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rescan_seq
Martin Asser Hansen edited this page Oct 2, 2015
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6 revisions
[rescan_seq} uses information from REBASE to locate restriction enzyme (RE) binding sites.
The positions reported as values to the RE_MATCHES key denotes the beginning postion of the
binding site (0-based), not the cleavage site - which may be outside the binding site.
The following extract from REBASE shows what RE that can be scanned for:
#
# REBASE version 908 emboss_e.908
#
# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
# REBASE, The Restriction Enzyme Database http://rebase.neb.com
# Copyright (c) Dr. Richard J. Roberts, 2009. All rights reserved.
# =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
#
# Rich Roberts Jul 28 2009
#
# REBASE enzyme patterns for EMBOSS (embossre.enz)
#
# Format:
#
# name<ws>pattern<ws>len<ws>ncuts<ws>blunt<ws>c1<ws>c2<ws>c3<ws>c4
#
# Where:
# name = name of enzyme
# pattern = recognition site
# len = length of pattern
# ncuts = number of cuts made by enzyme
# Zero represents unknown
# blunt = true if blunt end cut, false if sticky
# c1 = First 5' cut
# c2 = First 3' cut
# c3 = Second 5' cut
# c4 = Second 3' cut
#
# Examples:
# AAC^TGG -> 6 2 1 3 3 0 0
# A^ACTGG -> 6 2 0 1 5 0 0
# AACTGG -> 6 0 0 0 0 0 0
# AACTGG(-5/-1) -> 6 2 0 1 5 0 0
# (8/13)GACNNNNNNTCA(12/7) -> 12 4 0 -9 -14 24 19
#
# i.e. cuts are always to the right of the given
# residue and sequences are always with reference to
# the 5' strand.
# Sequences are numbered ... -3 -2 -1 1 2 3 ... with
# the first residue of the pattern at base number 1.
#
#
AanI TTATAA 6 2 1 3 3 0 0
AarI CACCTGC 7 2 0 11 15 0 0
AasI GACNNNNNNGTC 12 2 0 7 5 0 0
AatI AGGCCT 6 2 1 3 3 0 0
AatII GACGTC 6 2 0 5 1 0 0
AbsI CCTCGAGG 8 2 0 2 6 0 0
AccI GTMKAC 6 2 0 2 4 0 0
AccII CGCG 4 2 1 2 2 0 0
AccIII TCCGGA 6 2 0 1 5 0 0
Acc16I TGCGCA 6 2 1 3 3 0 0
Acc36I ACCTGC 6 2 0 10 14 0 0
Acc65I GGTACC 6 2 0 1 5 0 0
AccB1I GGYRCC 6 2 0 1 5 0 0
AccB7I CCANNNNNTGG 11 2 0 7 4 0 0
AccBSI CCGCTC 6 2 1 3 3 0 0
AceIII cagctc 6 2 0 13 17 0 0
AciI CCGC 4 2 0 1 3 0 0
AclI AACGTT 6 2 0 2 4 0 0
AclWI GGATC 5 2 0 9 10 0 0
AcoI YGGCCR 6 2 0 1 5 0 0
AcsI RAATTY 6 2 0 1 5 0 0
AcuI CTGAAG 6 2 0 22 20 0 0
AcvI CACGTG 6 2 1 3 3 0 0
