTCCCT-CCCTCCCTCCCTCCCTCCCT 438

  Tasmanian_Dev      16718 TGTTCCCTCCCTGGCTGCAACCCTTGCTCCCCCCCCCCCTCTGTCTCTCT 16767
                           ivi         vv  v vv    iv     i   i     --i   i  
  (CTCC)n#Simpl        439 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTC--CCTCCCT 486

  Tasmanian_Dev      16768 CCTTCCCT 16775
                             i     
  (CTCC)n#Simpl        487 CCCTCCCT 494

Matrix = Unknown
Transitions / transversions = 1.76 (65/37)
Gap_init rate = 0.05 (24 / 497), avg. gap size = 1.00 (24 / 24)


114 23.83 2.41 4.15 Tasmanian_Devil_Short_Consensus_IGS 17579 18117 (13464) (CTCC)n#Simple_repeat 1 530 (0) m_b1s252i20 23

  Tasmanian_Dev      17579 CTCCCTCATTCCCTCCCTTGCTCCTTNTNTTTC-CTATCCCTCYTTCTAT 17627
                                  vi         iv    i ?i? ii - iv      ?i  iv 
  (CTCC)n#Simpl          1 CTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCT 50

  Tasmanian_Dev      17628 CTCTCCCACTCTCCC-CCCTCCCTCTCYCTTTCTTCCTCCCCTCCCTCCC 17676
                            i     v i     -         - -  ii  i   -           
  (CTCC)n#Simpl         51 CCCTCCCTCCCTCCCTCCCTCCCTC-C-CTCCCTCCCT-CCCTCCCTCCC 97

  Tasmanian_Dev      17677 -CCC-CCATCCCTCCTTCTCTCCTTCTMCCTCCCTCTTTCTC-CYCTYCC 17723
                           -   -  v       i  i    --  ?        ii  i - ?  ?  
  (CTCC)n#Simpl         98 TCCCTCCCTCCCTCCCTCCCTCC--CTCCCTCCCTCCCTCCCTCCCTCCC 145

  Tasmanian_Dev      17724 TCCCTCCCTCCCTYCCCTCCCTTCGGTCCNCT-CCTCNCTCCCTCCCTGG 17772
                                        -       -  vv   -  -    ?          vv
  (CTCC)n#Simpl        146 TCCCTCCCTCCCT-CCCTCCC-TCCCTCC-CTCCCTCCCTCCCTCCCTCC 192

  Tasmanian_Dev      17773 CTCCCTCCHCCRCTCTTTCTCTCCCTCCYCTCCCTCGCTCTCTTCCTGGC 17822
                                   ?i ?   ii  i        -       v   i  i   vv 
  (CTCC)n#Simpl        193 CTCCCTCCCTCCCTCCCTCCCTCCCTCC-CTCCCTCCCTCCCTCCCTCCC 241

  Tasmanian_Dev      17823 TCCYCCTGGCT-CCTWCCACCCTCNNTATCTCTC-NGNTNNCCCTCTCTC 17870
                            - -   vv  -   ?  v     ?? vi   i -?v? ?? i i   i 
  (CTCC)n#Simpl        242 T-C-CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCC 289

  Tasmanian_Dev      17871 TCCCTCWTCCACCTCCCCTCCTYTCCTTCTCTCTCAACCCCCCTTCCMCT 17920
                                 --  v  ii      -?   i  i   - vv   i  i   -  
  (CTCC)n#Simpl        290 TCCCTC--CCTCCCTCCCTCC-CTCCCTCCCTC-CCTCCCTCCCTCC-CT 334

  Tasmanian_Dev      17921 CCCCCATTCCCTCCC-CATCCCCYTCTTCCCCYCCTTYCT-YCTACCTCC 17968
                              i vi        - vii   ?i i    i?   i?  -?  v     
  (CTCC)n#Simpl        335 CCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 384

  Tasmanian_Dev      17969 GTCTATCTTTCCTTCCYTCCCTCCCTTRCTTTCCTTDTTCCCTCCTTCMC 18018
                           v  iv  ii   i   ?        - ? i i   i?i       i  ? 
  (CTCC)n#Simpl        385 CTCCCTCCCTCCCTCCCTCCCTCCC-TCCCTCCCTCCCTCCCTCCCTCCC 433

  Tasmanian_Dev      18019 TCCTTCTCCCCCCYYCTTCTTCCCTCCCCTCCTCTCTCTCCCT-CCTCCC 18067
                              i  i i   i??  i i     -      -   i      -      
  (CTCC)n#Simpl        434 TCCCTCCCTCCCTCCCTCCCTCCCT-CCCTCC-CTCCCTCCCTCCCTCCC 481

