>input_sequence_85140
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--ATGGCGCCGCCCCAGGAGGGGGAGCAGTGCGGGCGGCCGGCCAGCAGCGTGTTGATCTGGGTGGTGACGGTGCTGCTG
CTCCTTGCCGTGCTCGGGGGCGGCGGGTGCCTCGTGGCCTACGTCCTGCTGCCGCCGAGCGAGGCGCCCGGATGGATCCC
ATGCGTCGGCTTGGGGCTCGTGTCGCTCCCCTGGGCGTTCTGGCTCGCCATGGTCGCCTACCGGTGCGTCACGGCGCGCT
CGGCCGACCGCGCCGTGGCGCCCGCGGCCGCCG---GCAGCTAA------------------------------------
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-----------------------------------
>chr4D_1_TraesCS4D01G097500
GTCAGTACCACGTGTGATCTCCTTCATATTTCTTGAAGAAGATACCTCTAATGTTCCCACTAGATCTTAGACCCGCCAAC
CTCCACTCTCGCCTTTCTGTTTATTTCCCGCAATCCTAATATTTAGTTCCACTTCTGACTGGATGAGAGCTCACCATCCA
AGGTGCCCTGCTTTCTGATTCTCTCTTTTATTTATCTTTCTTTCTT----TCTCATCTCTTTCTGATTATTTCTAACCTC
ATTCTTTATGG---------------------------------------------------------------------
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--------------------------------------------------------------------------TATAGG
GATTAGTTGAGCCCGAAACAAGGAGATGAACTTTTGGTCTATGAGTGTAT------------------------------
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---------------------------------------------------------------------------ATATG
CCTTATATGAAAAAAATAGTACTTAAATAAAAGATTAAAAAAATCTGAAATATTTTTGAAATAAACTTGATCGTCCATTG
TACTTGTGAATTTTTTTTCCACGATTTTTCCCCTTTGACTTCTTCTAAAAATAAATTTTCGGTCAAAATACTGTGGATAG
TGACCTATAATGGTAAATATTTTTTTGCCTTGAAGTCAACGCTGGTTTTTAATTCTTGAAAATTTATATACTAGTGCAAA
AGAAAGTCAAGTTTATTCACAAAAAACTTCTGAACTATTTCACATTTTTGTATTTTTTTCCTCATGTAGAGACAACCAGG
AACCGAGGGGTATTTCAGCACGTGAGAAAA-AAGAACTAGCTTATTATAGAATGCACAGTTAACTCGCCACCATTCTCTC
GTGACC--------------------TCTCCTTCCATTTTGGCCACCTTCCCTTGGTTTGAGCGCTCCGCCATTCCCCCG
TCGCT---CCTCTTGCATTCCTCGATCCACAAAAGGGCAAACAGCATAACAGATCAGAACTTTTTTGGCACATTTTC-CT
GTTCTTGGTCCACGAACAAGAAGGCAACAAGGTGAGGATCCGAGGC--CACTGGCGATGCACGCCGCCCTCTTCTT---G
CTCTCCTTGACCAGCGCCTCCGCGTCCGTCGTCGCCGCCCTTGCGTCTTCCTGAGCTCCGGTCCACCGGCGACGATAGAC
CGATGGCGCCGCCCCAGGAGGGGGAGCAGTGCGGGCGGCCGGCCAGCAGCGTGTTGATCTGGGTGGTGACGGTGCTGCTG
CTCCTTGCCGTGCTCGGGGGCGGCGGGTGCCTCGTGGCCTACGTCCTGCTGCCGCCGAGCGAGGCGCCCGGATGGATCCC
ATGCGTCGGCTTGGGGCTCGTGTCGCTCCCCTGGGCGTTCTGGCTCGCCATGGTCGCCTACCGGTGCGTCACGGCGCGCT
CGGCCGACCGCGCCGTGGCGCCCGCGGCCGCCG---GCAGCTAA--------------TTTCATTACTGAAGAGTAGGTA
ACCATTGTG-ATGTTAGTATCAAATCTGTCGTCAGTGAAAAAAGCATTTAGCAAGGAG----A-TCTGTGGGGATCGATT
ATGCATTGCAATGTTTGCATGGTTATGAAGTAAAAAAGTTGGTTATCTGAAAAGTGTGCCATGGTTATATTTTGTCTTTT
AACTCTT--TATGCTTTGCAGTGTGAAGCTGATTGGAGATCGACACAATTGATGTGAGGATTATATCAACTAAATTCGAC
CGACCCCCGCAAAAAAAT-----AAAAAATTCGACCGAGTTCGGTTTAAATCTTTTCGATCAAAATCCGACGTGATGGTA
