12 0.00 0.00 8.33 Tasmanian_Devil_Long_Consensus_IGS 863 888 (39545) (GCTT)n#Simple_repeat 1 24 (0) m_b1s252i0 1

  Tasmanian_Dev        863 GCTTGCTTGCTTGCTNNYGCTTGCTT 888
                                          --?        
  (GCTT)n#Simpl          1 GCTTGCTTGCTTGCT--TGCTTGCTT 24

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2)


38 0.00 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 2500 2532 (38240) (TC)n#Simple_repeat 1 33 (0) c_b1s251i0 2

  Tasmanian_Dev       2500 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 2532
                                                            
  (TC)n#Simple_          1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 33

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

18 0.00 0.00 1.72 Tasmanian_Devil_Long_Consensus_IGS 2536 2594 (37871) (TC)n#Simple_repeat 1 58 (0) m_b1s252i1 2

  Tasmanian_Dev       2536 TCTCTCYYTYTYTCTCYYKCTCTCTYTNCYCTMYCTCTCTCTCTCTCNNN 2585
                                 ?? ? ?    ???      ? - ?  ??             ???
  (TC)n#Simple_          1 TCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCT 49

  Tasmanian_Dev       2586 CTCTCTCTC 2594
                                    
  (TC)n#Simple_         50 CTCTCTCTC 58

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1)


51 0.00 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 3223 3270 (37502) (TC)n#Simple_repeat 1 48 (0) c_b1s251i1 3

  Tasmanian_Dev       3223 TCTCTCTCTCTCTCTCTCTCTCTCTCTCYCTCTCTCTCTCTCTCTCTC 3270
                                                       ?                   
  (TC)n#Simple_          1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 48

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)


15 0.00 2.33 10.00 Tasmanian_Devil_Long_Consensus_IGS 3656 3698 (36814) (GGA)n#Simple_repeat 1 40 (0) m_b1s252i2 4

  Tasmanian_Dev       3656 GGAGGGAGGAGGA-GAGAGAGGRRGGAGGAGGAGGGAGNNGGAG 3698
                              -         -   -    -?         -    ??    
  (GGA)n#Simple          1 GGA-GGAGGAGGAGGAG-GAGG-AGGAGGAGGA-GGAGGAGGAG 40

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.12 (5 / 42), avg. gap size = 1.00 (5 / 5)


32 9.76 0.00 1.72 Tasmanian_Devil_Long_Consensus_IGS 6905 6963 (33549) (TCTG)n#Simple_repeat 1 58 (0) m_b1s252i3 5

  Tasmanian_Dev       6905 TCTGTCTGTCTGTGTCTNCTGTCTGTCTGTGTCTCTGTCTGTCTGTGNNT 6954
                                        v v -            v v             v?? 
  (TCTG)n#Simpl          1 TCTGTCTGTCTGTCTGT-CTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGT 49

  Tasmanian_Dev       6955 CTGTCTGTC 6963
                                    
  (TCTG)n#Simpl         50 CTGTCTGTC 58

Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.02 (1 / 58), avg. gap size = 1.00 (1 / 1)


102 2.24 0.00 2.04 Tasmanian_Devil_Long_Consensus_IGS 6980 7129 (33643) (TC)n#Simple_repeat 1 147 (0) c_b1s251i2 6

  Tasmanian_Dev       6980 TCTCTCTCTCTCTCTSTSTCTCTCTCTCTCTGTCTCTCTCTCTCTGTCTC 7029
                                          ? ?             v             v    
  (TC)n#Simple_          1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50

  Tasmanian_Dev       7030 TCTCTCTCTSTSTNCTCTCTCTCTCTGTCTCTCTCTCNNNTCTSTCTCTC 7079
                                    ? ? -            v          -??   ?      
  (TC)n#Simple_         51 TCTCTCTCTCTCT-CTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTC 98

  Tasmanian_Dev       7080 TCTCTCTCTCTCTCTCTCTCTCTCTCATCTCTCTCTCTCTCTSTCTCTCT 7129
                                                     -               ?       
  (TC)n#Simple_         99 TCTCTCTCTCTCTCTCTCTCTCTCTC-TCTCTCTCTCTCTCTCTCTCTCT 147

Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.02 (3 / 149), avg. gap size = 1.00 (3 / 3)


302 26.87 3.81 3.81 Tasmanian_Devil_Long_Consensus_IGS 7841 8076 (32585) C L1ME3G_3end#LINE/L1 (446) 478 243 m_b1s551i0 7

  Tasmanian_Dev       7841 TTTCAGTTTCTAGCTACTACAAACAGGGCTKMYACAAACATTTGSYWYRT 7890
                             i  i   i v    i        iv   ??? ii     ---????? 
C L1ME3G_3end#L        478 TTCCAATTTTTCGCTATTACAAACAATGCTGCAATGAACAT---CCTTGT 432

