>input_sequence_66307
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-------------------------------------------------------------------ATGACTTTATATA
A-GCGCACGGCGCGAGGTGGCGACACGGGGGGCGCCGGACGACAAAGTACTACTAGTACCACTCC--CTCCCTGTCCGTC
TGCTCGACCCGATCAGCTCGCCACCAGCAAGCAACCGCTCTTTTTAGCCCCCACTCGCTCCACTCTCCTCACGATCCCTC
CCCCACTCCGGCCGGCCACGCACAGAGCGGAACGCTCCCCGACTCCGGCCAAGAGCTCCAGCCCCGATCGTCGT-CGTCC
-----------ATGGTGAGGTCCAACTCTATCGACAGCTGCTACTCCTCCATCCAGGACGTCACCTACAGGTACCTTCCG
CTTCCACTTCCAGTTCCATCCACACCTCCACTTTCTTCTCCACCGGCGAGACGGCTCTTGCACCAATGATTGGCGGTTCA
TAGCTCGACTTCTTTTCTGATTTGCTGCTGATGGCAGCTGCGGCTACTGCGGCTACGCGCTGAACCTGAGCTCGGCGGCG
CGGAACACGGCCGGCATCGGCTCCAAGTACGGCAAGAATATAAGGAAGAAGGGCGTCGTCGCCTTCGTCGCCGTCGACGA
GACGCGCTTCACGCAGGCCGACGAGGTCACCTGCGCGCCCCGCCTCCGCCCCTGGACCTGGCGCCTCTTCCGGCGGAGGT
CGCGCCTGCTCTGCGGCAAGTGCGGCGGCCGCATCGGCGCCGCCTACGAGGTCGACGATG---ACGAGGACCCCGCCGGC
CTGTCCGCGTGCGCCGGCTCGGACGA---CGACGGCGACGACCTGCGGACGAGCCCGGGCGACGATAGCGGCGGCGTCGG
CGCGTCCAGAAGGAGGAACTACCTGATCAGGATCGGCGCGCTGCAGCCCTCGACGGACGATCCTCCTCCCGCTGATCCCT
TCTCTCTATGA---------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G346100
AACTCGATCGGGTACCATTTAGGCCAAACTCAAAATGTTGGGACTAAAAATGGTTTGGTTCGTCCAAGTAGTTGATCATC
ACATCCCATCGTACTATAAGAAGCTACTTCCTCCGTCCCATAATGTAAGACGTTTCACATCCCATCGTACTATAAGAAGC
TACTTCCTCCGTCCCATAATGTAAGACGTTTTTTGACACTATGTCAAAAAACGTCTTACATTATGGGACGGAGGGAGTAC
TAATTATACGTATCGAGTGTAACTTTATCATCTCATATGTATAGGATGTGAATGAATTCATAAAATTATGTAACTTTATC
CTGCTCTTTCTAGACATGGTTCTCTCGAGTCTAAGCCAAGGGCATTTGCTTCACTTGGCTGTTGGCTGCACGACAGTAGT
TCCC---------------ATCTGACCATACTTGTGAAATCTGCAGGTTGTTGATCACACCACGCACTACTTCAAGAAGC
AGGACGGCGTAACCTTTGTGATCGAGGACTGAGACGCTGCATGTCACTGACCACGACCTATGCACAAAAGCTCAGCGCAC
CGTGTGCCTCACGGACGCTGTTCGGGCCCTGTCCCTCTGTATGATGCACGTCCAGTATGTATATGCAATAATGTACTGCA
AGTCACGTGTACTTCGTACGCTGCTCCTTTTTGGCTCCTTGAGCGTTTATTTGTGTCGTTGTTTCTGCTGACACACATCA
TAAATTCTTAGTACCAGGCCAAGCCGTGCCGCGCCGGCCATGCCCTAGCGAGCGAGCGGCAGCCGGCCGCGCCGTGCACA
TGGGCACGGAGGCCGGCGTGAATGCGCGGCCGCCGCCGGGCCCGGGCCCTCCCGGCGCGCGACACATGG----------C
GCGTCCACCCCGACGGTGGGTGCAGGCCCCGTCGGCATCCACGTCTGCCCGTCCGGCCGCCGTAGAGATAGTTGGCGTGC
CCGCAATGGTCAGAGCAGA--AGCAAAGCACCCATGCCGATTACCCGGCGCTCCCGATTAATTAGCAATGACTTTATATA
A-GCGCACGGCGCGAGGTGGCGACACGGGGGGCGCCGGACGACAAAGTACTACTAGTACCACTCC--CTCCCTGTCCGTC
TGCTCGACCCGATCAGCTCGCCACCAGCAAGCAACCGCTCTTTTTAGCCCCCACTCGCTCCACTCTCCTCACGATCCCTC
CCCCACTCCGGCCGGCCACGCACAGAGCGGAACGCTCCCCGACTCCGGCCAAGAGCTCCAGCCCCGATCGTCGT-CGTCC
-----------ATGGTGAGGTCCAACTCTATCGACAGCTGCTACTCCTCCATCCAGGACGTCACCTACAGGTACCTTCCG
CTTCCACTTCCAGTTCCATCCACACCTCCACTTTCTTCTCCACCGGCGAGACGGCTCTTGCACCAATGATTGGCGGTTCA
TAGCTCGACTTCTTTTCTGATTTGCTGCTGATGGCAGCTGCGGCTACTGCGGCTACGCGCTGAACCTGAGCTCGGCGGCG
