>input_sequence_85479
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----------------------------------------------------------------ATGGAGACGATGGTGG
CGAACGGCGGCGGGGAGGGCCGGGCGGCGGCGAGGTACGGGGACAGGGAGCAGCAGGGCGCCGGGTGCGGGGGCGC----
-----------GCGCCGCTTCCAGATGCCGCTGCACTACCCGAGGTACACCAGGGCCAACTACGAGGCCATGCCCGAGTG
GCAGCTCGACCGCCTCCTCTCCGACTACGGCCTCCCCGTCCACGGCAACGTCCACCAGAAGCGCAGCTTCGCCATGGGCG
CCTTCCTCTGGGGCGCCGGCAACTGA------------------------------------------------------
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-------------------------------
>chr3D_1_TraesCS3D01G155200
AACAATATT---TTACACAAATAATCTGAGCTCTCTCGGCCATTATT--TTTTGTGCCTCCGTAGAAAAGAGCTCCTAAG
AATGGGGTAGTCACTAGGCTAACGGATATACTCTGTTTTGTTTCTCTCTCACGGCTCAGCAAAATTGA------------
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-------------------CATCAGCCACACCTTCAATCCACGTAATATGAGCCGGTCCATGCATGCCTACAGCCCTGCA
TGACGATTAGTTGGGCCATGAAACAAGTGCCGCTCGACCTGCTCGATCATGTACTCTACGTTGTTACTGCACGTTTCCGT
CCCCACAAA------GTCCTCGACAATATCCGCAAAAAAGAGGTCCTCGACAAGAAAGCTGGATC-AGCACTAAATGGGC
GACAAACGCAAGGTCTCACGT-------ACCACGCCCGTAAACCCTCGTAACACCCGTCCGATCGATCATTTGGTGCGAG
CCAGAGCGAGTCGTGCCTGGCCGGCTCAACTTTTTTTTTTTAGGCAAACCTGGCCGGCTCAACTAAACAAGCACGCCCAG
CCGCCAGTCCAACAGGCGGGCCTGCTATGCCGTGCTGGCCATTTCTGCCACCTTTTCCCGCGCCCGGGCCTCGCAAGTTC
GCAACGGACGGCGCAGGGCGCCGTTGACATGCATGC---------ACGCGGGTGTCAACTGCCAAGGCACGGGCGTGGGA
CGTCCGCCGCCCGTGCGCGCGCCGCACCTGCCA-----CAAC-----------------------TGCCCGTTCCAACAC
ACACTGACACACGTAGCACAGGGTCTCCACACCGG-----------CCACACGGGCCACAGAGTTATAGCTGGCTCAGCT
GCATTCCTCGTGATAAACCAACCGAACTCTCCGT--CTGATATTTCCTATGGCGCGCGGGTCCTGGACTCCCGCCCGGCG
CTATAAAAGGCGACCACCTGGTCCGCTTCGTTGCCCAGCGAGCTCAGACCTTGGATTCGACCAAAGACGGCAGGGCGACG
CAGCCGCAT----CACCACCACCACCTACAAAGCTTCCTAACCTGGTCTCGAGGCAGGACGTACATGGAGACGATGGTGG
CGAACGGCGGCGGGGAGGGCCGGGCGGCGGCGAGGTACGGGGACAGGGAGCAGCAGGGCGCCGGGTGCGGGGGCGC----
-----------GCGCCGCTTCCAGATGCCGCTGCACTACCCGAGGTACACCAGGGCCAACTACGAGGCCATGCCCGAGTG
GCAGCTCGACCGCCTCCTCTCCGACTACGGCCTCCCCGTCCACGGCAACGTCCACCAGAAGCGCAGCTTCGCCATGGGCG
CCTTCCTCTGGGGCGCCGGCAACTGATCTCGCTGCCG-GCCGTACGTCTAGTCTTCTCCCTCGACCATGGAGCC------
--GTGCTCATGAAT----CATT---CATGACTAACTTACGATGGGCCTGGGAGACGAAGTGCTACTGTATTATTATCCGT
ATATGCAGAGATCGACTAGCTAGCTAGCTACCAAGTTTTTCG-----ATATAGTTTCTATTTGCTTGTTATGAAATGGCA
TGTATA-------------TGTGTC-TGTATGCTAATTTGGACGCGTTGATATTTTGAATTTCAAGT----------TAG
TGGTGGCTGATGTGTGAAACTGAGGATTGCGTATGTCTTAATTAAGCTTCTTAATGTATAGTTAATTTATGCTCTGCATG
