>input_sequence_66903
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-----------------------------------------------------------------ATGGAGTTATCGATG
AAGCTC-----ATGATCGACACCAAGTCCCAGAAGGTGTGCTTCGCCGAGGCCGGAAGCGACGTCCTGGAGTTCCTTGCC
GGCCTCCTGTACCTGCCGCTGGGCACCGCCCTCGGCCTACTGACCAAGGAGCGCATGGTTGGCTGCATCGGCAACGTGCT
CGGCAGCGTGGAGAAGCTAGGTGTGAACTACAAGAGCAAGGAGCGGTGCCTTAGCCCGGCCGTCACCGCCGCCACGCTCC
CCCTCCTCCAGCAGCTGTTGGGAATACAACTCAACAACGGTATTGACACCTTCTACACATGTGAAGGCCGTAACACTGGC
GCCTACTCAGGCGTAGGCACTAGCTGTGGATATCTATCGGTGATACCTAACAGAAGCTGCCCTACTTGCCGATGTTATAT
GACGAAGGCTATGACGCTCGCCGCTGAAACCAACCGGACCTTGGTGGCCGCGGCGCTGCCGACGACCACGCCGCTACCTG
TGGCCATGTACACTGTCGGGGACGACTTGACAGTGACTTCAGCCTCTTTTTTTGCGACGATCTCGCTGTTGGGCATCAAG
GACCTCAGCGCCTTACAAGAAAAGACAGTGAAGATCGGCAAGGAAGAGGTACGTAGTGCTCTAGTTTCTTTGAAGTCTTT
GAACTTTTAGGTGGT-GTTTTGCTCAAGTTGATCGGCTGGTGATTTAGCTTTTGTTTTGTGTGTGTTTGTGTACTTATGG
A-TTTTTTTAATGTAGGCACTAGAGATATTTGCTGCTTCCCTCAAGTCCAAGACCGTCCTGTCGGATGTCTTTTTGCCGA
AGAAGAATGCTCGCCTCAAGAGGGAACATCCTGACGGTGTCATTCATGTATGA---------------------------
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>chr3D_1_TraesCS3D01G131700
TGCACGATGAGAACGGTTGTTGAGGAAGAGGTTGTGAACGACAAGCCAAAGGAAGTAAGTAGTCCCATCAGGCTTCATGA
TGATGTCGAGGATTTCCTAGGAGATGGGTG--TACACCTAGTTGATGATGCAAGAGCCGATAGATATATAGTGAAGGATG
GCGAGGCGCATACAGCCGTCGGCGGAGCATTCGATGTGGTCGGTGAGCCTGTATGTGCAGAAGACTGACATGAATAGGGA
GTACCGCATATTATAGTTGGATTAATGGAGGTCGGGGATGACAGGAACATGTTGCTGGATGGGCACATGTTGGGTCGCAA
GGGTAGAGGGGGAGGGTTGGTGTTGGCGCCGAAGGAGATGGAAGATGCGCTGTCCATGGTAAGGACATGTGGAAGCGAGG
AAACGAGTATCACAATAATTAGAAAGAGGTTGAAACCATGTAAGAGTTTATACTGGGAAAAATATTATATATACCCATGT
ACACGAGTGAGAAGTACCTAACTAACCTAGCTAGGAACGGGTTATATCATATGGAGTAGGACAACAACACAATCATGCAC
TAACAACACTATCATCAGTATCTAACATGTATCCATACAAGCACATTGAAGTACTCTTACAATCTCCGCCCCAGTGTAAA
CTCTTACAATCTAAACCATTTAATA-------------------------------------------------------
---------------------------------------------GTATATATGCATTACACAAAGCATCCATTTATATG
TAATAAATGAAATATAAAATTTCCAACAAATCTTG-TAGTTAAAAAATGTTTATCTAGTGGTATTGGTTGCATGGTTTGT
ACATAGCTTGTGGGTTACATTTGATATTATCCACTAATCTGAAATTGTCTTCTCACACGGAGATCTCTTTGCGTTACAGT
TTAGAAAGATGGTATTGCTCCATCTGCTTTAATTCTTGGAAG--TCAACTTCTTTTCGATGATACAGAAATGCATGTTTT
CTTGTCAATTAACATTGCTCATTCAGAAGGTTTGAATTGGACTACAACAGAATAGCAAGCCTACTATGGAGTTATCGATG
AAGCTC-----ATGATCGACACCAAGTCCCAGAAGGTGTGCTTCGCCGAGGCCGGAAGCGACGTCCTGGAGTTCCTTGCC
GGCCTCCTGTACCTGCCGCTGGGCACCGCCCTCGGCCTACTGACCAAGGAGCGCATGGTTGGCTGCATCGGCAACGTGCT
CGGCAGCGTGGAGAAGCTAGGTGTGAACTACAAGAGCAAGGAGCGGTGCCTTAGCCCGGCCGTCACCGCCGCCACGCTCC
CCCTCCTCCAGCAGCTGTTGGGAATACAACTCAACAACGGTATTGACACCTTCTACACATGTGAAGGCCGTAACACTGGC
GCCTACTCAGGCGTAGGCACTAGCTGTGGATATCTATCGGTGATACCTAACAGAAGCTGCCCTACTTGCCGATGTTATAT
