>input_sequence_64045
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-----------------------------------------------------------------ATGCAGGACCTGTTC
TCGGTGCCCTCCTGCTTCTCGTCCGGCGAGAAGCAGCTGCCGGACGCGCCGGCGTCGGCGGCGCCGGCCACCAGGTCGGG
GCAGAGCGCGGTGACGCTGGTGTACCGCGCCGTGATCTCCGGGCAGAGCCGGCTGGTCACCGTGACGTGGTGCAGGAACC
TGCTGGCCCACGGCATGCAGGTGTCCATCGAGGGGTCGGCCGGCGGCGGCAAGGACAAGAGCGGCGGC------GGAAGG
GAGCACGGCAGCGGCGGCGGCATCGAGGGCGGCGGCGGCGGCGCCAATAAGAGCTGCAGCGCGTGCAAGGTGGAGATGCA
GCCGTGGCACTTCTGGCGCAAGTACGGGGCCAAGCAGTTCCAGGTGGACGGCCGGCCGGTGGACGTGGTGTGGGACCTGC
GGGCCGCGCGCTTCTCCGACGAGCCGGAGCCGGTGTCGGACTACTACGTGGCGGTCGTCTCCGGCGAGGAGGTGGTGCTC
CTGCTCGGCAACCAGAACAAGGAGGCGTTCCGGCGGACGGGGTCGCGGCCGTCGCTCTCGCTGGGGGACGCGGCCATGGT
GTGCAAGAAGGAGCACGTGTTCAGCAAGAAGCGGTTCCTGACCCGGGCCAGGTTCCACGAGAAGGGCAAGCTGCACGACA
TCAGCATCGAGTGCAGCAGCGGCAACCTCGGCGGCGGCG------GCACGGACGTGGACATGGCCATCAAGATCGACGGC
TGCGTCAACGTGCTCGTCAAGCACCTCCAGTGGAAGTTCAGGGGCAACGACTGCATCTCCATCAACAAGATGAAGGTGCA
GGTCTACTGGGACGCCCACGACTGGCTCTTCGGCACCGGCATGCGCCAGGCCCTCTTCATCTTCAAGCCCCAGGCCCCCT
CCCCCTCGCCATTGCCCGACTTCGCCGCCGCCCCCGCCGCCGACGAGTTCTCCGATTTCTGCCTCTTCCTCTACGCATGG
AAGATCGAATGA--------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G411600
ATCTGTTATTTGTTTCCTAAAACAAATTGAACCAATAAAAGGAATCAATTGATTTGCATAATTTAAGGAAGTTAGATCCG
TGATTTGTTATAGGTTAGGAAAGTTCTGGTTGTAATAAAGAGTGAAGAGAAAAATAAACCGATGAACCAGGATGGGAGGG
GGTGGTGGGAGAAGAGACGAAAAAAACCAGCGAAAATAAACCACGGAGACGATTCACCAACTCGTTCATTAAAAGTAGAG
ATCCCCAGAGGCCAGAGGCCAGAAATCCGGCGCCA----CACATCCCCACATGCCCTTCCATGTGCATGTGCCATGATCT
CCAGCATGTTGCCCACATGCCGCTGCTCGCCGTCG-----------CCGAGACCCCCAGACAGTAACCCCGGGCTCACTG
TACACTGCCTGAGAGCTATCACGCATCA----------GCCATGGCCTCTCG--TCGTCGACACTCATGGTGAAAGTTGG
CAGCGTAAGCTTAGTATATAGTGAAGCGTGGTAGTAGAAAAATG-----------------GAAAATATATACGATACTC
CTAGGATC---GGAGCATAGTGTAATGGCCCGCGGAGGAATCAAGGCTGGATCGGTCCCCGGGCCGGACCGGGCCTGCG-
----AGATGGCGCACGCATTTACTCGCTCCAAGCAATAGCAATAGCAATAGCAATAACAATAGCAATAGCAAGCGGATGA
AGAAGGTTCATGGTTTAAAACGCCACACCTCATGCCCATGGGG-----GGCAAGGCAACCCCCCAACTCACTTTCGTGCA
CAGCTCACTTTCCAGCGCGGTTCGGCTCGCTCGCCAGCCAGTCTACGGTCTCCTGCCCGACTGCCTCCCTCCCCTCCCCC
CCTC----------------------------------------------------------------------------
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----------GCCAAACCGAGCTCCGTCATCATGCTGGCTCCGCTGCTGCATGGATCCATGGCGCTCCCCCACCCCCGCG
