>input_sequence_82521
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------ATGGCTTCCTCTTCGTCCTCAAGGCTGCTCGCGGCGGCGGTGCTGGCGGCGCTGCTCGCCGGCGCGATGTGCGG
CGTGAAGGTGGCCTTCACGGTGGAGAAGGGGTCCGGCGCCAAGAAGCTGGTGCTGAAGATCGACTACGCCAGACCAGGCG
ACAGCCTCGCCGAGGTGGAGCTCCGGCAGCACGGCTCGGAGGAGTGGCAGCCCTTGACCAAGAAGGGTGGCTTCTGGGAG
GTCTCGTCCACCAAAGACCTCGTCGGCCCCTTCAACTTCCGCTTCATGTCCGAGAACGGCATGAGGAACGTCTTCGACGA
GGTCTTCTCCACCGATTTCAAGATCGGCGAAACCTACGCCCCGGAAAAGTGA----------------------------
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>chr4A_1_TraesCS4A01G007700
GATACAGGTGTATAATACAGTACATCTTAAAGTACAATTTTCTTAATCTTAGGACATTCCTTGGTTTTAAAATTAGAATC
GTGTGATATATCATCATGTCAATGCCACTTCAGTATTCATGTGGCACACGTGGTTAGCAACTCAAACTTGATGATTTTTT
CAAATATTGTTTATACTTAAGTATGCATATTGATAGTTTGTATGTGTATGCATTTCTAATATCAAAAATATGTTTCTCTA
TATTAAGATTAACATATAATCAACTTATTTATGTATTTCAAAAATTGTGTGTGCTATATTCATACGTATTTCTCATGAAT
GTCACATCATTTGCATAAATATTAGTACCATCTGGTAGGGCAATGAAAAAAATAGCGCGCTACAAAAAATAGCGTCGTCC
TTGAAAATATGCTATTAGCGTGCTATTAGCGAGAGATTTTATATTGATCAATTTAGTGAGACAATTCTCTACACTCTATA
GCGCGCTATTTTTTTTCAATGGGTAGAATACAGTGTCAACACTAAAAACATAAAAAAAAAACTTTACAGTGATGACTATT
GCCTTGTGACCAAACTGGAAAGCAAAGATAACAGTAATTGGAATTTCTATATTTTTCTTTATCCGCCTTCATGTT-----
-------------------------------------------------------------------------------T
TACCTTACATTACGTAAGAGTAATATCAGCCTTCAGATC---------------------------------AGGAGAAA
ATAACAGCTCATATATATCGACTTAGGACTATCTTAAAACGGCTCAAGACTA-GCACCAATTTAGGCCCACCACTTAATT
GCAGGCCAGCCGAAACAATTGTTCATGTCGTTTAAATACCGTGGTGACATGCGGCGCCGTTTCCTCCGATTGTATTGGCG
CGGCGGTCACGGCCAGCGCCGTTTCCTCCGACTGTGTTGCCCGGAGCACCGCCCGTCGGACGCTCTCTTCTGCCCATAAA
TACCGCGCACATGATCCATCAGAATCCACACAGCTCGAAGCATCCACACACCG--------CAGTCAAATCTCTCTATCA
GTCCAGATGGCTTCCTCTTCGTCCTCAAGGCTGCTCGCGGCGGCGGTGCTGGCGGCGCTGCTCGCCGGCGCGATGTGCGG
CGTGAAGGTGGCCTTCACGGTGGAGAAGGGGTCCGGCGCCAAGAAGCTGGTGCTGAAGATCGACTACGCCAGACCAGGCG
ACAGCCTCGCCGAGGTGGAGCTCCGGCAGCACGGCTCGGAGGAGTGGCAGCCCTTGACCAAGAAGGGTGGCTTCTGGGAG
GTCTCGTCCACCAAAGACCTCGTCGGCCCCTTCAACTTCCGCTTCATGTCCGAGAACGGCATGAGGAACGTCTTCGACGA
GGTCTTCTCCACCGATTTCAAGATCGGCGAAACCTACGCCCCGGAAAAGTGATCCTTCCGTCGGTGTGTCACATTAGTCG
ATTCGAGTTTTCCCTTGTTTCCGTTTCATTATATTTGCATGTATTCGCCCTCATGCGTGGATAATACATAATTATCGACG
CCTATGAGGTGCGTATACATACGGT-------------GCGGATGTGTTTGCTCTCCATT-----CATCCACTGCCTATG
