>input_sequence_63434
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-----------ATGGTACACTAGTGATCTCACTAGTATTCAGTTTCA-TTTTCAGTCAAGCAAATTGGATTCTCATCACA
TCTGAATCCTTAATTAATCCTTCTTTCATGTTTGTTTGTTTGTACTTACGTTCTTGTGTAAACAT-CCTTAAAAATCTCT
AAAAGGCTAGCTTTGTTTTGTCCCAAGAAAATACATAGATTTTGCTTT--AAAAAGCGTTCACTCCATTGCTGAAGTTCC
AAGCTGCACCTTTTGTTTCAGCAGCAGCAGCAGCAGCCGCCGCCTCCGAGGAGGATGGTCGCGTCGAAGAAGCTCATGAA
AGTCGGGCCATGGGGCGGCACCGGGGGCAACACGTGGGACGACGGCGGGCACACCGGGATCCGCGGCGTCACACTGTCGT
ACGACCACCGCTGCGTCGTCTTCATCGCCGTGGAGTACGACAGGAGCGGCCTCGCCGTCCCCGGCGAGCGGCACGGCGGC
GCCGGCGGCAACCACACCACCCAGGTTGGTACT--------------------TCGATCGGCAAGATCGCGTAAACGGCA
TATATGATACGGCAGAGCCGTGC-TTTTCTTGACTGGACTGTTGCGTGCATATGCGTAGATCAAGCTGAGCTTCCCGGAC
GAGCACCTGACGGCCGTGAGCGGCCGCTACGGCGCGGTGGCTCCCGGTGGCTCGCCAGTGATCCGGTCGCTGGCGTTCAG
GACGGAGCGCGCGGCGTACGGGCCGTTCGGCGCCGCCGAGGGCACGCCGTTCGAGTTCGCGGTGGAGGGCGGCGTGATCG
TGGGGTTCTGCGGGCGGAGCGGCTGGCAGCTGGACGCCGTCGGGATGTACGTGGCGCCGCTGCGGCCGGAGAAGCTGTAC
GACAAGGTGCATCACCTGGGGCTCATGGCCTACCGCTCGGTCATGCACCGGCTCGGGCCGGCGCCGGCACCGCCACAGGA
CGAGCTGCCGGAGGCGAGAGTTCAGCATCAGCGTCAGAACGGCAGTGTGGTTCAGACAAGTCGCAAGAATTACTAA----
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>chr1B_1_TraesCS1B01G380700
AACAAAGTTGGGAATCCATATCGTCTCTGTTCATCACCCATCACCACAAGATGGGCATGTAACAAATGTAAAGTACTCTC
CCTGTTCCAAATCAATTGAAGTTCTAGTTTTGTCCAAAGTCAAACTTGTTTAAGTTTGACTGATTATATAGAAAAATATA
CCAAC--------ATCTACATCATCAAATTAGTTTGCACTATATATATTTGACGCAACAAGTTCAACTCAGGACAAATCT
TTAACTTCAATTTATCTGGAGCAGAGGGACTAATTTAGTAGAGGTTGATTACAAAAAACATAGAAGTTTCTCGAGGAATT
TTAAAAATGTTACTTGCAGCAGAAGCTTTGTACCCAAACATCGACATTGAGAAGCTTTGTACCCAAGCTTCGAGGTTGGA
TTT-GCAGATTGAGCGGGAGCAGCCCCAACGCCACAAGCATATCGCCGTCGATGTTCCTAGCAATA---ACATCTGGCTG
CAGACTTTGCGATCAAAA-------GACCCCGGGGCATACCGGCTTTTCCAAT-AAAAGTTTCCAATTAATTAAAAGAAT
CTCTTTGTCGGATAAAAAAACATTGTCGAAAATTCAAAAAATCTGGCTCTAAACGTTGCGATCATAGAGGTAATGGATTC
AAAAAAATGTTATGCAGTTTTGGGCTTTTGGGAGATGCTAACCT------------------------------------
------------------------------------------------------GA------------------------
---------------------------------------------------------------------------ACGTC
AAAATTCTTGATTCATTGCTACCATAGCTTCTAGGTGAAGAAGAGCATGTTCCTGTACAGTATGCTTAGCTTTATGGAAA
GCAAAGCAGTATGCCTACTGATCTATCAAGAGAGAGCATCCAGTTCCGGTCTCCACTTATATTTCTCATCATCATGTACA
CTACAATCTTGCCAGCTGCCATTTTGGCTGGACCTGCCATTTTTTT--CACCAGCTACTTTAACCCGTATAAGTACACTT
GTTCTTAGAACATTAGGTAGCTAGCTGCTCATCTTACCACTTACCACCTGGTGTTATAGCCCTGCTGTACATATCTGGAG
TGGAGGCAAACATGGTACACTAGTGATCTCACTAGTATTCAGTTTCA-TTTTCAGTCAAGCAAATTGGATTCTCATCACA
