>input_sequence_78850
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----------ATGGCCATGATGGGCAT------------CATAGCGCCGGAGACGGCGTACGAGACGGAGGCCGTGTCTC
CGGCCACAGCCAGCGCCGCCGCGG---GCGCGCGGCAGCGGAGGGGCTTGCTCCGGAGGATGATGCCGCGGGGTCACTAC
TCGCCCGTCGGCGCCGAGCAGAAGACAGCGCCTGGAAGGGCGCCCGAGGTGGCACCGAT---------CGCTGCCGATGA
CTCGGAGGTCGCGGAGAAGCCGCGGCGCAGCTGGCTGCGGCGGCTGGTACCGCGGCAGCGGCAGCGCTGGAAGAACCTCG
GCGGAGCCGGCGCGTCGAGGCTGGCCGGACTGTCGCGATCGCTGCGGTGGAAGCGGCTGTCCATGAACCTGAGGGGCAGC
TGGGCGTCGGCGCTGCTGGACACCGTCGCGTTCCGCGTCATGTACGTGGTGGAAGCCATCGTGCTTGGTCTGGCGCTTTC
CTGCTTCTTCTGCTGCTGCGGCTGCCAGATATAG----------------------------------------------
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>chr3D_1_TraesCS3D01G242600
GTACGTGCGGTGATGTGGCTCGGCTTTTTTCTTTTTGCGGTGATCAGGTATGCTTGCGACGTTCCAGAGTGCAGGTGCAG
CGGGACTCGTACTATACTCTGCCATGCACCTTTTTACAGGCACGCAGGCGACGACAAATGGGAGAAGCACAGCCAGACAT
CTGGGGCAGCCGGTCCCAAACCTTGATC--AGCCAGCATTAACTAACGG-TTTATGGTCGCTCGAGGCTACCGAAACACT
GCGCTTTTTTGACCAAACGGCCGCTGCCCGACAAGAGGCAAATTTGCAAGCCGTTGGCGAGCGTAAGAAAACAACAACGA
TAGGCTAGCAGTAGCAGGGGAGCGTGTAGTGTAATGTAGGCCTGCGCTGCACGCCCGGGCCCGGCTGTCACGGCCAGTTC
GACTCCAGCAACACTCGAGAGTCGAGAACCATATACTCCTACCACCACCCTGTAT--GACCTGCCGCTGCCGGCCTTTTC
AGTTCAGATACGCCCTGCCCCTGCCCCTGCCCCTGCCCTGGCGTTCTAGAAAGTCCATGCACTTTGTTCAAATTCGCCAT
GTTTTGCAACTTGACAGCATAATAAACACTGTTCAACATATATTATGCATAATACAGTA------TATCCGTTACAGCAT
GCGATGCGC---AATAAACGGACCAGCGCAACACATATACAGCCA--------CCCAGCTGAGCTTGCGCTTGCGGTTGC
AAATAAAATCGGCAACGGCCTTTACAGCACGAGCTGAGCTGTTAAGCCGTCCGTCTGGCGGATGCCTTACGCACAAAGC-
------AGCAGCTCAAGCCACAATCTCTTCTTCTCCTTTGAAAAAGCACGATCGAAACGGCGATAGGTAGGTTTCGGCAC
GTCCA---GTCCCGAGATCGAAACGGTCTCCTTTATATTCTCCCGTCTCCGCCTGACCACACCCCGCACGTCGCT--CCC
CACGCCTTC-----GTCCCGTCTCGTACC-----------AATCTTCTTCACCTAGGCTAGCTATATACTAGGTCTTCTC
CCGCTCAGCCATGGCCATGATGGGCAT------------CATAGCGCCGGAGACGGCGTACGAGACGGAGGCCGTGTCTC
CGGCCACAGCCAGCGCCGCCGCGG---GCGCGCGGCAGCGGAGGGGCTTGCTCCGGAGGATGATGCCGCGGGGTCACTAC
TCGCCCGTCGGCGCCGAGCAGAAGACAGCGCCTGGAAGGGCGCCCGAGGTGGCACCGAT---------CGCTGCCGATGA
CTCGGAGGTCGCGGAGAAGCCGCGGCGCAGCTGGCTGCGGCGGCTGGTACCGCGGCAGCGGCAGCGCTGGAAGAACCTCG
GCGGAGCCGGCGCGTCGAGGCTGGCCGGACTGTCGCGATCGCTGCGGTGGAAGCGGCTGTCCATGAACCTGAGGGGCAGC
TGGGCGTCGGCGCTGCTGGACACCGTCGCGTTCCGCGTCATGTACGTGGTGGAAGCCATCGTGCTTGGTCTGGCGCTTTC
CTGCTTCTTCTGCTGCTGCGGCTGCCAGATATAGCTGGCCT--GCCTGCCCCTTGCTGTGATTCATGCAAGCCCCCTTCT
GCTTGCCATTGGGCGTGTAATCTTTGTACCGTCGTCCTTGTTTATT--------------------TAAGATGCTTATAT
AGTTCTCTAATGAAAAGGATTTTTTTTTTGCTACATCGCGTTGATCGTCGATCTTGTTGGACTCCATTGCATGTTCTTAT
GCA------------ACAGATGTCTAGTTGCGAGG-ACCACGTTGCTGGTATGCTGCTTTGCGTATTTGCGAAAAAAGAT
