>input_sequence_71463
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------------------------------------------------------ATGAGAGGGCGAGAGACGCCC---AA
GGCTCGCAGCGGCGCGGCGACCCCGAGCTGCCCGCAGAGCCCGCTCCGCATCACGCACGACGGCGAGTTCTACGCGCGCC
TGCTCACCAGGGAGAGCTCCCTCGCCAACCCCTCCTTCCGCTACTACGGCGCCGGCCCCGCCGCCGTGCCCTTCGGCTGG
GAGTCCCAGCCGGGCACGCCCAAGGACGCCACCTCCTGCTGCAG---GGCGCTCCC------CGCCGCCGTCCCGGCCAT
CACCCCCCCGCCGTCCTACCATGCGCGGGCCGTCTCGGCGTCGTCGTACGGCGACAGCGGCAGGCTGCAGGGCCGCAGGA
GCAAGGGCGCCCCCGCTGGCGACAGGAGCTGCAAGTGCTGCTGCGGCGGCTACAGGAGGCTCAAGTGGATCAAGATCGGC
TTCATCGCCGCCGTGTTCCGCCGGATCGCGCTCGGCAGGTCCCGGGTGTCCTCGTCGCCGTCCTCGTCCGCGGCGTCGGT
GCAGTCGTCCTCGTCGTCCACCCGCTGGCTCTTCTCCGGCGGCTCGAGCAGCTGCCTGGACGAGGCCGGTGCCCACCACT
ACCAGTACTACGAGGCGCCGGCGATGGCGGGGATGCTCTGCCTCGGGGTCCGGCCGAGCCCGTGGATGGTGAAGTTCTGC
GGCGGCCGGCGGGAGCCCGTCTGGGTGCAGGGCTGGCCGTAG--------------------------------------
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>chr1A_1_TraesCS1A01G299300
AGGCTGGAGCCCCGACAAGTCTTTGATGGAGGAGCATTCTGCAGGGTTGATGTTAAGAGAGTCGACCGTCGACCAGACGT
CAGCAACAATAGAGCAGTGGAGAAGTATGTGGGACGCTGATTCAATGGACGTGCAGAATGGGCATGAGTCGGAGTCTGTC
TAGTTCCGCA--AATCGACGCTCGTTGTTGTACAGTCTCCCACGATGCGCAAGTCAGATAAACAACCTGCAGCGGTTAGT
CGCATAGTTCTTTCCCCAAATAAAATCTGTGAACAAATCCTCCGGCCTAGAGAAGAAAGCAGCCTCATATGCATAAGCAA
TGGATAGGGGCTTATCGTTGACCCTACATAATGTACCATCAGGTATGTGCGGTATTAAGTCAACAGTGGCTAACAGGTCA
CGCGGGTATTGTAGTTCGGAGGAAGCAACGTTGGACAGACACGGCTGTAACGAGAGACAGAGGTCCACAGCTGAGAGCAC
GAACGCAACAGAGGCATTCGGTTTGGCGGTGTGGGAGTTTAAACATGTTA--AGATAGCTAGATCACAAATCAGGGTTCC
AC--ATTGTCACTCTAACTATATATGCTCGTACGAC----ACGTAGGATCGCTTGTTGGTTGCAGCGTGACCCTCCTTTC
ATTCATCACCT--TGTGAGCGGAATGTAACCCTATTGATATGGAATAAAACTCCCCTTTACTAAAAAAAATCAAAAAAAA
TCGAAC--------------------------------------------------------------------------
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---------TGACCCGTCGTGCGTTTGTATACATAATACACACAAGCACTGATTGGCACGTG------------------
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------------------------------------------------------------CCAGCGTGTCATTCCCCGCA
AGTGGGCA-GGAAAAAGGTGTGCGAGTAGTTTGGATCGCAAGTGACCACCGAGCAAGAGGAGCGACCCTCCTCCCGCATA
TAAAACGCGCCATCGGATCTCTCCACTTCTCGGATCGTTCGCGCTCCACACTCTCCCACGCAGCGACCAACACCCTCCCC
CATTCCATTCCCTCCGTCCACCGCACCACCTACCCAGAGATCATACCATCCACCATGAGAGGGCGAGAGACGCCC---AA
GGCTCGCAGCGGCGCGGCGACCCCGAGCTGCCCGCAGAGCCCGCTCCGCATCACGCACGACGGCGAGTTCTACGCGCGCC
TGCTCACCAGGGAGAGCTCCCTCGCCAACCCCTCCTTCCGCTACTACGGCGCCGGCCCCGCCGCCGTGCCCTTCGGCTGG
GAGTCCCAGCCGGGCACGCCCAAGGACGCCACCTCCTGCTGCAG---GGCGCTCCC------CGCCGCCGTCCCGGCCAT
CACCCCCCCGCCGTCCTACCATGCGCGGGCCGTCTCGGCGTCGTCGTACGGCGACAGCGGCAGGCTGCAGGGCCGCAGGA
GCAAGGGCGCCCCCGCTGGCGACAGGAGCTGCAAGTGCTGCTGCGGCGGCTACAGGAGGCTCAAGTGGATCAAGATCGGC