TATAATATTGCTCTGGGTACAGTTAGTTGGAGACATGTGTGACCTATCTATACTAGTATTCATACTGATGACATATTAAT
TAAGCTTCTTAATGTAAACTGCACAAAACATGTGTGACCTATCTGTACTAGTATTCATACTGATCTCGTGCTACCTGAAT
TAAGAGCATCTCCAGCCAAACCCCCTACTCCACTCATATGTATGGGCGTATAGCCCGAACAGAAAAAACATCACCTAACC
GGACCCCAAACTCAACCTATATGTTTGAATTGTCTCGCACACCTTAAACCCAGCTCATATGTGGGGCGTGTTAGAATATT
TCGAGACACAAGCTGATCTACCGAGGATTAAGCAATTGCATGAAGCGCGATCGAGATTTGTTAATGAGATTTACCAAACA
TCAGCAAAATCTTTGGAACATGACTATGGGTGCTCCTCTCCGTTGATACCGCGACAATACTGCACACCGGCCTCTCAGGA
GCCGACACATGCCGCGGCTTCCCTTGTGCACATGTGTTGTTATGTTGGCATAGATTATATTGTGTCTATTCCCATATTTA
TATAGGAGGCCTAGGATACAAGTGTTCTACTAGGACACGGCTCTATACCCTGTTTACGCACAATACGACTCTAAGTGCAT
ATGTAATCTATCTTATACACAATATTTGACA
>chr3B_1
AACAATATTTTATTACACAAATACAATGAGCTCCCTCGCCCATTTTTTCTTTTGTGACTCAGTGGAAAAGAGCTCCTAAG
ACTGGGGCGATATACAC-----------TACTCTGTTTTTTTTCTCTCACACAGCTCGGCAAAATTGA------------
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-------------------CATCAGCTACACCTTCAATCCACCTGATACGAGCCGGTCCATGCATGCCTACAGCCCTGCA
TGACGATTAGTTGGGCCATGAAACAAGTGCCGTTCGACCTGCTCGATCATGTACTCTACGTTGTTACTGCACGTTTTCGT
CCCTACAAA------GTCCTGGACAATATCCGCAAAAAATAGGTCCTCGACAAGAAAGCTGGATC-AGCACTAAATGGGC
GACAAACGCAAGGTCTCACGTGTCACGTACCACGCCCATAAACCCTCGTCACACCCGTCAGATCGATCATTTGGTGCGAG
CCAGAGAGAGTCGTGCCTGGCCGGCT---------------------------------CAACTAAACAAGCACGCCCAG
CCGCCGGTCCAAAAGGCGGGCCTGCTATGCCGTGCTGGCCATTTCTGCCACCTTTTCCCCCGCGCGGGCCTCGCAAGTTT
GCAACGGACGGCGCAGGGCGTCGTTGACCGACCTGCCT-----GCACGCGGCTGTCAACTGCCAAGGCACGGGCGTGGGA
CGTCCGCCGTCCA--CGCACGCCGCGCCTGCCAACTGCCAAC-----------------------TGCCCGTTCGAACAC
ACACTGGCACACGTACT---GGGTCTCGACATCGG-----------CCACACGGGCCACAGAGTTATAGCTGGCTCAGCT
GCATTCCTCGTGATAAACTA-CCAAACTCTCCGT--GCGATATTTCCGATGGCGCGCGGGTCCTCGACTCCGGCCCGGCG
CTATTAAAGGCGGTCGCCTTGCCCGCTTCGTTACCTAGCGAGCTCAGACCTTCGAT-----CAAAGACGGCAGGGCGACG
CAGCCACAT----CACCACCACCACCTACAAAGCCTCCTAGCCTGGTCTCTAGGT-GGACGTACATGGAGACGATGGTGG
CGAACGGCGGTGGGGAGGGCCGGGCGGCGGCGAGGTACGGGGACAGGGAGCAGCAGGGCGCGGGGTGCGGAGGCGC----
-----------GCGCCGCTTCCAGATGCCGCTGCACTACCCGAGGTACACCAGGGCCAACTACGAGGCCATGCCCGAGTG
GCAGCTCGACCGCCTCCTCTCCGACTACGGCCTCCCCGTCCACGGCAGCGTCCAGCAGAAGCGCAGCTTCGCCATGGGGG
CCTTCCTCTGGGGCGCCGGCAACTGATACCGCTGCCGG-CCGTACGTCTAGTCTTCTCCCGCGACCATGGAGCC------
--GTGCTCATGAAT----CATT---CATGACTAGCTTACGATGGACCTGGGAGACGATGTACTACTGTACTATTATCCGT
ATATGCAGAGATCGACTAGCTAGCTAGCTACGAAGGTTTTTCTATATATATAGTTTCTATTTGCTTGCTATGAAATGGCA
TATATA-------------TGTGTCTTGTATGCTAATTTGGACGCGTTGATCTTTTGAATTTCAAGTACTAGCTAGCTAG
