>input_sequence_80109
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----------------------------------------------------------------ATGAGTGACCGAAGGT
ACGGGTACTCGTACCCACACAACCAAGGTAACTCCCACGC-----------------------ATGATAGATAGACGAA-
-----TATATGTTTGTGTTTCTTGCATTCCATTTCCCTTTTC-CCCTTCTTGTTTGCTCACGCTCACTGCCTTGCATGAA
ACTGAAACTGGAACGCGCGCGCACATGCAGGGTATTACAACGGACCGCCGGTGATGGCGCCGCCGCAGTACGCCCCGCCG
CCGAGACGGCAGACGGGATTCCTCGAAGGATGGTA----ATAAAAAGCTACGAACCTGACGGTTTTTCTTAATTTCCTCT
GCGTAAACTATGTGGGCAGTGCTAATCTGAGGTGCTCT------GTGCTTGCATGCCCGC--AAACTACGTACGAATAGC
CTGGCTGCTCTGTGCTGCTGCTGCCTCGTCGACGAGTGCTGCTGCGACCCGTCCATCATATTCGTGAGCTGA--------
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>chr3A_1_TraesCS3A01G318900
AGAGAGCAGGCAAGCCGGATCCTGAAGCCACACAATGATGTCGATGTCTCGGAAATCTGTCAGGTACATTTCCTACGAAG
AGATGGTAGTCGCTACAAACCTGCGTTCCTGCCGATTTTCCTTTAGTTTTTCCTCAAAGGTGGCGATATCCCC----TAC
AGTTTCTGAATTCTGGCAACCTGCAACTGCAAATGCAGACGGTTATCTGAACCCTTATGCTTAGGTT-------------
-----TCACGGTTGTGCACCACGCGTCACTCCCGTGTGCCTGCTGGAAGGGC-----GGCATAGACACAGAAAACTCTAG
AGAAGGGCGATCTGG-TTGCTACGAATCGTGCA-----AAAGAAACAAAGAACCCAGCATCTACCCTTGAATCGTCGACC
GATTTCTGATGATTTAACCGGACCA-------------TGCATTCTCCTCGTCTCGCCGTCTCGAGTTGGCAACGTCGCT
TTACCTGCCTCTTACCAACG---AAGAAGAAGAAGATC-----------GTAGCTCGCGTTGCATGCAGAGGTT-TAGAT
TCCCAGCGTCTTTG------------GTGTCTGATGCTGGTTACCGAGTTGTGCCGTTCACATTACAAGGTGGCGCATTA
GCATCGATC-CTAGCGCTTGTTAGATAACTACTGT----AATTGTAAATAGCGACAGCAAGCAGAGATA-GAGTTCAATC
GTATGAATATGATGC--CCCCATTTGCTTGAAGTTAAAGGCAGGAATAATCCACGGAAGGTCAAAAAGGAAGGGCGG---
-AATTAAAAGGAAGCAAAGAGATAATAATCGGATAACGATCG---AGTAGCTTTATTCGTTTCCCCTCGC----TGCCGC
CTAGGATCGATGAGCTGCCGACAGCGGCGCGCCGAATGTTTCAGAAGCGCCACTAAAAGTGCAATCCACGGCAAAAATAT
AC--TAGCAGGCCACTTGATCTTCGGTTTGCAGCCGCTATTTATACTCCCTCTAGGTCCAGCACCGGCCGGTCCACTTCT
GCTAGC--AG---GCAGCCATCTGCAGCTAGGGTTCA---TAGTTC--ATAGTCAGTGACCAACATGAGTGACCGAAGGT
ACGGGTACTCGTACCCACACAACCAAGGTAACTCCCACGC-----------------------ATGATAGATAGACGAA-
-----TATATGTTTGTGTTTCTTGCATTCCATTTCCCTTTTC-CCCTTCTTGTTTGCTCACGCTCACTGCCTTGCATGAA
ACTGAAACTGGAACGCGCGCGCACATGCAGGGTATTACAACGGACCGCCGGTGATGGCGCCGCCGCAGTACGCCCCGCCG
CCGAGACGGCAGACGGGATTCCTCGAAGGATGGTA----ATAAAAAGCTACGAACCTGACGGTTTTTCTTAATTTCCTCT
GCGTAAACTATGTGGGCAGTGCTAATCTGAGGTGCTCT------GTGCTTGCATGCCCGC--AAACTACGTACGAATAGC
CTGGCTGCTCTGTGCTGCTGCTGCCTCGTCGACGAGTGCTGCTGCGACCCGTCCATCATATTCGTGAGCTGATCGAAACA
CGTACGCGGTCCAGACGACGGCCGACCGATCGACCGACCGACGAACCATCCGAGCCGAGCTACGTACCTAACGTACTGGT
AGTAGTACATGTGCGATTTATATATGCGTGTCGTGTGTATGTGTGCTTCCCTTGAGCTGTTGCTTTCAGCTATAGCAATA
GCATATGCCCCTAGAGGCCTAGAACAGAGTAGAACTGCAGAAAGAATAGCCAGCCCGTCCTGCCGTTCGGTTCAGCTCTC
