>input_sequence_85277
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-ATGAGGGGCGGCGGGCGGGCGCGGCAGAACGCGATCCGGTCGGGCATCGTGGTGCTGGGCGCCGCGGCCTTCGCCTACC
TCTCCTACCGCGTCGGCTTCAAGCCCTACCTCGACCGCGCCCAGGAGGCCATGGACTCCCAAATCCACAGCTCCGACCAC
GCCGCAGCCGCCG---------------CCGCCGCTGCTTCCGCCTCCTGGGAGGACCAGCCTGGTCACCCGGAGGGCGA
CGGCGGCCTCGCGCCGTCCAGGGACCCGGCCGCCGTGCTCCGCGACTGA-------------------------------
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>chr1D_1_TraesCS1D01G355700
GGATCTTTGATATTGCACTCTTTTCCTTTATAATTATTTTCTGAATGGTTTCTTATGGAAGGTTTTAATGAGGCAATAGT
AATGCAGGCATTATGATATGCCATTTTCTCCTTATTTTTCCGGTGGGTTTTTCAAAGGAGTTCTTGATGGCATATTGTAC
ATATCTCCTTATATTTTTTCTACAGGATTTTTGGAGGAGGCTGACCAAGATGTTGATGATGATGTTTACAAAAATAATTA
AAGCGGAGATTAGGAAGAATGTTAGGATTAATTAATTAGTTTAATTAAAGAAAATCCCTGCTTAGCAAAACCAACATAGG
GTTCCTCTCCCGACGGATCGCGTCCTAATATGACAGACGCGTCCTTCTAATCCCATCTCTTGTAATGATTGCGTATGTGC
GACGCGTCCCTTCTGAGGATATAGATCTGTACATCATCACAATCAATCAATATCGATTGTTACTATTCACTATTGTTTCT
-------------------------------------------TGGCTATAACTTATTGCGCAA---AACAACAGCGTAA
TTTTGAATACGTACTACTTAT--TCGCAAAAAAA------AA--------TACGGACCACTC-GGCTTGACAGAACTGCA
AACCTTTAGATAGTTGGCCACTGATCTTAGGCGTCGCAACAGACCAAGCTGGTTTGAAATAAATAATCTGGATTTCCTTT
CTATACCAGAAGCTGCTGTGGTGTAGTGGTTATCACGTCAGTCTTACACACTGAAGGTCTCCGGTTCGATCCCGGGCAGC
AGCAA---TTACTAAAGTTTTTATTCTCATATCTATTTATTT-------------ACCTCACTATTCTTTTTAGCCCCAC
CCCACCAAGATAACAGTCTCTGCATCTTTCGATCAGCTGCTCTTGTTGCAACCCAATTTCTTTTCCCCCAACCTTCAGA-
-----------------------GGGAAGACAGACTGTTGGTT---CAGCTGCAGAGTCACGGTGCGCCTGGAGCCTTCA
GGCCAGCACTAGGAGAGGAGAGTGAAGCGACTTGCCCATCGTCGCGTCAACCCGAGAGAGACAGA---------------
GATGAGGGGCGGCGGGCGGGCGCGGCAGAACGCGATCCGGTCGGGCATCGTGGTGCTGGGCGCCGCGGCCTTCGCCTACC
TCTCCTACCGCGTCGGCTTCAAGCCCTACCTCGACCGCGCCCAGGAGGCCATGGACTCCCAAATCCACAGCTCCGACCAC
GCCGCAGCCGCCG---------------CCGCCGCTGCTTCCGCCTCCTGGGAGGACCAGCCTGGTCACCCGGAGGGCGA
CGGCGGCCTCGCGCCGTCCAGGGACCCGGCCGCCGTGCTCCGCGACTGACGCGCCATCCA-----GGGGCGCCCGCGGCA
GCTTGGCTTGTTGTGGCATTTCGCCGAACACTTTGTAAGCGGATAATAAAATGTACTGGAACTGT----TTCTTTTTTTC
GCACTGTAATTCCCCTACTATTACTGCTGGCGTGGTTTCAAAGTG-TTTAACCTGTGTCTGATTCTATCATCGTACA---
CTTAGTTCACTGAAAACTCACCTGCGCTGCATATGCCTGCTCTGCACACACTGTCACACATATAGCCTGATGCGAAGATG
CTGAAACTGTGATTGGTGGCTCTAGTTGACCAGGCAGTTTTCATATCAAATGGATGTGCATATTATAGGTCCAGGAAGCA
GAGCATCTTCTAGATTCCAGCGACATTGTTGCATATTTGTGTGATCCTAATGGGAAAGTCTCATCTTCTTGTTGCTTCAT
GTTCTTGTTCCGACTTACTCACGGTAGCGATTAATCCCCTACCGTTGCAATCTGTGTGATGTAGATATGTTAGTTCTTCA
GGAACTTGAAGAGC--ATAGGTCTAAATGATTAAGCATCACTTTCCCTGCAGTTAGTGCCTAGACTTGTTTTGTTCGAGT
