>input_sequence_87278
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--------------------------------------------------------------------------ATGGGG
AAGGCAAAGCGTGCATCGATATTTATCAGGCTCGTTTCAGCAGCTGGAACTGGTTTTTTCTACGTGAAGCGTAAGAATCC
TCGGCGGATTACAGAGAAGCTTGAGTTCAGGAAGTACGATCCTCGTGTAAACAAGCATGTTCTATTTACGGAAGCCAAGA
TGAAGTGA------------------------------------------------------------------------
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>chr1D_1_TraesCS1D01G336000
GCATCTCCAGGCAACCGCGTGACG---TAGTAAACCCTACTCTCTCTTCCCGGTCCCACCCGCCAGCCGCACTACGGCAC
AAGCTGCTTCTTCTTCTTCTTCATTCCCGTCCCCTGCGCTCGCG------GCGGCGGCGGCGGCTTTCCACGGTAAATCT
CGAGGCAGGATCCGTTGAATAATTTTGGACAAGTCTTGGAGTATGTTGTAGCCTTGTAGATCCGAACCAGGGATCCTTGT
TTAGAGAGCCTTAGTCCACGCCGCCCGACCTCGCCGTCATCGCCTGGAACCGAAATTTCTTTGCGGGGA--GGGTCGATC
CCATCCAGCTTTTTCTTTGTGGATTCTGGGAAGTTTGATTGTTGTTGTGGTGGGCAATCGTCCTGGGAGCAGATTGATCG
TTGATGCGGTTTGTATCGTTAGGATGCAGTACAGCTAATGGGTCCATCAGGGTGTAGACAAAACTGCTTATTTACCATTG
AGTTTACTCAAGGCGTAGTATATCATATAAACATTCAGTGCATTTCTACTGGTT-ATTCAACCTACTTATGACTGCTGAA
TGACCAATCTAAGA--CTAACTATATGTATGTAAGGATCAAGGTA---CAATATAATG---TACTGGATAGCAGTTGAGT
TATCATGCCCAGACCAGGTCAGCAATGTGATCTCTAAAGTCTAGACAAGGCGATATGTACATAGAAAAATCCAAAACTGT
AGTAGATGTATCGGGTAACAGGCCATATGTGCAAACCCATATGACCAACGCGAACCTGTTTTTG----GAGAATTTCTTA
TTTAACTTATATTCTCCGGATGTGTCTCAAATTCTCAATCTTAACATTGTATGGC-------TTGCTGCAGTATTCTTTT
GCTAGATGTATGAGATTTCTCTTGATTTGCTATCCTCCTTTTGCTCCTTGTGTCTGCCTTTGACATTGCAGAAGCTTGAA
CTTT---ACTCTAATGTTCTGTTTGCCTGCAGCATTTTCAGTTTCCTTTTGCTGCGGAAGTTCATACCCACTAGATGGGG
AAGGCAAAGCGTGCATCGATATTTATCAGGCTCGTTTCAGCAGCTGGAACTGGTTTTTTCTACGTGAAGCGTAAGAATCC
TCGGCGGATTACAGAGAAGCTTGAGTTCAGGAAGTACGATCCTCGTGTAAACAAGCATGTTCTATTTACGGAAGCCAAGA
TGAAGTGAGACAGTGCAGCCTTTTTTTTTTCTTGACATAAGACCTCTACTGTTCATTTTCGTTGAAGACA---CTGCTAC
CTTTATT--AGCCTGTTCCAGATTCGAGAGTTTCATGTGG--------------------------------GCACCAAA
TCAGCATGGAT-----CTTGCTCTGCC-TGCCTGTTTATTTGTATTGTAAGTTTATCACTGAAATGAGCTGCAAGCCTGG
AAAAGTAATGCCCATCTA--GTGTTGTGATGATTATCATGTGGATGCTTGGTTCTGAAACTTAAAGCAGCCACAAATGAA
-GGGTAGAGGGTCTGAACCACCAAGATAAATGTAAGTTTTTCCTTTCCTTTTATGTTCTTTTCCTTTCCTGTTTAATACC
TAAAATATTTATGCCGTCTCCGTAACCGAGTATCAGATAGCTGAGAGGCATGATTTGCTATTACTGTTTATGTTTCGTGA
TTCAAGTATGAACTCTGAACGATGTTCTTTTGT---------GTGGATGACATCATATATCAACAAAACAAACAATACAT
CATATACATCTTGTGAAAAAAAGTAGGCTGTCGATCCTTGACCATCTTCAGAATTAGCATTGGCAAGTAGCTAGCTGTCT
AATTCTAAAAGGTCAGGTACTAACTTTCCGTGTCCTCAGACGCATGAAACTGACCGGCCGCTGTGAAGCTACTACTTGCT
TCACCCCAGCTCTGTAAGCACATCCTGGAGCTAGGATCATAGTCCCACAGTCCGGATGCCATCTGTCGCCAGAGTTTCTT