CATCTGTCTTGTTCCGTTTGTATCCGAATTTTGCTCAAGATTATGAAATGTATCTTTTTTTTATCTTGTCACCTTTATTT
TGGTTATGTTTGTTTCTACTTACTTTGAGGTAACGCGATACAAGATCAAAAGGTGGTATGTAAAGGATCTAAGAGGATGG
AGATATATTTGCGTTGCCTATTCCATTTTTTTT-TTGGTTAATATGAGGGCAAACCAGTCACAAA-CTAACTACCACAAA
AGTGAGGATATAAACATTCGGGAAAGTCAAGAACCATGTTCAGTTTCTTGTGAAACCAATAAACAT--------------
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---------------ATCAAATATATACATGCAATTAAAGTAAAT-CACCATATTATAGTTGCGCTTTATCCACTTATAC
CAACTCTAGCAGAGTCGCCAAATTTGTAATCGTCATGTTACATATGGAGCGGCTGGCCAGGCGATGTGCAAACTCAGAGT
CAACATATATCAGCCTCCACA---TTTTTACTTTTTCTTCATTAAAACAATTTGATTGCCTCCAAAATCAAACGTTTTAT
CACACCATTTC-AAAGCAATGGTGTACATAATTTTAACAAGTCATATGAACAAAATCATTTAATCGACGGCGTGTACAAA
TCAGATGTTCACGACGTGTTTGCCGTCGTCTTCTCCGACATGTGCATCGTCCCCTCCTATAACGTCCCTATAGAACGTAT
GGTCACCATTCACGTCTTCTTCCAAAATTCTCGCACCACTAGACGGCTAAGATGTTACCGCCAGAGAGTTTCGATTACGA
TCTGACGACTGGAAATCATTGCCACTTGGCACCAAGTAGGATAGGGGCTTCTTCTTGGAATCTGAA
>chr4D_1
GATACAGGTGTATAATAGAGTACATCTTAAAGTACAACTTTCTTAATCTTAGGACATTCCTTGGTTTTAAAATTAGAATC
ATGTGATATATCATCATGTCAATGCCACTTCAGTATTCATGTGGCACACGTGGTTAGCAACTCAAACTTGATGAATTTTT
TTAATATTGTTTATACTTAAGTATGCATATTGATAATTTGTATGCGTATGCATTTCTAATGTCAAAAATATGTTTCTCTA
TATTAAGATTAACATATAATCAACTTATTTATGTATTTCAGAAAT--TGTGTGCTATATTCGTACCTATTTCTCACGAAT
GTCACATCATTTGCATAAATATTAGTACCATCTA----------------------------------------------
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----------------------GTATAATACAGTGTCAACACTAAAAACATTAAAAAAAAACTTTACAGCGATGACTATT
GTCTTGTGACCAAACCGGGAAGCAAAGATAACAGTAATTAGAATTTCTATATTCTTCCTTATCGGCCTTCATGTTTTAGT
GACAGCATAATTTATTCCTTTATTTGTGGAAATGAAAAGTTCATACTAACCCCACATAATAATAATCACTGATAACATCT
TACCTTACATTACGCAAGAGTAATATCAGCCTTCAGATCAGGAGAAAATAACTTTTTTTTGAGACAAAGATCAGGAGAAA
ATAACTGCTCATATCA----ACTTAGG---------------------------------------------ACTTAATT
GCAGGCCAGCCGAAACAATTGTTCATGTCGTTTAAATACCGTGGTGACATGCGGCGCCGTTTCCTCCGATTGAATTGGCG
CGGCGGTCACGGCCAGCGCCGTTTCCTCCGACTGTGTTGCCCGGAGCACCGCCCGTCGGACGCTCTCTTCCGCCCATAAA
TACCGTGCACATGATCCATCAGAATCCACACAGCTCGAAGCATCCACACGACCACACACAACAGTCAAA--TCTCTATCA
GTTGAGATGGCCTCCACCTCGTCCTCAAGGCTGCTAGCGGCGGCGGTGCTGGCGGCGCTGTTCGCCGGCGCGATGTGCGC
CGTGAAGGTGAGCTTCACGGTGGAGAGGGGGTCCGGCGCCAAGAAGCTGGTGCTGAAAATCGACTACGCCAGACCAGGCG
ACAGCCTCGCGGAGGTGGAGCTCCGGCAGCACGGCTCGGAGGAGTGGCAGCCCTTGACAAAGAAGGGTGACTTCTGGGAG
