>input_sequence_66500
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-------------------------------------------------------------------------ATGGAGT
TCTCGCCAACCGCACCGGCCGGTGGCGAGGAATCCGAGAGGGTTTGCGCGTCGTCGTCGGTGGTGGAGAAAGAGCACATG
TTCGAGAAGGTAGTGACTCCCAGCGACGTGGGGAAGCTGAACCGCCTGGTCATCCCCAAGCAGCACGCCGAGCGCTACTT
CCCGCTCGATGGCGCTGCCGCAGCGCTGGCGGCGGAGGGTAGCGGCGGCAAGGGGATGGTCCTCAGCTTCGAGGATCGCG
CGGGAAAGGCGTGGCGGTTCCGGTACTCGTACTGGAACAGCAGCCAGAGCTACGTGATGACCAAGGGCTGGAGCCGCTTC
GTGAAGGAGAAGAGCCTCGGCGCCGGCGACACCGTCCTGTTCGGCCGCGGGGTCGGCGACGGCGCCGCGCGCGACCGCCT
CTACATCGACTTCCGCCGCCGGCGCCCGGCCGAATCCTACAGCGCCACCGTAGCTTTCCCGCCACCGGCGACGTCGTCTT
TGTCACATCGCCTGCCGCTCCTCCCGTCTGTGCCGTTCTGCCCGTGGCGGCGGGACTTCGGCACCACCTACGGCGTCCCC
CCCGCTGCCTCGGGGTCCAATCGTCATGTGCTATTCCTGCGGCAGCAGGTGCCAGCGGCTGTGGTGCTCAAGTCCGTGCC
GGTGCGCGCCGCGGCCTCCGTACTGGAGCCGCCGGCGAGGCCTATGCCTAAGCGAGTCCGGCTGTTCGGCGTGAACCTCG
ATAGCCCGGCCACGGAAGACGATGGCACCTGCGGAGTCACACAGACGGTGACCTCAACGCTCCTGCAGCAGCTGCTGCCC
TCGCCGTCGTCGTCAACGTCGTCGACGGCGGGTAAGGAGAGGCAGTGCTCCCTGGATCTTGGATTGTGA-----------
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>chr1A_1_TraesCS1A01G200500
ATCCAGTTTAATAAATAATATATATTTCCACTTTTTCACCTCATATCCAGATTATGGACAACCAAATCTCAACGAAATAT
AGTGCGACCATTTCCCGCAGCAATG-CACGAGGTTACCCTATCACCTAGTACCATGTA----------------------
----AAAAGAAACACATGTTGAGTGTCATTTTCAGAATGAGATTTCTTTCTTTTTCAGAATCGAGATTTCTTTTATATAG
TGGATGCAACCTA-----------------------------TTTTGTGGGAATACAACGCAACTCTTAGGTCATCCAAT
CCCATGATTCATGAGGGTCTGTGATGAAAAGC----TAGAAAATATCGTGCCC-CACACAGATTGTTCACCCATCGATCC
ATCCATT-TCACCGATAGCTCGTGCCAG--TATGCCACACAAATTGTTAACCGAAGGGGCTACCACAGCTAGCAAACCAA
TCAGAATCACACATCCAT-ATATAGAGAGCTGACCGAT--CACACACAATTGGGACGTTGAGAGGGACATGCTCCATCAC
ATGATCTCTCAAACCCTATCATTCGTAGCCTGTGGACCCCACACGTCCTCACAACCATCTCCCTCCCTCCTCCCCACCTC
TCGCCCCCTCTCATCTTCCTCCTTAAAGAAGAAAGCAGCTGGCATGGGCTGCTTGTATTGTTCCTGACCTTTTCTCTC--
CTACCTTATCCCATATACATACACTTATACCCACTACACACACA---------------CCAAGATCCAAGAACCTTCAT
TGTGCTCCCCCCTGATGAGCTAGCTAGCTACCCCCCGTTTCTGGC----ATCTGTTCACCCATGGCATACTCGCATATC-
---------------TATTCCAGTTTTCCAATCATCCGAAGAAATCTCG-AGGCCCATATTATAGTAAG-CTGATAGGCA
TAGCCCTAATTCTTTTCTCCAAGAATAGCTGATTATAGTACTGTTGCGTGCCATCCCGGCTCCCAGAAATAGCATACAAC
CAGTCAAAGTCAGCACCTTGGTGCCTCAAGCTCGGGAGGTTGGGAGGGAGCTAGCGCGCCAAGT-------CCATGGAGT
TCTCGCCAACCGCACCGGCCGGTGGCGAGGAATCCGAGAGGGTTTGCGCGTCGTCGTCGGTGGTGGAGAAAGAGCACATG