CTTCCTCCCGTTTACCCAGTTATTGTGGATGATGAAGCACCCAAGGTTCCTGCAAGCCAAGCGCAGATCGTGCCTCTCCC
AAAGTCCCTTGTAAGCTCCGTTGGGGAACAGGTCCTGGTCCAGGAACACGACGGTGAGGTTTGTGCTAGGCTCTAGGCAT
CTGTCGTTGCCGAGTCGGTTCACACCTTCCTTCCCACACAGGACGTCATAGAAGCTTGGCTGCTCTGATGAGTTTGATTT
GGCCGCGTGCTTCACTACCATCT
>chr1B_1
GCATCTCCAGGCAACCGCGTGACG---TAGTAAACCCTACTCTCTCTTCCCGGTCCCACCCGCCAGCCGCACTACGGCAC
AAGCTGCTGCTTCTTCTTCTTCGTTCCCGTCCCCTGCGCTCGCG------GCGGCGGCGGCGGCTTTCCACGGTAAATCT
CGGGGCAGGATCCGTTGAATAATTTTGGACAAGTCTTGGAGTATGTTGTAGCCTTGTAGATCCGAACCAGGGATCCTTGT
TTAGGGAGCCTTAGTCCACGCCGCCCGACCTCGCCGTCGTCGCCTGGAACCGAAATTTCTTTGTGGGGATGGGGTCGATT
CCATCCAGCTTTTTCTTCGTGGAATCTGGCAAGTTTCATTGTTGTTTCGGTGGGCAATCTCCCTGAGAGCAGATTGATCG
GTGGGCAATCGCCA----TTAGGATACAGTTCAGCTACTGGGTCCATCAGGGAGTAGACACAACTGCTTATTTACCATTG
AGTCTACTCCAGGCGTAGTATATCATATAAACATTCAGTGCATTTCTACTGGTT-ATTCAACCTATTTGTGACCGCTGAA
TGACCAATCTAAGACTCTAACTATATGTATGTAAGGATCAAGGTAGTACAATATAATG---TACTGGATAGCAGTTGAGT
TATCATGCCCAGCCCAGGTCAGCAATGTGATCTCTAAA-------CAAGGCGATATGTGCATAGAAAAATCCAAAACTGT
AGTACATGTATCAGGTAACAGGTGATATGTGCAAGCCCATATGACCAATC-GATCCCTTTTTTG----GAGAATTTCTTA
TTTAACTTGTATTCTCCGGAGGTGTCTC--------AATCTTAACATTGTATGGCATTTCTCTTGCTTTAGTATTCTTTT
GCTAGATGTACGAGATTTCTCTTGCTTTGCTATCCTCCTTTTGCTCCTTGTGTCTGCCTTTGACATTGCAGATGCTTGAA
CTTT---ACTCTAATGTTCTGTTTGCCTGCCGCATTTTCAGTTTTCTTTGCCGT-GGAAGTTCATACCCACTAGATGGGG
AAGGCAAAGCGTGCTTCCATATTTATCAGGCTCGTTTCAGCAGCTGGGACTGGTTTTTTCTATGTGAAGCGCAAGAATCC
TCGGCGGATTACAGAGAAGCTTGAGTTCAGGAAGTATGATCCTCGTGTAAACAAGCATGTTCTATTTACGGAAGCCAAGA
TGAAGTGAGACAGTGCAGCCTTTTTTTTTTCTTGACATAAGACCTCCACTGTTCATTTTCGTTGAAGACA---ATGCTAC
CTTTATT--AGTTTGTTCCAGATTCGAGAGTTTCATGTGG--------------------------------GCACCAAA
TCAGCATGGAT-----CTTGCTCTGCC-TGCCTGTTTATTTGTATTCTAAGTTTGTAACTGAAATGAGCTGCAAGCCTGC
AAAAGTACTGCCCATCTA--GTGTTGTGATGATTATCATGTGGATGCTTGGTTCTGAAACTTAAAGCAGCCACAGATGAA
-GGGTAGAGGGTCTGAACCACCAAGATAAATGTAAGTTTTTTCTTTCCTTTTATGTTCTTTTCCTTTCCTGTTTAATACC
TGAAATATTTATGCTGTCTCCGCAACCGAGTATCAGATAGCTGAGAGGCATGATTTGCTATTACTGTTTATGTTTCATGA
TTCAAGTATGAACTCTGAACAATGTTCTTTTGT---------GTGGATGACATCATATATCAACAAA-CAAACAATACAT
C--ATACATCTTGTGAAAAAAAGCAGGCTGTCGATCCTTGACCATCTTCAGAATTAGCATTGGCAAGTAGCTAACTGTCT
AATTCTAAAAGGTCAGGTACTAACTTTCTGTGTCCTCAGACGCATGAAACTGCTCGGCCGCTGTGAAGCTACTACTTGCT
TCACCCCAGCTCTGCAAGCATATCCTGGAGCTAGGATCATAGTCCCACAGTCCGGACGCTGTCTGTCGCCAGAGTTTCTT
CTTCCTCCCGTTTACCCAGTTATTGTGGATGATGAAGCACCCAAGGTTCCTGCAAGCCAAGCGCAGATCGTGCCTCTCCC
AAAGTCCCTTGTAAGCTCCATTGGGAAACTTGTCCCGGTCCAGGAACACAACAGTGAGGTTCGTGCTAGGCTCTAAGCAT
