>input_sequence_73099
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----------ATGAGCGGCCAAGTTTACCCGCCGCCGCCGGCGGCGATGGTGCCGCAGCCGCAGCCGCACGGGCAGGTGG
CCGCGAACAACTGGGCGGGCAACGACGCCAACACGCTGCTGGTGGTGGCGACGCTGATCACCACGCTCACGTACCAGCTC
GGGTGCAGCGTCCCCGGCGGGTACTGGCAGGACACGCTGGCGGCGGACGGCAAGCAGCAGCCGCACGAGGCCGGAGACCC
CATCATGCGCGACAAGCACCCGCAAAGGTACGCACATGGCGCATGCTCCTGGTTAGAAACTTAGATTCTGA----AATCC
CGGTGGTCATGCGGACGTCCCTTGACCGATGGCACGCATGCGTGCAGGTACTGGGTGTTCATGGCGGCGAGCTGGATGGG
GTTCCTGGCGTCCATGATGATGACGCTGAGCCTGCTGGTGCGCCTGCCGGTGGACTCGCGGCAGGTCCGGTGGTCCTTCG
CCGTCGCCTACTCCAGCCTGGTGCTCACCTTCATCGTGTCGCAGGCCAAGACGCACATCTCAGTCGACATCGCCATCTGG
TTGGTCACCGTCGTCTTCCTGTGGCTCATGATCAGCGTCCGCCCTGAGCACCGGGCGCGTATCCTCCGTTTCTTCTGCTG
CGACCGCGAGAACTGA----------------------------------------------------------------
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>chr4A_1_TraesCS4A01G084100
CATTAATACAAAATATCCAGATTTTTAGGTATATAAATTAAACATCAGATATTTT-ATGAAAGATAGATTTATTATATGC
ATCTTATACATTTTTTTATTAATAACTTGTACTCCTACATACAAAAGGTATCGGCCAAGATTGTATCTTGAAGATTGTTC
ATATCTAGTAAACCATATTGTCTTTTGGAA-CAGTGTGAGTATTAGTTTATTCATCATGATTATGATGACCG--------
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----------------------------------TGTCAAAATCTAAAACGTAGAATCAAC---CTCAAGTTCAGGTCGA
AACTCGAAATTTATATTGAGAGACAGAAAAAGGTAAATTCAGATGTGAATAGTGTCAAATGTTGTTTTTGGTCTTTTTAT
GACACTATCCATGCTAGATTTCACATTTTTGTTTCTTAATGTACATTTAGAGTTTGGACCTGGAATTTTTAGAAGTTGTA
GTCACATTCCTTGTAAACATTCATATTTTTTCCATAGTTTTTTAAAACATTTAAAATTGATCTTTTTTTTAAGTTGGAGC
ATGTGGAGCACCCCAAGGATGGGAGCGCCTGATATTTCCCCCTTTCTTAGATCACTCTTACTCT-GAGTAATCTTAGATC
ACTCTAAGTAATCTTGCAGTTTCCTGTCAAATCAGCCAGGCAGAAAAAGTTGAACTATGTGTACTCATTTAATGGCGTAC
ATCCGAATGTGCTGGCACCATTAAGTGAGCACACTCTAAATGACAGCATATCACCTGATTTGGATTCGAATAAAGCACTA
AATGAGAGCATATCTGGCACCACATTGCAGATTGCAGTACTAACTGACTGTAT--GGCTGCATCACACTGTCGAGTAGGA
AACGCAGTCGAGTAAGCAACCGCCGCGTCTGACCGTGACTTCGCCGGTGACCGGTCACGTGCCCGCCCGTCCTATAAACA
CAGCCGCTCCATCAGAGTCGACCAGACCAAAGCCTTCTGCCAGTCGCTCGTTGTCACTCGACAGTCGACACCATGTGGAA
CAACGGGGCGATGAGCGGCCAAGTTTACCCGCCGCCGCCGGCGGCGATGGTGCCGCAGCCGCAGCCGCACGGGCAGGTGG
CCGCGAACAACTGGGCGGGCAACGACGCCAACACGCTGCTGGTGGTGGCGACGCTGATCACCACGCTCACGTACCAGCTC
GGGTGCAGCGTCCCCGGCGGGTACTGGCAGGACACGCTGGCGGCGGACGGCAAGCAGCAGCCGCACGAGGCCGGAGACCC
CATCATGCGCGACAAGCACCCGCAAAGGTACGCACATGGCGCATGCTCCTGGTTAGAAACTTAGATTCTGA----AATCC
CGGTGGTCATGCGGACGTCCCTTGACCGATGGCACGCATGCGTGCAGGTACTGGGTGTTCATGGCGGCGAGCTGGATGGG
GTTCCTGGCGTCCATGATGATGACGCTGAGCCTGCTGGTGCGCCTGCCGGTGGACTCGCGGCAGGTCCGGTGGTCCTTCG
CCGTCGCCTACTCCAGCCTGGTGCTCACCTTCATCGTGTCGCAGGCCAAGACGCACATCTCAGTCGACATCGCCATCTGG
TTGGTCACCGTCGTCTTCCTGTGGCTCATGATCAGCGTCCGCCCTGAGCACCGGGCGCGTATCCTCCGTTTCTTCTGCTG
CGACCGCGAGAACTGACGCCCCAAGCTT-AGTGTTCTCATGTCTTTGTCGAGTATAAACTGCTGTGAGTTCAGAACTTTT
