>input_sequence_63938
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-----------------------------------------CTATATAAACACCCCCGACCCT--GAGAGATCTTCGTCC
ACCTCCTCCCTCCTGTTCCTTCAGCCACCGTG-----------AGCAATGGCGCCCAAGCGGAAGGGTGGCAACGGCCGG
AAGAAGACCGTCCTCCTCTCGATCGTCAAGGAGGACGCCCGCCATGTATGCTTCTCAAAGCGCAAGCGGGGCCTGTTCAG
CAAGACCAGCGCGCTGTCCCTGCTCACGGGCGCCCAGGTGGCCGCCGTCATCTTCTCGCCCGGCGGCAAGGTCTTCTCCT
TCGGCCACCCCTCCGTCGACGCCGTCGTCAACCGCTTCATGGCGGGGGACGCCGCGGTGGTCCAGGCCGCCGCCGACGAC
AACGGGTTGCAGACGCTGCAGCTGCAGCACGGCGACATGCGCACCGAGCTGGCGGACCAGAAGAAGCGGAAGAAGCGCGC
TGAGGAGGCCCTGGACAAGGAGCGCGCTGGGGGGGACCAGATTGCCTCGTGGCTCCACCCCGACGTGCGCGACATGGGGC
ATGACGACATGGCGGCCTTCGCCGCCGCGCTCTTGCAGGTCCAGGCCGCCGTCTCCGGACGCGCCAACCAGGTTCTCGTC
GAGGCCTTTCGCGTCGACATCAGCCGTATGCTCCAGGTGCCCCCGCCGCCGCCGCCTCCGCTCCAGCTCTTCGGTGCCAG
CACCATTGAGTTCGGTAGTAGCAGCAGCAGCGCCAACGCCGGGATGGAGATGCAACAGATGCAGATGGTTATGGAGATGC
CACCGCCGCCTGACTTCCCCGCAGTGATGGGGATGCAGCAGTTGGTTATGGAGATGCCACCACAGCCAAGGTTCGAGGCA
GCGATGGAGATGACGCCGCTGCAGGAGTTCGTCGCCGGGATGCAGAAGGTGCAGCGGCAGGGGCTCGGGCCGAACGCCGA
CTTCCCCTACTGAGGAGAAGAAAGACACCAGACAGAGTCCGACCGAGTCCGAGTCTCAGTTACTATATTCTAA-------
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>chr3D_1_TraesCS3D01G513800
TAGAGACCTCCACGACTTCTACCTTGTAGAAGGACCTTCCTCGTGACCTTTATCCTTAACAAAGAAAGAATCCGTGTGCA
ACTCGACAAAGACATGAGAAAAAATATCCGGTTTTTATGATCAACATGAGATGAAGTGAAAACTCGACATGTGGAGATGG
GGAAAAGATCTGATTTTTATGATCAAATGAAAGAAAACAAAGATTGTTCTAGGAAGATTGGAAATAATACTTGCGCGCGT
TTTGAGGAAAAAAACCAGCTTTGTACGAGCGGCATGTAGGAGCGTCGGCATCAGAATGGGCTGGCCTCCCCCTCGATGGC
CGTCATGATCGCTCTTGGCCTCCCTCCGCTCGTTCCGCTCGCCGGAGATGATCAGTACGTTGCCTCCTCGTGCACCTCCA
CCTTGAACTACTCCTTGTTTGTCAACCCCGCGGTGCGCAACGCTGAACACGTATGCCTCCGCCGTCTCCCCGGCTCTCTA
TGCCGGTGTCGTCGTGTCGCTCGCGGCAGGCGTGCTGCCGGAAGATGAGGCTTCGGTAGACCAAGGCGGCCGTGTCGAAG
AAAGCAAAGACAGTATGTACGTGCATGAGCTGGGCTGCGAACAATTGATTCTGAATGCGAAGGAGTACGTACACATGCAT
TTACGCACTTATATGAGACTATGAGTATTGAGTGTGTGATGCATAATGCTCTGCTCAGCTGCGGACAATC--TCGATCTG
CATTCTGCCGGCGGTGAAACGATGGATGGATCGAAGTAGGATGGTATGCTATGTTGAGATGAAGCCTCAACATACGTTCG
TAGTGACCAGATTGCAGTACGCTTCGAC----------------------------------------------------
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---------------------------GCGTGCCAGGTGATACGTACGTAGTGACGTATATTTCGACGCGTGCCAGGCCA
GCCCAGGCCAGCTCAGCTCAGCCAGGCAGAGAATATATACAGGATCAATTTTTTATTGGCCTCAATCAAAAGCTTCAATG
CAGTACCCAGCTCACCGTGGCAATTCGCTCTCCGGCCGCTGCTATATAAACACCCCCGACCCT--GAGAGATCTTCGTCC
ACCTCCTCCCTCCTGTTCCTTCAGCCACCGTG-----------AGCAATGGCGCCCAAGCGGAAGGGTGGCAACGGCCGG
AAGAAGACCGTCCTCCTCTCGATCGTCAAGGAGGACGCCCGCCATGTATGCTTCTCAAAGCGCAAGCGGGGCCTGTTCAG
CAAGACCAGCGCGCTGTCCCTGCTCACGGGCGCCCAGGTGGCCGCCGTCATCTTCTCGCCCGGCGGCAAGGTCTTCTCCT
