>input_sequence_87309
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-----------------------------------ATGGAGCCCCTGGAGGCGGCGATAGCGATCGTGTTCAACGCGCTG
CTGCTGGTGTTCATGGTGAAGCTCTTCTTCGCCATGTTCCAGATGAAGCTCGTCGTCATCCTCTTCTACCTCGTCGTCGT
CCTCTTCGCCCTCGCCTTCTCCGGCCGCGGCCCCGCCGGCTTCTAG----------------------------------
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>chr4A_1_TraesCS4A01G275000
TCTAGGCATTTTCCGTGATATGAGCTTATTTTTGCAAGGGATTTTTTTT--CAGGAGCTTTACTTTCCACTAAAAAGTGT
ACTTTGGCCCAGCAGTGAGTCTCCCAAAAAAAATAACACGCAGGCGGTTGTTGCAGAAAACAGAAAAATTCTTCCACGGA
AAATAACATGCATTTC-------------------------------------ACTGGCAAAACGTCTTGTATTTATGAA
CAGAGGTAGTACATTATTTGATAGTGTGATTTTTTTACGACTATTATCTACTCCCTCCGTTCCTAAATACTTGTCTTTCT
AGAGATTTCAACAAGTGACTGCATACGGCGCAAAATGAGTGAATCTACACTTTAAAATATGTCTGCATACATCCGTATGT
TGAGTCCATTTGAAATGCCTAGAAAGACAAGTATTTTGGAACGGAGGGAGTAGTACAAATGAATTTCACTGCAAATTGAA
TGTCAGAATTTTGAGCATGGCAGATCAAACTTTTTCTTGATGA-----ATTATGTTGTTACGAGAATGGTGATTT-TCTT
TAGCGAGCCTGACAAAGAATTGCCAGAATTTGCCATGCTTGCCAAAGAAAACTACCATAACGTTTGATTTGTCATGGTTA
AAA-----------------------------------------------------------------------------
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---------------TCTGACGTTGCCGCTACAGATTTGGTAG-------------------------------------
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--------------------------------------------------------ACATCACGCGGTCTACGGGAAAGT
GTGCCGATCCTTCGATTCCAGCGAGCTGACAGGA----------------------------------------------
---------------------------------------------------------------------------CATCC
GAAGATTCAGCGGGGGGACACCTCGGCAGCTGCCGCGCAGGTTCACACGGACGGACTCGCC-TTTCTTTCCTTGCCCCGA
CGCGCGATCGGCGTCGCCGAGAGCGAATTCCCCGCACCAAAGACTACGCGTCGCCGTCAACCCGCCGCAGGTCAGTAGGT
CACAGGTTTGCATCTTCCAGCCCCTT-----CCGGAGCCCCCACTCGGGCTC--------TCACTGACGGGCACCTTTAG
TTTCAGGGCACAGCCAATCACTCCGCCTTTTCAGCCACCGGTCTGGTCGGTC----------GGCGACGGTTGGGACCGG
AGGGAGG--------------------GAGGAGCGATGGAGCCCCTGGAGGCGGCGATAGCGATCGTGTTCAACGCGCTG
CTGCTGGTGTTCATGGTGAAGCTCTTCTTCGCCATGTTCCAGATGAAGCTCGTCGTCATCCTCTTCTACCTCGTCGTCGT
CCTCTTCGCCCTCGCCTTCTCCGGCCGCGGCCCCGCCGGCTTCTAGGTTAGGTCCTTCGTTTTTTTCCCCCTTGCTTCGG
TTGGCTCCCGATCCATCCTTCAGGCTGTACAGCAGTGCTTCA----TCTTCGAGAGAATACTAGTAGATCATACCTACCT
CGGTGCATGTC---------TGGTTGGTT------------AGGAGAGATCTAGTCTGTGATGGTGA--TGACTCCGAGC
TGCAAATTGTGTGAAGTCGGCCAATTAACAAGTGC-----TAGTACAGCTTTATATGAGCCCTAGTTGCAGATTGTGTGG
A-TTACTCGCCGCTTTCTTCGATTGCTCTGTGCAATTTTACTTGTGGATTCGTGATGTAGCCTCTGCTATG---GCTCCT
CTTCTTGAAAATCCAGAGACAGAGT--TCTTTTCTTTCTCCTAGTTCGTGATAGACAAACATTAATTAGTG-----TTCA
CTCCCAAAGGAGAGAAAATTACTATAAGAGGAACAGGCCTGACCGTTTTGTTTCTTATCTGAAGAAAAATCTCAATCATG
ATATTGGGATTAAATTGTGAAATTGTTTGTTCGTTCG---------AAGCAACCATATTCACCATAAGCCCCCTGAGATC
TTTTACAATGCAAGGTGCT-------------CAGAGAAATAAATTAGGTTTTTCTTAAGCACCGGTTTTTGTTTGTACA