ACTACCTTTGTCCTATAATATAAGAACGTTTTTGATATTAGTGTAGTGCCAAAAATGTTCTTATATTATGGGACGAAGTG
AGTATGATGCTAGCGGCTCGCGAGCGTGCATGTTAATGGTCACCCTCGCCGCCTCCCACGGTCTCGCGCAAAGGCTTTTT
GTGGATCACCATGACACGTTACACCCTGCTGTATCAAATTATTATTATTCCTTTCTGCGGCAATGAGGGCTATCAAATTC
TGTTCGATCCATAGTAAGGGGAACAGGTTCTGAAAAAATTCAAAGATATCGGATTTTTGGTGGGTCTGTCATTCTTTCTG
TCAGTTGACTAAGATTTAACAAAGTCTTAATCAAATGACATAGTATATAAAAAGAAAATCTAGAAAGAAAATTTTACACG
GATCTCCATGCAAGACGACTGAGACATAATCAAGTCTCAGTCGACTAAGATTTAGCAATGCTGATAATTAAACATCTATT
GAAGTTATGTGCTTTCATTTTCTTTGTTCGTTATTTTGTGCTAGAACTAGAAATTTAATATTCCCTCCGATCCATATTAG
TTATAGCAGCTTTAGTTGGGAGTATAACAATATAGCCGGGAGAAACCCTTATGGTTCCCTTAAAAAAGATTTAAGTCTTT
AATTACATATATCTTCTAAATAACTGTCTACTTCCTCGCCTTTTTTTGTCGATGTACTATCTCCATGCTTTTTCAGTGTT
GTGCAACTCGCCATAGAGATCGATGCACA
>chr3A_103
CATGCATC------------------------------------------------------------------------
-------------------------------TTTTACAGGCACGCAGGTGACGACAAATGGGAGAAGCACAGCCAGACAC
CTGGGGCAGCCGGTCCCAAACCTTGATCTCAGCCAGCATTAACTAACGG-TTTATGATCGCTCGAGGCTAC-------CT
GCGCTTTTTTGACCAAACGGCCGCTGCCCGACAAGAGGCGAATTTGCAAGCCGTTGGCGAGCGAAAGAAAACAACAACGA
TAGGCTAGCAGTAGCAGGGAAGCGTGCAGTGTAATGTAGGCCTGCACTGCACTGCAC-GCCCGGCTGTCACGGCCAGTTG
GACTCCAGCAGCACTCGAGAGTCGAGAACCATATACTCCTACCACCACCCTGTATGTGACCTGCCGCTGCCGGCCTTTTC
AGTTCAGATACGCCCTG------CCCCTGCCCCTGCCCTGGCGTTCTAGAAAGTCCATGCACTCTGTTCAAATTCGCCAT
GTTTTGCAACCTGACAGCATCATAAACACTGCCCAACATATATTATGCATAATACAGTAGGAGTATATCCGTGACAGCAT
GCGATGAGCAATAATAAACGGACCAGCGCAACACATATACTCCAGCACAACTTCCCAGCTGA------GCTTGCGGTTGC
AAATAACATCGGCAACGGCCTTTACAGCACGAGCTGAGCTGTTAAATCGTCCGTCTGGCGGATGCCTTACGCACAAAGCG
GCAGCCAGCAGCTCAAGCCACAATCTCCTTTTTTCCTTTGAAAAAAGCA---CGAAACGGCGATAGGTAGGTTTCGGCAC
GTCCA---GTCCCGAGATCGAAACGGTCTCCTTTATATCCTCCCGTCTCCGCCTGACCGCACCCCGCACGTCTTC-CCCC
CACGTCTTCGCCCAGTCCCGTCCAACAACGTACCATCTTGAATCTTCTTCGCCTAGGCTAGCTATATACTAGGTCTTCTC
CTGCTCAGCCATGGCTATGATGGGCATCATCAAGACCGACATAGCGCCGGAGACGGCGTACGAGACGGAGCCCATGTCTC
AGGCTACAGCCAGCTCCGCCGCGGCGGGCGCGCGGTACCGCAGGGGTTTGCTCTCGAGGATGATGCCGCGGGGGCACTAC
TCGTCCGTCGGCGCCGAGAAC------------GGAAGGGCGCCCGAGGCGGCACCGATGCCCCCGGCCGCTGCCGATGG
CTCGGAGGTCGCGGAGAAGCCGCGGCGCGGCTGGCTGCGGCGGCTGATACCGCAGCAGCGGCGGCGCTGGAAGAATCTGG
GCGGCGCCAGCGCGTCGAGGCTGGCCGGACTGTCGCGATCGCTGCGGTGGAAGCGGCTGTCCGTGAACCTGAGGGGCAGC
TGGGCGTCGGCGCTGCTGGACACCGTCGCGTTCCGCGTGATGTACGTGGTGGAAGCCATCGTGCTTGGCCTCGCGCTCTC
CTGCTTCTTCTGCTGCTGCGGCTGCCAGATATAGCTGGCCATGGCCTGCCCCTTGCTGTGATTCGTGCAAGCCCCCTTCT
GCTTGCCATTGGGCGTGTAATCTT-GTACCCCCGTGCCCCGTCCTTTAATTTTCTTATGTCAATTATAAGATGCTTAG--
--TTCTGCGATCAAGAGGAAT---TTTCTGCAATATCGTGTTGATCATCGATCGAGTTGGACTCCAT------------T
GCA------------ACATAAGTCCAGTTGCGAGGAACCACGTTGCTGGTATGCTGCTTTGCCTATTTGCGA--------