AC-TTATGCAGGGTCCACAGATTGGGAATGGGAACACAAGGAAAACATC------------------GACAGAGTAAACA
TGCCAAACTCCAACACAGCTAGTGATTTCATTTCAGATTTCACTGAATTATCAGCAAATAGCACACTTGCTCAATCGATT
CTTAGTAAACTAGCACAATGGACGTGCATCGCAACGA-AACTGCTAAAAGGCGAGGAGGTATGCCACTGGCTTGTCTCGG
CCAGTGGC-------------------------------------ATTAAAAAAGAGAACAAGAATATGAGGGCCGAATT
GCCGAAGGCTAGGCGTTCGAGCATCCAAAGCGACCATGGAAAGGGTCGT----------------TTGTGACATTTAAAG
TGCGAGATGACATTTCAAAATTTAAAACTTGGCAAGGTGGGGCATTAGGGAGGAAACAAAGCAATGATGACGACGGTCGG
ATAGGAGGGTGAGGCCT
>chr1A_1
GGATCTTTGATATAGCACTCTTTTCATTTATAAGTTTTTTCTGAATGGTTCCTTATGGAAGGTTTTAATGAGGCAATAGT
AATGTAGGCATTGTGATATGTCATTTTCTCCTTATTTCTGCAATGGGTTTTTCAAATGAGTTCTTGATGGCATATTGTAC
ATATCTCCTTATATTTTTCCTACATGATTTTTGGAGGAGGCTACTCAAGATGTTGATGATGATGTTTATAAGAATAATTG
AAGCGGAGATTAGGGAGAATGTTAGGATTAGTTAATTAGTTTAATTAAAGAAAACCCCTGCTTAGGAAAACCAACATACG
GTTTCTCTCCTGACGGACCGCGTCCTAATATAACAGACGCGTCCTTCTAATCCCATCTCTTGTAATGATCGCATATGTGC
GGCGCGTCCCTTCCGGGGATATAAATCTGTACATCATCACAATCAATCAATATTGATTGTTATTATTCACTACTGTTTCT
TTAAAATAACAAATGGCTATACCCCGCAAAAAAAATTAACAAATGGCTATAACTTATAGCC--A---AACAACAGCGTAA
CTTTGAATACGTACTACTTATATTCGCAAAAAAAGAAAAGAA--------TACGGACCACTT-GACTTGACAGAACTGCA
AACCTTTAAACGGTTGGCCACTGATCTTAGGCGTGGCGAAAGATCACGCTGATTAGAAATAAAATGTTTAGATTTCGTTT
CTACACCAGAAGCTGCTGTGGTGTAGTGGTTATCACGTCAGTCTTACACACTGAAGGTCTCCGGTTCGATCCCGGGCAGC
AGCACCTTTTTTCTATTAATCTTTTTCATC--------------------------------------------------
------------------------------------------------------------------------------TT
TTCGGCATGCCAACCCTTC-------AAGAGAAACTGCTGGTT---CAGCTGCAGCGTCACGGTACGC-TGGAACCTTCA
GGAAAACACT----------AGCGAACCTTCAGGCACATCGTCGCGTCAACCCGAGAGAGGCAGA---------------
GATGAGGGGCGGCGGGCGGGCGCGGCAGAACACGATCCGGTCGGGCATCGTGGTGCTGGGCGCCGCGGCCTTCGCCTACC
TCTCCTACCGCGTCGGATTCAAGCCCTACCTCGACCGCGCCCAGGAGGCCATGGACTCCCAAATCCACAGCTCCGACCAC
GCCGCAGCCGCAG---------------CCGCC------GCCGCCTCCTGGGAGGACCAGCCCGGTCACCCGGAGGGCGA
CGGCGGCCTCGCGCCGTCCAGGGACCCGGCCACCGTGCTCCGCGACTGACTCGCCCCGCCGTCAGGGGGCTTCCGCGGCA
GCTTGGCTCGTTGTGGCATTTCGCCGAACGCTTTGTAAGCGGATAATAAAG-GTACTGGAACTGAACTGTTTTGGCATTG
GAATG--AATTTCCTTGCTGGTATTGCTGGTATGGTCTCAAATAAG-TTAATCCATGCATGATTCTGTCATCATACA---
ATTAGTTCACTGAAAACTCACCTGCGCTGCTCA--------------------------------CCTGATGTGAAGATG
CTGAAACTGTGATTGGTGGCTGTAGTTGACCAGGCAGTTTTGAGATTAATTGGCTTTGCAAATTGTAGGACCAGGAAGCA
GAACATCTTCTAGATTCCAGCGACATTGTTGCAGATCTGTGTGATCCTAATGGGAAATCTCGT--------TTGCCCCAT
GTTCTTGCGCCGACTTACTCACGGTAGCGATTAATCCCCTATCGTTGCAATTTGAGTGATGTAGAGATGTTAGTTCTTCA
GGAGCTTGAAGAATGTAGGTCT----------------------------------------------------------