GACGAAGGCTATGACGCTCGCCGCTGAAACCAACCGGACCTTGGTGGCCGCGGCGCTGCCGACGACCACGCCGCTACCTG
TGGCCATGTACACTGTCGGGGACGACTTGACAGTGACTTCAGCCTCTTTTTTTGCGACGATCTCGCTGTTGGGCATCAAG
GACCTCAGCGCCTTACAAGAAAAGACAGTGAAGATCGGCAAGGAAGAGGTACGTAGTGCTCTAGTTTCTTTGAAGTCTTT
GAACTTTTAGGTGGT-GTTTTGCTCAAGTTGATCGGCTGGTGATTTAGCTTTTGTTTTGTGTGTGTTTGTGTACTTATGG
A-TTTTTTTAATGTAGGCACTAGAGATATTTGCTGCTTCCCTCAAGTCCAAGACCGTCCTGTCGGATGTCTTTTTGCCGA
AGAAGAATGCTCGCCTCAAGAGGGAACATCCTGACGGTGTCATTCATGTATGACTCGGTGCTTGCTATTTTAGAATTCTG
GATACCT----TTTTCGATATCATATTTACGAGGAAGGAGATGTATTTGAGTGACTTGGTACTAGTTTAACTTACTACCA
TAAGTTA--------TTTATAAAGTTAACTTCAAATTTTACTCCTTAAGTGCCAATCTGGG-TATCTCTTGCTCTATTTG
AGGAGTATAAAAATTGTCCTAGTTTCCTCCATAGTTAAGT--------------------------AAGTTTTGCATCAT
TCTATCAAGTGGGGCCCATTGTTAATTGGACATAGATAGATGAATCAGCCCTCACATCGGCGAATGATTCGTGCAAAATG
CGTCTCACGTGATAAATGGGGCCCCAACTTGGGCCGAACCATGTCACCACACCTGAGCCAGCCAGTCCCCTCTCCCTCA-
--------ACGCGAGGTAGGGATTTGGAAGCGACGGTGGTGACAACAGCTCGGTGGTGTGTTAGAGCAACTACAACCAGG
CGATTCAAACGGACGCGCGCTTTGTCCGCTTTTCGTTCGTCTGGATCGGTGAGGCGGACGGGCGCGTCCGCTTTTTAAAA
TGGGTTAGCAGATGCATGCCT--------------ATATCAGCCCGCGTACAAAGAAAAAAAA-----GATAAGCATGTG
GCTGAAAATAAACATATAATAACACATAATTAAACATAAATGACCGGTCAA-----------AGTTCACTTAAACATTAG
TTAAACAATGAAAAAACTCCGGGCCATACACTGCCCTAGGCGTCCGCCTTACCCTTC-CCTTGCCGTTGTTGTCGCCGTC
AGGGAGGTCAATGAAAACGGGAGGTGGACCAGCCCACTCGAATGCGACTTGATAGGCTGCCAAGGCTGCCTCCTCCGGT-
-----------GGCATTGCGGCGAGGCGGGCGCGCTCCTCCTCCTC------AACGGGCAGTGTCTCCTTGT--------
----CCTGCTCCCAACGCATCTGCCGCTCATCGCCGGTCGCCTCCTCGGCAAGCCAATGCGCCTTCTAGCGCTCAAGGTG
GGCCTCCTCCTTCTCTAGCATCGCAGCGTAGTGGACGGGAGG
>chr3A_1
TGCACGATGAGAACGGTTGTTGAGGAAGAGGTTGTGAACGACAAGCCAGAGGAAGTAAGTAGTCTCATCAGGCTTCATGA
TGATGTCGAGGATTTCCTAGGAGATGGGTGTATACACCTAGTTGATGATGCAAGAGTTGATAGATATATAGTGAAGGACG
ACGAGGCGCATACGGCCGTCGACGGAGCATTCGACGTGGTCGGTGAGTC-------------------------------
------CATATTGTAGTTGGATTAATGGAGGTCAAGGACGACAGGAGCATGTTGCTGGATGGGCACATGTTGGGTTGCAA
GGGTAGAGGGGGAGGGTTGGTGTTGGCGCCGAAGGAGATGGAAGATGCGTTGTCCATGGTTAGCACGTGTGGAAGCGAGG
AAACGAGTATCACAATAATTAGAAAGAGGTTGAAACCATGTAAGAGTTTATACTAGGGAAAATATTATATATACCCATCT
ACACGAGTGAGA-----CTAACTAACCTAGCTAGGAATGGCTTAGATCATATGGACTAGGACAACAACACAATCACGCAC
TAACAACACTAG---CAGTATCAAACATGTATCCATACAAGCACGTTGAAAAACTCTTACAATCCCCGCCCCAGTCTAAA
CTCTTACAATCTAAACCATTTAATA-------------------------------------------------------
---------------------------------------------GTATATATGCATTACA----GCATCCATTTATATG
TAATAAATGAAATATAAAATTTCCAACAAATCTTG-TAGTTAAAAAATGTTTATCTAGTGGTATTGGTTGCGTGGTTTGT
ACATAGCCTGTGGGTTACATTTGATATTATCCACTAATCTGAAATTGTCTGCTCACACGGAGATCTCTTTGTGCTACAGT
TTAGAAAGATGGTATTGCTCCACCTGCTTTAATTCTTGGAAAAGTTAACTTCTTTTCGATGATACAGAAATGCATGTTTT
CTTGTCAATTAACGTTGCTCATTTAGAAGGGTTGAATTTAACTACAACAGAATAGCACGCCTACTATGGAGTTGTCGATG
