>input_sequence_78045
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-----------------------------------------------------------CTATAAAAACACCACCTAGCC
TAAGCATCCACTCGCTACTGATCATCCAACACGAGGAAGCATCCAGGACTAC------ATACGAGATGGGCAAGACACTG
TTGCTCCTGCCCGTCCTGCTCGTCGCTTCCCGTAAGTGTTTGAATTCTCATGAATCAATCGGATGCATATGAATTTTGCT
CAAATTTGACTGC----------------AGTGGGCATGTCGACGACGGTGGTGCGGAGCGAGCTGGCGTGCGGCAGCCT
GAGGGAGCAGTGCATGGCCATGTGCATCCTAGCAAGCTGGTGCATGCACTGTTGCCAGGCCCGCGGATACGCCCACGGCC
GCTGCAGGGTCCTCCACGGCGAGACCACCTGCTACTGCTGCAAGGACGTGCCCCCC-TCCCCCTCCCCGGCTCCCGGCCC
GCAGAAGAGCTCCGCCGCCGGCGACCTCACTTTCTTGACCGACTGAGGAATATGCGGCGACATCCTCACTCTCTTTATGC
AT-------CAAGCGTGAGTTGGGCCAACTCCTGA---------------------------------------------
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>chr1A_1_TraesCS1A01G039000
TTAATATAAAGTAGTTCTAGCCCGAGCAAGCGGCACATGTTGTTGAATGGTGTTACTTAATCACCAACATTAAGGAAGGG
AACATATATATGAGAACATTAATTAATATTATCTATATAAACAAGGGAAACATAACTTTTCAAAAAATATTTCTCTTATC
CTCTACTTCACTAGGACCAGCATTTCC--TATATATAACTAAAATGCTTAGGTGTCAAATATATCCTTGACAAATTAATG
AGACCACTTAAGCTAAGAAGTGTTAAACTTCTCCCGACCTAGGCAGGCGGCAGCCCTTCCATGACCCCCACTCCCTCCAT
ATGCCCCTAGAGCGCCGAGAGGAGGTGTAAACTGTACTGCTTCTGTTTGGTCTCTGAGTAGCGGTGGCGAGACGATGGCA
TCGCCTTCGGTGTGGAATAAGGTATCTTCACCTTGCTCTAGTTCCGATGGTGCCTATCC------TCCGGAGGCATTCTG
AGGATGGTGTGTCCCTAGATCCCTTTCTCTGTGTCCGAATTTTACTTTTGCATGTTTGTCTTGGTGTCGCTGCCCCACGG
AGCGGACAACACGGATGTGTGTCTTAATCCCCCATCTTGAGTATTGACCAATGAAAGTTGACCAGCCTTGGCCTTGACCG
GGAGATTGTGAGATTTGTGTTCTTTGACTCCATCTAGCTGGATATGGGGCGTTCTACAGGCACATTCCAACATTTTCCTT
CTTCTGGGCAGCGATTTGCTATA--CAGATCACTGTCCTCGACATCTTCTGGTCTACATATTGGTCGCTAGTTCTACAAA
CTTCTGAGTTTCAACGGTTTCGCTCTGTTGAGACGGAGACCCAGAAG-GGCAACGAGCTTTACTCACCGTGCGCCGCTGA
TGGATGAAGGGGCAATAATACTGTGGCACCCCAATGACTTGGATGTATTTTTGAC-TTTTTGCAAGGGTGTTTTTGTAAG
AGTACATGCTACTCAA-----TAATAAGGATGTTATCCCTTTCCCC--ATGCTCTCCTCCTATAAAAACACCACCTAGCC
TAAGCATCCACTCGCTACTGATCATCCAACACGAGGAAGCATCCAGGACTAC------ATACGAGATGGGCAAGACACTG
TTGCTCCTGCCCGTCCTGCTCGTCGCTTCCCGTAAGTGTTTGAATTCTCATGAATCAATCGGATGCATATGAATTTTGCT
CAAATTTGACTGC----------------AGTGGGCATGTCGACGACGGTGGTGCGGAGCGAGCTGGCGTGCGGCAGCCT
GAGGGAGCAGTGCATGGCCATGTGCATCCTAGCAAGCTGGTGCATGCACTGTTGCCAGGCCCGCGGATACGCCCACGGCC
GCTGCAGGGTCCTCCACGGCGAGACCACCTGCTACTGCTGCAAGGACGTGCCCCCC-TCCCCCTCCCCGGCTCCCGGCCC
GCAGAAGAGCTCCGCCGCCGGCGACCTCACTTTCTTGACCGACTGAGGAATATGCGGCGACATCCTCACTCTCTTTATGC
AT-------CAAGCGTGAGTTGGGCCAACTCCTGAATAAATGGACAAGATCTGTCTAGTAGTTTTACGCGATCTTTCCAA
AAAGGATATGCATGTTTGCTAATTGCTATGCCAACTCGATCTTTTAGCTGCGTGTACCGTACCATCGGATGCAAAGGCCG
GGCGATAT----------------------------------TCACCCGCCATC-------------TAAGAAAACTTAT
GCCAACTTCCCAATTCTCCGGCTTCAAAACCACCATGGTTTTATCTAACCGTGTTCCCTATACTTACACACTTATCGCAA
AGTTGTAAGCTAATACTATCAAAAGTCCCTGTTTAATTGATTATGTGCGCAATGCGCATCCTTTTAATGGAAAAGTATTC
CTGTT--TTTCATCCAAGAGTTCTTGTTTGATGTCGTGCGTCCT----TTTCATGCAGATGACATCTACAAATTGTGTGG
CATCAACATTTTTCT-----AAATATCGCATATAATTTATGTTGAGTTGGA--AGTGATCAAAGAAATAAAAGGTAGTAT
