##maf version=1 scoring=autoMZ.v1
a score=6441.000000
s mm9.chr10               3009319 162 + 129993255 TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT
s oryCun1.scaffold_133159   11087 164 +     13221 TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT
q oryCun1.scaffold_133159                         99569899999998999999999999999999999999999999999999999999999999999999999757878999975999999999999999979999999999997899999999999997997999999869999996999988997997999999
i oryCun1.scaffold_133159 N 0 N 0

a score=103072.000000
s mm9.chr10     3012076 365 + 129993255 AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGC-----ACTCCCAACAGCAAGACACTAAGTT---------CACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCAC-----CAAATTAAATAACCAGTGAGCAGAGTTG--TGACGAGCATCAGGCTCTGGATTTAGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGAT--------------------------GAGTCAAGTGAAGGTCCTGAGACAA-------------------CAAGTCCTC----GGCTATGTGGGGGTGAGGG-------------ATGC----AG--------CTGGAACCTCAGGGA-TCTCTGT-AAGCAGTGGCATAAATGCTTGGCGG--GAGAGAGCATGTTAGAGCTCACACGACATAGGAAGCCACTGA--GACACTG
s ponAbe2.chr6 16160203 443 - 174210431 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCCAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTACTTATGAAGTGAGCAAGCAGTATTTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGCTGCTGTAGACTCCCTGACAGCGTAGGAACT--------AGAACTCTGAAGCAAGCCACTGGTGCCTAACAAATTCTTTCTAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACGTGGTTGAAAAGGCCATGGACTTGTGTTC
i ponAbe2.chr6 N 0 C 0
s panTro2.chr6 16379004 443 - 173908612 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGATGCTGTAGACTCCCTGACAGCATAGGAACTAGAACTCTGAAGC----AAGCCA----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC
q panTro2.chr6                          99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----------9999999999999999999999999999999999999999999999999----999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i panTro2.chr6 N 0 C 0
s hg18.chr6    15860456 443 - 170899992 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGATAGGGATGCTGTAGACTCCCT---GACAGCATAGGAAC-TAGAACTCTGAAGC---AAGC----CA--------CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCCATGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC
i hg18.chr6    N 0 C 0

a score=49128.000000
s mm9.chr10                      3012441 125 + 129993255 TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACCTGAATTG--AATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGCTCGACAC
s hg18.chr6                     15860899 114 - 170899992 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC
i hg18.chr6                     C 0 C 0
s panTro2.chr6                  16379447 114 - 173908612 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC
q panTro2.chr6                                           99999999999999999999999--99999999999999999999999999999999999999999999999999999999----------999999999-99999999999999999999999999
i panTro2.chr6                  C 0 C 0
s ponAbe2.chr6                  16160646 114 - 174210431 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTCTATATTGACCACCTGTCTTGACTGTTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC
i ponAbe2.chr6                  C 0 C 0
s otoGar1.scaffold_334.1-359464   180525 101 -    359464 TGGGCCCCCCTGACCTGGCCAAG--TCCTCACTCACCCGGGTTTACACTGACCACC-------------AAACTTGGGGAG----------CCCTTTGCT-GAGGGGCAACAGCAAACACGGGAAGC
q otoGar1.scaffold_334.1-359464                          99999999999999999999999--9999999999999999999999999999999-------------999999999999----------999999999-99999979999999999999999999
i otoGar1.scaffold_334.1-359464 N 0 C 0

a score=117109.000000
s mm9.chr10                      3012566 262 + 129993255 --TGTGGGCTCCTCACTTTCCTG-TCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTACAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCTGTCCTCTTTAGC-------TTATCTCAGGCAACCTATCTTATTTTGTT-TGCTTTC--AGAAGGCAAG---CGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtgCGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG
s hg18.chr6                     15861013 199 - 170899992 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTCTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------
i hg18.chr6                     C 0 C 0
s panTro2.chr6                  16379561 199 - 173908612 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------
q panTro2.chr6                                           999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999-999999999999999999999-------999999999999999999999------------------------------------------------------------------
i panTro2.chr6                  C 0 C 0
s ponAbe2.chr6                  16160760 199 - 174210431 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTGTCATTCCTGTCAATCAATCCTCTTGTTTTTTTCCTTCATTACC----TTATTTCTAGCAACATATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------
i ponAbe2.chr6                  C 0 C 0
s otoGar1.scaffold_334.1-359464   180626 204 -    359464 CACATGCACTCATCGTGTCTCTG-TCTTAGGCGTAGCCCTGGTTTCTGGGGAAAGCTGTCCAGAAAACCACCTGAAAACCCAGTCTCTGTGGTCATTGCTGGCAATCAGTCC-CTTATTTTTAGGTTGCCTTG------TTATTTCAGGTGACATAGCTTACTTTGTTTTGTTTTCCCAGAAGACAAGTGGTGACTTGTGTATGAGTTTTGA------------------------------------------------------------------
q otoGar1.scaffold_334.1-359464                          99999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999------9999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------------------------------------
i otoGar1.scaffold_334.1-359464 C 0 C 0
s cavPor2.scaffold_290371            310 205 -     39932 --TGCGTATCCCTTGCGATCCTGATCCGAGGTGTGGCTGTGGTTTTTGGTGAAAGCCATCCAGAAAAGAACTTCAAAACCTAGTCTAAATTGTTATTCCCTCCTGCCAATCCTCTTGTTTTTACCCCATAGTGACCTCGTTATTGCAA--AACATatcttattttgttctgttttcctggaagataaa---tgaattttgtgtgaGTTTGAG------------------------------------------------------------------
q cavPor2.scaffold_290371                                --99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999997999999999999999999999999999999999999999--99999999999999999999999999999999999999---999999999999999999999------------------------------------------------------------------
i cavPor2.scaffold_290371       N 0 C 0

a score=128047.000000
s mm9.chr10                      3012828 168 + 129993255 TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATGCACTTAGCACAGCCTGCCCTGAGGGAT----GAACACT--ATTGTTAA-AGAACTATTCCGCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT
s cavPor2.scaffold_290371            515 166 -     39932 -----GTGGGATGTCTTGACAGCTAAATAGTcttatatttaagcatttatGAAAATAATGAGGTTATCATGGTTCGCTCTAGTAGCTCTGAGACCTTT--ATTGTCAGCAAAGCTGTTTAGC--AGGAGGCAACTTCAGGTTCCGTGGGATTCTAGTGCCATCTGCTGGTCATAT
q cavPor2.scaffold_290371                                -----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--9999999999999999999999--999999999999999999999999999999999999999999999999999
i cavPor2.scaffold_290371       C 0 C 0
s otoGar1.scaffold_334.1-359464   180830 161 -    359464 -----GTGGACATTCGTGACAGGCAAATAGTGTTCTATTTAAACATTTGTTGAAATGATAAACTTAGCTCAGCC--CCTT---AGAAGTG-AGAGGCT--ACTGTCAGGGAAGCGGTTTTGCG-GAGCAGCAGCCTCAGGATCTGTGGGATTTTAGCGCCATCTGCTGGTCACAG
q otoGar1.scaffold_334.1-359464                          -----999999999999999999999999999999999999999999999999999999999999999999999--9999---9999999-9999999--99999999999999999999989-996999999999999999999999999999999999999999999999999
i otoGar1.scaffold_334.1-359464 C 0 C 0
s ponAbe2.chr6                  16160959 161 - 174210431 -----GTGGACTATCCTGACAACCAAATAGCGTTATATTTAAACATTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGTTTAGCT-AAGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAT
i ponAbe2.chr6                  C 0 C 0
s panTro2.chr6                  16379760 161 - 173908612 -----GCGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC
q panTro2.chr6                                           -----9999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999-------9999999999999999999-999999999999999999999999999999999999999999999999999
i panTro2.chr6                  C 0 C 0
s hg18.chr6                     15861212 161 - 170899992 -----GTGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTGTGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC
i hg18.chr6                     C 0 C 0
s echTel1.scaffold_288249          87492 169 +    100002 TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATGAGTTTGTCATAACT-GCCTCCTCCCAAGTG-GGAAGCTGAAGCACCAA-GTACTGACTCAGC--AGTCCCTGACCTCA-CATCCATGGAAATCTAGTGACATCTGCTGGACACAT
q echTel1.scaffold_288249                                99989999998979665899999999999676899897997899979878899999999999999999999999-999999999999999-99999999999999999-9999999999999--99999999999999-999999999999999999999999999999999999
i echTel1.scaffold_288249       N 0 I 7564

a score=98097.000000
s mm9.chr10                         3012996 222 + 129993255 AGATGTCTGCTGTGGAGA-------CCTGGCCAACTTTG----CTT--TCTTC-----AAAAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCA-----TTAGGAAGGCGACCTCTAGTGCACAAACCTTGAC-ATTTTCCCTTTTAATGGAA-TTTAACAGAAGTTCAGGATGTTCTTTGGGTAATTTACAATT---A----GGGGGCAAAAATCAAAAGTATTTCGAGCATATCAAAACTGTTAGCTATG
s cavPor2.scaffold_290371               681 177 -     39932 TGACGTCTGCAGCCACGG-------GCTGGCTAACTCCA--GTCTT--CCGCG-----CTAAAGCCGAC--------------------CACACCACATAGTGGGGAGAGTGACCTCTAGCGGAAAagctttgca-atttttttcttc----gAC-TCTGTCAG--GTTCAGAATTCCATTTAAACAATTTacagct---a----gaaaaggaaaagcagaggCATTT--------------------------
q cavPor2.scaffold_290371                                   999999999999999999-------99999999999999--99999--99999-----99999999999--------------------9999999999999999999999999999999999999999999999-999999999999----999-99999999--9999999999999999997999999999995---6----99999999999336991774687--------------------------
i cavPor2.scaffold_290371          C 0 N 0
s hg18.chr6                        15861373 184 - 170899992 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGC-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------
i hg18.chr6                        C 0 I 14
s panTro2.chr6                     16379921 184 - 173908612 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ATTCT-----ATAAGACTAAC--------------------AGGACCCCATGGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTAAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------
q panTro2.chr6                                              999999999999999999---9999999999999999999999999--99999-----99999999999--------------------9999999999999999999999999999999999999999999999-9999999999999999999-99999999-99999999999999999999999999999999---99999999999999999999----------------------------------
i panTro2.chr6                     C 0 I 14
s ponAbe2.chr6                     16161120 217 - 174210431 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTAGGCCGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTATAAATATTGAATGTAT-TCAAACCTGTCAATGATG
i ponAbe2.chr6                     C 0 I 2
s otoGar1.scaffold_334.1-359464      180991 226 -    359464 GGACGGCCGCCGCCACCACCGCTTTCCCTGCCAACTCCACCGTCTTAAATTCTGCAACAAAAGAAAAAT--------------------CGGACCCTGCAGTTACTAGAGCGACCTCTGGTGAACAAGCCTTGGATTTTTTTCTTTTTAATTGAATTTTACAAC-GGCTCAAAATGCAAGTTAGACAATTCATAGTGTATGTGTGGGGACCTGAGAGTGCAAATATTGCTGGCAT-TCAGCCTTGTTA------
q otoGar1.scaffold_334.1-359464                             999998999999999999999999999999999999999999999999999999999999999999999--------------------999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999699999999999999999999999999-999999999999------
i otoGar1.scaffold_334.1-359464    C 0 I 2931
s tupBel1.scaffold_114895.1-498454   167217 159 -    498454 TGATGGCTACAGCTGTCA---CTTTCTTGGACCACTCAGCTCTCTC--AAC-------GAAAGACAAAC--------------------TGGATCCTCCGG---GAGAGGAGACCTCTAGTGAGCAAACCTTGGA-ATTTTTCTTTAAAACAGAA-TTTATAAA-GGTTCA-AATGCCATTTAGACAACTTATAATT---A-----------------------------------------------------
q tupBel1.scaffold_114895.1-498454                          234233433332122232---1582112220212134443324332--133-------23732111754--------------------365002326236---2411112335242535353245936522224-1376645373578253554-58324573-545454-8444565585455465799967999---9-----------------------------------------------------
i tupBel1.scaffold_114895.1-498454 N 0 I 4145
e echTel1.scaffold_288249             87661 7564 +    100002 I

