>input_sequence_77713
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-----ATGGAGGAGGAGGAGGCCGCCGGCGTGAGGAAGCGGAAGCGGGGCGGGGAGGCCGTCCTCGCCGTGTCCGGCGGG
GAGGCGGGGCTCGTCGAGGGAGGCGGCGGCTTCTCGTGGAAGGAGGCGGAGATGGAGGAGGAGGAGGGGGAGGAGTACGA
GGGCATCGCGGAGGAGTCGGTGGAGGAGGTGATGCGGTGGCTGGAGCTGGAGATCTCCTCCTCGCCGGGCAAG------G
GCGGCGACGACGGGTTCGTGACCATCAACGGCAACGAGGAGAGCTGCGGCCCGTCCTTCTCCGCCGCGGCGTCCAGCGTG
ATGGCCTCCGTGGACACGCGCGCCGGCGCGCCGCCGCCCCCGACGGCCATCCCCTGGCCGTGGCCCGAGCCCG---ACGA
CGACACCAAGGCGGCGGCGGCGGCGGCGCACGGCGACGCCGACGCCGACGCGGACATGGCGGAGCTCGTCGACGAGGAGT
GGCTGGTGGAGCTGCTGACCGGCGGCGGGCCCGCGCTGGAGGTAGAGTAG------------------------------
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>chr3D_1_TraesCS3D01G106900
GCTACTGGGCCAGTAACCCAGTAGTCCAGTTGCCCCAGAGAATCCCTTTTCTTGCTCCCTTCCT-----TCCCCGGTGTG
CAGCTTCTTTCCTAAAAAAAAGCAAGAGATAGACGTGCGCGCTCGTC-GACACTCGTGTAAAACCTCTCCCGGAAGGAAC
T--ACCCAAAGCGTATCGCGCCCGTACAGCTCACACGATTAATCCGGAGACACGAATCCTTGTCGTGCAAGACACGAAGG
TGATGGCATGCAGGAGATCGGCGACGGACCTAAACAG-CCCCGCAGCTTTTGGCAACAACAAAGGCGCCAACGAAAACCG
CCGCAGATAGAGCGGA------ACACACGCACCAGCTGGCCACAATCAATACTACGTACGACCCAGAGAAATGCTACCCG
AACCCTCGCGGTCCGTCCGTCCT--C-------CCCGCACGCCACAACAACGGCGGTGCGGTGCGGCGCGGCGCGGGGCT
CTGGGCCTGCCGCGCT----TCCGTCACGAGCGCGAGATTGGGG---------TTCGTTTTTTGGCAAGAGCCCAACTGG
CACCCACCCACGCCCCATCCCCC-ATCCACCACGGGCCGAGCCACCCAGCGACGACGGTCAACAGCACCGACGAACGGAG
AAAAAGAAAGGGTTTGGTTTCTTTCCCCACTCGTCGCGTCCAAAAAGGACGCGGTTCCCCAGAGGAGGAGAGGAGAGGAG
AGGAGAGCGCGCTACGCGCCACGGCCACGCCACGCCGCGCGACGCGAACACGTCCTTTTCCTCGCGTAACGCCT-GAGGC
CGCCGGATGCGCGCCGGGGCGTGCCCCCGAGGCGGATCCGACGGCCCCGCGCCGCGCAGCCACGTCCCGCCCCACGCGCT
ATATAAACCGACGTGGACGCGGCAAGGCGCTCCACCGCGCTATCCTCCACCACGCCTCACTCTCCTA-TCTTCCTCCTCT
GTTTTCAGTTCCACTTGGCGGTTCCCTCCGCTCGCGCAATCTCTCTGAGTCGAGTTCGTGGGAGTGGGG-----TGGTAG
GGTGGATGGAGGAGGAGGAGGCCGCCGGCGTGAGGAAGCGGAAGCGGGGCGGGGAGGCCGTCCTCGCCGTGTCCGGCGGG
GAGGCGGGGCTCGTCGAGGGAGGCGGCGGCTTCTCGTGGAAGGAGGCGGAGATGGAGGAGGAGGAGGGGGAGGAGTACGA
GGGCATCGCGGAGGAGTCGGTGGAGGAGGTGATGCGGTGGCTGGAGCTGGAGATCTCCTCCTCGCCGGGCAAG------G
GCGGCGACGACGGGTTCGTGACCATCAACGGCAACGAGGAGAGCTGCGGCCCGTCCTTCTCCGCCGCGGCGTCCAGCGTG
ATGGCCTCCGTGGACACGCGCGCCGGCGCGCCGCCGCCCCCGACGGCCATCCCCTGGCCGTGGCCCGAGCCCG---ACGA
CGACACCAAGGCGGCGGCGGCGGCGGCGCACGGCGACGCCGACGCCGACGCGGACATGGCGGAGCTCGTCGACGAGGAGT
GGCTGGTGGAGCTGCTGACCGGCGGCGGGCCCGCGCTGGAGGTAGAGTAGGAGTAGGGTAGGGCGCAGCACTCGGGT---
