>input_sequence_79219
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---------------------------------------------------------------ACAACGATTAGCAAGCG
GACCATCA----ATT----TCTAGCGCATCTATCCATCCATCAAACTGCGACG-CAAACATTCTATCTGACAGCACTAGC
AGAGGCTGGTTCAGCGACAACAATGGCGTTCGTGCCGATCTGCGTGCAGTGCGGGACGAGGAGCAACCCGTGCCGGTGCA
AGGTGGTCGGCCCGACGCTGGGATTCGTGGCGCTCGTCGTGGCCGGAGTGGTGGAGTGGCCGCTGGGTGCTGCCGTGTAC
CTTTTCCGCCACCGCAAGGGCCGCCGCATCATGGGTCACCCGGCCAGGGTCGTGTACCCTCGCGTCACCGGCGCAATCCC
CATCTAATCGACCGCAGCATCTTCGTCTTCGGTGGTGATCTGTCACGAGGTACCGCCGTTGGCTTGTCAAGCTGTGTCAT
GTAATCTGGGAGATTCGTCTCCCCGACTTTCAGCGTTTGTTTAATAAAGCGAGGTTTTTGTT------------------
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>chr3A_1_TraesCS3A01G232000
TATGGCCTAGAGTTGGTTTTACAGCCACATTATAGATATACAACTCCAAA------------------------------
--------------------------------------------------------------------------------
----------------------------------------------CTTACATGTCTACATGATTGAAGCACCAGAGTGT
AACACAATCATTGTACGGTAATTTTCATCAGTTTATAGTTGGATATCTAAGCTATGCACATATATCTTACTAGTAAAATT
ATTTTACTATGTAATGTATACATATAGAATGGCGTTTTGGATCTTGGAAAATTCA---------------AAAAAAAAAG
TGTACAAGTAAACAAGGATATAAGGTGTATGCGTGTAAACTTTCAGAATAAAATACAATGCAGTGGCGACCTGTACAAAA
A-ACAAATTTATGATCTGAGAGAATGAATAGTATCACGTGTTAAAAAGCCTCGATTTTTTTGCACAACCCTTATCTCAAC
ATATTTCATCCTGAAAATTTACACACTTGTGTATTATGCCCTCATGTATGTCAGTATTTTCTTTAGAATTTTTTAAATGT
AAAAGTATGAATTTTCATGAATTTTGCATTTTGCATTTAGATGCCTCCATGAAGCTCGGCCTTCAAAAGCAATTTCAGTT
TCAAATGTCAATTATTAGTGCTTTTTCTGATGGTTTGACGGCATGTGCACTATACGTTTTTTTCCATACGAGGACGTATC
GGGTTTCACCATCATCTATCATCA------GATAACGGCATGTGCGCTAGTGTCAATTCACAAACTGGAGCTATTTTTT-
TTTTCACAAACTGGTGCTGAGGAGAGCATGTTATTATACATAGAACATAGTCTGATGTGCAATTACGTGTCCCG---TTG
CTTGTGCATCTTTCG-TTTGTTGAGAAAGTTCCAGAGAACTCTAAGAACAACTGAACACACGTGAGCGGAGTCCCGTGCA
ACGTGGAAGTGATCCAGCAAGCGGAGTCATCACCAACTTTTTGCAACCATGCTGCGAGCGCCACGCGTGCCGGCAGTCGC
GCCAACCGTCCTCAACGCAACGACGTTATATATATGCCCGAGATGCGAGAGACCGACCACATCACAACGATTAGCAAGCG
GACCATCA----ATT----TCTAGCGCATCTATCCATCCATCAAACTGCGACG-CAAACATTCTATCTGACAGCACTAGC
AGAGGCTGGTTCAGCGACAACAATGGCGTTCGTGCCGATCTGCGTGCAGTGCGGGACGAGGAGCAACCCGTGCCGGTGCA
AGGTGGTCGGCCCGACGCTGGGATTCGTGGCGCTCGTCGTGGCCGGAGTGGTGGAGTGGCCGCTGGGTGCTGCCGTGTAC
CTTTTCCGCCACCGCAAGGGCCGCCGCATCATGGGTCACCCGGCCAGGGTCGTGTACCCTCGCGTCACCGGCGCAATCCC
CATCTAATCGACCGCAGCATCTTCGTCTTCGGTGGTGATCTGTCACGAGGTACCGCCGTTGGCTTGTCAAGCTGTGTCAT
GTAATCTGGGAGATTCGTCTCCCCGACTTTCAGCGTTTGTTTAATAAAGCGAGGTTTTTGTTGTTGTAGTATTTGCAAGG
CTTCGCCGTGGTTGTACCAAATATTTGTTCGTCGATGTAAAGTAGAGTAGCCTTTTTGGTTACCCCGAGTGCTGTGTAAT
