>input_sequence_83876
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-------------ATGAAAAGCAGCACGCTGATGGTGATCATGGTCCTCCAGGCCACTCTGGTCATGGGGATCTTTATCC
TCCCGGACATGTGCAACGGAGATGTGCATGCAACGTCCGTGGGTGAGGGCAAGGCCATCGACCTCAACCTGGGCAAGCTA
AGGTGCTGCAGCAACTGCAACTCCTCCTCGGGCCTCTACACATGCGAAGACGTCGTGAAGATATGCGACCCTGTCTGCAA
GCGATGCGCCGTCGTGAAGAAGAACCTTGTCAAGGAGTTCAGGTGCACCGACACCTTCCTCGGTCTGTGCGAAAATCCGT
GCAAGAACCACTGA------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G039600
GTCCCAGAGGGA--TGATGAAGATCTACGTGAAGACGCTACGGCAAAATTTCTATAATCTTGAGGTGAGGAGCACAGATA
CCGTCTATAATGTCAAGGAGAAGATTTGGGCTGCGGAAGGCATTCCCCCGGGCCAGCAGAGCCTCATATTTGACGGCAAG
AAAATGAAGGATGACCGTACCTTGGCACACTATAATATCCAGATGTATGAAGTTCTCTATTTTGTGCTCAACCTACGTGG
TTGAATATTCATGGCATCATTTTTGCACCATGGGGTGTACTGCCGTGGTCTCCTTCGTACAGTACAGGCTTGTGTGATCT
GAATATTTTGTCAATCTTGTAGACTGTCTTGTCATATATTACATGCCACTTAGTAATTGAAGCTGTGCCCT---------
--------------------------GGCGAGTAT--TTGCTGAAGCACTCTTTGGAAGTTCCCTATATATAGTAATTTA
AATTGTTAGGTCAATGATTTTCAGTTTCATTTTATGTGCTGGCCACAAAGAACTGGTCTACCAC----TTGGCATTGTTG
ATAGCCAATAATATG--TCTGTGT-GCAGCGACGCGTGTGCATGACGCCAGTTAATTAGAATACGCATCTCGTTGTGGTT
AGCAGTCTTGATTACGATCAGCTTACTCCTTTTCTTTTTTGGGTGATTAGCTTACTTTCAATCA--GAGCTAATCTATGA
CGCACGAGCATACGCATAGCTCGATCGGACAATATAACAATACAATAGTGCGACAAATCACATG-----GCAATACATGA
AAGAGAACAAAGACCATTCCACACCTCTATCCCCGGCCATGACTCATAGACTTGTGTAACAAGCATTCAAACAAGAAAAA
CAATAAAAATAGTTCCATTTCCATCCTGGAGTTTGCAAAATTCTATGTCTTGAGACCTCAACGCACTCCTATATATACAT
GAAGCTGCTGTGGTGCGCTTTCGCCAACAAAAGCAGAGGCATCTATGCGAAGCAGATTCGGTACTGCATATAAATCGTTG
GAAGTAGCTAGCCATGAAAAGCAGCACGCTGATGGTGATCATGGTCCTCCAGGCCACTCTGGTCATGGGGATCTTTATCC
TCCCGGACATGTGCAACGGAGATGTGCATGCAACGTCCGTGGGTGAGGGCAAGGCCATCGACCTCAACCTGGGCAAGCTA
AGGTGCTGCAGCAACTGCAACTCCTCCTCGGGCCTCTACACATGCGAAGACGTCGTGAAGATATGCGACCCTGTCTGCAA
GCGATGCGCCGTCGTGAAGAAGAACCTTGTCAAGGAGTTCAGGTGCACCGACACCTTCCTCGGTCTGTGCGAAAATCCGT
GCAAGAACCACTGAAGATGAAAGTAGCTAATAAGCGGCACGCTAGCTGCTACTGTGATTTGATATGTGCTACGGTGCACA
GTAGGCATGTATGCCAGGATTGGGATTGGATGATTTTCGATCCATGTTATACGCGGAACAGTAAGTCGTTGTTTACGTGT
TTATTGACACAATAAAATCGGTGTTAGATATTGGTGGTTATATCATGGCAATCTCCACAATTTTGATTCTAGATATTGGT
GGAATAGTTCCTATAGGCTTGAGTCACGATGTTGTGGAAATTTATTGATGCACCGAATCACAAGATATTTGACGTGTTAG
GTTGATCATTTCTTGCGACGGCAACAAGCATCTTTTCTCCCGTGAGGATATTTTACATTATTTTAGAGAGCTAGTATTAA
TCGGTCACAAGTCGGAGTATGAAATATTGTCTGCATATCAAACATACATTGTTTTGCAAGTTCCTTAGTTGTGTCTGCTT
ATCCTATGGGACTGGCTAGAGGTCAGTTGACTGAAAATAAAATTTGGTCAGTTGACTGA---------------------