GTCTCCTGTAGCAAGGACCTCGTTGGGCCCTTCAACTTCCGCTTCATGTCCAAGAACGGCATGAGGAACGTCTTCGACGA
GGTCTTCTCCACCGATTTCAAGATCGGCAAAACCTACGCCCCGGAATATTGATCCTTCCGTCGGTGTATT--ATTAGTCG
ATTCAAGTTTTCCCTTGTTTCCGTTTCATTATCGTTGCATGTATTCGCTCTCATGCGTGGATAATACATAGTTATCGGCG
CCTATGAGGTCCGTATACATACGGTAGGAGAAGCAACGACGGGTGTGTTTGCTCTCCCG----TGCATCGACTGTCTATG
CTTCAGTCTTGTTCCGTTTGTATCCGAATTTTGCTCAAGATCATGAAATGTATGCTTTTTTTATCTTCTCACCTTGATTT
TGGCTATGTTTGATTCTACTTGCTTTGAGGTAACGCAATACAAGATCTAACGGTGGTATGTGAAGGATCTAAGAGGATGA
GGATATATTTGCATTGCCTATTCCAAATTATTT-TTTGTTAATATTAGCGCAAACCAGTCACAAAACTAACTACCACGAA
AATGAGGATATAAACATTCGGGAAAGTCGAGAACCATGTTCAATTTCTCATGAAACCAATAAATATATCTTTCCTAATAA
TAAAGCACGGATTGACTTTGTCGGGTTCACCGTCACAATACGCTTCTTCACGTGATTTTACGCTTTCAGTTTGAATTTAA
AATATATACACGAGGTTTACCCAAGGTGGTACTAATCTATATACGTGCCCATGCATCAAAACCATCAGGTTCGATGTGTG
TTCCTACCGACTTGGGCCTGCAGGCTGGGTCGTTGGCCCAGCTTCAGTTGAACGCGAGAAGAAGAAAAATAAATAAAATT
GGGATATGGACAATGGGATTCGAACTCTTGTCTGCTGTGTAGATGCTAACGTAGCAGACCAATCAATCCAGGCTTGTGGG
TATTACAACGTCGGTGTCTGGCTCTTTAACATAAAGCAAGGCGTACTGGGGCCAAGGGAGTTGGACGCTTGATGGGCACG
GGAGTGCTGGGCCGAGACTGCTGCCGCGGCCCACGGGGCGGACAAGGAACAGGCCGGAGGCTTTTTCATATTTGTTTACT
TATGAAATAGACCCACCTTGCTATTTTGCATTAATTTTTACCAATTTATATACGTTCTTAGGTTATCAGGCATCACGGAG
CTGCTTCGGAAATTAAGCAAAGAATAAGGCATGAATATCTCATTGAGAAACAAAGAAGGAAGGCCCATGGAAAGAGAGAG
AACGGAAATAGAGGGTAATTAATTGGAAAGTAACCGGCTGGCAAATGAGATTCATGACATGCTTGATATAAGGAAAAAGA
AAAAGAAAGAAAATAGACACTGATTGCGTGAGAAATAAAGAAGAAAGGAAAGAGAGAGGAAGGAAATAGGAGGATTGAGG
GAGGATCCTACCAAATAGATAGGACATGCGGGATTTGTGGGCGCCATATATTCTTTGTTGGCCTGAAATTTAGTATCAAT
GGCAGGCGTACTGGCCTCATTCATATCTTATATGAATATAAAAATGATGTGGCATTTTTTTCCTACATGCAATCCTCACT
AAATTCACGTCATTTTTTTTCTGTTGCAGCGGACAACATGACATGTTTTACTTCCACTTATGATCCTTACTAAATTTGCA
CCAATTTTATAACACATTGAATGGTATGTCTGCCATACAATCCTCACTAAATTTAAGTCATTTTTTAGAGGTAATATCAC
CGACAATCACACAACTTGCATTGGATGTGCAGTTTAGTGCTACAACTTGCAAAATACGTCTTTTTGTCAGCTAACTTGCG
TTTCGGTGCATATACGGTCACTCCATGCGTATTCGGCGCTTGCGTGGCATGCCACGTCTGCATGGAGCCACTGTCAGTGA
CCGAAGACGCTCTGGAGCAACCAGCGCGTGGTAAACTTGCATAGACCCCCTGAATCTGTCTGTCAGGCGTACGGGCACCG
GAGAGAGATAACAGAGATTGCTATAGAAAAGTGGTGGGTGTACAATCTTCATGACAGTTTCAGATTTTTGTCTCATTTTC
ATGGTTCAATTCTGTACAATGTTGTGCCGAAATTCAGTTGAAAACTGTGGCAAAATTCAGTTGAAAACTGTGCCAAAATA
CTGTCCAAAAATTCAGATTTTTATCTTTTTTTACTGGTTCAATTCTGTACAAAGTTGTGCCAAAATACAGTTGAAAACTG