  Tasmanian_Dev       7891 NNNGGKYCCTTT---CCYTYCTTAATGTATTTCTTTGRGGTAGAAGCCCR 7937
                           ???v ??i i  --- v?v?v vviv        ? i? i    v?  ??
C L1ME3G_3end#L        431 ACATGCNTCCTTGTGCACATGTGCGAGTATTTCTNTAGGATAGATNCCNA 382

  Tasmanian_Dev       7938 GTNGGAGCACTGCTGGATCAAGGGTTATGCACAGTTTGATAACTTTNGGG 7987
                            v? vi v i      i    i  v     i  v   i--  i   ?---
C L1ME3G_3end#L        381 GAAGTGGAATTGCTGGGTCAAAGGGTATGCGCATTTTA--AATTTTA--- 337

  Tasmanian_Dev       7988 GCAGA-ATTGCT-GATTGCTCTNCARRATGATTGGATCSG-KYMSRM-YY 8033
                           ii   - i   i-i     i  ?  ?? ? ii  v i ?i-??????-??
C L1ME3G_3end#L        336 ATAGATACTGCCAAATTGCCCTCCAAAANGGCTGTACCAATTTACACTCC 287

  Tasmanian_Dev       8034 CAGCAACAATGCRT--NAGTGCCAGNTTTCCTRRATCCCTCAACA 8076
                             v  i  i  i? --?   i  v ?  i  i?? -     iv  
C L1ME3G_3end#L        286 CACCAGCAGTGTATGAGAGTACCCGTTTCCCCACA-CCCTCGCCA 243

Matrix = 20p37g.matrix
Kimura (with divCpGMod) = 36.28
Transitions / transversions = 1.89 (36/19)
Gap_init rate = 0.06 (15 / 235), avg. gap size = 1.20 (18 / 15)

294 26.46 4.00 5.74 Tasmanian_Devil_Long_Consensus_IGS 7842 8266 (32395) C L1ME5_3end#LINE/L1 (460) 481 64 m_b1s551i1 7

  Tasmanian_Dev       7842 TTCAGTTTCTAGCTACTACAAACAGGGCTKMYACAAACATTTGSYWYRTN 7891
                            i  ii i iv  i  i       iv   ??? ii     ---????? ?
C L1ME5_3end#LI        481 TCCAACTCCCCGCCACCACAAACAACGCTGCAATGAACAT---CCTCGTA 435

  Tasmanian_Dev       7892 NNGGKYCCTTT-----CCYTYCTTAATGTATTTCTTTGRGGTAGAAGCCC 7936
                           ??v ??  i  -----  ?v?v v -- v         ? i  v vi   
C L1ME5_3end#LI        434 CATGTCCCCTTATGGACCTGTGTGA--GAATTTCTTTGGGATATATACCC 387

  Tasmanian_Dev       7937 RGTNGGAGCACTGCTGGATCAAGGGTTATGCACAGTTTGATAACTTTNGG 7986
                           ? v? vi v i      i   vi  v     ii vvi --   --  ? i
C L1ME5_3end#LI        386 AGGAGCGGAATTGCTGGGTCATAGGGTATGCGTATACT--TAA--TTTGA 341

  Tasmanian_Dev       7987 GGCAGAATTGCT-GATTGCTCTNCARRATGATTGGATCSGKY-MSRM-YY 8033
                           vvv  v i   i-         ?  ??   ii  v i ? ??-????-??
C L1ME5_3end#LI        340 CTAAGTACTGCCAGATTGCTCTCCAGAATGGCTGCACCAGTCTACACTCC 291

  Tasmanian_Dev       8034 CAGCAACAATGCRTNAGTG--CCAGNTTTCCTRRATCCC--TCAACAGTC 8079
                             v  i  i   ? ?  v --  vi?? i  i??    i--i     v i
C L1ME5_3end#LI        290 CACCAGCAGTGCATGAGGGTTCCTATNTCCCCACATCCTCGCCAACACTT 241

  Tasmanian_Dev       8080 GTCRYGWTTTTCCTGTC--ATCTTARNYAATGTGACRGGRNNTKGARTCR 8127
                            v ??v? iivv  v  --  i  v??? i v i i?  -?? ?i ? --
C L1ME5_3end#LI        240 GGCATTATCCAGCTTTCTAATTTTTGCCAGTCTAATAGG-TGTAAAGT-- 194

  Tasmanian_Dev       8128 NNARMYATCTCAGAGTTCTCTTAATTTGSANNNTTCTCAGATCAACAGTN 8177
                           ---???      vv   v i        ? --?     v   i vi i ?
C L1ME5_3end#LI        193 ---GATATCTCATTGTTGTTTTAATTTGCA--TTTCTCTGATTACTAATG 149

  Tasmanian_Dev       8178 GATTTGGNNNNCYTYYYTYATRWG-KKGAAAGAGGTTCNGAGTTCACATC 8226
                           ii    i???? --??? ?  ?? -?? vv  vvv   ? iv   ---- 
C L1ME5_3end#LI        148 AGTTTGAGCATC--TCTTCATATGCTTGTTAGCCTTTCGGGTTTC----C 105