CGGAACACGGCCGGCATCGGCTCCAAGTACGGCAAGAATATAAGGAAGAAGGGCGTCGTCGCCTTCGTCGCCGTCGACGA
GACGCGCTTCACGCAGGCCGACGAGGTCACCTGCGCGCCCCGCCTCCGCCCCTGGACCTGGCGCCTCTTCCGGCGGAGGT
CGCGCCTGCTCTGCGGCAAGTGCGGCGGCCGCATCGGCGCCGCCTACGAGGTCGACGATG---ACGAGGACCCCGCCGGC
CTGTCCGCGTGCGCCGGCTCGGACGA---CGACGGCGACGACCTGCGGACGAGCCCGGGCGACGATAGCGGCGGCGTCGG
CGCGTCCAGAAGGAGGAACTACCTGATCAGGATCGGCGCGCTGCAGCCCTCGACGGACGATCCTCCTCCCGCTGATCCCT
TCTCTCTATGATATGATATGATATGA-----------CACACTGTTGCTGAATTTTGTTCCTTTGTTCATAGTGGAGGAC
-GACCCCAGGGTTTGATGTGTGTAAGTTGATCCTACTGTAGTTTTTGTGTCCTGGTAATGGAGTGAGCCATGGTTGCAAT
TTTGAGCCACCTAGTATTTGTCAATGGCTTAATTCTAGCTTTCTGTGTGGGCTTTT-CTCTCTTGATATCTAAATTGTGG
ATTCTGTTTTGATTATCCACACATAAATATATTTCAGTTTGTCACCACTAATTTCATAAGCTGGATGACAAGATAAATTC
ATGTGATGGAGCTTTGTTATGTTATGTTTATTATCACCATCAGTTCTTCTATGCAGTCAACTCGCTGGGAATTCAGAATT
GGAGCACAACATCAAGGTTTGCAGTCAAGGCTCCAGGTAAGTCTATTCGCAAAAAAAAAAAAGGCTCCAGGTAAGTCCAT
GCAACCAGTACCCCAGTTAATCAGTTGGATGATTCCATGGTGAGAAACACCATTTTTCTGATCCAAGAATTTGTATATGC
AAAAATGCCAGT--------------------------------------------------------------------
-------------TATTTTCTTTCTATGCAGTGAGTAAATCTGGAAATTATACTTTTGAAATAATCACTATATCATATAC
AAGGAGCTCTTTTAGCTGCAGTAGTACAAATGTCAGTTTCCCCTATTAGCTAAGATACATACATTTTCAATAGAGATAAC
TGAATAAAATGTTGTAATGATCAAATCAAACAAAAAAAAGAATGTGA--AAAACGGTGAATATGATTTTCGTAGTTTACA
CTATCATTT--TGCTTCAAGTGGCTATTGAGTAGGCATCGGTGTGTCCTTCAAGAAGTGTCTGAATAGTATTAGTGCTTG
CCGAGGCCGGTGCAGAGGTACCTCATGCCCTGCACCTGCTACGGTGACGAGAGTTAGTCCTTTGTAAACCTGACTCCAAC
CTCCAACCTGCAAAACAGAGAGGAGAATTTGATGTC------AAAATGGTCTTTCTGGGACAGAATTTCTCAATT-
>chr3B_332
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-----------AGACATGGTTCTCTCGA-TCTAAGCCTAGGGCATTTGCTTCACCTGGCT-----CTGCACAACAGTGGT
TCTTTCCATCTGACCTGAGATCTGACCATACTTGTGGAATCTGCAGGACGTTGATCGCACCACGTACTACTTCAAGAAGC
AGGACGGCGTAACCTTTGTGATCGAGGAGTGAGGCGCCGCACGTCACGACCTTAGTT------ACAAAAACCCAGCGCAC
CGTGTGCCTCGCGGACGCTCTTCGT-------------------------------------------------------
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-----------------------------------GGCCATGCCCCAGCGAGCGAGCGGCAGCCGGCCGCGGCGTGCACA
TGGGCACGGAGGCCGGCGTGAATGCGCGACCGCCGCCGGGCCAGGGCCCTCCCGGCGCGCGACACATGGCACGCTCCGAC
GCGTCCACCCCGACGGTGGGTGCAGGCCCCGTCGGCATCCACGTCTGCCCGTCCGGCCGCCGTAGCGATAGTTGGCGTGC
CCGCAATGGTCAGAGCAGA--GGCAAAGCACCCATGCCGATTATCCGGCGCTCCCGATTAATTAGCAAGGACTTTATATA
A-GCGCACGGCGCGAGGTGGCGAGACGGGGGGCGCCGGACGACAAAGTACTACTAGTACTACT---ACTCCCTGTCCGTC
TGCTCGACCCGATCAGCTC------AGCAAGCAACCGCTCTTTTTAGCCCCCACTCTCCCCAC---------GACTCCCT
CGACAAAGT-------------------GGAACGCTCCCCGACTCCGACCAAGAGCTCGAGCGCCGATCATCGTCCGTCC
-----------ATGGTGAGGTCCAACTCCCTCGACAGCTGCTACTCCTCCATCCAGGACGTCACCTACAGGTACCTTCCA
CTTCCA------------TCCATGCCTCCA----CTTCTCCACCGGCGAGACGGTTCTTGCGTCAATGATTGGCGATTCA
