>input_sequence_73048
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---------ATGCGACTTTTTCTTCTT---------CTTCTTTGGTTGCTTTTAGCTCTTTTTGTCCGGCCATTTGGTGA
ATCACCGAGCCACATCCACATGATCGTTCTGCATTTCTCCAAATATATATGTACCAGCACCGTGCAGTTCAATCAGTCTA
-------GAGAGCAGTTCAAGATCGTAGCAACAGTTTGCTATTTAGGCTGTTTCTAGTAGCCACTAACTGTTGATTCTCG
CAACGGCAGCTCGATTGGCGACCGAAGCAATGGCGTCCATCCGGCGAGATCTGCTCGTGGCGCTCTGCGTGGCGGCGCTC
CTGGCCGTCGGGTCGGAGTCCCACGGGCTGGAGGACTTCGGCAGCGAGGGGAAGACGGAGGCGACGCCCGAGATGGCCTC
CTTCTTCGGCGCCAAGCCCGAGGCCGCCGTGCTCCCGGAGGCGCTGGACAACAACAAGGCCGCCAAGCCGGAGGCCGCCT
CGGCGATGCCCACCACCACCACCAGCACCAACCCACGCTCGTCCCCGCCGCGCAGATCCGTGGCCGTCGCGGCCGGCGTG
GCCTGCGGCGTCGCGGCCCTGGCGGTGGTCGGCGTGGCGGTCGCCGTCGCCTTCGTGGTGCGCGCCAGGCGCGGCGAGAG
GCGCGAGGCCGAGGTCCATCTCGGCTAA----------------------------------------------------
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>chr2D_1_TraesCS2D01G463900
TTACCACTCGCCTGATCGATCGAGAGTCACCGGCCAATGGCGATCAACCGTCCATGTGCGCTAGCACGTCGCAGTACATC
TCTCAGGACTCGAGGACGGCCCTGCTCGTACTCGCCCAACAACCAGCAGGCGAACGGCTGATGAGTTGCGTGACTTGACC
TC-GAGGAGTAG-------------------------------TATGATGAAGCGGACGACGCATGAGCTAATTATGGTC
ACCGGGCACTGCGCTCGCTGCACGAGGGC------CGATCGCTTGCCCGTGAAGCGCGGCTCGTGAACCGGGGGATAGAA
TAGACAGCCCCCTACGCGACCGAGGAAAAGTACAACGGAGTACAGTAACCGTAGCAAAGAATCTGGGCACG----GGATG
GATGGATTAGCGGTGGTACTGTACGAGACTGGCGCTCTGCTCTCCTAATAGTGGGTGGAAGCAAGCCGACAGAGAGGTTA
GTGAACCAAGTAAAGGCTTCCTCA----CATGCCTACCTAATGGTGGGGGAGGCCGGCCACCT-------------CT--
--------------------TTGTTTTCCCGCGGGCACGGGGCAGTGGTCAAAAATCATAATGGCTTCACACTCACTCCA
CCACCCAAATAACGACGAGCCCTACATCACATCTAC-----GTGCATCATGCGATGCATGGT-------AGTGAGTGAGT
GAGTGATCGGTTGATTAGATAGGGTTCTCACTCACTCACTCACGTCACGAGCCTCTCGCTCTCCACAGGCTCCCATACTC
GTGCTAACCAAACCAAGGAGCTCTTATATATACCGGGAATCTTCAAGAG------CTCTCACAAGCCACAAGTGCTATTT
TTCTCTGCTT-----TCTCCGTCG----------------CACACACACTATCCTTTCGTGAA-GCTCCGGAGGTACGTT
CGTGCTGT--------GCAAAGCTAGCGAGGAAATCTCCTCGCGTTGAGCTTTTCCTTTGTGGAATTCTGCACTTTGTTT
GTTTAGCATGGTCTGCTGCTGCTGCAGAAAGAACATGGTCGTCTAGCTGCTCCTGCTTGTAGTTGATTGACACTGAGATC
TGTCGGTGCATGCGACTTTTTCTTCTT---------CTTCTTTGGTTGCTTTTAGCTCTTTTTGTCCGGCCATTTGGTGA
ATCACCGAGCCACATCCACATGATCGTTCTGCATTTCTCCAAATATATATGTACCAGCACCGTGCAGTTCAATCAGTCTA
-------GAGAGCAGTTCAAGATCGTAGCAACAGTTTGCTATTTAGGCTGTTTCTAGTAGCCACTAACTGTTGATTCTCG
CAACGGCAGCTCGATTGGCGACCGAAGCAATGGCGTCCATCCGGCGAGATCTGCTCGTGGCGCTCTGCGTGGCGGCGCTC