CCGCCGCCTATGTATAGTAGCCTTCCTTGCTAGCCCATCATCCATCCATCCATCCATCCTCTCGTGTCTCTCAGTTCGTC
ATAGCTA------------------------------------------GCGAGGGGCAGACAGGATGCAGGACCTGTTC
TCGGTGCCCTCCTGCTTCTCGTCCGGCGAGAAGCAGCTGCCGGACGCGCCGGCGTCGGCGGCGCCGGCCACCAGGTCGGG
GCAGAGCGCGGTGACGCTGGTGTACCGCGCCGTGATCTCCGGGCAGAGCCGGCTGGTCACCGTGACGTGGTGCAGGAACC
TGCTGGCCCACGGCATGCAGGTGTCCATCGAGGGGTCGGCCGGCGGCGGCAAGGACAAGAGCGGCGGC------GGAAGG
GAGCACGGCAGCGGCGGCGGCATCGAGGGCGGCGGCGGCGGCGCCAATAAGAGCTGCAGCGCGTGCAAGGTGGAGATGCA
GCCGTGGCACTTCTGGCGCAAGTACGGGGCCAAGCAGTTCCAGGTGGACGGCCGGCCGGTGGACGTGGTGTGGGACCTGC
GGGCCGCGCGCTTCTCCGACGAGCCGGAGCCGGTGTCGGACTACTACGTGGCGGTCGTCTCCGGCGAGGAGGTGGTGCTC
CTGCTCGGCAACCAGAACAAGGAGGCGTTCCGGCGGACGGGGTCGCGGCCGTCGCTCTCGCTGGGGGACGCGGCCATGGT
GTGCAAGAAGGAGCACGTGTTCAGCAAGAAGCGGTTCCTGACCCGGGCCAGGTTCCACGAGAAGGGCAAGCTGCACGACA
TCAGCATCGAGTGCAGCAGCGGCAACCTCGGCGGCGGCG------GCACGGACGTGGACATGGCCATCAAGATCGACGGC
TGCGTCAACGTGCTCGTCAAGCACCTCCAGTGGAAGTTCAGGGGCAACGACTGCATCTCCATCAACAAGATGAAGGTGCA
GGTCTACTGGGACGCCCACGACTGGCTCTTCGGCACCGGCATGCGCCAGGCCCTCTTCATCTTCAAGCCCCAGGCCCCCT
CCCCCTCGCCATTGCCCGACTTCGCCGCCGCCCCCGCCGCCGACGAGTTCTCCGATTTCTGCCTCTTCCTCTACGCATGG
AAGATCGAATGAGCTCCCTCGCTCGCTCGCTGGCTAGCTAGGTGCTCTTACCTACATTCGTTTGTTACTGCCGCCACATT
ACAGAGCGGATGATGATGGACATTTCACCATGTTATGAGCAAGATACTACTACCATGTAATGTGACAATGTGT-------
---GTGTAAGAGGGGGAGTGAATGTCTGTCTGATTGAGGTTGAGGTTGAGGGCCTGAGGCCATTCTTCTCTGTTCCATTG
GAGCGTGTTGTGCATGCACATGGAGGATCGGCATGGAGGGGCACAGGATAGTCCTGGGGGCGAGGAACAGCCTGGTCCTG
ATGGAGAAACATGCATATGCATGGAGGGTGGCGACATGACAGGCAGAACGGCATATGGCCTTTCCCAATCAATCATGCTG
GTTTATCCAGGGGAACTCCAGCTAAGA--------GAACTGGTCCCTCCCAACTCCTAACTCCTA------TCTAGCAGT
A--CTCTACTCTACACTGCCTCTGATTTCTTTGTTATCATCTTCCACTCACTTACTTTGACCGGCCTAACTAACAAACTG
-----CCTCTGCTTTCCTCCGTTCAAGAACAAGGAGAGCAGGTATGGACAAGGACACAAGATA------CT---GGTACA
ATAGCT---GTATTTAACTCAGCTGTGCTATTGTTAATGGCGACTGGTCAAAGAGTGCACTGTTTTTCACCCAGGTTTTC
AGTGATGGTCACATTTGGACCATGCAGCTTTGGTAACCCCCATGCCCAAGTTGAGATCTCAGGGACGTCTACTGGGCC-A
GTTTTAATAGTGGCTAACAGATGCAGATGAAAGGCTAC-------------TACTATGTTTCATACAGACTAAAAAAAAT
ACA-CATACATAGGGTATACAGGGCTCAAGAAAAAAGTGAGCACAGTAGCTCCCTGGAGAACAGGTCAATCATGTAGTA-
--CATACCTACCATCAGCTGAGAAGTTGACAAAGTTTTATCCATTCCAATGCTCATGCCTTCCCCATTGGCTGACAGCCA
TTGTTTAAACCAGGAATGCCATAGAATCTAGAT
>chr3A_241
ATCCCCCAGC----------------------------------------------------------------------