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>chr3B_157
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----------------------------------------------------------------------------ACAT
CTGGAGCAGCCGGTCCCAAACCTTGATC--AGCCAGCATTAACTAACGGTTTTATGGTCGCTCGAGGCTACCGAAACACT
GCGCTTTTTTGACCAAACGGCCGCTGCCCGACAAGAGGCAAATTTGCAAGCCGTTGGCGAGCGAAAGAAAACAGCAACGA
TAGGCTAGCA------GGGAAGCGTGTAGTGTAATGTAGGCCTGCACTGCACTGCAC-GCCCGGCTGTCACGGCCAGTTG
GACTCCAGCAGCACTCGAGAGTCGAGAACCATATACTCCTACCACCACCCTGTATGAC--------CTGCCGGCCTTTTC
AGTTCAGATACGCCCTG------CCCCTGCCCCTGCCCTGGCGTTCTAGAAAGTCCATGCACTTTGTTCAAATTCGCCAT
GTTTTGCAACTTGACAGCATAATAAACACTGCCCAACATATATTATGCATAATACTC------TATATCCGTTACAGCAT
GCGATGAGCAATAAACGGATTAGCGCA-------------------ACAACTTCCCAGCTGACCTGA-GCTTGCGGTTGC
AAATAAAATCGGCAACGGCCTTTACAGCACAGGCTGAGCTGTTAAGTCGTCCGTCTGGCGGATGCCTTACGCACAAAG--
-----CAGCAGCTCAAACCACAATCTCTCCTTTG-------AAAAAGCA---CGAAACGGCGATAGGTAGGTAAGTTTCG
TTCGGCACGTCCCGAGATCGAAACGGTCTCCTTTATATTCTCCCGTCTCCGCCTGACCGCACCCCGCACGTCGCCTCCCC
CACGTCTTC-----GTCCCGTCCAACAACGTACCATCTTGAATCTTCTTCCCCTAGGCTAGCTATATACCTGCTCTTATC
CCGCTCAGCCATGGCCATGATGGGCAT------------CATAGCGCCGGAGACGGCGTACGAGACGGAGGCCGTGTCTC
CGGCCACAGCCAGCGCCGCCGCGG---GCGCGCCGCAGCGCAGGGGCTTGCTCCGGAGGATGATGCCGCGGGGGCACTAC
TCGCCCATCGGCGCCGACCAGAAGACAGACCCTGGAAGGGCGCCCGAGGTGGCACCGAT---------CGCTGCCCGTGA
CTCGGATGTCGCGGAGAAGCCGCGCCGCGGCTGGCTGCGGCGGCTGGTAAC---GCAGCGGCGGCGCTGGAAGAATCTGG
GCGGCGCCAGCGCGTCGAGGCTGGCCGGACTGTCGCGATCGCTGCGGTGGAAGCGGCTGTCCGTGAACCTGAGGGGCAGC
TGGGCGTCGGCGCTGCTGGACACCGTCGCGTTCCGCGTCATGTACGTGGTGGAAGCCATCGTGCTTGGCCTGGCGCTCTC
CTGTTTCTTCTGCTGCTGCGGCTGCCAGATATAGCTGCCCATGGCCTGCCCCTTGCTGTGATTCATGCAAGCT-CCTTCT
GCTTGCCATTGGGCGTGTAATCTTTGTACCCCCGTCCTTGTTTATC--------------------TAAGATGCTTAA--
--TTCTCTAATGAAGAGGATT---TTTTTGCTACATCGCGTTGATCGTCAATCTTGTTGGACTCCAT------------T
GCATGTTCTTATGCAACAGACGTCTAGTTGCGAGGAACCACGTTGCTGGTATGCTGCTTTGCGTATTTGAAAAAAAAAAG
G-------------------------------------------------------------------------------
-GTATGATGCTTGCCGCTCGCGAGCGTGCATGTTAATGGTTACCCTCACTGCCTGCCACCGTCTCGCGCGAAGGCTGTTG
GTGGATCACCATGACACGTTACACCCTGCCGTATCAAATTATTA------------------------------------
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>SNPs
SSSSSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----------------S-------------------------------
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---------------------------------------------------------------S----------------
-------------------S-------------------------S------SS-SSS---------------------S
----------S---------------------------------------------------------------------