a score=0.000000
s mm9.chr10                         3013218 219 + 129993255 agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggatctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacacagaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAAAAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT
e tupBel1.scaffold_114895.1-498454   167376 4145 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e otoGar1.scaffold_334.1-359464      181217 2931 -    359464 I
e hg18.chr6                        15861557  14 - 170899992 I
e panTro2.chr6                     16380105  14 - 173908612 I
e ponAbe2.chr6                     16161337   2 - 174210431 I

a score=40604.000000
s mm9.chr10                         3013437 166 + 129993255 TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAAGAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCAGACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA
s panTro2.chr6                     16380119 130 - 173908612 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA
q panTro2.chr6                                              999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------9999999999999999999999999999999999999099999999999999999999
i panTro2.chr6                     I 14 I 9106
s hg18.chr6                        15861571 130 - 170899992 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA
i hg18.chr6                        I 14 I 9085
s ponAbe2.chr6                     16161339 109 - 174210431 ---------------------CAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA
i ponAbe2.chr6                     I 2 I 8044
e tupBel1.scaffold_114895.1-498454   167376 4145 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e otoGar1.scaffold_334.1-359464      181217 2931 -    359464 I

a score=0.000000
s mm9.chr10                         3013603 1041 + 129993255 CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgctgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacccgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagttcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcatacctttaatatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcgttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggattccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactagagtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagtcattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaaccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgaggttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggtcctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGTGTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCTTGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAGTATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaaaaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGATTTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCTTGTTTGTTTTGGTCAATGCAG
e tupBel1.scaffold_114895.1-498454   167376 4145 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e otoGar1.scaffold_334.1-359464      181217 2931 -    359464 I
e hg18.chr6                        15861701 9085 - 170899992 I
e panTro2.chr6                     16380249 9106 - 173908612 I
e ponAbe2.chr6                     16161448 8044 - 174210431 I

a score=19159.000000
s mm9.chr10                         3014644 45 + 129993255 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG
s hg18.chr6                        15870786 46 - 170899992 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
i hg18.chr6                        I 9085 C 0
s panTro2.chr6                     16389355 46 - 173908612 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
q panTro2.chr6                                             99999999999999999999999-9999999999999999999-9999
i panTro2.chr6                     I 9106 C 0
s calJac1.Contig6394                   6182 46 +    133105 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT
i calJac1.Contig6394               N 0 C 0
s loxAfr1.scaffold_75566               1167 34 -     10574 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC
q loxAfr1.scaffold_75566                                   ------------99999699899-9999999999999869998-9997
i loxAfr1.scaffold_75566           N 0 C 0
e tupBel1.scaffold_114895.1-498454   167376 4145 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e otoGar1.scaffold_334.1-359464      181217 2931 -    359464 I
e ponAbe2.chr6                     16161448 8044 - 174210431 I

a score=40840.000000
s mm9.chr10                         3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6                        15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6                        C 0 I 401
s panTro2.chr6                     16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6                                             9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6                     C 0 I 400
s calJac1.Contig6394                   6228 53 +    133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394               C 0 I 2
s otoGar1.scaffold_334.1-359464      184148 52 -    359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464                            7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464    I 2931 I 2
s loxAfr1.scaffold_75566               1201 54 -     10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566                                   899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566           C 0 I 2
e tupBel1.scaffold_114895.1-498454   167376 4145 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e ponAbe2.chr6                     16161448 8044 - 174210431 I

a score=411.000000
s mm9.chr10                         3014742 36 + 129993255 AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA
s calJac1.Contig6394                   6283 28 +    133105 AAATGTA-----TGATCTCCCCATCCTGCCCTG---
i calJac1.Contig6394               I 2 I 54
s otoGar1.scaffold_334.1-359464      184202 31 -    359464 AGATTTC-----TGATGCCCTCACCCCCTCCGTGCA
q otoGar1.scaffold_334.1-359464                            9996999-----965974999999999999999999
i otoGar1.scaffold_334.1-359464    I 2 I 24
s loxAfr1.scaffold_75566               1257 27 -     10574 AGGCTTA-----TG----CCACCCCCCACCCCCACA
q loxAfr1.scaffold_75566                                   9999999-----99----997999999999999999
i loxAfr1.scaffold_75566           I 2 I 25
e tupBel1.scaffold_114895.1-498454   167376 4145 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e hg18.chr6                        15870885 401 - 170899992 I
e panTro2.chr6                     16389454 400 - 173908612 I
e ponAbe2.chr6                     16161448 8044 - 174210431 I

a score=0.000000
s mm9.chr10                         3014778 17 + 129993255 TCCCATGTCCACCCTGA
e loxAfr1.scaffold_75566               1284 25 -     10574 I
e calJac1.Contig6394                   6311 54 +    133105 I
e tupBel1.scaffold_114895.1-498454   167376 4145 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e otoGar1.scaffold_334.1-359464      184233 24 -    359464 I
e hg18.chr6                        15870885 401 - 170899992 I
e panTro2.chr6                     16389454 400 - 173908612 I
e ponAbe2.chr6                     16161448 8044 - 174210431 I

a score=-12243.000000
s mm9.chr10                         3014795 47 + 129993255 GTTTCAGGGGCAGCTCGCTG----------------TTAGCAG-CTAAGGCATGGTGTCTCTCA
s otoGar1.scaffold_334.1-359464      184257 60 -    359464 ---TCGGGAACAAGTTGCAGTCATGGATAT-TTGGTTTAGATGGTTTAGGTGGGGTGTATTTCT
q otoGar1.scaffold_334.1-359464                            ---899999999999999999999999999-999999999999999999999999999999999
i otoGar1.scaffold_334.1-359464    I 24 C 0
s calJac1.Contig6394                   6365 39 +    133105 -------------------GCCATGAATAT-----TTTAGAC-ATGCAGGTGTGGCGTGTTTCT
i calJac1.Contig6394               I 54 C 0
s hg18.chr6                        15871286 20 - 170899992 --------------------------------------------aGCAGGTGTGGCATGTTTCT
i hg18.chr6                        I 401 C 0
s panTro2.chr6                     16389854 20 - 173908612 --------------------------------------------aGCAGGTGTGGCATGTTTCT
q panTro2.chr6                                             --------------------------------------------99999999999999999999
i panTro2.chr6                     I 400 C 0
s ponAbe2.chr6                     16169492 20 - 174210431 --------------------------------------------aGCAGGTGTGGCATGTTTCT
i ponAbe2.chr6                     I 8044 C 0
s tupBel1.scaffold_114895.1-498454   171521 27 -    498454 ------------------------------------TTAGAAA-TGTGGGTGTGGCGCATCGCT
q tupBel1.scaffold_114895.1-498454                         ------------------------------------9999999-99999989998899999699
i tupBel1.scaffold_114895.1-498454 I 4145 C 0
s cavPor2.scaffold_216473              7816 26 -     10026 ------------------------------------TTAGAAA-TTTAGGTGTGGCATGGTTC-
q cavPor2.scaffold_216473                                  ------------------------------------4255831-1324566557465575854-
i cavPor2.scaffold_216473          N 0 C 0
s loxAfr1.scaffold_75566               1309 62 -     10574 GTT-TGAGAGCAAGTTTAGGACATCAATACGTTGTTTCAGAAA-TTGAGGTTTGCTGTATCTCt
q loxAfr1.scaffold_75566                                   999-999999999999999999999999999999999999999-99999999999999999999
i loxAfr1.scaffold_75566           I 25 C 0
e echTel1.scaffold_288249             87661 7564 +    100002 I

a score=320596.000000
s mm9.chr10                         3014842 186 + 129993255 C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGATCTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCTTCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtttttatttttt----tatt-tat-----------------------ttattttttttt------------cttt
s loxAfr1.scaffold_75566               1371 245 -     10574 tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGCCATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCCTCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATTCCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGACTTTGGCCAAATCT
q loxAfr1.scaffold_75566                                    999999999999999999999999999999999999999999999999-999999999999999999999999-9999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999-99999999999999-999---999999999999999999999999999999999999999999999999
i loxAfr1.scaffold_75566           C 0 C 0
s cavPor2.scaffold_216473              7842 198 -     10026 ---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCCTCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATTTCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt------------ctct
q cavPor2.scaffold_216473                                   ---610137---------77-200195531236266876425368858-778987956887868956898956-8988778987788768588885664786777656586678636299978766----89979789936989956687867689995888978886997659897789899998996778899997-989-----------------------998799999777------------9899
i cavPor2.scaffold_216473          C 0 C 0
s tupBel1.scaffold_114895.1-498454   171548 215 -    498454 CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGTCTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCCTCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATTTCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG------------ACTT
q tupBel1.scaffold_114895.1-498454                          989999999---------899999998999999999999999999999-999999999999999999999999-9999998999999999999999999999999999899999999999999999---998899999999973999999998999999999999999979999999999999-99999997699849-999---9999999999999-------999999999999------------9999
i tupBel1.scaffold_114895.1-498454 C 0 C 0
s ponAbe2.chr6                     16169512 219 - 174210431 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCCTCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTTCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT------------ACTT
i ponAbe2.chr6                     C 0 C 0
s panTro2.chr6                     16389874 168 - 173908612 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATTT------------------------------------------------------------------------
q panTro2.chr6                                              999999999---------999999999999999999999999999999-999999999999999999999999-99999999999999999999999999999999999999999999999999999--9999999999999999999999999999999999999999999999999999------------------------------------------------------------------------
i panTro2.chr6                     C 0 C 0
s hg18.chr6                        15871306 169 - 170899992 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTT------------------------------------------------------------------------
i hg18.chr6                        C 0 C 0
s calJac1.Contig6394                   6404 223 +    133105 TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGTCTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCCTCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATTTCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT------------ATTT
i calJac1.Contig6394               C 0 C 0
s otoGar1.scaffold_334.1-359464      184317 222 -    359464 TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCCTCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATTT-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT------------TCTC
q otoGar1.scaffold_334.1-359464                             999999999--------9999999999999999999999997999999-999999999999999999999999-9999999999999999999999999999999999999999999999999999---9999999999999999999999999999999999999999999999999999-9-99999999999999-999---99999999999999999999999999999999------------9999
i otoGar1.scaffold_334.1-359464    C 0 C 0
s ornAna1.chr2                     14750994 201 -  54797317 --CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTATCTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCCTCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGTTCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT----------------
i ornAna1.chr2                     N 0 I 5690
e echTel1.scaffold_288249             87661 7564 +    100002 I

