>input_sequence_87039
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----------------------------------------------------------------------------ATGC
TGGTGGTGGAGCTGGGCATATGGGTCATCCCGCTGACCCTCGTCTTCGTCCCGTGCCGGCGCATCGTCCTCCTCCTGTCC
AGGCTCCAGGAGCTTGGACGGACCATGATGCGCCCGAGGCTGGTGATCAGCTCGCGGGAAGAGGACATGTGGAGCCGCCT
GTCCAGGCTTAACTCCATGGCCTTCATGTTGTGA----------------------------------------------
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>chr1A_1_TraesCS1A01G188400
GTAGTATTTGCGGGTTGCATTATTGGGCCTGGCAAGAATCCAAGATGGAAGAACAGTGAAGAAATCGTCCGATGGTGCGG
CTCCAGGATGGTTTATG-GCACGGGAATCTGCAGAGAGACTGAGAGAGGGGCATGTGCATATGCTTTTGCTAATGAGGAC
GAGCGTCACCCACCGCACTAGCT--------CTTAAACAATTCGTGTCCCTGTTCCGGCCAGCAACTGGCTCCATGCTTG
ATCGTTCTGCTTTATAGA-----------GACCTCCTCTTGTTTCTGTGGGC-AAGCCACGGTGGTAACTGGACAGCAGT
CAACAATTAGACTAGCCAAAGTACAGGGTGTAAAAGACTGCATCAATTGCTGCTCC----------TTCCGTGCTCGATC
CA-----TTGAGACGATGAGATCTATCCATCAGTGGCCTTGCCTCCCCAATCTGGTTAATCTCTCTTTCAAGTAAAACCT
CATAAAAGCTTCTTGCTTGCATCCCTCTCTCTCCAAAAGTATCCACAGTATTGGAAATAACGCATGTTAATCAACAAAGC
ACAAAGGCGCCGTGCTTAATCCGCACCAAATTGCCACTTTTGGTGTTTGCTTCTCTACGCAAGCATCACTGCTCCGCCAA
CAACTATCCCAAGTCGTAAGACAGACACGGATGGCAGTGACAATGCCAAACCGAAAAAATCGGTCGCGAGTTATCT----
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-------------CAGGGAACCAAAGGCAGTGAAAGGACAAGGCAGCCTATGACCCTAAATGCACTATTTAATTTCAGAT
CACACACCGGTCACCGTCATGTGGAGTGGGAAGGGAAACCACCTAGCCTACC------TCACTGAGCTAGGACACAGCAC
ATTCCGCA------------------------------------------------------------------------
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-----------------------------------------------------------------GTAGATGGCGGGCAT
ATCATATCAGGAAATCAAGGCGGATCGGACGGCGTGCCCTCCACTAGAGCCTAGCTAGCTGAGCTCCGTTATATAAAGAG
CATGGAGCTAGCGACCCGGTGGGTGCGAGAGCAAAGCACAGTCCCACCATTTTTTTGCAGCGGCGGCGAAGCGAGGATGC
TGGTGGTGGAGCTGGGCATATGGGTCATCCCGCTGACCCTCGTCTTCGTCCCGTGCCGGCGCATCGTCCTCCTCCTGTCC
AGGCTCCAGGAGCTTGGACGGACCATGATGCGCCCGAGGCTGGTGATCAGCTCGCGGGAAGAGGACATGTGGAGCCGCCT
GTCCAGGCTTAACTCCATGGCCTTCATGTTGTGATGTGACGGCGGTGATGGTACTATGTGTGCCTGCTT-GCCCCTCTCC
TCGGTTGGTGTTCGATGCTAAGTTGTTTTTGCTTCTTCTTTTCTTGAGCCT----TGTATGTATCTGTAATAAGCTCACG
GTAGTTGAGATGTAT--TAAGATGTATATATATTTGGCGTAGCTTGGACTTTGATGTTAGATGTATATACTGGTGTGGTA
GAGGCAATGAAGTGAAATTAACGTCATGGTTCATCTAGCGGAATTTCTTGGACTAGTAGTATTTGTATTGTTTGACATGA
GAGATACTTTAACAAATACAT-----------------------------------------------------------
---------------ATTTCTCTTGAAGTAGGCTTTCATCCCCGCTTTATAAATAAAGCAACCATCACATCCATACAACA
AGAGTG----CACGAAGAAAGTAACCGAGTATATTGGAGCATCAGCACAAACACGGCGAAAAAAAAACATGAAAGAAAAC
GAAAAAAAGACCACCAAGTGGTCGGTGCCTCAAGCACACTGAGGCGTAGTAAGTCGGCATGGGGCAGCAGTCATCGCGTC
