>input_sequence_81842
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------ATGAGGACATCAAGCTTCCTGCTCATCGTCGCTGCCGCATTCCTCTACGCCATCGCCTCACCCGCCACGGGTTG
TGGGGAATGGATGGGCAACCAATTACGGAACACAAC-ATTAGAGAATGGATTGGAACCAATCGGAAACATCAACGACCAA
CGCATCCAGGTGCTCGGCAATTGGGTGGTGTTGGAGTTCGGAAAGTACACAAATTGTGTGCTCGAGTTCAACAAGGTGGT
GAGTGGCAGACAACAACATGCATTTTTATTGTACTACGAACTCATCATCGATGCATCGGACGTCCGCGGGGTAGACGGCA
AGTACAAGGCAAGGGTGCTCGTGCAGGAGGGGATTCACAGACCCTATCTCCTCTCCTTTGCCAAGGTGAACTAG------
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>chr2D_1_TraesCS2D01G586300
CCATGTATTTGTAATCAATATGATGATGAATGAAATACAGAGTTCACATAATTATTTCTATGTTTGTCATTGTATTTTGT
TTTCAAAACACATTGCACACGTGCATATGAGTTTTCCACG-------------------------------AGCATAGAA
TATAAACTCTTAATATGAACATACAAACATAATAAT-AAAATATCATTGCCTCTAGTGCATATTTTCAACACCCAAAGCT
TCCAGGGCCTTTTATCATTCAGAAAAAATCATCAAAAAGTTTCATCGTGTTTGGATTACCGTAGGTATGGATTTTCTGAA
AAACCAAAAGCGTGCGAAAACACCTGAACTGACACTGGGCACTAAATTAATATGTTAGTCCATAAAAATAATATAAAAGT
CATATAAAACATAAAAAGTGATAATATAATAGCATTTAGCAATAAAAAATTATAGATAGATTGGAGACGTATCATATTTC
CATGATAGCAATCTAGATATATTTTCTTATAGAAGTTTAAGTACATGCTTTCTACTACCTCTTATGAGCTTACAATGCCT
ATCTACTTTATCTCAACACAAATCCTTTTAATTTTGACCAAGTTATGGAGAAGATACTACTGACAGTTTGTTAGTGGGTG
AGCTAGTTACTACATCTGTTTCGAAATAGAACCATCTAGAAAGCATATATATTTAAACATTAATAACTTTAAGTAGGTCA
AAGCTTTTGGAAATGCATCAAATTGATTAACTTTTAAATAACTCTATAAAAAGTTCTTATAAATGCGCTTCTAAATGCCT
AGTTGGATATGCATCCAGTTGATTAACTTTTAAATAA---------CCCTACAAAAGGTTCTCA-TAAATGCACTTCTAA
ATGCTTAGTTGGATAAGTATCCAATTAATATTTGCCTCTTACAACGATGTCTATTTAACCACCCCTATCTCGCTTGTTTT
TCATCCAC----TCACATCACCGATTCAAACAAAGTCCCACATAACTATCTCAAGATCTAAAATCCCATTAAGCAATCCA
ATAGCCATGAGGACATCAAGCTTCCTGCTCATCGTCGCTGCCGCATTCCTCTACGCCATCGCCTCACCCGCCACGGGTTG
TGGGGAATGGATGGGCAACCAATTACGGAACACAAC-ATTAGAGAATGGATTGGAACCAATCGGAAACATCAACGACCAA
CGCATCCAGGTGCTCGGCAATTGGGTGGTGTTGGAGTTCGGAAAGTACACAAATTGTGTGCTCGAGTTCAACAAGGTGGT
GAGTGGCAGACAACAACATGCATTTTTATTGTACTACGAACTCATCATCGATGCATCGGACGTCCGCGGGGTAGACGGCA
AGTACAAGGCAAGGGTGCTCGTGCAGGAGGGGATTCACAGACCCTATCTCCTCTCCTTTGCCAAGGTGAACTAGGTGGGT
GGCAGTAACAACAGTAGTTATAATTGTGATGTTGCAAATATGTTTGCTGGG--TTT-CTAATTGAATAATAAATATTCCT
GTTGCATTGCCATGCATTTTGGAACATATCAAATTGCATTAAA-AAATCTGCAACTTGACTATGATAAGACCAGATGTTT
TTTTTTACAGGACAACATGATTAAGCTTTCCCATATAAATTTGCAGGTAGCATTTGCGTGCGACAATGAACACATATGTT
ATCTTTTTTTTTTTGAATGACCA-----TGACAAAATACATTTTTGGCGTG----------TACTCCCT-GAGCCAAAAG
CAATACCTGTGAAAGATGATCTTGTATTGTGGGACGGAGGGAGTATAACTTTAGCGTTGTTAGTTGCAAAAAAGTAACAA
GTCTGATTAGTTGTTGGATCACCAGC----ATACTGGAATAACAAAAAGGTACCATTCGCAGATCAATACCGCATAC---
---TATATGTCATCACCCATGGCGCACCTAG----GCCAAATCACCATCTACCAATGCAAAGATAATTTTATCCCAAGCT
TTAT---ACCTAGCTAAATAGGAGATCACGTGGGGAGAAGAACGCCAATATGAACAGACGGCGCGGAAGCGGC----CGT
AATCTAGCAGGTCGTCTAGGTCTCCGGTCAAGCACCCGCCATCCGACAA----GGCGCACCAAATCTTCGTGCAGGGTCG