CTGGCCGTCGGGTCGGAGTCCCACGGGCTGGAGGACTTCGGCAGCGAGGGGAAGACGGAGGCGACGCCCGAGATGGCCTC
CTTCTTCGGCGCCAAGCCCGAGGCCGCCGTGCTCCCGGAGGCGCTGGACAACAACAAGGCCGCCAAGCCGGAGGCCGCCT
CGGCGATGCCCACCACCACCACCAGCACCAACCCACGCTCGTCCCCGCCGCGCAGATCCGTGGCCGTCGCGGCCGGCGTG
GCCTGCGGCGTCGCGGCCCTGGCGGTGGTCGGCGTGGCGGTCGCCGTCGCCTTCGTGGTGCGCGCCAGGCGCGGCGAGAG
GCGCGAGGCCGAGGTCCATCTCGGCTAAGCCAGCCCCAAGCCGGCTTGATTTGAGTAGGACGTGTTCGTCAATTCATTAG
CGTCGTGGTTTGCGTTTAGTTAATCGTCTGCTTAGTT---TGATGAATGATTTCTTCCGTTCTTCCGCTGTTCGTGGGTG
TGTGTGATGGGGATTTGGAGAGCTACGTACGGAGCGGCACGCTGTAACATAAATAACGCTTCATTGGCATGCATGTTACT
GTGATGTTTAGACCTTGAATGGAGT--ATTTCACTAGGAATTCATCACCACTTTGTTGTTCTTAT---GACTTGTGGTTT
GGTTTATGAGTACCTACTCCGCTAATGATTAATGGCTAATTGTTGGAGAAACGTAAGCCAACTGACGGATGCTACG----
--TTCCAAGCG---------------------------------------------------------------------
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---ATTATGTTGCAGTGAGAAACATTTGCAAGCTTGTGGTGTCGGCAGTGGGAACGTGACAAATGTGGGACGGCGTTTTC
CGGCCCTGGAACATGGCAGGCAGCGCAGAGCCGCCATTAGCAGTACTGTTTCGCCGCCCGTGGGAGTGTGAAGACGACGA
AAACGGAGATGGAGCTCGCAGTCGCAGACCTGT-----------CTGTCACCTGGGCTGTGCCGTGCAGTCTCTGTGGTC
ACCTGAGGCGCGGTCCTCGAGAAGTAAACGCAGTGGGAACGAGCGAGCAGGCACTCACTGAAAGCCTGAACCAGACCCGA
CCGACCAAAGTGCATGTGGTAC---------TGCTTGTGAATTCTCGCTGCCCTCCGGGTCCGGGCCCGGGCTGCGGCGT
GGACGGACGCACGCCACGGGCGTGTAGA--GCAGCGTTGCCAAACGAGATCTAGGAGGAAGCA----------TGCGGGG
GAAGGGCTGGACCGGCGGCTCCATGGTCCAGTCGACGCCGTGCCCGTCGGCCGTCGCACAGCTCACGGCCTCGGCTGGAA
TCGCAACCGTCGGAGCATGCTGGCGTTGCCTTCCAGAACCAGACCCAAGTGGAAGGTTTCCGTGATGTGGTGAATATTTG
TGGGGTGAGAGATTTTTAGGCTATGT
>chr2A_9
CGCTCTGATCCATCGG---------GTCACCGGCCAATGGCGATCAACCGTGCATGTGCGCTAGCACGTCGCGGTACATC
TCTCAGGACTCGAGGACTGCCCCGCCCGTGTTCGTCCAACGAC-----------------------TGCGTGACTTGACC
TCAGAGGCCGTGATGGCCTGCCAAGACGTAGTAGCAGTGCTGCTATGACGAAGCGGACGACGCATGAGCTAATTATGGTC
ACCGGACACGGCGCTCGCTGCACGAGGGTCGATCTCGATCGCTAGCCCGTGAAGCGCGGCTCGTGAGGC--GGGATAGAA
TAGACAGCCCCCTACGCGACCGAGGAAGAGTACAACGGAGTACAGTAACCGTAGCACAGAATCTGGGCACGGGATGGATG
GATGGATCAGCGGTGGTACTGTACGAGACTAG----------TCCTAATAGTGGGTCGAAGCAAGCCGACAGAGAGGTTA
GTAAACCAAGTAAAGGCTTCCTCACATGCATGCCTACCTAATGGTGGGGGAGGCCGGCCACCT-------------CTCT
CTCTCTCTCTCTCCCCGCCTTTGTTTTCCCGGGGGCACGGGGCAGTGGTCAAAAATCATAATGGCTTCACACTCACTCCA
CCACCCAAGTAACGACGAGCCCTACATCACATCTACTCTACGTGCATCATGCGATGCATGGTGGTAGTGAGTGAGTGAGA