CATCGTGTCGCCAAACCAATCATGATCCCTCTGTCCACATATTGAGTTTCAGTGCTGCAAGAATAAAAAAACTTGAAG-A
TAGAGTCAGAGGCCAGCCTAAGAAAGACCCGCTCAATAACCATCTTGTTACGTGTCGTCCACAGGGTCCAAACTAACGCT
GCA-----------------CGTCTCCTCCTCCTAGTTTGGTTGGCCTAGTTTTAAAGAAACGGAGCTAGGTCTGAGGCC
TCCCAATCGGGCCCTAGAACCTCACGGATAAAACACCAAAGTAATAGCGCTGCCAAGAAGAGGGTATGAGTCCATGTCTC
CGGGATAGCACAAAGGGGGCACGATCCATCCCCAGGGTCCTGATGTTTGATCACCTCTGTCCCAGATGGGAGGCAATCTC
CCAACAATTGCCATAGAAATATTCGGCACAAGGCATGATATTGCCAAGACACGGCGTCCGGGAGCACCGTCCGCGGGGAG
GGGGGAGGTTTGCCCGC
>chr1D_1
GTAGTATTTGCGAGTTGCATTATTGGACTGGGCAGGAATCCAAGATGGAAGAACAGTGAAGAAATCGTCGGATGGTGCGG
CTCCAGGTTGGTTCATGAGCACGGGAATCTCCAG--------AGAGAGGGACATGTGCATATGCTTTTGCTAATCAGGAC
GAGCGTCACCCACCGCACTAGCT--------CTCAAACAAATCGTGTCCCTGTTCCTGCCAGCAACTGGCTCCATGCTTG
ATCGTTCTTATTTGTAGA-----------GA---TCTCTTGTTTCTGTGGGC-AAGCCACGGTGGTAACTGGACATCAGT
CAGCAATTAGACTAGCCAAAGTACAGGGTGCAAAGACT--GATCAATTGC-TCTGCTACCAACCGGTTCCGTCCTCGATC
CA-----TTGAGATGATGAGATCTATCTATCACA-GACTTGCCTCCCCAATCTGGTTAATTTCTCCTTCAAGTAAAACCT
CATAGAAGCTTCTTGCTTGCTTCCCTCTCTAAACTCTCTACACTCTACAGGGAAACAACACAAA-GTTAATCAATAAAGC
ACAAAGGCGCCGTGCTTAATCCACACCAAATTGCCACTTTTGGTGTTTGCTTCTTTACGCAAGTATCACTGCTCCGCCAA
CAACTATCCCAAATGGTAAGACAGACACGGATGGCAGTGACCATGCCAAACCGAAAAAACTGGTCGCGAGTTATCTAAGA
GTGTTTGTTTCCAGAGACTTTTTGGTGCAGGG------------------------------------------------
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---ACCAGAAAAAGTCCCTTTGAAAGACTTCTCAATCAAATAGGAGGGACTACTAGGGACTAAAAGTTGCTTTTTAGGAC
TTTTTCAACAA---------------------------------------------------------------------
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------------------------------TGCCCCTCCCTGCACCCATTGCCCCGCCGTCCCATGGTGTTGTTTGGTTG
TTATTTTTCTGTATACTAGGGGTAACATTGTCATTTAATAACCTCTAGGGAGGGACTAGGGACTTTTTAGTTCTGGAAAC
AAATTTTTTAGAGACTATGGACTTTTTAGTTGGGACTAGAATGAACCAAACAG---------------------------
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--------GGCCTCAGGCTACCAAAGGCAGTGAAACGACAAGGCAGCTGATGACGCTGAATGCACTAGTTAATTTCAGAT
CACACACCGGTCACCGTCACGTGGAGTGGGAAGGGAAACCACCTAGCCTACC------TCACTGAGCTAGGACACAGCAC
ATGCCGCGGTGGCAAATTTGACAAATTTGACCTATAAACGAAATCAAATCACAGAATGAACTATTCGTGAAACTATTTCA
CGCGGCTGACCTTTTTGTGTGACGCCCGACACGAAGGCGCCACACTACACTGTGCAACGTCTCACAGATAGGCGCTACAC
GGCCAGCGTCGCACCCGTGTAATCAGAAAATTACTAAATCAGTGTGCAGCGCCTGAGAGCTAGGCGCCACACTATACAGT
ATAGCGCCTAGCTCCTAGGCGTTGCACTAGTGCAGCGCCTGAGAGCTAGACGCCACGGGTCAGCCGCGTGAAATAGTTTC
ACGGACAGTTCATTTTGTGATTTGATTTCATCTATAGGTCAAATTTATCAAATTGCCCCGCCGCGGTAGATGGCGCGCGC
ATCATATCAGGAAATCAAGGCGGGCCGGATGGCGTGCCCTCCACTAGAGCCTAGCTAGCTGAGCTCCGTTATATAAAGAG
CATGGAGCTAGCGACCCGGTGGGTGCGAGAGCAAAGCACACTCCCACCATTTTTTTGCAGCAGCGGCGGAGCGAGCATGC