----AGGCAAGCCAAGGCGTAAGCGTACGCGCGTTTCCTTTTTCGGACGGTTGTACAGCGGGCAAGGGAAAAGCCAGGAA
AAAA-AGGGCGGTGGTTCGTTTTGGCGCGGCCCGGATCGGTCGCATCGCTTTCTTCCGCGGCATGGGCGGGCAGCG----
--ATCGGTCCGTTCATCAATGCGGTCGGTCTTGTGTGGT---GCGTTGAGGGGTGAGGTTGCGAGGAAATGGAAATGGTG
CTTGCTGGCGGCACGATCCGGCTGGCTGGCCC-TTGTCGCCTTGCCTGCTTTTGCGTCCGGTTTCTA----------CTA
TGGCTCAGTTGTCCTGTTCCATGCAACCTT--TTTTCTCGCCTTGACTGGCCGATAGCGAGCGGCGTTTGAATTCGATTT
CGATCGTACTCCTCCGTGCGTGC----TTCTTTCTCTTTCGCCAACCTACCCAACCCACATTCAAATAGTAGTGAGAGTT
ACTAGTA--------------GCGTGTACAATCAGTCTGTGGTAACCAATCTCAGAGTCCCGAGGAAAGAAGACCTAACT
ATCTA---------------------------------------AGCCAAGTTGAGTCGTGTTGGTAGGCGTGCGTCTCG
GCCGGAGCATGGACTAATTTCCACCGGTACATGTAGTAGTGCGTTCGTGTCCTTCGTGGTCTGGACGCATTAGATTCC--
---AAGAGGCAACGGTACGAAACAGATGCAGCAGGCAACATGGATAGCCATGAATCCGCGAGCGAGCGAGCACAGAGGA-
GCGCGGGGCTCGGTGGTCTGTGGTTTCAGGCTATCATCAGCTTCCGCGGCAGACTGCATGCAATGCAAGCAGCCTGCTGT
GTGGATAGTGCAGCGCAGCGCAGTGCAGGCTTTACTTACTTTCACTGTAGTGGTTTCAGGCTTCGGGCGCAGGCCGCAGC
ACAGCA----------CATGTCAAAGGCAGCACGTTTCATTAAGCATG----CATGTATGCAGCTACCACCACTATCTAT
CTAGCCAGGTCTAGCCGCCGTGCTTCATGTTTTTCGC
>chr3A_1
GCCACTGGGCCAGTAACCCAGTAGTCCAGTTGCCCCAGAGAAACCCTTTTCTTGCTCGCTTCCTTTCCATCCCCGGTGTG
CAGCTTCTTTCTTAAAAAAAA-CAAGAGATAGACGTGCGCGCTCGTCTGACACTCGTGTAAAACCTCTCCCGGAAGGAAC
TTAACCGAAAGGGTAACGCGCCTGTACAGCTCACAAGGTTAATCTCGACT----AATCCTTGTCGTGCAAGACACGAAGG
TGACGGCATGCAGGAGATCGGCGACGGTCCAAAACAG-CCCCGCAGCTTTTGGCAACACCAAAGGCGCCAACGAAAACCG
CCGCAGATAGAGCAAAACACACACACACACGCCAGCTGGCCACAATCAATAC-----ACGACCCAGAGAAATGCTTCCCG
AACCCCCGCGGTCCGTCCGTCCGTCCGTCGTCTCCCACAAGCC---ACAGCG----------GCTGTGCGGCCTGGGGCT
CTGGGCCTGCTGCGCTCGCCTCCGTCACGAGCGCGAGATTGGGG---------TTCGTTTTCTGGCGAGAGCCCAACTGG
CACCCACCCACGCCCCATCCACC-ATCCACCACGGGCCGAGCCACCGAGCGACGACGGTCAACAGCACCGACGAAGGAAG
AAAGAAAG-------GGTTTCTTTCCCCACCCGTCGCGTCCAAAAAAGCCGCGGTTCCCC------------------AG
GGGAGAGCGCGCTACGCGCCAC----ACGCCACGCAG-----CGCGAACACGTCCTTTTCCTCGCGTAACGCCTCGAGGC
CGCCGGATGCGC----------GCCCCCGAGGCGGATCCGACGGCCCCGCGCCGCGCAGCGACGTCCCGCCCCCCGCCCT
ATATAAACCCACGTGGACGCTCCACCGCGCT------CGCTATCCACCACCACGCCTCACTCCCCTCCTCCTCCACCTCT
GCTTTCAGTTCCACTTGGCGGTTCCCTTCCTTC---------CTCTGAGTCGGCTGCTGTGCCTGTGGGAGCACCGGTAG
GGTGGATGGAGGAGGAGGAGGCCGCCGGCGTGAGGAAGCGGAAGCGCGGCGGGGAGGCCGTGGCCCTGGTGTCCGGCGGG
GAGGCGGGGCTCGTCGAGGGAGGTGGTGGCTTCTCCTGGAAGGAGGCGGAGATGGAGGAGGGGGAGGGGGAGGAGTACGA
GGGCATCGCGGAGGAGTCGGTGGAGGAGGTGATGCGGTGGCTGGAGCTGGAGATCTCCTCCTCGCCGGGGAAGCCCGGCG