a score=-36127.000000
s mm9.chr10                         3015028 58 + 129993255 ccatttt----------ttattaggtatttagctcatttacatttccaatgctatac----caaaagtcccc
s loxAfr1.scaffold_75566               1616 33 -     10574 TCACTTCTA---------------------------------------CCTCCATTCCTTACAAAAGTTCTC
q loxAfr1.scaffold_75566                                   999999999---------------------------------------999999999999999999999999
i loxAfr1.scaffold_75566           C 0 N 0
s cavPor2.scaffold_216473              8040  8 -     10026 ctgtgtc----------t------------------------------------------------------
q cavPor2.scaffold_216473                                  6788989----------9------------------------------------------------------
i cavPor2.scaffold_216473          C 0 I 1372
s tupBel1.scaffold_114895.1-498454   171763  1 -    498454 T-----------------------------------------------------------------------
q tupBel1.scaffold_114895.1-498454                         9-----------------------------------------------------------------------
i tupBel1.scaffold_114895.1-498454 C 0 I 2374
s ponAbe2.chr6                     16169731 12 - 174210431 TTTTGCCTTTTC------------------------------------------------------------
i ponAbe2.chr6                     C 0 I 75
s calJac1.Contig6394                   6627 22 +    133105 TGCTTTTTCTCAAATCTCCACT--------------------------------------------------
i calJac1.Contig6394               C 0 I 3479
s otoGar1.scaffold_334.1-359464      184539 36 -    359464 TTTTTTCTATT------------GACTTTTGCCAAATATTCACTTCCA------------------------
q otoGar1.scaffold_334.1-359464                            99999999999------------9999999999999999999999999------------------------
i otoGar1.scaffold_334.1-359464    C 0 I 137
e ornAna1.chr2                     14751195 5690 -  54797317 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e hg18.chr6                        15871475  0 - 170899992 C
e panTro2.chr6                     16390042  0 - 173908612 C

a score=0.000000
s mm9.chr10                         3015086 2572 + 129993255 catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcccctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccgactaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagttcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctctagctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctgtgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataagatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccctggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgtaactccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcagtcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcctaggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaatgtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataaattaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgtatccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataaggctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatatatgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaaccgccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtgttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagccattctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgattaaggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaattctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccaccttcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaagatcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcagaaactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattgctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttctcctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttgaccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagttgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctcccttgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattccattggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgtagtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagagtttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaattcgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttggcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttccatcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagatctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgagaagggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggccattgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggtttaggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaagtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaattgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagccttgtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttggctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184575  137 -    359464 I
e hg18.chr6                        15871475    0 - 170899992 C
e panTro2.chr6                     16390042    0 - 173908612 C
e ponAbe2.chr6                     16169743   75 - 174210431 I

a score=12170.000000
s mm9.chr10                         3017658 85 + 129993255 TTTTTATTTGCAGGTTTCTTTAC----AGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTGTTGACCTTTATCAGATTTCTGCTTTAACC
s hg18.chr6                        15871475 83 - 170899992 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC
i hg18.chr6                        C 0 I 53
s panTro2.chr6                     16390042 83 - 173908612 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC
q panTro2.chr6                                             999999999999999999999999999999999999999999999------99999999999999999999999999999999999999
i panTro2.chr6                     C 0 I 53
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184575 137 -    359464 I
e ponAbe2.chr6                     16169743 75 - 174210431 I

a score=0.000000
s mm9.chr10                         3017743 418 + 129993255 ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggctgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaattagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaagagagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgccagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaatctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggagacctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184575 137 -    359464 I
e hg18.chr6                        15871558  53 - 170899992 I
e panTro2.chr6                     16390125  53 - 173908612 I
e ponAbe2.chr6                     16169743  75 - 174210431 I

a score=22499.000000
s mm9.chr10                         3018161 69 + 129993255 ATCCACAAAAGAGAC-----AAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAATTCCATTTTATTGA
s panTro2.chr6                     16390178 65 - 173908612 ACCTACAAAGG---------AAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA
q panTro2.chr6                                             99999999999---------999999999999999999999999999999999999999999999999999999
i panTro2.chr6                     I 53 C 0
s hg18.chr6                        15871611 65 - 170899992 ACCTACAAAGG---------AAAACAATTAACCACAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA
i hg18.chr6                        I 53 C 0
s ponAbe2.chr6                     16169818 61 - 174210431 -------------ACAAAGGAAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA
i ponAbe2.chr6                     I 75 I 97
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184575 137 -    359464 I

a score=4781.000000
s mm9.chr10                         3018230 129 + 129993255 AGGA-CAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATGAATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTA-CAGCCCCAGC
s hg18.chr6                        15871676  95 - 170899992 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTATGAA----------AAAGAATTTACACATATATAGATTTATTAGGTATATG
i hg18.chr6                        C 0 C 0
s panTro2.chr6                     16390243  95 - 173908612 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTGTGAA----------AAAGAatttacacatatatagatttattaggtatatg
q panTro2.chr6                                              99999999999999999999---------------------9999999999999999999-----9999999999999999999----------9999999999999999999999999999999999999
i panTro2.chr6                     C 0 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184575 137 -    359464 I
e ponAbe2.chr6                     16169879  97 - 174210431 I

a score=61520.000000
s mm9.chr10                         3018359 123 + 129993255 TT-CAAACATGCATACATGCATTCATGTCTCATAA-TAATTATTAACA-TTGTCTTAGGCCAGAGGCTCGACTGCCCCAAAGCAATCCACT-------TAAACTGTCCCTGAGAA-AGTCAttcctctccctaa
s panTro2.chr6                     16390338 131 - 173908612 -tataaatgtacaaatatatgtgtatgtCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--
q panTro2.chr6                                              -99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--
i panTro2.chr6                     C 0 I 2400
s hg18.chr6                        15871771 131 - 170899992 -TATAAACGTACAAATATATGTGTATGTCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAATGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--
i hg18.chr6                        C 0 I 2402
s otoGar1.scaffold_334.1-359464      184712 127 -    359464 TT-TATACATGTATGTGTAAATGTAGGTCCTGTAAGTAATTATTAACATTTGTCTTAGGTTAGAGGCCCGAGTGACACAAGCTAACCCATCC------TATCCTCCCTGTGTGAAGGGTCATCCTTTCTTCTGA
q otoGar1.scaffold_334.1-359464                             99-99999999999999999999999999999999999999999999999999667736999999999999999999999999999995666------677755798899998999967967999999999589
i otoGar1.scaffold_334.1-359464    I 137 I 2731
s ponAbe2.chr6                     16169976 129 - 174210431 ---taaatgtacaaatatatgtgtatgtgtcataaataATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATAGAAACTAAGCCATCCATATTTTATATTCTCTCTGGGAAGGGTCATCCTTTTCTTT--
i ponAbe2.chr6                     I 97 I 2523
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I

a score=0.000000
s mm9.chr10                         3018482 162 + 129993255 tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtccttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatggggagaggaggaaaggaggagaggggaggagaggaggggagGTAT
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184839 2731 -    359464 I
e hg18.chr6                        15871902 2402 - 170899992 I
e panTro2.chr6                     16390469 2400 - 173908612 I
e ponAbe2.chr6                     16170105 2523 - 174210431 I

a score=1520.000000
s mm9.chr10                         3018644 178 + 129993255 AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTC---TGAGTGTCAGTGATGTTCA-TGAGATTATCACCAGCAAGGATG--GCTGACGGGAACTG---CAAGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATG--------------------------CACTGTTTCAGCATCT
s canFam2.chr1                     78070420 204 - 125616256 AGAAAAGGCAAATGCCCCTGGGAGGGA-----TAGCACATTGA--GTTTATTCACATGCGTGTAAGTGATGGATACTGAGATCCTCTCC--TAAGGATGCGGTTGATGGAATCAGAAGCAAATACCACCAGCCAGAACTCTAAAATGAGAGGAAAGATCATGGATAGAATAGAATTGTAATATGAAATATAAAATTTCCCTATTGAAGAATTT
q canFam2.chr1                                              999999999999999999999999999-----99999999999--99999999999999999999999999999999999999999999--99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i canFam2.chr1                     N 0 I 160
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184839 2731 -    359464 I
e hg18.chr6                        15871902 2402 - 170899992 I
e panTro2.chr6                     16390469 2400 - 173908612 I
e ponAbe2.chr6                     16170105 2523 - 174210431 I

a score=1986.000000
s mm9.chr10                         3018822 110 + 129993255 CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACA----GAAGAGAACCTAACTTG-CTTAGGAGCATATGTACAGTTAATCAAGAC-----AAAAATAAGAATGGAGACt
s canFam2.chr1                     78070784 119 - 125616256 CTTTTTTTCCCTGCCCATTATTACTCACTTAAAATTCTCC-ACATTGTAAAGGGAATTCAAATCGACTTCTAGAGATGCACACAATTTAGCAAGATCAACTAAAAATAAGTATGGAAAAT
q canFam2.chr1                                              9999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999
i canFam2.chr1                     I 160 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184839 2731 -    359464 I
e hg18.chr6                        15871902 2402 - 170899992 I
e panTro2.chr6                     16390469 2400 - 173908612 I
e ponAbe2.chr6                     16170105 2523 - 174210431 I