TGGTGGCTGATGTGTGAAACTGAGGATTGCGAATGTC----TTAAGCTTCTTAATGTATAGTTAATTTATGCTCTACATG
TATAATATTGCTCTGGGTATAGCTAGTTGTGTTTCAAAGTGCAGCAAAACATA---------------------------
--------------------------------TGTGACCTATCTGTACTGGTATTCATACTGATCTCGTGCTACCTGAAT
TAAGAGCATCTCTAGCCAGACCCCCTACTCC-------TGTCCGTGCGGACACCCCGAACAGAAA-AACATCACCTAACC
GGACCCCAAACTCAACCTATATGTTTGGGTTGTCTCGCACACCTCAAACCCAGCTCATATGTGGGGCGTGTTAGAATATT
TCAAGACAGAAGTTGATCTACCAAAGATTAAACAATTGCATGAAGCGCGATCGAGATTTGTTAACGAGATTTATCAAACA
TCAGCT-AATCTTTGGAACATGACTATGGGTGCTCCTCTCTG-TGATATTGTGACAATACTGCACACCGGCCTCTCAAGA
GCCGACACATGCTGCGGCTTCCCGTGTGCACATGTGTAACAATGTTGGCATAGATTACATCGTGTCTATTCCCATATT-A
TATAGGAGGCCTAGGATACAAGTGTTCTACTAGGACACGGCTCTATACCCTGTTTAGGTACAATACCACTCTAGGTGCAT
ATGTAACCTACCTTATACACAATATTTGACA
>chr3A_4
---AATATT---TTACACAAGTAATATGAGCTCTCTCGGTCATTATT--TTTTGTGCCTCCGTAGAAAAGAGCTCCTAAG
AATGGGGTAGTCACTAGGCTAACGGATATACACTGTTTTGTTTCTCTCTCACGGCTCGGCAAAATTGCGAAAATGCTACA
CCTACGAAGAGGTGCCACGTACCCTACGTAACTTTCCAAAACATCAATCAAACTACCGCCCCCCTGATTCTAGGGTGGGC
CCGTGCGGCAAACAAATACAAATCAAAAGCTGCCAGATCAGCAATTACGTCAAGAACGTAATAATCCGTTCGTAGGTGTA
GCAAAGCCCGCAAAATTGGCATCAGCTACACCTACAATCCACCTGATACGAGCCGGTCCATGCATGCCTACAGCCCTGCA
TGACGATTAGTTGGGCCATGAAACAAGTGCCGCTCGACCTGCTCGATCATGTACTCTACGTTGTTACTGCACGTTTCCGT
CCCTACAAAAAAGAGGTCCTCGACAATATCCGCAAGAAAGAGGTCCTCGACAAGAAAGCTGGATCAAGCACTAGATGGGC
GAGAAACGCAAGGTCTCCCGC-------ACCACGCCCGTAAACCCTCGTAACACCCGTCAGATCGATCATTTGGTGCGAG
CCAGAGCGAGTCGTGCCTGGCCGGCT---------------------------------CAACTAAACAAGCACGCCCAG
CCGCCAGTCCAAAAGGCGGGCCTGCTATGCCGCGCTGGCCATTTCCGCCACCTTTTCCCG-----------CGCAAGTTC
GCAACGGACGGCGCAGGGCGTCGTTGACATGCATGCAT-------ACGCGGGTGTCAACTGCCGAGGCACGGGCGTGGGA
CGCCCGCCCGT------------GCGCCTGCCAACTGCCCG-------------------------------TCGAACAC
ACACTGGCACACGTACT---GGGTCTCCACACCGG-----------CCACACGGGCCACAGAGTCATAGCTGGCTCAGCT
GCATTCCTCGTGACAAACCAACCGAACTCTCCGT--CTGATATTTCCCATGGCGCGCGG--------CTCCCGCCCGGCG
CTATAAAAGGCGGTCGCCCGGCCCGCTTCGTTGCCCAGCGAGCTCAGACCTTCGAT-----CAAAGACGGCAGGGCGACG
CAGCCACAT----CACCGCCACCCCTTACAAAGCCTCCTAGCCCGATCTCGAGGTAGGACGTGCATGGAGACGATGGTGG
CGAACGGCGGCGGGGAGGGCCAGGCGGCGGCGAGGTACGGGGACAGGGAGCAGCAGGGCGCCGGGTGCGGGGGCGC----
-----------GCGCCGCTTCCAGATGCCGCTGCACTACCCGAGGTACACCAGGGCCAACTACGAGGCCATGCCCGAGTG
GCAGCTCGACCGCCTCCTCTCCGACTACGGCCTCCCCGTCCACGGCAGCGTCCACCAGAAGCGCAGCTTCGCCATGGGCG
CCTTCCTCTGGGGCGCCGGCAACTGATCTCGCTGCCGGGCCGTACGTCTAGTCTTCTCCCTCGACCATGGAGCC------
--GTGCTCATGAACCATGCATT---CATGACTAACTTACGATGGACCTGAGAGATGATGTGCTACTGTGTTATTATCCGT