AcyI GRCGYC 6 2 0 2 4 0 0
AdeI CACNNNGTG 9 2 0 6 3 0 0
AfaI GTAC 4 2 1 2 2 0 0
AfeI AGCGCT 6 2 1 3 3 0 0
AfiI CCNNNNNNNGG 11 2 0 7 4 0 0
AflII CTTAAG 6 2 0 1 5 0 0
AflIII ACRYGT 6 2 0 1 5 0 0
AgeI ACCGGT 6 2 0 1 5 0 0
AgsI TTSAA 5 2 0 3 2 0 0
AhaIII tttaaa 6 2 1 3 3 0 0
AhdI GACNNNNNGTC 11 2 0 6 5 0 0
AhlI ACTAGT 6 2 0 1 5 0 0
AjiI CACGTC 6 2 1 3 3 0 0
AjnI CCWGG 5 2 0 -1 5 0 0
AjuI GAANNNNNNNTTGG 14 4 0 -8 -13 25 20
AleI CACNNNNGTG 10 2 1 5 5 0 0
AlfI GCANNNNNNTGC 12 4 0 -11 -13 24 22
AloI GAACNNNNNNTCC 13 4 0 -8 -13 25 20
AluI AGCT 4 2 1 2 2 0 0
AluBI AGCT 4 2 1 2 2 0 0
AlwI GGATC 5 2 0 9 10 0 0
Alw21I GWGCWC 6 2 0 5 1 0 0
Alw26I GTCTC 5 2 0 6 10 0 0
Alw44I GTGCAC 6 2 0 1 5 0 0
AlwFI gaaaynnnnnrtg 13 0 0 0 0 0 0
AlwNI CAGNNNCTG 9 2 0 6 3 0 0
Ama87I CYCGRG 6 2 0 1 5 0 0
Aor13HI TCCGGA 6 2 0 1 5 0 0
Aor51HI AGCGCT 6 2 1 3 3 0 0
ApaI GGGCCC 6 2 0 5 1 0 0
ApaBI gcannnnntgc 11 2 0 8 3 0 0
ApaLI GTGCAC 6 2 0 1 5 0 0
ApeKI GCWGC 5 2 0 1 4 0 0
ApoI RAATTY 6 2 0 1 5 0 0
ApyPI atcgac 6 2 0 26 24 0 0
AquIII gaggag 6 2 0 26 24 0 0
AquIV grggaag 7 2 0 26 24 0 0
ArsI GACNNNNNNTTYG 13 4 0 -9 -14 24 19
AscI GGCGCGCC 8 2 0 2 6 0 0
AseI ATTAAT 6 2 0 2 4 0 0
Asi256I gatc 4 2 0 1 3 0 0
AsiGI ACCGGT 6 2 0 1 5 0 0
AsiSI GCGATCGC 8 2 0 5 3 0 0
AspI GACNNNGTC 9 2 0 4 5 0 0
Asp700I GAANNNNTTC 10 2 1 5 5 0 0
Asp718I GGTACC 6 2 0 1 5 0 0
AspA2I CCTAGG 6 2 0 1 5 0 0
AspCNI gccgc 5 0 0 0 0 0 0
AspEI GACNNNNNGTC 11 2 0 6 5 0 0
AspLEI GCGC 4 2 0 3 1 0 0
AspS9I GGNCC 5 2 0 1 4 0 0
AssI AGTACT 6 2 1 3 3 0 0
AsuI ggncc 5 2 0 1 4 0 0
AsuII TTCGAA 6 2 0 2 4 0 0
AsuC2I CCSGG 5 2 0 2 3 0 0
AsuHPI GGTGA 5 2 0 13 12 0 0
AsuNHI GCTAGC 6 2 0 1 5 0 0
AvaI CYCGRG 6 2 0 1 5 0 0
AvaII GGWCC 5 2 0 1 4 0 0
AvaIII atgcat 6 0 0 0 0 0 0
AviII TGCGCA 6 2 1 3 3 0 0
AvrII CCTAGG 6 2 0 1 5 0 0
AxyI CCTNAGG 7 2 0 2 5 0 0
BaeI ACNNNNGTAYC 11 4 0 -11 -16 23 18
BaeGI GKGCMC 6 2 0 5 1 0 0
BalI TGGCCA 6 2 1 3 3 0 0
BamHI GGATCC 6 2 0 1 5 0 0
BanI GGYRCC 6 2 0 1 5 0 0
BanII GRGCYC 6 2 0 5 1 0 0
BanIII ATCGAT 6 2 0 2 4 0 0
BarI GAAGNNNNNNTAC 13 4 0 -8 -13 25 20
BasI CCANNNNNTGG 11 2 0 7 4 0 0
BauI CACGAG 6 2 0 1 5 0 0
BbeI GGCGCC 6 2 0 5 1 0 0
Bbr7I gaagac 6 2 0 13 17 0 0
BbrPI CACGTG 6 2 1 3 3 0 0
BbsI GAAGAC 6 2 0 8 12 0 0
BbuI GCATGC 6 2 0 5 1 0 0
BbvI GCAGC 5 2 0 13 17 0 0
BbvII gaagac 6 2 0 8 12 0 0