AGCATCGATCAACTTGACTCCTCTTTTCGGAAAATGCTCTTTATGTAGTGCTCCCTCCGATCTTCTCTTTTTCGAAAAAT
GCTCCTTATGTAATGTTTCCTCCTATACCAAATAAAATAAATGTCATGGTTTTTTTATTAATCAACTTAAAATGTCTGAT
ACAATCATTCATTACAAACTTTGTCACCCATGACGAAATAGAATGAAAAAGAAAATTATCATATCTATTATCAAAACTAA
ACTTTGCAACCTGGTGGCCTCTAAATTTGCCCTCATGTTGATCTTTGAAATATGTAAATTCACCAGCATCTTTGAGACAT
TTACCACCGCCTTCTTTAAATCAACAAGGGAGGACCTGTCCATACAATCTCTTCCAAGAACAGAGGCAGCAAAGGAGCGA
TCAGTTTCCTCCAAAATGATGGGCATGTCTAGTGTTGTACTAATATACAGGCCGAT-AGGAACGCTCTAAATTCCGCTTC
CTCGACGCTATAGCAAACTCTAATACAATCTCAGAAAGAAAGAATAATTTGTCCACAATGGTTTCTTACAAACTCTAATA
CAATCCTAGAAAGAAAGAATAATTTGTCCACAATGGTTTCTCACAACCACCCACTCTTATGTTGATATTAATATTGTAGA
CCTTTAATATTGTACTCCCTTCTTTTTGGTTTATAGGGCTTATCTCAAGCTCAATTTGGTTGTTCATCATCACATATTCA
GACTTCAAAGTGCATTAAATCATTGCATGCAAGTATGAAGAGAAAACTAATCAATGCATGCACTGCGTGCATGCATTGCA
TTGCAATTAATGCATTCGTAAACATAATTTTTTTAGGAAAATAAAAGCATTAATTAGATGCTTTTGTAAACTATAAAAAA
TATTCCATCACTCATCATTTATC
>chr3D_1
TATGGCCTCGAGTTGGTTTTACAGCCACATTATAGATATATGAGGCTAATTGGTTCGTTGCCAAAGTTTGGCATTGCCAA
TATTTGGCAAGCCAACATTTGGCAAAACCAAAAGCTGCCAAACATTGGCGACTTTTTGAGAAGTGGGCAATAACCAATTC
GTAGCCAACCAATTGAGAGCCAAATTTTTAGACTTGCCAACAATTTCTTACATATCTACATGATTGAAGCACCAGACTGT
AGAACAATCATTGTACGGTAATTTTCATTAGTATATACTTGATTATCTAAGCTATGCACATATATCTTACTAGTAAAATT
ATTTTACCATGTAATGTATACATATAGAATGACGTTTTGGATCTGGGTCTTCATGGAGGCCGATTTTTTTT-AAAAAAAT
TGTACGAGTAAACAAGGATGTGAGGTGTATGTGTGTAAAATTTCAGAATAAAATACAATGAAGTGGCGTCTTATA-AAAA
AGACAAATTCATGGCCTGAGAGGATGAATAGAATCATGTGTTAAAAAGCCTC---TTTTTTGGACAACCCTTACCTTAAC
GTATTTCATCCTGAAAATTTACACACTTGTGTATAATGCCTTCATGTATGTCAGTATTTTTTTAGAATTTTTTGAAATAT
AAAAATGTGAATTTTCGTGAATTTTGCATTTTGCATTTAGAGGCCTCCATGAAGCTCGGCCCCCAAAAGCAATTTCAATT
TTAAATGTCAATTATTAATACTTTTACTGATGGTCTGACGGCATGTGCACTATACGTGTTTCTCCATACGAAGATGGATC
GGGTTTCACTATCATCTAGTATTATCATCAGATAACGGCATGCGCACTAGTGTCAATTCACAAACTGGAGCTAATTTTT-
T-TTCACAAACTGGTGCTGAGGAGATCATGTTATTATACATAAAACATAGTCTGATGTGCAATTACGTGCCCCC---CTG
CTTGTGCATCTTCCGTTTTGTTGAGAAAGTTCG-GAGAACTCTAAGAACAACTGAACAGACGTGAGCGGAGTCCCGTGCA
ACGTGGAAGTGATCCAGCAAGCGGAGTCATCACTAACTTTTTGCAACCATGCTGCTAGTGCCACGCGTGCCGGCAGTCGC
ACCACCCGTCCCCAACGCAACGACGTTATATATATGCCCGAGATGCGAGAGACCGACCACATCACAACGATTAGCAAGCG
GACCATCA----ATTAATTTCTAGCGCATCTATCCATCCACTAAACTTTGACA--AAGCATTCTATCTGACAGCACTAGC
AGAGGCTGGTTCGGCAACAACAATGGCGTTCGTGCCGATCTGCGTGCAGTGCGGGACGAGGAGCAACCCGTGCCGGTGTA
AGGTGGTTGGCCCGACGCTGGGATTCGTGGCGCTCGTCGTGGCCGGAGTGGTGGAGTGGCCGCTGGGCGCCGCCGTGTAC
CTTTTCCGCCACCGCAAGGGTCGCCGCATCATGGGTCACCCGACCACGGTCGTGTACCCTCGCGTCACCGGCGCAATCCC
CATCTAATCGACCGCAGCATCTGCCTCTTCGGTGGTGATCTGTCACGAGGTACCGCCGTTGGCTTGTCAAGCTGTGTCAT