TTGTCGTCTAAAAAGTTCAGAAGTTGTAAACTTTGTTTAGACTCGGAGTAATAAC-AAAAGGGAACGCCTAA--------
-----------------TCTTTCAGTCGATTTTGTCAAAGCCGTTTGGATTTACTG---GTTCGTCCTCCTTCCGCCAGC
CACTATCCATCTTCCTCCTCCCGCTAGTCGACATTCTGCCGAGCCTGACCGCGTGCGGCCCAGCCTTGTTTGACCTGATC
ATCCCTCTAAACCC------------------------------CGCACTCAAACAATCGAGCTTCTGATTGGCCTCCAC
AGGTGACATCGCGGCCACGTCGCCGCTAGCTCCGGCTCGCTTTAGGCGAGACCTCGACGGGGAGTCCCCGTCTCGGCCTC
GGGGTTACATGCACACGAGAACCGACCCATGCAAACAAAACCTCA-----------------------------------
-------------------------ATTGCATGAGGAATAAATGTGTAAGTAACAAAATGAAACTTCAAGTTGCTGATGG
AGACATGTCGGCGATCTCGACCGAGCAGCGCCATTGCTGGGATTCCTCTTCCCCACGCGGCACATACCCTTTTTGTGGTG
GTTGACAACCTTTTTTTTTTCTTTTGAGAATGATGGTTGACAACTAACAGACAAATCCTTGCAGCAAATAAGAATGCGCT
GCGTACCCT-GATCTTGGCCGGCTCAACAAGGCTTATGAGCACTTATTTATTTGTTTATTTATGTGCTTTTTACCTAGAT
AATGTTCTATTTTCTCAACAAAAAAAAAACTTTTGCCTACACCTAGTTTGGCTCCCTATAATTTAACTTTGATTTATTCA
ATTTATGCT----TATGAAATTGATTCTGAAAGAGTTTAATTTCAATATTTTACTCGGATGCCACATGACAATGAAAATT
ACTCATTTCTAATTTCTTAAGAATTTGAATTTCGTGTTCACACATACTCCCTCTCTCTACAATTGTAAGTCATTTCTTGA
CACTATACGTCTTACATTTTA
>chr4B_2
-ATTAATACAAAATATCCAGATTTTTAGGTATA--AATTAAACATCAGATTTTTTTATGAAAGATAGATTTATTATATGC
ATCTTATACATTTTTTATTAACTTG----------TACATACAAAAGGTATATGCTAAGATTGTATCTTGAAGATTGGTC
ATATCTA---AACCATATTGATTTTTCGAA-CAGTGTGAGTATTACTTTATTCATCATGATTTTTTTATGATTTTTTTTT
TGAGAAGGAGGATCATCCT-GGCCTCTGCATCCGACATATGCATGCGTCCATATTATTAAAAGGTGTCAACAAAATACAA
AGTCTGCAATCTAGATGATTTTTTTAATGATGACTGTCAAAATCTAAAACGTAGAATCAAC---CTCAAGGG--------
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-----------------------------------------CTTTGTTAGGTCACTCTTACTCAAGACTGATCTTAGATC
ACTCCAGGTAATCTCGCAGTTTCCTGTCAAATCAGCCAGTCAGAAAA-GTTGGACTATGTGTACTCATTTAATGGCGTAC
ATCCGAATTTGCTGGCACCATTAAATGAGCACACTCTAAATGACAGCATATCACCTGATTTGGATTCGAATAAAGCACTA
AATGAGAGCATATCTGGCACCACATTGCAGATTGCAGTA---ACTGACAGTAT--GCCTGCATCACACTGTCGAGTAGGA
AACGCAGTCGAGTAAGCAACCGCCGCGTCTGACCGTGACTTCGCCGGTGACCGGTCACGTGCCCGCCCGTCCTATAAACA
CAACCGTTCCATCAGAGTCGACCAGATCAAAGCCTTTTGTCAGTCGCTCGCTGTCAC-------TCGACACCATGTGGAA
CAACGGGGCGATGAGCGGCCAAGTTTACCCACCGCCGCCGGCGGCGATGGCGCCGCAGCCGCAGCCTCACGGGCAGGTGG
CGGCCAACAACTGGGCGGGCAACGACGCCAACACGCTGCTGGTGGTGGCGACGCTGATCACCACGCTCACGTACCAGCTC
GGGTGCAGCGTCCCCGGCGGGTACTGGCAGGACACGCTGCCGGCGGACGGCAAGCAGAAGCCGCACGAGGCCGGTGACCC
CATCATGCGCGACAAGCACCCGCAAAGGTACGCACAGGGTACATGCTCCTGGTTAGAAACTTAGATTCTGATCGAAAGCC
CGGTGGTCATGCGGACGTTCCTTGACTGATGGCATGCATGCGTGCAGGTACTGGGTGTTCATGGCGGCGAGCTGGATGGG
GTTCCTGGCGTCCATGATGATGACGCTGAGCCTGCTGGTACGCCTGCCGGTGGACTCGCGGCAGGTCCGGTGGTCCTTCG
CCGTCGCCTACTCTAGCCTGGTGCTCACCTTCATCGTGTCGCAGGCCAAGACGCACATCTCAATCGACATCGCCATCTGG
TTGGTCACCGTCGTTTTCCTGTGGCTCATGATCAGCGTCCGCCCTGAGCACCGGGCGCGTATTCTCCGTTTCTTCTGCTG
CAACCGCGAGAACTGACGCCCCAAGCTTTAGTGTTCTTATGTCTTTGTCGGGTATAAACTGCTGTGAGTTCAGAACTTTT