a score=0.000000
s mm9.chr10                         3018932 339 + 129993255 gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaaaaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtgggggcatggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatccaaaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacccacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaatggcaccactcctggtccaagaatatacaaaccatgaca
e canFam2.chr1                     78070903   0 - 125616256 C
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184839 2731 -    359464 I
e hg18.chr6                        15871902 2402 - 170899992 I
e panTro2.chr6                     16390469 2400 - 173908612 I
e ponAbe2.chr6                     16170105 2523 - 174210431 I

a score=228.000000
s mm9.chr10                         3019271 106 + 129993255 GAGACCAAATG------------TGGCGCTCACG-TGAGGCCAGGAGTAAATCGCACACACAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG
s canFam2.chr1                     78070903 106 - 125616256 GAGGC-AAATGGAAAATGCCCCACGATGTCCAGGCTGTGTCCATGTGTGA--CGCACATGCTGTCC----------CACCTGCTTCTATTCACTTGACACACATAGGTCCCAAACCTGG
q canFam2.chr1                                              99999-99999999999999999999999999999999999999999999--99999999999999----------9999999999999999999999999999999999999999999
i canFam2.chr1                     C 0 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184839 2731 -    359464 I
e hg18.chr6                        15871902 2402 - 170899992 I
e panTro2.chr6                     16390469 2400 - 173908612 I
e ponAbe2.chr6                     16170105 2523 - 174210431 I

a score=10938.000000
s mm9.chr10                         3019377 88 + 129993255 CCCCAGCATTCTGGCAGACACAGTG-AAAAGAGACAGATGGTCACTAATAAAATCTGT-ATAAATTAG-ATCTCAGAGGATGGATGGACCA
s felCat3.scaffold_205680             72509 88 -    119354 CCCAAGTGTTCTGATAGCTAATGTGAAAAAGAAGCATGTGCCCACCAGTAAGCTTTGTGGTGAACTAGAATCTCAGAGGATG---GGACTC
q felCat3.scaffold_205680                                  9999999999999999999999999999999999999999999999999999999999999999999999999999999999---999999
i felCat3.scaffold_205680          N 0 C 0
s canFam2.chr1                     78071009 88 - 125616256 CCCAAGTGTTCTGATTGCCTCTGTGAAAAAGAAACATGGGCCCGCTAATAagatttgcaatgacctagaatctcagaggatg---ggactc
q canFam2.chr1                                             9999999999999999999999999999999999999999999999999999999999999999999999999999999999---999999
i canFam2.chr1                     C 0 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                   6649 3479 +    133105 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184839 2731 -    359464 I
e hg18.chr6                        15871902 2402 - 170899992 I
e panTro2.chr6                     16390469 2400 - 173908612 I
e ponAbe2.chr6                     16170105 2523 - 174210431 I

a score=36924.000000
s mm9.chr10                         3019465 47 + 129993255 AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT
s calJac1.Contig6394                  10128 47 +    133105 aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC
i calJac1.Contig6394               I 3479 C 0
s panTro2.chr6                     16392869 40 - 173908612 -------atattttgaaatggcttttcatgttattctgatgTGTTTT
q panTro2.chr6                                             -------9999999999999999999999999999999999999999
i panTro2.chr6                     I 2400 C 0
s hg18.chr6                        15874304 40 - 170899992 -------atattttgaaatggcttttcatgttattctgatgTGTTTT
i hg18.chr6                        I 2402 C 0
s canFam2.chr1                     78071097 44 - 125616256 ---aggtatatttaaaaatagctcttcatgttgttctaatgtgtgtt
q canFam2.chr1                                             ---99999999999999999999999999999999999999999999
i canFam2.chr1                     C 0 C 0
s felCat3.scaffold_205680             72597 43 -    119354 ---ACGTGTTTTTAAAAATAG-TTTTCATGTTGTTCTGATGTGTGTT
q felCat3.scaffold_205680                                  ---999999999999999999-9999999999999999999999999
i felCat3.scaffold_205680          C 0 I 193
e ornAna1.chr2                     14751195 5690 -  54797317 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184839 2731 -    359464 I
e ponAbe2.chr6                     16170105 2523 - 174210431 I

a score=20303.000000
s mm9.chr10                         3019512 92 + 129993255 TGCATCATTAAGACTAGAGTTCCT---------------TTCTGTCTT---TGCTTTCTTG--------ACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg
s calJac1.Contig6394                  10175 86 +    133105 --CCTCATGAAGGCCCAAGTTCCTAAA-----ACATTAATTCTCTTCC---TATTTCCTAGCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC----------------------
i calJac1.Contig6394               C 0 C 0
s panTro2.chr6                     16392909 93 - 173908612 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------
q panTro2.chr6                                             --9999999999999999999999999-----9999999999999999---9999999999------999999999999999999999999999999999999999999---------
i panTro2.chr6                     C 0 C 0
s hg18.chr6                        15874344 93 - 170899992 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------
i hg18.chr6                        C 0 C 0
s canFam2.chr1                     78071141 97 - 125616256 --CCTCATCTAAACCCAGGTTCTTACAGGCTTATATTTTTTCTTTCTTCAACCCTTCCTCA--------TCAGTGTCTTGCCTGCCAGTCATTCCTAC-----------TTTGTTCGG
q canFam2.chr1                                             --99999999999999999999999999999999999999999999999999999999999--------99999999999999999999999999999-----------999999999
i canFam2.chr1                     C 0 C 0
e felCat3.scaffold_205680             72640 193 -    119354 I
e ornAna1.chr2                     14751195 5690 -  54797317 I
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184839 2731 -    359464 I
e ponAbe2.chr6                     16170105 2523 - 174210431 I

a score=0.000000
s mm9.chr10                         3019604 98 + 129993255 tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctggaactcactttgtagaccagactggccttgaactcagaaa
e felCat3.scaffold_205680             72640 193 -    119354 I
e canFam2.chr1                     78071238  0 - 125616256 C
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                  10261  0 +    133105 C
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184839 2731 -    359464 I
e hg18.chr6                        15874437  0 - 170899992 C
e panTro2.chr6                     16393002  0 - 173908612 C
e ponAbe2.chr6                     16170105 2523 - 174210431 I

a score=45.000000
s mm9.chr10                         3019702 42 + 129993255 tctgcctgcctctgcctcccaag--------------------------------tcctgggattaaaggcgtg
s felCat3.scaffold_205680             72833 74 -    119354 tctgtctctctctctctctcaaaaataaacattaaaaaaaaCCAAACAAACAAACTCAAGTTCTTAAAGGTTTA
q felCat3.scaffold_205680                                  99999999999999999999999999999999999999999999999999999999999999999999999999
i felCat3.scaffold_205680          I 193 C 0
e canFam2.chr1                     78071238  0 - 125616256 C
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                  10261  0 +    133105 C
e tupBel1.scaffold_114895.1-498454   171764 2374 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      184839 2731 -    359464 I
e hg18.chr6                        15874437  0 - 170899992 C
e panTro2.chr6                     16393002  0 - 173908612 C
e ponAbe2.chr6                     16170105 2523 - 174210431 I

a score=-16865.000000
s mm9.chr10                         3019744 33 + 129993255 -----------------cgccaccactgccctgcCT------------TAAACTGCTCTTAA
s ponAbe2.chr6                     16172628 27 - 174210431 -----------------CGCCAGCAATTCC------------------CACATGGGTATTGG
i ponAbe2.chr6                     I 2523 C 0
s tupBel1.scaffold_114895.1-498454   174138  4 -    498454 ----------------------------------------------------------TTGA
q tupBel1.scaffold_114895.1-498454                         ----------------------------------------------------------9999
i tupBel1.scaffold_114895.1-498454 I 2374 C 0
s calJac1.Contig6394                  10261 13 +    133105 -------------------------------------------------ACATGGCTACTGG
i calJac1.Contig6394               C 0 C 0
s otoGar1.scaffold_334.1-359464      187570 11 -    359464 ---------------------------------------------------ATTGGTGTTGA
q otoGar1.scaffold_334.1-359464                            ---------------------------------------------------87784564678
i otoGar1.scaffold_334.1-359464    I 2731 C 0
s oryCun1.scaffold_156751               192 41 -      4726 --------------------CACCATTGTCTTGCCTGTC-TCAGGTCCCATAGGGGTGTTGA
q oryCun1.scaffold_156751                                  --------------------9999999999999999999-9999999999999999999999
i oryCun1.scaffold_156751          N 0 C 0
s felCat3.scaffold_205680             72907 62 -    119354 TGATTTCTCTTTCTCTTACTCATCAGTGTCTTGTCTTTCAGTCATTCCCACATTGGTGTAGA
q felCat3.scaffold_205680                                  99999999999999999999999999999999999999999999999999999999999999
i felCat3.scaffold_205680          C 0 C 0
e canFam2.chr1                     78071238  0 - 125616256 C
e ornAna1.chr2                     14751195 5690 -  54797317 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e hg18.chr6                        15874437  0 - 170899992 C
e panTro2.chr6                     16393002  0 - 173908612 C