TCGGCCACCCCTCCGTCGACGCCGTCGTCAACCGCTTCATGGCGGGGGACGCCGCGGTGGTCCAGGCCGCCGCCGACGAC
AACGGGTTGCAGACGCTGCAGCTGCAGCACGGCGACATGCGCACCGAGCTGGCGGACCAGAAGAAGCGGAAGAAGCGCGC
TGAGGAGGCCCTGGACAAGGAGCGCGCTGGGGGGGACCAGATTGCCTCGTGGCTCCACCCCGACGTGCGCGACATGGGGC
ATGACGACATGGCGGCCTTCGCCGCCGCGCTCTTGCAGGTCCAGGCCGCCGTCTCCGGACGCGCCAACCAGGTTCTCGTC
GAGGCCTTTCGCGTCGACATCAGCCGTATGCTCCAGGTGCCCCCGCCGCCGCCGCCTCCGCTCCAGCTCTTCGGTGCCAG
CACCATTGAGTTCGGTAGTAGCAGCAGCAGCGCCAACGCCGGGATGGAGATGCAACAGATGCAGATGGTTATGGAGATGC
CACCGCCGCCTGACTTCCCCGCAGTGATGGGGATGCAGCAGTTGGTTATGGAGATGCCACCACAGCCAAGGTTCGAGGCA
GCGATGGAGATGACGCCGCTGCAGGAGTTCGTCGCCGGGATGCAGAAGGTGCAGCGGCAGGGGCTCGGGCCGAACGCCGA
CTTCCCCTACTGAGGAGAAGAAAGACACCAGACAGAGTCCGACCGAGTCCGAGTCTCAGTTACTATATTCTAAATAAATC
GTTC-AGATCCATGTAAGATCCATCTACGTGGGTCCAAGATCTATGCATTAGTTGGTTCAATTATCTTAGTAGCAATTAA
ATTTATGGCATTGTAATCTTTTTTGTATCGGTAGTACAATGGCTGGAAATTCGTGAATGAAATACTATTAAGCCTTTTCT
TTTGGTTCTCTCCATGCTTGCAACATAAAAAAAGATCCACATGTACGTGTTAATTGTTCAAAAATCCCATGTATACCGCT
ATACTATGTGTACATGCACAACTCTATACCGTAAGATTCAATGTGTGTTAGGCCTGATTACTGCCTATTGGTGGGACTGA
TGCGTTGGTCGGTGGGTTTGCGAGTTGTAACATGACTCTATAAACGAACTAAAACATGAATACATGATCCAGCGGGCCAA
GTAACGATCACCATTTTTCCCACAAAAAATCTCAAAAACCTATCAAACACCAGGTACAAAATCCCGGTAAGTCGAAACCA
TTGTGAAGTCATGATTTTATCAACAGGCAGAGAGCGGTGAAAATGACGGGTGGTTCGCACCAGACAACAAGGACCCGACG
ATAGGGCGACTGGACTAGGATGCAAAAATTGCTGAAAAGGAAGAGCAACTTACATAATGAAAGTTGATTTTGCAAAAAGA
ACTACATAATGAAAGTCAATTCACAAAAAATAATTACATAATGAAAGTTAATGTAGAATTAAAATTGAACATCATTTTGA
AGCAAAATTTGTTGCGGCGGCCGAAATAAGAACCCTCGCTATGGTGAACTCTCGTTGTTGAAACTAATCAGTTAGTTTGG
GATTTAGGTTGTACTTGTCGAACATAGATTATTTTAATAAACTATGAAATAGTTGTATTTTTCTCTCATTAAACTCCGCC
ACAGCTCGGAACTGTTCCTGCCTTCGGCAATGCCGCAGATGTGCCACTATCTCCTCGCAAAATACAACGTGCAGTGCATG
TTTGTTACTTTTCACCTCATGCATGGATGGGCCC
>chr3A_442
GCTGAC--------------------------------------------------------------------------
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-----------------------------------------------CACGTATGCCTCCGCCGTCTCCCCGGCTCTCTA
TGCCGGTGTCGTCGTGTCGCTCGCGGCAGCCGTGGTGCCGGAAGACGGGGCTTCGGTAGACCAAGGCGGCCGTGTCGAGA
AAACCAAAGACAGTAGGTACGTGCATGAGCTGGGCTGCGAACAATTGATTCTGAACGCGAAGGTGCACGTACACATGCAT
TTACGCACTTATATGAGACTATGAGTATTAAGTGTGTGATGCATAATGCTCTGCTCAGGTGCGTGGATAATTTCGATCTG
CATTCCGCCGGCGGTGAAACGATGGATGGATCG-AGTAGCATGGTATGCTATGTTGAGATGAAGCCCCACACGGTGACGA
TGGTGCATGGCAAAAGACATGATCTTTGAGTCCGCCCGCCCGCCCATGGGTCCTGGAACGATCGCCGCGTTCAGCACGCC
GGCCGGCCAGTACCGACGTTGTGCTAGATTTTGTGCGACAAATAACAGTACATGCATGCATGAGCCGCTGCCGTACGAAG
CGTACTGCAATGGGTAGGAGTGGTGCAGCGTACCAGGTGATACGTACGTAGTGACGTACATTTCGACGGGT---------
--------------------GCCAGGCAGAGAATATATACAAGATCAATTTTTTATTGCCCTCAATCAAAAGTTTCAATG
