>input_sequence_65237
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-------------------------------------------------------------------------------A
TGGCATCTCAGGCTCGCGAGCTCCGCTTCCTCCTCGCCGTCGCCGTGTTCTCGGCCGCCGCGGCCGTGGCGGGCGCGCGG
TACGGCGCCGCCGGGCAGTGCGGCCCGGTGGGGGCGATCGTCACCGAGCAGCTCTACTCGTCCCTGTTCCTGCACAAGGA
CGACGCCGTCTGCCCCGCCAAGGGGTTCTACACCTACGCGTCCTTCATCCGGGCCACCAAGAAGTTCCCCAGGTTCGGCG
CCACCGGCGACCTCGTGACGCGCAAGCGCGAGATCGCCGCCTTCCTCGCGCAGATCTCCCATGAGACGACCGGCGGCTGG
GCCACCGCGCCGGACGGCCCCTACTCCTGGGGCCTGTGCTACAAGGAGGAGATCAGGCCGCAGAGCAACTACTGCGACGC
CACCGACAAGCAGTGGCCCTGCTACCCCGGCAAGTCCTACCACGGCCGAGGCCCCATCCAAATCTCATGGTACTGATAAA
TCCCCCGAGTCTACCTGCAAATTTCACCCATGGCGCCGGCACACGTGCTGAT------------------------CTCT
GACCTCTGGCCGGCTGATGAACAGGAACTTCAACTACGGGCCGGCGGGGCAGGCGCTGGGGTTCGACGGGCTGCGGTACC
CGGAGCTGGTGGCCAACTGCTCCGACACGGCGTACCAGACGGCGCTGTGGTTCTGGATGACGCCCAGGGAGGCCAAGCCG
TCGTGCCACCAGGTGATGGTCGGCGAGTACTGCCCCAGCCGGGCCGACGTCGCCGCGAACCGCACGGCCGGGTTCGGGCT
GGTCACCAACATCGTCAACGGCGGCCTCGAGTGCAACATCACCGAGGACGCGCGGGTCAACAACCGGATCGGCTTCTACC
GGCGGTACTGCCAGGTCCTCGGCGTCGACGTCGGGCCCAACCTCGACTGCGCGCACCAGCTCCCGTACTAG---------
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>chr3A_1_TraesCS3A01G312500
GATATTGTATTGTTGTTGAGGCCGGATGTAATCGGTACCATTTTCCTTTTTGGATGGAAAAACTATGCAGCCTATTACTC
AAGAACGTCACATTCGGAGGTCACCATCTTCACATTAATATATACTGATTTTTGTAGGGGGGGAAAGGTGAAAGGAAGAT
GAAAAAAT-AAAGGTCGGCCGTGATTTGCAGGCCGTGCACATATCTTCCACTCTATAGCAGTCAACGCTTGCTCTAACAG
ACACGCATGCTC-------ACCTCCTTCGAGAAAAGAACAGACGCAT---TATATTGCAGCACTAACCGGTCGTATTGCG
CCAACGAACTCCACTCATCATGTAAGCTGCTGACCTGGTTTAGATTAGATGCCCTGCGCTCCCGCATCCATGCTGAATGG
TCTTCCTATTTGCTGCAATGATTTCTCAATTTCCGGCATGTAATGCTTGGACGCACCACAGCTCCACTTACAATCCATAA
GCTATAGCTGAATCTTCTGGATTTGTATAGCTCCACTTGCCAATTCAACTAGGAACAAATAGGACGCAGTCCGTCCCCCA
TGTAATAACGTTTGTTGCTTGGACGCCCATCCATGGCCGTTTCTTGGTCAGAC-GACCACTGTGCCGTCGCCGTTACGAC
CTCTTCCTCTTCCT------CTCGCTCCTTTCTTTACTCAGCCTGCCTGCATGCATGGCCTGTGCAGGCAAGAGCTGCGG
CATGGGCGCTCCGCTTGCTTCTGTTACACGTCCCGGTGGTGATCGAGAGCGAGGCCCAGACCGGCTCGCACTATCCTCTG
CCTTGCGCTGACATGATCAAGATCAAGTCAACCGATGGTGGCGCG------------GTCGACGGCCGCGCCACTAGCTG
CATGCGTCGCCCCCACCCACCACACCACTGCCGGCCGCCGTTGTCCCA-TCCCCGTGTCCTCACGCCCCTCCACCGGTAG
AGCC--------AGCGGATATATAATGCGCACGCGTGTCCTCATGCCGAGCAAGCAGCCAATAAGCACTCACTCCAGCAA
TGGCATCTCAGGCTCGCGAGCTCCGCTTCCTCCTCGCCGTCGCCGTGTTCTCGGCCGCCGCGGCCGTGGCGGGCGCGCGG
TACGGCGCCGCCGGGCAGTGCGGCCCGGTGGGGGCGATCGTCACCGAGCAGCTCTACTCGTCCCTGTTCCTGCACAAGGA