CCCATGGAG------GAGTGTGGTCGGAGCTAGTTGTGGCGAAGGGCTCTCGCGACTCGCCAACGACAGCATTGATTGTA
TCTGACGCAAATATTTTAGATTGATCTGGGTTTTTTTCTCTCATTGATTTTGAGAAGGCTAGATCGATCTGATTATTACA
CCTGAGTAAGGAACTTGCGTCCTCGGGGGATCAGTGAATCAAGTGGAATCAACTCGGCCACGAGCCCACCACTCGAACTG
TCCCTGCGTAACAATTTGTCGTGCCAGGCCGGCTGCCAAAACATGCTTTTTTTGGTCTGATTAAAATTTAGTCACACATC
AATTT
>chr2A_1
CCATGTATTTGTAATCAATACGATGATGAATGAAATACAGAGTTCACATAATTATTTCTGTGTTTGTCATTGTATTTTGT
TTTCAAAACACATTGCACATGTGCATGTGAGTTTTCGAATGAATCACACATTCCAGGATCATATTAGTTATAGCATAGAA
TATAAACTCTTAATATGAACATACAAATATAATAAAAAAAATATCATTGCCTCTAGTGCATATTTTCAACACCCAAAGCT
TCTAGGGCCTTTTATCATTCAGAAAAAATCGTCAAAAAGTTTCATCGTGTTTGGATTACCGTAGTTATGGATTTTCTGAA
AAACCAAAAGCGTGCAAAAACACCTAAACTGACACTGGGCACTAAATTAATATGTTAGTCCATAAAAATAATATAAAAGT
CATATAAAACATAAAAAGTGATAATATAATAGCATTTAGCAATAAAAAATTATAGATAGGTTGGAGACGTATCATGTTTC
CATGATAGCAATCTAGATATATTTTCTTATAGAAGTTTAAGTACATGCTTTCTACTACCTCTTATGAGCTTACAATGCCT
ATCTACTTTATCTCAACCCAAATCCTTTTAATTTTGACCAAGTTATGGAGAAGATACTACTCACAGTTTGTTAGTGGGTG
AGCTAGTTACTGCATCTGTTTCAAAATAGAACCATCTAGAAAGCATATAT--TTAAACCTTAA-----------------
---------------------------TAACTTTTAAATAACTCTATAAAAGGTTCTCATAAATGCGCTTCTAAATGCCT
AGTTGGATATGCATCCAGTTGATTAACTTTTAAATAA---------CCCTACAAAAGGTTCTCA-TAAATGCACTTCTAA
ATGCTTAGTTGGATAAGAATGCAATTAATATTTGCCTCTTACAACTATGTCTATTTAACCATCCCTATCTCGCTTGTTTT
TCATCCACTCAATCACATCATTGATTCAC-CAAAGTCCCATATAACTATCTCAATATCTAAAATCCCATTAAGCAATCCA
ATAGCCATGAGGACATCGAGCTTCCTTCTCATCGTTGCTGCCGCATTCCTCTACGCCATCGCCTCACCCACCACGGGCTG
TGGGGAATGGATGGGCAACCAATTGCGGAACACAAC-AATAGAGAATGGATTGGAACCAATCAGAAATATCAACGACCAA
CGCATCCAGGTGCTCGGCAATTGGGCGGTGTTGGAGTTCGGAAAGTACACAAATTGTGTGCTCAAGTTCAACAAGGTGGT
GAGTGGCAGACAACAACATGCATTTTTATTGTACTACGAACTCATCATCGATGCATCGGACGTCCGCGGGGTAGACGGCA
AGTACAAGGCAAGGGTGCTCGTGCAAGAGGGGGTTCACAGACCCCATCTCCTCTCCTTTGCCAAGGTGAACTAGGCGGGT
GGCAGTAACAACAATAGTTATAATTGTGATGTTGCAAATGTGTTTGCT--GGGTTT-CTAATCGAATAATAAATATTCCT
GTTGCATTGCCATGCATTTTGGAACATATCAAATTGCATTAAAAAAATCTGCAACTTGACTATGATAAGACCAGATGTTC
TTTT-TACAGGACAACATGATTAAGCTTTCCCATATAAATTTGCAGGTAGCATTTGCGTGCGACAATGAACACATCTGTT
ATCTT-TTCTTTTTGAATGACCA-----TGACAAAATAGATTTTTGGCGTGCAGGAGCATATACTCCCT-GAGCCAAAAG
CAATACCTGTGAAAGATGATCTTATATTGTGGGACGGAGGGAGTATAACTTTAGCGCTATTAGTTGCAAAAAAGTAACAA
GTCTGATTAGTTGTTGGATCGCCAGC----ATACTGGAATAACAAAAAGGTACCATTCGCAGATCAATACCGCATAC---
---TATATGTCATCACCCATGGCGCACCTAG----GCCAAATCACCATCGACCAATGCAGAGATAACTTTATCCCAGGCT
TTAT---ACCTAGCTAAATAGGAGATCACGTGGGGAGAGGAACGCCAATCTGAACAGACGGCGCGGAAGCGAC----CGT
AGTCTAGCAGGTCGTCTAGGTCTCCGGTCAAGCACCCGCCATCCGACAA----GGCGCACCCAATCTTCGTGCAGGGTTG
CCTATGGAG------GAGTGTGGTCGGAGCTAGTTGTGGCGAAGGGCTCTCGCGACTCGCCAACGACAGCATTGATTGTA
TCTGATGCAAATATTTTAGATCGATCTGGGTTTTTCTCTCTCTTTGATTTTGAGAAGGCTAGATCGATCTGGTTATTACA
CTTGCGTAAGGAACTTGCGTCCTCGGGGGATCAGTGAATCAAGTGGAATCAA----------------------------