CAGTACCCAGCACACCGTGGCAATTCGCTCTCCGGCCGCTGCTATATAAACACCCCCGACCCTGAGAGAGATCTTCGTCC
ACCTCCTCCCTCCTCTTCCTTCAGCCACCCTG-----------AGCAATGGCGCCCAAGCGGAAGGGTGGCAACGGCCGG
AAGAAGACCGTCCTCCTCCCGATCGTCAAGGAAGACGCCCGCTATGTGTGCTTCTCAAAGCGCAAGCGGGGGCTGTTCAG
CAAGGCCAGCGCGCTGTCCCTGCTCACCGGCGCCCAGGTGGCCGCCGTCGTCTTCTCGCCCAGCGGCAAGGTCTTCTTTT
TCGCCCACCCCTCCGTCGACGCCGTCGTCAACCGCTTCATGGCGGGGGACGCCGCGTTGGTCAAGGCCGCG-CCGCCGAC
AACGGGTTGCAGACGCTGCAGCTGCAGCACGGCGAGATGCGCTCCGAGCTGGCGGACCAGAAGAAGCGGAAGAAGCGCGC
TGAGGAGGCCCTGGACAAGGAGCGCGCTGCTGGGGACCAGATTGCCTCGTGGCTCCACCCCGACGCGCGCGACATGGGGC
ATGACGACATGGCAGCCTTCGCCGCCGCGCTCTTGCAGGTCCAGGCCGCCGTCTCCGGACGCGCCAACCAGGTTCTCGTC
GAGGCCTTTCGCGTCGACATCAGCCGTATGCTCCAGGTGCCCCCGCCGCCGCCCCCTCCGCTCCAGCTCTTCGGTGCCAG
CACCTTTGAGTTCGGTAGCAGCAGCAGCAGCGCCAACGCCGGGATGGAGATGC---------------------------
CACCGCCGCCTGACTTCCCCGCAGTGATGGGGATGCAGCAGTTGGTTATGGAGATGCCACCGCAGCCAGGGTTCGAGGGA
GGGATGAAGATGATGCCGCTGCAGGAGTTCGTCGCCGGGATGCAGATGGTGCAGCAGCAGGGGCTCGGGCCGAACGCCGA
CTTCCCCTACTGAGGAGAAGAAAGACACCAGACAGAGTCCGATCGAGTCGGAGTCTCAGTTACTATAATCCAAATAAATC
GTGCAAGATCCATGTAAGATCCATCTACGTGGGTCCAAGATCTATGCATTAGTTGTTTCAAT-----------CAATTAT
ATTTATGGCATTGTAATCTTTTTTGTATCGGCAGTACAATGGCTGGAAATTCATGAATGAAATACTATTA----------
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>chr3B_907
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---------------------------AGAAAATATATACATAATCTTC-TTTTATGGTACTAAATCATGATTCTGAATG
CAGTACCCAACTCAGCCAAGCAATTTCCTCTCCGACCACTGCTATATAAACCCCCT-GACCCT--GAGAGATCTTCATCC
ACCTCCTCTCTCCTCTTCCTTCATCCACGACCCTGAGCGAGCAAGCAATGGCGGCCAAGCGGAAGGGTGGCAACGGCCGG
AAGAAGACCGTCCTCCGTCTGATCCTCAAGAAGGACGCCCGACATGTGTGCTTTTCCAAGTGCAAGCGGGGTCTATTCAG
CAAGGCCAGCATGGTGACCATGCTCTCCGTCACCCAGGTGGATGCCGTCGTCTTCTCGCCCAATTGAAAGGCCTTCTCCT
TCAATCATTCATCCACCAACGTCGTTGTCAACCGCTTCATGGCGGGGAC-GGCGTGGAGCTTGAGGGTGCCACCGCTGAC
AACGGATTGTAGACGTTGCACTGACAGCACAGTGAGATCCGGACAGAGCTAGCATAGAGGAAGAAGCAGAAGAAGCACCC
GGACGAGGCCCTGGCCGAGATGCGTGCCTGCGAAGAACAGATTACCGCATGGCTTGACCCCGACATGCGCAAGATGGGGT
ATGAGAACATGGAGGCCTTAGTTACCGCACTCATGCACATGAAGGCCACCGTCTCTGAACGCGCCAACAAGGTTCTTGTG
GAGGCCTATCACATCGATATCTGTCCTAAGGTCTCCGTGCCCCCGCCTCCACCGCTTCCGCTCCAGCTCTTCGATGCCAC
CACCTATGAGTTCG------------------------------------------------------------------
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>chr3D_1076
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-------------------------------------------------GGCGCCCAAGCGGAGGGCCGGCAAAGGGCGG
CAGAAGATCGCCATCCGGCGGATCGAGAAGAAGGACGCCCGGCAGGTATGCTTCGCTAAGCGCCGGCAGGGTCTGTTTAA
CAAGGCCAACGAGCTGGCGGTGCTGTGCGGCGCCCAGGTGGCCGCCGTCACCTTCTCGGACGGCGGAAAGGCCTTCTCCT