AAGCTCATGTCATGATCGACACCAAGGCCCAGAAGGTGTGCTTCGCCGAGGATGGAAGCGACGTCGTGGAGTTCCTCGCG
GGCCTCCTGTCCCTGCCGCTGGGCACCGTAGTCGACCTACTGACCAAGGAGCGCATGGTCGGCTGGATCGGCAACGTGCT
CGGCAGCGTGGAGAAGCTAGATGCGAACTACAAGAGCAAGGAGTTGCGCCTTAGCCCAGCCGTCACCCCGGCCACGATCC
CCCTCCTAAAGCAGCTGTTGGGCACACAACTCAGCAACGGTACTGACACCTTCTACACATGTGAAGGCCGTAAAACTGGC
GCCTACCCAGGCGTAGGCACTAGCTGTGGATATCTATCGGTGATACGTAACAGAGTCTGCCCTAGATGCAACTGTTATAT
GCACAGGGCTATGACGCTCGCCGCCGAAACGAATGGGACCCTGGTGGCCGCGGCACCATCGACGACCACGCCGTTACCTG
TGGGCATGTACACTGTCGGGGATGAC------------------------------------------------------
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>chr3B_1
TGCATGATGAGAACGGTTGTTGAGGAAGAGGTTGTGAACGACAAGCTAGAGGAAGTACGTAGTCTCATCAGGCTTCATGA
TGATGTCGAGGATTTCCTAGGAGATGGG--TATACACCTAGTTGATGATGCAAGAGTTGATAGATATATAATGAATGACG
GTGAGGCGCATACGGTCATCGACAGAGCATTCGACGTGGTCGGTGAGCCCGTATGTGCAGAAGACTGACATGAATAGGGA
GTACCACATATTGTAGTTGGATTAATGGAGGTCAAGGGCAACATGAACATGTTGCTGGATGGGCACATGTTGGATCGCAA
GGGTAGAGGGGGAGGGTTGGTGTTGGCGCCGAAGGAGATGGAAGATGCGTTGTCCATGGTAAGCACGTGTGGAAGCGAGG
AAACGAGTATCACAATAATTAGAAAGAGGTTGATACTATGTAAGAGTTTATACTGGGAAAAATATTATATATACCCATGT
ACATGAGTGAGAAGTACCTAACTAACCTAGCTAGGAACGGGTTAGATCATATGGACTAGGACAACAACACAATCATGCAC
TAACAACACTAG---CATTATCCAACAGGTATTCATACAAGCACGTTGAAAAACTCTTAAAATCTCAGCCCCAGTCTAAA
CTCTTACAATCTAAACCATTTAATACTCCTTCCGTCCCAAAAAATAAATGTCTTGACCTTAGTACAACTTTGTACGAAAG
CTAGTACTATAAAGTTGAGACACTTATTTTGGGACGGAGGAAGTAGTATATATGCATTACACAAAGCATCCATTTACATG
TAATAAATGAAATATAAAATTTCCAACAAATCTTGGTAGTTAAAAAATGTTTATCTAGTGGTATTGGTTGGGTGATTTGT
ACGTAGCTTGTGGGTTACATTTCATATTATCCACTAATCTGAAATTTTCTGCTCACACGTAGATCTCTTTGTGTTACAGT
TTAGAAAGATGGTATTGCTCCATCTGCTTTAATTCTTGGAAAAATCAACTTCTTTTCGATGATACAGAGATGCATGTTTT
CTTGTTAATTAACGTTGCTCACTCAGAAGGTTTGAATTGAACTACAACAGAATAGCACGCCTACTATGGAGTTATCGATG
AAGCTC-----ATGATCGACACCAAGTCTCAGAAGGTGTGCTTTGCCGAGGCCGGAAGCGACGTCGTGGAGTTCCTCACC
GGCCTCCTGTCCCTGCCGCTGGGCACCGCCCTCGACCTACTGACCAAGGAGCGCTTGGTCGGCAGCATCAGCAACGTGCT
CAACAGCGTGGAGAAGCTAGATGCGAACTACAAGAGCAAGATGCGGTGCCTTAGCCCGGCCGTCAACCCCGCCGCGCTCC
CCCTCCTACAGCAGCTGTTGGACACACAACTCAGCAACGGTGACAC------CTACACATGTGGAGC-------------
-----------------------CTGTGGATATCTATCGGCGATAGATGACAGAGTCTGCCCTAGATGCAAATGTTATAT
GCGCAGGGCTATGACGGTCGCCGCCGGAAAAAACGG---------------------------GACCACGCCGGTACCTG
TGGGCATGTACACTGTCGGGGATGACCTGTCCGTGACTTCGGCCTCTTTTTTCGCGACGATCTCGCTGTTGGGCATCAAG
GATCTCAGCGCCTTGCAGGAAAAGACAGTGAAGATCGGCAAGGAAGAGGTACGCAGTGCTCTAATTTCTTTAGAGTCTTT
GAACTTTTAAGTGGTGGTTTTGCTCAAGTTG--------GTGATTTAC---TTTTTTTATGTGTGTTTGTGTATGTATGG
A-TTCTTTTAATGTAGGCACTAGAGATATTTGCTGCTTCCCTCAAGTCCAAGACCGTCCTGTCGGATGTCTTTCTACCGA
AGAAGAATGCTCGCCTCAAGAGAGAACATCCCGAGGGAGTCATTCACATATGACTTGGTGCTCCCTATTTTAGAATTCCA