CGACGCCGTCTGCCCCGCCAAGGGGTTCTACACCTACGCGTCCTTCATCCGGGCCACCAAGAAGTTCCCCAGGTTCGGCG
CCACCGGCGACCTCGTGACGCGCAAGCGCGAGATCGCCGCCTTCCTCGCGCAGATCTCCCATGAGACGACCGGCGGCTGG
GCCACCGCGCCGGACGGCCCCTACTCCTGGGGCCTGTGCTACAAGGAGGAGATCAGGCCGCAGAGCAACTACTGCGACGC
CACCGACAAGCAGTGGCCCTGCTACCCCGGCAAGTCCTACCACGGCCGAGGCCCCATCCAAATCTCATGGTACTGATAAA
TCCCCCGAGTCTACCTGCAAATTTCACCCATGGCGCCGGCACACGTGCTGAT------------------------CTCT
GACCTCTGGCCGGCTGATGAACAGGAACTTCAACTACGGGCCGGCGGGGCAGGCGCTGGGGTTCGACGGGCTGCGGTACC
CGGAGCTGGTGGCCAACTGCTCCGACACGGCGTACCAGACGGCGCTGTGGTTCTGGATGACGCCCAGGGAGGCCAAGCCG
TCGTGCCACCAGGTGATGGTCGGCGAGTACTGCCCCAGCCGGGCCGACGTCGCCGCGAACCGCACGGCCGGGTTCGGGCT
GGTCACCAACATCGTCAACGGCGGCCTCGAGTGCAACATCACCGAGGACGCGCGGGTCAACAACCGGATCGGCTTCTACC
GGCGGTACTGCCAGGTCCTCGGCGTCGACGTCGGGCCCAACCTCGACTGCGCGCACCAGCTCCCGTACTAGCCCGAGGGA
CTAGCCTCACGTTCCTCGACCGGGAGAAAACCATAGCCTCACGTGC----TAGTTGCTTGAATTTGTAGTTTAGTTAAGC
CTACAAAGAAAAACACTTGTATTTTGTTAGTAATAACAAATCTAATAAATTAAGGTTTCTTTCTTCAAGAACATTGATCG
TACTATCAACAAGTGAAATTGAAGCAAGCACAAATGACAAATATCCTGAGCAAATTGAAAGCTACACCAAGATTCTCTAA
AGTCTTCGTGTC--------------------------------------------------------------------
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-------------------------------------------------------TAACTTCATTGTTCGCACTTAATTG
TGCTTTCTTGTATTCGACAACGATTTTTATTTTATCTTTTGTGGGAAGTATTTGACAACAAAATTGTAGAGGACAAGCCC
CACAAGGTGGAGTAGCCTTTTTTTTAAAAGAGAGGGGCTTGCTCGCCAATAAACTAAGGCC-----CTTACAGAATGAGT
GCAAAGTAAAGTGAACCAAAACATACAAGATCACAAGTGTCCGAACAAAGTGGCGCATCGCTTGCAAGCTAGACACTAGG
CCTAGGAAATAACGTGGGTCGCCCACGGAGAGTCCCTGAATGGAAGAAGACGATCACATGATGGCTTCCCTGGCCTACAT
TGTCCCGTCTCGATGCGGCACGAAGAGCTTGACACTTTGCACAAAGATTGCTGACAAGACGATCATGTTGTGGCCAGTCT
TGTTGTTTCCCAAATGCTCTCTAAAACTGTAGAAGGACAACAACTTAATACACAAGATCGGTCGGATGCTTGAATTCAAG
ACCTTCCATTGGTTTTCAGCATTCCAAAGTGGCCATACTAATGCAAAAAATCCCACCCAATAAATTTTTCTATCGTTTTT
GTGGATCCCTTGCATAAGTTTATGGAATTCAGCAAACCTAGCCGGATTCCACAAGCAACCCGTGGTGTGTCTCGGATCAC
ACTCCATACAAATTTGGCCACTATACATCAAAAGAATATGTGGTCACAATTTTCATTGAGGCCGCACCAAATGCAAGTGC
CGT
>chr3D_145
AAGAGT--------------------------------------------------------------------------
---------------------------------------------------------------------GAAAGGAAGAA
AAAAGAAAAAAAGGTTGGCCGTGATTTGTAGGCCGTGCACATATCTTCCACTCTATAGCGGTCAACGCTTGCTCGAATAG
ACACGCATGTATGC---TTACCTCCTTCGGAAAAAGAAGAGACGCATTCTTGTATTGCAGCACTAACCGGTCGTATTGCG
CCAACGAACTCCACTCACCATGTAAGCTGCTGACCTGGTT------AGATACCCTGCGCACCCGGCCGCATGCTGAATGG