CAGCGGCACGACGGGTGGGTGGTGTGTGTTGCATGTATGTATGTATCTGATGTGATCCCCTAAAAAAAAGTATCTGATGT
GAGTCTACGAATAAGATGA---GGAAAAAGAAAAGTTCGGCACCTTCTATGATGTGAGCCTATGACATCCTGAATTTTAC
AAAAATAACATTATCAATATCAG-------GCTCACAGGAGATGCACCGGTAAGGTAGAAAGTCAAAACTGAGTGCCATG
ACGAACGCAAACACACGCCCCCTCCAGAGAATTGAATCGCACCGAACAGAGTCAAACAGAGTGAAGCGGAACATACAGGA
AGCGAAGAGGCACATTGGTTCGAACAAGAACCTGAAGAGACAGGC-----------------------------------
---TAAGGCTAGCACTGGTAGTGTGCGCAATCTGTGGCAGGAGCCGATGGTTTCGTCTCTCCGGTTGCGCGGGGAGTGGC
GGCCCGGAGGCGGAATCGGTGCAGCGGCGATCCACGAAGAATATGTGCAGCGGCGGCTGGGGGTGGACAAAGGGCATCCT
GCCCGTCTTCTCGCGCGTTGCGTTCCGCGGGCGCGGCGTGGAGACTCCTCCAGGCTCCAGCAACCGCAAGAGCTACTAGC
CCCGCCCACGAAGTTCTCAAAGAACAAAATGCGCCCATGAACATGGCCGACTCAACATACTCTCTCCGTCCCAAAATAAA
TATAAATCAACTACATTTATTTTGGGATGGAGGGAATAGATGTTGACATTTGCAATATATTATTTTAACGAGATCTAATT
>chr3B_58
---------------------------------------------------------TGTCAGGTACATTTCTTACGAAG
TGATGGCAGCCGCTGCAAATCTGCGTCCCTGCCGGTCTTCCTTTTGTTTCTCCTCAAAGGTGACGATCCCCTAATAATAC
AGTTTCTGAATTCTGCCAAC------CTGCAAATGCAGGCGGTTATCTGAACCCTTATGTTGGGTTAGTTCTCGCGGTCT
CCGAATCAGAGTTTTGCAGCACGCGTCACTCCAGTGTGTGT-CTAGAAGGGC-----AGCAAAGCCACAGAAAACCCTAG
AGAAGGGCAATCTGG-TTGCTACGAATCGTGTGAG-----AGAAACAAAGAATCCAGCATCTGCACGATGATCGCTTATT
ATCATCGGTTCGTGCACGTTCCCGAGAGCCAATG----------------GTCTCGCCATCTCGAGTTGGCGACGTCGCT
TTACTTGCCTCTTCCCAATGAAGAAGAAGAAGAATAGAAGATCGTAGGAGTAGCTCGCATTGCATGCAGAGGTT-TAGAT
TCCCAGCTAGCGTCTCTGGTTTCTCAGTTTCTGATGCTGGTTATCGAGTTGTGCCGTTCACATTA---------------
-------------GCACTTGTTAGATTACTGCTGT----AATTGTAAACAGCGACAGCAAGCAGGGATAAGAGTTCGATC
GT---------ATGATGCCCCATTTGCTTGAAGTTAAAGGCAGGAATAATCCACGGAAGGTCAAAAAGGAAGGGCGG---
-AAATTAAAGGAAGCAAAGAGATAATCA---GATAACAATCAAGTAGTAGCTTTATTCGTTTCCCCTCGCGCGCTGCCGC
CTAGGATCGATGAGCTGCCGACAGCGGCGCGCCGAATGTTTTAGAAGCACCACTAAAAGTGCAATCCACGGCAAAAATAT
ACACTAGCAGACCGCTTGATCTTCGGTTTGCAGCCGCTATTTATACTCTCTCCAGGCCCAACACCGGCCGGTCCACTTCT
CCCTCATAAG---GCAGCCATCTGCAACTAGGGTTCATAGTAGTTC--ATAGTCAGTGACCAACATGAGTGACCGAAGGT
ACGGGTACTCGTACCCACACAACCAAGGTAGCTCCCACGTTTATTACTACAGCTCCACGCATGATAATAGATAGACGAGT
AGGAGTATCTGTTTGTGTTTTTTGCATTCCGGTTACTCTTTTTCCCTTCTTGTTTGCTCACGCTCACTGCCTTGCATGAA
ACG------GGAACGCGCGCGCGCACGCAGGGTATTACAACGGACCGCCGGTGATGGCGCCGCCGCAGTACGCCCCGCCG
CCGAG---------------------------------------------------------------------------
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>chr3D_224
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-----TCACAGTTCTGCACCACGCGTCACTCCAGTGTGCCTGCTGGAAGTTCAGCATAGCATAGACACCGAAAACTCTAG
AGAAGGGCCATCTGGTTTGCTACGAATCGTGTGAAGTGAAAGAAACAAAGAATTCAGCATCTGCACACTGTTCGCTCATT