TTGTCGTCTAAAAAGTTCAGAAGTTGTAA-CTTTGTTTAGACTCGGAGTAATAAC-AAAAGGGGACGCCTAGGCGTCACT
TATATTAATTA-AAAAGTCTTTCAGTCGATTTTGTCAAAGCCGTTTGGATTTACAGGTACGCAA---TCCTTCTGCCAGC
CACTATTCATCTTCCTCCTCCCGCTAGTCGACATTCTGCCGAGCCTGACAGCCTGCGGCCCAACCTTGTTTGACCTGATC
ATCCCTCTAAACCTCGCACCGAGCTCCCGGGCTGGCAGCCTTCACGCACTCAAACAATCGAGCTTCTGATTGGCCTCCGC
ACGTGACATCGCGGCCACGTCGCCGCAAGCTCCGGCTCGCTTTAGGCGAGACCTCGACGGTGAGTCCCCGTCTGGGCCTC
GGGGCTACACG--CACGAGAACCGACCGATGCAAACAAAACCTTAACTTTTTTTTGAAATTGATTGGATTGCTTATCACA
TGTGTTACGTGCTAACAAAAACTCGATTGCATGAGAAATAAATGTGCC--------------------------------
----------------------------------------------------------------------TTTTTTGGTG
GTTGACAACTTTTTTTTTTT-----GAAAATGATGGTTGACAAGTAACCGACAAATCCTTGCAGCAAATAGGAATGCGCT
GCGTACTCTAGATCGTGGCCGGCCCAACAAGGCTGATGAGCACTTATTTATTTGTTTATTTATGTGCTTTTTACCTAAAC
AATGTTCTATTTTATCAAAAAAAA----ACTTTTACCTACACCTAGTTTGGCTCCCTATAATTTAACTTTGATTTATTCA
ATTTATGCTAGAATATGAAATTGATTCTGAAAGAGTCTAATTTCAATATTTTACTC------------------------
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>chr4D_2
-ATTAATACAAAATATCCAGATTTTTAGGTATA--AATTAAACATCAGAGTTTTTAATGAAAGATAGATTTATTATATGC
ATCTTATACATTTTTTATTAACTTG----------TACATACAAAAGGTATCTGCCAAGATTGTATCTTGAAGATTGGTC
ATATT---TAAACCATATTGATTTTTCAAACCAGTGTGAGTATTACTTTATCCATCATGATTTTTTTATGATTTTTTTT-
-----AGGAGGATCACCCCCGGCCTCTGCATCCGACAAATGCATGCGGCCATATTATTAAAATGTGCCAACAAAATACAA
AGTCTGCAACCTAGATGATCTTTTTAATGATGACTGTCAAAATCTAAATCGTAGATCACTCTTACTCAAGGG--------
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-----------------------------------------CTTTGTTAGGTCACTCTTACTCAAGAGTGATCTTAGATC
ACTCCAAGTAATCTTGCGGTTTGCTGTCAAATCAGCCAGTCAGAAAA-GTTGGACTATGTGTACTCATTTAATGGCGTAC
ATCCGAATTTGCTGGCACCATTAAATGAGCACACTCTAAATGGCAGCATATCACCTGATTTGGATTCGAATAAAGCACTA
AATGAGAGCATATCTGGCACCACATTGCAGATTGCAGTA---ACTGACAGTATACGCCTGCATCACACTGTCGAGTAGGA
AACGCACTGGAGTAAGCAACCGCCGTGTCTGACCGTGACTTCGCCGGCGACCGGTCACGTGTCCGCCCATCCTATAAACA
CAGCCGTTCCATCAGAGTCGACCAGATCAAAGCCTTCTGTCATTCGCTCGTTGTCAC-------TCGACACCATGTGGAA
CAACGGGGCGATGAGCGGCCAAGTTTACCCGCCGCCGCCGCCGGCGATGGTGCCGCAGCCGCAGCCGCACGGGCAGGTGG
CGGCTAACAACTGGGCGGGTAACGACGCCAACACGCTGCTGGTGGTGGCGACGCTGATCACCACGCTCACGTACCAGCTC
GGGTGCAGCGTCCCCGGCGGGTACTGGCAGGACACGCTGGCGGCGGACGGCAAGCAGAAGCCGCACGAGGCCGGAGACCC
CATCATGCGCGACAAGCACCCGCAAAGGTACGCACAGGGCACATGGTCCTGGTTAGAAACTTAGAATCTGA----AATCC
TGGTCGTGCG--GGACGTTCCTTGACTGATGGCATCCATGCGTGCAGGTACTGGGTGTTCATGGCGGCGAGCTGGATGGG
GTTCCTGGCGTCCATGATGATGACGCTGAGCCTACTGGTGCGCCTGCCGGTGGACTCGCGGCAGGTCCGGTGGTCCTTCG
CCGTCGCCTACTCCAGCCTGGTGCTCACCTTCATCGTGTCGCAGGCCAAGACGCACATCTCAATCGACATCGTCATCTGG
TTGGTCACCGTCGTCTTCCTGTGGCTCATGATCAGCGTCCGCCCTGACCACCGGGAGCGTATCCTCCGTTTCTTCTGCTG
CAACCGCGAGAAGTGACGCCCCAAGCTT-AGCGTTCTCATGTCTTTGTCGATTATAAACTGCTGTGAGTTCAGAACTTTT