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>chr2D_771
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--TTGGATATGGATCCAATTGATTAACTTTTGAATAAAGTTTGTCCCCGTATAAAAGGTTGTCA-TAAATGCCATTGTAA
ACGCCTACTTGGATAAGCATCCAATTAATGTTTGCCTCTTATAACAATGTCTATTTAAGCACCGCTACCTCAATTGTTTT
GGATCCAC----TCACATCACCAATTCAC-CAAAGTCCCACATAACTATCTCAAGATCAAGAACCCCACTAGACAATCCA
ATAGCCATGAGGACATCTAGCTTCCTCCTCATCATCGTTGTTGCGTTCCTCTATGCCATCGGCTCACCTGCCATAGGCTG
TGGGGAACGGATGGGCAACCAATTGTGGAACACGGC-AATTGAGAATGGATGGGAACCAATCGGAAACATCAACGACCAA
CACATCCAGGAGCTCGGCCGTTGGGCGGTGTTGGAGTTCGGCAAGCATGTGAACTGCGTGCTCAAGTTCAACAAGGTGGT
AAGTGGCAGGCAACAACTTGTTTCTGGAATGAACTACGAACTCATCATCGAGGCATCAGACATTGGCGGGAAAGAAGACA
AGTACAAGGCAGAGGTGTACGAGCAGACGTGGACTCACAAACGCCAGCTCCTCTCATTCGCCAAGGTGAAATAGGCGGGT
AGCAATAACTTCGGTAGTAATAATTGTGATGTTGCAGATTTGTTAACT--G--TTT-TTTATCGACTAATAATTTATCCT
CTTGCGTTGCCATGC---TTGTAACATATCAAATAGCAT---AC--ATCTACAACTTGACAATGATAAGAGCAGA-----
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>chr2A_773
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----GGATATGGATCCAATTGATTAACTTTTGAATAAAGTTTGCCCCTGTATAAAAGGTTGTCA-TAAATGCCATTGTAA
ATGCCTACTTGGATAAGCATCCAATTAAATTTTGCCTCTTATAACAATGTCTATTTAAGCACCGCTACCTCAATTGTTTT
GGATCCAC----TCACATCACCAATTCAC-CAAAGTCCCACATAACTATCTCAAGATCAAGAACCCCACTAGACAATCCA
ATAGCCATGAGGACATCTAGCTTCCTCCTCATCATCGTTGTTGCGTTCCTCTATGCCATCGGCTCACCCGCCATAGGCTG
TGGGGAACGGATGGGCAACCAATTGCGGAACACGGC-AATAGAGAATGGATGGGAACCAATCGGAAACATCAACAACCAA
CACATCCAAGAGCTCGGCCGTTGGGCGGTGTTGGAGTTCGGCAAGCATGTGAACTGCGTGCTCAAGTTCAACAAGGTGGT
AAGTGGCAGGCAACAACTTGTTTCTGGAATGAACTACGAACTCATCATCGAGGCATCAGACATTGGCGGGAAAGAAGACA
AGTACAAGGCAGAGGTGTACGAGCAGACGTGGACTCACAAACGCCAGCTCCTCTCATTCGCCAAGGTGAAATAGGCGAGT
GGCAATAACTTCGGTAGTAACAATTGTGATGTACCAGATTTGTGAGCT--GGGTTTATTTATCGACGAATAATTTATCGT
CTTGCATTGCCATGC---GTGGAACATATCAAATAGCAT---AC--ATCTACAACTTGACAATGATAAGAGCAGA-----
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>chr2B_773
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----GGATATGGATCCAATTGATTAACTTTTGAATAAAGTTTACCCCCGTATAAAAGGTTGTCA-TAAATGCCATTGTAA
ATGCCTACTTGGATAAGCATCCAATTAATGTTTGCCTCTTATAACAATGTCTATTTAAGCACCGCTACCTCAATTGTTTT
GGATCCAC----TCACATCACCAATTCAC-CAAAGTCCCACATAACTATCTCAAGATCAAGAACCCCACTAGACAATCCA
ATAGCCATGAGGACATCTAGCTTCCTCCTCATCATCATTGTTGCGTTCCTCTATGCTATCGGCTCACCTGCCATAGGCTG
TGGGGAACGGATGGGCAACCAATTGTGGAACACAGC-AATAGAGAATGGATGGGAACCAATCGGAAACATCAACGACCAA
CACATCCAGGAGCTCGGCCGTTGGGCGGTGTTGGAGTTCGGCAAGCACGTGAACTGCGTGCTCAAGTTCAACAAGGTGGT
AAGTGGCAGGCAGCAACTTGTTTCTGGAATGAACTACGAACTCATCATCGAGGCATCAGACATTGGCGGGAAAGAAGACA
AGTACAAGGCAGAGGTGTACGAGCAGACGTGGACTCACAAACGCCAGCTCCTCTCATTCGCCAAGGTGAACTAGGCGAGT
GGCAATAACTTTGGTAGTAATAATTGTGATATACCAGATTTGTTAGCT--GGGTTTATTTATCGACGAATAATTTATCGT
CTTGCATTGCCATGC---GTGGAACATATCAAATAGCAT---AC--ATCTACAACTTGACAATGATAAGAGCAGA-----