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>chr1B_4
---TCTTTGATATTGCACTCTTTCCCTTTATAAGTTTTTCTTGAATGGTTTCTTATGGAAGGTTTTAATGAGGTAATAGT
AATGCAGGCATTACGATATGCCATTTTCTCCTTATTTTTCCAGTGAATTTTTTGAAGGTGTTCTTGATGGTATATTGTAC
ATACCTCCTTATATTTTTCCTACAGGATTTTTGGAGGGGGCTGATCAAGATGTTGATGACGATGTTTACAAAAATCATTG
AAACAGGGATTAGGAAGAATGCTAGGATTAATTAATTAGTTTAATTAAAGGAAATCCCTGCTTAGCAAAACCAACATAGG
GTTTCTCTCCCGACGGATCACGTCCTAATATGACAGACGCGTCCTTCTAATCCCATCTCTTGTAATGATCGCGTATGTGC
GACGCGTCCCTTCCGGGAATATAAATCCGGACATCATCACAATCAATCAACAGCGATTGTTATTATTCGTTACTGTTTCT
TTACAATAACAAATGGCTATA------------------------------ACTTATTGCGCAAAACAACATCAGCGTAA
CTTTGAATACGGACTAGTTAT--TCGCAAAAAAC------AAAAGAAGAATACGGACAACTTAGACTTGACAGAACCGCA
AACCTTTAGATGGTTGGCCACTGATCTTAGGCGTGCCAAAAGACCACGCTAGTTTGAAATATAAGAGCTGTTGTTCGTTT
GTAAAACAAAAGCTGCTGTGGTGTAGTGGTTATCACGTCAGTCTTACACACTGAAGGTCTCCGGTTCGATCCCGGGCAGC
AGCAA---TTTTTTATCAATCTCTTCCATCTTTTCCCGTACTGTAACTGCACAACATCTCACGACTCTTTTTGGTCCCGC
TGCGATCTCACGATTCTT----------------------TCTAGTTGCGACGAAATTTCTGTTGTTCCAACAAACATTT
TTCGGCATGCCAACCCTTTAACTGGGAAGAGAGACTGTTGGTTCAGCAGCTGCAGAGTCACGGTAGCAC-----------
----AACACT----------AGTGAACCTTCAGGCACACCGTCGCGTCAACCGAGAGAGAGGAGGGGTGGTTAAAATGGC
GATGAGGGGCGGCGGGCGGGCGCGGCAGAACGCGATCCGGTCGGGCATCGTGGTGCTGGGCGCCGCAGCCTTCGCCTACC
TCTCCTACCGCGTCGGCTTCAAGCCCTACCTCGACCGCGCCCAGGAGGCCATGGACTCCCAAATCCACAGCTCCGACCAC
GCCGCAGCCGCCGCCGCGGCCGCCGCTTCCGCC------TCCGCCTCCTGGGAGGACCAGACTGGTCACCCGGAGGGCGA
CGGCGGCCTCGCGCCGTCCAGGGACCCGGCCACCGTGCTCCGCGACTGACGCGCCGTCCA-----GGGGCTTCCGCGGCA
GCTTGGCTTGTTGTGGCATTTCGCCGAACAGGTTGTAAGCGGATAATAAAATGTACTAGAACTGT----TTTTCGCACTG
GAATTC-----TCCCTACTGTTATCGCTGGTATGGTTTCAAAGTATTTTAATCTGTGCCTGGTTCTATCATCATGCTCTT
ATTAGTTCATTGAAAACTCACCTGCGCTGCAAATGCCTGCCCTGC--------TCACACATGTAGCCTGATGTGAACATG
CTGAAAATACGATTGATGGCTCTAGTTGACCAGGCAGTTTTCAGATCAAATGGCTGTGCAAATTACAGGACCACGAAGCG
GAGTATCTTCTAGATTACAGCGACATTGT--CAGATTTGTGTGATCCTAATGGCAAAATCTCATCTTCTTGTTGCCTCAG
GTTCTTGTTCCGACTTACTCACGATAGCGATTAATCCGCTACCATTACAATTTGTGTGATGTAGAGAT-TTGGTTCTTCA
GGAACTTGAAGAGAGAATAGGTCTAAATGATTAAGCATCACTCTCCCTGCAGTTAGTGCCTAGACTTGTTTTGTTCGAGC
CCTTTATGCAGGGTCGACAGACTGGGAATGGGAGCACAAGCAAAACAGTGGTTCGAGAGTTGCTGCAGACAGAGCAAACA
TGCCAAACTCCAACAGAGCTAGTGATTTGATTTCAGATTTCACTGAATTATCAGCAAATCGCACACTTGCTCTATCGATT
CTTATTAAACTAGCACAATGGGCGTGCATCGCAACGAGAACCGCTAGAAGGC---GAGGTATGCCACTGGGTTAGGAAAT
CATCGGAAGATGTTTGCGTCCTATGACTGTTATGTGGTTCCAACGATTAGAAAAGAGAACAAGAATATGAGGGCCAAATT
GCAGAATGTGAGGCGTTCGAGCATCCAAAGTGACCATTGATATGACAAAATGTGGTCCGAATTGCTTGTGACATTTAAAG