Bbv12I GWGCWC 6 2 0 5 1 0 0
BbvCI CCTCAGC 7 2 0 2 5 0 0
BccI CCATC 5 2 0 9 10 0 0
Bce83I cttgag 6 2 0 22 20 0 0
BceAI ACGGC 5 2 0 17 19 0 0
BcefI acggc 5 2 0 17 18 0 0
BcgI CGANNNNNNTGC 12 4 0 -11 -13 24 22
BciVI GTATCC 6 2 0 12 11 0 0
BclI TGATCA 6 2 0 1 5 0 0
BcnI CCSGG 5 2 0 2 3 0 0
BcuI ACTAGT 6 2 0 1 5 0 0
BdaI TGANNNNNNTCA 12 4 0 -11 -13 24 22
BetI wccggw 6 2 0 1 5 0 0
BfaI CTAG 4 2 0 1 3 0 0
BfiI ACTGGG 6 2 0 11 10 0 0
BfmI CTRYAG 6 2 0 1 5 0 0
BfoI RGCGCY 6 2 0 5 1 0 0
BfrI CTTAAG 6 2 0 1 5 0 0
BfuI GTATCC 6 2 0 12 11 0 0
BfuAI ACCTGC 6 2 0 10 14 0 0
BfuCI GATC 4 2 0 -1 4 0 0
BglI GCCNNNNNGGC 11 2 0 7 4 0 0
BglII AGATCT 6 2 0 1 5 0 0
BinI ggatc 5 2 0 9 10 0 0
BisI GCNGC 5 2 0 2 3 0 0
BlnI CCTAGG 6 2 0 1 5 0 0
BlpI GCTNAGC 7 2 0 2 5 0 0
BlsI GCNGC 5 2 0 3 2 0 0
BmcAI AGTACT 6 2 1 3 3 0 0
Bme18I GGWCC 5 2 0 1 4 0 0
Bme1390I CCNGG 5 2 0 2 3 0 0
BmeRI GACNNNNNGTC 11 2 0 6 5 0 0
BmeT110I CYCGRG 6 2 0 1 5 0 0
BmgI gkgccc 6 0 0 0 0 0 0
BmgBI CACGTC 6 2 1 3 3 0 0
BmgT120I GGNCC 5 2 0 2 3 0 0
BmiI GGNNCC 6 2 1 3 3 0 0
BmrI ACTGGG 6 2 0 11 10 0 0
BmrFI CCNGG 5 2 0 2 3 0 0
BmsI GCATC 5 2 0 10 14 0 0
BmtI GCTAGC 6 2 0 5 1 0 0
BmuI ACTGGG 6 2 0 11 10 0 0
BoxI GACNNNNGTC 10 2 1 5 5 0 0
BpiI GAAGAC 6 2 0 8 12 0 0
BplI GAGNNNNNCTC 11 4 0 -9 -14 24 19
BpmI CTGGAG 6 2 0 22 20 0 0
Bpu10I CCTNAGC 7 2 0 2 5 0 0
Bpu14I TTCGAA 6 2 0 2 4 0 0
Bpu1102I GCTNAGC 7 2 0 2 5 0 0
BpuAI GAAGAC 6 2 0 8 12 0 0
BpuEI CTTGAG 6 2 0 22 20 0 0
BpuMI CCSGG 5 2 0 2 3 0 0
BpvUI CGATCG 6 2 0 4 2 0 0
BsaI GGTCTC 6 2 0 7 11 0 0
Bsa29I ATCGAT 6 2 0 2 4 0 0
BsaAI YACGTR 6 2 1 3 3 0 0
BsaBI GATNNNNATC 10 2 1 5 5 0 0
BsaHI GRCGYC 6 2 0 2 4 0 0
BsaJI CCNNGG 6 2 0 1 5 0 0
BsaMI GAATGC 6 2 0 7 5 0 0
BsaWI WCCGGW 6 2 0 1 5 0 0
BsaXI ACNNNNNCTCC 11 4 0 -10 -13 21 18
BsbI caacac 6 2 0 27 25 0 0
Bsc4I CCNNNNNNNGG 11 2 0 7 4 0 0
BscAI gcatc 5 2 0 9 11 0 0
BscGI cccgt 5 0 0 0 0 0 0
Bse1I ACTGG 5 2 0 6 4 0 0
Bse8I GATNNNNATC 10 2 1 5 5 0 0
Bse21I CCTNAGG 7 2 0 2 5 0 0
Bse118I RCCGGY 6 2 0 1 5 0 0
BseAI TCCGGA 6 2 0 1 5 0 0
BseBI CCWGG 5 2 0 2 3 0 0
BseCI ATCGAT 6 2 0 2 4 0 0
BseDI CCNNGG 6 2 0 1 5 0 0
Bse3DI GCAATG 6 2 0 8 6 0 0
BseGI GGATG 5 2 0 7 5 0 0
BseJI GATNNNNATC 10 2 1 5 5 0 0
BseLI CCNNNNNNNGG 11 2 0 7 4 0 0
BseMI GCAATG 6 2 0 8 6 0 0
BseMII CTCAG 5 2 0 15 13 0 0
BseNI ACTGG 5 2 0 6 4 0 0
BsePI GCGCGC 6 2 0 1 5 0 0