TTCGAGAAGGTAGTGACTCCCAGCGACGTGGGGAAGCTGAACCGCCTGGTCATCCCCAAGCAGCACGCCGAGCGCTACTT
CCCGCTCGATGGCGCTGCCGCAGCGCTGGCGGCGGAGGGTAGCGGCGGCAAGGGGATGGTCCTCAGCTTCGAGGATCGCG
CGGGAAAGGCGTGGCGGTTCCGGTACTCGTACTGGAACAGCAGCCAGAGCTACGTGATGACCAAGGGCTGGAGCCGCTTC
GTGAAGGAGAAGAGCCTCGGCGCCGGCGACACCGTCCTGTTCGGCCGCGGGGTCGGCGACGGCGCCGCGCGCGACCGCCT
CTACATCGACTTCCGCCGCCGGCGCCCGGCCGAATCCTACAGCGCCACCGTAGCTTTCCCGCCACCGGCGACGTCGTCTT
TGTCACATCGCCTGCCGCTCCTCCCGTCTGTGCCGTTCTGCCCGTGGCGGCGGGACTTCGGCACCACCTACGGCGTCCCC
CCCGCTGCCTCGGGGTCCAATCGTCATGTGCTATTCCTGCGGCAGCAGGTGCCAGCGGCTGTGGTGCTCAAGTCCGTGCC
GGTGCGCGCCGCGGCCTCCGTACTGGAGCCGCCGGCGAGGCCTATGCCTAAGCGAGTCCGGCTGTTCGGCGTGAACCTCG
ATAGCCCGGCCACGGAAGACGATGGCACCTGCGGAGTCACACAGACGGTGACCTCAACGCTCCTGCAGCAGCTGCTGCCC
TCGCCGTCGTCGTCAACGTCGTCGACGGCGGGTAAGGAGAGGCAGTGCTCCCTGGATCTTGGATTGTGAATTCAAGGCCA
GATTAAAGACTAGTACTTAGTACTGACACGCGAACTTGATCCAGTCCAGAGAGGCAATGCGTGATTGGGGCAGCCTGCGT
ACGTATATAGCTCCTGCATTATGTGTAACATTCAGATCAGATGGGTTGTTTCTTGACGATATGCATCTT--ACGTATGAT
TATTTGCTTGCTAAACTAGCTAGTTAATTATATTGTTCTTCATTTTAGTCTGAGTTTTCCCCTTGACAATGAAAGAATGT
ATCAAACCTCTCTGAACCTCTGCATCATGAGATACATTCACACAGATTATGGCTTGATACGCCC-CGTTCTATAGATTTA
TGGCTCCCCTTC----------------------------------ATTGACAAAAGAAAAGTATTTATCGCTTCCCTTT
ATATACTTATTACACTACAGTGTACAGTCTCGTTCCCT-GCTCCCTGCATATGATAACAATTAGCACCAATGTAGGAGTA
TATGCAACTCATGCTTGGGTACGTTTCACTTTCAAGTTTCTTGAAGCAGTGTCGTTCTGGAGATCGATCACAAGGCTCTC
CTCCCTAAGCAAGGTAGGGGCTAG----AGGAGGTCAGGTCAGTGTCAGAACCTAATCCTTCTCCTACATGTACAGATAT
CCGCATCGATCTGCTATGAACATTGTCGTGCTAGCTTCTTGGGTTGGTTCTCGTGCGCAATTCTTTCCCAGCTGCCTCAT
GCATCTGATGTCTACCGATTTCTGACGCGCTTCTGACTTTGTTTGCTGCACCGCATGCATGCTGCAAATCTCTGCAGTTC
GTCCAAGACTCTTCTGAAATTATGCCGGCTGCTTCAGC-CTTGAAATTAATACTGTTACTAGCCAGCCATGTCAACTGGT
TGTGAGAAC---------TGAGAAGTAATACTGTTATGAAGCTTTGTGG--TGCTATCGTGCAACCACCGTGCGGTGGAA
CACCCCTCTCCAGTTCAAATATTCTTCAGGGCACAGTATTTGTATATAGCACCTTCAGTCCATAGTAAATTAAACTGGCA
TGT
>chr1D_1
ATCAAGTTCAATAAATCATATGTATTTTCATTTTTCATTCTCATATCCAGATTTTAGACAACCAAATCTCAACGAAATAT
ATTGCAACCAATTCCCGCCGCAAACACACGAGGTAATCCTATCATCTAGTAGTACTATGTAAAAAGAAACACATGTTCAC
CCGCAAAAAAAACACATGTTGAGTGTCATTTTCAGAATGAGATT------------------------TCTTTTATATAG
TAGATACGATCTATACCAATTTGTAGTGTCAAATGACGAATTTTCTGTGGAAATACAACGCAACTCTTCGGTCATCCAAT
CCCATGATTCATGAGGACCTGTGATAAAAAGCTATGTAGAAAATATCGTGCCCACACACAGATTGTTCACCCATCGATCC
ATCCATTCTGACCGATCGCTCGTGCCAGCATATGCCACACAGTTTGTTAACCGAAGGGGTTACCACAGCTAGCAGACCAA