a score=367532.000000
s mm9.chr10                         3019777 183 + 129993255 GGCAATGTCA-GGCTATGCGT------TCTAGACAGGGCACAAGAAAAGCTTTTAGCAGCAGAATAAACTTTT-AAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGA-TACAGT------GGAAAG-----A----------GGCCTTTGAGAAT---GCATGAGAGAATAT---TTCCTGTA------AGAGTTGAACAATTTAGAATTTACc
s oryCun1.scaffold_156751               233 193 -      4726 GGCAACATCATGACCTTATGT------TCTAA----GGGACAGGAAAAGCTTTTTCCAGTAGAATAAGCCTTT-AGAGGAAACTGCTTCCCTTGCTAGTAATCAAGTGTTCAAAGTGA-TACAACAAAGAAAAAAAA-----A----------GCCTTTTGGGAAT-CAGGATGGAATAATATTACTTCCCCTATTTCTCAGAGCTAAATAGTTTAGGATT----
q oryCun1.scaffold_156751                                   999999999999999999999------99999----9999999999989999999998999999999999999-99999999999999999999999999999999999998989999-999899799999999999-----9----------9997999999998-978998999999999999999978999999979689999999999999999979----
i oryCun1.scaffold_156751          C 0 I 37
s hg18.chr6                        15874437 190 - 170899992 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGGAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A----------TTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----
i hg18.chr6                        C 0 C 0
s panTro2.chr6                     16393002 191 - 173908612 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----
q panTro2.chr6                                              9999999999999-9999999------9999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999-99999-------999999-----9---------999999999999999999999999999999999999999999999999999999999999999999999----
i panTro2.chr6                     C 0 C 0
s ponAbe2.chr6                     16172655 190 - 174210431 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCGGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTCTTTTTGAGAATGCAGCACAGAATAATATTATTTCCCTTATTTCT-AGAGTTAAACAATTTAGGATT----
i ponAbe2.chr6                     C 0 I 21
s calJac1.Contig6394                  10274 187 +    133105 GGCAACACCGTGA-TACATAT------CCGAGATAAAGTACAGGAAAAGC-TTTTGCAGTGGACGAAAATGTT-GAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAA-----------------GTTTTTTGAGAATGTGGGATAGAATAATATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT----
i calJac1.Contig6394               C 0 I 21
s otoGar1.scaffold_334.1-359464      187581 197 -    359464 GGCAACGCCGTGA-TCCTTGCTGTAGATAAAGACAAAGTGCAGGAAAAGCCCTTTACGGTAGAATAAAAGGTT-AAAGGAAATTGCTTTTCTTGATAGCAATCAGGTGACCAAAGTGATTATAA-------AGAAAA-----A----------ATGTTTTGAGAATGCTGGAAAGAATAATTTTATCCACCCTCCATTTCAGAGTTAAATAATTCAGGATT----
q otoGar1.scaffold_334.1-359464                             5466765345564-89977768969797886996999557766667768677897764536465578775526-67697777697779896767576676677696675376877786786858-------478887-----7----------56858859779666569356677477759968759378767656876769557597655596536566----
i otoGar1.scaffold_334.1-359464    C 0 I 358
s tupBel1.scaffold_114895.1-498454   174142 196 -    498454 GGCAATGTCATGA----ATGT------TCTAGATAAAGTACAGGAAAAGCTTTTTGCAGTAGGATAAACTTTT-AAAGGAAATTGCCTTCCTTGACAGCAATCAGGTGACCAAAGTCATACTGA-------AAAAAA-----AAACAAAAACAAACTTTTGTGGATGCAGTATAGAAGCATATTATTTTCCCTATGTCT--AAGTTAAATAACTTGGGCTT----
q tupBel1.scaffold_114895.1-498454                          9999999999999----9999------9999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999-------999999-----999999999999999999999999999999999999999999999999999999999--99999999999999999999----
i tupBel1.scaffold_114895.1-498454 C 0 I 623
s felCat3.scaffold_205680             72969 186 -    119354 GACATC---ATAA-AGTACAT------TCTAGATAAAGTGCAGGAAAAGCATTTTG-AGTAGAATAAAATGTT-GTAGGAAATTGCTTTCTTCAAGAGACATTAGGTGATTAAAGTAA-TATAA-------AGGGAA-----T----------TTTTTTTGAGAATACAGGATACAATAATATTATTTCCCCTACATCTAAGAGttaaataatttaaaatt----
q felCat3.scaffold_205680                                   999999---9999-9999999------99999999999999999999999999999-9999999999999999-99999999999999999999999999999999999999999999-99999-------999999-----9----------99999999999999999999999999999999999999999999999999999999999999999999----
i felCat3.scaffold_205680          C 0 I 27
s canFam2.chr1                     78071238 193 - 125616256 ------ATCATGA-TGTAAAT------TCCGGGTAAAGTACAACAAAAGGATTTTG-AACAGGATAAAATGTTAATAGGAAATTACTTTCTTTGAGAGCAATCAGGTGATTGAAGGAA-TATAA-------AGGGAAAAAACA----------AAGTTCAGTGAATCCAAGTTAGAATAATATTGTTTCCCTTACTTCTAAGAGttaaataatttaaaatttaat
q canFam2.chr1                                              ------9999999-9999999------99999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999-99999-------999999999999----------999999999999999999999999999999999999999999999999999999999999999999999999
i canFam2.chr1                     C 0 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I

a score=0.000000
s mm9.chr10                         3019960 757 + 129993255 actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacagttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgagggatgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaatgcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactcaggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttgctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgcagatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggatggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccggggactaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagcagaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagagaaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccctcttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggagggagaacatttgaaatgtaaataaataaaataataaaaaa
e felCat3.scaffold_205680             73155  27 -    119354 I
e canFam2.chr1                     78071431   0 - 125616256 C
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                  10461  21 +    133105 I
e tupBel1.scaffold_114895.1-498454   174338 623 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      187778 358 -    359464 I
e hg18.chr6                        15874627   0 - 170899992 C
e panTro2.chr6                     16393193   0 - 173908612 C
e ponAbe2.chr6                     16172845  21 - 174210431 I
e oryCun1.scaffold_156751               426  37 -      4726 I

a score=8951.000000
s mm9.chr10                         3020717 44 + 129993255 TGTCAAACATGCATAAAGATATACT-GAGGAGCCCATGAATTTTA
s canFam2.chr1                     78071431 33 - 125616256 tGTT------------TAACATAATAGAGGGGCCCATGAATTTTA
q canFam2.chr1                                             9999------------99999999999999999999999999999
i canFam2.chr1                     C 0 I 9
s panTro2.chr6                     16393193 38 - 173908612 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA
q panTro2.chr6                                             ----999999---99999999999999999999999999999999
i panTro2.chr6                     C 0 I 11
s hg18.chr6                        15874627 38 - 170899992 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA
i hg18.chr6                        C 0 I 11
e felCat3.scaffold_205680             73155 27 -    119354 I
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                  10461 21 +    133105 I
e tupBel1.scaffold_114895.1-498454   174338 623 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      187778 358 -    359464 I
e ponAbe2.chr6                     16172845 21 - 174210431 I
e oryCun1.scaffold_156751               426 37 -      4726 I

a score=0.000000
s mm9.chr10                         3020761 157 + 129993255 TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaagattttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaagtgctgagatcatacctctgcaccatcctgcccACCT
e felCat3.scaffold_205680             73155  27 -    119354 I
e canFam2.chr1                     78071464   9 - 125616256 I
e ornAna1.chr2                     14751195 5690 -  54797317 I
e calJac1.Contig6394                  10461  21 +    133105 I
e tupBel1.scaffold_114895.1-498454   174338 623 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              8048 1372 -     10026 I
e otoGar1.scaffold_334.1-359464      187778 358 -    359464 I
e hg18.chr6                        15874665  11 - 170899992 I
e panTro2.chr6                     16393231  11 - 173908612 I
e ponAbe2.chr6                     16172845  21 - 174210431 I
e oryCun1.scaffold_156751               426  37 -      4726 I

a score=85471.000000
s mm9.chr10                         3020918  96 + 129993255 GAGGTTTGTGACTTTTAATA----------CTGATTGTTATCTAACATCACAGAATTCTCAGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA
s hg18.chr6                        15874676  73 - 170899992 ---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA
i hg18.chr6                        I 11 C 0
s panTro2.chr6                     16393242  73 - 173908612 ---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA
q panTro2.chr6                                              ---------------------------------9999999999999999999999999999999999999999999999999999999999999999999999999
i panTro2.chr6                     I 11 C 0
s canFam2.chr1                     78071473  75 - 125616256 --------------------------TAATAAAATAATTCTGTACCATTATGAAGTTCTCAGCTCTTAAGGAAAAA-----GTGATTTGTTAATTACTTAGGACAA
q canFam2.chr1                                              --------------------------99999999999999999999999999999999999999999999999999-----9999999999999999999999999
i canFam2.chr1                     I 9 C 0
s felCat3.scaffold_205680             73182  76 -    119354 ---GTCCATGAATTTTAATGGTGAAGTAATGAAATAATTCTTTAATATCAC----------------------AAA-----GTAATTTATTAATTATTTAGGACAA
q felCat3.scaffold_205680                                   ---999989999999999999999999999999999999999999999999----------------------999-----9999999999999999999999769
i felCat3.scaffold_205680          I 27 C 0
s cavPor2.scaffold_216473              9420  82 -     10026 GAGTTCTGCAAATtttaata----------ggaaaagaagatTAATATTACAAAGTTTTCAGTTCTGATGGAAaaa----------gtgtgatttttttaaa----
q cavPor2.scaffold_216473                                   99679966799668566465----------8567828838346568788268865663676558367765776667----------6965686997776684----
i cavPor2.scaffold_216473          I 1372 I 28
s oryCun1.scaffold_156751               463 102 -      4726 -AGATCCATGAATTTTAATA---AAGCAATGAGATAATTATTTAATGTTGGAAAATCCTCAAGTCTTAAGGAAAAAAGTGTTTGACTTGTTAATGACTTGGGATGA
q oryCun1.scaffold_156751                                   -9999997999999999999---99999999999999999999999999999999998677999969999999999999999999999999999999999999999
i oryCun1.scaffold_156751          I 37 C 0
s calJac1.Contig6394                  10482 100 +    133105 GGGGTCCATGAATTTTAATA-----GTAACAAAATGGTTATTCAATATTGCAAAATCCTCAGC-TTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA
i calJac1.Contig6394               I 21 C 0
s ponAbe2.chr6                     16172866 101 - 174210431 GGGGTCCATGAATTTTAATA-----GTAATAAAATGGTTATTTAATATTGCAAAATCCTCAGCTTTTAAGGAAAAACGTGTTTGACTTATTAATTATTTAGGACAA
i ponAbe2.chr6                     I 21 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I
e tupBel1.scaffold_114895.1-498454   174338 623 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e otoGar1.scaffold_334.1-359464      187778 358 -    359464 I

a score=105724.000000
s mm9.chr10                         3021014 40 + 129993255 ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG
s oryCun1.scaffold_156751               565 40 -      4726 ATCTTGATGAAGTCATTCCAACTTGGATGATTTAGGAATT
q oryCun1.scaffold_156751                                  9999999999999969999699999999999999999999
i oryCun1.scaffold_156751          C 0 C 0
s otoGar1.scaffold_334.1-359464      188136 40 -    359464 ATCTTGGTGAAGTTATTCCAATTTATGTGATTTAGGAATG
q otoGar1.scaffold_334.1-359464                            9999999999999999999999999999999999999999
i otoGar1.scaffold_334.1-359464    I 358 C 0
s calJac1.Contig6394                  10582 40 +    133105 ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG
i calJac1.Contig6394               C 0 C 0
s hg18.chr6                        15874749 40 - 170899992 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG
i hg18.chr6                        C 0 C 0
s panTro2.chr6                     16393315 40 - 173908612 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG
q panTro2.chr6                                             9999999999999999999999999999999999999999
i panTro2.chr6                     C 0 C 0
s ponAbe2.chr6                     16172967 40 - 174210431 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG
i ponAbe2.chr6                     C 0 C 0
s canFam2.chr1                     78071548 40 - 125616256 ATCTCAGTGAAGTCATTCTGACTCGCATGATTTAGGAATG
q canFam2.chr1                                             9999999999999999999999999999999999999999
i canFam2.chr1                     C 0 C 0
s felCat3.scaffold_205680             73258 40 -    119354 ATCTCAGTGAAGTTATTCTGACTTGCATGATTTAGGTATG
q felCat3.scaffold_205680                                  9999989999989988999997999979997996167779
i felCat3.scaffold_205680          C 0 C 0
s dasNov1.scaffold_56749               3116 40 -     10470 ACATCAGTGAAATCATTCCGACTCGTATGACTGAGCGATG
q dasNov1.scaffold_56749                                   9759855999977756667495765475885678385647
i dasNov1.scaffold_56749           N 0 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I
e tupBel1.scaffold_114895.1-498454   174338 623 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I
e cavPor2.scaffold_216473              9502 28 -     10026 I