BseRI GAGGAG 6 2 0 16 14 0 0
BseSI GKGCMC 6 2 0 5 1 0 0
BseXI GCAGC 5 2 0 13 17 0 0
BseX3I CGGCCG 6 2 0 1 5 0 0
BseYI CCCAGC 6 2 0 1 5 0 0
BsgI GTGCAG 6 2 0 22 20 0 0
Bsh1236I CGCG 4 2 1 2 2 0 0
Bsh1285I CGRYCG 6 2 0 4 2 0 0
BshFI GGCC 4 2 1 2 2 0 0
BshNI GGYRCC 6 2 0 1 5 0 0
BshTI ACCGGT 6 2 0 1 5 0 0
BshVI ATCGAT 6 2 0 2 4 0 0
BsiI cacgag 6 2 0 1 5 0 0
BsiEI CGRYCG 6 2 0 4 2 0 0
BsiHKAI GWGCWC 6 2 0 5 1 0 0
BsiHKCI CYCGRG 6 2 0 1 5 0 0
BsiSI CCGG 4 2 0 1 3 0 0
BsiWI CGTACG 6 2 0 1 5 0 0
BsiYI ccnnnnnnngg 11 2 0 7 4 0 0
BslI CCNNNNNNNGG 11 2 0 7 4 0 0
BslFI GGGAC 5 2 0 15 19 0 0
BsmI GAATGC 6 2 0 7 5 0 0
BsmAI GTCTC 5 2 0 6 10 0 0
BsmBI CGTCTC 6 2 0 7 11 0 0
BsmFI GGGAC 5 2 0 15 19 0 0
BsnI GGCC 4 2 1 2 2 0 0
Bso31I GGTCTC 6 2 0 7 11 0 0
BsoBI CYCGRG 6 2 0 1 5 0 0
Bsp13I TCCGGA 6 2 0 1 5 0 0
Bsp19I CCATGG 6 2 0 1 5 0 0
Bsp24I gacnnnnnntgg 12 4 0 -9 -14 24 19
Bsp68I TCGCGA 6 2 1 3 3 0 0
Bsp119I TTCGAA 6 2 0 2 4 0 0
Bsp120I GGGCCC 6 2 0 1 5 0 0
Bsp143I GATC 4 2 0 -1 4 0 0
Bsp1286I GDGCHC 6 2 0 5 1 0 0
Bsp1407I TGTACA 6 2 0 1 5 0 0
Bsp1720I GCTNAGC 7 2 0 2 5 0 0
BspACI CCGC 4 2 0 1 3 0 0
BspCNI CTCAG 5 2 0 14 12 0 0
BspDI ATCGAT 6 2 0 2 4 0 0
BspD6I gactc 5 2 0 9 11 0 0
BspEI TCCGGA 6 2 0 1 5 0 0
BspFNI CGCG 4 2 1 2 2 0 0
BspGI ctggac 6 0 0 0 0 0 0
BspHI TCATGA 6 2 0 1 5 0 0
BspLI GGNNCC 6 2 1 3 3 0 0
BspLU11I acatgt 6 2 0 1 5 0 0
BspMI ACCTGC 6 2 0 10 14 0 0
BspMII tccgga 6 2 0 1 5 0 0
BspNCI ccaga 5 0 0 0 0 0 0
BspOI GCTAGC 6 2 0 5 1 0 0
BspPI GGATC 5 2 0 9 10 0 0
BspQI GCTCTTC 7 2 0 8 11 0 0
BspTI CTTAAG 6 2 0 1 5 0 0
BspT104I TTCGAA 6 2 0 2 4 0 0
BspT107I GGYRCC 6 2 0 1 5 0 0
BspTNI GGTCTC 6 2 0 7 11 0 0
BspXI ATCGAT 6 2 0 2 4 0 0
BsrI ACTGG 5 2 0 6 4 0 0
BsrBI CCGCTC 6 2 1 3 3 0 0
BsrDI GCAATG 6 2 0 8 6 0 0
BsrFI RCCGGY 6 2 0 1 5 0 0
BsrGI TGTACA 6 2 0 1 5 0 0
BsrSI ACTGG 5 2 0 6 4 0 0
BssAI RCCGGY 6 2 0 1 5 0 0
BssECI CCNNGG 6 2 0 1 5 0 0
BssHII GCGCGC 6 2 0 1 5 0 0
BssKI CCNGG 5 2 0 -1 5 0 0
BssMI GATC 4 2 0 -1 4 0 0
BssNI GRCGYC 6 2 0 2 4 0 0
BssNAI GTATAC 6 2 1 3 3 0 0
BssSI CACGAG 6 2 0 1 5 0 0
BssT1I CCWWGG 6 2 0 1 5 0 0
Bst6I CTCTTC 6 2 0 7 10 0 0
Bst98I CTTAAG 6 2 0 1 5 0 0
Bst1107I GTATAC 6 2 1 3 3 0 0
BstACI GRCGYC 6 2 0 2 4 0 0
BstAFI CTTAAG 6 2 0 1 5 0 0
BstAPI GCANNNNNTGC 11 2 0 7 4 0 0
BstAUI TGTACA 6 2 0 1 5 0 0
BstBI TTCGAA 6 2 0 2 4 0 0