TGGTAGATGTTTATTTAGGCACCCCTTCTGTAAAGATAAAAAAACTCAATTTATTTTTTACTAAACGTCTTGCATTGTAC
AAGGTCTAATAATGCTGCCAACAATAACTTCTGGGAATGGCTTTATTG----------AGATGGACTTGCAACGGTACGA
---------------------------------------------AAGCAAACTTACACACC-----AGTAACTTCGTTC
GATGCATTTTGTTTCATTCTAGTATGAAAACTCTAATTTCTCCGGGAACCGTCAATTTTGTTTCATTCTAGT--------
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-----ATACAAACTTCTCTTTCGGTCTTGCATACATTTTTGGATTCTTGTTGAG---TATAAGCATTCTTAAAATTTCTC
GCGTTTGGAATTTTAATGTGCATGTCTTGTTCCCGGGTTTGTTCTCAAAAGAAAATACCATCATCTC
>chr4B_8
-------ATTTTTCATGATATGAGCTTATTTTTTGTAAGGAAAGAAAATGCCAGGAGCTTTACTTTCCACTAAAAAGTGC
TTTGGCAGTTT------------CCAAAAGAAATAGGCG------GGTGGTTGCAGAAGACAG-AAAATTCTTCCACGAA
AAATAATACTAATATGTATCTATCTCTCACTTCTGAAATACACCATCTGTTGAACTGCCAAAACGTTTCATATTTAGAAA
CAGAGATAATACGTCATTTGATACTTTGGTTTTTTTACGACTGTGTGTTT------------------------------
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-----------------------------------------------------TACAAATGAATTTCACTACATTGAACA
TTAGTTT-TTTTTAGCACGGCGATCAATTTATTTTTTTGATATAAATTATTATGTTGTTGCGAGAATGGTCATTTCTCTT
TAACGAGCATGACAAAAATCTAGCAGAATTTGCCATGCACGCTAATTATTTTTACCATAACATTTGATTTGTCATGGTTA
AAAGAAAAAAATCTGACGTCGCCCCTCAAACTTGGTAGACATCACGGGTCAACGGGCATGGATCGTGCTTTTTGAAATAA
AATTATACTTCCTCCGTCCGAAAATACTTGTCCTAGAAATGAATAAAATTGATGTATCTACAACTAGAATAATTCTAGAT
ATAACTAAAATAAGTCTAGATACAACCATTCCTAGAACGTGGTGCCACAGAATAATGCTCTGGTCGTATGCCCTTTTCGT
TATACTATAAGATTACTTTTGGTAGTGGCTCTGTCTTTTCACTAGAAATAGGAACATCTAATTATTTTCCGTGGTATGCG
CAAGGGAAAAGGAATGTCAGGGGCTATACTTTCCACTCAAAAGCACTTTGGCAGTCTCCCGGAGAATAACCCGTAGGCGG
TGGTTCCAGAAAACAGGAAACAAATACTCCATCCGCACTTTGGCACAAATTTTAGCAAGTTTCATTCTTCCATGGAAAAC
AACATGTAGTATTATGTAGGGAAACCCCTCGCTTCTGAAAATAAGTACTAGTACATGATTTGACAGCGTGATTTACTAAG
TCAGCGACATTTATTTTGGGACGGAGAGAGAGAGTATGATTGAAGTTTCATTCTTCCATGCAAAACGACATGTATGGGGT
GTTTGGTCGGAAGAGACTAGACTTTTTTGGTGGGCTAGGGACTAAGAAAAAAGATCCTTCAGTAGAGTTTTTTTCTAGTC
CCTGTAGAAAAAGTCCTTCCTGTTTGGTTACATAAGGACTAAAAAAGACTTTTTCTAGTCTAGACCCTGTAACCAAACAC
CTTCTATGTATCTCTCATTTTTGAAAATAGTGCATGATTTTTTTTAAGAAAAATGGAGGAGGACCCCTGGCCTCTGCATG
TGGACGATGCATGCGGCCACTTTATTAATTATTCATAAAGACCTTACAAAGTCATACAACAGTAAGACTAAAGTCACCGT
CTAGGCAACATCTGTAGCTACTCCTATCCAGTTAATGAAAGGATGCTGATAGTCTGGGCCTAATACCAAACAAACCTTAC
AGCCAAACCTAAACATCTAAGACCTGAGGTCCAAACCAGGACGCCTGCCGGGTATGGGGCACCTACCAGTCCGGCGAATT
CCTCAACCAGGACGCCTGTCGGGTATGAGGCCGCCGCAGCCACCTGCCATCAATCCATCTTCCGAGCTGTACTGTTGCAT
CTACCGTGCCAGGTCTCTCTGCCATCGACGCCACCAGGACGCCAGACAACGTCTTCCTCCTGCGCGAGTCCATTCTCGCA
CATCGAATGCCGAATTTACACTGCGTCACGCCCTCGAGATCCGTCGCCATCAATGTGTAGGATGAAGCACCGCTCCACCA
AAGAAGTCGTCCGCTGGTCCCGCGAGATCGAGTGCATCTCCAAGAATGCCGCCTCCAAGGGGGTAACGACACATGATTGC
CGCCAACATCCGATCAGCTGATCTAGGGTTTCCCCTGGAGTTATTGAGTGGAGCTGGGAGCTTCACCTCGATGATGCCTT