TCGTCGTCTAAGAAGTTCAGAAGTTGTAA-CTTTGTTTAGACTCGGAGTAATAACAAAAGGGGGACGCCTAGACGTCACT
TATATTAATTTTAAAAGTCTTTCAGTTGATTTTGTCAAAGCCGTTTGGATTTACTGCTGGTTCGTCCTCCTTCCGCCAGC
CACTATTCATCTTCCTCCTGCCGCTAGTCGACATTCTGCCGAGCCTGACCACCTGCGGCCCAGCCTTGTTTGACCTGATC
ATCCCTCTAAACCCCGCACCGAGCTCCAGGGCTGGCAGCCTTCACGCACTCAAACAATCAAGCTTCTGATTGGCCTCCGG
ACGTGACATCGCGGCCACGTCGCCGCTAGCTCCGGCTCTCTTTAGGCGAGACCTCGACGGGGAGTCCCCGTCTCGGCCTC
GGGGCTACACGAACACGAGAACTGACTGATGTAAACAAAATCTCA-----------------------------------
-------------------------ATTGCATGAGGAATAAATGTGTAAGTAACAAAATGGAACTTCGAGTTACTGATGG
AGACATGTCGGCGATCTCGACCGAGCAGCGCCATTGCTGGAATTCTTCTTCCCCACGCGGCACATACCCTTTTTGTGGTG
GTTGACAAGTTTTTTTTTGG-------GAATGATGGTTGACAACTAACCGACAAATCCTTGCAGCAAATAGGAATGCGCT
GCGTACCCTAGATCTTGGCCGGCCCAACAAGGCCTATGAGGACTTATTTATTTGTTTATTTATTTGCTTTTTACCTAGAT
AATGTTCTATTTTCTCAACAAAAA-AACACTTTTACCTACACCTAGTTTGGCTCCCTATAATTTAACTTTGATTTATTCA
ATTTATGCTAGAATATGAAATTGATTCTGAAAGAGTTTAATTTCAATATTTTACTCGGATGCCACATGACAATGAAAATT
ATTCATTTCTAATTTGTTAAGAATTTGAATTCCGTGTTCACACATACTCCCTCTTTCTACAATTGTAAGACATTTCTTGA
CACTATATGTCTTACATTTTA
>chr4A_1046
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-------------------------------------------------------CAGCAGCAGCTCGGCGGGCAGGGAC
---CGAACACCTGGGTCGGCAACGACGCCAACACGCTGCTGGTGGTGGCCACGCTGATCACCACGCTCACCTACCAGCTC
GGCACCAACATCCCCGGCGGGTACTGGCAGGAGACAAAGTCGGTGGACGGCAGGGAGCTTTACCGCGCCGGC---GACCC
CATCATGCGCGACCTGCACCGCCCAAGGTACGCGCGCGCCGTGAAAACCACTCGATCGGTCGTTCATGCCATGCCAGTAT
CGGTTGACATGCCGGAT------------------------GTGCAGGTACTGGCTGTTCATGGCGGCGAGCTGGGCTGG
GTTCGCGAGCTCGATGGTGATGACGCTGAGCCTGCTGGTGCGGATGTCGGCGGACTCGCGGCACGTGCGGTGGTCGTTCG
TGGTGGCCTACTCCAGCCTCGTGCTCACCTTCGTGGTGTCGCAGCCCAGGACTCACCTGTCCATGGACATCCTCGTCTGG
GCGGGCGTCCTCGCCTTCCTCTGGCTCGTCATCAGCGTCCACCCGGAGCACCGCACGCGCATCGTCC-------------
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>chr4B_1046
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-------------------------------------------------------CAGCAGCAGCTCGGCGGGCAGGGAC
---CGAACACCTGGGTCGGCAACGACGCCAACACGCTGCTGGTGGTGGCCACGCTGATCACCACGCTAACCTACCAGCTC
GGCACCAACATCCCCGGCGGGTACTGGCAGGAGACAAAGTCGCTGGACGGCAGGGAGCTGTACCGCGCCGGC---GACCC
CATTATGCGCGACCTGCACCGCCCAAGGTACGCGCGCGCCGTGAAAACCACTCGATCGGTCGTT-----CATGCCAGTAT
CGGTTGACATGCCGGAT------------------------GTGCAGGTACTGGCTGTTCATGGCGGCGAGCTGGGTTGG
GTTCGCGAGCTCGATGGTGATGACGCTGAGCCTGCTGGTGCGGATGTCGGCGGACTCGCGGCACGTGCGGTGGTCGTTCG
TGGTGGCCTACTCCAGCCTCGTGCTCACCTTCGTCGTGTCGCAGCCCAGGACGCACCTGTCGATGGACATCCTCGTCTGG
GCGGGCGTCCTCGCCTTCCTCTGGCTCGTCATCAGCGTCCACCCGGAGCACCGCACGCGCATCGTCC-------------
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>SNPs
S--------------------------------SS---------------S-----------------------------
----------------SS-S-S-SSSSSSSSSSSS-----------------S------------------------S--