TCTTTAATACA-ATTTTCATCGTACTAGACTTTGTTCCTCCACCATTTGGTGCTTATTTAATAATATTAGTCGCCACCCA
---CGTGAGCATTAATTGTTAGCAAATACAATAAAAAATAACTATATCGCCATATCTCT--------------------A
TATCTCTATATCAATATCGCTA--TCTCTATTTATATCTACATCTATCTCTATCTCTATCTATTTGTATCTATATCCATT
ATCTATTATCGCTTACTTATGTTATATTGTTATATT-ATTTTGTTTCATACTTATAATTTTATTTTACTTAAATCATTAT
TTATTTATTTTTGGGTAAAGACATGGATATTTTGTTATA--TTTCCAAAGCTTCGCTAGCTGTGAGCTATGAAAGGGGCG
GTTCTAGCCATTGTAGGAGCTAGATGATACCCCACACATTGTTGTGTGGACATTTTGCAACATATTTCGATGAGATTCGA
TGTATGAAACATGAATATTTGGAGTAATAATATAAGAGCTAAAAATCAAAATACGTCTGATTTATTGTGTTTGATTATTG
TATA
>chr1D_1
TTAATATATAGTAATTCTAGCCCGAGCAGGCGGCACA---TGTTGAATGGTGTTACTTAATCACCAACATTAAGGAAGGG
GACATATATATGATAACAGTAATAAATGTTATCTATACAAACAAGGGAAACATAACTTTTCAAAAA-TATTTCCTTTATC
CTCTACTTCACTAAGACCAGTATTTCCTATATATATAACTAAAATGCTTAGGTTCCGAATATATCCTTGATGAATTAACG
AGACCACTTAAGCTAAGAAGTGTTAAACTTATTCCCACCTAGGCAGGCGACAACCCATCCCCC-CCCCCTCCCCCTCCAT
ATGCCCCTCCGGCGAGGGGATGAGGTGAAGATCCCAGTGCTTCTGTTTGTTCTCCGAGTGGCGGTGGCGAGATGACAACA
TCGCCTTCGGTGTGGAATAAGGTATCTTCATCTCGCTCTCATTCCGATGGTGCCTCTTTGTATTGTCGGGAGGCATTTGG
AGGATGGTGTGTCCCTAGATTCGTTTCTCTGTGTCCGAATTTTTCTTCTGCATGTTTGTCTCGTTATCGCTATCATGCAG
AGCGGACAACACGGATGTGCGTCTTGGTCCTCCATCTCGAGTATCGACTGATGAATGTTGGCCAGCCTTGGCCTCGATGG
GGAGCTTGTGAGATTTGTGTTCTTTGACTCTGCCTAGCCCGACATGGGGCGTTCTACAGGCACATTCCAAAATTTCCCTT
CTTCCGTGCGGCGATCTACATA--GCAGATCGCTATCGTCGGCATCTTCTGATCTACATATCGGCCGCTAGTTCTACAAA
CTTCTGAGTTTCAACAGGTTTGCTTCGCTGAGACGGAGACCTAGAGGCGGCAACTAGGTTTGCTCACTGCACACCGCCGA
TGGATGGAGGAGGAATAATACTGTGGTACCCCAATGACTTGGATGTATTTTTGAGTTTTTTGCAAGGGTGTTTTTG-AAG
GTTACATGCTACTCAA-----TAATAGGAATGTTATCCCTTCCCCCC-ATGCTCTCCTCCTATAAAAACACCACCTAGCC
TAAGCATCCACTCGCTAAAGATCATCCAAGACGAGGAAGAATCCAGGAGC------ATATACGAGATGGGCAAGAGACTG
TTGTTCTTGGCCGTCCTCCTCGTCACTTCCCGTAAGTGTTCGAATTCGCACGATTCAATCGGATGCATATGAATTTTGCT
CAAATTTGACTGCG----CGCACGCCTGCAGTGGGCATGTCGACGACGGTGGTGCGGAGCGAGCTGGCGTGCGACAAGCT
GAGGGAGCAGTGCATGGCCATGTGCATCCTGGCAAGCTGGTGCATGCACTGTTGCCAGGCCCGCGGCTACGTCGACGGTC
GCTGCAGGGTCCTCCACGGCGAGACCACCTGCTACTGCTGCAAGGACGTGCCCCCC-TCCCCCTCCCCGGCTCCCGGCCC
GCAGAAGAGTTCCGCCGCCGGCGACCTCACTTTCGTCGCCGACTGAGGAATATGCGGCGACATCCTCACTTTCTTTATGT
AT-------CAAGCGTGAGTTGGGCCAAGTTCTGAATAAATGGACAAGATCTGCCTAGTAGGTTCATGCAATCTTTCCAA
AAAGGATATGCATGTTTGCTA-------TGCCAACTCGATCTTTTAGCTGCGTTTACCGTACCATCGGATGCAAAGGCCG
GGCACCACGTTGGGCTCTGACGATTTGAAAATTAGTCTGGCCTCACCCGTTATC-------------TAAGAAAACTTAT
GGCAACTTCCCAATTATCCGGCTTCAAAACCACCGTGGTTCTGTCTAACTTTGTTCCCCATACCTACACACTTATCTCAA
AGTTGTAAGCTAATACCATCAGAAATCCCCGTTTAATTGATCATGTGTGCAGTGCGCATCCTTTTAACGGAAAAGTATTC
CTGTT--TTTCATCCAAAAGTTCTTGTTTGATGTCGTGCGTCCT----TTTCATGCAGATCACATCTACAAATTGTGTGG
CATCAACATTTTTTTTTTGAATATATCACATAGAATTTATGTTGAGTTGGAAGAGTGATCAAAGAAATAAAAGGTC---T
TCTTTAATATG-TTTTTCATCGTACTAGATTTTCTTCCTTCACCAGTTATTGCTTATTTAATAATATTAGTCGCCACCCA
---CATGAGCATTAA-TGTTAGCAAATACAATAAAAAAAT-----------ATATCGCT--------------------A
TATCTGTATATCTATATCGCTA--CCTCTATCTATATCTACATCTATCTCTATCTTTATCTATTTGTATCTATATCCATT