-------------------CCACAAGTTTGTTTCGGTCAAAACTTTAGATTAGTTGTACGTGTTCAGGGCATGCACACTC
ACACCTAGCCAAACAGGCACAAATCACATGCTTGGTCCAACAGACGAGAGCATTCCAATATAATTTTTCACATGTTATAT
AGTATTTGCGTGTATACATTTTATACTCACTCAACATCCCAAAAGTATCCATAAAAAACAATTAAGAAAATGAAAAAAGA
AAAGCCAAAAAGGTATACGAATAGAAGAAAAACATGAAACATTGTCCCTCTATGAAAAGACGAAATGGCTTCAGCGCAAT
AAGGAATCGACTGACCCAAAACAGTGGTCAGTCAAAAATTTCGGCCCAAAACATGACTGTAGACACAACAGAAAAAAAAA
AACAAGAACACGAATCTTGGAGCTGAAATCCAATTGACTGACCCAAATTTATTTTCAAACGACTTACATGTAGCTAAAGT
GTATCTTATTACCT
>chr3A_1
GTCCCAGAGGGA--TGATGAAGATCTACGTGAAGACGCTACGGCAAAATTTCTATAATCTTGAGGTGAGGAGCACAGATA
CCGTTTATAATGTCAAGGAGAAGATTTGGGCTGCGGAAGGCATTCCCCCGTGCCAGCAGAGCCTCATATTTGACGGAAAG
AAAATGAAGGATGACCGTACCTTGGCACACTATAATATCCAGATGTATGAAGTTCTCTATTTTGTGCTCAACCTACGTGG
TTGAATATTCATGGCATCATTTTTGCACCATGGGGTGTACTGCCGTGGTCTTCTTCGTACAGTACAGGCTTGTGTGATCT
GAATATTTTGTCAATCTTGAAGACTGTCTTGTCATATATTACATGCCACTTAGTAATTGAAGCTGTGCCCT---------
--------------------------GGCGAGTAT--TTGCTGAAGCACTCTTTGGAAGTTCCCTATATATAGTAATTTA
AATTGTTAGGATAATGATTTTCAGTTTCATTTTATGTGCTGGCCACAAAGAACTGGTCTACCAC----TTGGCATTGTTG
ATAACCAATAATATATCTCTGTGT-GCAGCGACGCGTGAGCATGACGCCAGTTAATTAGAATACGCATCTCGTTGTGGTT
AGCTGTCTTGATTACAATCAGCTTACTCCTTTTCTTTTTTGGGTGATTAGCTTACTTTCAATCT--GAGCTAATCTATGA
CGCACGAGCATACG-ATAGCTCGATCGGACAATATAACAATACAATAGTGCGATAAATCACATG-----GCAATACATGA
AAGAGAACAAAGACCATTCCACATCTCTATCCCCGGCCATGA--------CTTGTTTAACAAGCATTCAAACAAGAAAAA
CAATAAAAATAGTTCCATTTCCATCCTGGAGTTTGCAAAATTCTATGTCTTGAGACCTCAACGCACTCCTATATATACAT
GAAGCTGCTGTGGTGCGCTTTCGCCAACAAAAGCAGAGGCATCTATGCGAAGCAGATTCGGTACTGCATATAAATCGTTG
GAAGTAGCTAGCCATGAAGAGCAGCACGCTGATGGTGATCATGGTCCTCCAGGCCACTCTGGTCATGGGGATCTTTATCC
TCCCGGACATGTGCAACGGAGATGTGCATGCAACGTCCGTGGGTGAGGGCAAGGCCATCGACCTCAACCTGGGCAAGCTA
AGGTGCTGCATCAACTGCAACTCCTCCTCGGGCCTCTACACATGCGATGACGTCGTGAAGATATGCGACCCTGTCTGCAA
GCGATGCGCCGTTGTGAAGAAGAACCTTGTCAAGGAGTTCAGGTGCACCGACACCTTCCTCGGTCTGTGCGAAAATCCGT
GCAAGAACCACTGAAGATGAAAGTAGCTAATAAGCAGCACGCTAGCTGCTACTGTGATTTGATATGTGCTACGGTGCACA
GTAGACATGTATGCCAGGATTGGGATTGGATGATTTTCGATCGATGTTATACGCGGAACAGTAAGTCGTTGTTTACGTGT
TTATTGACACAATAAA-------------ATTGGTGGTTATATCATGGCAATCTCCACAATTTTGATTCTAGATACTGGT
GGAATAGTTCCTTTAGGCTTGAGTCACGATGTTGTGGAAATTTATTGATGCACCGAATCACAAGATATTTGACGTGTTAG
GTTGATCATTTCTTGCGACGGCAACAAGCATCTTTTCTCCCGTGAGGATATTTTACATTATTTTAGAGAGCTAGTATTAA
TCGGTCACAAGTCGGAGTATGAAATATTGTCTGCATATCAAACATACATTGTTCTGCAAGTTCCTTAGCTGTGTCTGCTT
ATCATATGTGACTGGCTAGAGGTCAGTTGATTGAAAATAAAATTTGGTCAGTTGTACGTGTCCACAAGTTCCTTAGCAGT