GCGGCGACGACGGGTTCGTGACCATCAACGGCAACGAGGAGAGCTGCGGCCCGTCCTTCTCCGCCGCGGCGTCCACCGTC
ATGGCCTCCGTGGACACGCGCGCGGGCGCCCCGCCGCCCCCGACGGCCATCCCCTGGCCGTGGCCCGAGCCCAACAACGA
CACCACCAAGCCGGCGGCGGCGGACGGCAA---------CGACGACGACGCGGACATGGCGGAGCTCGTCGACGAGGAGT
GGCTGGTGGAGCTGCTGACCGGCGGCGGGCCCGCGCTGGAGGTAGAGTAG------GGTAGGGCGCAGAGCGCTCGGGTA
GGCAAGGCAAGGCAAGGCGCAAGCGTACGCGCGTTTCCTTTTTCGGACGGTTGTACAGCGGGCAAGGGAAAAGCCAGGAA
AAAAGAGAGCGGTGGCTCGTTTTGGCGCGGCCCGGGTCGGTCGCATCGCTTTCTTCCGCGGCATGGGCGGGCAGCGGCAG
CGATCGGTCCGTCCATCAATGCGGTCGGCCTTGTGCGGTGGTGCGTTGAGGGGTGAGGTTGCGAGGAAATGGAAATGGTG
CTC-----------------GCTGGCTGGCCC-TTGTCGCGTTGCCTGCTTTTGCGTCCGGTTTCTACTGCTGGCCACTA
TGGCTCAGTTTTCCTGCTCCGTGACGCC-T--TTTTCTCGCCTTGACTGGCCGATAGCGAATGGTGTTTGAA------TT
CGATCGTACTCCTACGTGTT--------------TCTTTCGCCAACCTACCCAACCCACACTCAAAAAAAAAAAGCAACC
CAACCCACATTAAATCAGCTAGCGTCTACAGTTAGTAGCTGTTAACCAATCTCAGAGTCCCGAGGA--------------
-----------------------------GTAGTACTAAAATGAATCCAAGTTGGGTCGTGAAGTTAG----GCGTCTCG
GCCGGAGCGTGAACTAATTTCCACCGGTGCATGTGGTGGTACGTTCATGTCCTTCGTAGTCTGGGCGCATTAGATTCC--
---AAGAGGCAACGGTACGAAGCAGATGCAACAGGCAACATGGATAGCCATGAATCCGCGAGCGAGCGAGCACAGAGGTG
GCGCGGGGCTCGGTGGTCTGTGGTTTCAGGTTATCATCAGCTTCCACGGCAGACTGCATGCATTGCAAGCAGCCTCCTGC
GTGGAT----------AGTGCAGTGCAGGCTTTACTTGCTTTCACTGTAGCAGTTTCAGGCTTCGGCCGCAGACAGCAGC
ACAGCAGAGCACACCACAGGTCAAAGGCAGCACGTTTCATCACACATGCTGACATGCATGCAGCTACCACCACTATCAG-
---GCCAGGCCTAGCCGCCGTGCTTCTCATGTTT---
>chr3B_78
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--GCTTCTTTCCTAAAAAAAA-CAAGAGATGGACGTGCGCGCTCTTC-GACGCTGGTGTAAAACCTCTCCCGGAAGGAAC
T--AACCAAAGCGTAACGCGCCTGTCCAGCTCACAAGGTTAATCCGGAG----GAATCCTTGTCGTGCAAGACACGAAGG
TGATGGCATGCAGGAGATCGGCGACGGATCAGAACAGCCCCCGCAGATTTTGGCAACAACAAAGGCGCCAACGAAAACCG
CCGCAGATAGAGCAAAACACACACT------CCAGCTGGGCACAACCAATAC-----ACGACCCAGAGAAATGGTTCCCG
AACCCTCGCGGTCCGCCCGTCCGTCC-------CCCGCACGCC---ACAACGGCTGTGCGGCGCGGCGCGGCGC------
---GGCCTGCTGCGCT----TCCGTCACGAGCGCGAGATCGGGGGCGGAGCGTTTCGTTTTCTGGCGCGAGCCCAACTGG
CACCCACCCACGCCCCATCCCCCCATCCACCACGTGCCGGGCGGGCGAGTGACCCCGGTCAACAGCACCGACGAACGGAG
AAAAAGAAAGGGTTTGGTTTCTTTCCCCACCCGTCGCGTCCAAAAAAGACGCGGTTCCCGA---GAGGAGAGGAGAGGAG
AGGCGAGCGCGCTACGCGCCACGGCCACGCCACGCAGCGCGACGCGAACACGTCCTTTTCCTCGCGTAACGCCTCGAGGC
CGCCGGATGCGCGCTGGGGCGTGGCCCCGAGGCGGATCCGACGGCCCCGCGCCGCGCAGCCACGTCCCGCCCCCCACGCT
ATATAAACCGACGTGGACGCGGCCCGGCGCTCCACCGCGCTATCCACCACCACGCCTCACTCTCCTA-TCCTCCTCCTCT