TGGTGGTGGAGCTGGGCATATGGGTCATCCCGCTGACCCTCGTCTTCGTCCCGTGCCGGCGCATCGTCCTCCTCCTGTCC
AGGCTCCAGGAGCTTCGCCGGACCATGATGCGGCCGAGGCTGGTGATCACCTCGCGGGAAGAGGACATGTGGAGCCGCCT
GTCCAGGCTTAACTCCATGGCCTTCATGCTGTGACGGCGG---------GGTACTATGTGTGCCTGCTTTGCCCCTCTCC
TCGTTTGCTGTTCGATGCCAAGTTGTTTTTGCTTCTTCTTTTCTTAAGCCT----TGTAT----CTGTAATAAGCTCGCG
GTAGTTGAGATGTAGTATAAGATGTGTATATA-TTGGCGTAGCTTGGACTTTGATGTTAGATGCATATACTGGTGTGGTA
GAGGCAATGAA-------------------------------ATTTCTTGGACTAGTAGTTTTTGTATTGTTTGACATGA
GAAATACTTTAACAAATACATACTCCCTCTGTCCCAAAATAAGTGACTCAACTTAACTTTGTACTAAAATTCCTACAAAG
TAGGACGGAGGGAGTATTTCTCTAGAAACAGGCTTTCGTCATA-CTTTACAAATAAAGCAATCATCACATTCATACAACA
AATTCAAGTTCACGAAGATAGTAACAGAGTCTGCTGGGGCATGAGCACAAACACACGC--AAAAAAACATGGAAGAAAAC
GAAAAAAAGACCAAT---TGGTCGATACCTCAAGCCTCATGAGGCGAAGCAAGTCGGCATGAGGCAGCAGTCATCGTGTT
CGTCATGTGGACAAACCGATCGCGATCCCTCTATCCAGATAGCGAGTTTCGGTGCTGCAAGAATACAAGGAATTTGAAAA
TAGAGATAGAGGCCCACCTAAGAAAGACCTGCTCAATAACCATCTTGCTACGCGTCGTCCACAGGGTCCAAACTAACGCT
ACATAACAAGCTAGAAGAGGCGTCTCCTACTCCCAGTTTGGTTGTCCCAGGTTTAAAGAAACACGAGTAGGTCTGAGGCC
TCCTAGTCGGGCCCCAGAGCCTCACGGATAAAGCACCAAAGTAATCGCGCCGCCGAGAAGAGGGTATGAGTCCATGTCTC
CGGCATAGCACAAAGGGGGCACGACCCATCCCCAGGGTCATGATGTTTGATCACCTCTGTCCTAGATGGGAGGCAATCTC
CCAACAATTGCCATAGAAAGATTCAGCACAAGGCACGATAT---------------------------------------
-----------------
>chr1B_4
---GTGTTTGCGGGTTGCATTGTTGGGCCTGGCAAGAATCCAAGATGGAAGAACAGTGAAGAAATCGTCTGATGGTGCGG
CTCCAGGTTGGTTCATGGGCGCGGGAATCTGCAG--------AGAGAGGGACATGTGCATATGCTTTTGCTAATCAGGAC
GAGCGTCACCCACCGCACTAGCTGCATCGCTCTTAAACAATTCGTGTTCCTATTCCGGCTAGCAACTGGCTCCATGC-TG
ATCGTTCTTCTTATTGGGGACCTCCTCCTGA---CCTCCTGTTTCTGTGGGCAAAGCCACGGTGGTAACTGGACAGCAGT
CAGGAAATAGGCTAGCCAAAGTACAGGGTGTAAAAGACTGGATCAATTGCTTCTGCTACCAATCGGTTCCATGCTCGATC
CATTAAGTTGAGATGATGAGATCTATCTATCAGA-GCCTTGCCTCACCAATCTGGTTAATCTTTCTTTCAAGTAAAACCT
CATAAAAGCTTCTTGCTTGCATCCCTCTCTCTCT-AAAGTATCTACAGAATTGGAAATAATGCATGTTAATCAATAAAGC
ACAAAGGCGCCGTGCTTAATCCGTACCAAATTGCCACTTTTGGTGTTTGCTTCTCTACGCAAGCATCACTGCTCCGCCAA
CAACTATCCCAAGTGGTGAGACGAA----GATGGCAATGACCATGCCAAACCGAAAAAACTGGTTGCGAGTTATCTCAGG
CCAACTCCACCGCACGACCCCAAACGGATGTTCAGTTTGGTTGGATTTTGTTCCTTTGGGAAGGCAATGGGTTCGCGAAA
GTCCGCTTCTATTCGTTGGGTCGTGGGTGCGCCCAACACGCGGCCGCACCCCAAATCATGTCTGTGTTGGACGTGATTAA
AAAAACAGAAAAACTTAAATAAAATGACTAAAAAGGTAAATAAATGCAGTTAAAAAAACATAAAACGTAAGTTAGGGGTC
ACAGCCACAAAACGGTCTAGTTTCACGGTTCACTTAACGGCCCACTGCCATAATTAATATAAAAACAAAATAAAAAAACG
CCGCCCGCGTGCTCCTGCCGTGGCCGTCGCCGTCTTCAGTGGCTGCCGGTGTTGTCGTCGTCGTTGACGAGGTCGACGTA
CTCCGACGGCGTCCAGAGGTGGGCCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTCCCGCTCCGGTGACATCGGCGG
CGTGGGGCACCAGTTCACGTCCCCCACGGCGTCGGCCATCTCCGTAGCCGTGCACGACCAACTCCACAGCTGGCCCACCA