TGCCAAAATACTGTCCAAAAATTCAGTAAACGTTTTGGCAAAATTTAGAACATGTACAGAACATCCAAATAAAAAGAGAG
GACTGGGATTCGAACCCAGGTCCTGCCAATATTACTTGACAACGTATTGCCAATTGGGTAATGAGTAGATTCTGCTCATA
TCTCTCCACCCACCAGTTTTCTATAGCAATCTCTGTTATCTCTCTCCGGTGCCCGTACGCCTGACAGACAGATTCAGGGG
GTCCGTGCAAGTTTACCACGCGTTGGTTGCTCCAGAGCATCTTCGGTCACTAACAGTGGCTCCATGCAGACGTGGCATGC
CACGCAAGTGCTGAATACGCATGGAGTGACCGTATCTGCACCGAAACGCAAGTTAGCTGACCAAAAAGACGTATTTTGCA
AGTTGTAGCACTAAACTGCACATCCAATGCAAGTTGTGTGACTATCAGTGATATTACCTCCATTTTTTACCGGTGTAACC
CACGGGCATATATGCTATATTTTGTATAAATGGAGGTATAATATTATTTCGCCTTCCATTTGGTATGTCCATGTCGTTTC
TCCATACTTAGTTAGGCTATTCTACCAAATAGAGGAAGGAAATAGGAGGATTGAGGGAGGATCATACCAAAATAGATAGG
ACATGCGGGATTTGTGGGCGCCATATTAATCTTTGTTGGCCTGAAATTTAGTATCAATGGCAGGCGTACTGGCCTCATTC
ATATCTTATATGAATATAAAAATGACGTGGCATTTTTTTTCCTACATGCAATCCTCACTAAATTCACGTCATTTTTTTTT
CTGTTGCAGCGGACAACATGACATGTTTTACTTCCACTTATGATCCTTACTAAATTTGCACCAATTTTATAACACATTGA
ATGGTATGTCTACGCATACAATCCTCACTAAATTTAAGTCATTTTTTACCGGTGTAACCCACGGGCATATATGCTATATT
TTGTATAAATGGAGGTATACTATTATTTCGCCTCCCATTTGGTATGTCCATGTCGTTTCTCCATACTTAGTTAGGCTATT
CTACCGATAGTCTATCCTAGGCCACCAGGCATCTGCCCCGTTCATCCGTGTTACGTTCCACCAATAAAAAAACAGCGCCC
TCCCGACCCGTCTGTGCAACCCGGTCCAACAAATCAGACCCACCAGCCCGTTTAGGAGATGAGGCAAAATAGTAGACCGT
GATAGCAATCAAACTGCAACCTCCACTGTTCTTTGGTGTTGATCGTTTTAACCCACAAAAAAAAGGTGTTGATCATTTTA
AACTAAAATTGAATTTGGTGTTTGTTTGTGTCCTTTACGGACTGGAACTGAACTACTACGATGTAAAATCTGGATACACA
AATACAAGGCGCAAGCATTAGATTGTGCAGATGTGGCCGGGATCTCAAACACGACCGTTCGCTGGTCTGTACATGTAGAC
GATGCAATTCTTTATTGGTTCCAAGCTTAGGTGGAACGTTCCCGTGTAGTGGACATCGTGAGAGACAATGAGGACAAAGA
AAATAAGTGGTAACAGGGATGGGACGCTAAGGGTGATAATTTGTTTCTCCCGTTGCAACGCACGGGCACTTTTGCTAGTC
AATAAAAGTATGTGTATCAAATATATACATGCAATAAAAGTAAAT-CACCATATTATAGTTGCACTTTATCCACTTATAG
CAACTCTAGCAGAGTC-ACATATTTGCAGTCGTCATGTTGAATATAGAGCAGCTGGCCAGGCGACGTGCAAACTCAGAGT
CGGCATATCTTAGCCTCCATGTTTTTTTTACGTTTTCTTCATTAAAACACTTTGATTGCCTCCAAAATCAAATGTTTTAT
CACACAATTTCGAAAGCAATTGTGTATATGATTTTAACATGTTGCATGAACAAAAGCATTTAATCGACGACACGTATAAA
TCACATGTTGATGACGTGTGTGCTATCCTCTTCTCCAACGTGTGCATTGTCCCCTCATCTAACATCTCTATAGAACGTAT
GGTCACCATTCACGTCTTCTCCCAAAATTCTCGCACCACTAGACGGCTGAGATGTTGCCGCCAGAGAGATTGGATTACGA
TCTGGTGACTGAAAATCATTGCCACCTGGCACCAAGTAGGATAGGGGGTTCTTCTTGGAAGCTGA-
>chr4B_636