TCTTCCAA-TTGCTGCAATGATTTCCCAATTTCCGGCATGTAATGCTTGGACGCACCACAGCTCCACTTACGACTCATAA
TCTATAGCTGAATCTTCTGGATTTGTGTAGCTCCACTTGCCAATTCAACCCGGAACAAACAGGACGCAATCCGTCCCCCA
TGTAATAAGGTTTGTTGCTTGGACGCCCATCCATGGCCGTTTCTTGGTCAGACTGACCACTGTGCCGTCGCCGTTACGAC
CTCTTCCTCTTCCTCTTCCTCTTGCTCCTTTCTTTATTCAGCCCGCCTGCATGCATGGCCTGTGTAGGCAAGAGCTGCGG
CATGGGTGCTCCGCTTGCTTCTGGTACACGTCCCGGTGGTGATCGAGAGCGAGACCCAGACCGGCTCGCACGATCCTTTG
CCTTGCGCTGACATGATCAAG------TCAACCAATGGTGGCGCG------------GTCGACGGCCGCGCCACTAGCTG
CATGCGTCGCCCCCACCCACCACACCACTGCCGGCCGCCATTGTCGCATTCCGCATGTCCTCACGCCACTCCACCGGTAA
GGCAGTCGGTGGAGCGGATATAAAACGCACACGCGTGTCCTCATGTCGAGCAAGCCGCCAATAAGCACT----CCAGCAA
TGGCACCTCACGCGCGCGGCCTCCGTTTCCTCATCGCCGTTGCCGTGTTCTCGGCCGCCACGGCCGTGGCGGGGGCGCGG
CACGGCGCCGCCGGGCAGTGCCGCCCGGTGGGGGCGATCGTCACCGAGGAGCTCTACTCGTCCCTGTTCCTGCACAAGGA
CGACGCCGTCTGCCCCGCCAAGGGGTTCTACACCTACGCGTCCTTCATCCGCGCCACCAGGAAGTTCCCCAAGTTCGGCG
CCACCGGCGACCTCGTGACGCGCAGGCGCGAGGTCGCCGCCTTCCTCGCGCAGATCTCCCACGAGACGACGGGCGGGTGG
GCGACCGCGCCGGACGGCCCATACTCGTGGGGCCTGTGCTACAAGGAGGAGATCAGCCCGCAGAGCAGCTACTGCGACGC
CACGGACAAGCAGTGGCCGTGCTACCCCGGCAAGTCCTACCATGGCCGAGGCCCCATCCAAATCTCATGGTACTGATAAA
TTCCCTGAGCTTACCTGCAAATTTCACTCATGGCGCCGGCTCGTTAGAATGCACACATCTGACCTCTGAGTCTGACCTCT
GACCTCTGGCCGGCTGATGAACAGGAATTTCAACTACGGTCCGGCGGGGCAGGCCCTGGGGTTCGACGGGCTGCGGAACC
CGGAGCTGGTGGCCAACTGCTCGGACACGGCGTTCCAGACGGCGTTGTGGTTCTGGATGACGCCCAGGGAGACCAAGCCG
TCGTGCCACCAGGTGATGGTCGGCGAGTACCGCCCCAGCAGGGCCGACGCCGCCGCGAACCGCACGGCCGGGTTCGGGCT
GGTCACCAACATCGTCAACGGTGGCCTCGAGTGCAACGTCGCCGACGACGCGCGGGTCAACAACCGGATCGGCTTCTACC
GGCGGTACTGCCAGGTCCTCGGCGTCGACGTCGGGCCCAACCTCGACTGCGCGCACCAGCTCCCGTACTAGCCCGAGGGA
GTACCCTCACGTTTCTCGATCGGGAGAAAACCATAGCCTCACGTGCTACGTAGTTGCTTAAATTTGTAGTTTAGTTAAGC
CTACAAAGAAAAACACTTGTATTTTGTTAGTAATAA---ATCTAATAAATTAAGGTTCCTTT-------AACATTGATCA
TACTATCAACAAGTGAAATTGAAGCAAGCACGAATGACAAATATCCTGAGCAAATTGAAAGCTACACCAAGAT--TCTAA
AGTCGTCGTGTC--------------------------------------------------------------------
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-------------------------------------------------------TAACTTCATTGTTCGCACCTAATTG
TGCTTTCTTGTATTCGATAAAGATTTTTTTTGA-----------GAAGTATTCGATAATGAAATTGTAGAGGACAAGCCG
AACAAGGCGGAGTGA-C-TTTTTTTAAAAGAGAGGGGCTTGCCAGGCAATAAACTGAGGCCCTTCTCTTACAAAAAGAGT
GCAAAGTAAAGTAAACGAAATCATACAGGGTCACAAGTGACCGAACAAAGTGGCACCTCGCTTGCAAGCTAGACACTAGA
CATAGGAAACAATGAGGGTCACCCACGGAGAGTCTCTGAATGGAAGAAGACGATCAGACGATGGCTTCTAGCCCT--CAT