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-----------CCAGAGGCCAGAAATCCGGCGCCGCAGCCACATCCCCACATGCCC-------------TGCCATGATCC
CCGGCATGTTACCCACATGCCCCTGCCCGCCGTCG-----------CCGAGCCCCCAGGACAGTAACCCCGAGCTCACCG
CCCTCTTACCTGAGACCGAGAGCCATCGGCCATGCATGGCCATGGCCTCTCG--TCGTCGATACTCATGGTGAAACTTGG
GAGC--------------------------GTAGTAGAAAAACG-----------------GAAAATATATGCGATGCTC
CTAGGATCGGAGGAGCATAGTGTAGTGGCCCGCGGAGGAATCAAGGCTGGATCGGTCCCCGGGCCGGACCGGGCCTGCGC
TGCGAGATGGCGCACGCATTTACTCGCCCCGAGCGACGGCGAGCGAGCGGAG----------------------GGAGAA
AGAAGGTTCCCGGTTTAAAACGCCACGCCCCATGCCCATGGGGGGCAAGGCAAGGCAGCCCCCCAACCCACTTTCGTGCA
CAGCTCACTTTCCAGCGCGGTTCGGCTCGCTCGCTACCCATAGCCAGCCAGCGTCTCCTNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNGCCGAACCGAGCTCCGTCATCATGCCGGCTCCGCTGTTGCATGGATCCATGGCGCCCCCCCACCCCCTCG
CCGCCGCCTATGTATACTAGCCTTCCTCCTCCTTAGCCCAT-----CATTCATCCATCCCCGAGTGTCTCTCAGCTCGTC
GGCTCGTCATAGGCTCATCACTAGTGGATAGGCGCCTTGGTCGAGTCGGGTGAGGGGCAGGCAGGATGCAGGACCTGTTC
TCGGTGCCCTCCTGCTTCTCGTCGGGCGAGAAGCAGCTGCCGGACGCGCCGGCGTCGGCGGCGCCGGCGACCAGGTCGGG
GCAGAGCGCGGTGACGCTGGTGTACCGCGCGGTGATCTCCGGGCAGAGCCGGCTGGTCACCGTCACGTGGTGCAGGAACC
TGCTGGCCCACGGCATGCAGGTGTCCATCGAGGGGTCGGCCGGCGGCGGCAAGGACAAGAGCGGCGGC------GGCAGG
GAGCACGGCAGCGGCGGCGGCATCGAGGGCGGCG---------CCAATAAGAGCTGCAGCGCGTGCAAGGTGGAGATGCA
GCCGTGGCACTTCTGGCGCAAGTACGGGGCCAAGCAGTTCCAGGTGGACGGCCGGGCGGTGGACGTGGTGTGGGACCTGC
GGGCGGCGCGGTTCTCCGACGAGCCGGAGCCGGTGTCGGACTACTACGTGGCGGTGGTCTCCGGCGAGGAGGTGGTGCTC
CTGCTCGGCAACCAGAACAAGGAGGCGTTCCGGCGGACGGGGGCCCGGCCGTCGCTGTCGCTGGGGGACGCGGCCATGGT
GTGCAAGAAGGAGCACGTGTTCAGCAAGAAGCGGTTCCTGACCCGGGCGAGGTTCCACGAGAAGGGGAAGCTGCACGACA
TCAGCATCGAGTGCAGCAGCGGCAACCTCGGCGGCGGCGGCGGCGGCACGGACGTGGACATGGCCATCAAGATCGACGGC
TGCGTCAACGTGCTCGTCAAGCACCTCCAGTGGAAGTTCAGGGGCAACGACTGCATCTCCATCAACAAGATGAAGGTGCA
GGTCTACTGGGACGCCCACGACTGGCTCTTCGGCACCGGCATGCGCCAGGCCCTCTTCATCTTCAAGCCCCAGCCCCCCT
CGCCCGA---------------CTCCGACGCCGCCCTCGCCGACGAGTTCTCCGATTTCTGCCTCTTCCTCTACGCATGG
AAGATCGAATGAGCTAGACT----------TAGCTAGCTAGACACCCTG-CCTACATTCGTTTGTTACTGCCGCCACATT
ACAGAGCGGCTGATGATGGACATTTCACCATGTTACGAGCAACATACTTCTACCATGTAATGTAAGTATGTAACGATGTG
TGAGTGTAAGAGGGGGAGTGAATGTGTGTCTGATTGAGGTTGAGGCTGAGGCCAT---GCCATTCTCTTCTGTTCCATTG
GAGCTTCTTGTGCGTGCACATGGAGGATCGGCGTGGAGGGGCACAGGGTAGTCCTGGGGGCGAGGAACAGCCAGGTCCTG
ATGGGGAAACACGCAT------GGAGGGTGGCGACATGACAGGCAGAAGGGCATATGGCCTTTCCCGATCAATCATGCCG
GTTTATCCAGGGGAACTCCAGCTAAGAGAAGTAGAGAACTGGTCCCTCCTAACTCCTAACTCCTACTCGTATCTAGCAGT
