>input_sequence_82940
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--------------ATGGCGTCCCGTCGTCCCATGGCCGCCGCGCCTGCCGTCCTCCTCC---TCCTGCTCCTGCTCGTC
GCCACAGGTACGTCCGACCGTCGGCAGTGTGCTTCTTACTTCCCAGTGAGAAGATGCATGCATGGACGGTGACCGGTGCT
TAATTACTATGCTTCGT-CGTGTGCA---------TGCAGAGATGGGGACGACGAAGGTGGCAGAGGCCCGGACGTGCCT
GTCGCAGAGCCACAAGTTCAAGGGCACCTGCCTCAGCGACAGCAACTGCGCCGGCGTGTGCCGCACTGAGAACTTCCCCG
ACGGCGAGTGCAACTCCCACCGCCTCGAGCGCAAGTGCTTCTGCAAGCGGACCTGCTAA---------------------
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>chr1A_1_TraesCS1A01G014800
AAAACACTTACGTGCGCGTAGAGCTCGCTGGAGTTGGTTTCGTGGG-CGCTGCGTCGCTGAGAGGCTATAAGTCATGATG
TACTGCTCGTGTGTGTAGATTGGATTGAGTTCGAGCTCAAGGGATAACGCCATTGTCGGGGCGGGCGTTGGTGCACCAGG
AAAAACCACCGTGTCCTATGCCTTCTTCTTCCCTACTTCCTCCTTGGTTCGAGCCAGAGAGAGAAGTGTGCAGAGAGACA
GAGAGAGGTA------GAGCTAGGGCCAGCTAGGGTAAGGGCTCGGTTCCAACACTGCCCATTTTGAGCGTCTGAAAATG
GACCTTCTTTGTCAATTTCGAGGACAAACGGACCAGACGAGCGGTCGACATTATTTGCAAAAAAGAAAAAAGATTAATAT
TTCATGGTGTGCGATTTACAATTGTGTTTTCTTGGATGTTTTTTGCAATGTACTAAACCGCAAATGTGGTGGTTTAATTC
TTGTTTTTTTACTCCGACGACAAGGTACTGATTCGGTGACCACATTTGATCGGCCCCCAATTGATCGTATCCCATGTCTA
TCCGCTTGTCGTCTTGTCAATGCATCAAAGAGAACTTGAGTAGGCCGGCAAAATAAGTAAAGTTTGCAGAAAGCAATGAA
TCCCAGCACTGAGCTTCGCAGGCAAAAGCATCGGCATTCAGTGCTCTGCCGACGAGCTCCACTCACTCAGCCGTGGCCCT
---GACGTC--------------AGC-AGCAGATGTCGGCAGGCATGCATGCGATCGACC--------GGACAGCCCTGG
CCCTGCTGCCATGGCAAGAT----GGATGCATGCGATCTAGATTAATATATCCCACCAACCACCACTAATCTCTACTCTA
CA------------------------------------------------TCTCTCTCTGGCTATATA------------
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---AACCCCTGCCTCGTCTTCTAGTTGTA--------------TCCACGCCACCTTGGCTTTGCTAGACAAGACAGCCCC
-----ACGTAGT---AGCAGCAGCAGCAGCGGAGAGCGCGGTCGGTTCTCTA----GCATCTCCG--GTGAAGCGAGCAA
GCAGAGAG------ATGGCGTCCCGTCGTCCCATGGCCGCCGCGCCTGCCGTCCTCCTCC---TCCTGCTCCTGCTCGTC
GCCACAGGTACGTCCGACCGTCGGCAGTGTGCTTCTTACTTCCCAGTGAGAAGATGCATGCATGGACGGTGACCGGTGCT
TAATTACTATGCTTCGT-CGTGTGCA---------TGCAGAGATGGGGACGACGAAGGTGGCAGAGGCCCGGACGTGCCT
GTCGCAGAGCCACAAGTTCAAGGGCACCTGCCTCAGCGACAGCAACTGCGCCGGCGTGTGCCGCACTGAGAACTTCCCCG
ACGGCGAGTGCAACTCCCACCGCCTCGAGCGCAAGTGCTTCTGCAAGCGGACCTGCTAAGCAAGACCAGTCCGCGCGACA
TCATCCGATCCGACGGATGCTACTT-----GCCAGAGCATCTATGCCCGCCGT---CAGTTAGATCTGTTCGTCCCTACA
TTTCTTTCACGTCCGTCAGTAGTTTGTTCGTGTGTTCCGTTTACAATAGTGGTT-ATCTCCATGCATCCGGAGGTTTAGT
CTAATTAGTTCGCCGGCCGCCGTGCGTTCGTGGCTCTTTAATCTATGCGGCGATGTAACATGGTCATTGCGTTGTTTCAG
GCTTTCAGCATGGACTGATATCCATATGCAATGCATCTGTTGGTGGCCTCAATTTGAAAAATATTTGTGAATTTGAAAAA
CTTATGCACAAATTTTAATTGATGTTAGCGAATTTGAAAAAATGCTCATGGATTTAAAAATGATCATGAATTTAAAAAAG
GAGTAGAAAATTGAAATGGTAAAGAAAAAACAGGAAAACAAACCTCAAAAAGAAAAGCAGTAAACCAGAATTAAACAAAG
AAAAGAAAAGAAAAATAAAAAAACTGGCTGGAAGCTGAGAGAGAGCCTACATGGGCCAGCCCACTTACCGACATAGATGA
TGATCTAGCAGGATGTGCGCAAACATATAAATTCCATCAACCCCTCAAAAAAATATAAATTCCAACATAGTTACCTAAAA
AAATTATAAATTCCATCATACAGAAATTTTGATGCGGCTGCAAACAGGGAGAAAGGAAACCAGCATGGGTGTCATGAAAA
ATGATGACAAGACCAAACTATCTGAGAGGTCTAGGCTTCAAGGATCTGGAACTTTTCAATTTGGCTTTCCTAGCAAAACA
GTTTGGAGAATTTTGCTGGAGTCGGCATCTTAGAGCGCAAGGATCCTTATGGCATCATATTTTCTTGGTGGTACAATCCT
TAACACTAGTGCAGAAAAGCCTAATTATGGCGCACAATGTAATTTGCACGCCACAAACGTTTTGTGCACAAAAAAAATTG
TTTTTAACATCATGTAACATTTAGCCTT
>chr1D_1