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>chr3B_806
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----------------------------------------------CCCTATAAAAGGTTGTGCGTAAATGCCATTGTAA
ATGCTTACTTGGATAAGCATCCAATTAATGTCTGCCCCTTATAACAATGTCTATTTAAGCACCCCTATCTCACTTTTTA-
GGATCCAC----TCACAACACCAATTCAC-CAAAGTCCCACATAACTATCTCAAGATCTAGAACCTCATTAGACAATCCA
ATAGCCATGAGGACATCTAGCTTCCTCCTCATCATCATTGTTGTATTCCTCTATGCCATCGGCTCACCTGCCACAGGCTG
TGGGGAACCGATGGGCAACCAATTATGGAACACGGC-AATAGAGAATGGATGGGAACCAATTGGAAACATCAATGACCAA
CACATCCAGGAGCTCGGCCGCTGGGCGGTGTTGGAGTTCGACAAGCACGTGAACTGCGTGCTCAAGTTCAACAAGGTGGT
GAGTGGCAGACAACAACTTGTTTCTGGAATGAACTACGAACTCATCATCGACACATCAGACATTGGCGGGAAAGACGACA
AGTACAAGGCAGAGGTGTACGAGCAGGAGTGGACTCACAAACGTCAGCTCCTCTCGTTCGCCAAGGTGAAATAGGCGGGT
AGCAATAACTTCTGTAGTAATAATTGTGATGTTGCAGATTTGTTAGCATGGT-TTT-TTAATCGACTAATAATTTATCCT
CATGCATTGCCATGC---TTGTAACATATCAAATAGCAT---AC--ATCTACAGCTTGACAAGGATAAGAGCAGA-----
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>chr2B_980
CCT-----------------------------------------------------------------------------
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--------------------------------------------------------------------TTAAGCAATCCA
ATAGCCATGAGGACTTCGAGCTTCCTTCTCATCGTCGCCGCCATGTTCCTCTATGCCATCGCCTCACCCGCCACGGGTTG
TGGGGAATGGATGGGCAACCAATTGCGGAACACGACAAATAGAGAATGGATTGGACCCAATCGGAAACATCAATGACCAA
CACATCCAGGTGCTCGGCAATTAGGCGGTGATGGAGTATGGAAAGTACACGAATTGTGTGCTCAAGTTCAACAAGGTGGT
GAGTGGCA------------------------------------------------------------------------
AGTACAAGGCAGGGGTGCTCGTGCAAGAGGGGACTCACAGACCCAATCTCGCATGA------------------------
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-----------------------AGCATATATACTGGAATAACAAAAAGGTAGCATTCGCTGATCAAAACTTACTGCATG
AAGTATATGTCGCACCT--------ACCTAG----GCCAAATCTCCATCTACCAATGCAAAGATAATTTTATCCCAAGCT
TTATTATACCTAGCTAAATAGGAGATCACGTGCGCCAATG-------ATATGAAGACACGGCGCGGAAGCGATCGAACGT
AGTCTAGCAGGTCGTCTAGGTCTCCGGTCAAATACCCGCCATCCGACGATCGTGGCGCACCAAATCTTGGTGCAGGGTCG
CCCATGGCCATGGATGAGTGTGGTCGGAGCTAGTTGTGGCGAAGGGCTCTCACGACTCGCCAATGACAACATTGATTGTA
T-------------------------------------------------------------------------------
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>chr2B_1441
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-----------------------------------------------TGGG--TTT-CTAATCGACTAACAAATATTCCT
GTTGCATTGCCATGCATTTTGGAACATATCAAATTGCAT---AAAAAACTGCAACTTGACTATGATAA-ACCAGATGTTT
TTTTTCACAGGTCAACATGCTTAAGTTTTCCCATACAAATTTGCAGGTAGCATTTGCGTGCGAAAATGAACACATCTGTT
ATTTT-TTTTCAAAAAAAAAATTTGACCTGACAAAATACATTTTTGGCGTGCGGGAGCATATACTCCCTAGAGCCAAAAG
CAATACCCGTGAAAGACGATCTTACATTGTGGGACGGATGGAGTATAAGCTTAGCGCTGTTAGTTGCAAGGAAGTAACAA
GTCTGATTAGTTGTTGGATCACCAGCATATATACTGGAATAACAAAAAGGTACCATTCGCTGATCAAAACTTACCGCATG
AAGTATATGTCATCACCCATGTCGCACCTAGCTAGGCCAAATCTCCATCCACCAATGCAAAGATAATTTTATCCCAGGCT