TGTCCCGTCTCAAGGCGGCGCGAAGAGCTTGACACTTTGCACAAAGATTGTTGATCAGATGATCATGTTGTGGTCGATCC
TATTGTCTCTCCAGTGATCTCCCAA-------------------TTTATACACAAGATTGGTTCGATGCTTGAATACAAG
ACCTTC----------------TCCAAAGTTACCATGCTAATGCAGCAAATCCCACACAACAAATTTTCCTATCTTTTTT
GTGGGTCCCTTGCACAAGTTTATGGAATTTGGCAAACCTAGCCGGATTCCGCGAGAACCCCCTGGTGTTTCA--GATCAC
ACTCCATATAAATTTGGCCACTATGCATGAGAAGAATATGTGGTCACAATTTTCATTGACACCACACCAAATGCAAGTGT
CGT
>chr3B_171
AGGC----------------------------------------------------------------------------
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---------------CGGCCGTGATTTGCAGGCTGTGCACATATCTTCCACTCTAGAGCAGTCAACGCTAGCTCGAATAG
ACACGCATGCTTACCAGTTACCTCCTTCGGAAAAAGAAGAGACGCATTCTTATATTGCAGCACTAACCGGTCGTATTGCG
CCAACGAACTCCACTCACCATGTAAGCTGCTGACCTGGTTTCGATTAGATACCCTGCGCACCCGGCCGCATGCTGAATGG
TCTTCCCA-TTGCTGCAATGATTTCCCAATTTCCGGCATGTAATGCTTGGACGCACCACGGCTCCACTTACGATTCATAA
TCTATAGCTGAATCTTCTGGATTTGTATGACTCCACTTGCCAATTCAACTAGGAACAAACAGGACGCTATCCGTCCCCCA
TGTAATAAGGTTTGTTGCTTGGACGCCCATCCATGGCCGTTTCTTGGTCAGACGGACCACTTTGCCGTCGCCGTTACGAC
CTCTTCCTCTTCCT------CTTGCTCCCTTTCTTATTCAGCCCGCCTGCATGCATGGCCTGTGTAGGCAAGAGCTGCGG
CATGGGTGCTCC----GCTTCTGGTACACGTCCCGGTGGTGATCGAGAGCGAGACCCAGACCGGCTCGCACGATCGTTTG
CCTTGCGCTGACATGATCAAG------TCAACCAATGGTGGCGCGGTCAGAAACTGCGTCGACGGCCGCGCCACTAGCTG
CATGCGTCGCCCCCACCCACCACACCACTGCCGGCCGCCATTGTCGCATTCCCCATGTCCTCGCGCCACTCCACCGGTAA
GGCAGCCGGTGGAGCGGATATAAAACGCACACGCGTGTCCTCATGTCGAGCAAGCCGCCAATAAGCACT----CCAGCAA
TGGCACCTCAGGCGCGCGACCTCCGTTTCCTCATCGCCGTCGCCGTGTTCTCGGCCGCCGCGGCCGTGGTGAGCGCGCGG
CATGGCGCCGCCGGGCAGTGCGGCCCGGTGGGGGCGATCGTCACGGAGGAACTCTACTCGTCCCTGTTCCTGCACAAGGA
CGACGCCGTCTGCCCCGCCAAGGGGTTCTACACCTACGCGTCCTTCATCCGCGCCACCAGGAAGTTCCCCAAGTTCGGCG
CCACCGGCGACCTCGTGACGCGGAAGCGCGAGGTCGCCGCCTTCCTCGCGCAGATCTCCCACGAGACGACGGGCGGCTGG
GCCACCGCGCCGGACGGCCCCTACTCCTGGGGGCTGTGCTACAAGGAGGAGATCAGCCCGCAGAGCAACTACTGCGACGC
CACCGACAAGCAGTGGCCGTGCTACCCCGGCAAGTCCTACCACGGCCGAGGCCCCATCCAAATATCATGGTACTGACAAA
TCCACAGAGCTTACCTGCAAATTTCACTCATGGCGCCGGCTCGGTAGAACGCACACGTG-------------------CT
GACCTCTGGCCGGCTGATGAACAGGAACTTCAACTACGGCCCGGCGGGGCAGGCCCTGGGGTTCGACGGGCTGCGGAACC
CGGAGCTGGTGGCCAACTGCTCGGACACGGCGTTCCAGACGGCGCTGTGGTTCTGGATGACGCCCAGGGAGACCAAGCCG
TCGTGCCACCAGGTGATGGTCGGCGAGTACTGCCCCAGCAGGGCCGACGCCGCCGCGAACCGCACGGCCGGCTTCGGGTT
GGTCACCAACATCGTCAACGGTGGCCTCGAGTGCAACATCGCCGACGACGCGCGGGTCAACAACCGGATCGGCTTCTACC
GGAGGTACTGCCAGGTCCTCGGCGTCGACGTCGGGCCCAACCTCGACTGCGCGCACCAGCTCCCGTACTAGCCTAAGGGA