GTAATCTGGGAGATTCGTCTCTCCGACTCTCAGCGTGTGTTTAATAAAGCGAGGTTTTTGTTGTCGTGGTATTTGCAAGG
CTTCGCCGTGGCTGTACTTAATATTTGTTCGTCGATGTT-----GAGTAGCTGTTTTGGTCACCCCGAGTGCTCTCTCCT
CCC-----------TGACTCCTCTTTACGGAAAATGCTCTTTATGTAGTGCCCCCTCCGATCTTCTCTTCTTTGAAAAAT
GTTCCTTATGTAATGTTTCCTCCTATCCAAAATAAAATAGGTGTCGTGGTTTTAG-------------------------
-------TTTATTATAAACTAAA---------------------------------------------------------
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>chr3B_23
----------------------AGCCACATTATAGATATACAACTCCAAA------------------------------
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----------------------------------------------CTTGCATATCTACATGATTGAAGCACCAGACTGT
AGAACAATCATTGTACGATAATTTTCATTAGTATATACTTGGTTATCTAAGATATGCAC--ATATTTTACTAGTAAAATT
ATTTTACTATGTAATGTATACATATAGAATGACATTTTGGATCTCGGCCTTCATAGAGGCCAAATTTTTGAAAAAAACAT
TATACAAGTAAACAAGGATGTGAGGTGTATGTGTCTGGAATTTCAGAATAAAATACAATGAAGCGGCAACCTGTATAAAA
AGACAAATTCATGG--------------TAGTATCATGCATTTAAAAGCCTCTTTTTT--TGCACAACCCTCATCTCAAC
GTATTTAATCCTGAAAATTTACACACTTATGTATTATGCCATCATGTATGCCGGTATTTTTTCAGAATTTTTTAAAATGT
AAAAATATGAACTTTAATGAATTTTGCATTTTGCGTTTAGAGGCTTTCATGAAGCTCGGCCTCCAAAAGCAATTTCAGTT
TCAAATGTCAACTATTAATACTTTTTCTGATGGTCTGACGGCATGTGCACTACACGTTTTTTCCTGTACCAAGATGGATC
GGGTTTCACTATCATCTATTATCATCAGAGATG-ACGGCATGCGCACTAGTGTCAATTCACAAACTGGAGCTAAATTTTC
T-TTCACAAACTAGTGCTGAGGAGATCGTGTTATTATACATAAAATATA-TCTGACGCGCAATTACGTGTCCCATCATTG
CTTGTGCATCTTCCG-TTTGTTGAGAAAGTTCCAGAGAACTCTAAGAACAATTGAACACACGTGAGCAGAGTCCCGTGCA
ACGTGGAAGTGATCCAGCAAGCGGAGTCACCGCTAACTTTTTGCAACCATGCTGCTAGCGCCACGCGTGCCGGCAGTCGC
ACCACCCGTTCCCAACGCAACGACGTTATATATATGCCCGAGATGCGAGAGACCGACCACATCACAACGATTAGCAAGCG
GAGTAGCGGACCATCAATTTCTAGCGCATCGATCCATCCATCAAACTTCGAACACAAGCATTCTATCTGACAGCTCTAGC
GGAGGCTGGTTCAGTAACAACAATGGCGTTCGTGCCGATCTGCGTGCAGTGCGGGACAAGAAGCAACCCGTGCCGGTGCA
AGGTGGTCGGCCCGACGCTGGGATTCGTGGCGCTCGTCGTGGCCGGGGTGGTGGAGTGGCCGCTGGGCGCCGCCGTGTAC
CTTTTCCGCCACCGCAAGGGCCGCCGCATCATGGGTCACCCGGCCAGGGTCGTGTACCCTCGCGTCACCGGCGCAATCCC
CATCTAATCGACCGCAGCATCTTCCTCTTCGGTGGTGATCTGTCACGAGGTACCGCCGTTGGCTTGTCAAGCTGTGTCAT
GTAATCTGGGAGGTTCGTCTCTCCGACTCTCAGCGTGTGTTTAATAAAGCGGGGTTTTTGTTGTCGCAGTATTTGCAAGG
CTTCGCCGTGGCTGTACCTACTATTTGTTCGTCGATGTGAAGTAGAGTAGCTGTTTTGGTCACCCCGAGTGCTGTGTAAT
AGTATCGATCAACTTGACTCCTCTTTTCGGAAAATGCTCTTTATGTAATGCTCCCTCCGATCTTCTCTTTTCTGAAAAAT
GCTTCTTATGTAATGTCTTTTTTTAGAAAAAAAACTCCATCATG-----------TATTAATCAACTTAAAATGTCCG-T
ACAATCATTTATTACAAACTCCGCCACACAGGGCGGAACAGAATGAAAAAGAAAATCATCAGATCTATTATCAAAACTAA
ACTTATCTCGGGA---GCCACCAAATTTGCCCT---GTTGATCTTTGAAATATGCAAATTCAACAGCATCTTTGAGATAT
