>input_sequence_86257
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-----------------ATGGGGCTGTGGTCATTTCTTGAGGGTGTCCTGCTTATTGCTAATGCTTTGGCAATATTGAAT
GAAGACCGTTTTCTTAATCCCAGAGGATGGAGCTTCGCTGACGCTAGAGGCATGCATGGAGCAAACACTTTCAAAGGACA
GATGATTGGCCTCATATACGCGGCTCAATACATGAGATTTCCATTGATCCTTCTTGATGGAATCACTATACTTGTGAAGT
TCGTTACATTCTGA------------------------------------------------------------------
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>chr1D_1_TraesCS1D01G279100
AGCCCAACTCATACCATGGGCTTTCGAAAGAAAAAGGAATCGGAGCCAGCCTGCTTCTTGTTCTAACCGTCCGTCTCTCT
CCCGTCAAAAAAAAAAACCGTCCGTCTCTATCTCCTCCTCCACTCCGGCAACCGGCCGGAGCCGTTCTCCGCTCCAGAAA
AG-------GACAGGGACCGGAGCCGTTTTCCCAGTGGCGGAATCAGAACTCGTCAAC---------------------T
C---------------GCCGTCCGGGCGAACTGGGACCGCAGACCCGTCCGGACTCGGCTTAATTTCTTCTCTGGTCGGT
AAGGAACCCTAGCTCGCTTGCCTGTTTTTGATCCGTGAGAGGATACACCATCAAATCCATGGTTCTATTA--------GG
TTTGTATATATTTTCTTC-AGAGCGCGCGATCGATCTCCTCCCACCCGTAGGGGGGGTCGCCCGTTCGGTACCCG-----
-----------------------------------ACTGAATCACCATAGTTCTCCCTCGTGCAGTTCTTTTCTCTTTCT
TGGTTCATGTATACATATGTCGGGATAAAACAGCATAATTCATAATCAGTGCA-----------------------GGAT
TTATACCGTTATAGG--AAAATT--TAATTGGAAAATCAGAACTGCTGTGATTAAACTTATTTTGAATGGGGCTGTTTGT
GTCCGATTAATTTGCTGCAAGCCCAGGCAATAAAGATGGGTTGCCTTAACGGAGGGACTGCGACAGTAGGATGTA-----
----------TCACGCCAAGATCATAATGCTCTCAGACAATCCTCCTGGT--CATTAAAAAATAAGCTTATGCCGGATGA
ACTCTCGTGCGCGATACACCATACTAGGATTCATTCTGTGGAAGAGGTTATGGGTTAGGAAATGTTTCAGACAGAATAAG
GTGCTGGAGTGAAGAAGCTACAAAAGCACCTTTAGAAAAAGGACCGAGAACTACATTACAATTGCAATCTATAATGAAGA
TTTGGAAAC-AAAATTCAGAGGGTTAAAAAGGACTGTGTTATGGGCTCCTTTCCTTGTGACTGATGTCCGACTGTGATCC
CTTCTTATTATGCAGGCATGGGGCTGTGGTCATTTCTTGAGGGTGTCCTGCTTATTGCTAATGCTTTGGCAATATTGAAT
GAAGACCGTTTTCTTAATCCCAGAGGATGGAGCTTCGCTGACGCTAGAGGCATGCATGGAGCAAACACTTTCAAAGGACA
GATGATTGGCCTCATATACGCGGCTCAATACATGAGATTTCCATTGATCCTTCTTGATGGAATCACTATACTTGTGAAGT
TCGTTACATTCTGACAGTGGGAAGTGGTATGCTATACAG---TTCTTCCATTTGCTTCCTTGAAGATTGAGATATTTG--
----------GCTTTATGCAAATTTTCTCGTGCTTCACCCCTTCTTCCAATACTCTT-TTGTTGATGGTTGTATAGCTGT
GCCTTTTATATGCACACTGTTGACATGTGCAGTTGTGCTCAGTTAGTAATTTATTGGTTGTCCG-------CAACACACT
AGACGGTAGGTGCCTAACTGTGATCTTTCATTGTTCTTTTGTATGTACATGATGTATTTGCATTTGTCCATTGTAATTTT
TTCTTGTTATTCCTGATAAATTTTTGCATGATGGGATTTTTATTATCAAGCAAATGGAACACTCATGTTTCCATTTTCAT
AGAAGTATCAGAGAAGTTCTTATGTG-TATGATTTAGAGTGCCTCTCATAAACCAGACACTGTATAGTATTATATGGTTG