TAGCTCGATTTTCTTTC--ATTTGCTGCTGATGGCAGCTGCGGGTACTGCGGCTACGCGCTGAACCTGAGCTCGGCGGCG
CGGAACACGGCGGGCATCGGCTCCAAGTACGGCAAGAATATCAGGAAGAAGGGCGTCGTCGCCTTCGTCGCCGTCGACGA
GACGCGCTTCACGCAGGCCGACGAGGTCACCTGCGCGCCCCGCCTCTGCCCCTGGACCTGGCGCCTCTTCAGGCGGAGGT
CGCGCCTGCTCTGCGGCAAGTGCGGCGGCCGCATCGGCGCCGCCTACGAGGTCGACGAGG---ACGAGGACCCCGCCGGC
CTGTCCGCGTGCGGCGGCTCGG---A---CGACGACGACGACCTGCGGACGAGCCCGGGCGACGATAGCGGCGGCGTCGG
CGCGTCGAGGCGCAGGAACTACCTCATCAGGATCGGCGCGCTGCAGCCCTCGACGGACGATCCCCCTCCTGCTGACCCCT
TCTCTCTATGATATGATATG-----A-----------CACACCGTTGCTGAATTTTGTTCCTTTGTTCATATTGGAAGAC
AGACCCCAGAGTTTGATGTGTGTAAGTTGATCCTACTATAGTTTTTGTGTCCTGGTAATGTAGTGAGCCATGGTTGCAAT
TTTGAGCCACCTAGTATTTCTCAATGGCTTAATTCTAGCTTTCTGTGTGGGTTTTTGCTCTCTTGATATCTAAATTATGG
ATTCCGTTTTGATTATCCACAGATAAATATATTTCAGTTTGTCATCACTGATTCCATAAGCTGGCTGACAAGATAAATTC
ATGTGATGAACCAT-----TATTATGTTTATTATAAATATCAGTTCTTGTATGCAGTCAACTCGCTGGGAATTCGGAATT
GGAGCACAACATTAAGGTTTGCAGTCAAGGCTCCAGGTC----------------------------------AGTCCAT
GCAACCAGTACCCCAGTTAATCAGTTGGATTCAATGGGACT-AGAAACACCATTTTTCTGTTCCAAAAAATTGGATATGC
AA-AATGCCCGT--------------------------------------------------------------------
-------------TATTTCCTTTCTGTGCAATGAGTGAATCTGGAAATTGTACTTCTCAAATAATCACTATATCATATAC
AAGGAGCTCTTTTAGCTGCAGTAGTACAAATGTCAGTTTCCCCTATCTGCTAAGATACATACATTTTCAATAGAGATAAC
TGAATAAAATGTTGTAATGATCAAATCAAACAAAAAAAA-AAGAATGTGAAAACGGTGAATATGATTTTCGTAGTTTACA
CTATCATTT--TGCTTCAAGTGGCTATTGAGTTGGCATCGGTGTGTCCTTCAAGAAGTGTCTGAATAGTATTAATGCTTG
CCGAGGCCGGTGCAGAGGTACCTCATGCCCTGCACCTGCCACGGTGACGAGGGTTAGTCCTTTGTAAACCTGACTCCAAC
CTCCAACCTGCAAAATAGTTAA-AGCATTTGATGTAAGATTGAAACGGTTCATTCTCGGACAGAATTTTCTCA---
>chr3A_729
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-----------------------CCGTGCCGCGCCGGCCATGCCCCAGCGAGCGAGCGGCAGCCGGCCGCGCCGTGCACA
TGGGCACGGAGGCCGGCGTGAATGCGGGGCCGCCGCCGGGCCCGGGCCCTCCCGGCGCGCGACACATGGCGCGCTCCGGC
GCGTCCACTCCGACGGTGGGTGCAGGCCCCGTCGGCATCCACGTCCGCCCGTCCGTCCG-----GCGATAGTTGGCGCGC
CCGCAATGGTCAGCAGAGCAGAGCAAAGCACCCATGCCGATTACCCGGCGCCCCCGATTAATTAGCGAGGACTTTATATT
AGGCGCACGGCGCGAGGTGGCGCGACGGGGGGCGCCGGACGACAAAGTGCTGCTAGTACTACTAGTACTCCCCGTCCGTC
GGCTCGGCCCGATCAGCTCGCCACCAGCAAGCAACCGCTCTTTTTAGTCCCCACTCGCTCCAC---------GATCCCTC
CCCCACTCCGGCCGGCCACGCGCAAAGCGAAACGCTCCCCGACTCCGGCCAAGAGCTCCAGCGCCGCCGCCGCCGACCGT
CGTTCGTCCATATGGTGAGGTCCAACTCCATCGACAGCTGCTACTCCTCCATCCAGGACGTCACCTACAGGTACCTTCCG
CTTCCACTTCCACTTCCGTCGACGCTTCCA----TTTCTCCGCCGGCGACGGGTTCATTGACCCCTCCGGTTCCTCCTGG
TTCGCCGGC-----------------------GGCAGCTGCGGGTACTGCGGCTACGCGCTGAACCTGAGCTCGGCGGCG
CGGAACACGGCCAACATCGGCTCCAAGTACGGCAAGCAGATCAGGAAGAAGGGCATCGTGGCCTTCGTCGCCGTCGACGA
GACGCGCTTCACGCAGGCCGACGAGGTCACCTGCGCGCCCCGCCTCCGCCCCTGGACCTGGCGCCTCTTCCGGCGGAGGT