  Tasmanian_Dev       8227 NNNNCTCTGAA--ARKTGTTCATATCCNTTTGACCCTTTGTC 8266
                           ????  v i  --i??           -    v  v   v  
C L1ME5_3end#LI        104 TCTTCTGTAAATTGCCTGTTCATATCC-TTTGCCCATTTTTC 64

Matrix = 20p37g.matrix
Kimura (with divCpGMod) = 37.73
Transitions / transversions = 1.09 (51/47)
Gap_init rate = 0.08 (33 / 424), avg. gap size = 1.24 (41 / 33)


388 23.68 2.79 3.76 Tasmanian_Devil_Long_Consensus_IGS 9056 9270 (31391) L1ME4c_3end#LINE/L1 342 554 (276) m_b1s551i2 8

  Tasmanian_Dev       9056 AAAAGTTATCAAACTRTNNNKCATACCCTTTGATCCMWYRGTGTTACTAC 9105
                             i  ii  v   v ? ?---            i  ????i vii   v 
  L1ME4c_3end#L        342 AAGAGCCATAAAAATGTT---CATACCCTTTGACCCAGTAATTCCACTTC 388

  Tasmanian_Dev       9106 TGGGA--TTATANNNMARGAGATTAT--AANNNNNNGAAAGGGACCTGTA 9151
                                --    -???? ?  i  v  --  ??????    ii --  i  
  L1ME4c_3end#L        389 TGGGAATTTAT-CCTAAGGAAATAATTCAAAAGAAGGAAAAAG--CTATA 435

  Tasmanian_Dev       9152 TGTGCMYGAATGTTTGTNGYAGCCCT-TTTGTAGTRKY-WAAAACTGGAA 9199
                             ii ??ii     ii ? ?   vi -   i  i ???-?    i     
  L1ME4c_3end#L        436 TGCACGAAGATGTTCATTGCAGCGTTATTTATAATAGCGAAAAATTGGAA 485

  Tasmanian_Dev       9200 ACTGAATGGATGTNCATCAGNTTGGAGARTGGCTGAATAAATTGTGGTAT 9249
                             vivv ii    ?  v  -? v  i  ?   i i i      i     i
  L1ME4c_3end#L        486 ACAACCTAAATGTCCAACA-ATAGGGGAATGGTTAAGTAAATTATGGTAC 534

  Tasmanian_Dev       9250 NNNGAATRTTATGGAATATTA 9270
                           ???? v -iv           
  L1ME4c_3end#L        535 ATCNACT-CGATGGAATATTA 554

Matrix = 20p37g.matrix
Kimura (with divCpGMod) = 31.11
Transitions / transversions = 2.38 (31/13)
Gap_init rate = 0.06 (12 / 214), avg. gap size = 1.17 (14 / 12)

274 21.81 3.86 6.97 Tasmanian_Devil_Long_Consensus_IGS 9152 9358 (31303) L1MC2_3end#LINE/L1 433 633 (458) m_b1s551i3 8

  Tasmanian_Dev       9152 TGTGCMYGAATGTTTGTNGYAGCCCT-TTTGTAGTRKYWAAAACT-GGAA 9199
                             ii ??        i ? ?   ii -  ii  i ????      -    
  L1MC2_3end#LI        433 TGCACACGAATGTTTATAGCAGCTTTATTCATAATTGCCAAAACTTGGAA 482

  Tasmanian_Dev       9200 ACTGAAT--GGATGTNCATCAGNTTGGAGARTGGCTGAATAAATTGTGGT 9247
                           i --  i--i     ? v   -? v  v  ?   v i  i   i      
  L1MC2_3end#LI        483 GC--AACCAAGATGTCCTTCA-ATAGGTGAATGGATAAACAAACTGTGGT 529

  Tasmanian_Dev       9248 ATNNNGAATRTTATGGAATATTACNT-GTTCTGTAARGAAATGA-CNNNC 9295
                            i???v - ?iv           i?i- ivv iv  ?       - ??? 
  L1MC2_3end#LI        530 ACATCCA-TACAATGGAATATTATTCAGCGATAAAAAGAAATGAGCTATC 578

  Tasmanian_Dev       9296 AGG--ATGATTTCAGAAAGGCCTGGAGAGACTTACCNNNNNNRRSYRRTG 9343
                            i -- i  ------    i v     -  ---   ????????????  
  L1MC2_3end#LI        579 AAGCCACGA------AAAGACATGGAG-GA---ACCTTAAATGCATATTG 618

  Tasmanian_Dev       9344 CTGAGTGAAATGAGC 9358
                             i       vi   
  L1MC2_3end#LI        619 CTAAGTGAAAGAAGC 633

Matrix = 20p37g.matrix
Kimura (with divCpGMod) = 25.72
Transitions / transversions = 2.27 (25/11)
Gap_init rate = 0.10 (20 / 206), avg. gap size = 1.10 (22 / 20)


28 0.00 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 10200 10226 (30546) (T)n#Simple_repeat 1 27 (0) c_b1s251i3 9