GATGCAAACGTAATGGACCCCAACATCTGAACAAACT--TTCATAATCATGCGACTAAACTGCACGTGTTGTTTGT--AA
CACACAAAAATACAAGTTTTCCGAAGCAATCCCTATCTGAATATATTATCCAAAGATGTATGGAGAACATATTATATGGT
TGTTCCCATTAAAAATACATATTATATGGTTGTGCATATGCCGACCAATTTCTTAAACCGCTGTGATCAAAAGGTAAAAT
CTGTCTAGGACACATCTAGATGTGACATAAGACATAGTTATGTCACATCTAAACTGATGTCCACTCTATTTGTGGTCTAT
TGTTTTGTCCTAGTTTTTTTTGCTTTTTGTTGCTGCATTATATATTTATGGGAGCTTAGATGTGACATCCTTAAAAAAAT
CTATATGTGAATTATACAAACTGAAATAATTCACTATTTTCCCAATGACGGTGAAAGAGCTATGGTCATCATGTTGTTGA
AATTATAGAACATTTCCCTGCAAAAAGAAAAAAAGTATAGAACCTGTAGCCCATTTTATCATTTTCAATAATTCCTCAAA
AATTCCAAGAGGTTCATATGGTCCATAATGCACGAATAAAAAGTATGAAAGTTTAGTCCCACCTCGATTGTGGAGGGTGT
GTGAAGATGACTCATACATGAGTGCCCCTCCTCCG
>chr5A_1
GTCAGTACTATGTGTGATCTCCTTCATATTTCTTCATGAAGATACCTCTAATGTTCCCACTAGATCTTAGACCCGCCAAC
CTCCACTCTCGCCTTTCTGTTTATTTCCCGCTATCTGAATCTTTAGTTCCACTTCTGACTACATGAGAGATGA-------
------CCTGCTTTCTGATTCTCTCTTTTATTTCTCTTTCTTTCTTTCTTTCTCATCTCTTTCTGATTATTTCTGACCTT
ATTCTTTATTAGTGTGATAAAAGCCGTCCCTGCTTTCATTTTGTGTTGTTTTTTCCTTGTTTCCCCTTTTTAGCGGTGGA
TTACTATCTGTTTGTTGGGATTTATTGGTATGTATTGTTGTTCCGTATACCCTCACGTGGCTAACTAGAGCATAACAACA
TATACGGTGTGGTTAGTACTACCCTACCATTTTGTGATGGGATAGTATGGTTGTATTGTTCCATTCCAAACCCTTGTGTC
AGTGCCACTACACTTCTGTACTGATTGGTACTAGAGGACGAGAATTATAGTGAGAAATAGTGGATTTCTTTTCTTTGGGT
TTCTGTTGGGCTGACTTTTATGACCTCTCGGTTCTGGATTTCTGATCGCGGCTTATCTTGAATACTTTTTTTCATATAGG
ATTTAGTCAATCATACTTATGAGTATTCCTCTAATAGCGTGATAAAACGTTGCAACTCTCGTATATCTTTAGCGACTAGT
GTTTTGATTCTTTATTAGTGTGATAAAAGTTGTCCCTGCTTTTTTCATCCATCAACTGGAATCGCTTTGATTTCGCAATC
ATACCTTTGACCGTATAATATTTCCATGACATCAGATCAAAACGTTCACAGAGATCAGTGAGAGTTCCTATATCAATATG
AGGAATACTAGTACAATAGTACCGGAATCTAAGACTTCG-----------------------------------------
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----------------------------------------------------------------------------TCTC
TTGAATAAGTAATTCATATTCCCATATCTCTTTCGTTTTTGGCCGGTTTTGTGGTAAGCGTGATAGATTGAATCAACAAG
CACTAGTGTGAT--------------------------------------------------------------------
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-----------------------------------------------------------------------------CTA
CTGCTTGCCGTCAGTACTACGTGTGATCTCCTTCATATTTCTTGATGAAGATAC--------------------------
-------------------------CTCTAATGTTCCCACTAGATCTTCACTCTCGCCTTTCTGTTTATTTCCCGCGATC
CG------------------------------------------------------------------------------
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------------------------------------------------AATC-TTTAGTTCCACTTCTGACTGGATGAGA
GATGACCTGCTTTCTGATTTTCTCTTTTATTTCTCTTTCTTTCTTTCTTTCTC---------------------------