Bst2BI CACGAG 6 2 0 1 5 0 0
BstBAI YACGTR 6 2 1 3 3 0 0
Bst4CI ACNGT 5 2 0 3 2 0 0
BstC8I GCNNGC 6 2 1 3 3 0 0
BstDEI CTNAG 5 2 0 1 4 0 0
BstDSI CCRYGG 6 2 0 1 5 0 0
BstEII GGTNACC 7 2 0 1 6 0 0
BstENI CCTNNNNNAGG 11 2 0 5 6 0 0
BstF5I GGATG 5 2 0 7 5 0 0
BstFNI CGCG 4 2 1 2 2 0 0
BstH2I RGCGCY 6 2 0 5 1 0 0
BstHHI GCGC 4 2 0 3 1 0 0
BstKTI GATC 4 2 0 3 1 0 0
BstMAI GTCTC 5 2 0 6 10 0 0
BstMBI GATC 4 2 0 -1 4 0 0
BstMCI CGRYCG 6 2 0 4 2 0 0
BstMWI GCNNNNNNNGC 11 2 0 7 4 0 0
BstNI CCWGG 5 2 0 2 3 0 0
BstNSI RCATGY 6 2 0 5 1 0 0
BstOI CCWGG 5 2 0 2 3 0 0
BstPI GGTNACC 7 2 0 1 6 0 0
BstPAI GACNNNNGTC 10 2 1 5 5 0 0
BstSCI CCNGG 5 2 0 -1 5 0 0
BstSFI CTRYAG 6 2 0 1 5 0 0
BstSLI GKGCMC 6 2 0 5 1 0 0
BstSNI TACGTA 6 2 1 3 3 0 0
BstUI CGCG 4 2 1 2 2 0 0
Bst2UI CCWGG 5 2 0 2 3 0 0
BstV1I GCAGC 5 2 0 13 17 0 0
BstV2I GAAGAC 6 2 0 8 12 0 0
BstXI CCANNNNNNTGG 12 2 0 8 4 0 0
BstX2I RGATCY 6 2 0 1 5 0 0
BstYI RGATCY 6 2 0 1 5 0 0
BstZI CGGCCG 6 2 0 1 5 0 0
BstZ17I GTATAC 6 2 1 3 3 0 0
Bsu15I ATCGAT 6 2 0 2 4 0 0
Bsu36I CCTNAGG 7 2 0 2 5 0 0
BsuRI GGCC 4 2 1 2 2 0 0
BsuTUI ATCGAT 6 2 0 2 4 0 0
BtgI CCRYGG 6 2 0 1 5 0 0
BtgZI GCGATG 6 2 0 16 20 0 0
BthCI gcngc 5 2 0 4 1 0 0
BtrI CACGTC 6 2 1 3 3 0 0
BtsI GCAGTG 6 2 0 8 6 0 0
BtsCI GGATG 5 2 0 7 5 0 0
BtuMI TCGCGA 6 2 1 3 3 0 0
BveI ACCTGC 6 2 0 10 14 0 0
Cac8I GCNNGC 6 2 1 3 3 0 0
CaiI CAGNNNCTG 9 2 0 6 3 0 0
CauII ccsgg 5 2 0 2 3 0 0
CciI TCATGA 6 2 0 1 5 0 0
CciNI GCGGCCGC 8 2 0 2 6 0 0
CdiI catcg 5 2 1 4 4 0 0
CdpI gcggag 6 2 0 26 24 0 0
CelII GCTNAGC 7 2 0 2 5 0 0
CfoI GCGC 4 2 0 3 1 0 0
CfrI YGGCCR 6 2 0 1 5 0 0
Cfr9I CCCGGG 6 2 0 1 5 0 0
Cfr10I RCCGGY 6 2 0 1 5 0 0
Cfr13I GGNCC 5 2 0 1 4 0 0
Cfr42I CCGCGG 6 2 0 4 2 0 0
ChaI gatc 4 2 0 4 -1 0 0
CjeI ccannnnnngt 11 4 0 -9 -15 26 20
CjeNII gagnnnnngt 10 0 0 0 0 0 0
CjePI ccannnnnnntc 12 4 0 -8 -14 26 20
CjuI caynnnnnrtg 11 0 0 0 0 0 0
CjuII caynnnnnctc 11 0 0 0 0 0 0
ClaI ATCGAT 6 2 0 2 4 0 0
CpoI CGGWCCG 7 2 0 2 5 0 0
CseI GACGC 5 2 0 10 15 0 0
CsiI ACCWGGT 7 2 0 1 6 0 0
CspI CGGWCCG 7 2 0 2 5 0 0
Csp6I GTAC 4 2 0 1 3 0 0
Csp45I TTCGAA 6 2 0 2 4 0 0
CspAI ACCGGT 6 2 0 1 5 0 0
CspCI CAANNNNNGTGG 12 4 0 -12 -14 24 22
CstMI aaggag 6 2 0 26 24 0 0
CviAII CATG 4 2 0 1 3 0 0
CviJI RGCY 4 2 1 2 2 0 0
CviKI-1 RGCY 4 2 1 2 2 0 0
CviQI GTAC 4 2 0 1 3 0 0
CviRI tgca 4 2 1 2 2 0 0
