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0
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1 ##maf version=1 scoring=lastz.v1.04.22
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2 # lastz.v1.04.22 --strand=both --ambiguous=iupac --traceback=160M --format=maf --action:target=multiple
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3 #
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4 # hsp_threshold = 3000
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5 # gapped_threshold = 3000
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6 # x_drop = 910
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7 # y_drop = 9400
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8 # gap_open_penalty = 400
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9 # gap_extend_penalty = 30
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10 # A C G T
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11 # A 91 -114 -31 -123
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12 # C -114 100 -125 -31
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13 # G -31 -125 100 -114
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14 # T -123 -31 -114 91
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15 a score=5613
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16 s Merlin.Merlin 960 60 + 172788 ATTTTCTGTAGCAGTTCAAACTGTAGAAAATGATGAAGTTATTTTAACTTTACCAGCTTT
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17 s merlin1.Merlin 960 60 + 60 ATTTTCTGTAGCAGTTCCAAACTGTAGAAAATGATGAAGTTATTTTAACTTACCAGCTTT
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18 a score=5667
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19 s Merlin.Merlin 1020 60 + 172788 CGTAATTTTCCGCAAATAAAACAATGGGGAGCTATGCTCCCCATTTTTACAATCCAAGTA
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20 s merlin2.Merlin 0 60 + 60 CGTAATTTTCCGCAATAAAACAATGGGGAGCTATGCTCCCCATTTTTACAATCACAAGTA
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21 a score=5721
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22 s Merlin.Merlin 1080 60 + 172788 TTTTCGAAGTAGAGTTTCGGGTCGAATTAATGACGTGAGACAACCCTCCAGCAGCTCCTC
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23 s merlin3.Merlin 0 60 + 60 TTTCGAAGTAGAGTTTCGGGTCGAATTAATGACGTGAGTACAACCCTCCAGCAGCTCCTC
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24 a score=5613
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25 s Merlin.Merlin 1140 60 + 172788 CAAGTCTAGATAATCTACTTAAACTTCCATTAAGAGACATTTCACTATTAATTCCAGTTA
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26 s merlin4.Merlin 0 60 + 60 CAAGTCTAGGATAATCTACTTAAACTTCCATTAAAGACATTTCACTATTAATTCCAGTTA
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27 a score=5703
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28 s Merlin.Merlin 1200 60 + 172788 TAGAATTAACAGCTCTATCTTCAATCCAATCAAGAGCAGCTTGACGTCCAACAGCACCCG
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29 s merlin5.Merlin 0 60 + 60 TAGAATTAACAGCTCTATTCAATCCAATCCCAAGAGCAGCTTGACGTCCAACAGCACCCG
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30 a score=5649
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31 s Merlin.Merlin 1260 60 + 172788 TTTGCATTACTCTGTAAGCAAATGTAACATCGAAAACCGCAATTTGGTTATCTCCTTCAT
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32 s merlin6.Merlin 0 60 + 60 TTTGCATTACTCTGTAAGCAA TGTAACATCGAAAACCGCAATTATGGTTATCTCCTTCAT
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