>input_sequence_60713
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---------------------------------------------------------------------ATGCCCTTCAC
CGGCGTGTCTGTCATCACCGATGGAA------GAGCGCCACGATCTTCCTCGCCAACCGCAAGCAGCAACACCTCCAGCG
GCTACCACCTGCTCATAGTCGAGGGGTACTCGCGCACCAAGAGCAGCACACACACGGGAGAGTGCATCAGGTCTTGCCCT
TTCATGGTTGGCGGCTACCTTTGGTGCATCCAGTACTACCCCAATGGCGCCAAGTCGGAGAACGCAGATTTTATATCTCT
TTATCTTGGTCTTCTTAACAATGACGATGCTGCACTTGCAAGCCCATTGAAGTTGCAGTTCGAGATTAGTTTCGTCGATC
AGATTTACAATCAAGAATCCACGCAGATTCGCGCTGGCCAAGTATATGAATTGCCTAGAAGCA---TATGTGCGGCCTAT
CACCAGTTAATCAGA-GGGACACCTTGGAAAGATCAAAGTACCTTAAGGATGACAGTTTCACCCTCCGTTGTGACATCGT
GGTCATTGGCGATGCT---AACAGCAGGGACACTGCCACCACTTCTCCGTCCATCAAGGTGCCTTCTTCGGACATGCAAC
AGCATTTCAGCGATCTTCTTCTGGCCGAGGAGGGAACGGACGTGACGTTCAAGGTCGGCGGCGAGACGATCGCCGCACAC
CGTTGTGTGCTAGCGGCCCGATCTGCCGTCTTCAAGGCAGAGCTCTTTGGCACCATGAAAGAAGGCATGATGACTACAAG
CGTCATACAGGTTGACGACATGGACGCGCAAGTTTTCAGGGCGATGCTTGGGTTCATTTACAGTGACTCGCCGTCGGAGA
TAGAGGAGGAAGAAGATGCAGATGTGATGTGGCAGCACCTGCTCATCGCTGCTGACAGGTATGATCTCCGGCGACTAAGG
CTGATGTGTGAAGAGAAGCTGTCCGAGTACGTCGACGTGACCACGGCCACGACCATCTTGACGCTAGCTGAGCAGCACAA
CTGTCGCGGGTTGAAGGAGACGTGCTTGGAGTTTCTCAACTCTCCTGCAAACCTGCAAAAAGTCATGGCGTCCGGTGGTT
TGGATAGTCTTGCTGCATGCTGCCCCTCTGTTCTGAAAGATCTCATTGCCAAGCTTAATTAA------------------
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>chr3D_1_TraesCS3D01G103600
GTACGCTTCCTACAGTGGAGGGTTAACCAAGGTTTGGCCTGGAGGAGGTGCCTTTCGGTCTACCTTCCATGGTTGGTGTG
TTGTGAGGCAGAGAGTTGGCGGTGGCTCGAGACATGGGTGTCAAGGCGACGACCCCGGATGGTGTCTACATGATTGGCTC
TCCGGCGGGCATCATGGCAGCGGCGGTAGCTATGCTTCTTGGTAGTGTGGGCAGCGAGGGGTGTAGTGGGGGTTGCTCGG
GCTCGCCTTCTGCTATGGCAGTGGCGACGCTCAAATCTAGGACCCGAAGACTTGTTTTCGTCGCGACTATCCTGGGTACC
TCGTGGTGACACGGGTGAGCTGTCGAGCGAAAGCTTCGCACTTTGGTGCCGACGACGGTGCCGCGCCGCTTGCAGGTGAC
GCTATCTTCTTGAAGACATTGATGTGGTTCTTGTTCTTCCCTTCGTATCAGAGTTCCGAGTGAAGACCATTGTCTGTCTT
GGACTCGACAGCGGCGACACCTAGTGTCGTTTCTCCCCCCGAGGGTGTTGTCGTGGACCTTAGGTGTTCTTGGATGTGTC
GTCGTGTTGCATTCATGGTGTTAGCTTTCGGTGGACGTAGTCGTGGTCCAGTTATGCCCAAATTTGCTTTGTAACAAGAA
CTCCTTCATGCCGGGCTTAAGACATGCCGGGCGACGAACGTTTGTTTTTTACAGGCACGAGAATCTTGTTGGCTTCAGTT
GCTCGTCAGATTTAACTGGAAGTTGCATTGAAACGACACCTATCTATTCATTGTGCCCTCGGGAGTGGAAACGATGACTG
TTTCAGCTCTCGAGGAGACGGACGGCGCAACC--------TTCCTAAACTTTTGCAGTTACGTTCACATACGAGA--CGC
ATGGGTTCCCGTACTGAAAGAGTCATTCCCTATAGCAGAGTATATATAGCGGGTGTGCATTGCGTATAAATGGAGCGTCT
TCCTCGTCTCCAATTTCCCTCATTGCCAAGTGATCGAGAACGCCAC-------------------GATCATGCCCTTCAC
CGGCGTGTCTGTCATCACCGATGGAA------GAGCGCCACGATCTTCCTCGCCAACCGCAAGCAGCAACACCTCCAGCG
GCTACCACCTGCTCATAGTCGAGGGGTACTCGCGCACCAAGAGCAGCACACACACGGGAGAGTGCATCAGGTCTTGCCCT
TTCATGGTTGGCGGCTACCTTTGGTGCATCCAGTACTACCCCAATGGCGCCAAGTCGGAGAACGCAGATTTTATATCTCT
TTATCTTGGTCTTCTTAACAATGACGATGCTGCACTTGCAAGCCCATTGAAGTTGCAGTTCGAGATTAGTTTCGTCGATC