CTGTCATCGCCGAGGCGGTTCACACCCCCCTTCCCACACAAGACGTCATAGAAGCTTGGCTGCTCTGATGAGTTTGATTT
GGCCGCGTGCTTCACTACCAT--
>chr1A_1
GCATCTCCAGGCAACCGCGTGACATACTAGTAAACCCTACTTTCTCTTCCCGGTCCCACCCGCCAGCCGCACTACGGCAC
AA------GCTTCGTCTTCTTCATTTCCGTCCCCTGCGCTCGTGGGATCTGCGGCGGCGGCGGCGTTCCACGGTAAATCT
CTGGGCAGGATCCGTTGAATAATTTTGGACAAGTCTTGGAGTATGTTGTAGCCTTGTAGATCCGAATCAGGGATCCTTGT
ATAGAGAGCCCTAGTCCACGCCGCCCGACCTCGCCGTCGTCGCGTGGAACCGAAATTTCTTTGCGGGGA--GGGTCGATC
CCATCCAGC--TTTCTTTGTGGATTCTGAGAAGTTTGATTGTTGTTGTGGCGGGCAATCTTCCTGGGAGCAGATATATCG
TTGATGCGGTTTGTATCGTTAGGATGCAGTACAGCTAATGGGTCCATTAGG-AGTAGACACAACTGCTTATTAACCATTC
GGTTTACTCAAGGCGTAGTATATCATATAAGCGTTAATTGCATCAGTACTGGTTCATTCAATCTACCTATGAGCACTGAA
TGACCAATCTAAA--------TATGTGTATGTAAGGATCAAGGTA---CGATATAATGTACTACTGGATGGTAGTTGCGT
TATCATGCCCAAACAAGGT--------------------------------GATATGTATGTAGATATGTCCAAAACTGT
AGTAGGTGTATCAGGTAACAAGTGATATGCAACTTGG--TATGACCAATGTGAACCCTTTTTTGTGTGGAGAATTTCTTA
TTTTACTTCTATTCACCCGATGTGTCTCTTTCTTAACTCT----------------------------------------
------TGTATGAGATTTCTCTTGCTCTGATATTCTCTTTATGCTCCTTGTGTCTGCCTTTGGCGTCGCAGAAGCTTGAA
TATTACCACTCTGATGTTGTGTTTGTCAGCCCCATTTTCAGTTTCCTCTGCTGTGC-AAGTTCATACCCACTAGATGGGG
AAGGCAAAGCGTGCATCTATATTTATCAGGCTCGTCTCAGCAGCCGGAACTGGATTTTTCTACGTGAAGCGCAAGAATCC
TCGGCGGATCACAGAGAAGCTTGAGTTCAGGAAGTATGATCCGCGTGTAAACAAGCATGTTCTATTTACGGAAGCCAAGA
TGAAGTGAGACGCTGCAACCTTTC---TTTCTTACCATAAGACCTCTACCGTTCATTTTGGTCGAAGACGATGATGCTAC
CTTTATTTTAGCGGGCTCTAGATAATTTAGTTTCATGTAAACAACTCTAATGAGCACGTTTTGATCTCGTCAGCACCGAA
TCAGCATGGATTTTCACTTGCTCTGCCTTGCCTGCTTATTTGTAT--------TGTAACTGAAATGAGCTGCAAGCCTGC
AAATGTACTGTCCCATTTTGGTGTTGTGATTTTTGTCA-GTGAATGCCTGCTTCTGAAACTTACAGCACCCACAGATGAA
GGGGTAGAGGGTCTGAACCACCAAGATAAATGTAAGTTTTTCCTTCCCTTTTATTTTCTTTTCCTTTCCTGTTTAACACC
TGAAACATATATGCTGTCTCCGCAACCGATTATAAGATAGCTGAGAGGCATGAATTGCTATTACTGATTATGTTTCGTGA
TTCATGTTTGAACTCTGAACAATGTTCTTTTGTTTGTTTTGTGTGCATGACATCATATATTAACTAA-CAAACAATACAT
--TATACATTTTGTCAAAACAAGCAGGCTGTCGATCCTTGAACATTTTCAGAATTAGCATTGGCAAGTAGCTAACTGTCT
ACAAT---AAGGTCAGGTACTAACTTTCCATGTCGTCAGACGCGTGAAACTGCTCGGCCACTGTGAAGCTACTACTTGCT
TCACCCCAGCTCTGCAAGCACATCCTGAAGCCAGGATCATAGTCCCACAGCCCGGATTCCATCTGTCGCCAGAGTTTCTT
CTTCCTCCCGTTTACCCAGTTATTGTGGATGATGAAGCACCCGAGCTTCTTGCAAGCTGAGCGCATGTCATGCCTTCCCC
AGAGCCCCTTGTAAGCTCCGTTGGGGAACAAATCCCGGTCCAGAAACACGACGGTGAGGTTTGTGCTAGGCTCTAGGCAT
CTGTCGTTGCCGAGTCGGTTCACACCTTCCTTCCCACACAGGACGTCATAGAAGCTTGGCTGCTCAGATGAGTTTGATTT
GGCCGCGTGCTTCACTACCATCT
>SNPs
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--------S-----------------------------------------------------------------------
--S-----------------------------------------------------------------------------
--------------------------------------S-----------------------------------------
-----------------------------------------------------------S--------------------
----------------------------------------------------S-------S-------------------
-------------------------------------------------------------------------S------
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--------------------------------------SSSSSSS-----------------------------------
------------S---------SS----------S-------------S-S-----SS----------------------
--------S-------------------SSSS-SSS-------------------------------SS-----------
------------------------S-------------------------------------------------------
------------------------------S------------------SS-SSS-------------------------
-----------------S-----------------------------------------------------S--------
------------------------------------S-------------------------------------------
-------------------------------------------------------------------------S------
------------S-------------------------------------------------------------------
----------------------------------------------S-------S-S----------------------S
-------S------------------------------------------------------------------S-----
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-S------------S-------S---------------------------------------------------------
--------------------S----------------------------------------------S------------
-S---------------------S-------------------------------------------------S------
----------------------------------------------------SS--------------------------
--------------S-----------------------------------------------------------------
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------------------------------S----S--------------------------------------------
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>forward_380
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----------------------------------------GTTGTTGTGGTGGGCAATCG--------------------
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>reverse_1784
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-----------------------TAGGCTGTCGATCCTTGACC-------------------------------------
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