GAGAGATCGGTTGATTAGATAGGGTTCTCACTCACTCAC----GTCACGAGCCTCTCGCTCTCCACAGGCTCCCATACTC
GTGCCAACGG-----AGGCGCTCTTATATATACCGGGAATCTTCATGGCCTGAGCCTCCCACAAGTCACAAGTCTTACGC
TGCTCTGCTCCGCTCTCTCCGTCG----------------CACACACACTATCCTTTCGTGAAAGCTCCCGAGGTACGTT
CCATGGTGC-------------------------------CGCGTTGAGCTTTTCCTTTGTGGAATTCTGCACTTTGTTT
GTTTAGTATGGT---CTGCTGCTGCAGAAAGAACATGGTCGTCTAGCTGCTCCTGCTTGTAGTTGAT----ACTGAGATC
TGTCGGTGCATGTGACATTTTCTTCTACTAGTAGTACTTCTTTGGTTGCTTTTCGCTCTTTTTGTCCGGCCATTTGGTGA
ACCACCGAGCCG------CATGATCGTTCTGCATTTCTCCACATATATATGTACTAGCACCTTGCACCTCATTCAGTCTA
AAATCTAGAGAGCAGTTGACGATCGTAGTAACAGTTTGCTGTTTAGGCTG-TTCTAGTAGCCACTGACTGTTGATTCTCG
CAACGGCAGCTCGATCGGCGACTGAAGCGATGGCGTCCTCCCGGCGAGATCTGCTCGTGGCGCTCTGCGTGGCGGCGCTC
CTGGCCGTCGGGTCGGAGTCCCACGGGCTGGAGGACTTCGGCAGCGAGGGGAAGACGGAGGCGACGCCCGAGATGGCCTC
CTTCTTCGGCGCCAAGCCCGAGGCCGCCGTGCTCCCGGAGGCGCTGGACAACTCCATGGCCGCCAAGCCGGAGGCGGCAT
CGGCGATGC---CCACCACCACCAGCACCAACCCGCGTGCGTCCCCGCCGCGCAGATCCGTGGCCGTCGCGGCCGGCGTG
GCCTGCGGCGTCGCGGCCCTGGCGGTGGTCGGCGTGGCCGTCGCCGTCGCCTTCGTGGTGCGCGCCAGGCGCGGCGAGAG
GCGCGAGGCCGAGGTCCATCTCGGCTAAGCCCGCCGGCTTGGT--TTCAT-----TAGGGGTTGCTCGTCAATTCATTAG
CGTCGTGGTTTGCGTTTAGTTAATTGCGTGTTTAGTTCGATGATGAATGATTTCTTCCGTTCTTCCGCTGTT--TGTGTG
TGTGTGATGGAGACTTGGGGAA--------------GCACGCTGTAACATAAATAACGCTTCATTGGCATGCATGTTACT
GTGATGTCTAGACCTTGAATGGAGT--ATTTCACTAGGAATTCATGGCTACTTTGCTGTTCTTATTATGACTTGTGGTTT
GGTTTATGAGTACCTACTCCGCTAATGACTAATGGCTAATTGTTGGAGAAACCTACGCCAACTGAAGGATGCTACA----
--TTCCAAGCCTCAATTATGTGGAACCGGCTCCTCTACCGTGCCTGCTGGGCACGGCAGGGTGCCGTGCCTTCTTACCCC
GCACCTTACACATTGATATGGGCCAGAAAGGCCAGACTCTTTGATGAAAGTTTATCTAATCAGCCCAACTGTTCACCGGA
TGCATCACGTTCAACTAAAAAAAACTGATGTATCACACGCCTGCACGTGTCACCTAATTAACTATTTCCCAAACCCAAAA
AGAAACTATTTCCCCCTAGAAAAGCTAACTCACTATTTCTACTTTTATTTTTTTAGATAACACTTCGATCTATTCATATT
CAATCATGACAGTACAATAAACACCATAAATAATAAAAAAATACACCCAGATGCGTAGACCACCTAGCGACGACTACAAG
TACTAAAGCGAGCCGAAGGCACGCCGCCGTCATCGCCCCTCCCTCGCTGGAGCCGGGCAAAACTTGTTGTATACACAGTT
CAGAAGTCATCGTGCTAAGACCCCATAGGACCGACACGGCAGAATAACAACCGCCGCCGAGAAAGGGTAGCGTAGATTGG
AAGAATCCAACCTGAAGACACACGAACGTAGATGAACTACGGCCAGATCCAAGCAAATCCAAATCCACCAAAGATAGATT
CGCCGGAAACACATCTCCATATGCCCATCGACGATGCTAGAGACACCATTGGGACGGGGGCTAGGCGGGGAGGAATTTAT
TTAATATTCAAGGAGCCGCCGCCATCTCGTCTTCCTGAGCAGGACATAAGTCCTAACAAAACTCGAAGAAACATCTGAAA
ACGGGGCCCTTTCACTATCATTGTCTCAATAAACTAATTACCTATTATGAATATACATGAGCAACATTCTAAAATGAAAA