ACTCTCTACTCTACACTGCCTCTGATTTCCTTGTTATCATCTTCCACTCACTCACTTTGACCGGCCTAACTAACAGACTA
ACATCCCTCTGCTTTCCTCCGTTCAAGAACAAGGAGAGCAGGTATGGACAAGGACACCAGATAGGAGCACT---AGTACA
ATAGCTGTAGTATTTAACTCGGCTGTGCTATTGTTGACGGCGACTGGTCAAAGAGTGCACTGTTTTTCACCCAGGTTTTC
GGTAATGGTCACATTTGGACCGTGCAGCTTTGGTTATCCCCATGCCCAAGTTGAGGGTTCAGGGATGTCCACTGGGCCGA
TTTTATTTAGTAACCAACAGATGAAAGAGAAAAAGGCTACTACAGATCAGATACTATGTTTCATACAGGCAAAGAAAAAT
GAAGCAAATATAGGTTATACAGGGCTCAAGAGAAAAGAAAGTACAGTAGCTCCCTGGAGAACAGGTCAATCATGTAGTAG
TACATACCTACCATCAGCTGAGAAGTTGACAAAGTTTTATCCATTCTAATGCTCATGCCTTCCCCACTGGCTGACATACA
TTGTTTAAACCAGGAGTGCCATAGAATCTAGA-
>chr3B_252
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-----------CCAGAGGCCAGAAATCCGGCGCCA----CACATCCCCACATGCCCCTCCATGTGCCAATGCCATGATCT
CCAGCATGTTGCCCACATGCCCCTGCTCGCCGTTGCCGCGACCGCCCCGAGCCCCCAAGATAGTAACCCCGAGCTCACTG
CACACTACTTACCTGAGGAGC--CATCA----------GCCATGGCCTCTCATCTCGTCAATGCTCATGGTGAAAGTTGG
CAGC--------------------------ATAGTAGAGCACTCCGTAGTAGAAAAATGAAGAAAAAAAATAGTATACTC
CTAGGATC---GGAGCATAGTGTAATGGCCCGCGGAGGAATCAAGGCTAGATCGGTCCCCGGGCCGGACCGGGCCTGCG-
----AGATGGCGCACGCATTTACTCGCTCCAAGCAAGCGATG--------------------------GCAAGCGGAGGA
AGAAGGTTCCTGGTTTAAAACGCCACCCCCCATGCCCATGGGGGGCAAGGCAAGGCAACCCCCCAA--------------
---CTCACTTTCCAGCGCGGTTCGGCTCGCTCGCCAGCCAGCCTACGGTCTCCTGCCCGACTGCCTCCCTCCC-TCCCCC
CCTC----------------------------------------------------------------------------
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----------GCCAAACCGAGCTCCGTCATCATGCCGGCTCCGCTGTTGCATGGATCCATGGCGCTCCCCCACCCCCGCG
CCGCCGCCTATGTATAGTAGCCTTCCTTGCTAGCCCATCATCGATCCACTCATCCATCCTCTCGTGTCTCTCAGTTCGTC
GTAGATA------------------------------------------GTGAGGGGCAGACAGGATGCAGGACCTGTTC
TCGGTGCCCTCCTGCTTCTCGTCCGGCGAGAAGCAGCTGCCGGACGCGCCGGCGTCCGCGGCGCCGGCGACCAGGTCGGG
GCAGAGCGCCGTGACGCTGGTGTACCGCGCGGTGATCTCCGAGCAGAGCCGGCTGGTCACCGTGACGTGGTGTAGGAACC
TGCTCGCCCACGGCATGCAGGTGTCCATCGAGGGGTCGGCCGGCGGCGGCAAGGACAAGAGCGGCGGCGGCGGGGGCAGG
GAGCACGCCAGCGGCGGCGGCATCGAGGGCGGCGGCGCC---------AAGAGCTGCAGCGCGTGCAAGGTGGAGATGCA
GCCATGGCACTTCTGGCGCAAGTACGGGGCCAAGCAGTTCCAGGTGGACGGCCGGCCGGTCGACGTGGTGTGGGACCTGC
GGGCCGCGCGGTTCTCCGACGAGCCGGAGCCGGTGTCGGACTACTACGTGGCGGTCGTGTCCGGCGAGGAGGTGGTGCTG
CTGCTCGGCAACCAGAACAAGGAGGCGTTCCGGCGGACGGGGGCCCGGCCCTCGCTGTCGCTGGGGGACGCGGCCATGGT
GTGCAAGAAGGAGCACGTGTTCAGCAAGAAGCGGTTCCTGACCCGGGCGAGGTTCCACGAGAAGGGCAAGCTGCACGACA