ATCTCTTATCGCTTACTTATGTTATATTGCTATACTAATTTTTTTTCATACTTGTAATTTTATTTCACTTAAACTATTTT
GTAATTATTTTTGGGTCAGGACATGGATATTTTGTTATA--TTTTTAAAGCTTCGGTAGCTGTGAGCTATGAAAGGGGCA
GTTCTAGCCATCGTAGGAGCTAT------------------TTGTGCGGACATTTTGCAAGATATTTCGATGAGATTCGT
TGTATGAAGCATGAATATTTGGAGTAATACTATAAGAGCTAAAACTGAAAATACATATGATCTATTGTGTTTGATTATTG
TATA
>chr1B_484
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-----------TCCCTAGGTCCGTTTCTCGGTGTCTGGTGTTTTCTTGTGCATGTTTGTCTCGGTGTCTCTGTCCTGCAG
AGCGGGCCATACAGATGTGCATCTTGGTCCTCCGTGTCGAGTATTGACCGATGAAGGTTG----GCCTTGGCCTCAACAG
GGAGCTTGTGAGATTTGTGTTCCCTGACTCCGTCTAACCGGACATGGGGCGTTCTACATGCACATTCCAATATTTTCCTT
CTTCCGGGCGGTGATTTGCTATATGCAGATTGCTGTCACCGGCATCTTCTGGTCTGCATATTGACTGCTAGTTCTACAAA
CTTTCGAGTTTCAATAGTTTTGCTCCGTTGAGACGGAAACCCAGGGGTGGCAACAAGCTTTGCTCTGCACACACCGCCGA
TGGATGGAGGAGGAATAATGCTATGGCACCCCAATGACCCAGATGTACTTTTCAG-TTTTTGCAAGGGTGTTTTTGTAAG
GGTACATGCTACTCAATACTGTAATAAGAATGTTATCCCTTCCCCCCTATGCTCTCCTCCTATTAAAACACCACCTAGCC
CAAGCATCCACTCGCTAAAGATCATCCAAGACGAGGAAGAATCCAGGAGTATATTTATATACGAGATGGGCAAGAGACTG
TTGTTCCTGGCCGTCCTCCTCGTCGCCTCCCGTAAGTGTTCGAATTCGCACGATTCAATCGGATGCATATGAATTTTGCT
CAAATTTGACTGCGTGCACGCACGCACGCAGTGGGCATGTCGACGACGGTGGTGCGGAGCGAGCTGGCGTGCGGCAGCCT
GAGGGAGCAGTGCATGGCCATGTGCATCCTGGCAAGCTGGTGCATGCACTGTTGCCAGGCCCGCGGCTACGTCGACGGCC
GCTGCAGGGTCCTCCACGGCGAGACCACCTGCTACTGCTGCAAGGACGTGCCCCCCCTCCCCCTCCCCGGCCCCCAGCCG
GCAGAAGAGCTCCGCCGCCGGTGACCTCACTTTCTTGCCTGGCTGAGAAATATGCGGCGACATCCTCACTTTCTTTATGT
ATGATAGCTCAAGCGTGAGTTGGGCCATGTTTTGAATAAATGGACTAG-------------TTCTATGCAATATTTCCAA
AAAGGATATAT---------------------------------------------------------------------
------------------------------------------TCACCGGTTATCTATCTATCTATAATAAGAAAACTTAT
GCCAACTGCCCAACTCCCCGGCTTCAAAACCACCGTGGTTTTATCTAACTGTGTTCCCCATACCCACGGCCTTATCGCAA
AGTTGTAAGCTAATACCATCAAAAGTCCCCATTTAATTGATCATGTGCACA-------TCCTTTTAGCGAAAAGTGTGTT
CTTTTTGTTTCATCCAAAAGTTCTTGTTTTACGACATGCTTGCACCCATTTCATGCAGATAACATCTACAAATTGTGTGG
CATCAACATTTTGTTTTTGGAAATGTCACATAGAATTTCTTTTGAGTTGGAAGAAAAAACAAAGAAATAAAATGTC---T
TCCGTAATATTTTTTTTCATCGTACTAGACTTGTTTCCTTCACCATTTGTTGCTTGTTTAGTTTTATTAGTCGCCACCAT
CACCGTGAGCATTAATTGTTAGCAAGTACAATAAAAAATAACCTATTGTAGAATAAGTTATTGCTATGTTCTTTACATAA
TATCTCTATATCTATATATATGTGTCTCTATCTATATCTGCATCTATCTCTATCTTTATCTACTTGTATCTACATCCATT
ATCTATTATCACTTACTTATATTAT--------ATT-ATTTTGTTTCATACTTGTAATTTTATTTTATTTAAATTATTTT
GTATTTATTTTTGGGTAAAGACATGGCTATTTTGTTACTTTTTTTAAAAGCTTCGGTAGGTGTGAGCTATGAAAGGGGCA
GTTGTAGCCATTGTAGGAGCTA----------------------------------------------------------
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>SNPs
--------S----S--------------S--------SSS----------------------------------------
S------------S----S----S---S---------S----------------------------S------SS-----
-------------S------S--------------------------------SS-S-------------SS------S-
------------------------------S-S--S-------------S--S---S---SSSS-----S-S--------
--------SSS---SS-S--S------S-S-SSSS-S------------S----S----S------------S--SSS--