GTTTTCAGTTCCACTTGGCGGTTCCC----TTC---------CTCTGAGTCGGCTGCTGTG------GGAGCGCTGGTAG
GGTGCATGGAGGAGGAGGAGGCCGCCGGCGTGAGGAAGCGGAAGCGGGGCGGGGAGGCCGCGGTCGTCGTGGTGTCCGGC
GAGGCGGGGCTCGTCGAGGGAGGCGGTGGCTTCTCGTGGAAGGAGGCGGAGATGGAGGAGGGGGAGG------AGTACGA
GGGCATCGCGGAGGAGTCGGTGGAGGAGGTGATGCGGTGGCTGGAGCTGGAGATCTCCTCCTCGCCGGGGAAG------G
GCGGCGACGACGGCTTCGTGACCATCAACGGCAACGAGGAGAGCTGCGGCCCGTCCTTCTCCGCCGCGGCGTCCACCGTG
ATGGCCTCCGTGGACACGCGCGCCGGGGCGCCGCCGCCCCCGACGGCCATCCCCTGGCCGTGGCCGGAGCCCG---ACG-
--ACACCAAGGCGGCGGCGACGGCGTCAGCGGCGGACGGCGACGACGACGCGGACATGGCCGAGCTCGTCGACGAGGAGT
GGCTGGTGGAGCTGCTGACCGGCGGCGGGCCCGCGCTGGAAGTAGAGTAG------GGTAGGGCGCTCGGGGAGTTGT--
---------AGGCAAGGCGTAAGCGTACGCGCGTTTCCTTTTTCGGACGGTTGTACAGCAGGCAAGGAAAAAGCCAGGAA
AAAAAAGGG-GGTGGTTCGTTTTGGCGTGGCTCGGGTCGATCGCATCGCTTTCTTTCGCGGTATGGGCGGGCACCG----
--ATGGATTCATTCATCAATGCGGTCGGTCTTGCTT----GTGCGTTGAGAGGTGAGGTTGCGAGGAAATGGAAATGGTA
CTTGCTGGTGACACGATCGGGCTGGCTGGCTCTTTGTCGCGTTGCCTGCTTTTGCGTCCGGTTTCTAG---------CTA
TGGCTCAGTTTTCCTGTTCCGTGCTAGAACCCTTTTCTCGCCTTGACTGGCCGATAGCGAGCGGCGTTTGAATTCGATAT
CGATCGTACTACTCCTGCGTTTTGTTTTTCTTTCTCTTTCGCCAACCTACCCAACCCACATTCAATCAG-----------
-CTAGCG--------------GCGTGTACGATCAGTCTCTGTTAACCAATCTCAGAGTCCCGAGGAAAGAAGACCTATCT
ATCTACAGTAAGCAGGACTAGTAGTAGGAGTAGTACTAAAATGAATCCAAGTTGGG----------AG----GCGTCTCG
GCCGGAGCATGAACTAATTTCCGTCGGTACAT---GTAGTGCGTTCGTGTCCTTCGTGGTCTGGACGCATTTTTTATATT
CCAAAGAGGCGACGGTACGAAACAGATGCAGCAGGCAACATGGATAGCCATGAATCCGCGAGTGAGCGAGCACAAAGGA-
GCGCGGGGCTCGGTGGTCTGTGGTTTCAGGCT---ATCAGCTTCCACGGCAGACTGCATGCAATGCAAGCAGCCTGCTGT
GTGGACAGT-----GCAGCGCAGTGCAGGCTTTACTTACTTTCACTGTAGTAGTTTCAGGCTTGGGCCGCAGGCCGCAGC
ACAGCACAG-----CACAGGTCAAAGACAGCACGTTTCATTACGCATGCATGCAGGCATGCAGCTACCACGACTATCAG-
---GCCAGGTCTAGCCGCCGTGCTTCTCATGTTT---
>SNPs
--S---------------------------------------S--------------S----------------------
---------------------S----------------------------------------------------------
---------------S------S------------S-S-----------SSSS---------------------------
------------------------------S-------------------------------------------------
-------------SS-------------S-S---------------------SSSSS------------------S----
----------------------S--------------------SSS--------S------S------------------
----------S--------------------------------------------------S----S-------------
----------------------------------------------S---------------------------------