TCAGAATCACACATCCAT-ATATAGAG--CTGACCGATCACACACACAATTGGGTCGTTGAGAGGGACATGCTCCATCAC
ATGATCTCTCAAACCCTATCATTCGTAGCCTGTGGACCCCACACGTCCTCATAGCCATCTCTCTCCCTCCTCCCCACCTC
TCGCCCCCTCTCATCTTCCTCCTTAAAGAAGAAAGCAGCTGGCATGGGCTGCTTGTATTGTTCCTGACCTTT--TCTC--
CTACCTTATCCCATATACATACACTCATACCCACTACACACACA---------------CCAAGATGCAAGAACCTTCAT
TGTGCTCCCCCCTGATGAGCTAGCTAGCTACCCCCCGTTTCTGGC----ATCTGTTCATCCATGGCATAATCGCATATCG
TAGCACACACACATCTGTTCCAGTTTTCCAATCATCCGAAGAAATCTCGGAGGCCCATATTATAGTAAG-CTGATAGCCA
TAGCCCTAATTCTTTTCTCCAAGAATAGCTGATTATAGTATTGTTGCGTGCCATCCCGGCTCCCAGAAATAGCATAC---
CAGTCAAAGTCAGCACCTTGGTGCCTCGAGCTCGGGAGGTTGGGAGGGAGCTAGCGCGCCAAGT-------CCATGGAGT
TCTCGCCAACCGCACCGGCCGGTGGCGAGGAACCCGAGAGGGTTTGCGCGTCGTCGTCGGTGGTGGAGAAAGAGCACATG
TTCGAGAAGGTAGTGACTCCCAGCGACGTGGGGAAGCTGAACCGCCTGGTCATCCCCAAGCAGCACGCCGAGCGCTACTT
CCCTCTCGATGGCGCTGCCGCAGCGCTGGCGACGGAGGCTAACGGCGGCAAGGGGATGGTCCTCAGCTTCGAGGACCGCG
CGGGAAAGGCGTGGCGGTTCCGGTACTCGTACTGGAACAGCAGCCAGAGCTACGTGATGACAAAGGGCTGGAGCCGCTTC
GTGAAGGAGAAGCGCCTCGGCGCCGGCGACACCGTCCTGTTCGGCCGCGGGGTCGGCGACGGCGCTGCGCGCGGCCGCCT
CTTCATCGACTTCCGCCGCCGACGGCCGGCCGAAGCTTACAGCGCCACTGTAGCTTTCCCGCCGCCGGCGACATCGTCTT
TGTCACATCGCCTGCCGCTCCTCCCGTCTGTGCCGTTCTGCCCGTGGCGGCGGGACTTCGGCACCACCTACGGCGTTCCC
CCCGCTGCCTCGGGGTCCAACCGTCATGTGCTATTCCTGCGGCAGCAGGTGCCAGCGGCTGTGGTGCTCAAGTCCGTGCC
GGTGCGCGCCGCGGCCTCCGTACTGGAGCCGCCGACGAGGCCTATGCCTAAGCGAGTCCGGCTGTTCGGCGTGAACCTCG
ATAGCCCGGCCACGGAAGACGATGGCGCCTGCGGAGTCACGCAGATGGTGACCTCGACGCTCCTGCAGCAGCTGCTGCCC
TCGCCGTCGTCGTCAACGTCGTCGACGGCGGGTAAGGAGAGGCAGTGCTCCCTGGATCTTGGATTGTGAATTCAAGGCCA
GATTAAAGACTAGTACTGAGTACTGACACGCGAACTTGA-----TCCAGAGAGGCAATGCGTGGTTGGGGCAGCCTGCGT
ACGTATATAGCTCCTGCATTATGTGTAACATTCAGATCAGATGGGTTGTTTCTTGACGATATGCGTCTTGCACGTATGAT
TATTTGCTTGCTAAACTAGCTAGTTAATTATATTGTTCTTCATTTTAGTCTGAGTTTTTCCCTTGACAATG-AAGAGTGT
ATCAAACCTCTCTGAACCTCTGCATCATGAGATGCATTCACACGGATTATGGCTTCATGCGCCCTCGTTCTATAGATTTA
TGGCTTCCCTTCGTTAGTAAAAGAAAAATATTTATGGCTCCCCTTCATTCGCAAAAGAAAAATATTTATGGCTCCCCTTT
ATCACTTACAC-----------TACAGTCTCGTTCCCTGGCTCCCTGCATATGATAACAATTAGCACCAATGTA----TA
TATGCAACTCATGCTTGGGTACGTTTCTCTTTCAAGTTTCTTGAAGCAGTGTCGTTCTGGAGATCGATCCCAAGGCTCTC
CTCCCTAAGCAAGGTGAGGTGAGGACTAAGGAGGTCAGGTAGGTGTCAGAACCTAATCCTTCTCCTACACGTACAGATAT
CCGCATCGATCGGCTATGAACATTGTCTGCTGCCG------------------------------------------CAT
GCATCTGACATCTACTGATTTCTGATGCGCTTCTGACTCTGTTTGCTCCACCGCATGCATGCCGCAAATCTCTGCAGTTC