a score=115790.000000
s mm9.chr10                         3021054 50 + 129993255 CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAG--------------------GACTTACATGCAG
s cavPor2.scaffold_216473              9530 38 -     10026 CTCATTTGGGAGTTCAGAGTT--------GCTATAAA--------------------TACTTGTGA----
q cavPor2.scaffold_216473                                  788777667898846665666--------98766677--------------------876665669----
i cavPor2.scaffold_216473          I 28 C 0
s oryCun1.scaffold_156751               605 69 -      4726 CTAATTTGGGCTCTTACATTTTATAACTGCCTAATGGAGTCTTCTTTTTTCCT-CCTTAATTACACGTAT
q oryCun1.scaffold_156751                                  99999999999997999799999999999999999999999799799999997-9979999999495999
i oryCun1.scaffold_156751          C 0 C 0
s otoGar1.scaffold_334.1-359464      188176 69 -    359464 CTAACTTGGGGACACAGG-TTCATAAAGGCTTAATGGAGCCCACTGGTCCCTTCCCCAGACTCTATGTAC
q otoGar1.scaffold_334.1-359464                            999999999999999999-999999999999999999998999999689999999999999999999999
i otoGar1.scaffold_334.1-359464    C 0 C 0
s calJac1.Contig6394                  10622 70 +    133105 CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGCCTATATGTAT
i calJac1.Contig6394               C 0 C 0
s hg18.chr6                        15874789 70 - 170899992 ACAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCCTTCCTTCCCTAGACTATATGTAT
i hg18.chr6                        C 0 C 0
s panTro2.chr6                     16393355 70 - 173908612 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT
q panTro2.chr6                                             9999999999999999999999999999999999999999999999999999999999999999999999
i panTro2.chr6                     C 0 C 0
s ponAbe2.chr6                     16173007 70 - 174210431 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT
i ponAbe2.chr6                     C 0 C 0
s canFam2.chr1                     78071588 70 - 125616256 CTAATTTGGTGACTCAAATTTCATAATTGCTTAATGAAAGCTGATGTTTTCTTCCCTACACCATATGTAT
q canFam2.chr1                                             9999999999999999999999999999999999999999999999999999999999999999999999
i canFam2.chr1                     C 0 C 0
s felCat3.scaffold_205680             73298 70 -    119354 CTAATTTGGTGACTTGAATTTCATAATTGCTTAAGGAAGCCTGCTGTTTCCTTCCCAAGACTATATGCAT
q felCat3.scaffold_205680                                  9769999999975699868977669777966666596959759669595666758736585676666655
i felCat3.scaffold_205680          C 0 C 0
s dasNov1.scaffold_56749               3156 70 -     10470 CTAATTGGGGGACTCACATTTTAAAATTGCTAACCGAAGCCTGCTGTTTTCTTCTCTAGACTATAAGTAT
q dasNov1.scaffold_56749                                   5556576999664654656985688667655565647767537567688856666555556565555656
i dasNov1.scaffold_56749           C 0 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I
e tupBel1.scaffold_114895.1-498454   174338 623 -    498454 I
e echTel1.scaffold_288249             87661 7564 +    100002 I

a score=44222.000000
s mm9.chr10                         3021104 32 + 129993255 CTGTTAGTGCTGTTTT---AATGTACCTCGCAGTA
s cavPor2.scaffold_216473              9568 27 -     10026 -----ATTACTTTCTT---AATGTAAATTTTTATA
q cavPor2.scaffold_216473                                  -----55455868746---7957999989884575
i cavPor2.scaffold_216473          C 0 C 0
s oryCun1.scaffold_156751               674 30 -      4726 TTGCTAGTA--TTCTC---AATGTAATATTTTATA
q oryCun1.scaffold_156751                                  999979999--96665---6999999999999999
i oryCun1.scaffold_156751          C 0 C 0
s otoGar1.scaffold_334.1-359464      188245 32 -    359464 TTGCTGGTGTTCCCTT---AATATAATGTTTTATA
q otoGar1.scaffold_334.1-359464                            9999999999999999---9999999999999999
i otoGar1.scaffold_334.1-359464    C 0 C 0
s calJac1.Contig6394                  10692 30 +    133105 TTACTCGTG--CCCTT---AATATAGCATTTTATA
i calJac1.Contig6394               C 0 C 0
s hg18.chr6                        15874859 30 - 170899992 TTGCTGGTA--CTCTT---AATATCACATTTTATA
i hg18.chr6                        C 0 C 0
s panTro2.chr6                     16393425 30 - 173908612 TTGCTGGTA--CTCTT---AATATCACATTTTATA
q panTro2.chr6                                             999999999--99999---9999999999999999
i panTro2.chr6                     C 0 C 0
s ponAbe2.chr6                     16173077 30 - 174210431 TTGCTGGTG--CTCTT---AATATAACATTTTATA
i ponAbe2.chr6                     C 0 C 0
s canFam2.chr1                     78071658 25 - 125616256 TTGCTGGTGCTCTCAA---AATGTAGCA-------
q canFam2.chr1                                             9999999999999999---999999999-------
i canFam2.chr1                     C 0 I 196
s felCat3.scaffold_205680             73368 25 -    119354 TTGCTGGTGCTCTCAA---AATATAACA-------
q felCat3.scaffold_205680                                  8677668566555658---876555655-------
i felCat3.scaffold_205680          C 0 I 6
s dasNov1.scaffold_56749               3226 33 -     10470 TTGCTGGTG--ATCTGATTAATGTAACATTTTATG
q dasNov1.scaffold_56749                                   856647736--775356546747663745776545
i dasNov1.scaffold_56749           C 0 C 0
s echTel1.scaffold_288249             95225 21 +    100002 CTGTTAATG--CTCTG------------TTTTATG
q echTel1.scaffold_288249                                  999999999--99999------------9999999
i echTel1.scaffold_288249          I 7564 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I
e tupBel1.scaffold_114895.1-498454   174338 623 -    498454 I

a score=43757.000000
s mm9.chr10                         3021136 44 + 129993255 AGGCAAATGAGGTGATAAGA-------TTGTGTT-----TAC----TCCCTCTGTGC----------TTG
s cavPor2.scaffold_216473              9595 43 -     10026 AG-CAGATGAGATAACAGTG-------ATATATT-----cat----tctctgtgtgt----------atg
q cavPor2.scaffold_216473                                  49-96766988786798889-------8679566-----756----66896967579----------888
i cavPor2.scaffold_216473          C 0 C 0
s oryCun1.scaffold_156751               704 42 -      4726 AAGCAAATGAGGTGATGAGG---------GCATC-----TAT----TTCTTATTTGT----------GTG
q oryCun1.scaffold_156751                                  99998999999999999999---------99999-----999----99999999999----------999
i oryCun1.scaffold_156751          C 0 C 0
s otoGar1.scaffold_334.1-359464      188277 45 -    359464 AAACAAATGAGATCACA-GG-------ACATATG-----TA--CTTGTCCCCCACGT----------GTG
q otoGar1.scaffold_334.1-359464                            99999999999999999-99-------9999999-----99--99939999999999----------999
i otoGar1.scaffold_334.1-359464    C 0 I 15
s calJac1.Contig6394                  10722 45 +    133105 AAGCAAATGAGATCACA----------GCACATG-----TATATTTTTTCTCCGTGT----------GTG
i calJac1.Contig6394               C 0 I 15
s hg18.chr6                        15874889 47 - 170899992 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG
i hg18.chr6                        C 0 I 15
s panTro2.chr6                     16393455 47 - 173908612 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG
q panTro2.chr6                                             99999999999999999999-------9999999-----999-99999999999999----------999
i panTro2.chr6                     C 0 I 15
s ponAbe2.chr6                     16173107 47 - 174210431 AAACAAATGAGATCACAAGG-------GCATATG-----TAT-TTTTTTCTCTGTGT----------GTG
i ponAbe2.chr6                     C 0 I 15
s eriEur1.scaffold_266115               358 65 +      4589 taaataataagataagatgaaagCATAGCATGTA-----TTTTCTtgccctctccttctctgtctctgtc
q eriEur1.scaffold_266115                                  9999999999999999999999999999999999-----9999999999999999999999999999999
i eriEur1.scaffold_266115          N 0 I 9
s canFam2.chr1                     78071879 51 - 125616256 tAGAAAATGAGATACC-----------GTGTGTA-----TATGCTTTCTCTCTGTGT---GGGGTCTGTG
q canFam2.chr1                                             9999999999999999-----------9999999-----999999999999999999---9999999999
i canFam2.chr1                     I 196 I 9
s felCat3.scaffold_205680             73399 51 -    119354 AAGCAAATGAGATAAG-----------ACACGTG-----TATTCTTCCTCTCTGTGT---GGTGTCTGTG
q felCat3.scaffold_205680                                  9755596656454353-----------5346324-----243451535354422233---3635339999
i felCat3.scaffold_205680          I 6 I 9
s dasNov1.scaffold_56749               3259 46 -     10470 AGGAAAGTGAGAGGACCAGG-------GCAAATA-----AATATTCTTTCTCTGTGT----------A--
q dasNov1.scaffold_56749                                   55569764556657658568-------6768555-----858686457859535656----------5--
i dasNov1.scaffold_56749           C 0 C 0
s echTel1.scaffold_288249             95246 51 +    100002 AAGAAGGTGAGATGACAAGG-------GTGTATAGATAGGATATTCTTGCTTTGGGT----------G--
q echTel1.scaffold_288249                                  99999999999999999999-------999999999999999999999999999999----------9--
i echTel1.scaffold_288249          C 0 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I
e tupBel1.scaffold_114895.1-498454   174338 623 -    498454 I

