>input_sequence_72954
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--ATGGTACTC-----------------------------CCTCTTCTTCTTAATCTTAATCAGTTCACGCTCAATTAGT
TCGTCGTGGATTTGTCGATAACTTTGGTGGATTTTTGGTTGCGCGTGAACATTGCAGGCGAACGCGGTGTCGGGCGTGGC
GGTGAGCGAGGAGTGCGTGAGGGCGTTCCAGGAGCTGCGGGCGGGGCGGGCGCACCGGTTCGTGGTGTACAAGATGGACG
ATGCCGTGCAGCGGGTGGTGGTGGACAAGGTGGGCGGCCGCGACGCCGGCTTCGACGACCTCGCCGCGGCGCTCCCCGCC
GACGACTGCTGCTACGCCGTCTACGACCTCGACTTCACCGTCGGCGACGCCACCGCCAAAGGCGCCGACGGGGAGGCGCC
CCGCAGCAAGATATTCTTCATCTCCTGGTACGTACTCCTGTGCTACGCTTAAATAGGAGTACTTCAAATC----------
-ATGCAACTACGTACGTGAGCCGCACGATGATGACATATGTG----TGATTATTGATGAAGGTCGCCGGCGAGTGCGGAG
GTGAAGAGCAAGATGATCTACGCCAGCTCCAACGAGGGGTTCGAGAAGGAGCTGGACGGCACGCAGATCGACGTGCAGGC
CACCGACCCCAGCGAGCTCACCCTCGACATCCTCAAGGACCACGCCACCTAA----------------------------
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>chr5A_1_TraesCS5A01G478800
TTCTTCGAAACGTGATGTGAGCTGTGTCTTGGCTGTGTGCGGTGAATCGATAATCTTTTTACCCGTTTCCATTAGGGCCT
TTCCATTATCCAGTATACTGTAGTGGAACTATCATCCCTCTTGGTCGTGGGCTTTGCATGAATGGAGAAAACAAAAAACT
TAAGGCCTCATTCGGTTTGAAGGATTTCTATAGGAAAAACGTAGGAATAAGGATTTCACAAGAAAATTTTCTATAGATGC
ATTTGGTTTGGAGAAAATGTGTACGGGGATTTCATAGGAATACTATTCATTTCCTTTGTTTTTGGATGAATCTACACATC
CACTCAAAGCTCATTTTATGCGTAGAAACGAGGCAAGACAATTCTTTAGGATGGCACTTGCCATCTTATCAAATTTCTAT
ACTACTCTAAATTCCTACATTTTGCTTTCCTCCAAACCGAATGAGGCTAAAGGGTTACATGCAATGGTCAA-CTTGAATG
GCACCACAGGAATTCGCAGATCAATTCTAGTTCT------ACTCACCTGGATACGCAAAACGAACCTTCCA--CCGTGAT
TGACAGGCGTACTAACCGAAATATGCACGTCACTGCGGATGAAGCACAATCGAACTGCTGAGCTGATCTTCGCGAATCAA
GCTAGATATAATGCTG---ATGGAAAGGGCGCGCCCTCAA------TCTGCTGACCGACCACGCAAGCGGATCTGGCCAC
CATCAGTCGAGACGAC------CTTTCCAAGCTTCGATTCTTGGGCGTGAGTCACTCCAATTCTTCTTCTTCCCGCTGCC
ACATCGCCATGTCGAGAACAGTCCGCCCGACGGAGAGCGACACCACAGCGCCCACACGTGT-------------TCACCT
CGCTCACATTGGACACGACACACAAT-----CATCTTATTTAAGCACCAGGCGACACCACGCTGAAATAACAACAAAAAA
CCACTGCGAAATACTCCTACTACTAGCAGTTCTTCGCTGCAGCATCATCACACAGATTTAAGGTTCAATCTCCAGACAGA
AAATGGTACTC-----------------------------CCTCTTCTTCTTAATCTTAATCAGTTCACGCTCAATTAGT
TCGTCGTGGATTTGTCGATAACTTTGGTGGATTTTTGGTTGCGCGTGAACATTGCAGGCGAACGCGGTGTCGGGCGTGGC
GGTGAGCGAGGAGTGCGTGAGGGCGTTCCAGGAGCTGCGGGCGGGGCGGGCGCACCGGTTCGTGGTGTACAAGATGGACG
ATGCCGTGCAGCGGGTGGTGGTGGACAAGGTGGGCGGCCGCGACGCCGGCTTCGACGACCTCGCCGCGGCGCTCCCCGCC
GACGACTGCTGCTACGCCGTCTACGACCTCGACTTCACCGTCGGCGACGCCACCGCCAAAGGCGCCGACGGGGAGGCGCC
CCGCAGCAAGATATTCTTCATCTCCTGGTACGTACTCCTGTGCTACGCTTAAATAGGAGTACTTCAAATC----------
-ATGCAACTACGTACGTGAGCCGCACGATGATGACATATGTG----TGATTATTGATGAAGGTCGCCGGCGAGTGCGGAG
GTGAAGAGCAAGATGATCTACGCCAGCTCCAACGAGGGGTTCGAGAAGGAGCTGGACGGCACGCAGATCGACGTGCAGGC
CACCGACCCCAGCGAGCTCACCCTCGACATCCTCAAGGACCACGCCACCTAACCAATCAAGCAATCCCTCCAGTG----T
GTATGATTGACGGTTCACGCGTGCACGTTACGTGCGTGC------TAGTTTTGTGCTGTGCATGTATCTTTGCCCTTTTC
GATTGTGTTGTGTGCTTCCAACTGGATCGTGTCGTCGACCCCAAGAGAATGATGATGATTTTCCATTGT----ACTATGT
GGTGTGCAAATAATTGACTCTATCCTCAAGTGAAACACGTAATTTTTTCCGATAAAAGGTGCTTTTATTAACTTAAAATG
TAGCATCAAGCAGATACAAAA-TATGATAAATAAAT-CCGACCTCTGTATAATCAAGATGCACACAGCCAAACATCAAAA
