>input_sequence_84357
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-------------------------------------------------------ATGGGGTGGCTGCGGTCGCTCATGG
CGCCCATCAAGAAGCTCTGGATTCGCGTGCATTCCGCGCAGAAGAAGAGTATGTTCCTTCGTCTCTCTCTGCACTCTG--
----------------------------TTTCTTCCAGATTGCTCCTGTTTGTGAAT-TCTGATTCTGATTCTGCGTGGT
GCTGATCGTTGCTTTTGGTTGTGTGGTGGTAACAGAGAGAGGGATCTACATCCTGTACGAGGACGTCAAGTCGTGCCCGT
GCGAGGACGTGCAGATCCTCTGGTCCATCCTCGTCGAGTCCCACCCGCCGCCGCCGCTGCGGCTGAAGCAGTGA------
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>chr2A_1_TraesCS2A01G196100
TGAATGAAATGAGTGAATTAATAAACGGGTCAGTCCCTCTCCCTCCCTCTCCGCTCGATTTGACGATTTGACGATTTCTC
CCCTCGT-------GATCGCTCGAGATACTTAAACCGTCGCACTCTCCTTCTTCTTCTTCTTCTT---TCCGACTATTCA
TTTTGGCCCGTGGGGCAACGGCGATGCCCCAACTGACGCCCTGCGCGCCTTCGGACGGACACCTGGACGACGGGCGCGCG
---GCAGGCCATGTAGGCGCCAGCTTGTGGGTCATGGCTGCCCTGTGCCACGCCCTGTTCAGTGCTCACCGACGGGGAAA
ATGGCATGATTTTGTTGTGTGGTGGCTGCTGTGTCACTGAGACGTGCAAAAATGCATAGCAGTAGTC-------------
------ATACAGGAGCAGGAGAAGGGCGCCACGCCGACGGCCTGGCGAACGATTTCCCACGTTCGGAACGATGAAACCCT
GCTGAAATGCCAATGTTCCGAGCGTGGCTTCTGTCTGTCTCTCCCCAAAGCAGTGGAGCCATGGACGAATGGACTCCTGG
CTCGTTCTGCCGACAGCGTAGGCCACGGCGGCCATAAAGCTTAAATAAGACCTGACCTGACAGGGCCGAGGGGACACCCT
TTCTGTTTTCTCCTCGACTGATAATAAGACGAGAAAATTGAAAAATTGGC-------------------------GCGCC
AATTCGTTTGTTTATTATTATTCATTGGTATTCGTAGGGGCAGATATGGATGGATGGCGACGCGGCACCAAGAGCGTTAA
AGCCTATGATTAGGATA---------------------------------------------------------------
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--------------------------------------------------CAAGGGAAGCCCGGCAACGTGATGTTATGA
ATAGTGGCCGAGCCG-----AGCCAAGCAGCGGCAGAGACTTACTTCACAGGGCCTCAAAGCGACTCCGTCTCTTCCCCC
TCACGTCTCCTCCTCCTCGTCCCTTCTACAAGGTAGCTTGGCGTTGCTATTTCATCTCGTCTCCCGGCTGGTCAGTGCAC
GCACGAGCAGGGCAAAACGGGGGGGAGTGCTCGTGCTCAGCTGAGGGTCTCGCTCATGGGGTGGCTGCGGTCGCTCATGG
CGCCCATCAAGAAGCTCTGGATTCGCGTGCATTCCGCGCAGAAGAAGAGTATGTTCCTTCGTCTCTCTCTGCACTCTG--
----------------------------TTTCTTCCAGATTGCTCCTGTTTGTGAAT-TCTGATTCTGATTCTGCGTGGT
GCTGATCGTTGCTTTTGGTTGTGTGGTGGTAACAGAGAGAGGGATCTACATCCTGTACGAGGACGTCAAGTCGTGCCCGT
GCGAGGACGTGCAGATCCTCTGGTCCATCCTCGTCGAGTCCCACCCGCCGCCGCCGCTGCGGCTGAAGCAGTGATGGACC
GGCCGGCCGGT-CCCTGCCGCCGTCCGTCGATCGAGCACGGCGCTCCGACGTACCGATGGCCTCCCGGCGGCAGCCTACC
GATCCCG----------ACAGACTGTCGGTGGCTCGGTGTAGTGTACATAAAGATGATCGAGCGAGCGAGCGGCAGTTCC
GTGTCGCCATGATAGTAGGAAAGTAGGTGTCCCCTCGGCCTCTCCCTTGTGAGCCACGGAAATGGCGTGCGTGCGTGCAT
GGCCGGTGAGCTCCCCTCTCGCG-----CGCATGTGTCCTTCACCGACACTGCGACTCTGTGAAGCAA-GTTTTTTTTTC
TTCCTCCTCCCGTTTCTTTTCTCTTCTTTCTTATTTTCCTTTTTGGAAAAAAAGGGGA-AGCACGTGTAAGGCCTGGTTG
GTGGCCCGGGTCAATGGCCGCGCGTGCCTGTATTATCATCTTGTAAATACGAGAGAGGATACGAGTGAGAAGGCTGTATA