TGAACTCATATTTGAAAAATGGTTTTGCTTAATCTCAGCCATATTTTACGGAGAGCATTTTTTTGTTAAAATATATTTGT
ATTTTGCTTCGAGCGGGCAACAGTACCATTTCCTACATTTGCATATTTTGAAAAGTTAGCAAATATATTCAAGTATTAGA
AACTATAAATCCAGAAAAGACAAAAAATTGAGAAACAACATGCAGACAACAGTCGACTTATATACTTAACCAAATTTAAA
TCGACCAAAATTTTGACAAACAAAAAAACGCCATGAGAACATGCAGCCATGAACTAATGCTGTTAATTTTTTTATAGAAG
ACTAATATTGTTAATCAATAAAAAAATTGAGAACCATGTTGTTAATCAGCGGGCATCAGGTGAGCTTTTAGTAGTTTCCT
GGGCTAGACCATTGCTTCGCCGGGGTAAAGAAGGCACGGCACCCTGCCGTGCCAAGCGGGCACGGTAGAGGAGCCGGTTC
CCAATTATGTTGCAGTGAGAGCCGCTTGCAAGCTTGTGGTGTGGGCAGTGGGAACGTGACAAATGTGGGACGGCGCTTTC
CGGGCCTGGAACATGGCAGGCAGCGCAGAGGTGCGATTAGCAGTACTGTTTCGCCGCCCGTGGGGTGTGG-AGCCGACGA
AAACGGAGATGGAGCTCGCAGTCGCAGAGCTGTAGCAGTA----------------------------------------
---------------------------------------------------------CTGCAAGCCTGAACCAGACCCGA
CCGACCAAAGTGCATGTGGCAC---------TGCTTGCGAATTCTCGCTGCCCTCCGCGTC-------------------
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>chr2B_12
CTGG----TCCATCGG---------GTCACCGGCCAATGGTGATCAATCGTGCATGTGCGCTAGTACGTCGCGGTACATC
TCCCAGGACTC-AGGACGGCCCCGCCCGTGTTCGTCCAACAACCAGCAGGCGAACGACTGATGAGTTGCGTGACTTGACC
TC-GAGGCCGTGATGGCCTGCCAAGACGTAGTAGGAGTGCTAC---GACGAAGCGGACGACGCATGAGCTAATTATGGTC
ACCGGACACTGCGCTCGCTGCACGAGGGTCGATCTCGATCGCTTGCCCGTGAAGCGCGGCTCGTGAGGC--GGGATAGAA
TAGACAGGCCCCTACGCGACCGAGGAAAAGTACAAGGAGGTACAGTAACCGTAGCACAGAATCTGGGCACGGGGATGGAT
TAG----CAGTGGTAGCACTGTACGAGACTAGCGCTCTGCTCTCCTAATAGTGGGTGGAAGCAAGCCGACAGAGAGGTTA
GTAAACCAAGTAAAGGCTTCCTCA----CATGCCTACCTAATGGTGGGGGAGGCCACCCCCTCTCTCTTCAACCTCCT--
--------------------TTGTTTTCCCGCGGGCACGGGGCAGTGGTCAAAAATCATAATGGCTTCACACTCACTCCA
CCACCCAAATAACGACGAGCCCTACATCACATCTAC-----ATGCATCATGCGATGCATGGT-------AT----TGAGT
GAGTGATCGGTTGATTAGATAGGGTTCTCACTCACTCAC----GTCACGAGCCTCTCGCTCTCCGCATACTCCCATACTC
GTGCCAACGG-----AGGCGCTCTTATATATACCGGGAATCTTCAAGAG------CTCTCACAAGTCACAAGTGCTATTT
TGCTCTGCTT-----TCTCCGTCGCGCGCGCGCGCACACACACACACACTATCCTTTCGTGAA-GCTTCCGAGGTACGTT
CCTTCCTTGGTGCCGCGCAAAGCTAGCGAGGAAATCTCCTCGCGTTGAGCTTTTCCTTTGTGGAAATCTGCACTTTGTTT
GTTTAGTATGGC---CTGCTGCTGCAGAAAGAACATGGTCGTCTAGCTGCTCCTGCTTGTAGTTGATTGACACTGAGATC
TGTCGGTGCATGTGACTTTTTCTTCTT---------CC---TTGGTTGCTTTTAGCTCTTTTTGTCCGGCCATTTGGTGA
ATCGACT---------CACATGATCGTTCTGCATTTCTCCAAATATATATGTAGCAGCACCGTGCAGTTCATTCAATCTA