AAAACGCTTACGTGCGCGTAGAGCTCGCTGGAGCTGGTTTCGTGGGGCGCTGCGTTGCTGAGAGGCTTTTAGTCACGATG
TACTGCTCGTGTGTGTAGTGTGGGTTGAGTTCGTGCTCAAGGGAAACGCCG-TTGTCGCGGCGGGCGTTCGTGCGCCAGG
AAAAACCACCGTATCCTATGCCTTCTTCTTCCCTCCTTCCTCCTTGGTTTGAGCCAGAGAGAGAACTGTGGAGGGAGACA
GAGAGAGGTAGTGGTAGAGCTAGGGCCAGCTACGGCAAGGGCTCGTTTCCAACACTGCCCATTTTTAGCGTCTGAAAATG
GTCCTTTTCTGTCAACTTCGAGGACAAACGGACCAAACAAGCGATCGACATTATTTGCAAA----AAAAAAGATTAATAT
TTCATGGTGTGAGATTTACAATTGAGTTTTCTTGGATGTTTTTTGCAATGTACTAAACAGCAAATGTGGTGGTTTAATTC
TTGTTTTTTTACTCCGACGACAAGGTACTGATTCGGTGACCACATTTGATCGGGCCCCAATTGATCGTAT-CCATGTCTA
TCCGCTTGTGGTCTTGTCAATGCATAAAAGAGAAATTGAGTAGGCCGGCAAAATAAGTAAAGTTGGCAGAAAGCAATGAA
TCCCAGCTCTGAGCGTCGCAGGCAAAAGCATCGGCATTCAGTGCTATGCCGATGAGCTCCACTCACTCAGGCGTGGCCCT
---GGCC--------------TGAGC-AGCACATGTCGGCAGGCATGCATGCGATCGACTGAATTATTGGACACCCCTGG
CCCTGCTGCCATGGCAAGGT----GGA--------------ATTAATATATCCCACCAACCACCACTAATCTCTACTGTA
CA------------------------------------------------TCTCTCTCTGGCTATATA------------
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---AACCCCTGCCTCGTCTT------GTAGTTGTATCCACAGTTCCACAACACCTTGGCTTTGCTAGACAAGACAGACTC
CAAG-------------------------------------------------------TCTCCG--GTGAAGCGAGCAA
GCAGAGAG------ATGGCGTCCCCAAGTCGCACGGCCGCCACGCCCGCCGTCCTCCTCC---TCCTGCTCCTGCTTGTC
GCCACAGGTACGTCGA--------CAGCGTGCTTCTTTCTTGCCGGTGAGAAGATGCATGGATAGACGGTGACCGATGCA
TAATTACTATGGTTCGTACGTGTGCA---------TGCAGAGATGGGGACGACCAAGGTGGTGGAGGCCCGGACGTGCCT
GTCGCAGAGCCACAAGTTCAAGGGCACCTGCCTCAGCGACAGCAACTGCGCCGGCGTGTGCCGCACCGAGAACTTCCCCG
ACGGCGAGTGCAACTCCCACCGCCTCGAGCGCAAGTGCTTCTGCAAGCGGACCTGCTAAGCAAGAA-------------G
TC-----ATCCGATGGATGCTACGT-----ATCAGAGCATCCATGCGTGTGCCGGCCAGTTAGATCTGATCGTCCCTGCA
TTTGTTTCACGTCCGTCAGTAGTTTCTTCGTGTGTTTCGTTTACAATAATGGTTCATCTCCATGCATCCGGAGGT-----
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>chr1A_590
TGAC----------------------------------------------------------------------------
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----------------------------------------TAGGCGGGTAAAATAAGTAAAGTTGGCAGAAAGCAATGAA
T-CCAGCGGTCAGCGTGGCAGGGAAAAGCATCGGCGTTCACTGCTGTGCCGACGAGCTCCACTCACTCAGCCGTAGCCCG
GCCGGCC--------------TGAGCAAGCACATGTCGGC-------------ATCGAGTGAATTATTGGAGACA-----
-CCTGCTGCCATGGCAACGT----GGA--------------ATTGATATCTCCCGCCCACCACCACTAATATCTACCTAC
CGTACCCCTCTCTCGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCTATATA------------
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---AACCCCTGCCTCTTCTT------GTG--------------TCTGCACCACCTTCGCATTGCTAG---------CCCC
-----ACGTAGAC---------GCAGCAGCAGCGAGCTCTGTCGGTTCTCTATCTAGCATCTCCGGTGTGAAGCGAGCAA
GCAGAGAGAGAGAGATGGCGTCCACTCGTCGCATGGCTGCCGCGCCGGCCGTCCTCCTTC---TCCTCCTCCTGCTCGTC
GCCACAGGTACGCCCGCCCATCCATGGTTCCTGACTCC---TGAC---------------CATCTGTGCTCAGCGATACT
TAATAATTACTTG----------CTGTGGTTGCATTGCAGAGATGGGGACGATGAAGACGGCGGAGGCCCGGACGTGCCT
GTCGCAGAGCCACAAGTTCAAGGGCACCTGCCTCAGCAACAGCAACTGCGCCGCCGTGTGCCGCACCGAGAACTTCCCCG
ACGGCGAGTGCAACACGCACCTCGTCGAGCGCAAGTGCTACTGCAAGCGGACCTGCTAAGCAACACCAGTCCGCGCGACG
TC-----CTCCGGTGGATGCTTGCTACTGGGCTAGAGCATCCAT----GCCGT---CCCTTAGATCTGTTCGTCCCTAC-
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>chr1B_650