TTCATCGCCGCCGTGTTCCGCCGGATCGCGCTCGGCAGGTCCCGGGTGTCCTCGTCGCCGTCCTCGTCCGCGGCGTCGGT
GCAGTCGTCCTCGTCGTCCACCCGCTGGCTCTTCTCCGGCGGCTCGAGCAGCTGCCTGGACGAGGCCGGTGCCCACCACT
ACCAGTACTACGAGGCGCCGGCGATGGCGGGGATGCTCTGCCTCGGGGTCCGGCCGAGCCCGTGGATGGTGAAGTTCTGC
GGCGGCCGGCGGGAGCCCGTCTGGGTGCAGGGCTGGCCGTAGGCCGGGCAGGCCCCA--TCGCCGTCCGGTCGCCGTCAT
GCACGTCGTTCCGTTCCACTTCCAGTCCATGCAGCG----GGCTGGGCCACCATAATTAAAGTTGTCTA---TCGACACG
ACTTGAGGTTGATCGATCGTTCCATTGGTTCCTGCC-------------TCGATCCGGTGTATGTTCCTGCGTCTGATAG
CTCTAGGGATCCAGCATAAGTGCATGGTTCGTTTTGGTCGTTTAGCGTTGGCGTGTCGCTGTGGCCGCTGCCGGCCGGAG
GACACACGACACGAGCATGTCGCCATTTCACCTTTGGAACG-TTTGTTGCTGTTGTCTAGTGGT------------CTAT
GG-----AGAAATAGAATGCTTGTTGTCGATCGCGACTAGATCCGACAGTTTCACGTGTCTCGAGACTCGGAGCCTCA-C
CGTCTGGAACTAATCCCACGTTACGTCTTGATCTCCGCTTGCATTTTATAATTGTTTGGGGGCGCATGATTATTGAGGAC
GTTGCCATGTTTGAGAGTTGCCTGAAATTTTTGTCGGTGCGAGGGTGCTAACATCGACGGTGGACTAATTTTACACTGCT
CTCAGAGATTGATTCTTTCTCGTTCATCAGCTGCGTAGTGGACCAATACTGTAACTTCTCCAAATGTTTGAAATAC----
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---------------------------------------------------ACACTATTTGTTGTACTTTCTCATCATAC
TCTATTTGGAGCTACACACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNCACACACACATTTATCATGTAGTAACTTGAGTGCAAAGACGCGCAGTAGTAATTC
GCCTACATTTGCGTCGGC
>chr7A_1
AGGTTGTAGCCCCGACAATTCTTCGATGGAGGCACAGTCGGCAGGGTTGATGTTAAGAGAGTCGACCGCCGACCAGACGT
CAACAGTAGTAGAGCAGTGGAGAAGCATGTGGGCCGTTGATTCAGTTGACGTGCAGAATGGGCATGAGTCAGAGTCTGTC
AAGTTCCGCCGGAATCGACGCTTGTTGGTGAACAGTCTCCCACGGTGCGCAAGCCAGATAAACAACCTGCAGCGGTTAGT
CGCATAGTTCTTCCCCCAGATAAAATCTGCGAACAGATCCTCCGGTCTAGATGAGAAAGCAGATTCATATGCATAAGCGA
CGGACAGGGGCTTATCGTTGACCCTACATAATCTATCATCAGGTACGTGCGGCATTAAGTTAACAGTGGCTAGCAGGCCA
CGCATGGATTGAAGTTCGGAGGAAACAACGTTGGACAGACGCGGCTGTAGTGAGAGACAGAGGTCCGCAACAGAGAGCAC
GAACACGGCAGAGGCATTAGGTTTGGTGGTGTGGGAG-------------------------------------------
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>chr1B_511
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--------------------------------GGGAGTTTAAACATGTTATAAGATAGCTAGATCACAAATCAGGGTTTC
AC--GTTTTCACTCTAAC----TATGCCCGTACAAC----ACGTAGCACCGCTTGTTGGT--------------------
----------------------------------------TGGAATAAAACTCCCCTTTGCTTGATTTTTTTT----AAA
TCAAAC--------------------------------------------------------------------------
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---------TGATCAGTCGTGCGTTTGT-------ATACACACAAGCACTGATTGGCACGTGAACCAACCTGTGGTTGGA
TGGTTAGATGGACTGTGGTATCCCCAGCCCATCAGGGTTCAAATGCTGATGCTCACATTTATTCCTGGATTTATTTCGGG
ATTTTCGGCGATACGCACTCAGTCGGAGGAGACGTTCCCGTCGACGACGAGGCGCCTACGGTGACTTCGTAAATCTCAAG
ATGATATGCCGACTCAGTCTTTCAGAGGTGCTCATAGGGATAGGGTGTGCGTGTGTGCGTTTATAGGGGTGAGTGTATGC