-------GAGAGCAGTTCAAGATCGTAGCAACAGTTTGTTATTTAGGCTGTTTCTGGTAGCCACTAACTGTTGATTCTCG
TAACGGCAGCTCGATCGGCGACCGAAGCAATGGCGTCCATCCGGCGAGATCTGCTCGTGGCGCTGTGTGTGGTGGCGCTC
CTGGCCGTCGGGTCGGAGTCCCACGGGCTGAAGGACTTTGGCAGCGAGGGGAAGACGGAGGCGACGCCCGAGATGGCCTC
CTTCTTCGGCGCCAAGCCCGAGGCCGCCGTGCTCCCGGAGGCGCTGGACAACAACAAGGCCGCCAAGCCGGAGGCGGCCT
CGGCGATGC---CCACCACCACCAACACCAACCCACGTTCGTCCCCGCCGCGCAGATCCGTGGCCGTCGCGGCCGGCGTG
GCCTGCGGCATCGCGGCCCTGGCGGTGGTCGGCGTGGCGGTCGCCGTCGCCTTCGTGGTGCGCGCCAGGCGCGGCGAGAG
GCGCGAAGCCGAGGTCCATCTCGGCTAAGCCGGCCACGAGACTGCTTCAT-----TAGGGCGTGTTCGCCAATTCATTAG
CGTCGTGGTTTGCGTTTAGTTAATCGTCTGCTTAGTT---TGATGAATGATTTCTTCCGTTCTTCCGCTGTT--TGTGTG
TGTGTGATGGAGATTTGGGGAGC----TACGGAGCGGCACGCTGTAACATAAATAACGCTTCATTAGCATGCATGTTACT
GTGATGTTTAGTTTAGACCTTGTTGTCATTTCACCAGGAATTCATCAGCGCTTTGTGGTTCTTG---------GTGGTTT
GGTTTACGAGTACCTACTGACTCCAT----------TAATGGTCGGAGAAACCTAAGCCAACTGAAGGATGCTAGTAGTA
GATTCCAAGCG---------------------------------------------------------------------
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---ATAATGTTGCAGTGAGAAACATTTGCAAGTTTGTGGTGTCGGCAGTGGGAACGTGACAAATGTGGGGCGGCGTTATC
CGGCCCTGGAACATGGCAGGCAGCGCAGAGCTGCTATTAGCAGTGCTGTTTCGCCGCCCGTGGGGTGAGG-AGACGACGA
AAACGGAGATGGAGCTCGCAGTCGCAGAGCTGTGGCAGACCTGTCTGTCACCTGGGCTGTGCCGTGCAGTCTCTGTGGTC
ACCTGAGGCGCGGTCCTCGAGAAGTAAACGCAGTGGGAACGAGCGGGCAGGCG----CTGAAAGCCTGAACAAGGCCCAA
CCGACCAAAGTGCATGTGCTCCTACTGCTTGTGCTTGTGAATTCACGGTGCCCTCCGGGTCCGGGCGGT------GGCGT
GGACGGACGGACGCTCACGCGCGTGCAAATGCAGCGTCACGAAACGAGATCTAGGAGGAAGAGCGTGCGGCGGTGCGGGG
GAGGGGCTGGACCGGCAGCTTCATGGTCCAGTCGACACCCTACCCGTCG-------------------------------
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>SNPs
S-SS-SSSSS-S-SSSSSSSSSSSS--------------------------S--------------------S-------
----------------------S--S---SS---S---------------------S-----------------------
-------SSSS-------------------------------------S-------------------------------
-----S----------------------S-------------------------------------SS-SS---------
--------------------------------------------------------S-----------------------
-------S----------------------S-------------------------------------------------
--S-----------------------------------------------------------------------------
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---------------------------------------SSSS-------------------------------------
----S---SSSSSSS---S----------------------------------------------S--------------
-S-------------------------------------------------------------------S----------
-S-S-SS-------------------------------------------------------------------------
------S-----SSS-----------------------------------------------------------------
------------S-------------------------------------------------------------------
-----------SSSSS-------------------------------------------------------S--------
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---------------S----------------------------------------------------------------
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---------------------------------------------------------------------------S----
---------SSS-------------------------S------------------------------------------
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-------------------------------S---S-S--S-S----S--SSSSS----S--------------------
------------------------------------------------------------------------SS--S---
----------S-------S----SSSS-----------------------------------------------------
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----------------------------S-----------------------S------------S---------S----
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-------------------------------S--S-----------------------------SSSSS-S---------
----------------------------S---------------------------------------------------
---------------------------------------------S------SSSSS-----------------------
------------------------------------------------------------------SSSSSSSSS-----
---------S----SSSS-SSSSSSSS----------SS-S--------------------SS-----------------
--S-------------S---S---------------S--S-S-------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_169
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---------------------------------------------------------------------CGTGACTTGAC
CTCGAGGAG-----------------------------------------------------------------------
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>reverse_2133
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----------------------------------------------------GTAAGCCAACTGACGGATGC--------
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