AGATTTACAATCAAGAATCCACGCAGATTCGCGCTGGCCAAGTATATGAATTGCCTAGAAGCA---TATGTGCGGCCTAT
CACCAGTTAATCAGA-GGGACACCTTGGAAAGATCAAAGTACCTTAAGGATGACAGTTTCACCCTCCGTTGTGACATCGT
GGTCATTGGCGATGCT---AACAGCAGGGACACTGCCACCACTTCTCCGTCCATCAAGGTGCCTTCTTCGGACATGCAAC
AGCATTTCAGCGATCTTCTTCTGGCCGAGGAGGGAACGGACGTGACGTTCAAGGTCGGCGGCGAGACGATCGCCGCACAC
CGTTGTGTGCTAGCGGCCCGATCTGCCGTCTTCAAGGCAGAGCTCTTTGGCACCATGAAAGAAGGCATGATGACTACAAG
CGTCATACAGGTTGACGACATGGACGCGCAAGTTTTCAGGGCGATGCTTGGGTTCATTTACAGTGACTCGCCGTCGGAGA
TAGAGGAGGAAGAAGATGCAGATGTGATGTGGCAGCACCTGCTCATCGCTGCTGACAGGTATGATCTCCGGCGACTAAGG
CTGATGTGTGAAGAGAAGCTGTCCGAGTACGTCGACGTGACCACGGCCACGACCATCTTGACGCTAGCTGAGCAGCACAA
CTGTCGCGGGTTGAAGGAGACGTGCTTGGAGTTTCTCAACTCTCCTGCAAACCTGCAAAAAGTCATGGCGTCCGGTGGTT
TGGATAGTCTTGCTGCATGCTGCCCCTCTGTTCTGAAAGATCTCATTGCCAAGCTTAATTAA-TTAAGCAATAAAAGTAT
AGTAATATGGTAGTACTTGTCGCTATATATCAGACATGCCGCCAAGAAGTAGTATTTGATCCTTGAGAGATCAGATGCGG
GAACTTTTTATATTTTCGTCATATAGTATTTGATCCTGTTGAGATANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAAAAATAGAAACCGTTAAATCTCAGTCGA
TTAAGATTTAGTCAAGTCTCAATCAACCTGTTTTTTGTTTTTTGAGGGGCAGTCAACTGGTTGTCTGTTGGATTGTTTGT
CTGCTTGAAGATTAGTGCGCTGCTGGCTTTGTGTCTACACGGGCCAATTTTGAGGGGCAGTCAACTGGTTGTCTGGTACA
GAGATTGGTTGGCCTGCTGTTTGTCTTTGCTTGTCTTTTCCCGTCGGGCTTGGGTTTGCTTGCGTGATGGGCTAGCGAGG
GGCTGGAGCCTTTTTCGTTGTCAGTGGCTCTTTTTCGTTTTTGGTTGCGCTGCCATTTTTATTTTTGGTTGTTTTTCATT
TTTCATTTTTTTGGCGGGGGATTTTTCATTTTCCATTTACTCTTTTGTACAGTATGTGTCTGATTTTCTTTCTTATGTTT
TCTTTTCTTCCTGTATTTTGTGT
>chr3A_660
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-------------------AGACGTGCCGGGCGACGAACGTTTCCTTTTTACAGGCACGAAAAACTTGCTGGCTTCCGTT
GCTCGTCAGATTTAACTGGAAGTTGCACTGAAACGACACCTGTCTATTCAT--TGCCCTCGGGAGTGGAAGCGAGGACTG
TCTCAGCTCTCGAGGAGACGGACGGCGCAGTCTCCTCATTTTCCTAAACTTTTGCAGTCACGTTCACATACGAGAGACGC
GTGCGTTCCCGTACTGAAAGAGTCATCCCCTAGAGCAGAGTATATATAGCGGGTGTGCATTGTGTATAGATGGTGCGTCT
TCCTCGTCTCCAATTTCCCTCCTTGCCAAGTGGTCGGGAGCTCACCTGGGTGGAGTCGCTTCGTGGATCATGCCCTTCAC
CGGCGTATCTGTCATCACCGATGAAGGAGCGCGAGCGCCACGATCGTCCTCGCCAACCACAAGCAGCAACACCTCCAGCG
GCTACCACCTGCTCATAGTCAAGGGGTACTCGCGCACCAAGATCAGCACACCGACGGGAGAGTGCATCAGGTCTCGCCCT
TTCATGGTTGGCGGCTACCTTTGGTGCATCCAGTACTACCCCAATGGCGCCAAGTCGGAGAATGCAGATTTTATATCTCT
TTATCTTGGTCTTCTAAATAAT---GATGCTGCACTTGCAAGCCCATTGAAGTTGCAGTTTGAGATTAGCTTCGTCGATC
AGATATACAATCAAGGATCCACGCAGATTCGCGCTAGCCAAGTATATGAATTGCCTAGAAGCAATCTATGTGCGGCCTAT
CACCAGTTCATCAGAAGGGACACCTTGGAAAGATCAAAATACCTTAAGGATGACAGTTTCACCCTCCGCTGTGACATCGT
GGTCGTTGGGGATGCCATAAACAGCATGGACACCGCCACCGCTTTTCCGTCCATCAAGGTGCCGCCTTCCGACATGCAAC
AGCATTTCAGCGATCTTCTTCTGGCCGAGGAGGGAACGGACGTGACGTTCAAGGTCGGCAGCGAGACGATCGCAGCGCAC
CGGTGTGTGCTGGCGGCCAGATCTGCCGTCTTCAAGGCAGAGCTCTTTGGCACCATGAAAGAGGGTACGGCCACTACAAG
CGTCATACAGGTCGACGACATGGACGCGCAAGTTTTCAGGGCGATGCTCGGGTTCATTTACAGTGACTCGCCGCCGGACA