---ATCGGTTCGTGCACGTTCCCGAGAGCCAATGAACCTGTATTCTCCTCGTCTCGCCATCTCGAGTTGGCGACGTCGGG
TTACTTGCCTCTTCCCAACGACCAAGAAGAAGAAGATC-----------GTAGCTCGCATTGCATGCAGAGGTTATAGAT
TCCC----AGCGTCTCTGGTTTCTCCGTTTCTGATGCTGGTTACAGAGTTGTGCCGTTCACATTACAAGGTGGCGCATTA
GCATCGATCTCTAGCGCTTGTTAGATTACTACTGTAATCAATTGTAAACAGCGACAGCAAGCAGAGATA-GAGTTCGATC
GTATGAGTATGATGATGCCCCATTTGCTTGAAGTTAAAGGCAGGAATAATCCACGGAAGGTCAAAAAGGAAGGGCGCAAT
TAATTAAAAGGAAGCAAAGAGATAATCA---GATAACGATCG---AGTAGCTTTATTCGTTTCCCCTCGC----TGCCGC
CTAGGATCGATGAGGTGCCGACAGCGGCGCACAGAATGTTTTAGAAGCACCACTAAAAGTGCAATCCACGGCAAAAATAT
ACGAG----------TTGATCTTCGGTTTGCAGCCGCTATTTATACTCTCTCCAGGCCCAACACCGGCCGGTCCACTTCT
CCCTCGTAAGGCAGCAGCCATCTGCAACTAGGGTTCATAACTTCATATATAGCCAGTGACCAACATGAGTGATCGAAGGT
ACGGGTACTCGTACCCACACAACCAAGGTAACTACTACTTGT-----------TCCACGCATGATG--------------
----------GATTGTGTGTCTTGCATTCCATTTCCTTTC--TCCCTTCTTGTTTGCTCACGCTCACCGCCTTGCATGAA
ACTGAAACTGGAACGCGCGCGCACATGCAGGGTATTACAACGGACCACCGGTGATGGCGCCGCCGCAGTACGCCCCGCCG
CCGAGACGGCAGACGGGCTTCCTCGAAGGATGGTACGTAATAGAAAGCTAAGAACCTGACGGTTTTTCTT----TCCTCT
GCGTAAACTATGTGGGCAGTGCTAATCTGAGGTGCTCTGTGTTCGTGCTTGCATGCCCTGCAAAACTACGTACGAACAGC
CTGGCTGCTCTGTGCTGCTGCTGCCTCGTCGACGAGTGCTGCTGCGACCCGTCCATCATATTCGTGAGCTGATCGAAACA
CGTACGCTATCCAGACGACGGCCGACCGACCGACCGACCGACGAACCATCCGAGCCGAGCTACGTACCTAACGTACTGGT
AGTAGTACATGTGCGATTTATATATGCGTGTCGTGTGTATGTGTGCTTCCCTTGAGCTGTTGCTTTCAGCTATAGCTATA
-CATATGCTCCTAGAGGCCTAGACCAAAGTAGAACTGCAGAAAGAATAGCCAGCCCGTCCTGCCGTTCGGTTCAGCTCTC
CAGCGGCACGACGGGTGGGTGGTGTATGTATGCAT----------------------------------GTATCTGATGT
GAGTCTACGAATAATATGATGAGGAAAAAGAGAAGTTCAGCACCTTCTATGATGTGAGCCTATGACATCCTGAATTTTAC
AAAAATAGCATTATCAATATCAGGTTCACCGCTCACAGGAGATGCACCGGTAAGGTAGAAAGTCAAAACTGAGCGCCATG
ACGGACGCAAACACACGCCCCTTCCAGAGAATTTAATCGCGCCGAGCCGAGTCAAACAGAGTGAAGCGGAACCTGCAGGA
AGCGAAGAGGCACAT-GGTTCCAACAAGAACCTGAAGAGACCTTTGTCGGAAAAAAAAAGAACCTGAAGAGACAGGCTAA
CGTTAAGGCTAGCACTAGCAGTGTGCGCAATCTGTGGCAGGACTCGCCTCTCCA---------GTTGCGCGGGGAGTGGC
GGCCCGGAGGCGGAATCGGTG-----GCGATCCACGGAGAATATGTGCAGCGGCGGCTGGGCGTGGACAAAAGGCATCGT
GCTCGTCTTCTGGGCGCGGGGTCTGAGGCC----------------CCTCCAGGCTCCAGCAACCGCAAGAGCTA-----
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>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------------S-------
S-----S--S----S----S------S-------S-S-------S----S------------S----SS--SS-------
---------------S----SSSSSS------------S--------------------S-SS-S-S-------------
---------S---S------------------S------------------------S----------------------