CACCGGTGAG------TGATGGTGTCGAGGAAAAAGAATTGTGAGTGTGGCATTGAAAGATGGGGTTGAAAGATGGCCTG
ATTGATGCTCTGTTCCCTGTGGCTCGCGTGCAGGGGAGGTGGGCGTGGTTTGACCTGACCACAGCGCGCACACGTAGTAC
GTGCGTGTGGGGGATGGGTGAGCGCGCGCACGGGTGGCGTGGTTAATGCCGGGGCCGGACCGGGGATCGTTTTCGTCGGC
CCGTGCGGTTGCAGGCTCATTGGTCGACGTCGGGGTGGTTGGTTTGTTCCGAG-----------------TTCGCCGTCA
TCATCGGGATGGGTTCGCCGTGTCCGCTGCTTCCAGCTGAGACGGGGAGGAGCACGGCACGATCATCCCGTGTTTCTCTG
GCCCCTGCCTGCGAGTGTGTAGTCTTTTCCGCCTCAGGCCCGCGCGTCGGCCGCCCAACACCCACCGGTCCTATTTAATT
GGTAATCGTTTGGAATCGGCGCACCGGCCGAACGCTCGGCCGGTTCCCCTCGCTCGCTCGCTCTTTTTCCACGCA
>chr2B_10
---------TGAATGAATGAATAAACAGGCCAGTCCCTCTCCCTCTCTCTCCGCTCGGTTTGACGATTTCTCCTCCT---
--CTCGT-------GATCGCTCGAGATACTTAAACCGTCGCACTCTCCT------TCTTCTTCTT---TCCTACTATTCA
TGTTGGCCCGTGGGGCAATGGCGATGCCCCAACTGACGCCCTGCTCACCTTCGGACGGACACCTGGACGGGCACGCAGCA
GGAGTAGGCCATGTAGGCGCCAGCTTGTGGGTCATGGCTGGCCTGTGCCACGCCCTGTTCAGTGCTCACCGACGGGCAAA
AATGCCATGA----TTGCGTGGTGGCTGTTGTGTAACTGGGACGTGCAAA--TGCCTAGCAGTAGCAGGAGCTGCTCGTC
ATACAGATACAGGAGCAGGAGAAGGGCGCCACGCCGACGGCCTGGCGAGTAATTTGCCACGTTCGGAACGATGAA-CCCT
GCTGAAATGCCAATGTTCCAAGCGTGGTTTCTGTCTCTCCA----CAAAGCAGTGGAGCCACGGACGAATGGACTCCTGG
CTCGTTTTGCCGACAGCGTAGGCCACGGCGGCCATAAAGCTTAAATAAGACCTGACCTGACAGGGCCGAGGGGACACCCT
TCCG--TTTCTCCTCGACTAATAATAAGATGAGAAAACAGAAAAATTGGCGCGACCGAACGAGCGCAACGCTTCTGCGCC
AATTCGTTTGTTTATTACATTATTC----ATCCGTAGGGGGAGATATGGATGGATGGCGACGCGGCACCAAGAGCGTTAA
AGCCTATGATTAGGATA---------------------------------------------------------------
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--------------------------------------------------CAAGGGAAGCCCGGCAACGTGATGTTATGA
ATAGTGGCCGAGCCGGGCAGAGCCAAGCAGGGGCAGGGACTTACTTCACAGAGCCTCAAAGCGACTCCATCTCTTCCCCC
TCACGTCTCCTCCTCGT-GTCCCTTCTACAAGATAGCTTGGCGTTGCTATTTCATCTCGTCTCCCGGCTGGTCAGTGCAC
G----AGCAGGGCGGCTGGGGGAGA-------GTGCTCAGCTCAGGGTCTCGTTCATGGGGTGGCTGCGGTCGCTCATGG
CGCCCATCAAGAAGCTCTGGATTCGCGTGCATTCCGCGCAGAAGAAGAGTATGTTCGCTCGTCTCTCTCTCTCTCTGTCT
CTCCGCG-------------------CTTTGCTTTCAGATTGCTCTTGTTTGCAAAATTCAGA----------------T
GCTGATTGTCGCTTTTGGTTGTGTGGTGGTAACAGAGAGAGGGATCTACATCCTGTACGAGGACGTCAAGTCGTGCCCGT
GTGAGGACGTGCAGATCCTCTGGTCCATCCTCGTCGAGTCCCACCCGCCGCCGCCGCTGCGGCTGAAGCAGTGATCGACC
GGCCGGCCGGT-CCCTGCCGCCGTCCGTCGATCGAGCACGGCGCTCCGACGTACCGATGGCCTCCCGGCGGCA----ACC
GATCCCGACATGCTTCGACTGACTGTCGGTGGCTCGTTCTAGTGTACATAAAGATGAT----CGAGCGAGCGGCAGTTCC
GTGTCGCCATGATAGTAGAAAAGTAGGTGTTCCCTCGGCCTCTCCCTTGTGAGC-ACGGAAATG--------GCGTGCAT
GGCCGGTGAGCTCCCCTCTCGCTAGCATCGCATGTGTCCTTCACCGACACTGCGATTCTGCGAAGCAAGGTTTTTTTTTC
T---------------TTTTCTCTTCTTTCTTCTTTTCCTTTTTGGAAAAAAGGGGGA-GGCACGTGTAAGGCTCGGTTG
GTGGCCCGGGTCAATGGCCGCGCGTGCCTGTAT---------------------------ACGAGAGAGAAGGCTGTAAG
