>input_sequence_86494
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----------------------ATGGAGCTCCCGGCCGCCTCCGTCCCCCACTCCGTCTGCACGGCGTACAGCAACCTCG
TCACGACGACGGCGGCGGCGGCGCAGCATCGGCGCACGCGGCGGCCGCCGCC---GCGCCCGCGGCAGGGCAGGTGCTGC
GCCATGCTGAAGCAGCACAAGACGAGGCTGTACATCCTCGGGCGGTGCGTGTCCATGCTCCTCTGCTGGCACGACCGCGA
CGACTCCGACTGA-------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G122100
ATCGAACCAATAAGCTTGAGTGCCTCGCCTTCCTGGCCCCCACCAAGAAAAGGCTGACACAAACATTAGTCACCACAGTG
GAGCAAATGGACTCAGATGAAGGGCAATAGTTCTTTTATTCAAATTGGTTAGAGCAATGGCGAAGCTTGCACCAAAAAGC
TGGGCGGGCCGGCAATAAGAGATTGTTACTAGCTAGTATTTTATGACTCATGGTCTGGCTATAAATGCGAGGAGGAGCTC
CAGAACTGAGCAGGACATGGCTCATTCGGCCTTGCCTAAGCTCCGCCAGTGGGTTGGAGGTGGGCAAATAACCAACAACA
TCACGTAGCAAAGTCGAATAAGTTTCTCTAGATCAGACAGGGTTTGGGGCCTGGTTATCAGATAGTGTTTATAGTTAGGC
TCACGTGTTAGGTTGCTCATAGTAGGGCGTATCATATACTAGTATCATGCACATAAGAGTAATGTATGTATACAATACCT
GGCTCTATAATTCATAGTAATATTTCAGTATCTTTCCATGAAAAACTGTTAGTATTTTACATGACCTTATTTATTGTTTT
GAATAATCTGTAGTAGCCCATCTTCTCTCAATTAATGTCATGTGATGGTAACATTACGTTTAGTTGCCATTGCATAAGGT
T-GCATGACACTAAAAATAATAGTACCCCCTTGCGAGAGAT------TTTCTTTTTTAGGGGGCGAGAGATTTTTATATG
AGAG------------------------------------------AAAAACAACATGCGAGAGGGCAAAATCGTCAGTG
CCCAGTAACCATCCAGTCCACCGAATCCGGCCCACCGCCACGTGCTGACATGCACCCCACCTCACTAGGGCCCGGCCCTG
GACCAGCT----------GATCCATCCACCCGACCGGGCCTATTTAACTACCGGCATCGATCTTTCTTCATCGCTCTCCT
CCAGACCAAGACTCCCCGTGCCAGTGCCTCTCAAAACTCT--CTACACGTGTCGAAGCATCCCCGCGTTCGTTAGGCCGC
GACGCCCGCTCGT-CTGAAAACATGGAGCTCCCGGCCGCCTCCGTCCCCCACTCCGTCTGCACGGCGTACAGCAACCTCG
TCACGACGACGGCGGCGGCGGCGCAGCATCGGCGCACGCGGCGGCCGCCGCC---GCGCCCGCGGCAGGGCAGGTGCTGC
GCCATGCTGAAGCAGCACAAGACGAGGCTGTACATCCTCGGGCGGTGCGTGTCCATGCTCCTCTGCTGGCACGACCGCGA
CGACTCCGACTGAGCCCCTCCGGCTATGTCTGGTGCAGGCCTTTTTTTTC------------------TTCTTGATTTTG
TCATTGTTCTTTTGTGTGTGAACAGAAGCGTCATACAC----ACTCGAAGAGAGATGCTGGAAATATTGGCTGGTTAGTT
TGGCAGATGATGGAATGAAACCAAGCAAATGTACATGAAAA-AGTTTCTTTTATAAGTATATGATTATATTGCCATTTCC
C----CGTTA--------------------------CTAAGAGAAAACTGTGATATCTATATGCTTTTTTTAACTGAAAT
GTCTATATGCTGAATGAACAAAAACTTATTACTTGTTCTTGTAGTAATCAGGGCCTAATTTGATACT--TGTATAGGGCC
TTTAGTTTCCCGGTTACGGCCTTGCTCTCGATCGTGTGTGTAGACGGCCTCAAGGTGGACGCCCATGTCGCGGCGGCACA
GGGGGCACGTCGTCACCGTCTCGAACCACCGCGCAAGGCAGCGGACGAGGAAGGTGTGTGAGCATGGCAGCCTCACGGTG
CCGTCGTCGTCGCCGCCGCCCTCAGCAGCCGCGATATCCTGATCCTGAGTTCCTGACATATGCAGCAGCAAC-AGCGGTC
CGCCACGGACAGCCCACACTGGGCGGTGGCCTCCCGGCACGCGAGCGCCAGCAGCCTGGCCTCGCTG---------CAGA
CGGCCCGCACGAAGACGGCCAGGGAAAACTCGAGGGTGAAGCGCGGCGCGTCGCCGCCGTGATCC---TCCTCGCCGAGC
CGGGCCCTCTCCGTGATGGTTCCGGCGAGGTCGTCGGGCAGGAAGCCGCCGTCCCAGTGGGCGGCGGCGAGGTCGAAGTC
GCGGAGGGCCGGCGTCCGCGTGAGCATCCGGTGGATCTCGTCGCGGCAGGCCGAGCGGCTCCGGAAGAAGGCCCTGGGGC
CGTCGAGCAGGAACGTGCGGTCGAAGCTCCGGGGCGCGTCCTCGTCGTGCTGGGCCTGGAGGCGGTGGAGGGGCTGGCTG
GTGCATGAAGAACCCCCCAGCTCCAGCAGCCCGTAGACGAC
>chr3A_542
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-------------------------------------------------------------TGACCTAATTTATTGTTTT