-----------------SSSSSS---------------------------------------------------------
-------------------------------SS-----------------------------------------------
------S---------------------------------SS-SS-----------------S--SSS------------
----------------------------------------------S---------------------------------
--------------------------------S------------SSSSSSS----------------------------
----------------------------------------------------------S---------------S-----
----S-----------------SSSS-S----------------------S-----------------------------
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----------------------------------------S--------------------------------S------
----------------------------SS--------------------------------------------------
----------------------------S------------------------S--------S------------S--S-
----S---S-----------------------------------------------------S-----------------
--------------------------------------------------------------------S--------S--
----------------------------------------S---------------------------------------
------------------------------SS---------------------------------------------SSS
SS------------S------SSS-------------------------------------------SSSSSSSSSSSS-
--------------------S--------------------------------------------------------S-S
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
S----------S--S-------------------------S------S-S----S----S---------S------S--S
-----------------------------S--------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_63
-------------------------------------------TCAGGTATGCTTGCGACGTT-----------------
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>reverse_1518
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-----------------------------------------------------------------------------TTC
CTGCTTCTTCTGCTGCT---------------------------------------------------------------
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>forward_498
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------------------------------------------------------------------------------TC
AGTTCAGATACGCCCTGC--------------------------------------------------------------
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>reverse_2239
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------------------------------------------------------------------------------CG
GATCTCCATGCAAGACGA--------------------------------------------------------------
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