  Tasmanian_Dev      10200 TTTTTTTTTTTTTTTTTTTTTTTTTTT 10226
                                                      
  (T)n#Simple_r          1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0)


16 21.33 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 11315 11377 (29310) (A)n#Simple_repeat 1 63 (0) m_b1s252i4 10

  Tasmanian_Dev      11315 AAAATAAATAAATCAATNNAAAAAAAAAAAAACAATAAATTAATAANNNA 11364
                               v   v   vv  v??             v  v   vv  v  ??? 
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50

  Tasmanian_Dev      11365 AAWWAAAWAAAAA 11377
                             ??   ?     
  (A)n#Simple_r         51 AAAAAAAAAAAAA 63

Matrix = Unknown
Transitions / transversions = 0.00 (0/10)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)

18 13.24 2.94 2.94 Tasmanian_Devil_Long_Consensus_IGS 11316 11383 (29304) (AAAT)n#Simple_repeat 1 68 (0) m_b1s252i5 10

  Tasmanian_Dev      11316 AAATAAATAAATCAATNNA-AAAAAAAAAAAACAATAAATTAATAANNNA 11364
                                       v   ?? -   v   v   vv       v     -?? 
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAA-ATA 49

  Tasmanian_Dev      11365 AAWWAAAWAAA-AATTAAAT 11383
                             -?   ?   -  v     
  (AAAT)n#Simpl         50 AA-TAAATAAATAAATAAAT 68

Matrix = Unknown
Transitions / transversions = 0.00 (0/7)
Gap_init rate = 0.06 (4 / 67), avg. gap size = 1.00 (4 / 4)


23 13.13 6.94 1.32 Tasmanian_Devil_Long_Consensus_IGS 11889 11960 (28727) (TAAAA)n#Simple_repeat 1 76 (0) m_b1s252i6 11

  Tasmanian_Dev      11889 TAAAAT-AAAT-AAAT-CAATAAAAAAAAAANWYAAACAAT-AAAT-TAA 11933
                                 -    -    -v       v    v??? v v   -    -v  
  (TAAAA)n#Simp          1 TAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAA 50

  Tasmanian_Dev      11934 TAAAATAAAATNAAAAAAAAATTAAAT 11960
                                      -    v     v    
  (TAAAA)n#Simp         51 TAAAATAAAAT-AAAATAAAATAAAAT 76

Matrix = Unknown
Transitions / transversions = 0.00 (0/8)
Gap_init rate = 0.08 (6 / 71), avg. gap size = 1.00 (6 / 6)

25 16.31 0.00 2.94 Tasmanian_Devil_Long_Consensus_IGS 11891 11960 (28727) (AAAT)n#Simple_repeat 1 68 (0) m_b1s252i8 11

  Tasmanian_Dev      11891 AAATAAATAAATCAATAAAAAAAAAANWYAAACAATAAATTAATAAAATA 11940
                                       v      v   v  ???  vv       v   -    -
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAT-AAAT- 48

  Tasmanian_Dev      11941 AAATNAAAAAAAAATTAAAT 11960
                               ?  v   v  v     
  (AAAT)n#Simpl         49 AAATAAATAAATAAATAAAT 68

Matrix = Unknown
Transitions / transversions = 0.00 (0/9)
Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2)

23 23.45 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 11890 11954 (28733) (A)n#Simple_repeat 1 65 (0) m_b1s252i7 11

  Tasmanian_Dev      11890 AAAATAAATAAATCAATAAAAAAAAAANWYAAACAATAAATTAATAAAAT 11939
                               v   v   vv  v          ???   v  v   vv  v    v
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50

  Tasmanian_Dev      11940 AAAATNAAAAAAAAA 11954
                               v?         
  (A)n#Simple_r         51 AAAAAAAAAAAAAAA 65

Matrix = Unknown
Transitions / transversions = 0.00 (0/12)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0)


18 9.50 7.81 4.55 Tasmanian_Devil_Long_Consensus_IGS 12477 12540 (28147) (TAAAA)n#Simple_repeat 1 66 (0) m_b1s252i9 12

  Tasmanian_Dev      12477 TAAAAT-AAAT-AAAT-CAATAAAAAAACCAAT-AAAT-TAATAAAATAA 12521
                                 -    -    -v       v  --   -    -v          
  (TAAAA)n#Simp          1 TAAAATAAAATAAAATAAAATAAAATAA--AATAAAATAAAATAAAATAA 48

  Tasmanian_Dev      12522 AATNNNAAAAAAATTAAAT 12540
                              -??  v     v    
  (TAAAA)n#Simp         49 AAT-AAAATAAAATAAAAT 66

Matrix = Unknown
Transitions / transversions = 0.00 (0/5)
Gap_init rate = 0.13 (8 / 63), avg. gap size = 1.00 (8 / 8)

23 12.96 0.00 2.33 Tasmanian_Devil_Long_Consensus_IGS 12479 12522 (28165) (AAAT)n#Simple_repeat 1 43 (0) m_b1s252i10 12