GTTTGCTTATCCTATGTGTCCACAAGTTTGTTTCGGTCAAAATTTTAGATTAGTTGTACGTGTTCAGGGCATGCACACTC
ACAGCTAGCCAAACAGGCACAAATCACATGCTTGGTCCAACAGACGAGAGCATTCCAATATAATTTCTCACATGTTATAT
AGTATTTGCGTGTATACATTTTACACTGACTCAACATCCCAAAAGTATCC--AAAAAACAATTAAGAAAATGGAAAA-GA
AAAGCCAAAAAGGTACACGAATAGAAGAAAAACATGAAGCATTGTCCCTCTATGAAAAGACGAAATGGCTTCAG------
-------------------------------------ATTTCGGCCCAAAACATGACTATATACACAACAG--AAAAAAA
AACAAGAGCACGAATCTTGGAGCTGAAATCCAATTGACTGACCCAAATTTATTTTCAGACGACTTACATGTAGCTAAAGT
GTATCTTATTACCT
>chr1D_3
CCCGAGAGGGAGTCGGATGAACATCTACGTGAAGACTTTACGAGGTAAATTCTATAATCTTGAGGTGAGGAGCACAGATA
TCATCTATAATGTCAAGGAGAAGATCTGGGCTACGGAAGGCATTCCCCCTAACCAACAGTGCCTCATATTTGGCGGCAAG
ATAATGGAGGATGGCCGTACCTTGACACACTACAATATCCAAATGTATGA--TTCTTTATTTTCTGCTCAACTTAAGTGG
TTGAATATGCATCACATGGTTATTGCACCATGAGGTGTACTGCCGTGGTCTTCATACACACTACAA----TGTGTGATCT
CAATATTTTGACATTCTTGTAGACTTTCTTGTCTTGTATTACATGCCACTTAGTAATTGAAATTGTCGGCGGGAGTATTG
C------------CGATAATGTGTTGTGGGAGTACTCTTGCTGAAGCACTCTTTGGAAGTTCTCAACATATAGTAATTAA
AATTGTT-GGTTAAGGATTTTCAGTATCATTTTGTGTGATGGCTACAATGAATTGGCCCACTACGTAGTTGCCATTGTTT
ATAACCAATAATATGTCTGTGTGCAGCAACCTCGCGTGTGCATGCTGCCAATTAGTATGAATCCCC------TTGTGGCT
AGTTGTCTTGATTATGATCAGCTTACTCCTTTTTTTTTGCCGATGATTAGATTACTTGCATGTT--GAGCTAATCTATGA
CCCATGAACATACA-ACTGTTCCATCGGC-AAT------ATATAATAGTGCGT-----CAAATCACATTGCAATACATGA
AAGAGAACAAAGGCCATTCCACA---------------------------------------------------------
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>chr3D_8
-------AGGGA--GGATGAACATCTACGTGAAGACCTTACGAGGAAAACTCTATAATCTTGAGGTAGACAGCGCAGATA
CCATCTATAATGTTAAGGAGAAGATCTGGGCTAAGGAAGGCATTCCACTGGACCTGCAGCGCCTCATATTTGAAAACAAG
TTAATGAAGGATGACCGTACCTTGGCAACGTACAATATCCAGATGTATGAAGTTCTCTATTTGGGGCTCAACCTACGTGG
TTGAATATGCATGGCATGGTTATTGCATCATTAAATGTATTGTCGTGCTCT---TCGTACGGTACGGGCCTGTTCGATCT
GAATATTTTGTCAT--------------TTGTCGTGTATTACGTGCCACTTAGTAATTGAAACTGTATCCAGGAGACTGG
ACTATATATTGCTCGTTAATGTGTTGGGCGAGTACTCTTGCTGAAGCACTATTTGGAAGTTCTTAATATATAATATTTTG
AATTGTTGGGTTAATGATTTTCAGTATCATTTTGTGTGCGAGCTACAATGAATTGGCCTACAAC----TTGACATTGTTG
ATAACCAATAGTATATGGTTGTGTAGCGACGTGT-GTGTCCATGACGCCAATTAGTGCGTAT------CTCGTTGTGGTT
AGCTGTCTTCATCACGATCAGCTTACTC--TTATTTTTGCGGGCGATTAGCTTCCTTTCATGTCGCGAGCTAATCTATGA
CGCACGGACATACG-ACTGTTTGATTTGATAAT------ATATAATAGTGCCA-----CAAATG-----GCAATGCATGA
AAGAGAAGAAAGACCATTCCA-----------------------------------------------------------
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>SNPs
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---------------------------------------------------S----------------------------
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-----------S--------------------------------------------------------------------
---S----------------------------------------------------------------------------
---S-----------------------------------------------------------S----------------
--------------S--------------------------------------S--------------------------
-----------------------S------------------SSSSSSSS-----S------------------------
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------------------S-------------------------------------------------------------
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----------S------------------------------------S--------------------------------
------------S-------------------------------------------------------------------
-----------------------------------S--------------------------------------------
----S-------------------------------------S-------------------------------------
----------------SSSSSSSSSSSSS----------------------------------------------S----
------------S-------------------------------------------------------------------
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-----------------------------------------------------S--------------S-----------
---S----S---------------------S-----------------------SSS-S---------------------
------------------------------------------S-------------------------------------
---S--------------------------------------------------------------S-------------
-----------------------S---S----------------------SS--------------------S----S--
---------------S----------------------S-----------------------------------SSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------------------S--S---------SS-------
-------S-------------------------------------------------S----------------------
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>forward_847
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---------------------------TATCCCCGGCCATGACTCAT---------------------------------
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>reverse_2248
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-------CGACTGACCCAAAACAGTGG-----------------------------------------------------
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