DdeI CTNAG 5 2 0 1 4 0 0
DinI GGCGCC 6 2 1 3 3 0 0
DpnI GATC 4 2 1 2 2 0 0
DpnII GATC 4 2 0 -1 4 0 0
DraI TTTAAA 6 2 1 3 3 0 0
DraII RGGNCCY 7 2 0 2 5 0 0
DraIII CACNNNGTG 9 2 0 6 3 0 0
DraRI caagnac 7 2 0 27 25 0 0
DrdI GACNNNNNNGTC 12 2 0 7 5 0 0
DrdII gaacca 6 0 0 0 0 0 0
DrdIV tacgac 6 2 0 26 24 0 0
DriI GACNNNNNGTC 11 2 0 6 5 0 0
DsaI ccrygg 6 2 0 1 5 0 0
DseDI GACNNNNNNGTC 12 2 0 7 5 0 0
EaeI YGGCCR 6 2 0 1 5 0 0
EagI CGGCCG 6 2 0 1 5 0 0
Eam1104I CTCTTC 6 2 0 7 10 0 0
Eam1105I GACNNNNNGTC 11 2 0 6 5 0 0
EarI CTCTTC 6 2 0 7 10 0 0
EciI GGCGGA 6 2 0 17 15 0 0
Ecl136II GAGCTC 6 2 1 3 3 0 0
EclXI CGGCCG 6 2 0 1 5 0 0
Eco24I GRGCYC 6 2 0 5 1 0 0
Eco31I GGTCTC 6 2 0 7 11 0 0
Eco32I GATATC 6 2 1 3 3 0 0
Eco47I GGWCC 5 2 0 1 4 0 0
Eco47III AGCGCT 6 2 1 3 3 0 0
Eco52I CGGCCG 6 2 0 1 5 0 0
Eco57I CTGAAG 6 2 0 22 20 0 0
Eco72I CACGTG 6 2 1 3 3 0 0
Eco81I CCTNAGG 7 2 0 2 5 0 0
Eco88I CYCGRG 6 2 0 1 5 0 0
Eco91I GGTNACC 7 2 0 1 6 0 0
Eco105I TACGTA 6 2 1 3 3 0 0
Eco130I CCWWGG 6 2 0 1 5 0 0
Eco147I AGGCCT 6 2 1 3 3 0 0
EcoHI ccsgg 5 2 0 -1 5 0 0
EcoICRI GAGCTC 6 2 1 3 3 0 0
Eco57MI CTGRAG 6 2 0 22 20 0 0
EcoNI CCTNNNNNAGG 11 2 0 5 6 0 0
EcoO65I GGTNACC 7 2 0 1 6 0 0
EcoO109I RGGNCCY 7 2 0 2 5 0 0
EcoRI GAATTC 6 2 0 1 5 0 0
EcoRII CCWGG 5 2 0 -1 5 0 0
EcoRV GATATC 6 2 1 3 3 0 0
EcoT14I CCWWGG 6 2 0 1 5 0 0
EcoT22I ATGCAT 6 2 0 5 1 0 0
EcoT38I GRGCYC 6 2 0 5 1 0 0
Eco53kI GAGCTC 6 2 1 3 3 0 0
EgeI GGCGCC 6 2 1 3 3 0 0
EheI GGCGCC 6 2 1 3 3 0 0
ErhI CCWWGG 6 2 0 1 5 0 0
EsaBC3I tcga 4 2 1 2 2 0 0
EsaSSI gaccac 6 0 0 0 0 0 0
EspI gctnagc 7 2 0 2 5 0 0
Esp3I CGTCTC 6 2 0 7 11 0 0
FaeI CATG 4 2 0 4 -1 0 0
FaiI YATR 4 2 1 2 2 0 0
FalI AAGNNNNNCTT 11 4 0 -9 -14 24 19
FaqI GGGAC 5 2 0 15 19 0 0
FatI CATG 4 2 0 -1 4 0 0
FauI CCCGC 5 2 0 9 11 0 0
FauNDI CATATG 6 2 0 2 4 0 0
FbaI TGATCA 6 2 0 1 5 0 0
FblI GTMKAC 6 2 0 2 4 0 0
FinI gggac 5 0 0 0 0 0 0
FmuI ggncc 5 2 0 4 1 0 0
FnuDII cgcg 4 2 1 2 2 0 0
Fnu4HI GCNGC 5 2 0 2 3 0 0
FokI GGATG 5 2 0 14 18 0 0
FriOI GRGCYC 6 2 0 5 1 0 0
FseI GGCCGGCC 8 2 0 6 2 0 0
FspI TGCGCA 6 2 1 3 3 0 0
FspAI RTGCGCAY 8 2 1 4 4 0 0
FspBI CTAG 4 2 0 1 3 0 0
Fsp4HI GCNGC 5 2 0 2 3 0 0
GdiII cggccr 6 2 0 1 5 0 0
GlaI GCGC 4 2 1 2 2 0 0
GluI GCNGC 5 2 0 2 3 0 0
GsaI CCCAGC 6 2 0 5 1 0 0
GsuI CTGGAG 6 2 0 22 20 0 0
HaeI wggccw 6 2 1 3 3 0 0