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-------------------------------------------------------------------------------T
TACCTTACATTACGCAAGAGTAATATCAGCCTTCAGATC---------------------------------AGGAGAAA
ATAACAGCTCATATCA----ACTTAGGACCATCTTAAAACGGCTCAACACTAGGCACCAATTTAGGTCCACCACTTAATT
GTAGGCCAGCCGAAACAATTGTTCATGTCGTTTAAATACCGTGGTGACATGCGGCGCCGTTTCCTCCGATTGTATTGGCG
CGGCGGTCACGGCCAGCGCCGTTTCCTCCGACTGTGTTGCCCGGAGCACCGCCCGTCGGACGCTCTCTTCCGCCCATAAA
TACCGTGCACATGATCCATCAGAATCCACACAGCTCGAAGCATCCACACGACCACACACAACAGTCAAA--TCTCTATCA
GTTGAGATGGCCTCCTCCTCGTCCTCAAGGTTGCTCGCGGCGGCGGTGCTGGCGGCGCTGTTCGCCGGCGCGATGTGCGC
CGTGAAGGTGGCCTTCACGGTGGAGAAGGGGTCCGGCGCCAAGAAGCTGGTGCTGAAAATCGACTACGCCAGGCCAGGCG
ACATCCTCGCGGAGGTGGAGCTTCGGCAGCACGGCTCGGAGGAGTGGCAGCCCTTGACCAAGAAGGGCGACTTCTGGGAG
GTCTCGTGTAGCAAGGACCTCGTCGGGCCCTTCAACTTCCGCTTCATGTCCAAGAACGGCATGAGGAACGTCTTCGACGA
GGTCTTCTCCACCGATTTCAAGATCGGTAAAACCTACGCCCCGGAAGAGTGATCCTTCCGTCGGCGTGTT--ATTAGTCG
ATTCAACTTTTCCCTTGTTTCCGTTTCATTATCGTTGCATGTATACGCCCTCATGCGTGGATAATACATAATTATCGACG
CCTATGAGATGTGTATACATGCGGTAGGAGAAGCAACGGCGGATGTGTCTGCTCTCCGGCCCATGCATCCACTGTCTATG
CATCAGTCCTCTTCCGTTTGTATCCGAATTTTGCTCAAGATTATGAAATGTATGCTTTTTTTATCA-------TTGATTT
TGGCTATCTTTCATTCTACTTACTCTGAGGTAACGCAATACAAGATCTAACGGTGGTATGTGAAGGATCTAAGAGGATGA
GGATATGTTTGCATTGCCAATTCCAAATTATTTTTTGTTTGATATGAGCGCAAACCAGTCACAAAACTAACTACCACAAA
AGTGAGGATATAAACATTCGGGAAAGTCAAGAACCATGTTCAATTTCCCGCAAAACCTATAA------------------
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---------------ATCAAATATATACATACAATTAAAGTAAATTCACCATATAATAGTTGCGGTTTATCCACTAATAG
CAACTCTAGCAGGTCA-CCATATTTGCAATCGTCATG-------------------------------------------
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>SNPs
-----------------S-------------------S------------------------------------------
S-------------------------------------------------------------------------S-----
SS---------------------------------S--------S---------------S-------------------
----------------------------------------S----SS--------------S---S---------S----
---------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSS---S-------------------------S-----------------S----------
-S-------------S--S--------------------S-------------S---S-----S----------------
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--------------S-----------------------------------------------------------------