GGTGTCACCACTTCTATGATAGAGTATATTTCATTAGTTATTATTG-----------------------GGTTTT--TTA
TCATATGTGTTCAATGTCAAACGTGGGTTTCATTTATTGGACGTTGGAGTGATTGCTCTGAATAAAGGTTATGGCCA-TT
CCTAT-TGTGTAGAATTTCTGAAGATACACGAGCTTAGAAGCCATTGATGGAATATACATTTAGAAGAGGAAATTTAGTT
ATATTT---AATTAAAAAATATAATCCCTTGAAATTTGAATGTT-TTTTTCTCAAACTATAAACTTGAATGTCATCATCA
AAGACGGAAGCAACATTTGGATAAATTCTTGCATGTGCTCATGACGGAGTATAGAACCATGATTTTGTAATTTTTTTAAA
CTAAAAATACAAATAAAATGATAAATTATGATACACAATTGCTACTAGTCGTCATATTTACTGTACCATAAATATACATA
AAATTTTCCAAAATCTCCATGC--AAAAAATGAAAATCTTCTATTTTTAGTATGAATCTATTTT--TCCTAAGAAGAGGA
CGATTTGTAATTATTTTAAACTTCCAGCCTTAA
>chr1B_16
---------------ATGTGCTTTCGAAAGAAAAAGGAATCGGAGCCAGCCGGCCTTTTGTTCTAACCGTCCGTCTCTAT
CCCCTCCTCC-----------------------CCC------CTCCGGCAA--GGCCGGAGCCGTTCTCCGCTCCGTAGA
AAAGAAAAGGACAGGGACTAGAGCCGTTCTCCCGGTGGCGGAATCCGAACTCGTCAACTCGACGAGCCAAACCTCGCCGT
C---------------GCCGTCCGGGCGAACTGGGACCGCAGACCCGTCCTGACTCGGCTTAATTTCTTCTCTGGTCGGT
AAGGAACCCTAGCTCGCCTGCCTGTTTTTGATTCGTGAGAGGGTTCACCATCAAATCCATGGTTCGATTA--------GG
TTTGTAT----TTTCTTC-AGAGCGCGCGATCGATTTCCTCCCACCCGTAGGATTTATACCGTGGTT-------------
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-------TGTATACATATGTCGGGATAAAACAGCATAATTCATAATCG--GCA-----------------------GGAT
TTATACCGTGGTTGGGAAAATTT--TAATTGAAAAAGCAGAACTGCAGTGATTGAACTTATTTTGAATGGGGCAGTTTGT
GTCAGATTAATTTGCTGCAAGCCCAGGCAATAAAGATGGGTTGCGTTAACCGAGGGACTGTGACTGTAGGATGTA-----
----------TCACGCCAAGATCATAATGCTCTCAGATAATCCTCCTGGT--CATTAAGAAATAAGCTTATGCCGGATGA
ACTCTAGTGCGCGATACAC--CACTAGGATTCATTCTGTGGAAAAGGTTATGGGTTAGGAAATGTTTCAGACAGAATAAG
GCGCTGGAGTGAAGAAGCTACAAAAACACCTTTAGAAAAAGGACCGAGAACTACATTACAATTGCATTCTATAATGAGGA
TTTGGAAAC-AAAATTCAGAGGGTTAAAAAGGACTGTCTCATGGGCTCCTTTCCTTGTGACTGATGTCCGACTGTGATCC
CTTCTTATTTTGCAGGCATGGGGTTGTGGTCATTTCTTGAGGGTGTCCTGCTTATAGCTAATGCTTTGGCAATATTGAAT
GAAGACCGTTTTCTTAATCCCAGAGGATGGAGCTTCGCTGACGCTAGAGGCATGCATGGAGCAAACACCTTCAAAGGACA
GATGATTGGCCTCATATACGCTGCTCAATACATGAGATTTCCATTGATCCTTCTTAATGGAATCACTATACTTGTGAAGT
TTGTTACATTCTGACAGTGGGAAGTGGTATGCTATATAG---TTCTTCGGTTTGCTTCCTCGAAGATTGAGATATTTGCA
CTCAACT-AGGCTTCATGTAAATCTTCTCGTGCTTCACCCCTTCTTCCGATAGTCTT-T-GTTGATGGTTGTATAGCTGT
GCCTTGTGTATGCACCCTGTTGAGATGTGCAGTTGTGCTCAGCTACTAATTTATTGGTTATCCGGGACAAACAACAAACT
AGACGGCAGGTGCCTAACTCTGATCTTTCATTGTTCTTTTGTATGTGCATGATGTATTTGCATTTGTCCGCTGTAATTTT