CATGAAGGAAACCATGATAAGGACATCGTCATCACCGGCTTCGGCCATCGACCGGAGACCAAGTTTTCACCCGGATCCAT
CCCAAGTAATCCACCCTACAACCCGTGCATCGTCTCGACCGCCTTCAAAGCCCCAGATCTAGCTGCCTAGATCCGGCGAC
CAACCGCAACAGCAGTGCCACCGTAGGAGCCCTGGCGCACCGGCCACTGCCTGAGTGTGCCACCACTGGAGCCTAGGAGG
AGGGCTCCAACCCCGCCTCGTCAAGCCGCGAGAGCCGCCGAGATGGATCCTGCGTGCTCGTCACCGTCTCTGATCCGAAC
CAATCCGTAGATCGGATCGCCGTCACAGATCTGCCTTGGACAGGGACTGCACCACGCCATGCCGCCACGGGAAGTCCTAG
CTTCACCGGCCGCCAGGGCCGCCGCCCCGGGATCTAGACAGAACATTGCAGCTGCCACCGGCCATGTTTTGCCACCGCCG
ACCGGCCAAGCCGCCGGCCACTGCGACCTCCGCCGACATGACCATGCAATCCCACTGACCCCACTCCATGCACAACCAAC
CGGCCTACCAACTCCGACGAAGAAGAAGGCCACCACCACCAAGCCTAGGGCTGGCGCCCCAGACATCCTCGTGTTGCAGA
TCAAGTTCAGAAGCAGCGCACCGCTGACGGCGATTGAGATCGGTAGCATAACGAATTAGCCCGACTGAGTCAAGGCCAGA
CCCGCCGTTGCTGGTGCCGTCCTCCACCGCCGCTGCCGCACCACATCCATGTCGCCCCCGATATGCGCCACCGCCGCCGA
TCTGGCCGGAAAGGAGCGCCGCCTCCCAACCAGATTGAGATCCGAGGAGAAAACCGTCGCCGTCGCCACGCCACAAGGGC
TTTGCCCTATGACGCCCCGGGCGACGGCGGCGGAGGTGAGGCGCGGCTGTAGGAGGAGGGCGGGGGCTCCCCGGTGCGGG
GCGGCGCCGCCGCACGGGGGAGTTGCTACAAATTAGTGCATGACTTGGCGGTGTGATTTTTCAAGACTGTTTTCTACGAA
TGGATTTCGCCACAAATTGACCGCCAGACATTGTGGCATGGCAAATCAAACTTCTTTTACGGTATAAACTATGTCGTCAC
GAGGAAGGCGATTTTCTTTAGCAAGCTTGGTAAAAAATCGTTCTGCCATGGAAAACGTAATTTGCCATAGAAAAACGTTC
TGCCATGATTAGAAATCTGATGTTACCGCTACAGACTTGGTAGTAGTCCTGGCCATCTTAGGTCCGGCCCTGTTGGCCCA
CCCAGGCCCGGCCCTAAAATCTAGGGCCTAGGCCCGATGGGCTTGCCCATGGGCCGGGCTTGGGCCTGACTTTTGAGCCC
ACCAATAGGGCCTGGACGGGCTTGGGCTTGGCATATTGGCATTTTAAGAAAGAGGCCCGGCCCACGGCCCTAAGCCCTAA
GGGCTTTTTACCAGATGGGCCGGGCTTGGGCTTGAAAAGTAGGCCCAATGATAGGGCCTGTGAGGGGCTGGGCCTCAGTT
TTCTGCCGTGGGCTTTTTCAGGCCCGGCGCGGTCCATGGCCAGATATACTTGGTAGACATCACGGGGTCTACGGGAAAGT
GTGCAGATCCTTCGATTCC----AGCTGACAGGACCGCGGGAATTGGCCGGACGGTGGCGAAGCTGACAAGTGACATGGA
AGGGGATCCCTCGGCCGCGTCCCTGTGTGTACGCGTAGGCTCGACCTACCTTTAATTATAACCTTCCGTGTCGGCCATCC
GAAGATTCAGCG--GGGACACCTCGGCAGCTGCCGCGCAGGTTCACACGGACGGGCTCGCC-TTTCTTTCCTTCCCCCGA
CGAGCGATCGGCGTCGGCGAGAGCGAAATCCCCGCACCAAAGAATACGCGTCGCCGTCAAGCC-----------GTAGGT
CACAGGTTTGCATCTTCTCGCCCCTT-----CCGGAGCCCCCACTCGGCCAC--------TCACTGACACCTTT------
-------------------ACTCCGCCTTTTCAGCCACCGGTCTGGTCGGTCTCGCCGGGGCGGCGTCGGTTGGGACCGG
AGGGAGGTACGCGAGGGGCGGACGGTGGAGGAGCGATGGAGCCCCTGGAGGCGGCGATAGCGATCGTGTTCAACGCGCTG
CTGCTGGTGTTCATGGTGAAGCTCTTCTTCGCCATGTTCCAGATGAAGCTCGTCGTCATCCTCTTCTACCTCGTCGTCCT
CCTCTTCGCCCTCGCCTTCTCCGGCCGGGGCCCCGCCGGCTTCTAGGTTAGGTCCTTCGTTTTTTTTCCCCTTGCTTCGG
TTGGCTCCGGATCCATCCTTGGAGCTGTAACAGCGGTGC-------------------------TAGACCATACCTACCT
CGGTGCATGTC---------TGGTTGGTTGGTTTAACAAACTGGGGAAATTTAGTCTACAGTATCATGGTGACTCCGGGC
TGCAAATTGTGTGAACTCGGCGAATTAAGAG--------GTAGTACAGCTTTATATGAGCCCTAGTTG-AGATTATGTGG
ACTTAGTCGGCGCTTTCTTCGATTGTTCTGTACAATCTTACTTGTGGATTCGTGATGTAGCCTCTGCTAGGCGTGCTCTT
CTTCTTGAAAATCCTGAGGCAGAGTGTTCTTTTCTTTCTCCTAGTTCGTGATCGACAAGCATTAATTTAGTGTTCATTCA