TTGGGCACCCCTCCGCCGAGGCCGTCGTCGACCGCTTCCTGGCGGGGGGAGGCGCGTTGGTCCAGGGCGCCGACGACGAC
AACGAGCTGAAGGAGCTGCACCTGCTGCACGGCGAGCTGCGCACGCGGCTGAAGGAGGTGAAGGCGCAGAAAGGGCGCGT
GGTGGAGGCCATGGCGAAGGAGCGCGCCTCGGGGGATCAGATTGCGGCGTGGCTCGACCCCGAGTTGGGCGACATGGGGG
GGGAGGAGATGATGGCCTTCGCCGTCAAGCTGATGGTGGCGCGGGCCGCCGTCTCGGAGCGCGCATACCAGGTGCTCTTG
GAGGCGCAGA------ACGTCAGCCGCATGCTGCAGGCGCCCCCGCCGCCACAGCAG------CAGCTCTTCGGCGGTAG
CACCTTTGAGTTTGGTGGCAGCA---GCAGTGGCAACGCCGGGATGGAGATGCAACAGATGCAGATGGTGATG-------
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>chr3A_2128
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--------------------------------------------------------------TACTATTAAGCCATTTCA
-TTGGTTCTCTCCATACTTGCAACATAAAAAAAGATCCACATGTACGTGTTAATTGTTCAGAAATCCCATGTATACCGCT
ATACTATGTGTACATGCACAACTCTAAACCGTAA-ATTCAATGTGTGTTAGGCCTGATTACTGCCTATTGGTGGGACTGG
TGCGTTGGTCGGTGGGTTTGCGAGTTGTAACATGACTCTATAAACGAACTAAAACATGAATACATGATCCAGCGGGCCAA
GTAACGATCACC----------------ATCTCAAAAACCTATCAAACACCGGGTACAAAATCCTGGTAAGTCGAAACCA
TTGTGAAGTCATGATTTTATCAACAAGAAGAGAGCGGTGAAAATGACGGGTGGTTCGCACCAGACAACAAGGACCCGAT-
-------GACTGGACTAGTATGCAAAAATTGCTCAAAAGGAAGAGCAACTTACATAA-------TGATTTTGCAAAAAGA
ACTACATAATGAAAGTCAATTCATAAAAAATAATTACATAATGAAAGTTAATGTAGAATTAAAATTGAACATCATTTTGA
AGTAAAAATTTTT-------------------------------------------------------------------
-----------------------------------AATAAACTATTAAATAGTTGTATTTTTTTCTCATTAAACTTCGCT
GCAGCTCAGAACTGTTCCTGCCTTCGGCAAGGCCGCGGATGTGCCACTACCTCCTCGCAAAATACAACATGCAGTGCATG
TTTGTTACTTTTCACCTCATGCATTGATGGGCCC
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------------------------------
-----------------------------S----S----------S-S------------------------------SS
---S-----------S---------------------------------------S-------S-S--------------
-----------------------------S----------------------------S----SSS-SSS----------
-----S---------------------------S-----S--------------------------S--SSSSSS-SSSS
-S---SSSS-SSSSSSSS-S-S-SSSSS----------------------------------------------------
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-------------------------------S--------------------------S---------S--SSSSSSSSS
SSSSSSSSSSSSSSSSSSSS---------------------S----------------S-------------S-------
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--------------S--------------S--------------------------------------------------
------------------S----------------------------------------------------S--------
----S----------------------S----------------------------------------------------
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-----------------------------------S--------------------------------------------