TCTGAATCCTTAATTAATCCTTCTTTCATGTTTGTTTGTTTGTACTTACGTTCTTGTGTAAACAT-CCTTAAAAATCTCT
AAAAGGCTAGCTTTGTTTTGTCCCAAGAAAATACATAGATTTTGCTTT--AAAAAGCGTTCACTCCATTGCTGAAGTTCC
AAGCTGCACCTTTTGTTTCAGCAGCAGCAGCAGCAGCCGCCGCCTCCGAGGAGGATGGTCGCGTCGAAGAAGCTCATGAA
AGTCGGGCCATGGGGCGGCACCGGGGGCAACACGTGGGACGACGGCGGGCACACCGGGATCCGCGGCGTCACACTGTCGT
ACGACCACCGCTGCGTCGTCTTCATCGCCGTGGAGTACGACAGGAGCGGCCTCGCCGTCCCCGGCGAGCGGCACGGCGGC
GCCGGCGGCAACCACACCACCCAGGTTGGTACT--------------------TCGATCGGCAAGATCGCGTAAACGGCA
TATATGATACGGCAGAGCCGTGC-TTTTCTTGACTGGACTGTTGCGTGCATATGCGTAGATCAAGCTGAGCTTCCCGGAC
GAGCACCTGACGGCCGTGAGCGGCCGCTACGGCGCGGTGGCTCCCGGTGGCTCGCCAGTGATCCGGTCGCTGGCGTTCAG
GACGGAGCGCGCGGCGTACGGGCCGTTCGGCGCCGCCGAGGGCACGCCGTTCGAGTTCGCGGTGGAGGGCGGCGTGATCG
TGGGGTTCTGCGGGCGGAGCGGCTGGCAGCTGGACGCCGTCGGGATGTACGTGGCGCCGCTGCGGCCGGAGAAGCTGTAC
GACAAGGTGCATCACCTGGGGCTCATGGCCTACCGCTCGGTCATGCACCGGCTCGGGCCGGCGCCGGCACCGCCACAGGA
CGAGCTGCCGGAGGCGAGAGTTCAGCATCAGCGTCAGAACGGCAGTGTGGTTCAGACAAGTCGCAAGAATTACTAAGT--
-----GGTCAGCGTGTACTTACTACTCAGTACTACTCATTAGCTAGAATGGCAAATTCATGGCTGGGTCTCTGTCGTACA
---GATTGATTCGGCTGGTATATATGAAACCAGAAAT----GCTTAATGCAGGAGATTTACTACAAGGCGACATGGTTTG
GTACTCTCGAATGACAACAAAATAATATTCTCGAAGAAGAAACCACAACAAGAACAACAACGATGATGATGATGATGTCG
ATGAACCACAAATAACAAGAGAGAAGTCCATGTTTCAATCATGAAATGTCACAAATGTTTAAGAATCAACCCTAAACTTT
GAAATCGTCTAAGTTTCAATCCTAGACGATCAAAACCCATGCAAGATTTTAACCGCATTTTTTTTGCAAGATTCGACCCT
GCCCTCTCCTCACATCGTTTTCTGCTGAGTTGGACATGTTTTAACCCTTTGACCGCCCCATCATTCAAGTGACCCGCCAC
GCCAATCAGTCCACTTAACGTAGCCCATGCTCTCTCTCTCTCTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-------------------------------------------------
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----------------------------------------------------------------------------TTCC
TTAAAGTAGGTGTCTT-CTGGTTTATCGAACCAACAAGAGTTTAGAAACACACACGATGATCAACACCTACACACACAGA
TACAAAACTGGCTTGGCCCCAAACAGAAGGGGGATGATAGGCGCCGGTGCACCGGCCCAAACTTTGGGCCGGTCGCACCC
CAGCCATACGATGCGA
>chr1D_1
AACAAAGTTGGGAATCCATATCGTCTCTGTTCATCACCCATCAA-ACAAGATGGGCATGTAACAGATGTAAAGTACTCTC
CCCGTTCCAAATCAACTGAAGTTCTAGTTTTGTCCAAAGTCAAACTTGTTTAAATTTGACTGATTCTATAGAAAAATATA
CAACTCAGGACAAATCTACAACTTCAAATTAGTTTGCACTATATATATTTGACGCAACAAGTTCAACTTAGGACAAATCT
ACAACTTCAATTTATCTGGAGCGGAGGGAGTAATTTAGTAGAGGTTGGTTACAAAAAACATAGAAGTTTCTTAAGGAATT
CTAAAAATGTCCCTTGCAACAGAAGCTTTGTACCCAAACGATTACATTGAGAAGCTTTGCACCCAAGCTCCGAGGTTGGA
TTTTGCAGATTGAGCGGGAGCAG--CCAACGCCACAAGCATATCGGCGGCGATGTTCTTAGC---A---ACATCTGGCTG
CAGACGTTGCGATCAAAA-------GACCCCAGGGCATTCCGGCTTTTCCGATGAAAAGTTCCCAATTAATTCAAAAAAT
CTCTTTGACAAA-AAAAAAACTTTGTCGAAAATTCAAAAAATCTGGCTCCAAACGTTGCGACCATAGAGGTGATGAATTC