----------------------------ATCTCTTTCTGATTATTTCT--------------------------------
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>chr4B_637
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--------GGTTTTGCAGCATGTGAGAAAAGAAGAAGTAGCTTATTATAGAATGCACACTTAACTCGCCACCATTCTCTC
TTGACC--------------------TCTCCCTCCATTTTGGCCACCC-----TGGTTTGAGCGCTCCGCCATTCCCCCG
TCGCTGCTCCTCTTGCATTCCTCGATCCACAAAAGGGCAAACAGCATAACAGATCAGAACTTTTTTGGCACATTTTCTCT
GTTCTTGGTCCACGAACAGGAAGGCAACAAGGTGAGGATCGGAGGCCACACTGGCGATGCACGCCGCCCTCTTCTT---G
CTCTCCTTGACCAGCGCCTCCGCGTCCGTCCTCGCCGCCCTTGCGTCTTTCTGAGCTCCGGTCCACCGGCGACGATAGAC
CAATGGCGCCGCCCCAGGAGGGGGAGCAGTGCGGGCGGCCGGCCAGCAGCGTGTTGATTTGGGTGGTGACGGTGCTGCTG
CTCCTCGCCGTGCTCGGCGGCGGCGGGTGCCTCGTGGCCTACGTCCTGCTGCCGCCGAGCGAGGCGCCCGGATGGATCCC
CTGCGTCGGCCTGGGCCTCGTGGCGCTCCCCTGGGCGTTCTGGCTCGCCACCGTCGCCTACCGGTGCATCACGGCGCGCT
CGGCCGACCGCGCCGTGGCGCCCGCGGCCGCCG---GCAGCTAA--------------TTTCATTACTTAAGAGTAGGTA
ACCATTGTG-ATGTTAGTATCAAATCTGTTGTCAGTGAGAAAAGCATTTAGCAAGGAG----AATCTGTGGGGATCGATT
ATGCATTGCAATGTTTGCATGGTTATGAAGTAAGAAAGTTGGTTATCTGAAAAGTGTGCCATGGTTATATTTTGTCTTTT
AACTCTT--TATGCTTTGCAGTGTGAAGCTGATTGGAGATCAACACAATTGATGTGAGGATTATATCAACTAAATTCCAC
CGACTCCCGCAAATAAAAAATAAAAAAAATTCGACCGAGTTTGGTTTAAATC-TTTCGATCAAAATCCGACGTGATGGTA
GATGCAACCGTAATGGACCACAACATCTGAACAATTT--TTCATAATCATGAGACTAAACTGCACGTGTTGTTTAT--AA
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>chr4A_637
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--------GGTTTTGCAGCATGTGAGAAAAGAAGAACTAGCTTATTATAGAATGCACAATTAACTCGCCACCATTCTCTC
TTGACC--------------------TCTCCTTCCATTTTGGCCACCTTCCTTTGGTTTGAGCGCTCCGCCATTCCCCCG
TCGCTGCTCCTCTTGCATTCCTCGATCCACAAAAGGGCGAACAGCATAACAGATCAGAACTTTTTTGGCACATTTTTTAT
GTTCTTGGTCCACGAACAAGAAGGCAACAAGGCGAGGATCGGAGGC--CACTGGCGATGCACGCCGCCCTCTTCTTCTTG
CTCTCCTTGACCAGCGCCTCCGCGTCCGTCCTCGCCGCCCTCGCGTCTTCCTAAGCTCCGCTCCACCGGCGACGATTGGT
CGATGGCGCCGCCCCAGGAGGGGGATCAGTGCGGGAGCCCGGCCGGCAGCGTGTTGATCTGGGTGGTGACGGTGCTGCTG
CTCCTCGCCGTGCTTGGCGGCGGCGGGTGCCTCGTGGCCTACGTCATGCTGCCGCCGAGCGAGGCGCCCGGATGGATCCC
CTGCGTCGGCCTGGGCCTCGTGGCGCTCCCCTGGGCGTTCTGGCTCGCCACCGTCGCCTACCGGTGCGTCACGGCGCGCT
CGGCCGACCGCGCCGTGGCGCCCGCGGCCGCCGCCGGCAGCTAATTGTAATTGGGCTCTTTCATTACTGAAGAGTAGGTA
ACCATTGTGGATGTTAGTATCGAATCTGTTGTCAGT-AAAAATGCATTTAGCAAGGAGAATCAATCTGTGGGGATCAATT
ATGCATTGCAATATTTGCATGGTTATGAAGTAAAAAAGTTGGTTATCTGAAAGTTGTGGCATGGTTATATTTTGTCTTTT
AACTCATTATATGCTTTGCAGTGTGAAGCTGATTGGAGACAGACAAAATTGATGTGAGGAT--TATCAACTAAATTCGAC
CGACCCCCGCAAAAAAAA-----AAAAA--TCAACCGAGTTTGGCTTAAATCATTTCGATCAAAATCCGACGTGATGGTA
GAGGCAAATATAATGGGCACCAACATCTGGAAAAAAAAATTCATAATCATGCGACTAAACTGCACGTGCTGTTTGTGTAA