GGCCCGGGTGGAACGCGGTCACCGGCGCCTCCTCCATCGCCTCCTCCGCGGCCACAATCTCCAGCTCGGGGATGGCGACG
TCGCCGACCGCAGAGAGGGCCATCATCTCCTCGAGGCCCTCCCATTGGTGCTCGTCGTGCGTCTTCATGGAGTCCCCCAT
GACACGCGCCATGAGACGGGCCTCCTCCTCCGCTGTCATGCGAGGAGGTGGTGGTGGCGACGGAGAGGGGTGAAGGCGAC
GACGTGGGCGTGAGGCCGCGCACCCGCGTACGCTCGCGCTCCTAAGGAGCACGCGCTGCGCGCTCTGGACGTGGCCGCCA
CGGCCCCGACGATGTGCCGGCGAAGAATGACGCGCGCCGCACGTCGTGCTCGTCCTGGAGCCACGTGTCCCGGAGCCGGG
AGTTAGGAGCGTACCTATCGTCGTAGTATAGGTCGTCAGGGAGGAGGCGGCGACGGCGCTCGATCTTCTCGCGGCGCGCA
CGGCCGCTCACCGGGTCCGGCGGGATCGGCACGCAGTCGGCGGAGAGGTGCTAGTTGTTGGGGAGGTGCACGTCGCTCCA
CGGGAGCGGCATTCTCGTCTCCCAATAGCGGCGGCATACATCCGCGACGATGTACTGCCGGTCGCGCTCGCCGGAGGCCG
TAGGGCCGATGGTGAAGGGGGCAGGCGCGGGGGCCCGACACGGTGGTGATGCGGGCTCCTCCTTCACGTCGCGGCGGCGG
CGGCCCGAGGACGAGCCAGCCTCGCGGTCGTGCTTCCCCTTGCAGCCGTAGTTCCATAGCCCCATGGCTGCGAGGCTTCC
GGCCGCCGAGTTCGAGGCTAGGGTTTGGGGGTTTGGGGGTGTCGGGTTTCAAGGAGGCCGTGGGGTTGAGTGAGGAGTGT
GGACGATGACCGGTCCATGGCTTCCCCATTTAAGAAGGACCGTGACCATTCGCCTGGGCGGATGACATGTAAGGCTGGCC
GCGCGTGCGCATTGGTGTTGGCGGGTGGGAGGTAGGTGGCCGTCTGCCACGCGTCCCCGACGCGGACGAGCGACGTGTCC
GTTTGCTGTCCGCCGCAACCCAAATCCGACGCATATTTGCATTCGAAATGGATCGACCGGAACATAAAACGGACAAAATG
GATTCGGACGTCACACGCTGGGCCGACCGGTTTATCCTTTTATCCCAAAAGGACGAGACTGGACGGGATGGGGTCGTGTG
GTGGAGTTGGCCTCATGCTACCATAGGTAGTGAAAGGACAAGGCAGCCTATGACGCTAAATGCAGTAGTTAATTTCGGAT
CACACACCAGTCACCGTCAAGTGGAGCGGGAAGGGAAACCACCTAGCCTGCCTCACTGTCACTGAGCTAGGACACATCAC
ATGCCGCA------------------------------------------------------------------------
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-----------------------------------------------------------------GTAGATGGCGGGCAT
ATCATATCAGGAAATCAAGGCGGGTCGGATGGCGTGCCCTCCACTAGAGCCTATGTAGCCTAGCCCCGTTATATAAAGAG
CATGGAGCTAGCGACCGA-TGGGTGCGAGAGCAAAG--CACTCCCACCATTTTTTTGCAGCGGCGGCGAAGCGAGGATGC
TGGTGTTGGAGTTGGGCACATGGGTCATCCCGCTGACCCTCGTCTTCGTCCAGTGCCGGCGCATCGTCCTCCTCCTGTCC
AGGCTCCAGGAGCTTCGCCGGACCATGATGCGCCCGAGGCTGGTGATCACCTCGCGGGAAGAGGACATGTGGAGCCGCCT
GTCCAGGCTTAACTCCATGGCCTTCATGCTGTGACGGCGG---------GGTACTATGTGTGCCTGCTT-GCCCCTCTCC
TCGTTTGTTGTTCGATGCCAAGTTGTTTTTGCTTCTTCTTTTCTTGGGCCTTGTATGTAT----CTGTAATAAGCTCGCG
GTAGTTGAGATGTAGTA--AGATGTATATATA-TTGACGTAGCTTGGACTTT----------------------------
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>SNPs
---------------------------------------------------------------------S----------
-------S-----S--------------------SSSSSSSS--------S-----------------------S-----
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--------S----S-----------------SSS----------------------------------------------
--S-------------------------------------S----------S--S-------------------------