A-AAAAATGTTATGCAGTTTTGGCCTTTTGGGAGATGCTAACACTAAACCACTGGCGGAGCTATGTACAAAGCTGCAGGT
GCCGTGGCCCCCCCAGCCTTGGCTAGTTTTGTGAAGAATTTTTTTTTTAGAGGGCTGAGATTGAATTTTTTTAGGTATTT
TATCCCTTGGAAATTGAGTGTTTTGTCCTCAGCCCCCCCAATAATCACCGTCTAGCTCCGCCACTGCACTGAACGACGTC
ATATTTCTTGATTCTTTGGTACCATAACTTGTAGGTGAAGAAGAGCATGTTCCTGTACAGTATGCTTAGCTTTATGGAAA
GCAAAGCAGTATGCCTACTGATCTCTCAAGAGAGAGCATCCAGTTCTGCTCTCCACTTGTATTTCTCATCATCATGTATA
CTACAATCTTGCCAGCTGCCATTTTGGCTGGACCTGCCATTTTTTT--CACCAGCTACTTTAACCCATATAAGTACACTT
GTTCTTAGAAGATTAGCTAGCTAGCTGCTCATCTTACCACTTACCGCCTGGTGTGATAGCCCTGCTGCACATATCTGGAG
TGGAGGCAAACATGGTACACAAGTGATCTCACTAGCATTTACTTTCATTTTTCAGTCAAGCAAATCGGATTCTCATCACA
TCTGAATTCTTAATCAATCCTCCTTTCA----TGTTTGTTTGTACTTGCGTTCTTGTGTAAACATTCCTTAAAAATCTCT
AAAAAGCTAGCTTTGTTTCGTCCCAAGAAAATACATAGGTTTTGCTTT--AAAAAACATTCACTCCCTTGCTGAAATTCC
AAGCTGCATCGTTTGTTTCAGCAGCAGCAGCTGCCGCCGCCGCCGCAGAGGAAGATGGTCGCGTCAAAGAAGCTCATGAA
GGTCGGGCCATGGGGCGGCACCGGCGGGAACCCGTGGGACGACGGCGGGCACACCGGGATCCGCGGCGTCACACTGTCGT
ACGACCACCGCTGCGTCGTCTCCATCGCCGTGGAGTACGACAGGAGCGGCCTCGCCGTCCCTGGCGAGCGGCACGGCGGC
GCCGGCGGCAACCACACCACCCAGGTTGGTACTTGGTACGTACGTCGATGCGCTCGATCGGCAAGATCGCGTT-------
------------CACAGCCGTGCTTTTTCTTGACTGGACTGCTGCGTGCGTATGCGTAGATCAAGCTGAGCTTCCCGGAC
GAGCACCTGACGGCCGTGAGCGGGCGGTACGGCGCGGTGGCGCCCGGCGGCTCGCCGGTGATCCGGTCGCTGGCGTTCAG
GACGGAGCGCGCGGCGTACGGGCCGTTCGGCGCCGCCGAGGGCACGCCGTTCGAGTTCGCGGTGGAGGGGGGCGTGATCG
TGGGGTTCTGCGGGCGGAGCGGCTGGCAGCTGGACGCCGTCGGGATGTACGTGGCGCCGCTGCGGCCGGAGAAGCTGTAC
GACAAGGTGCATCACCTGGGGCTCATGGCCTACCGCTCGGTCATGCACCGGCTCGGGCCGGCGCCGGCGCCGCCGCAGGA
CGAGCTGCCGGAGGCGAGAGTTCAGCATCAGCGTCAGAACGGCAGTGTGGTTCAGACAAGTCGCAAGAATTACTA-GT--
-----GGTCAGTGTG--------------------TCACTAGCTAGAATGGCAAATTCATGGCTGGATCTCTGTTGTACA
TATGATTGATTCAGCTAGTATATATGAAACCAGAAATATACGCTTAATACAGGAGATTTACTAC----------------
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>chr1A_1
AACAAAGTTGGGAATCCATATCGTCTCTGTCCATTACCCATCACCACAAGATGGGCATGTAACAAATGTAAAGTACTCTC
CCCGTTCCAAATCAATTGAAGTTCAAGTTTTGTCCAAAGTCAAACTTGTTTAAGTTTGACTGTTTCTATAGAAAAATATA
TCAAC--------ATCTACAACATCAAATTAGTTCGCACCATATATATTTGATGCAACAAGTTCAACCCAGGACAAATCT
ATAACTTCATTTTATCTGGAGCAGAGGGAGTAATTTAGTAGAGGTTGATTACAAAACACATAGAAGTTTCTCAAGGAATT
TTTAAAATGTTACTTGCAACAGAAGCTTTGTACCCAAAAGACGACATTGAGAAGCTTCGTACCCAAGCTTCGAGGTTGGA
TTT-GCAGATTGAGCCTGAACAGCCCCAACGCCACAAGCATATCGGCGGCGATGTTCTTAGC---AGCAACATCTGGCTG
CAGACGCTGCGATCAAAATTCAGAAGAGCCCTGGGCATTCCGGCTTTTCCAATGAAAAGTTCCCAATTAATTCA------
-----------------------------------AAAAAATCTGGCTCCAGACGTTGCGATCATGGAGGTAATGAATTC