  Tasmanian_Dev      12479 AAATAAATAAATCAATAAAAAAACCAATAAATTAATAAAATAAA 12522
                                       v      v   iv       v   -       
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAAT-AAATAAA 43

Matrix = Unknown
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.02 (1 / 43), avg. gap size = 1.00 (1 / 1)


19 15.99 0.00 3.12 Tasmanian_Devil_Long_Consensus_IGS 13060 13125 (27562) (AAAT)n#Simple_repeat 1 64 (0) m_b1s252i11 13

  Tasmanian_Dev      13060 AAATAAATAAATCAATNNNAAAAAAAAACAATAAATTAATNAAATAAAAT 13109
                                       v   ???v   v   vv       v   -    -    
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAAT-AAAT-AAAT 48

  Tasmanian_Dev      13110 NNAAAAAAAWATAAAT 13125
                           ?? v   v ?      
  (AAAT)n#Simpl         49 AAATAAATAAATAAAT 64

Matrix = Unknown
Transitions / transversions = 0.00 (0/8)
Gap_init rate = 0.03 (2 / 65), avg. gap size = 1.00 (2 / 2)


13 6.76 3.33 6.90 Tasmanian_Devil_Long_Consensus_IGS 13635 13694 (26993) (AAAATA)n#Simple_repeat 1 58 (0) m_b1s252i12 14

  Tasmanian_Dev      13635 AAAATAAATNAATCAATNNAAAAA-AAYAATAAATTAAT-AAANNWAAAA 13682
                                   --   v  v??     -  ?      --   -   ???    
  (AAAATA)n#Sim          1 AAAATAAA--AATAAAAATAAAAATAAAAATAAA--AATAAAAATAAAAA 46

  Tasmanian_Dev      13683 TAAAATTAAAAA 13694
                                v      
  (AAAATA)n#Sim         47 TAAAAATAAAAA 58

Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.10 (6 / 59), avg. gap size = 1.00 (6 / 6)

18 12.03 1.52 4.69 Tasmanian_Devil_Long_Consensus_IGS 13636 13701 (26986) (AAAT)n#Simple_repeat 1 64 (0) m_b1s252i13 14

  Tasmanian_Dev      13636 AAATAAATNAATCAATNNAAAAAAAYAATAAATTAATAAANNWA-AAATA 13684
                                   ?   v   -?  v   v?       v      ??? -    -
  (AAAT)n#Simpl          1 AAATAAATAAATAAAT-AAATAAATAAATAAATAAATAAATAAATAAAT- 48

  Tasmanian_Dev      13685 AAATTAAAAAATTAAAT 13701
                              -    v  v     
  (AAAT)n#Simpl         49 AAA-TAAATAAATAAAT 64

Matrix = Unknown
Transitions / transversions = 0.00 (0/6)
Gap_init rate = 0.06 (4 / 65), avg. gap size = 1.00 (4 / 4)


16 14.94 2.63 0.00 Tasmanian_Devil_Long_Consensus_IGS 14211 14248 (26439) (AAAT)n#Simple_repeat 1 39 (0) m_b1s252i14 15

  Tasmanian_Dev      14211 AAATAAATAAATCAATAAA-AAAACAATNAATCGATAAA 14248
                                       v      -   vv   ?   vi     
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAA 39

Matrix = Unknown
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.03 (1 / 37), avg. gap size = 1.00 (1 / 1)


19 22.55 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 15394 15464 (25223) (A)n#Simple_repeat 1 71 (0) m_b1s252i15 16

  Tasmanian_Dev      15394 AAAATAAATAAATCAATAAAAAAAAAAAAAACAAACNRTAAATTAATAAA 15443
                               v   v   vv  v              v   v??v   vv  v   
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50

  Tasmanian_Dev      15444 ATANNNNNAAAWAAAAAAAAA 15464
                            v ?????   ?         
  (A)n#Simple_r         51 AAAAAAAAAAAAAAAAAAAAA 71

Matrix = Unknown
Transitions / transversions = 0.00 (0/12)
Gap_init rate = 0.00 (0 / 70), avg. gap size = 0.0 (0 / 0)

19 14.04 4.08 0.00 Tasmanian_Devil_Long_Consensus_IGS 15395 15443 (25244) (AAAT)n#Simple_repeat 1 51 (0) m_b1s252i16 16

  Tasmanian_Dev      15395 AAATAAATAAATCAATAAA-AAAAAAAAAAACAAA-CNRTAAATTAATAA 15442
                                       v      -   v   v   i   -v??     v     
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAA 50

  Tasmanian_Dev      15443 A 15443
                            
  (AAAT)n#Simpl         51 A 51

Matrix = Unknown
Transitions / transversions = 0.20 (1/5)
Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2)


17 23.36 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 16575 16630 (24057) (A)n#Simple_repeat 1 56 (0) m_b1s252i17 17

  Tasmanian_Dev      16575 AAAATAAATAAATCAATNAAAAAAAAAAACAATAAATTAATAAAAWWAAW 16624
                               v   v   vv  v?           v  v   vv  v    ??  ?
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50