GTTCAAGACTCGTCTGAAATTATGCCAGCTGCTTCAGCTCTTGAAATTAATACTATTACTAGCTAGCCAAGTAGCCATAT
CATGTAG-----TAGTTGTGAGAAGTAATACTGTTATGAAGCTTTGTGTGCTGCTATCGTGCAACCACCGTGCGGTGGAA
CACCTCTCTCCAGTTCA---------------------------------------------------------------
---
>chr1B_137
A-------------------------------------------------------------------------------
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----AAAAAAAACACATGTTGAGTGTCATTTTCAGAATGAGATTTCTTT------------------------TATACAG
TAGATACGATCTATACTAATTTGTAGTGTCAAATGACGAATTTTCTGTGGAAATACAACACAACTCTTCGGTCATCC-AT
CCCATGATTCATGAGGACCTGTGATAAAAAGCTACGTAGAAAATATCGTGCCCACACACAGATTGTTCACCCATCGATCC
ATCCATTCTCACCGATCGCTCGTGCCAGCATATGCCACACAGTTTGTTAACCGAAGGGGTTACCACAGCTAGCAAACCAA
TCTGAATCACACATATCCCATATATAGAGCTGACCGAT--CACACACAATTGGGTCGTTGAGAGGGACATGCTCCATCAC
ATGATCTCTCAAACCCTATCATTCGTAGCCTGTGGACCCCACGC--CCTCACAGCCATCTCTCTCCCTCCTCCCCACCTC
TCGCCCCCTCTCATCTTCCTCCTTAAAGAAGAAAGCAGCTGGCATGGGCTGCTTGTATTGTTCCTGACCTTT--TCTCTC
CTACCTTATCCCATATACATACACTCATACCCACTACACACACACACACACACCAAGATCCAAGAACCAAGAACCTTCAT
TGTGCTCCCCCCTGATGAGCTAGCTAGCTACCCCCCGTTTCTGGCATCTATCTGTTCATCCATGGCATAATCGCATATCG
TAGT--ACACACATCTATTCCAGTTTTCCAATCATCCGAAGAAATCTCGGAGGCCCATATTATAGTAAGCCTGATAGCCA
TAGCCCTAATTCTTTTCTCCAAGAATAGCTGATTATAGTACTGTTGCGTGCCATCCCGGCTCCCAGAAATAGCATAC---
CAGTCAAAGTCAGCACCTTGGTGCCTCGAGCTCGGGAGGTTGGCAGGGAGCTAGCGCGCCAAGGCCCAAGGCCATGGAGT
TCTCGCCAACCGCACCGGCCGGTGGCGAGGAATCCGAGAGGGTTTGCGCGTCGTCGTCGGTGGTGGAGAAAGAGCACATG
TTCGAGAAGGTAGTGACCCCGAGCGACGTTGGGAAGCTGAACCGCCTGGTCATCCCCAAGCAGCACGCCGAGCGCTACTT
CCCTCTCGATGGTGCTGCCGCAGCGCTGGCGACGGAGGCTAACGGCGGCAAGGGGATGGTCCTCAGCTTCGAGGACCGCG
CGGGAAAGGCGTGGCGGTTCCGGTACTCGTACTGGAACAGCAGCCAGAGCTACGTCATGACCAAGGGCTGGAGCCGCTTC
GTGAAGGAGAAGCGCCTCGGCGCCGGCGACACCGTCCTGTTCGGCCGCGGGGTCGGCGACGGCGCTGCGCGCGGCCGCCT
CTTCATCGACTTCCGCCGCCGACGCCCGGCCGAAGCTTACAGCGCCACCGTATCTTTCCCGCCGCCGGCGACATCGTCTT
TGTCACATCGCCTGCCGCTCCTCCCGTCTGTGCCGTTCTGCCCGTGGCGGCGGGACTTCGGCACCACCTACGGCGTCCCC
CCTGCTGCCTCGGGGTCCAACCGTCATGTGCTATTCCTGCGGCAGCAGGTGCCAGCGGCTGTGGTGCTAAAGTCCGTGCC
GGTGCACGCCGCTGCCTCCGTACTGGAGCCGCCGACGAGGCCTATGCCTAAGCGAGTCCGGCTGTTCGGCGTGAACCTCG
ATAGCCCGCCCACGGAAGACGGCGGCGCCTGCGGAGTCACGCAGATGGTGACCTCGACGCTCCTGC---------TGCCC
TTGCCGTCGTCGTCAACGTCGTCGACGGCGGGTAAGGAGAGGCAGTGCTCCCTGGATCTTGGATTGTGAATTCAAGGCCA
GATTAAAGACTAGTACTGAGTACTGACACGCGAACTTGA-----TCCAGAGAGGCAATGCGTGATTGGGGCAGCCTGCGT