TTACAACATCCTCCTTTAAATCAACAAGGGATGACATGTTCATACAATTTCTTCCAAGCACAAAGGGCACAACGGAGCAA
TCAATTTTT---AAAATAACAGATACGTCTAGTGTCATTTCAATATACAGGCCCGGCAGGGACGCTCTAAGTTTCGCTTC
CTGACACTAT----------------------------------------------------------------------
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>SNPs
--------S-----------------------------------------------------------------------
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-----------------------------------------------------S----------------------S---
-SS-------------------------S---S----S----S-------------------------------------
-------------------------------S------------S--SSSSSSS-------------------------S
-------------------S-S---------S-------S--------------------S--------------S----
---------S---SS-------S-------------S---------------SS--------------------------
S---------------------------------------S-------------------S--SSS-S-----S------
----S------------------------------------S--------------------S-----------------
-----------------S-S--------------S------------------------------------S--S-S---
---------S---------S----------------------S--S---------------------------S------
-S-----------------------S----------------S------------------------------S------
------------S-------------------------------------------------------------------
---------------------------------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-------------------
------------------------------------------------------------------------S-------
----------------------------S----------SS----S-------SS---------------------S-S-
---------S----------SS-S---S--S-S--S--S-----------------S----S------------------
----SS-SSSSSSSSS---S-S-----------SSS------------------S-------S--------------S--
----S--SS---S------------------S---S---S--------S---------S---S---SSS---S-----S-
---S---SSSSS-----S-SS-SS-S---------SS-SSS------------SSS----S---------S--S------
--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSS
>forward_810
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----------------------------------------------------------------------AGGACGTATC
GGGTTTCACC----------------------------------------------------------------------
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>reverse_2234
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-------------------------------------------------------------------------CCGCTTC
CTCGACGCTATAG-------------------------------------------------------------------
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