GAATAATCTATAATAGCCCATCTTTTCT-AAATAATGTCATGTAACGTTAACATTACGTTTAGTTGCCATTGCATAAGGT
TTGCATGACACAGAAAGTAATAGTACCATATAGTGAGAGAGTTTATATTTTTTTTTGAGGGGGCCAGAGATTTTTATAAG
AAAAACAGCATGTTTTTTTTCGACAAAGAAAAACAGCATGTGTGCCAAAAAAAACATGCGAGAGGCCAAAATCGTCAGTG
CCCAGTCACCATCCAGTTCACCGAATCCGGCCCACCGCCACGTGCTGACATGCACCCCACCT---------------CAC
GGGGGCCCGGCCCTGGAAGATCCATCCACCCTACCGGGCCTATTTAACCACCGGCATCGATCTCTCTTCATCGCTCTCCT
CCAGACCCAGACTCCCAGCACCAGTCCATCTCAAAACTCTCTCTACACGTGTCCACGCATCCTCGCGTTCGTTAGGCCGC
GACGCCCGCTCGT-CTCAAAACATGGAGCTCCCGGCCGCCTCCGTCCCCCACTCCGTCTGCACGGCGTACAGCAACCTCG
TCACGACGACGGCGGCG------CAGCATCGGCGCTCCCGGCCGCCGCCGCCGCGGCGCCCGCGGCAGGGCAGCTGCTGC
GCCATGCTGAAGCAGCACAAGACGAGGCTGTACATCCTCGGGCGGTGCGTCTCCATGCTCCTCTGCTGGCACGACCGCGA
CGACTCCGACTGAGCCCCTCCGGCTATGCTTGGTGCAGGCCTTTTTTCTT------------------TTCTTGTTC---
-----------TTTTGTGTGAACACAAACGTCATATATACATACTCGAAGAGAGATGATGAAAGTGTTGGCTGGTTAGTT
TGGCAGATTATGGAATGGAACCAAGCAAATGTACATGAAAA-AGTTTCTTCTATAAGTATATGATTACATTGCCATTTCC
CGGCCCGTTACTCCCTTTTTAGCATTTCCAATAATTATGAGAGAAATCTGTAATATCTATATGCTTTTTTTAGCTGAAAT
GTCTATATGCTGAATGGGCAAAAACTTATTACTTGTTCTTTTAGCAATCAGGGTCCAATTTTATACTCCTGTATATGGCC
TTTAGTTTCTCGGCCACGGCCTTGCTCTC----GTGTGCGTAGGCGGCCTCAACGTGGACGACCATGTCGCGGCGGCACA
GGGGGCACGTCGTCACCTTCTCGAACCACCGCGCAAGGCAGCGGACGTGGAAGGTGTGTGAGCACGGCAGCCTCAAGTTG
CCGTCGTCGTTGCCGCC---CTCAGCAGCCGCGGTATCCTGATCCTGA--------CATATGCAGCAGCAAATAGCGGTC
CGCCACGGACAGCCCACATTGGGCGGCGGCCTCCCTGCACGCGAGCGCCAGCAGCT---------TG---------CAGA
CGGCCCGCACGAAGACGGTCAGGGACAGGTCGAGGCTGAAGCGCGGCGCGTCGCCGCCGTGATGGCCTTCCTCGTCGAGC
CGGGCCCTCTCCGTGATGGTTCCGGCAAGGTCGTCGGGTAAGAAGCCGCCGTCCCAGTTGGTGGCGGCGAGGTCGAAGCC
GCGGAGGGCCGGCGTCCGCGTGAGCATCCAGTGGATCTCGTCGCGGCAGGCCGAGCGGCTCCG-----------------
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>chr3B_719
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-----------------------------------------------AAAACAACATGCGCGAGGGCAAAATCGTCACTG
CACAGTCACCATCCAGTCCACCGAATCCGGCCCACCGCCACGTGCTGACATGCACCCCACCT---------------CTG
GACCAGCT----------GATCCATCCACCCGACCGGGCCTATTTAACTACCGGCATCGATCATTCTTCATCGCTCTCCT
CC-------------CAGCACCAGTCCATCTCAGAACTCTGTCTACACGTCTCGACGTATCCTCGCGTTCGTTAGGCCGC
GACGCCCCGCTCGCCTCAAAACATGGAGCTCCCGGCCGCCTCCGTCCCCCACTCCGTCCGCACGGCGTACAGCAACCTCG
TCACGACGACGGCGGCGC---CGCAGCATAGGCGCTCCCGGCGG---------------CCGCGGCAGGGCAGGTGCTGC
GCCATGCTGAAGCAGCACAAGACGAGGCTGTACATCCTGGGGCGGTGCGTGTCCATGCTCCTCTGCTGGCACGACCGCGA
CGACTCCGACTGAGCCCCTCCGGCTATGCTTGGTGCAGGCCTTTTTTTTTTCCTTGTTGATTTTTTTGTTCTTCTTC---
-----------TTTTGTGTGAACACAAACGTCATATATACATACTCGAAGAGAGATGATGAAAGTGTTGGCTGGTTAGTT
TGGCAGATTATGGAGTGAAATGAATCAAATGTACATGAAAATAGTTTCTTTTGTAAGTATATGATTACATTGCCATTTCC
C----CGTCACTCCCCTTTTAGCATTTCCAATAATTCTGAGAGAAAACTGTAATATCTATATGCTTTTTT-AGCTGAAAT
GTCTATATGCTGAATGAACAAGAACTTATTACTTGTTCTTTTAGCAATCAGGGTCCAATCTTATACT--TGTATAGGGCC
TTTAGTTTCTCGGTTACGGCCTTGCTCTCGATCGTGTGTGTAGACGGCCTCAAGGTGGACGACCATGTCACGGCGGCACA