CACCAGACACCGGCGATGATGGTGTTGAGGGAAAAGAATTGTGAGTGTGGCATTGA-------------AAGATGGCTTG
ATTGATCCTGTGTTCCCTGTGGCTCGCGTGCAAGGGAGGTAGGCGTGATTTG----------------------------
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>chr2D_43
------------------------------------------CTCTCTCTCCGCTCGATTTGACGATTTCTTCCCCT---
--CTCGTGAGTCGTGATCGGTCGAGATACTTAAACCGTCGCACTCTCCT------TCTTCTTCTTCTTTCTGACTATTCA
TGTTGGCCCGTGGGGCAATGGCGATGCCCCAACTGACGCCCTGCTCATCTTCGGACGGACACCTGGACGACGGGCGCGC-
--AGCAGGCCATGTAGGCGCCAACTTGTGGGTCATGGCTGACCAGTGCCACGCCCTGTTCAGTGCTCACCGACGG-----
----------------------TGGCTGTTGTGTCACTGAGACGTGCAAAAATGCATAGCAGTAGCAGGAGCTGCTCGTC
ATACAGATACAGGCGCAGGAG-AGGGCGCCACGCCGACGGCCTGGCGAATGATTTGCCACGTTCGGAACGATGAAATCCT
GCTGAAATGCCAATGTTCCAAGCGTGGTTTCTGTCTCTCCA----CAAAGCAGTGGAGCCATGGACGAATGGACTCGTGG
CTCGTTTTGCCGACAGCGTAGGCCACGGCGGCCATAAAGCTTAAATAAGACCTGACCTGACAGGGCCGAGGGGACACCCT
TCC-GTTTTCTCCTCGACTAATAATAAGATGAGAAAACTGAAAAATTGGCGCGACCGAACGAGCGCAACGCTCCTGCGCC
AATTCGATCGTTTGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAAGGGAAGCCCGGCAACGTGATGTTATGA
ATAGTGGCCG----------AGCCGAGCAGCGGCAGAGACTTACTTCACAGGGCCTCAAAGCGACTCCATCTCTTCCCCC
TCACGTCTCCTCCTCG---TCCCTTCTACAAGATAGCTTGGCGTTGCTATTTCATCTCGTCTCCCGGCTGATCAGTGCAC
GCACGAGCAGGGCGGCCGGGGGAGA-------GAGCTCAGCTTAGGGTCTCGTTCATGGGGTGGCTGCGGTCGCTCATGG
CGCCCATCAAGAAGCTCTGGATTCGCGTGCATTCCGCGCAGAAGAAGAGTATGTTCGCTCGTCTCTCTCTCTCTCTCTCT
CTCTCTCTCTGCTTTGTTCTGATCGTCTATTCTTTCAAACTGCTCTGGTTTGCGAAACTCAGATTCTGATTCTGCGTGGT
GCTGATCGTTGCTTTTGGTTGTGTGGTGGTAACAGAGAGAGGGATCTACATCCTGTACGAGGACGTCAAGTCGTGCCCGT
GCGAGGACGTGCAGATCCTCTGGTCCATCCTCGTCGAGTCCCACCCGCCGCCGCCGCTGCGGCTGAAGCAGTGATCGACC
GGACGGCCGGTCCCCTGCCGCCGTCCGTCGATCGAGCACGGCGCTCCGACGTACCGATGGCCTCCCGGCGGCAGCCTACC
GACCCCGGCATGCTTCGACAGGCTGTCGGTGGCTCGGTGTAGTGTGCATAAAGATGAT----GGAGCGAGCAGCAGTTCC
GTGTCGCCATGATAGTAGAAAAGTAGGTGTTCCCTCGGCCTCTCCCTTGTGAGCCACGGAAATGGCGTGCGTGCGTGCAT
GGCCGGTGAGCTCCCCTCTCGCTCGCATCGCATGTGTCCTTCACCGACACTGCGGTTCTGTGAAGCAAGGTTTTTTTTTC
----------------TTTTCTCTTCTTTCTTCTTTTCCTTTTTGGAAAAAAAGGGGAAGGCACGTGTAAGGCTCGGTTG
GTGGCCCGGGTCAATGGCCGCGCGTGCCTGTATTATCATCTTGTAAATACGAGAGAG-ATACGAGTGAGAAGGCTGTAAG
CACCAGACACGAGCGATGATGGTGTTGAGGGAAAAGAATTGTGAGTGTGGCATTGA-------------TAGATGGCCTG
ATTGATCCTGTGCTCCCTGTGGCTCGCGTGCAAGGGAGGTGGGCGTGGTTTGACCTGACCACCGCGC-CACACGTAGTGC
GTGTGTGTGGGGGATGGGTGAGCGCGCGCACGGGTGGCGTGGTTAATGCCGTGGCCGGACCGGGGATTGTTTTCGTCGGC
CCGTGCGGTTGCAGGTTCATTGGTCGACGTCGGGGTGGTTGGTTGCTTCCGAGGGTCCGTCTGCCGCCGCTTCGTCGTCA
TCATCGGGATGGGTTCGCCGTGTCCGCTGCTTCCAGCTGAGACGGGGAGGAGCACG------------------------
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>SNPs
SSSSSSSSS---S-----S-------S--S---------------S-----------------------SS-SSSS-SSS