GCGTGTATATGAGCGCTTGTGTCTGTACTTATGTTAAAAAAAAGCACTGATTGGCACGTGCCAGCGTGTCATTCCCCGCA
AGTGGGCA-GGAAAAAGGTGTGCGAGTAGTTTGGATCGCAAGTGACCACCGAGCCAGAGGCAGACTCC----CCCGCATA
TAAAACGCGCCATCGGATCTCTCCACTTCTCGGATCGTT-------CACACTCTCCCACGCAGCGACCAACACTCTCCCC
CATTCCAT----TCCGTCCACCACAGTACCTACCCAGAGATCGTACCAT-CACCATGAGAGGGCGAGAGACGCCC---AA
GGCTCGCAGCGGCGCGGCGACCCCCAGCTGCCCGCAGAGCCCGCTCCGCATCACGCACGACGGCGAGTTCTACGCGCGGC
TGCTCACCAAGGAGAGCTCCCTCGCCAACCCCTCCTTCCGCTACTACGGCGCCGGCCCCGCCGCCGTGCCCTTCGGCTGG
GAGTCCCAGCCGGGCACCCCCAAGGACGCCTCCTGCTG---CAG---GGCGCTCCCAGCCGCCGCCGCCGTCCCGGCCAT
CACTCCCCCGCCGTCCTACCACGCGCGGGCCGCCACGGCGTCGTCGTACGGCGACAGCGGCAGGCT---GGGCCACAGGA
GCAAGGGCGCCGCCGCCAGCGACAGGAGCTGCAAGTGCTGCTGCGGCGGCTACAGGAGGCTCAAGTGGATCAAGATCGGC
TTCATCGCCGCAGTGTTCCGCCGGATCGCGCTCGGCAGGTCCCGGGTGTCCTCGTCGCCGTCCTCGTCCGCGGCGTCGGT
GCATTCGTCCTCGTCGTCCACCCGCTGGCTCTTCTCCGGCGGCTCGAGCAGCTGCCTGGAGGAAGCCGGTGGTCACCACT
ACCAGTACTACGAGGCGCCGGCGATGACGGGAATGCTCTGCCTCGGGGTCCGGCCGAGCCCGTGGATGGTGAAGTTCTGC
GGCGGCCGGAGGGAGCCCGTCTGGGTGCAGGGCTGGCCGTAGGCCGGGCATGCCTCTTCTTGCCGTCCGGTCGCCGTCAT
GCACGTCGTTCC-----ACTTCCAGTCCATGCAGC-----GGCTGGGCCACCATAATTAAAGTTGTCTACTATCGACACG
ACTTGAAGTTGATCGATCGTTCCATTGGTTCCTGCCCATGGCTGCTCGATCGATCCGGTGTCTGTTCCTGCGTCTGGTAG
CTATAGTGATCCAGCATAAGTGCATGGTTCGTTTTGGTCGTTTAGCGTTGGCGTGTTGCTGTGGCCGCTGCCGGCCGAG-
--CACACGACACGAGCATGTCGCCATTTTACCTTTGGAACG-TTTCTTGCTGTTGTCTAGTGGGTGTGACTGTGGGCTAG
ACTAAGAAGAAATAGAATGCTTGTTGTCGATCGCGACTAGATCCGACAGTTTCACGTGTCTCGAGACTCGGAGGCTCAAC
CGTCTGGAACTAATCCCACGTCC-----TGATCTCCGCTTGCATTTTATAATTGTTTGGGAGCGCATGGCTATTGAGGAC
GTTGCCATGTTTGAGAGTTGCCTGAA--TTTTGTCGGTGCGAGGATGCTAACGTCGACAGTGGACTA------------T
CTCAGATACTGATTCTTTCTCGTTCATCAGCTGCGTAGTGGACCGATACAGTAACTTCTCCAAATGTTTGAAATTC----
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---------------------------------------------------ACAG--TTTGTTGTACTTTATCATCAT-C
TCTATTTGGAGC--------------------------------------------------------------------
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>chr1D_512
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---------------------------------GGAGTTTAAACATGTTA--AGATAGCTAGATAACAAATCAGGGTTTG
ACATATTGTCTCTCTAAC----CATGCTCGTATAACACGTACGTAGCACCGCTTGTTGATTGCAACGTGGTCCTCCTTTC
ATTTATGACCTTGTGTTAGCGGATTGTAACTCTGTTGCTATGGAATAAAACTCTCTTTTACTCGAGTCAGTTTGTCTTTA
CTCCCACTCCAGTTTACTATAGTTACCTCATTCGTGTTCTCCGAGATGTTCGAGGCACGATTTCTCATCGCCTGTTCTTT
TCTCGCTTCAATTTCTTACAGCTTAAGGTCTATTCGGATGCTACATGGGCTAGCGATCCCTCAAATCGCTGTTCACTTTC
TGCTTACAGTGTTTTTTTATCGTTCTCTTGTTGCCTGGAAGATGAAGAAACATACTGCAATTCGTGCAGAACGCGAGCTA
CGACTCTTTTGACGCGTCGTGCGTTTGT-------ATACACACAAGCATTGATTGGCACGCTCCCCCGTC----------