CGTGAGACGACATTTCAAATTTTGAAACTGGGCAAGGTGGGGCATTAGAGAGGAAACAAAGCAACGACGACGACGGTCGG
ATAGGAGGGTGAGGCCT
>SNPs
---------------------------------S-S--------------------------------------------
-----------------------------------------S--------------------------------------
------------------S-------------------------S----------------------------------S
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---S-----------------------------------------------------------------S----------
-------------S-S-------S--------------------------------------S---------S-------
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S------------------------------------------------------------S--S---------------
-----------S----------------------S----S------S----------------SS-----------S---
---S----------------------------------------------------------------------------
----------SS-S-SSSS-S-S---SSSSS-S-SSSSSSS---------------S-----S-S-------S-S---S-
SS-SSSSSS-SS-SSS-SSSSSSSSSSSSSSSSSSSSSSS---S-----S--SS-------S--SSS-----SSS--SS-
------------------------------S---------------------------------S--------S------
--SS-S----SSSSSSSSSS------S-SS-SS--S------------------------S-------------------
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---------------------------------SSSSSS-----------------------------------------
-------------------------------S-----------------------S--------------SS--------
-----------------------------------------------------------------------S-SSSS--S
-S-S-SS----S-------S---S------SS------------S------S-----S--------------S-------
S------------------------------S--------S----SSSSSSSS--------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-----SSS---------------S--SSSSSSS
-SSSS-SS-----------------------------------------S-------------------------S----
--S---S-SS--------------------S------S--S-S-SSSSS-------------------------------
S-S----S-----------S---S-----S------------------S---------------S--S------------
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>forward_894
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--------------------------------------------------------------------------CCCCAC
CCCACCAAGATAAC------------------------------------------------------------------
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>reverse_2329
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--------CTAGGCGTTCGAGCATCCAA----------------------------------------------------
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