a score=32886.000000
s mm9.chr10                         3021180 24 + 129993255 -------------------TCCC-------AGAGAGTCTGA-TAGGAGGAG
s cavPor2.scaffold_216473              9638 32 -     10026 -------------------tgcctTTGTATAGTGGCTCTGAGTATAAAGTA
q cavPor2.scaffold_216473                                  -------------------67576649966655666885655548785776
i cavPor2.scaffold_216473          C 0 C 0
s oryCun1.scaffold_156751               746 27 -      4726 -------------------TGCCTGTGTATAGCATTTCTGAATATA-----
q oryCun1.scaffold_156751                                  -------------------999999999999999999999999999-----
i oryCun1.scaffold_156751          C 0 C 0
s ponAbe2.chr6                     16173169 25 - 174210431 -----------------------TCTG---AGTGTGTATGAATATGAAGTA
i ponAbe2.chr6                     I 15 C 0
s panTro2.chr6                     16393517 25 - 173908612 -----------------------TCTG---AGTATGTATGAATATGAAGTA
q panTro2.chr6                                             -----------------------9999---999999999999999999999
i panTro2.chr6                     I 15 C 0
s hg18.chr6                        15874951 25 - 170899992 -----------------------TCTG---AGTATGTATGAATATGAAGTA
i hg18.chr6                        I 15 C 0
s calJac1.Contig6394                  10782 25 +    133105 -----------------------TCTG---AGTATGTCTGAATATGAAGTG
i calJac1.Contig6394               I 15 C 0
s otoGar1.scaffold_334.1-359464      188337 25 -    359464 -----------------------TCTA---AGTGTGTCTGAACATGATGTG
q otoGar1.scaffold_334.1-359464                            -----------------------9999---999999999999999999999
i otoGar1.scaffold_334.1-359464    I 15 C 0
s tupBel1.scaffold_114895.1-498454   174961 25 -    498454 -----------------------TCTC---TGAGTGTCTGAACTTGAGGTA
q tupBel1.scaffold_114895.1-498454                         -----------------------9999---999999999999999999999
i tupBel1.scaffold_114895.1-498454 I 623 C 0
s eriEur1.scaffold_266115               432 19 +      4589 -----------------------TCTC---AGTGTGTCTGACCAG------
q eriEur1.scaffold_266115                                  -----------------------9999---999999999999999------
i eriEur1.scaffold_266115          I 9 C 0
s canFam2.chr1                     78071939 25 - 125616256 -----------------------TCTG---AGTGTGTCTGAATGTGAGGTA
q canFam2.chr1                                             -----------------------9999---999999999999999999999
i canFam2.chr1                     I 9 C 0
s felCat3.scaffold_205680             73459 25 -    119354 -----------------------TCTG---AGTGTTCCTGAATGTGAGGTG
q felCat3.scaffold_205680                                  -----------------------9999---999999999999999999999
i felCat3.scaffold_205680          I 9 C 0
s dasNov1.scaffold_56749               3305 47 -     10470 T-TGTGTGCCTTTGCGGAGCATTTCTG---AGCGTGTCTGAACTTGAGGTA
q dasNov1.scaffold_56749                                   7-3659557766555777595699547---965955937797755656587
i dasNov1.scaffold_56749           C 0 C 0
s echTel1.scaffold_288249             95297 48 +    100002 TGCCCAGGACTGCGCATGGTATTTCTT---GGTGTGTCTGAAGGTGAGATA
q echTel1.scaffold_288249                                  999999999999999999999999999---999999999999999999999
i echTel1.scaffold_288249          C 0 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I

a score=309116.000000
s mm9.chr10                         3021204 71 + 129993255 TGCACTGGTTTTCC-TGCAGTGGTTCTCAGTAATAGGAAGACA-ACAGAATTTGAAGTATCCGGCTTTGGCCA
s echTel1.scaffold_288249             95345 73 +    100002 GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAAATATTCTTGGCTA
q echTel1.scaffold_288249                                  9999999999999999999999999999999999999999999999999999999999999999999999999
i echTel1.scaffold_288249          C 0 C 0
s dasNov1.scaffold_56749               3352 70 -     10470 TGCATTGATTTTCAGTGAGGGAAATCACAC---TAAGAGAGCATTTTGAATTTATAATAAATGCTCTTGGCTA
q dasNov1.scaffold_56749                                   579663579997957596666783594865---8458696597898258979678997999677999997699
i dasNov1.scaffold_56749           C 0 C 0
s felCat3.scaffold_205680             73484 72 -    119354 TGCATTGATTTTCA-TGCATTGATTCACATGAATAGGAATGCATTTTGAAATTATAGCAAATGTTTTTGGCTG
q felCat3.scaffold_205680                                  99999999999999-9999999999999999999999999999999999999999999999999999999999
i felCat3.scaffold_205680          C 0 C 0
s canFam2.chr1                     78071964 71 - 125616256 TGCATTAATTTTCA-TGCGTTGATTCACATGAATAGGAATACA-TTTGAATTTATAGGAAATGCTTTTGGCTG
q canFam2.chr1                                             99999999999999-9999999999999999999999999999-99999999999999999999999999999
i canFam2.chr1                     C 0 C 0
s eriEur1.scaffold_266115               451 70 +      4589 -GCACTGATTCTCG-AGGGTTGATTCCCAGTAAGAGGAAACTG-CGTGAGTTTACAGTACATGGGCTTGGCTG
q eriEur1.scaffold_266115                                  -9999999999999-9999999999999999999999999999-99999999999999999999999999799
i eriEur1.scaffold_266115          C 0 C 0
s sorAra1.scaffold_2476                3312 70 -      4997 TGCATTGATTTTTA-AGTATTGATTCACATGAAAAGGAAAGCA-CTTCAATTTATGATAAAT-GATTTGGCCA
q sorAra1.scaffold_2476                                    89999999999989-9999999999999999999999999999-999999999799999999-9999999999
i sorAra1.scaffold_2476            N 0 C 0
s tupBel1.scaffold_114895.1-498454   174986 71 -    498454 TGCATTGAATTCCA-TGTGTTATGTCACATTAATAGGAAACGA-TTCTAATTGATAGGAAATGCTTCTGACCA
q tupBel1.scaffold_114895.1-498454                         99999899899999-9999999999999999999999999999-99999999999999999999999999997
i tupBel1.scaffold_114895.1-498454 C 0 C 0
s otoGar1.scaffold_334.1-359464      188362 67 -    359464 TG----GATTTTTA-CACATTGATTCACCTTAACGGGAAAACA-TGTGAATTTGTAGGAAAGGCATTTGGCCA
q otoGar1.scaffold_334.1-359464                            88----99999999-9899999899943848888999999999-66359999569699999923799351281
i otoGar1.scaffold_334.1-359464    C 0 I 6280
s calJac1.Contig6394                  10807 71 +    133105 TGCATTGGTTTTTA-TGCCTTGATTCACATGAATAGGAAAACG-TTTGAATTTATAGGAAATGGTTTTGGCCA
i calJac1.Contig6394               C 0 C 0
s hg18.chr6                        15874976 71 - 170899992 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAATG-TTTGAATTTATAGTAAATGGTTTTGGCCA
i hg18.chr6                        C 0 C 0
s panTro2.chr6                     16393542 71 - 173908612 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAACA-TTTGAATTTATAGTAAATGGTTTTGGCCA
q panTro2.chr6                                             99999999999999-9999999999999999999999999999-99999999999999999999999999999
i panTro2.chr6                     C 0 C 0
s ponAbe2.chr6                     16173194 71 - 174210431 TGCTTTGATTTTTA-TGCATTGATTTACATGGATAGGAAAACG-TTTGAATTTATAGTAAATGGTTTTGGCCA
i ponAbe2.chr6                     C 0 C 0
s oryCun1.scaffold_156751               773 65 -      4726 ------TCTTTACA-TACTTTGATTTACATCGACGGGAAAACA-TTTGCATTTATAGCAATGGCTTTTGGTCA
q oryCun1.scaffold_156751                                  ------99999994-9999999999999899999999999999-99999999999999899999999999999
i oryCun1.scaffold_156751          C 0 C 0
s cavPor2.scaffold_216473              9670 71 -     10026 GGCATTGATTTCCA-TGCATTAATTCACATTAATAGGAAAACA-GTCCAATTTATAGTAAATGGTTTTGGCCA
q cavPor2.scaffold_216473                                  77888768786695-3886758796446556688656665478-68687676669688688666687574686
i cavPor2.scaffold_216473          C 0 C 0
e ornAna1.chr2                     14751195 5690 -  54797317 I