AATACCTTCTGTTTTCGATATCATATTTATGAGGAAGGAGTCATATGTGAGTGACTTGGAACTACTTTCACTTACTGCCA
TAAGTTATTC----------ATAGTGAATTCCAAATTTTACTCCCTAAGTGTCAATTTGGGATATTTCTTGCCCTATTTG
AGGAGTATAAAAATTGTCCTAGTTTATACCATAGTTAAGCAAGTT-----------------------------------
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>chr3A_1514
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-----------------------GACCTGTCTGTGACTTCGGCCTCTTTTTTCGCGACGATCTCGCTGTTGGGCATCAAG
GACCTCAGCGCCTTGCAGGAAAAGACAGTGAAGATCGGCAAGGAAGAGGTACATAGTGCTCTAATTTCTTTTGAGTCT--
GAACTTTTAGGTGGTGGTTTTGCTGAAGTTGATCGGCTGGTGATTTACCTTTTGTTTTGTGTGTGTTTGTGTATGTATGG
ATTTTTTTTAATGTAGGCACTAGAGATATTTGCTGCTTCCCTGAAGTCCAAGACCGTCCTGTCGGATGTCTTTCTGCCGA
AGAAGAATGCTCACCACAAGAGAGAACATCCTGAGGGAGTCATTCATGTATGACTCGGTGCTTGCTGTTTTAGAATTCTA
AATACCT----TTTTCGATATCATATTTATGAGGAAGGAGATGTATTTGAGTGACTTGGTACTTGTTTAACTTACTACCA
TAAGTTAATAAGTTATTTATATAGTGAATTCCAAATTTTACTCCTTAAGTGTCAAGTTGGGATATTTCTTGGTCTATTTG
AGGAGTATAAAAATTGTCCTAGTTTCTTCCATAGTTAAGCAAGTTAGTCTACTTTTATCCATTTTAAAGTTTTGCATCAT
TCTGTCAAGTGGGGCCCATTGTTAATTCGATATAGATAGATGAGTCAGCCCTCACATCGGTGAAGAATTCGTGCAAAATG
CGTCTGACGTGATAAATGGGGCCCCAACTTGGGCCGAACCATGTCACCACACCCGAT----CCAGTCCCCTCTCCCTCGA
GGCCTCTGACGCGAGGTAGGGATTAGGAAGTGGAGGTGGTGACAGCAGCCTGGTGGTGTGTTAGAG--------------
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>chr6B_2305
AGCAACCAAACATGA-----------------------------------------------------------------
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CGATCCAAACGTACGCGTGATTTATCCACTTTTCGTCCTTTTAGGTTGGTGAGGCAAACAGGCGCGTCCGCTCTTTGATT
TGGGTTGGCAGGTGCGGCCAATGGAAGGCAGAGCCATATTTGCCCGCGTGCAAAGAAAAAAATTATATGATAAATATGTG
ACCGAAATTAAACAC--AATAACACATAATTAAACATAAATGACCGGTCAAGCGCCGGTCAAAGTCCACTTACACATCAG
TTAAACAATAAAAAAA-TCCAGGCCACACGCTGCCCTAGGCGTCTGCCTTATCCTTGTCCTTGCCGTCGTTGTCGCCCCC
GGTGAGGTCGATGATGACGGGAGGCAGACCAGCCCACCCGAACGCGGCTTGACAGGCCGCCAGGGTTGCCTCCTTCGGCG
TCTGCGGCGGGGGCATAGTGGTGAGGCAGGTGCGCTCCTCCTCCTCCTCCTCAAGGCGCAGCGCCTCCTCGTCTCGGCGC
AGCTCCTGCTCCCGATGCATCTGCTGCTCACCGTCAGCCGCCTCCTCGGCGAGCCAATGCGTCTTCCAACGCTCTAGGTG
GGCCACTTCCACCTCTAGCGTCGTGGCATAGTGGACGGGAGG
>SNPs
------------------------------------------------S---------------S---------------
--------------------------------------------------------SS--------------------S-
-------------S-------S------------S--------------S------------------------------
-----S------S--------------------SS---S-----------------------------------------
-------------------------------------------------S-------------S--S-------------
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--------------------------------------------S----------S------------------------
-----------SSSS-------S---------------------S-----SS-----------------------S----