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----------------------------------------------------GGCACGTGCCAGCGTGTCATTCCCCGCA
AGTGGGCAAGGAAAAAGGTGTGCGAGTAGTTTGGATCGCAAGTGACCACCGAGGAGTCAAGAG----CTCCTCCTGCATA
TAAAACGCGCCATCGGATCTCTCCACTTCTCGGATCGTCCGCGCTCCACACTCTCCCACGCAGCGACCAACACCCTCCCC
CATTCCATTCCGTCCGCCCACCACACCACCTACCCAGAGACCATACCAT-CACCATGAGAGGGCGAGAGACGCCCCCCAA
GGCTCGCAGCGGCGCGGCGACCCCGAGCTGCCCGCAGAGCCCGCTCCGCATCACGCACGACGGCGAGTTCTACGCGCGGC
TGCTCACCAGGGAGAGCTCCCTCGCCAACCCCTCCTTCCGCTACTACGGCGCCGGCCCCGCCGCCGTGCCCTTCGGCTGG
GAGTCCCAGCCGGGCACGCCCAAGGACGCCACCTCCTGCTGCAGGAAGGCGCTCC---------CCGCCGTCCCGGCCAT
CACCCCGCCGCCGTCCTACCACGCGCGGGCCGCCACCGCGTCGTCGTACGGCGACAGCGGCAGGCTGCAGGGCCGCAGGA
GCAAGGGCGCCCCCGCCGGCGACAGGAGCTGCAAGTGCTGCTGCGGCGGCTACAGGAGGCTCAAGTGGGTCAAGATCGGC
TTCATCGCCGCCGTGTTCCGCCGGATCGCGCTCGGCAGGTCCCGGGTGTCCTCGTC------------CGCGGCGTCGGT
GCAGTCGTCCTCGTCGTCCACCCGCTGGCTCTTCTCCGGCGGCTCGAGCAGCTGCCTGGACGAAGCCGGCGCCCACCACT
ACCAGTACTACGAGGCGCCGGCCATGACGGGGATGCTCTGCCTCGGGGTCCGGCCGAGCCCGTGGATGGTGAAGTTCTGC
GGCGGCCGGAGGGAACCCGTCTGGGTGCAGGGCGGGCCGTAGGCCGGGCAGGCCTCCTCTCGCCGTCCGGTCGCCGTCAT
GCACGTCGTTCCGTTCCACTCCCAGTCCATGCAGCGGTCGGGCTGGGCCACCATAATTAAAGTTGTCTACCATCTATACG
ACTTGAAGTTGATCGATCGTTCCATTGGTTCCTGCC-------------TCGATCCGGTGTCTGTTCCTGCGTCTGATAG
CTCTAGTGATCCAGCATAAGTGCATGGTTCGTTTTGGTCGTTTAGCGTTGGCGTGTTGCTGTGGCCGCTGCCGGCCGGG-
--CACACGACACGGGCATGTCGCCATTTTACCTTTGGAACGTTTTGTTGCTGTTGTCTAGTGGGCGTGGCTGTGGACTGT
GG-----AGAAATGGAATGCTTGTTGTCGATCGCGACTAGATCCGACAGTTTCACGTGTCTCGAGACTCGGAGCCTCA-C
CGTCTGGAACTAATCCCACGTTT-----GGATCTCCGCTTGCATTTT------GTTTGGGTGCGCATGACGATTGAGCAC
GTTACCATGTTTGGGAGTTGCCTGAAATTTTTGTCGGTGCGAGGGTGCTAACATTGACGGTGGACTAATTATGCACAGCT
CACAGATACTGATTCTTTCTCGTTCAGCAGCTGCGTAGCGGACCAATACAGTAACTTCTCCAAATGTTTGAAATTCTAGG
ATCGACCAAATACAGTCTCAACTTCGGGGTGAAAACCCTACGTCTGACCATTTGGTTATACCTGGCAATGGTGGCGTTCT
CCACGTCATTAACTTGATGAAGGCATTGCTCGGAGTTTAATCAGATTTAATCTTCAAGGTGAAAACCCACGATCTAACCT
TCGATGGTTGGTCGGGCGACGGCGGCGCTTGCACGTCGTTCTCTTCCTGGAGACGTCGCTTTTAAAGAACTTCCCTTGTA
GTCCTTGTGTTGTCAAGAGATGGTTTGTGCCGATGGTCACTGTTGTATGCTGTCAATCATTGCTTTTATCGCTTTCGGGG
TTTTTATTTTCTTTTTCTTTTGCCTAGGCATAGCTTTGGTCTTGATGACTTTGCTATTTGCCGACGTGATTTTTTATATG
CGTGTGTTAGTGTTGGTTGTGTGCATCCTAGTTATGCAGAGGCCGGGTGTGTACTCACTATAATTGTATCCCTCGATGCT
ATATTTTGAGTCAATTAAGAACACCCTTTATCGAAAAAATGTTTGAAATTCACACTATTTGTTGTACTTTCTCATCATAC
TCTATTTGGAGCTACACAC-------------------------------------------------------------
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>SNPs
---S--S-----------S----S--------SS--S--S----------------------------S-----------
--S--SS-S----------------S-------S--S-------S-S-----------------------S---------
S--------S------------S----S--S-------------S--------S--------------------------