ATATGCAGAGATCGACTAGCTAGCTAGCTACGAAGTTTTTCG-----ATATAGTTTCTATTTACTTGCTATGAAATGGCA
TATAGTATATAAATATGTGTGTGTC-TGTATGATAATTTGGACGCGTTGATCTTTTGAATTTCAA-TACTAGCTAGCTAG
TGGTGGCTGATGTGTGAAACT-----------------------------------------------------------
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>chr3A_583
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------------------------------------------------------------------------GCAAGTTC
GCAACGGACGGCGCAGGGCGTCGTTGACCTGCATGCACGCACGGCACGCGGGTGTCAACTGCCAAGGCACGGGCGTGGGA
CGTCCGCCGTCCA--CGCACGCCGTGCCTGCCAACTGCCCCTTCCAACCGGGCCAAGCCAGCCGTTGCCCGCTCGCGG--
---CTCGCACACGTACA---CGGCCTGCACACACCACGCCGGCTGAACACACGGGCCACAAAGTTATAGCTGGCTCACCT
GCATTCCTCGTGATTAACTAACCAAAGCGCTCCGGCGTGATATTTCCTATGCCGCGCCCGGCCGGAGCTAC---------
CTATAAAAGGCGATCGCCTGTGCGGTGTGACTGTGTG-----------------------------------GTGCAACA
CAGTCACACCACACACCACCACCACGCACAAAGCTTCCTAGCTTCATCTCGAGGGCGGC----CATGGAGACGATGGCGG
CGAACGGCGGTGGGAAGGGCCGGGCGGCGGCGAGATACGGGGACAGGGAGCAGCA---------------GGGCGC----
-----------GCGCCGCTTCCAGATGCCGCTGCACTACCCGAGGTACACCAGGGCCAACTACGAGGCCATGCCCGAGTG
GCAGCTCGACCGCCTCCTCTCCGACTACGGCCTCCCCGTCCACGGCAGCGTCCACCAGAAGCGCAGCTTCGCCATGGGCG
CCTTCCTCTGGGGCGCCGGCAACTGATCTGCCGACC-GGCCGTACGTCTAATCTTCTCCCTGGACCATGGAGCAGACGAG
CAGTGCTCATGAATCATTCATGAGGCATGACTCATCTACGATGGACCTGAGAGATAG-------------TATTATCCGT
ATACGCATAGGTCGAATAGCTAGCTAGCTACCAAGT--------------------------------------------
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>chr3B_745
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-------------------------------CCGG-----------ACACACGGGCCACAAAGTTATAGCTGGCTCAGCT
GCATTCCTCGTGATTAACTAACCAAAGCCCTCCGGCGTGATATTTCCTATGCCGCGCGCGGCCGGAGCTAC---------
CTATAAAAGGCGATTGCCTGTGTGGTGTGACTCTGTG-----------------------------------GTGCAGCA
CAGTCACACCACACACTACCACCACGCACAAATCGTCCTAGCTTGATCTCAAGGGCGGC----CATGGAGACGATGGCGG
CGAACGGCGGTGGCAAGGGCAGGGCGGCGGCGAGGTACGGGGACAGGGAGCAGCA---------------GGGCGCGGGG
TGCGGAGGCGCGCGCCGCTTCCAGATGCCGCTGCACTACCCGAGGTACACCAGGGACAACTACGAGGCCATGCCCGAGTG
GCAGCTCGACCGCCTCCTCTCCGACTACGGCCTCCCCGTCCACGGCAACGTCAATCAGAAGCGCAGCTTTGCCATGGGCG
CCTTCCTCTGGGGCGCCGGAAACTGATCTGCCGACC-GGCCGTACGTCTAATCTTCTCCCTCCACCGTGGAGC-------
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-------------------------------
>SNPs
-------------------------S------------------------------------------------------
---------------------------------------------------------S----------------------