ATCT-----AAAAAAAAGA----AAACGAGAAACCGACATATCGGCAACAGTAGAGTCATATAGGACCAACATTGTGTCT
ATGTCGAAAAAGGTGGTGGGCTGATCCGGAAAATAAAAATAAACGAGAAACCTACATATCAACAACAGTAATACTCTGCC
TACATATCAACAACAGTAATACTTTGCCTATGTCGAAGAAAGTAGTGGGCTGATCCGGAGACTATGCTATCACCTATGTT
AGGTAAAAATCTTTTTGGTCACT---------CGCTCCAACTGCGTATACACCATCTTAAACAGCGGTTGGTACTCCGTC
CGTTGTAGCCTAGACTACATATGAAGCGAGTGCGTACAGTGGAAAATAACCTACAAAGCAAAAAAGTTTATGTTATTAAA
AACCAAAATATTTCTACATAGTCAAAGCGACCACAATAAGGCATACGCTCCCATCCTTAATAACGTTTTGACCCTACTTG
AAATATCGTCCAACCAATGACAAAAAATATTAGCAACACTTGTGGGCGGATATAAATTATGACCAAAAATATTGACAACA
CTTGTGGGCGGATATAAATTGGACGTTCCCATCCTCAATAACATCTTGATCCTATTTGAAATACCGTCCAACCAATGACA
AAAATATTGGCAACACTTGTGGGCGGATATAAATTGAACGTTATTT
>chr5D_450
A-------------------------------------------------------------------------------
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--------------------------------------------------AGAGTTACGTGTGATGGTCAA-CCTGAATG
GCACGGCGGGAATTCGCAGCTCAATTCAATTTCT------ACTCGCCTGGATACGCAAAG-GAACCTTGGACGCCGTGAT
TGACAGGTGTACCAACCGAAATGTGCATGTCACTGCG---GAAGCACAATCCAACTGCTTAGCTGATCTTCGCGAATCGA
GGC----AGATGATTTCAAATGGA--------------AA------ACCGCCGACCGACCACGCAACCGGAACTGGCCAC
CATCCCCAC--CAGATAGATGACTTTTCCAGCTTCGATTCTTGGGCGTGAGTCACTCCAATTCTTCTTCTTCCCGCTGCC
ACATCGCCACATCCAGAACAGTCCGCCCGACGGAGAGCGACACCCCAGCGCCCACACGTGTACACCTCCCCAGTTCACCT
CACTGACACTGGACACGACACACAACACAACCATCCTATTTAAGCACCAGGCGACACCACGCTGAAATAATAACAAAAAT
CCACTGCAAAA------AACCACTAGCAGTTCTTCGTTGCAGCATCATCACACAGATTTAAGGTTCAATCTCCAGATAGA
AAATGGTACGCAATGTCCATACGATCTGCTTCCGAT------TCTCCCTGTTCTTTTTACTCAGTTCGTGCTTTGTTAAT
TTGTAATGGACTCGTGAAGAACTTTGGTGGATTTTGGTT---GCGTGAACATTGCAGGCGAACGCGGTGTCGGGCGTGGC
GGTGAGCGAGGAGTGCGTGAGGGCGTTCCAGGAGATGCGCGCGGGGCGCGCGCACCGCTTCGTGGTGTACAAGATGGACG
ACGCCGTGCAGCGGGTGGTGGTGGACAAGGTGGGCGGCCGCGACGCCGGCTTCGACGACCTCACCGCGGCCCTCCCCACC
GCCGACTGCCGCTACGCCGTCTATGACCTCGACTTCACCGTCGGCGACGCCACCGCCAAAGGCGCCGACGGGGAGGCGCC
GCGCAGCAAGATTTTCTTCATCTCCTGGTACATTTCT----------CTTAAATAGCACTCGTGCTCCTGTATATGTG--
--TGTGACCAACTGTGTGGGCTGCACGATGACATGGTGGTGTTGGTTGGTTAATAATGAAGGTCGCCGGCGAGTGCGGAG
GTGAAGAGCAAGATGATCTACGCCAGCTCCAACGAGGGGTTCAAGAAGGAGCTGGACGGCACGCAGATCGACGTGCAGGC
CACCGACCCCAGCGAGCTCACGCTCGACATCCTCAAGGACCACGCCACCTAACCAATCAATCAATCCCTCCCGTGTGTAT
GTATGATTGACGGTTCACGCGTGCACGTTACGTGCGTGCGTGTGCTAGTTTTGTGCTGTGCATGTATCTTTGCCCTCTTC
GATTGTGTTGTGTGCTTCCAACTGGATCGTGTCGTCCGCACGA--AGAATGATGATGATTT-CCCTTGT----ACTACGT
GGTGTGCAAATAATTGACTCTTTCCTCAAGTGAAACACGTAAT-------------------------------------
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>chr5B_451
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--------------------------------------------------AGAGTTACGTGCAATGGTCAAACTTGAATG
GCACGGCCGGAAATCGTTGGAACAGTCAATTTCCTATTTCACTCACCTGGATACGCAAAG-GAACCTTCCA--CCGTGAT
TGACAGGCGTACCAACCGAAATGTGCACGTCACTGCG---GAAGCACAAACCAACTGCTGAGCTGATCTTCGCGAATCGA
GGTACGTAGATGATTTCGAATGGACAAGGCACGCCCTGACCCTCAGTCTGCCGACCGACCACGCAACCGGAACTGGCCAC
CATCCCCACTCCAGATAGATGGCTTTTCAAGCTTCGATTCTTCGGCGTGAGTCACTCCAATTCTTCTTCTTCCCGCTGCC