--------------SSSSSS---------S-----------------S------------------S-------------
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----------------------------------------------------------------------S---------
-----S-------------------------------------------SS-S----------------SS---------
--SS-------S-----S------------------------------------------S------------------S
---------------------------------------------------------S----------------------
----------S----------------------------------------------------------S----------
-------SS-S---S-----------S------------------------S----------------------------
----------------------------S-----------------S----------------------SSS--------
----S---------------------------SS----------------------------------------------
---------------------------------------------------------SSS--------------S-----
----S------------------------------------------------SS------------S-------S----
---S--------S-----------------------S----------S--S----------S-----------------S
S-----------S------------SS--S------------------S-------------------------------
------------------------------------------S-----S--------------S----------------
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-------------------------------------------------------------------------------S
----------------S---S-----S------------SS----S----S-------------S---------------
-SS-----S-S--------SS----------S-----------------S----------------------S-------
-----S--------------S-----S--S---------S--SSS----------S-------------S-SS---S---
---S-----S-S-------S---SS--S--------S--S-------S--------S-S----S--S-------------
--------------------S---------------------------S-------S-----------S--S--------
----SS-----S-------------S---------------------S------------S----S
>forward_1110
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--------------------------------------------------TCCACACACCGCAGTCAAAT----------
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>reverse_5560
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---------------------------------------ATGTGCATCGTCCCCTCCTA---------------------
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