TTCCCAAGGGAAAGAAATTTATA--------AACTGGGATGACAGTTTTGTTTCTTGTCTGAAGAAAACTGTCAATCATG
ATTTTGGGATTAAATTGTGAAATTGTTTGTTTGTTTCTTCAATTCAAAGCAACCATATTCACCACAAGCCCCCT------
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-------AATAATGCTGCTAACAATAACTTCTGGGACTGGCTTTATTGAGCTGTTAAAGTCATATATGATACTATCATAG
ACTAGTATCATATGCATGATACTAACTTGTGATATTATCCATTATAACCAGCCTGACACACCAGGCTAGTAACTTCGTTC
GAT-------------------------------AATTTCTCCCGGAACCGTCCACCTCGTCATGTGGCTTCAATAATTG
AAGAAGCTTCTCGGAATGCAAAATAATTAGATAATCTATTCGCCACACGGCCACCGAGTTGTTCAAGACTTTCCAATAGA
AAAAGGAAAAGGAGAGAACACGTTATCACCTCGGCTATCATCCATCACTTCACTTGTAACGACGCGAATCAGCGGAATCA
TGTCCATACAAATTTCTCTTTCGGTCTTGCATAC-TTTTTGGATTCTTGTAGGAGTATATAAGCATTCTTAAAATTTCTC
GCGTTTGGAATTTTATGC-GCATATCTTGTTCCCAGGTTTTTTGTCATAACAAAATACCGTCATCTC
>chr4D_685
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---------------------------------------------------------------------------CATCC
GAAGATTCAGCG--GGGACACCTCGGCAGCTGCCGCGCGGGTTCACACGGACGGACTCGCCTTTCCTTTCCTTCCCCCGA
CGCGCGATCGGCTTCGGCGAGAGCGAATTCCCCGCACCAAAGAATACGCGTCGCCGTCAAGCC-----------GTAGGT
CACAGGTTTGCATCTTCCAGCCCCTTCTCTTCCGGCGCCCCCACTCGGAACGGCCACTCATCACTGACGGGCACCTTTAG
TTTCAGGG----------CACTCCGCCTTTTCAGCCACCGGTCTGGTCGG---------GGCGGCGTCGGTTGGGACCGG
AGGGAGG--------------------GAGGAGCGATGGAGCCCCTGGAGGCGGCGATAGCGATCGTGTTCAACGCGCTG
CTGCTGGTGTTCATGGTGAAGCTCTTCTTCGCCATGTTCCAGATGAAGCTCGTCGTCATCCTCTTCTACCTCGTCGTCGT
CCTCTTCGCCCTCGCCTTCTCCGGCCGCGGCCCCGCCGGCTTCTAGGTT-----------TTTTTCCTTCCTTGTTTCGG
CTGGCTCCGGATCCACCTTTCGAGCTGTACAGCAGTGCTTCACACATCTTCCAGAGAATACTAGTAGATCGTACCTACCT
ACCTCGGTGGATGGATGTTTTGGTTGTTTGGTTTAACAAACAGGGGAAATTTAGTCTGTGATGATGA--CGACTCCGAGC
TGCAGATTGTGTCAACTCGGCGAATTGAGAAGTACAGTAGTAGTGCAGCTTTATATGAGCCCTAGTTGCAGATTATGCCG
ACTTACTCGGCGCTTTCCTCGATTGTTCTGTGCAATTTTACTTGTGGATTCGTGATGCAGCCTCTGCTAGGGGCACTCCT
CTTCTTGAAAAACATTAAT----------------------------------------------TTAGTG-----TTCG
TTCCCAAGGGAAAGAAAATTGTA--------GAC---------AGTTTTGTTTCTTATCTGAAGAAAAATGTCAATCATG
ATTTTGGTATT-AATTGTGAAATTGTTTGTTTGTTCG---------AAGC-------------------CCCGTAAGTTC
TTGTACAATCTAAGGTGCTTAGAAGAGGTGCTCAGAGAAATAAATCAGGTTTTTTTTAAGGGCCGGTGTTTGTTCCTACA
A-GTAGACGCTTAAGTAGGCATCCTCTCCTGTAGAGATAAAAAACTCGGTTTATTTTACT--------------------
--------ATAATGCCGCCAGCAATAACTTCTGGGAATGGCTTTATTGAGATGTTAAAAGATGAATTTGCAACGGTATGA
---------------------------------------------AAGCAAACTGACACACCG-----GTAACTTCGGTC
GATGC---------------------------------------------------------------------------
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>SNPs
SSSSSSS-----S-S------------------SSS-S---SSSSSSS-------------------------------S
SS-SSSSSSSSSSSSSSSSSSSS------S-----SSSSSSSSSS---S---------S----S--------------S-