  Tasmanian_Dev      16625 AWAAAA 16630
                            ?    
  (A)n#Simple_r         51 AAAAAA 56

Matrix = Unknown
Transitions / transversions = 0.00 (0/10)
Gap_init rate = 0.00 (0 / 55), avg. gap size = 0.0 (0 / 0)

20 16.12 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 16576 16618 (24069) (AAAT)n#Simple_repeat 1 43 (0) m_b1s252i18 17

  Tasmanian_Dev      16576 AAATAAATAAATCAATNAAAAAAAAAAACAATAAATTAATAAA 16618
                                       v   ?  v   v   vv       v      
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAA 43

Matrix = Unknown
Transitions / transversions = 0.00 (0/6)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)


17 15.14 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 17136 17174 (23513) (AAAT)n#Simple_repeat 1 39 (0) m_b1s252i19 18

  Tasmanian_Dev      17136 AAATAAATAAATCAATNNAAAAAACAATAAATTAATAAA 17174
                                       v   ?? v   vv       v      
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAA 39

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


24 18.24 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 18311 18354 (22333) (A)n#Simple_repeat 1 44 (0) m_b1s252i20 19

  Tasmanian_Dev      18311 AAAAAAAAAAAACAATAAATTAATAAAATAAAATAAAAAAAAAA 18354
                                       v  v   vv  v    v    v          
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 44

Matrix = Unknown
Transitions / transversions = 0.00 (0/7)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)


15 15.03 8.22 0.00 Tasmanian_Devil_Long_Consensus_IGS 18875 18947 (21740) (AAATA)n#Simple_repeat 1 79 (0) m_b1s252i21 20

  Tasmanian_Dev      18875 AAAT-AAAT-AARTCAATNNAAAAAAAAAAACAAACAAT-AAAT-TAATA 18920
                               -    -  ? v  v??   v    v  v v v   -    -v    
  (AAATA)n#Simp          1 AAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATA 50

  Tasmanian_Dev      18921 AAATAAAATNNNA-AAAA-AAAATTAAAT 18947
                                    ??? -    -     v    
  (AAATA)n#Simp         51 AAATAAAATAAAATAAAATAAAATAAAAT 79

Matrix = Unknown
Transitions / transversions = 0.00 (0/9)
Gap_init rate = 0.08 (6 / 72), avg. gap size = 1.00 (6 / 6)

20 20.24 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 18893 18941 (21746) (A)n#Simple_repeat 1 49 (0) m_b1s252i22 20

  Tasmanian_Dev      18893 AAAAAAAAAAACAAACAATAAATTAATAAAATAAAATNNNAAAAAAAAA 18941
                                      v   v  v   vv  v    v    v???         
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 49

Matrix = Unknown
Transitions / transversions = 0.00 (0/8)
Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0)


12 17.71 1.45 2.94 Tasmanian_Devil_Long_Consensus_IGS 19475 19543 (21144) (AAAT)n#Simple_repeat 1 68 (0) m_b1s252i23 21

  Tasmanian_Dev      19475 AAATAAATAAATCAATNNNNNAA-AAACCAATAAATTAATNAAAATAAAA 19523
                                       v   ?????  -   iv       v   --       v
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAAT--AAATAAAT 48

  Tasmanian_Dev      19524 TNNNAAAAAAAAAATTAAAT 19543
                           v???   v   v  v     
  (AAAT)n#Simpl         49 AAATAAATAAATAAATAAAT 68

Matrix = Unknown
Transitions / transversions = 0.12 (1/8)
Gap_init rate = 0.04 (3 / 68), avg. gap size = 1.00 (3 / 3)


19 17.04 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 20094 20136 (20551) (A)n#Simple_repeat 1 43 (0) m_b1s252i24 22

  Tasmanian_Dev      20094 AAAAAAAAACAATAAAWTAATAAAATAAAATNNAAAAAAAAAA 20136
                                    v  v   ?v  v    v    v??          
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 43

Matrix = Unknown
Transitions / transversions = 0.00 (0/6)
Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0)


24 12.25 6.06 1.45 Tasmanian_Devil_Long_Consensus_IGS 20653 20718 (19969) (TAAAA)n#Simple_repeat 1 69 (0) m_b1s252i25 23

  Tasmanian_Dev      20653 TAAAAT-AAATAAATCAATNNAAAAAAACAAT-AAAT-TAATAAAATAAA 20699
                                 -       vi  v??    v  -   -    -v           
  (TAAAA)n#Simp          1 TAAAATAAAATAAAATAAAATAAAATAA-AATAAAATAAAATAAAATAAA 49

  Tasmanian_Dev      20700 ATAAAATTAAA-AAATTAAA 20718
                                  v   -   v    
  (TAAAA)n#Simp         50 ATAAAATAAAATAAAATAAA 69

Matrix = Unknown
Transitions / transversions = 0.17 (1/6)
Gap_init rate = 0.08 (5 / 65), avg. gap size = 1.00 (5 / 5)