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----S-------------S--------------------------------------------------S---SSSSSSS
-------------------------------------------------------------S------S---------S-
-S----S------S--------------------------------S--------S------------------------
------------------------------------------S------S-----------------S--S---------
--S----------------------------------------------------S------SSSSSSSSSSS------S
-------------------------------S--------------------S---------------------S----S
S--------------S--------------------------------------------S-------------------
--------------------------S-------S--------------------------------------------S
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------------SSSSSSSSSSSSSSSS-----------------------S------------S---------------
-------------------------S-S--------------------------------------------------SS
SSSSSSS-----------S--------------S-----------------------SSSSSSS----------------
-----------------------S--------------------------------------------------------
--S----S--S--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----------S----------------S------------S---S
S------S----------------------S-----S------------S------------------S-----------
------------------------S---------
>forward_162
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--------------------------------------------------------------CTCGACATGTGGAGATGG
GG------------------------------------------------------------------------------
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>reverse_1215
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--------------GTTCCTTCAGCCACCGTGAG----------------------------------------------
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>forward_342
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--TCATGATCGCTCTTGGCCTC----------------------------------------------------------
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>reverse_2123
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------------------------------------------CCGAGTCCGAGTCTCAGTTAC-----------------
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>forward_1034
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------------------------------------------------------CGTATATTTCGACGCGTGCC------
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>reverse_2726
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-----GCGACTGGACTAGGATGCAA-------------------------------------------------------
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