CGCGCCTGCTCTGCGGCAAGTGCGGCGGCCGCATCGGCGCCGCCTACGAGGTCGACGAGGAGGACGAGGACCCCGCCGGC
CTCTCCGCGTGCGGCGGCTCGG---ACGACGACGACGACGACCTGCGGACGAGCCCGGGCGATGAT---------GTCGG
CGCGTCCAGAAGGAGGAACTACCTGATCAGGATCGGCGCGCTGCAGCCCTCGACGGACGATCCTCCTCCTGCCGATCCCT
TCTCTCTATGATATGATATG-----ATATTGATATGACACACCGCTGCTGAATTTTGTTCCTTTGTTCATAGTGGAAGAC
-GACCCGAGAGCTTGATGTGTGTAAGTTGATCCTGCTATAGTTTTTGTGTCCTGGTAATGGAGTGAGCCATGGTTGCAAT
TTTGAGCCACCTAGTATTTGTCAATGGCTTAATTCTAGCTTTCTGTGTGGGTTTTTGCTCTCTTGATATCTAAATTATGG
GTTCTGTTTTGATTATCCACAGATAAATATATTTCAGTTTGTCATCACTGATTCCATAAGCTGGCTGACAAGATGAATTC
ATGTGATGGAGCAT-----TGTTATGTTTATTATCACCATCAGTTCTTGTATGCAGCCAACTCGCTGCGAATTCCGAATT
GGAGCACAACATTAAGGTTTGCAGTCAAGGCTCCAGGTA----------------------------------AGTCCAT
GCAAGTAGCACCTCAGTTAGTAAGTTGGATTA---CATGGTGAGAAACACCATTTTTCTGATCCAAGAATTTGTATATGC
AAAATGCCAGTTACTCCCTCCGTCCCACAATGTAAGACGTTTTTGCAAGTTAAACAAGCTTGAAAAACGTCTTACATTAT
GGGACGGATGGAGTATTTTCTTTCTATGCAGTGAGTAAATCTGGAAATTATACTTCTCAAATAATCACTATATCATATAC
AAGGAGCTCTTTTAGCTGCAGTAGTACAAATGTCAGTTTCCCCTATTATCTAAGATACATACATTTTCAATAGAGATAAC
TGAATAAAATGTTGTGATGATCAAATCAAACAAAAAAAG-AATGTGA--AAAACGGTGAATATGATTTTTGTAGTTTACA
CTATCATTTTCTGCTTCAAGTGGCTATTGAGTAGGCATCGGTGTGTCCTTCAAGAAGTGTCTGAATAGTATTAGTGCTTG
TCGAGGCCGGTGCAGAGGTACCTCATGCCCTGCGCCTGCTACGGTAACGAGGGTTAGTCCTTTGTAAACTTGACTCCAAC
CTCCAACCTGCAAAACAAAGAGGATTATTGATAT--AGATCGAAACTGGTCTTTCTGGGACAGAATTTTCTCGATT
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSS-----------------S--------S----------------S-----SSSSS------S-----S--
--SS--------------------------------S----------SS-------S-------S---------------
----------------------------S----S---S---S-----SSS-SSS-SSSSSSSS------S-S--------
----------S--------S----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSS----------------------S----------------------------------
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-----------------------------------------------------------------S--------------
--------------------------------------------------------------------S-----------
-----------------------S-----------------------------------S---SS---------------
---------------------------------------------------------------SSSSSSSSS--------
---------------------S--S-------------------------------------S------S----------
----------------------------S---------------------------------------------------
------------S----S-----S------SSSS--------------------S------S-------------S----
-----------SS----SS------------------------S------------------------------------
-----------------------------------------S--------------------------------------
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----------------------------------------------------------S---------------------