ACGTATATAGCTCCTGCATTATGTGTAACATTCAGATCAGATGGGTTGTTTCTTGACGATATGCATCTTGCACGTATGAT
TATTTGCTTGCTAAACTAGCTAGTTAATTATATTGTTCTTCATTTTAGTCTGAGTTTTTCCCTTGACAATG-AAGAATGT
ATCAAACCTCTCTGAACCTCTGCATCATGAGATACATTCGCACGGATTATGGCTTCATGCGCCC-CGTTCTATAGATTTA
TGGCTTCCCTTCGTTAGCAAAAGAAAATTATTTATGGCTTCCCTTCATTCGCAAAAGAGAAATATTTATGGCTTCCCTTT
ATCACTTACAC-----------TACAGTCTCGTTCCCTAGCTCCCTGCATATGATAACAATTAGCACCAATGTA----TA
TATGCAACTCATGCTTGGGTACGTTTATCTTTCAAGTTTCTTGAAGCAGTGTCGTTCTGGAGATCGATCCCGAGGCTCTC
CTCCCTAAGCAAGGTGAGGTGAGGACTAAGGAGGTC----AGGTGTCAGAACATAATCCTTCT---ACACGTACAGATAT
CCGCATCGATCGGCTATGAACATTGTCTACTGCCG------------------------------------------CAT
GCATCTGATGTCTACTGATTTCTGATGCGCTTCTGACTCTGTTTGCTCCACCGCATGCATGCCGCAAATCTCTGCAGCTC
GTTCAAGACTCGTCTGAAATTATGCCAGCTGTTTCAGCTCTTGAAATCAATACTATTACTAGCTAGCCAAGTAGCCATAT
CAAGTACATATATAGTTGTGAGAAGTAATACTGTTATGAAGCTTTGTG--CTGCTATCGTGCAACCACCGTGCGGTGGAA
CACCTCTCTCCAGTTCAAATATTCTTCAGGGCACACTATTTGTATATAGCACCTTCAGTCCATAGTAAATTAAACTGGCA
TGT
>SNPs
---S----S-------S----S-----S--S----SSSS--------------S-S------------------------
-S---S----S-------S----SS---------S-S-------S------SS-SSSS----------------------
--------S----------------------------------------SSSSSSSSSSSSSSSSSSS------------
-S---S-S-S----------------------------------S-----S-----------------S-----------
----------------SS-------S------------------------------------------------------
----------------S------------------------SS----------------S--------------------
------------------------------------------------------S-------------------------
-----------------------------------------------------S-------S------------------
------------------------------------------------------------------------SS------
-------------------------S------------------------------------------------------
----------------------------------------------------------S----------S----------
-----------------------------------------------------------------------------S--
-----------------------------------------------------------------------------SSS
---------------------------S----------------------------------------------------
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---S---------------------------S------S--S---------------------------------S----
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------------S----------------------------------------------------S-------S------