-------S------------SS----S------------------S----------------S-SS-SSSSS--------
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----------------------------------------------------------------------SSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----S----S------------S-----S----------
----S----------------------------------S-------S----S---------------------------
--------S---------------S-------------------------------------------------------
---------------------------------------SSS------S-------S-----------------------
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------S-------------------S------------S-----------------SSSSSSS----------------
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-S------------------------------------------------------------------------------
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------------------------------------S-------------------------------------------
------------------S-------S-------S---------------------------------------------
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--------------------------------------------------------------S-----------------
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-S------------------------------------------------------------------------------
-----------------------------S---------------------------------S-------S--------
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------S---------------------------------------------S---------------------------
------------------------------------------------------------------------------S-
-S------------------------------------------------------------------------------
----S----S-S---------------S----------------------------------------------------
------------------------------------------------------------S------S----S-------
----------------------------------------S----S----------------------------------
---------S----------SSSSS-----------------------S---------------------S---------
-----------------------S--------------------------------------------------------
------------------------S--S------S---------------------------------------------
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-S-------------S---------------S----------------------S--------------S----------
-------S-------------
>forward_679
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-------------------TGGGAGCGCCTGATATTTCC-----------------------------------------
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>reverse_2007
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------CCATCTTCCTCCTCCCGCTA------------------------------------------------------
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