19 12.60 2.78 4.23 Tasmanian_Devil_Long_Consensus_IGS 21811 21882 (18805) (TAAAA)n#Simple_repeat 1 71 (0) m_b1s252i26 24

  Tasmanian_Dev      21811 TAAAAT-AAATAAATCAATAAAAAAAMAAYANNNNAAT-TAATAAAATAA 21858
                                 -       vi  -  v    ?  - ????   -v          
  (TAAAA)n#Simp          1 TAAAATAAAATAAAATAA-AATAAAATAA-AATAAAATAAAATAAAATAA 48

  Tasmanian_Dev      21859 AATNNAAAAAAAAAAAAATTAAAT 21882
                              -?   v    v     v    
  (TAAAA)n#Simp         49 AAT-AAAATAAAATAAAATAAAAT 71

Matrix = Unknown
Transitions / transversions = 0.17 (1/6)
Gap_init rate = 0.07 (5 / 71), avg. gap size = 1.00 (5 / 5)

18 20.45 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 21812 21876 (18811) (A)n#Simple_repeat 1 65 (0) m_b1s252i27 24

  Tasmanian_Dev      21812 AAAATAAATAAATCAATAAAAAAAMAAYANNNNAATTAATAAAATAAAAT 21861
                               v   v   vv  v       ?  ? ????  vv  v    v    v
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50

  Tasmanian_Dev      21862 NNAAAAAAAAAAAAA 21876
                           ??             
  (A)n#Simple_r         51 AAAAAAAAAAAAAAA 65

Matrix = Unknown
Transitions / transversions = 0.00 (0/10)
Gap_init rate = 0.00 (0 / 64), avg. gap size = 0.0 (0 / 0)


55 0.00 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 26460 26509 (14263) (TATTA)n#Simple_repeat 1 50 (0) c_b1s251i4 25

  Tasmanian_Dev      26460 TATTATATTATATTATATTATATTATATTATATTATATTATATTATATTA 26509
                                                                             
  (TATTA)n#Simp          1 TATTATATTATATTATATTATATTATATTATATTATATTATATTATATTA 50

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0)


16 12.13 0.00 3.57 Tasmanian_Devil_Long_Consensus_IGS 27291 27319 (13417) (TC)n#Simple_repeat 1 28 (0) m_b1s252i28 26

  Tasmanian_Dev      27291 TCTCTCTGTCTCTGTCTCTGTNCTCTCTC 27319
                                  v     v     v -       
  (TC)n#Simple_          1 TCTCTCTCTCTCTCTCTCTCT-CTCTCTC 28

Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.04 (1 / 28), avg. gap size = 1.00 (1 / 1)


16 8.18 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 27910 27935 (12801) (AATC)n#Simple_repeat 1 26 (0) m_b1s252i29 27

  Tasmanian_Dev      27910 AATCAATCAATCAATCAATGAATAAA 27935
                                              v   v  
  (AATC)n#Simpl          1 AATCAATCAATCAATCAATCAATCAA 26

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


20 7.03 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 28733 28762 (11974) (AATC)n#Simple_repeat 1 30 (0) m_b1s252i30 28

  Tasmanian_Dev      28733 AATCAATCAATCAATCAATCAATGAATAAA 28762
                                                  v   v  
  (AATC)n#Simpl          1 AATCAATCAATCAATCAATCAATCAATCAA 30

Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0)


14 0.00 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 29144 29164 (11572) (ACAA)n#Simple_repeat 1 21 (0) m_b1s252i31 29

  Tasmanian_Dev      29144 ACAAACAAACAAACNAACAAA 29164
                                         ?      
  (ACAA)n#Simpl          1 ACAAACAAACAAACAAACAAA 21

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


19 22.91 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 29712 29774 (10962) (A)n#Simple_repeat 1 63 (0) m_b1s252i32 30

  Tasmanian_Dev      29712 AAAATAAATAAATCAATAAAAAAAAACAATAAATTNNNNNATAAAATAAA 29761
                               v   v   vv  v         v  v   vv????? v    v   
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50

  Tasmanian_Dev      29762 AWAAAAAAAAAAA 29774
                            ?           
  (A)n#Simple_r         51 AAAAAAAAAAAAA 63

Matrix = Unknown
Transitions / transversions = 0.00 (0/11)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)


13 7.51 3.12 6.45 Tasmanian_Devil_Long_Consensus_IGS 29995 30026 (10710) (AATA)n#Simple_repeat 1 31 (0) m_b1s252i33 31

  Tasmanian_Dev      29995 AATAAATTAATNAAATAAAATAAA-AAAAAAAT 30026
                                  v   -    -       -   v    
  (AATA)n#Simpl          1 AATAAATAAAT-AAAT-AAATAAATAAATAAAT 31

Matrix = Unknown
Transitions / transversions = 0.00 (0/2)
Gap_init rate = 0.10 (3 / 31), avg. gap size = 1.00 (3 / 3)