TTCTTGTTATGCCTGATAATTTTTTGCATGATGGACTTTTTATTATGAAGG-AATGGAACACTCATGTTCCCATTTTCAT
AGAAGCATCAGAGAAGTTCTTATGTGATATGATTTGGAGTGCCTCTCATAAACCAGGCACTGTA--GTATTATATGTTTG
GTTTTCACCACTTCTATGGAGTAGAGTATTTCACTAGTTAATCCATATATGTAATACTTCTCAATTATTGGTTTC--TTA
TCATATGTGTTCAATGTCAAACGTGGGTGTCATTTATTGGACCTTGCAGTGATTGCTCTGAATACAGGTTATGGCCA-TT
CCTATATGTGTATAATTTCTGAAGATACACGAGCTTAGAAGCCATTGATGGAATATACATTTAGAAAAGGAAATTTAGTT
ATATTTAATATTGAAAAATATTTAATCCTTGAGATTTGAATTTTCTTCTTCTTGAACTATT-ACTTGACTGTCATCATCA
AAGACGGAAGCGACATTTGGATAAATTCTTGCATGTGCTCACGACGGAGTGTAGAACCATGATTTAGTAATTTTTGAAAA
CTTAAA--------AAAATGATAAAATATGATACACAGTTGCTACTAGTCGCCAAATTTATTGTACCGTAAATATACAAA
ACATTTTCCAAAATCCTCCATGAAAAAAAAAGAAAATCCTATATTTTCAGTACAAATCTATTTTGTTCCTGAGAAGAGGA
AATTTTGTAATTATTTTAAACTTCCATCCTTAA
>chr1A_97
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----------------ACCGTCCGTCTCTATCTCCC------CTCCGGCAACCGGCCGGAGCCGTTCCCCGCTCCGTAAA
AG-----AGGACGGAGACCAGAGCCGTTCTCGCAGTGGCGGAATCCAAAATCGTCAAC---------------------T
CGACGACCCAAACATTGCCGCCCGGGCGAACTGGGATCGCAGACCCGTCCTGACTCGGCTTAATTTCTTCTCTGGTCGGT
AAGGAACCCTAGCTCGCTCGCCTGTTTTTGGTTCGTGAGAGGGTTTACCATCAAATCCATGGTTCGATTCGCCGATTCGG
TTTGTATTTTTATTAATAAAGAGAGCCCAATCGATCTGTGTCCACCCATAAGTTTCTCCGG--GTTCTGTACCCCATGCA
TGTCTGCAGTTTGTTTTTCAGTTTTTGTGAGACCAACCGAATCACCATAGTTCTCCACCGTGTAATTTTCTTCTTGGTCC
GTTT----------ATATGTCACGGTGAAACATCATAATTCATAATTCGTGTTATACTTGTCAGGTTCTCGTGTTTGCAT
TTATACCATTATTAGGAAAAGACGCTTACTGGGAAATCATAACCGGAACGACTGAACCTTTTCTGAATGGGCCTGTTTGT
GTCAAATTAATGTGCTGCAACCCC--------AAGATGGGTTCAGTTAATGGAGGGACAGTGACTGCATCCAGTCGGATG
TATCATGGGTTCAAGACAAGTTGATACTGTTCTTACATAATCGTCCTAGCCCCAGTAAGAAATAATCTTAGATG------
---------------ATAC--TAGTATGATTCATCCAGTCAAAAAATTCATGTCAATTATCATTGCTCCCGTGGTACAGT
ATCTTTCAACCACAC------------------------------------------ACAATTGCAATCTACGATAAAAA
TTTGGAAAGGAAAATTCAGAGGGTTAAAAAGGACTCTCTTATGGGCTCCTTTCCTTGTGACTGATGTCCGAGTGTGATCC
CTTCTTATTTTGCAGGCATGGGGCTGTGGTCATTTCTTGAGGGTGTCCTGCTTATTGCTAACGCTTTGGCAATATTAAAT
GAAGACCGTTTCCTTTCTCCCAGAGGATGGAGCTTCGCTGACGCTAGAGGCGTGCAGGGAGCAAACACCTTCAAAGGACA
GATGATTGGCCTCATATACGCAGCTCAATACATGAGATTTCCATTGATCCTTCTTAATGGAATCACTATACTTGTGAAGT
TTGTTTCATTCTGACAGTGGGAAGTGGTACGCTATGCAGCTCTTCTTCGGTTTGCTTCCTTGAAGATTGAGATATTTGCA
CTCAAACCAGGCTTTATGTATATCTTCTCGTGATTCACCCCTTCTTCCAATAGTCTTCT-GTTGATGGTTGTATAGCTGT
GCCTTGTATATGCACACTGCTGAGATGTGCAGTTGTGCTCAGCTAGTAATTTATTGGTTATCCG-------CAACACACT