CACACAAAAATACAAGTTTTCCTAAGCAATCCCCATTTGAATATATTACCCAAAGATGTATGGAGAACAGATTATATGGT
TGTGG-------------------------------TATGCTGATCAATTTCTTAAACCGCTGTGATCAAAAGGTGAAAT
C-------------------------------------------------------------------------------
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-----------------------------------
>SNPs
--------S-S-----------------------S-S-------------------------------------------
-------------------------------S---SS---S-------------------SS-------S-S-SSSSSSS
SSSSSS---------------------------S----------------------------------------S----S
---------SS---------------------------------------------------------------------
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SS-----SS-S-SSSSSSSSSS-SSS-SSS--SS-S-SS-SSS-SSSSS-------------------------------
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SSSS---SS-SS-S--------SSS---SS----S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSS---S--S-----S-------------------------------------S---------------------
S--------------------------------------------------S----------------------------
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----------------------------------------S---------------------------------------
------------------------------S-------------------------------------------------
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-----------------S--------------------------------------------------------------
S---------S----S------S---------------------------SS----------------------------
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-----------------------------S--------------------------------------------------
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-----------------S-----------------------S----------S---------------------------
-----------------------------------S--------------------------------------------
----------------------S-------------------------S--------------------S----------
---SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----S--S------------------------------S----
-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_1208
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--------------------------------------------------------------------GAGACAACCAGG
AACCGAGG------------------------------------------------------------------------
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-----------------------------------
>reverse_2864
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---------------------------------------------------------------TCGATTGTGGAGGGTGT
GTG--------------------------------