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----------------CGCAGGCAAAAGCATCGCCATTCACTGCTCTGCCGACGAGCTCCACTCACTCAGTCGTAGCCCG
GCCGTAGGCCCCTGGCCGGCTTGAGCAAGCACATGTCGAC-------------ATCGAGTGAATTATTGGAGACCCCTGC
T-CTGCTGCCATGGCAACGTACATGGA--------------ATTGATATCTCCCACCCACCNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNAACTCCTGCATCGTCTT------GTA--------------TCTACACCACCTTGGCATTGCTAGACAGGACAGCCTA
TATTGACGTAGACGCAGCAGGAGCAGCAGCAGCGAACTCTGTCAGTTCTCTA----GCATCTCCG--GTGAAGCAAGCAA
GCAGAGAG------ATGGCGTCCCCTCGTCGCATGGCCGCCGCGCCCGCCGTCCTCCTCCTCGTCCTGCTCCTCCTCGTC
GCCACGGGTACGCCCGTCCGTCCGTCCATGGATAGTAGTAATGAG---------------CATCTCTACTCACCGGCCGG
CACTTACTTATTGAGTTATTGGACTGTGGTTGCATTGCAGAGATGGGGACGATGAAGACGGCGGAGGCCCGGACGTGCCT
GTCGCAGAGCCACAAGTTCAAGGGCACCTGCCTCAGCAACAGCAACTGCGCCGGCGTGTGCCGCACCGAGAACTTCCCCG
ACGGCGAGTGCAACTCCCACCGCCTCGAGCGCAAGTGCTTCTGCAAGCGCACCTGCTAAGCAAGCCCAGTCCGCGCTACT
GG-----CTCTGGCTAGCTAGACTGCTAGATC---AGCAGCCAT----GCCGT---CAGTTAGATCTGTTCGTCCCTACT
TTTGTTTCCGT---------------------------------------------------------------------
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>SNPs
-----S---------------------------S---------------------S-----------S-S-----S----
------------------SS---S---------S----------S-SSS-SS------S----------S----S-----
------------S---------------------S--------------S---------------S----S--S------
--------------------------------S--S---------S-------------------S--------------
-S----S-S------S-------------------S--S----S-----------------SSSS---------------
-----------S------------S---------------------------------S---------------------
-----------------------------------------------------S----------------S---------
---------S---------------S--------S-----------------------------S---------------
-------S------S-----------------------------------------------------------------
----S--S-----------------------S---------------------------S-------------S------
------------------S--------SSSSSSSSSSSSSS------------------------------------S--
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--------------------SSSSSS----------------------S-------------------------------
-----------S--------S---------S-S----S-S----------------------------------------
------------------------S-----S---------------S---------------------------------
----------------S-----S--------------S---S--S------------------S----------------
-----------S--------------------------------------------------S-----------------
------------------------------------------------------------------S-------------
-------------------------------------------------------------------------------S
--SSSSS----------------------------------S----SS--------------------------------
---S---------------------S----------S-----------S--------------------------SSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_356
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----------------TTCGAGGACAAACGGACCAG--------------------------------------------
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>reverse_2324
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---TCTAGCAGGATGTGCGCAAA---------------------------------------------------------
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