--S------------------S------------S-S--------------------------S--------S-------
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--------------------S-----------------------------------------------------------
----------------------------------S---------------------------------------------
--------------------------S-------------S----S---------S------------------------
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-----------------S---------------------SSSSS------------------------------------
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----------------------------------------------------------S------------S--------
-------------------------------------------S-----------S--S---------------------
-----S-------------------------------------------SS----------S-------S----------
--SSSS-SSSSSSSSSSSSSSS----------------------------------------------------SSSS--
---------------------------S-----------------------------------------S----------
---------------SS--SSSS-----------------SS---------------------------S----------
-----------S---------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---
---------------S---------S------------S--------S--------------S-----------------
--S--------S--------------S---------------------------S--------S-----S--SSS-SSS-
SS--SSS-S---------------------------------------S-------------------------------
----S------------------------------S--------------------------------------------
---
>forward_105
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-----GACCATTTCCCGCAGCAATG-------------------------------------------------------
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>reverse_1593
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------------------------------------------------------------------------GTCGTCTT
TGTCACATCGCC--------------------------------------------------------------------
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>forward_117
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-----------------GCAGCAATGCACGAGGTTAC-------------------------------------------
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>reverse_2041
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----------------------------------------CCAGTCCAGAGAGGCAATGC--------------------
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