-AAAAAATGTTACGCAGTTTTGGCCTTTTGGGAGATGCTAACACTATGTAGAAGTTCATGCTCTAGTCAATCCAACCAAA
AGACCGATTTGATGAAAGAGATTATTAGGCAATACATTTATACGTCAACACACCGA------------------------
---------------------------------------------------------------------------ACGTC
AAATTTCTTGATTCTTTGCTACCATACTT--TAGGTGAAGAAGAACATGTTCCTGTACGCC-----TAGCTTTATGGAAA
GCAAAGCAGTATGCCTACTGATCTCTCAAGAGAGAGCATCCAGTTCCGTTCTCCACTTACATTTCTCATCATCATGTATA
CTACAATCCTGCCAGCTGCCATTTTGGCTGGACCTGCCCTTTTTTTTTCACCAGCTACTTTAACCCATATAAGTACACTT
GTTCTTAGAAGAT----TAGCTAGCTGCTCATCTTACCACTTACCA--------------CCTGCTGCACATATCTGGAG
TGGAGGCAAACATGGTACACTAGTGATCTCACCAGTATTCAGTTTCA-TTTTCAGTCAAGCAAATCGGATTCTCATCACA
TCTGAATTCTTAGTTAGTCCTCCTTTCA----TGTTTGTTTGTACTTACGTTCTTCTGTAAACATTCCTTAAAAAT-TCT
AAAAAGCTAGCCTTGTTTTGTCCAGAGAAAATATATAGATTTTGGTTTAAAAAAAGCATTCACTCCGTTGCTGAAATTCC
AAGCTGCACCGTTTGTTTCAGCAGCAGCAGCAGCCGCCGCCGCCTCCGAGGAAGATGGTCGCGTCCAAGAAGCTCATGAA
GGTCGGGCCTTGGGGCGGCACCGGGGGCAACCCGTGGGACGACGGCGGGCACACCGGGATCCGCGGCGTCACCCTGTCGT
ACGACCACCGCTGCGTCGTCTCCATCGCCGTGGAGTACGACAGGAGCGGCCTTGCCGTCCCCGGCGAGCGGCACGGCGGC
GCCGGAGGCAACCACACCACCCAGGTTGGTACTTGGTACGTACGTCGGTACACTCGATCGGCAAGATCACCTT-------
------------CACAGCCGTGCTTTTTCTTGACTGGACTGCTGCGTGCGTATGCGTAGATCAAGCTGAGCTTCCCGGAC
GAGCACCTGACAGCCGTGAGCGGCCGGTACGGCGCGGTGGCGCCCGGCGGCTCGCCGGTGATCCGGTCGCTGGCGTTCAG
GACGGAGCGCGCGGCGTACGGGCCGTTCGGCGCCGCGGAGGGCACGCCGTTCGAGTTCGCGGTGGAGGGCGGCGTGATCG
TGGGGTTGTGCGGGCGGAGCGGCTGGCAGCTGGACGCCGTCGGGATGTACGTGACGCCGCTGCGGCCGGAGAAGCTGTAT
GATAAGGTGCAGAAGCTGGGGCTCATGGCCTACCGCTCGGTCATGCACCGTCTCGGGCCGGCGCCGGCTCCGCCGCAGGA
CGAGCTGCCGGAGGCGAGAGTGCAGCATCAGCATCAGAACGGCAGTGTGGTTCAGAAAAGTCGCAAGAATTACTA-GTGG
TCACTGGTCAGTGTG--------------------TCATTAGCTAGAATGGCAAATTCATGGCTGCATCTCTGTTGTGCA
TATGATTGATTCAGCT----------------------------------------------------------------
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>chr1B_2237
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------CACAAATAACAAGAGAGAAGTCCATGTTTCAATCCTGAAATGTCACAAATGTTTAAGAAGCAACCCTAAACTTT
GAAATCATCTAAGTTTCAATCCTAGACGATCAAAACCCATGCAAGATTTTAACCGGAAAAAAAA-GCAAGATTCGACCCT
GCCCTCTCCTCACATCGTTTTTTGCTGAGTTGGACATGTTTTAACCCTTTAACCGCCCCATCATTCAAGTGACCCACCAC
GCCGATCAGTCCACTTAACGTAGCCCACGCCCAAACTCTCTCCCCCCTCCCTCCCGACCTAGCACACCGCTCCCCACCAG
TCGTCACTACCGCCAACAACACCCGACCCACTGCCACCCATCCGATAAACAGAGGCGTCGCTACACCGNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTGCAAGGGTTTGTAGCAAACAACATTTTTTCC
TTAAAGTAGGTGTCTTTCTGGTTTATCGAACCAACAAGAGTTTAGAAACACACACGATGATCAACACCTACACACACAAA
TACAAAACTGGCTTGGCCCCGAACAGAA----------------------------------------------------