17 7.75 6.82 0.00 Tasmanian_Devil_Long_Consensus_IGS 30212 30255 (10481) (AAAT)n#Simple_repeat 1 47 (0) m_b1s252i34 32

  Tasmanian_Dev      30212 AAATAAATAAATCAATAAA-ANNNAAA-AAA-CAATAAATTAATAAA 30255
                                       v      - ???   -   -v       v      
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAA 47

Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3)


19 23.93 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 30793 30858 (9878) (A)n#Simple_repeat 1 66 (0) m_b1s252i35 33

  Tasmanian_Dev      30793 AAAATNAATAAATCAATNAAAAAAACAATAAATCAATAAAATTNNNNAAA 30842
                               v?  v   vv  v?       v  v   vv  v    vv????   
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 50

  Tasmanian_Dev      30843 AAAAAAAAAAAAAAAA 30858
                                           
  (A)n#Simple_r         51 AAAAAAAAAAAAAAAA 66

Matrix = Unknown
Transitions / transversions = 0.00 (0/12)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)

17 23.82 0.00 1.39 Tasmanian_Devil_Long_Consensus_IGS 30794 30866 (9870) (AAAT)n#Simple_repeat 1 72 (0) m_b1s252i36 33

  Tasmanian_Dev      30794 AAATNAATAAATCAATNAAAAAAACAATAAATCAATAAAATTNNNNAAAA 30843
                               ?       v   ?  v   vv       v   -    v????  v 
  (AAAT)n#Simpl          1 AAATAAATAAATAAATAAATAAATAAATAAATAAAT-AAATAAATAAATA 49

  Tasmanian_Dev      30844 AAAAAAAAAAAAAAACATTAAAT 30866
                             v   v   v   vv v     
  (AAAT)n#Simpl         50 AATAAATAAATAAATAAATAAAT 72

Matrix = Unknown
Transitions / transversions = 0.00 (0/13)
Gap_init rate = 0.01 (1 / 72), avg. gap size = 1.00 (1 / 1)


20 8.88 0.00 5.26 Tasmanian_Devil_Long_Consensus_IGS 31394 31433 (9303) (AATC)n#Simple_repeat 1 38 (0) m_b1s252i37 34

  Tasmanian_Dev      31394 AATCAATCAATCAATCAATCAATAAAANTAAATCAATAAA 31433
                                                  -v  - v       v  
  (AATC)n#Simpl          1 AATCAATCAATCAATCAATCAAT-CAA-TCAATCAATCAA 38

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


16 0.00 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 31959 31976 (8760) (T)n#Simple_repeat 1 18 (0) m_b1s252i38 35

  Tasmanian_Dev      31959 TTTTTTTTTTTTTTTTTT 31976
                                             
  (T)n#Simple_r          1 TTTTTTTTTTTTTTTTTT 18

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0)


18 12.57 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 32713 32739 (7997) (A)n#Simple_repeat 1 27 (0) m_b1s252i39 36

  Tasmanian_Dev      32713 AAAAAAAAAAAGAAAGAAAAAGAAAAA 32739
                                      i   i     i     
  (A)n#Simple_r          1 AAAAAAAAAAAAAAAAAAAAAAAAAAA 27

Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0)


43 0.00 0.00 0.00 Tasmanian_Devil_Long_Consensus_IGS 34327 34363 (6409) (TG)n#Simple_repeat 1 37 (0) c_b1s251i5 37

  Tasmanian_Dev      34327 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 34363
                                                                
  (TG)n#Simple_          1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 37

Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0)


1047 6.24 3.68 1.81 Tasmanian_Devil_Long_Consensus_IGS 40610 40772 (0) SSU-rRNA_Hsa#rRNA 542 707 (1162) m_b1s551i4 38

  Tasmanian_Dev      40610 TCGASSCYCTGKAATTAGA--TAGTACACT--AAATCCTTTAACGAGGAT 40655
                               ?? ?   ?    i  --v   v    --                  
  SSU-rRNA_Hsa#        542 TCGAGGCCCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGAT 591

  Tasmanian_Dev      40656 CCATTTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATT-CAGCT-CA 40703
                                -                                   -     -  
  SSU-rRNA_Hsa#        592 CCATT-GGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCA 640

  Tasmanian_Dev      40704 ATAGCGTATATTAAAGTTACTCACGGTTAAAAAGCTCGTAGTTAAGATCT 40753
                                             i  -i i                  -i     
  SSU-rRNA_Hsa#        641 ATAGCGTATATTAAAGTTGCT-GCAGTTAAAAAGCTCGTAGTT-GGATCT 688

  Tasmanian_Dev      40754 TGGGATCGAGCTGGCGGTC 40772
                                v  i  v       
  SSU-rRNA_Hsa#        689 TGGGAGCGGGCGGGCGGTC 707

Matrix = 20p37g.matrix
Kimura (with divCpGMod) = 6.73
Transitions / transversions = 1.50 (6/4)
Gap_init rate = 0.04 (7 / 162), avg. gap size = 1.29 (9 / 7)