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--------------------------S---------------S-S---S-------------------------------
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---S----------------------------------------------------------------------------
-----------------------------------------------------------S--------------------
--------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------------------
------------S--------------------------------------------------S----------------
--------------------S-----------------------------------------------------------
---------S--SSS---S------S------------------------------------------------S-----
------S--------SSSSS------------------------------------------------------------
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-------------S-S-----S------------------------------S---SSSSS-------------------
-----S----------------------------------S-------------S-------------------------
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--------------------------------------------S------------S----------------------
-------------------------------------------------------------------S------------
-S-------------------------------------------------S----------------------------
-------------------------------S-----SSSS----------------------------------S----
-------------------S--S------SSSSSSSSS---SSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----------------S------------------------------
------------S-----S------------SSSSSSS---SS-S---S-S-S------------S--------------
---------------------------SS---------------S-----------------------------------
--S-----S---S---------S-S------S--------------------------------S--------S------
-----SS---------------------------------S-S-----SS-S-------------------------S--
------------S----------S-------------SSSS----------------S--S-----------------S-
--------------------------------------------------------S-S-------S------S------
------S---S--------------------
>forward_1177
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-------------------------------------GCGAGCTCAGACCTTGGATT-----------------------
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>reverse_2272
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-------------------------------GCAATTGCATGAAGCGCGAT-----------------------------
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-------------------------------