ACATCGCCACGTCCAGAACAGTCTTCCCGACGGACAGGGACACCCCAGCGCCCACACGTGT-------------TCACCT
CGCTGACACTGGACACGACGCACAAC-----CATCCTATTTAAGCGCCAGGCGAGGCCACGCTGAAATAAT-ACAAAAAC
CCACTACAGAA------TACTACCAGCAGTTCTTCGTTGCAGCATCATCACACAGATTTAAGGTTCAATCTCCAGACAGA
AAATGGTACGCAATGTTACATTTACTTATGACCTGCCTCTCCTGGTCCTCTTCTTCTTAATCAGTTCACGCTAGC-TAAT
TCGTTGTGGATTTGTGAATAACTTGGGTGTATTTTTCA--------------TGCAGGCGAACGCGGTGTCGGGCGTGGC
GGTGAGCGAGGAGTGCGTGAGGGCGTTCCAGGAGCTGCGCGCGGGGCGCGCGCACCGGTTCGTGGTGTACAAGATGGACG
ACGCCGTGCAGCAGGTGGTGGTGGACAAGGTGGGCGGCCGCGACGCCGGCTTCGACGACCTGGCCGCGGCACTCCCCGCC
GACGACTGCCGCTACGCCGTCTACGACCTCGACTTCACCGTCGGCGACGCCACCGCCAAAGGCGCGGACGGGGAGGCGCC
GCGCAGCAAGATCTTCTTCATCTCCTGGTACGTTTCT----------CTTAAATAACACTCGTGGTCCTGTGTATCAGCA
TATGTGACCAAATGTGTGGGCTGCACGATGACATGTTGGTGTTGGTTGGTTATGTAA-AAGGTCGCCGGCGAGTGCGGAG
GTGAAGAGCAAGATGATCTACGCCAGCTCCAACGAGGGGTTCAAGAAGGAGCTGGACGGCACGCAGATCGACGTGCAGGC
CACCGACCCCAGCGAGCTCACGCTCGACATCCTCAAGGACCACGCCACCTAACCAATCAATCAAGCCCC--------TAT
GTATGATTGACGGTTCACGCGTGCACGTTACGTGCGT----GTGCTAGCTTTGTGCTGTGCATGTATCTTTGCCCTCTTC
GATTGTGTTGTGTGCTTCCAATTGGATCGTGTCGTCGACCCCAAGAGAATGATGATGATTT-TCCATTGTACCACTACGT
GGTGTGCGAATAATTGACTCTTTCCTCAAGTGTAACACGTAAT-------------------------------------
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>chr3A_1863
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------------------------------------------TTTTTTTCAATAAAGGCCGCTTTTATTAACTTAAAATG
TAGCATCAAGCCGATACAAAGC-ATGATGAGTAATACCCGGCCTTTGCATAACAAAGATGTACACAGCCAAACACCAAGA
GTCTGACAGAAAAAAATGAAAATAAATGAGAAACCGACATATCGGCAACAATAGAGTCATATAGGACCAACACTCTGCCT
ATGTCGAAGAAGGTGGTGGGCTGATCCGA---------------------------------------------------
----------------------------------------------------------AGATTATGTTGTCACCCATGTT
GGGTAAAAACCTTCTCGGCCACT---------CGCTCCAACTGCGTATACACCGCCTTGAACAACGGTTGGTACTCCGTT
TGTTGTAGCGTAGACCACATACGAAGCGTGTGCGTACAACGGAAAATAACCTGCAAAGCAGAAGTGTTTATGTTACTAAA
AACCAAATTATTTCTACCTAGCCAAAGCGACCACAATAAGGCATACGCTCCCACCCTCAATAACGTTTTGACCCTATTTG
AAATACCGCCCAACCAAT------------------------------------------GACCAAAACTATTGACAACA
CTTGAAGGCGGATATAAATTAGACC-------------------------------------------------------
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>chr2A_1863
TTTTTTCGATAAGGTGCGT-------------------------------------------------------------
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--------------------------------------------------------------TTTTATTAACTTAAATTG
TAGCATCAAGCGAATACAAAAATATGATGAGTAACACCCGGTCTCTGCGTAACGAAGATGCACACAGCCAAACACCAAAA
GTTTGATAAAAAAG---GAAAATAAATGAGAAACCGACATATCAGCAACAGTAGAGTCATATAGGACCAACACTCTGCCT
ATGTCAAAGAAGGTGGTGGCC-----------------------------------------------------------
---------------------------------------------------GATCCGGAGATTATACTCCCACTCATGTT
GGGTAAAAACCTCCTTAGCCACCCGCTCCAACCGCTCCAACCGCGTACACACCACCTTGAACAGTGATTGGTATTCCGTT
CGTTGTACTGTAGACCACATACGAAGCAAGTGCGTACAACGGAAAATAACCTGCAAAGCAAAAAAGTTTATGTTATTAAA