a score=891219.000000
s mm9.chr10                         3021275 146 + 129993255 CTTTCTCTGACATTACTGTAACTGAAGTAGCTC-AGAAGCACAAAAGGTCACATCATGCATCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGC-----------------------CACGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG
s cavPor2.scaffold_216473              9741 169 -     10026 CCTTTGCTGATGTTACTGTAAGCGAACTAGCTG-AAAAGCACAAAAGGTCATGTCAGGCATTTATGCAAAATTTACTAGTTCCGTTCATAAAGGCACCTCGCATTTTATTACTTAGTTCATGTGTCTCGCAGGAAATCCAGTCACGCCATCATTTCCTTCCATATTTCAA
q cavPor2.scaffold_216473                                   668536545547664539866666666666668-8787886799997788875886655536666688786768476688854689668876558688874778656675665668746666788474786888875667457786687996867886548798845555
i cavPor2.scaffold_216473          C 0 C 0
s oryCun1.scaffold_156751               838 158 -      4726 TCGTCTCTGATGTTACTCTAGCTGAAAGCGCTC-CAAAGCACAAAAGGCCATGGCAGGCATTTATGTCAAATGTACTAGCACTGTTTATAACAGCACCTTGTGTTGTATTACTTTGTTCA-----------GGAAATCCAGTCACGCCGCGATTTCCTTCCACATTTCAA
q oryCun1.scaffold_156751                                   999999879999999999999999999997999-99999799999999898999999988999999988999999989996999999999988897996999999999999979999987-----------899998987999799998998999999999777999899
i oryCun1.scaffold_156751          C 0 C 0
s ponAbe2.chr6                     16173265 169 - 174210431 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTCATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTATCTTTCAGGAAATTCAGTCACGCCATCATTTCCTTCCATATTTCAT
i ponAbe2.chr6                     C 0 C 0
s panTro2.chr6                     16393613 169 - 173908612 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT
q panTro2.chr6                                              999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i panTro2.chr6                     C 0 C 0
s hg18.chr6                        15875047 169 - 170899992 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTATCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT
i hg18.chr6                        C 0 C 0
s calJac1.Contig6394                  10878 169 +    133105 CCTTCTCTGATATTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGCAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT
i calJac1.Contig6394               C 0 C 0
s tupBel1.scaffold_114895.1-498454   175057 156 -    498454 TCCTCTCAGATGTTCCTGTAACCAAAGTAGCTC-AGAAGCACAAAAGGTCATGCCAGGCATTGATGTAAA-------------GTTTCTGAAGGCATCTCGTGTTTTATTACTTTGTTCATGTGCCTTACAGGAAATCCAGTCGGGCCATCATTTCCTTCCATATCTCAG
q tupBel1.scaffold_114895.1-498454                          999999999999999999999999999999999-999999999999999999999999999999999999-------------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i tupBel1.scaffold_114895.1-498454 C 0 C 0
s sorAra1.scaffold_2476                3382 170 -      4997 CCTTCTCTGATGTTACTGTAACTGAGGTAGCTCAAAAAGCACAAAAGGTCATGTCAGGCATTGATGTAAAATATACCAGTGCTGTTTATAAAGACCCCTTGCATATAATGTTGTTGATCATGAACTTTTCCGGAAATCCTGTAATCTCATCATTTCCTCCCATATTCCAG
q sorAra1.scaffold_2476                                     99999999999999997999999999999999999999999999999999999999999999999999999999999979999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i sorAra1.scaffold_2476            C 0 C 0
s eriEur1.scaffold_266115               521 156 +      4589 CCTTCTCTGATCTGACTGTAACCGAAGTCTCTC-GAAAGCACAAAAGCTCACGGCAGGCCTTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgca------gatgtctctcacgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCC-------TTCCTG
q eriEur1.scaffold_266115                                   999999999999999999999999999999999-999999999999999999999999799999999999999999999998987999899999999999999------999999999999999999999999999999999999999999999998-------999989
i eriEur1.scaffold_266115          C 0 C 0
s canFam2.chr1                     78072035 168 - 125616256 CTGTCTCTGATGTTACTGTAACTGAAGTAGCTC-AAAAGCACAAAAGGTCATGTCAGGC-TTTATGTAAAATTTACTAGAGCTGTTTATAAAGGCACCTCGTGTAATATTGCTTTGTTCATGTACTTTACAGGAAATCCTGTCATCCTGTTACTTCCTTCCATATTTCAA
q canFam2.chr1                                              999999999999999999999999999999999-9999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i canFam2.chr1                     C 0 C 0
s felCat3.scaffold_205680             73556 169 -    119354 CTGTCTCTGATGTTACTGTAACTGAAATAGTTC-AAAAGCACAAAAGGTGATGTCAGGCATTTATGTAAAATTTACTAGTGCTGTTTATAAAGGTACCTTGTGTATTATTGCTTTGTTCATGCACTTTATAGGAAATCCTGTCATCCTGTCATTTCCTTCCATAGTTCAG
q felCat3.scaffold_205680                                   999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i felCat3.scaffold_205680          C 0 I 34165
s dasNov1.scaffold_56749               3422 168 -     10470 CCTTCTCTGATGTTACTGTAACTGAAGAGGCTC-AAAAGCACAAAAGGTCATGTCGGGCATTGATGTAAAATTTACTAGTGCTG-TTTATAAAGGACCTTGTGTTCTATTACTTTTTCTATCCCCCTTACAGGAAATCCTGTCATACCATCATTTCCTTCCATAAGTCAC
q dasNov1.scaffold_56749                                    989999999999999937699999999999999-79999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i dasNov1.scaffold_56749           C 0 C 0
s echTel1.scaffold_288249             95418 169 +    100002 CCATCTCTGATATTACTGTAATGGAATTACTTT-GAAAGCACAAAAGGTCAGGACAAGCGTGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCATTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG
q echTel1.scaffold_288249                                   999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
i echTel1.scaffold_288249          C 0 C 0
s ornAna1.chr2                     14756885 169 -  54797317 CCACCTCTGATATCACTGTAACTCAGCTACCCA-GAAGATAGGAAAGGTCATATCAGCCAATCATGTGCAACTTAATAGCCCTGTTCATAAAGCTGCTTTGTGTTTTATGAGGCTATTCATTCACCTTAGGGGAAATCCTGTCAAGCCATCATTTCCTTCCATATCTTCA
i ornAna1.chr2                     I 5690 C 0
e otoGar1.scaffold_334.1-359464      188429 6280 -    359464 I

a score=30254.000000
s mm9.chr10                         3021421 44 + 129993255 -ACGTTGCTCATTGT-----AATTGAAGCATTTATTACCAA--------TG--------------CCTTCCC
s cavPor2.scaffold_216473              9910 47 -     10026 -CTGTTCCTTGTTACA----AATAAAAGTATGTTTTGCTGA--------CG-------G-----CCCCTCTG
q cavPor2.scaffold_216473                                  -476754645667788----868678677444665235455--------76-------4-----36669356
i cavPor2.scaffold_216473          C 0 C 0
s oryCun1.scaffold_156751               996 37 -      4726 -TGGTTCCTCATTATG----GATTAAAGCATTCACTGCTAA--------T----------------------
q oryCun1.scaffold_156751                                  -999999999899999----887999999999999999999--------9----------------------
i oryCun1.scaffold_156751          C 0 I 2345
s ponAbe2.chr6                     16173434 45 - 174210431 -CTGTTGCTCATTATA----AATAAAAGTGTTTATTGCTAA--------T--------------GCTTTCTC
i ponAbe2.chr6                     C 0 I 4
s panTro2.chr6                     16393782 45 - 173908612 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC
q panTro2.chr6                                             -999999999999999----999999999999999999999--------9--------------99999999
i panTro2.chr6                     C 0 I 4
s hg18.chr6                        15875216 45 - 170899992 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC
i hg18.chr6                        C 0 I 4
s calJac1.Contig6394                  11047 43 +    133105 -CTGTTTCTCATTATA----AAT--AAGTGTTTATTGCTAA--------C--------------GCTTTCTC
i calJac1.Contig6394               C 0 I 701
s tupBel1.scaffold_114895.1-498454   175213 35 -    498454 -CTGCTCCTCATGATA----AAT-ATAGCGTTTGTTGCTAA-------------------------------
q tupBel1.scaffold_114895.1-498454                         -999999999999999----999-99999999999999999-------------------------------
i tupBel1.scaffold_114895.1-498454 C 0 I 10695
s sorAra1.scaffold_2476                3552 48 -      4997 -CTGTTCCTTCTTAGATTaaaaaaaGAGCGTTTATGACCAG--------CA-------GGTTCC--------
q sorAra1.scaffold_2476                                    -9999999999999999999999999999999997669755--------99-------999999--------
i sorAra1.scaffold_2476            C 0 N 0
s eriEur1.scaffold_266115               677 35 +      4589 -CTCCTTGTTCTTGAAGC----------CGTTTTTTATTGT--------CA-------GTG-----------
q eriEur1.scaffold_266115                                  -98959997997999999----------9999999999999--------89-------999-----------
i eriEur1.scaffold_266115          C 0 N 0
s canFam2.chr1                     78072203 40 - 125616256 -CTGTTTCTCATTATA----AATAAAAGCATTTATTGCTAA--------TG-------T------------C
q canFam2.chr1                                             -999999999999999----999999999999999999999--------99-------9------------9
i canFam2.chr1                     C 0 C 0
s dasNov1.scaffold_56749               3590 44 -     10470 -CTGTTCCTCTTTAT-----AATAAAAGCATTTACTGCTAA--------CGGCTCCTC--------------
q dasNov1.scaffold_56749                                   -99999999999999-----999999999999999999999--------999999999--------------
i dasNov1.scaffold_56749           C 0 I 904
s echTel1.scaffold_288249             95587 38 +    100002 -CTGATCCTCATTATA----AATAAAAGTGTTTGTTACTAA--------TG---------------------
q echTel1.scaffold_288249                                  -999999999999999----999999999999999999999--------99---------------------
i echTel1.scaffold_288249          C 0 N 0
s ornAna1.chr2                     14757054 45 -  54797317 ACTG-TCCTCATTGTA----CAGGGACTCTTTTATTACTAAAGATCCCCC----------------------
i ornAna1.chr2                     C 0 C 0
e felCat3.scaffold_205680             73725 34165 -    119354 I
e otoGar1.scaffold_334.1-359464      188429 6280 -    359464 I

a score=-9167.000000
s mm9.chr10                         3021465 29 + 129993255 CCCT--ACACTGTC----AAGTGGGAGGAGACAGT--------------------
s cavPor2.scaffold_216473              9957 28 -     10026 AGCC--acactgg-----gggtggggtgggatggt--------------------
q cavPor2.scaffold_216473                                  7667--6878566-----66544895554554677--------------------
i cavPor2.scaffold_216473          C 0 N 0
s ponAbe2.chr6                     16173483 24 - 174210431 -------CCCTGTG----GGGGCGATAGGAGCAGC--------------------
i ponAbe2.chr6                     I 4 I 9
s panTro2.chr6                     16393831 24 - 173908612 -------CCATGTG----GGGGCGATAGGGGCAGC--------------------
q panTro2.chr6                                             -------9999999----99999999999999999--------------------
i panTro2.chr6                     I 4 I 9
s hg18.chr6                        15875265 24 - 170899992 -------CCATGTG----GGGGCGATAGGGGCAGC--------------------
i hg18.chr6                        I 4 I 9
s canFam2.chr1                     78072243 31 - 125616256 CCCTGAACCACATG----GGGGGTGTGTGTGTGTG--------------------
q canFam2.chr1                                             99999999999999----99999999999999999--------------------
i canFam2.chr1                     C 0 I 13
s ornAna1.chr2                     14757099 45 -  54797317 ----------TGTGTCATAGGAGTTTGGATGTAGCCCTCTTTCATCTTTGCTGGC
i ornAna1.chr2                     C 0 C 0
e dasNov1.scaffold_56749               3634 904 -     10470 I
e felCat3.scaffold_205680             73725 34165 -    119354 I
e calJac1.Contig6394                  11090 701 +    133105 I
e tupBel1.scaffold_114895.1-498454   175248 10695 -    498454 I
e otoGar1.scaffold_334.1-359464      188429 6280 -    359464 I
e oryCun1.scaffold_156751              1033 2345 -      4726 I

a score=15763.000000
s mm9.chr10                         3021494 42 + 129993255 TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt
s ponAbe2.chr6                     16173516 46 - 174210431 TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT
i ponAbe2.chr6                     I 9 I 943
s panTro2.chr6                     16393864 46 - 173908612 TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT
q panTro2.chr6                                             9999999999999999999999999999999999999999999999
i panTro2.chr6                     I 9 I 10
s hg18.chr6                        15875298 46 - 170899992 TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT
i hg18.chr6                        I 9 I 931
s canFam2.chr1                     78072287 46 - 125616256 TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT
q canFam2.chr1                                             9999999999999999999999999999999999999999999999
i canFam2.chr1                     I 13 I 1
s ornAna1.chr2                     14757144 36 -  54797317 TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----
i ornAna1.chr2                     C 0 C 0
e dasNov1.scaffold_56749               3634 904 -     10470 I
e felCat3.scaffold_205680             73725 34165 -    119354 I
e calJac1.Contig6394                  11090 701 +    133105 I
e tupBel1.scaffold_114895.1-498454   175248 10695 -    498454 I
e otoGar1.scaffold_334.1-359464      188429 6280 -    359464 I
e oryCun1.scaffold_156751              1033 2345 -      4726 I