AGACGGTATGTGCCTAACTGTGATCTTTCATTGTTCTTTTGTATGTACATGATGTATTTGCATTTGTCCACTGTAATTTT
TTCTTGTTATTCCTGATATTTTTTTGCATGATGGGATTTTTATTATCAAGC-AATGGAGCACTCATGTTTCCATCTTCAT
AGAAGCATCAGAGAAGTTCTTATGTG-TATGATTTAGAGTGCCTCTCATAAACTAGACACTGTATAGTATTATATGGTTG
GGTGCCACCACTTCTATGATAGAGTATATTTCATTAGTTATTATTG-----------------------GGTTTTTTTTA
TCATATGTGTTCAATGTCAAACGTGGGTGTCATTTATTGGACGTCGGAGTGATTGCTCTGAATAAAGGTTATGGCCAATT
CCTAT-TGTGTAGAATTTTTGAAGATACACAAACTTAGAAGCCATTGATG------------------------------
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>SNPs
SSSSSSSSSSSSSSS---S--------------------------------S--S-S---------------------S-
---S--SSSSSSSSSS-------------------SSSSSSS---------------------------------SS---
-------------------S--------S----------------S----------------------------------
--------------------------------------------------S-----------------------------
--------------------------------S---------S-S--------------------S--------------
-------S-S------------------------------------------SSSSS----SS----S------S-----
-------------------------------------S------------------SS----S-S--S-S----SSS--S
SSS-SSS----------------------------------------S--------------------------------
------------S-------S-------------------------S------S--------------------------
---S----------------------------------------S---------------S---S---------------
-------------------------------------S--------------------S---------------------
-----S-------------SS----------------------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-----SSS-S-SS------S--------S-----S----SS------SS------S-----------
-----------S-----------------------------S--------S--------------S---------SS---
--S---SSSSSSSS-----------S-----------S-------------S--S-----S------S----------S-
-S-------------SS-SSSS--------S-------S-S------S----SS----------------S---------
SSS-----------------------S------
>forward_206
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--------------------------TTTTCCCAGTGGCGGAATCA----------------------------------
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>reverse_1464
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-----------------------TTTCTCGTGCTTCACCCCTT-------------------------------------
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