GGGGGCACGTCGTCACCGCCTCGAACCACCGCGCAAGCCAGCGGACGTGGAACGTGTGTGAGCATGGCAGCCTCACGGTG
CCTTCGTCGTCGCCGCCGCCCTCAGCAGCCGCGATATCCTGATCCTGA--------CATATGCAGCAGCAGC-AGCGGTC
CGCCACGGACAGCCCACACTGGGCGGTGGCCTCCCTGCACGCGAGCGCCTGCAGCT---------TGGCCTCGCTGCAGA
CGGCCCGCACGAAGACGGTCAGGGACAGGTCGAGGCTGAAGCGCGGCGCGTTGCCGCCGTGATGGCCTTCCTCGTCGAGC
CGGGCCCTCCCCGTGATGGTTCCGGCGAGGTCGTCGGGCAGGAAGCCGCCGTCCCAGTTGGCGGCGGCGAGGTCGAAGTC
GCGGAGGGCCGGCGTCCGCGTGAGCATCTGGTTGATCCCGTCGCGGCAGGCCGAGCGGCTCCGGAAGAAGGTCCTGGGGT
CGTTGAGCAGGAACGTGCGGTCGAAGCTCCGGGGCGCGTCCTCATCGTACTGGACCTGGAGGTGGTGGAGGGGCCGGCTG
GTGCGT---GAGCCCCCCAGCTCCAGCAGCTCGTAGACGAC
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------S------------
---------S--S-----------S---S--S-----------S-S-S--------------------------------
-----------SS---S----------SSS-S-S------S---------S-----S-------S-------------S-
-S-S----------------------------------------------------------------------------
------S-------------------------------------------------------SSSSSSSSSSSSSSS---
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-------S--------S-SS-----S-S---------------------------S------S-----------------
----------------S---------------------------------------------------------------
-----------------SSSS--------------S-S------------------------------------------
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----------------------------SS-------------------S------------------------S-SSSS
SSSSSSSSSSS--S----------S--S-------S-S-------------------S--S--S-S--------------
--------S----------------------------------------------------------S------------
--------------------------------------S------------S--------------------S-------
----------------------------------------S---S--------S-S-----S------------------
---------S---------------------------------------------------S------------------
-----------------------------------------------S--------------------------------
------------------------------------------------SSSSSSSS------------------------
-----------------------------------S-------------------SSSSSSSSSS---------------
------------------S------S-SS------S---------------------------SS---------S-----
----------------------------------------------------------S---------------------
-----------------------------------------------------------------------S-------S
---S---------------------------------------S----S----S--------S-----------S-----
----S-SSS--S------------------S----------
>forward_681
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---------------------AGTACCCCCTTGCGAGAGAT---------------------------------------
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>reverse_1808
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-----------------------------------------------AGGAAGGTGTGTGAGCATGG-------------
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