TTAC---ACCTAGCTAA-TAGGAGATCAC---------------------------------------------------
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>SNPs
--------------------S--------------------------------------S--------------------
-------------------S------S---------S-SS----------------------------------------
---------------------------S-------S--------------------------------------------
--S---------------------------S---------------------------------S---------------
---------------S---------S------------------------------------------------------
-----------------------------------------------------------S---------------S----
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-----------------S-------------------------------------------S------------------
-----------S----------S---------------------------SS------S----SSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSS------------------------S-----S----------------------
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-----------------S---------------------------S----------------------------------
----------------------------SS--------------------------------------------------
-----------------S--------S-----------------------------------------------------
--------------------------------------S-----------------------------------------
-------------------------S-------------------------------------S----------------
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--------------------------------------------S------------------------------S----
---------------------------------------S----------------------S-----------------
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---------------------------------------------------------------------------S----
-----S--------------------------------------------------------------------------
-----------------------S--------------------------------S-----------------------
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--------------------------------------S--------------------------------S--------
-S------------------------------------------------------------------------------
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-----S---------------S-------------S------S----------------------------S--------
-S--S-----------------------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSS
>forward_346
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------AAAGCGTGCGAAAACACCTG------------------------------------------------------
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>reverse_2410
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---------AACAATTTGTCGTGCCAGGC---------------------------------------------------
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