-------------S--------SSS---------S---------------------------------------------
---------------------------------------------------------------------S----------
--------------------SSSSS-----------------S---------------------------------S---
---------S---------------------------S------------------------------------------
---------------------------------------------------S------------------------S---
---------------------S----------------------S----S---S----------S---------------
------------S-SSSSS-----------------------------S-------------------------S-----
------------S--------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-------
------------------------------S-SSS---------------------------------------------
---------S----------------------------------------------------------------------
-------------------------------------------------------S-S----------------------
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---------------------------------------S----------------------------------------
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---------------------------------------------------S----------------------------
-------------------------S---------S---------S----------------------SSSS-S--
>forward_121
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---------------------AGCTACTTCCTCCGTCCCAT---------------------------------------
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>reverse_1373
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------------GTTCCATCCACACCTCCACT------------------------------------------------
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>forward_177
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-----------------------------------------------------------------------------AGC
TACTTCCTCCGTCCCAT---------------------------------------------------------------
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>reverse_1391
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------------------------------CTTTCTTCTCCACCGGCGAG------------------------------
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>forward_465
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---------------------------------------------GGTTGTTGATCACACCACGC---------------
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>reverse_2384
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---------------------------------------------------------------GCTCCAGGTAAGTCCAT
GCA-----------------------------------------------------------------------------
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