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-----------------------------------------------------------------------S--------
--------------------------------------------------S--------------------S--------
-----------------------------------------S--------------------------------------
-------------S-------------------------S-----------------S----------------------
-----------------------------------------------------------------S----------S---
----------S-----------------------S------------------------S--------------------
--------------------S--S-------------------------------------------S------------
-------S--------------S-S--------S--------S------------------------------S------
------S---------------------------------------S-------SS--------SS---SS---------
-SSS-S------------------S-----S---S-----S-------------S-SSS--------------S------
---S------------------S---S--S-S--------S-----------S---------------------------
--------------S--S---------------------------------------------S-------SS-------
-----------------------------------------------S-------------------------SS-----
-------------------------------------------------------------------------S------
----------------------S-----------S--S-----------------------------------------S
S----------------------------S--------------------------------------------------
---------------------S---S--S-S--------------------S----S--------S--------------
--------------------------S------------S----------------------------------------
---S-----------------------S--S------------S----------------S---SS--------------
-----S-----------------------------------------------S--SSSSS-----------------S-
------------------------S-----S-SS----------S----SS---------------SSSSSSSSSSSSSS
----S------S-----S-S---S---S--------S-S-S-S-S-S--------SS--S------------S---S-SS
------S----S---SSS-SS------------------SS--------S------------S----------SS-----
S-S----S------SSS------------------------------------------------S------S----S--
---------S------S---S-----S--S--------------S------S----S----------S---------SS-
S-S------S----SS--------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-S-S------------S----------S----S-S-----S-----
----S-S---SS-------S---SS--S--------------
>forward_636
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--------------------------------------------------------TTACAATCTCCGCCCCAGTG----
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>reverse_2445
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--------------------------------------------ACAGCTCGGTGGTGTGTTAG----------------
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