------------S-----S----------S-----S---------S-----SS---------SS--------------S-
S---S---------------------------S--S---------S------S-------S-----------S----S--
---SS-S----S------------S---------------S--------SS---------------S--S-S--------
----S-SS----------S-------S---------------------------------------------------S-
------------------SSSS-----------S------------S-S---------------S----SS---------
---S--S---------S------S------S--S---S------------------------SS-SSS-S-SSSSSS---
--S-----------------------------------------------------------------------------
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----------------------------SSSSSSS---------------------------------------------
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------------------------------------------------------------SSSSSS--------------
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-----------S----------S--------------------------S------------------------------
------------------------------------------------------------------------------S-
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---------------------S----------S-S---------------------------------------------
----------------S---------------------------------------------------------------
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---------------------------------------------------------------S----------------
--------------------------S-----------------------------------------------------
---------S--------------------------------------------S-S-----------------------
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------S------------------------------------------------------S------------------
------S-------------------------------------------------S---------------------SS
SS--------------------------S----------------------------------S----------------
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----------------------SSSSSS--------------------------------S--------S----------
----------------------------------------------------------------------S-S---S---
------S-S----------------------------------------S------------------------S-----
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-------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSS
>forward_625
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---------------------------------------------GGATCGCTTGTTGGTTGCAG---------------
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>reverse_2744
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-----------------------CGTCTTGATCTCCGCTTGCA-------------------------------------
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