HaeII RGCGCY 6 2 0 5 1 0 0
HaeIII GGCC 4 2 1 2 2 0 0
HaeIV gaynnnnnrtc 11 4 0 -8 -14 25 20
HapII CCGG 4 2 0 1 3 0 0
HgaI GACGC 5 2 0 10 15 0 0
HgiAI gwgcwc 6 2 0 5 1 0 0
HgiCI ggyrcc 6 2 0 1 5 0 0
HgiEII accnnnnnnggt 12 0 0 0 0 0 0
HgiJII grgcyc 6 2 0 5 1 0 0
HhaI GCGC 4 2 0 3 1 0 0
Hin1I GRCGYC 6 2 0 2 4 0 0
Hin1II CATG 4 2 0 4 -1 0 0
Hin4I GAYNNNNNVTC 11 4 0 -9 -14 24 19
Hin4II ccttc 5 2 0 11 10 0 0
Hin6I GCGC 4 2 0 1 3 0 0
HinP1I GCGC 4 2 0 1 3 0 0
HincII GTYRAC 6 2 1 3 3 0 0
HindII GTYRAC 6 2 1 3 3 0 0
HindIII AAGCTT 6 2 0 1 5 0 0
HinfI GANTC 5 2 0 1 4 0 0
HpaI GTTAAC 6 2 1 3 3 0 0
HpaII CCGG 4 2 0 1 3 0 0
HphI GGTGA 5 2 0 13 12 0 0
Hpy8I GTNNAC 6 2 1 3 3 0 0
Hpy99I CGWCG 5 2 0 5 -1 0 0
Hpy166II GTNNAC 6 2 1 3 3 0 0
Hpy178III tcnnga 6 2 0 2 4 0 0
Hpy188I TCNGA 5 2 0 3 2 0 0
Hpy188III TCNNGA 6 2 0 2 4 0 0
HpyAV CCTTC 5 2 0 11 10 0 0
HpyCH4III ACNGT 5 2 0 3 2 0 0
HpyCH4IV ACGT 4 2 0 1 3 0 0
HpyCH4V TGCA 4 2 1 2 2 0 0
HpyF3I CTNAG 5 2 0 1 4 0 0
HpyF10VI GCNNNNNNNGC 11 2 0 7 4 0 0
Hsp92I GRCGYC 6 2 0 2 4 0 0
Hsp92II CATG 4 2 0 4 -1 0 0
HspAI GCGC 4 2 0 1 3 0 0
ItaI GCNGC 5 2 0 2 3 0 0
KasI GGCGCC 6 2 0 1 5 0 0
KflI GGGWCCC 7 2 0 2 5 0 0
KpnI GGTACC 6 2 0 5 1 0 0
Kpn2I TCCGGA 6 2 0 1 5 0 0
KspI CCGCGG 6 2 0 4 2 0 0
Ksp22I TGATCA 6 2 0 1 5 0 0
Ksp632I ctcttc 6 2 0 7 10 0 0
KspAI GTTAAC 6 2 1 3 3 0 0
Kzo9I GATC 4 2 0 -1 4 0 0
LguI GCTCTTC 7 2 0 8 11 0 0
LpnI rgcgcy 6 2 1 3 3 0 0
Lsp1109I GCAGC 5 2 0 13 17 0 0
LweI GCATC 5 2 0 10 14 0 0
MabI ACCWGGT 7 2 0 1 6 0 0
MaeI CTAG 4 2 0 1 3 0 0
MaeII ACGT 4 2 0 1 3 0 0
MaeIII GTNAC 5 2 0 -1 5 0 0
MalI GATC 4 2 1 2 2 0 0
MaqI crttgac 7 2 0 28 26 0 0
MauBI CGCGCGCG 8 2 0 2 6 0 0
MbiI CCGCTC 6 2 1 3 3 0 0
MboI GATC 4 2 0 -1 4 0 0
MboII GAAGA 5 2 0 13 12 0 0
McaTI gcgcgc 6 2 0 4 2 0 0
McrI cgrycg 6 2 0 4 2 0 0
MfeI CAATTG 6 2 0 1 5 0 0
MflI RGATCY 6 2 0 1 5 0 0
MhlI GDGCHC 6 2 0 5 1 0 0
MjaIV gtnnac 6 0 0 0 0 0 0
MlsI TGGCCA 6 2 1 3 3 0 0
MluI ACGCGT 6 2 0 1 5 0 0
MluNI TGGCCA 6 2 1 3 3 0 0
MlyI GAGTC 5 2 1 10 10 0 0
Mly113I GGCGCC 6 2 0 2 4 0 0
MmeI TCCRAC 6 2 0 26 24 0 0
MnlI CCTC 4 2 0 11 10 0 0
Mph1103I ATGCAT 6 2 0 5 1 0 0
MreI CGCCGGCG 8 2 0 2 6 0 0
MroI TCCGGA 6 2 0 1 5 0 0
MroNI GCCGGC 6 2 0 1 5 0 0
MroXI GAANNNNTTC 10 2 1 5 5 0 0
MscI TGGCCA 6 2 1 3 3 0 0
MseI TTAA 4 2 0 1 3 0 0
MslI CAYNNNNRTG 10 2 1 5 5 0 0