TCAGCATCGAATGCAGCAGCGGCAACCTCGGCGGC---------GGCACGGACGTGGACATGGCCATCAAGATCGACGGC
TGCGTCAACGTGCTCGTCAAGCACCTCCAGTGGAAGTTCAGGGGCAACGACTGCATCTCCATCAACAAGATGAAGGTGCA
GGTCTACTGGGACGCCCACGACTGGCTCTTCGGCACCGGCATGCGCCAGGCCCTCTTCATCTTCAAGCCCCAGGCCCCCT
CGCCGTCA------CCCGACTTCGACGCCGCCATCGCCGCCGACGAGTTCTCCGATTTCTGCCTCTTCCTCTACGCATGG
AAGATCGAATGAGCT----CGCTCGCTCGCTAGCTAGCTAGATGTTCTTACCTACATTCGTTTGTTACTACCGCCACATT
ACAGAGCGGATGATGATGGACATTTCACCATGTTGTGAGCAACATACTACTACCATGTAATGTAACGATGTGC-------
-GAGTGTAAGA-GGGGAGTGAATGTCTGTCTGATTGAGGT------TGAGGCCAT---GCCATTCTCTTCTGTTCCATTG
GAGCGTGTTGTGCATGCACATGGAGGATTGGAGCGGAGGGGCACAGGATAGTCCTGGGGGCGAGGAACAGCCTGGTCCTG
ATGGGGAAACATGCAT------GGAGGGTGGCGACATGACAGGCAGAAGGGCATATGGCCTTTCCCAATCAATCATGCTG
GTTTATCCGGGGGAACTCCAGCTAAGA--------GAACTGGTCCCTCCTAACTCCA-------A------TCTAGCAGT
A--CTCTACTCTACACTGCCTCTGATTTCTTTGTTATCATCTTCCACTCACTTACTTTGACCGGCCTAACTAACAAACTA
ACATCCCTCTGCTTTCCTCCGTTCAAGAACAAGGAGAGCAGGTATGGACAAGGACACAAGATA------CTACTAGTGCA
ATAGCT---GTAATTAACTCAGCTGCACTATTGTTAATGGCGACTGGTCAAAGAGTGCACTGTTTTTCACCCAGGTTTTC
AGCAATGGTCACATTTGGACCATGC-------GTAATCCCCATGCCCAAGTTGAGATCTCAGGGATGCCCACTGGGCC-A
GTTTTAATAGTGCCTAACAGATGCAGATGAAAGGCTAC-------------TACTGTGTTTCATACAGACTAGAACAATG
ATAATTCAAAATGGTGCCCA--GGTTCAAGAAAAAAGAAAGTACAGTAGCTCCTTGGAGAACAGGTCAATCATGTAGTAG
TACATACCTACCATCAGCTGAGAAGTTGACAAAGTTTTATCCATTCCAATGCTCATGCCTTCCCCATTGATTGACATGCA
TTGTTTAAACCAGGAATGCTATAGAATCTAGA-
>SNPs
---SSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSS---------------------------------------------S---------SSS-----------
---------------------S-----------------------------S----S--------------S--------
S-----S---SSSS--SSSS-SS--------------------------------------S------------------
----SSSSSSSSSSSSSSSSSSSSSSSSSS--------------------------------------------------
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------------------------------------SS--S-SS-SSSSSSSSSSSSSSSSSSSSSSS---------S--
---------S----------------S--S-------------------------------------S------------
-----------------------------------------S-------------------------------S------
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-----------------------------------S----------S---------------------------------
------------------------------------------S------S------------------------------
S-------------------------------------------------S-----------------------------
--------------------------------------------------------------------S-----------
------------------------------S-------------------------------------------------
----------------------------------------------------------------------------S---
-------------------------------------S-SSSS-------------------------------------
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----------S---------------------------------------------------------------------
------------------------------------------S-S-----------S-----------------------
------------------------------------------------S-------------------------------
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-S-----SSSSSSS------------------S-----------------------------------------------
---------------SSSS------------S---------S--------------------------------------
------------------------------------------S--------------------S--S-----S-------
---------------------------------------------S-----S-S-SSS--------SS------------
--------------------------------S-----------------------------------------------
----S-----------SSSSSS--------------------------S-------------------------------
-------------------------------------------------S------------------------------
-------------------------------------------------------------------------------S
--------------------------------------------------------------------------S-----
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---S--------------------------------S----------------------------S---S----------
------------S-------------------------------------------------------------------
-S----S-S-----S----------------------SS--S--------------------------------------
----------------------------------------------------------------------------SS--
--------------------------------S
>forward_487
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-------------------------------------------------------------------TGGTGAAAGTTGG
CAGCGTA-------------------------------------------------------------------------
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>reverse_2673
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--------------------------------ATGGAGGGGCACAGGATAGT----------------------------
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