------------------------------S---------------S--------------SSS----------------
-----------------------------------S--------------------------------------------
--------------S----------------------------------------------------------S------
------------------------S--------------------S------------------------S---------
---------------------------S-SS--SSSSSSSSS----------SS-S-SSS-SSSSS--------------
-------------------------------------------------------------SS---S-------------
--------------------------S----------------------------------S------------------
---------------------------------------------------------------------S----------
---------------------------------------------------------------------------S----
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-S-------------------------SS-S-SS----S-----S-----------------------------------
--------------------------------------------------SSSSSS------------SS-S--S-S---
-----------S--------------------------------------------------------------------
-----------------------------------S--------------------------------------------
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--------S-S-------S---------------------S---------------------------------------
----------S---------S---S---S---------------------------------------------------
------------------SS-SS-------------------------------------------S--S-SSSSS-SSS
S----S--------------------------------S--S-----------------------------------S--
---------------------------------------------S--------S------SS-S---SSSS--------
-----------S----------------------S---------------------------------------------
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---------------------------------------------S----------------------------------
---------SSSSS-------------------------------------S--------------S-------------
------------------S-----------------------S-------------S--------------------SSS
SSS-----------------------SSS-S---SSS
>forward_1013
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---------------------------------GCGCAATCTCTCTGAGTCGA---------------------------
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>reverse_2206
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---------------------------------------------GCCAAGTTGAGTCGTGTTGG---------------
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