------S-SSS--S-S-----------------------------------------S--------S-SS------SS--
-----S--S---S-S--------S-S--S-------------S-SSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----------------S--SSSSSS-
-SSSSSSS----S----S---SSSSS-SSSS----S-----SS----------------S----------S---------
--S-----S-------S-SS-SS---------------SS--S--SS-SSSS---------S------------------
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--------------------S---S----------S--------------------------------------------
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----------------------------------------------------------------S---------------
----S--------------SSSS---------------------------------------------------------
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------------SS-----------------------------------------------------------S------
----------------S--------------------------S----------------S--SSSSSSSSSSS------
------------------------------------------------S-S-----------------------------
--------SSSSSSSSSS------------------------------------------------S-------------
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--------S------------SS----------------------------S----------------------------
--------------------------------------------S--S--S------------S----------------
---------------S-----S------S----S----------------------------------------S-----
---------S---------------S-------------------------------------------S----------
--------------S---S---------------------------------S-----S---------------------
S------S---S---------SSSSSSSSSS---S--SS----S--------------------------S---------
--S----------------------------S--------------------------------S---------S--S--
--S------SS----------------------------------S--------S-----SS-----S------SS----
SS-----S-S---SS------S--SS--SSSS-SSSSS---------SS--------SSSSSSSSSSSSSSSSSSSSSSS
SSSSSSS--------------------------------------------------------S-S-----------S--
------------------------------------------------------S-------------------------
-----SSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------S---------S-SS-S--SSSS-SSSSSS--------
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------------S---------------------S---------------S-SS--------------------------
---------------SSSS----S----------S-----S--S---S--S--------S-------
>forward_99
-------------------------------------------------------------------------------T
ACTTTGGCCCAGCAGTGAG-------------------------------------------------------------
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>reverse_4911
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------------------------------GAACAGGCCTGACCGTTTTG------------------------------
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