--------S----------------------SS-------------------S---------S-S-SSSS----SSS-SS
SSSS--S-S-SS-SS-SSSSSS-S----------------S-----------------S------------S--------
----S--------S--------------------------------------------S---------------------
-------SSSSS-S--------------S---------------------------------------------------
--------------------------S---------------------S---------------------------S---
------S-------S-----------------------------------------------------------------
--------------------------S-SSS-------------------------------------------------
-----------------------------------------S------S-------------------------------
----------S--S----------------------------------S---S---S---S-------------------
S-SSSS--------------------S-----------------------------------------------------
---------------------------------------S--------------------------------------S-
--------S---------------------------S----S--------------------------------------
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-----------------S------------------------S-------S-------------------SSSS------
----------------------------------------------------------SS----------------S---
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-------SS--------------------S--------------------------------------------------
----------------------------------------------------------------------------S---
S-------S--------------S--S-----------------------------------------------------
-------------------------S---SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----------
--------------S----------------S------S-----------------------------------------
-------S-----------------------------------------------------------------S------
---S-----------------S-----------S------S----S-S------------------------S-S-----
---------------S-----S-------------------SSSS-----------------------------------
----------------S-S-----------------------SS--SSSS-SSSSSSSSSSSS-----------------
---------------------SSSSS----------S------------------------S---------S------S-
--S--------S-SSSSSS-SSS-SS-SSSSSSSSSSSSSSSSSSS-----------------------------SSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_353
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-------------TGGTTGCTACGAATCGTGCA-----------------------------------------------
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>reverse_2288
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-----------------------------------------------TGGTTTCGTCTCTCCGGTTG-------------
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