GTAGCCTCACGTTTCTCGATCGAGAGAAAA-CATAGCCTCACGTGC----TAGTTGCTTGAATTTGTAGTTTAGCTAAGC
CTACACAGAAAAACACTTGTATTTTGTTAGTAATAACAAATCTAATAAATTAAGGTTTCTTTCTTAAACAACATTGATCG
TACGGTCAACAAGTGAAATTGAAGCGAGCACGGATGACAAATATCCTGACCAAATTGAAAGCTACACCAAGATTCTCTAA
AGTCGTTGTGTCTTCGGAAGTAAGTTTAGGATAAGGTTTCCGATCCGGTTGGTGTTCTGATATTTTGCGCTTTCATATTC
TAGTTCCTCATTTGAGCGATACCCACTTGGAGCTGACCTTCACTTTTCAGAGACAGGGGCAAGCCGATAATTTGTAGCCT
CCCTGGTGGGAGTATATCGAATATAAGGCTGCCCTCAGGCAATCCCAACCCATAATAAGACTGATGAAAGNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNCAACAAAGGGGTGGGAGCGATGTGCCGCCTTTAACTTCATTGTTCGCTGCTAATTG
TGCTTTCTTGTATTCTATAACGATTTTGTTTTTTGTTTTTGCGGGAAGTATTCGATAATGAAATTGTAAAGGACAAGCAG
CACAAGACGGAGTCACC-TTTTTTTTAAAGAGAGGGGCTTGCCCGGCAATAAAGTCAGGCCCTTCTCTTACAAAAAGAGT
GCAAAGTAAAGTAAACGAAATCATACAGGGTCACAAGTGACCGAACAAAGTGGCACCTCGCTTGCAAGCTACACACTAGA
CCTAGGAAACAATGAGGGTCGCCCATGGAGAGTCTCTGAATGGAAGAAGACAATCACACGATGGCTCCTAGCTCT--CGT
TGTCCCGTCTCAAGGCGGCACGAAGAGCTTGACACTTTGCGCAAAGATTGCTGATAAGATGACCATGTTGTGGTCGGTTC
TATTGTCTCTCCGATGGTCTCTAAAGCTGTAGAAAAAAAACAAGTTTATACACAAGATCGATTGGATGCTTGAATACAAG
ACATTCCATTGGTTTCTAGCATTCCAAAGTGACCATGCTAATGCCTC---------------------------------
GTGGGTCCCTTGCACAAGTTTATGGAATTCAGCAAACCTAGCCGAATTCCACGATCAACCCGTGGTGTTTCA--GATCAC
ACTCCATATAAATTTGGCCACTATGCATGAGAAGAATATGTGGTAACAATTTTCATTGAGACCACACCAAATGCAAGTGT
CGT
>SNPs
S-S-S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----------S
S---S--S------------------------------------------------------------------S--S--
-----------S-----------------SS-------S-----------------------------------------
-----------------S-----------------------S--------S--------S----SSSS------------
------S-S----------------S---------------------------------------------S--S-----
S----------------------------------------------------------S--------S-----------
--------S-----------------------------------------------------------------------
----------------------S-------------S------S--------------------S---------------
------S----------------S-----------------------------S-----------------S-----S--
---------------------SSSSSS------S----------------------------------------------
---------------------------------------S-----S--------S------------S-----------S
S--S------------------S--S--S----------------S---------S-------------SSSS-------
-----S-------S-----S-----S------S-----------------------------------------------
S-----------------------------------------------S-------------------------------