-------------S-------------S-----SS---------------------------------------------
----------------------------------S--------S----S-------------------------S-----
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--------------S--------------------------S-----------------SS-------------------
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-----------------SS-----------------------------------S------------S------------
-------------------S------------------------------------------------------------
--S-----------------------------------------------------------------------------
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-----------------------S-----S--------------------------------------------------
----------------------------------------S---------------------------------------
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---------------S-S-------------------------------S------------------------------
----------------------------S-----S-SSSSSSSSSSSSS-------------------------------
---S---S----------S-----------------------------------------SSSS-------------S--
--------------S-----------------S------------------------------S----------------
-----------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------------S-------------------
--S-----------------------------------------------------------------------------
-----------------------S---SS--------S--SSSS-----S-----------S--------S---------
-SSSSS------------S------S----S-SS---S----S-----------SSSSSS-----------S--------
-------------SSSSS------S-S--------SSSS-------S--S-----------S--------------S--S
-S--S---S-S------S---SS---------S----S---SS-------S--------------S--SS-S--SS-S--
-----SS-------SS-------------S-----------------S----S---------------------------
S---------------------------S----S----------S--S--S-----------SSSSS-------------
---S-S--------S---S-------------S------------S----S---S-------------------------
---S--------------------S--------------S----------------------S-----------------
-------------------S----S----------S-----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSS
>forward_2658
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------------------------------------------------------------------------------GG
TCGCGAGTTATCTCAGGG--------------------------------------------------------------
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>reverse_4404
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---CAATCGGGCCCTAGAACCTC---------------------------------------------------------
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