AA-CAAATTATTTCTACATAGCCAAAGCGACCACAATAAGGCATACGCTCCCACCCTCAATAACATTTTGACCCTATTTA
AAATAGCGTCCAACCAAT------------------------------------------GACCAAAAATATTGTCAACA
CTTGTGGGCGGATATAAATT------------------------------------------------------------
-----------------------------------GAACGCTATTT
>SNPs
--S--SSS-SSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--S-----S---------------------
----SS-S-----------S-------S-S-----------------------------SS-------------------
------------S---------S--------------SSS-----------S--------------------------S-
-S--SS--S-SSSS-S--------S-S---S------S-------------S--------------S----S--------
----SSSSSSSSS--S----------S-----------------------------------------------------
---------S---S------------------------------S-----------------------------------
----S---S----------------S---------S----------------------------------S--------S
-------S---SSSSSS-------------------S-------------------------------------------
---------S-------------------------------------S----SS------------------SSS---S-
----S----------SS--------------------S-SSS--------------------------------------
---------------------------------------S--------S-------------------------------
-S--------------------------------------------------------------------S---------
---------S----------------------------------------------------------------------
S-----------S--------------------SSSSSSSSSSSSSS---------S-S-SS-S-SSS-S----------
----SS--S-SS-SS---S--S---------SSSSS-SSSSS------S-----S-------------------------
------------------------------------------S-------------------------------------
---------------------S--------------------------------------S----------S--------
----------------------------------------------------------------------------S---
-------------------------------------------------------------S--S------------S--
---------------------S--------------------------S-S-----S-SS--------------------
-----------S----------------S-S---SS----S------S----SS--------------------S-----
S---------------S---------S---------------------------------------------S-S--S--
--------S-------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----------S------S-----S-----
S--------S---S----S-----------------------------------S---S--------------------S
---------S-----S-----S----------------SS------------S---------------------------
-------S-------------S-------------------------------S---S------------------S---
-----S------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------------------
--------------------S---SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----S-----
>forward_612
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--------------------------------CTGCGGATGAAGCACAATCG----------------------------
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>reverse_2288
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-----------------------------------------------GGCTGATCCGGAGACTATGC-------------
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