------------------------------S--S-----SS--------------S-SS--------S---------SS-
----------------------S--------------------S---S-------------S----------S--SS-S-
-------------------S-----SS---S------S-----------S-----S----S-------------S---S-
----S--------------------------S------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--------------------------------------
-----------------SS----------S---------S--------S--S-----------------------S----
---S-----S-------S----------------------S------S--S--S--------------------------
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------------------------------S-----------------------------------S----S-S------
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-------------------------------------S--------------------------------S--------S
----------------------------S-S----------------------S------------S--S----------
---------------------SSSSSSS-------------------------S--------------------------
---SSS-S-----------------------------------------SS-----------------------------
----------------------------------S--------------S--------S----S----------------
----------------S------------S-----------S---------S---------------S------------
-----------------S------------------------------------------S-------------------
-------------S-------------S----S------------------------------------------SSSS-
---------SS-S--------------------S-----S---------S------------------------------
------------------------------------------SSSS-SSSS-----S-----------------------
------------S------------------S-----------------------S------------------------
-----------------------------S-----------------------S--------------------S---S-
S-------------------------------------------SS---------S-----------------------S
----------------------SSSSSSSSSSSSSSSSSSS-----S-------------S------------------S
--------S--------------------S--------------S-S-------S-S----S------------------
----
>forward_553
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-----------------------------------------------------GTTTGTCTTGGTGTCGCTGC-------
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>reverse_1478
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-------------------------------------ACCGACTGAGGAATATGCGG-----------------------
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>forward_1130
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----------------------------------------------------------------------CAAGACACTG
TTGCTCCTGC----------------------------------------------------------------------
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>reverse_2480
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-------------------------------------------------------------------------------G
GTTCTAGCCATTGTAGGAGCT-----------------------------------------------------------
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