----------------
>SNPs
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--S--------------------------------------------------------------S--------------
--------------------S-----------------------------------------------------------
S----------------------------S------------------------------------------S-------
------------------S--------------------SS---------------------------------------
---------------------------------------------S--S--------S----SSS---------------
-----S-------------------------S------S----------------------S----------S---S---
-------S-SS-S--------S---------------------------S-------------------------S----
-----------------------S------------------SS------------------------------------
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---S----------S-----------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----------------------------------------------------------
------------------------------------------------------------------------SSSSSSSS
SSSSSSSSSSSS--S--------------------------S-------S------------------------------
--------------------------S--------------S-----S--------S-----------------------
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--------------------------------------------------------------------S-----S-----
---------------------------------------------------------------------------S----
-----------S---SSSSSSSSSSSSSSSSSSSS-------------------------------S-------S-----
------------S---S-------------------------------S---------------SSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSS----------------------------------S------------------------S--------------
------S------------------------------------------------S-SSSSSSSS---------------
---------------------S----------------------------S------------------------S----
---S-----------------------S--S-SSS-------S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------
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------------------------------------------------------------------------------S-
--------------------S-------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSS
>forward_1009
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-----------------------------GAGAGAGCATCCAGTTCCGG-------------------------------
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>reverse_2691
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--------------------------------------------------GACCGCCCCATCATTCAAGT----------
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