TAGAGGAGGAAGAAGATGCAGATGTGATGTGGCGGCACCTACTCATCGCTGCTGACAGGTATGATCTCCGGCGACTAAGG
CTGATGTGTGAAGAGAAGCTGTCCGAGTACGTCGATGTGTCCACGGCCACGACAATCTTGACGCTAGCTGAGCAGCACAA
CTGTCGCGGGCTGAAGGAGACGTGCTTGGAGTTTCTCAACTCTCCTGCAAACCTGCAAAAGGTCATGGCGACCGGTGGTC
TGGATAGTCTTGCCGCATGCTGCCCCTCTGTTCTCAAAGATCTCATTGCCAAGCTTGCCAGGCTTAAGCAATAAAAGTAG
AGTAATATGCTAGTACTTGTTGCTATCTCAAAACATGTCGCC----AAGAAGTATTTGATCCTAGAGAGATCAGATACGG
GAA-TTTTTATATTTTCGTCATATAGTATTTGATCCTGTTG---------------------------------------
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>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSS----S-------------------SS---------------S--S----S-------S---
---------------------------S-------------S---------SS-----------------S---S-----
-S---------------------------SS---------------------------S---------------------
S--S----------------------S-----S-----------------------------S-----S----S------
---------------------S----------S---S--S-S-SS-----------------------------------
------S----------------S-S-------------------S------------S---------------------
--------------------S---------------------S--------SS---------------------S-----
--------------------------------------------------------------S-----------------
---------------S--S---SSS-----------------------------------S--------S----------
----S----------S-------------------S--------------------------------------------
--------S-----------------------------S-----------------------------S-----------
----S----S-----S----------S------S------S---S------------------SS----S----------
-----------------------------------------------------------S-------------S--S---
--S--------S------S-------------------------------------------S--S-S-SSS--------
------------S-----------------------------------S------------------------S----S-
---------------------------------S------S---------------------------------------
-----------------------------------S---S-------------S--------------------------
----------S-------------------------------------------------S---------S--------S
-------------S--------------------S---------------------SSSSSS-----------------S
---------S----------S-----S-SSS-SSSSSS-SS-SSSS---S-------------S------------S---
---S-------------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSS
>forward_655
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---------------------------------------------------------------------------AAGAA
CTCCTTCATGCCGGG-----------------------------------------------------------------
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>reverse_2189
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----------------------------ATCAGACATGCCGCCAAGAA--------------------------------
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