SS-----------------------------------------------SSSSSS-------------------------
-S----------------S-------------------------S-S--------------------------------S
----------------------------------------S-----------------------------------S---
-SS--SSSSSSSSS---S----------S------------------------------------SS-------------
-------------------------------------------------S-----S------------------------
-------------------S-------S--------S--SSSSSS-----------------------------------
------S-------------------------------------------------------------------------
-S-S---------------S---------S-------S------------------------------------------
-----------------SSS-SSSSSSSS--S--------S---------------------------------------
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--------------------------------------------------------------------S-----------
---------------S-S--------------S-----------------------------------------------
-------------SSSSS----S-SSSSSSSS----------S---------S---------------------------
--------------------------------------------------------SS------------SSSSSSSS--
----------------------------------S----------S------S---S---S-------------------
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---------------------------------------------------------------------------S----
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----------------------------------------------------------SSSS------------------
------------------S-----------S-------------------------------------------------
----------------------S--------------------------------S------------------------
-SSSSSSSSSSSSSSS----------------S--------------------------S-------------SS-----
---------------------------------------------------------S--------------------SS
----S-SS-S---------------S----S-------------------------SSSSSSSSSSSSS-----------
------S--S----------------------S-----------------------------S----S----------S-
---S-----------------------------------------------S---------------S------------
---------------S----------------------------SS----------------------------S-----
--------------------------------------------------------SSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_349
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---------TTTTGTTGTGTGGTGGCTGC---------------------------------------------------
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>reverse_2543
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--------------------------------------------------------------TCATCCCGTGTTTCTCTG
GC------------------------------------------------------------------------------
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