---------------------------------------------------S-------S-----------S--------
--------------------------------S----------------------------S--------S---------
--------------------------------------------------------S-----------------------
------------------S-------------------------------------------------------------
-----S---SS----------------S------------S-SSSS-SSSSS----------------------------
---------------------------------------S--------------S---------------------S---
----------------------S----------S-------------------------------------S--------
---------------------------------------S---------S------------------------------
---------------------S------------------S----S----------------------------------
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S------------S-----S------------------------------------------------------------
-----------------------------------------------------------------S--S-----------
-------------------------------S------------------------------------------------
----S---------------------------------------------------------------------------
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-------------------------------------------------------------------------S------
-----------------S----------S----SSS-----S----------S--S--SS-------------------S
-------S-----SS--S------------------------S--S---------S----------------S--S----
------------S---S---S------S-S---------S--------------S-S----------------------S
---------S--S-S-------------------S-----------------------S---------SSSSS-SSS---
-----------S-S----------------------------------------S----S-------------S-S---S
-S----S--S-S----S--------S--------SS-S-----S--S---------------S------------S----
---------------SS--------------S----S--------SS---------S---S-------S-----S-----
----S---------S-------------------------------------S---------------S--SSS------
--------S---------------S---S-S-----------------------------S--S---------------S
---
>forward_104
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----ACGTCACATTCGGAGGTCAC--------------------------------------------------------
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>reverse_2001
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CTAGCCTCACGTTCCTCGAC------------------------------------------------------------
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