  Tasmanian_Dev      18068 -CCCCCCCT-CTTCTCTCTCCTCCCTTCCTCTGTCTCTCTCCTTCCCTTC 18115
                           -   i    - i  i   -      -   -  vi   i    i     i 
  (CTCC)n#Simpl        482 TCCCTCCCTCCCTCCCTC-CCTCCC-TCC-CTCCCTCCCTCCCTCCCTCC 528

  Tasmanian_Dev      18116 CT 18117
                             
  (CTCC)n#Simpl        529 CT 530

Matrix = Unknown
Transitions / transversions = 2.48 (67/27)
Gap_init rate = 0.07 (35 / 538), avg. gap size = 1.00 (35 / 35)


19 8.35 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 18730 18755 (12826) (T)n#Simple_repeat 1 26 (0) m_b1s252i21 24

  Tasmanian_Dev      18730 TTTTCCTTTTTTTTTTTTTTTTTTTT 18755
                               ii                    
  (T)n#Simple_r          1 TTTTTTTTTTTTTTTTTTTTTTTTTT 26

Matrix = Unknown
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0)


26 0.00 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 18948 18972 (12708) (TATTA)n#Simple_repeat 1 25 (0) c_b1s251i5 25

  Tasmanian_Dev      18948 TATTATATTATATTATATTATATTA 18972
                                                    
  (TATTA)n#Simp          1 TATTATATTATATTATATTATATTA 25

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0)


16 4.94 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 19262 19283 (12322) (G)n#Simple_repeat 1 22 (0) m_b1s252i22 26

  Tasmanian_Dev      19262 GGGGGGGGGTGGGGGKGGGGGG 19283
                                    v     ?      
  (G)n#Simple_r          1 GGGGGGGGGGGGGGGGGGGGGG 22

Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0)


26 0.00 6.25 0.00 Tasmanian_Devil_Short_Consensus_IGS 19724 19755 (11925) (CTGTCTCT)n#Simple_repeat 1 34 (0) c_b1s251i6 27

  Tasmanian_Dev      19724 CTGTCTCTCTG--TCTCTGTCTCTCTGTCTCTCT 19755
                                      --                     
  (CTGTCTCT)n#S          1 CTGTCTCTCTGTCTCTCTGTCTCTCTGTCTCTCT 34

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.03 (1 / 31), avg. gap size = 2.00 (2 / 1)


14 8.18 3.85 0.00 Tasmanian_Devil_Short_Consensus_IGS 19781 19806 (11830) (AAAC)n#Simple_repeat 1 27 (0) m_b1s252i24 28

  Tasmanian_Dev      19781 AAACAAA-AACAAAACAAACAAACAAA 19806
                                  -  vv               
  (AAAC)n#Simpl          1 AAACAAACAAACAAACAAACAAACAAA 27

Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1)


17 6.12 5.56 2.70 Tasmanian_Devil_Short_Consensus_IGS 19780 19815 (11821) (AAAAC)n#Simple_repeat 1 37 (0) m_b1s252i23 29

  Tasmanian_Dev      19780 AAAACAAAAACAAAAC-AAAC-AAACAAAATAAATCAA 19815
                                -          -    -        i   v   
  (AAAAC)n#Simp          1 AAAAC-AAAACAAAACAAAACAAAACAAAACAAAACAA 37

Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3)


20 10.85 5.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 20334 20373 (11263) (AATC)n#Simple_repeat 1 42 (0) m_b1s252i25 30

  Tasmanian_Dev      20334 AATCAATCAATCAATCAATGAAT-AA-AAATAAATCAATAAA 20373
                                              v   -  -v   v       v  
  (AATC)n#Simpl          1 AATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAA 42

Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2)


18 0.00 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 20734 20756 (10880) (AAAC)n#Simple_repeat 1 23 (0) m_b1s252i26 31

  Tasmanian_Dev      20734 AAACAAACAAACAAACAAACAAA 20756
                                                  
  (AAAC)n#Simpl          1 AAACAAACAAACAAACAAACAAA 23

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)


19 26.05 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 21293 21349 (10287) (AAAAA)n#Simple_repeat 1 57 (0) m_b1s252i27 32

  Tasmanian_Dev      21293 AAAATAAATAANATCAATAAAAAAAACAATAAATTAATAAAATAAAATAA 21342
                               v   v  ? vv  v        v  v   vv  v    v    v  
  (AAAAA)n#Simp          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50

  Tasmanian_Dev      21343 AAAAAAA 21349
                                  
  (AAAAA)n#Simp         51 AAAAAAA 57

Matrix = Unknown
Transitions / transversions = 0.00 (0/12)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.0 (0 / 0)


29 19.25 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 21855 21908 (9728) (A)n#Simple_repeat 1 54 (0) m_b1s252i29 33

  Tasmanian_Dev      21855 AAAATAAATAAATCAATAAAAAAACAATAAATCAAAAAAAAAAAAAAAAA 21904
                               v   v   vv  v       v  v   vv                 
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50

  Tasmanian_Dev      21905 AAAA 21908
                               
  (A)n#Simple_r         51 AAAA 54

Matrix = Unknown
Transitions / transversions = 0.00 (0/9)
Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0)

23 17.97 1.64 3.33 Tasmanian_Devil_Short_Consensus_IGS 21856 21916 (9720) (AAAT)n#Simple_repeat 1 60 (0) m_b1s252i30 33

  Tasmanian_Dev      21856 AAATAAATAAATCAATAAA-AAAACAATAAATCAAAAAAAAAAAAAAAAA 21904
                                       v      -   vv       -   v   v   v   v 
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAAT-AAATAAATAAATAAATA 49

  Tasmanian_Dev      21905 AAAACATTAAAT 21916
                             v - v     
  (AAAT)n#Simpl         50 AATA-AATAAAT 60

Matrix = Unknown
Transitions / transversions = 0.00 (0/9)
Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3)


31 9.30 8.45 1.32 Tasmanian_Devil_Short_Consensus_IGS 22421 22491 (9145) (TAAAA)n#Simple_repeat 1 76 (0) m_b1s252i31 34

  Tasmanian_Dev      22421 TAAAAT-AAAT-AAAT-CAATAAAA-AAAAAAAAAAACAAT-AAAT-TAA 22464
                                 -    -    -v       -    v    v v   -    -v  
  (TAAAA)n#Simp          1 TAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA 50

  Tasmanian_Dev      22465 TAAAATAAAATAAAATAAAAATTAAAT 22491
                                           -     v    
  (TAAAA)n#Simp         51 TAAAATAAAATAAAAT-AAAATAAAAT 76

Matrix = Unknown
Transitions / transversions = 0.00 (0/6)
Gap_init rate = 0.10 (7 / 70), avg. gap size = 1.00 (7 / 7)


14 15.26 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 22949 22977 (8659) (CTCT)n#Simple_repeat 1 29 (0) m_b1s252i33 35

  Tasmanian_Dev      22949 CTATCTCTCTGTCTCTGTCTCTCTCCCTC 22977
                             v       v     v        i   
  (CTCT)n#Simpl          1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTC 29

Matrix = Unknown
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)


22 7.96 5.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 22999 23038 (8598) (AATC)n#Simple_repeat 1 42 (0) m_b1s252i35 36

  Tasmanian_Dev      22999 AATCAATCAATCAATCAATCAAT-AA-AAATAAATCAATAAA 23038
                                                  -  -v   v       v  
  (AATC)n#Simpl          1 AATCAATCAATCAATCAATCAATCAATCAATCAATCAATCAA 42

Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2)


22 3.45 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 24275 24306 (7330) (A)n#Simple_repeat 1 32 (0) m_b1s252i36 37

  Tasmanian_Dev      24275 AAAAAAAAAAAAAAARAAAANAAAAAGAAAAA 24306
                                          ?    ?     i     
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32

Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)


13 9.26 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 25122 25144 (6492) (CATG)n#Simple_repeat 1 23 (0) m_b1s252i37 38

  Tasmanian_Dev      25122 CATTCATGCGTGCATGCATGCAT 25144
                              v     i             
  (CATG)n#Simpl          1 CATGCATGCATGCATGCATGCAT 23

Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)


53 0.00 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 25885 25929 (5751) (TG)n#Simple_repeat 1 45 (0) c_b1s251i7 39

  Tasmanian_Dev      25885 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 25929
                                                                        
  (TG)n#Simple_          1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 45

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0)


20 4.35 0.00 0.00 Tasmanian_Devil_Short_Consensus_IGS 27911 27934 (3746) (C)n#Simple_repeat 1 24 (0) m_b1s252i38 40

  Tasmanian_Dev      27911 CCCCCCCCCCCCCCCCCCCCTCCC 27934
                                               i   
  (C)n#Simple_r          1 CCCCCCCCCCCCCCCCCCCCCCCC 24

Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)