MspI CCGG 4 2 0 1 3 0 0
Msp20I TGGCCA 6 2 1 3 3 0 0
MspA1I CMGCKG 6 2 1 3 3 0 0
MspCI CTTAAG 6 2 0 1 5 0 0
MspR9I CCNGG 5 2 0 2 3 0 0
MssI GTTTAAAC 8 2 1 4 4 0 0
MstI tgcgca 6 2 1 3 3 0 0
MunI CAATTG 6 2 0 1 5 0 0
MvaI CCWGG 5 2 0 2 3 0 0
Mva1269I GAATGC 6 2 0 7 5 0 0
MvnI CGCG 4 2 1 2 2 0 0
MvrI CGATCG 6 2 0 4 2 0 0
MwoI GCNNNNNNNGC 11 2 0 7 4 0 0
NaeI GCCGGC 6 2 1 3 3 0 0
NarI GGCGCC 6 2 0 2 4 0 0
NciI CCSGG 5 2 0 2 3 0 0
NcoI CCATGG 6 2 0 1 5 0 0
NdeI CATATG 6 2 0 2 4 0 0
NdeII GATC 4 2 0 -1 4 0 0
NgoAVIII gacnnnnntga 11 4 0 -13 -15 24 22
NgoMIV GCCGGC 6 2 0 1 5 0 0
NhaXI caagrag 7 0 0 0 0 0 0
NheI GCTAGC 6 2 0 1 5 0 0
NlaIII CATG 4 2 0 4 -1 0 0
NlaIV GGNNCC 6 2 1 3 3 0 0
NlaCI catcac 6 2 0 25 23 0 0
Nli3877I cycgrg 6 2 0 5 1 0 0
NmeAIII GCCGAG 6 2 0 27 25 0 0
NmeDI rccggy 6 4 0 -13 -8 13 18
NmuCI GTSAC 5 2 0 -1 5 0 0
NotI GCGGCCGC 8 2 0 2 6 0 0
NruI TCGCGA 6 2 1 3 3 0 0
NsbI TGCGCA 6 2 1 3 3 0 0
NsiI ATGCAT 6 2 0 5 1 0 0
NspI RCATGY 6 2 0 5 1 0 0
NspV TTCGAA 6 2 0 2 4 0 0
NspBII cmgckg 6 2 1 3 3 0 0
OliI CACNNNNGTG 10 2 1 5 5 0 0
PabI gtac 4 2 0 3 1 0 0
PacI TTAATTAA 8 2 0 5 3 0 0
PaeI GCATGC 6 2 0 5 1 0 0
PaeR7I CTCGAG 6 2 0 1 5 0 0
PagI TCATGA 6 2 0 1 5 0 0
PalAI GGCGCGCC 8 2 0 2 6 0 0
PasI CCCWGGG 7 2 0 2 5 0 0
PauI GCGCGC 6 2 0 1 5 0 0
PceI AGGCCT 6 2 1 3 3 0 0
PciI ACATGT 6 2 0 1 5 0 0
PciSI GCTCTTC 7 2 0 8 11 0 0
PctI GAATGC 6 2 0 7 5 0 0
PdiI GCCGGC 6 2 1 3 3 0 0
PdmI GAANNNNTTC 10 2 1 5 5 0 0
PfeI GAWTC 5 2 0 1 4 0 0
Pfl23II CGTACG 6 2 0 1 5 0 0
Pfl1108I tcgtag 6 0 0 0 0 0 0
PflFI GACNNNGTC 9 2 0 4 5 0 0
PflMI CCANNNNNTGG 11 2 0 7 4 0 0
PfoI TCCNGGA 7 2 0 1 6 0 0
PhoI GGCC 4 2 1 2 2 0 0
PinAI ACCGGT 6 2 0 1 5 0 0
PlaDI catcag 6 2 0 27 25 0 0
PleI GAGTC 5 2 0 9 10 0 0
Ple19I CGATCG 6 2 0 4 2 0 0
PmaCI CACGTG 6 2 1 3 3 0 0
PmeI GTTTAAAC 8 2 1 4 4 0 0
PmlI CACGTG 6 2 1 3 3 0 0
PpiI GAACNNNNNCTC 12 4 0 -8 -13 25 20
PpsI GAGTC 5 2 0 9 10 0 0
Ppu10I atgcat 6 2 0 1 5 0 0
Ppu21I YACGTR 6 2 1 3 3 0 0
PpuMI RGGWCCY 7 2 0 2 5 0 0
PscI ACATGT 6 2 0 1 5 0 0
PshAI GACNNNNGTC 10 2 1 5 5 0 0
PshBI ATTAAT 6 2 0 2 4 0 0
PsiI TTATAA 6 2 1 3 3 0 0
Psp03I ggwcc 5 2 0 4 1 0 0
Psp5II RGGWCCY 7 2 0 2 5 0 0
Psp6I CCWGG 5 2 0 -1 5 0 0
Psp1406I AACGTT 6 2 0 2 4 0 0
Psp124BI GAGCTC 6 2 0 5 1 0 0
PspCI CACGTG 6 2 1 3 3 0 0
PspEI GGTNACC 7 2 0 1 6 0 0
PspGI CCWGG 5 2 0 -1 5 0 0
PspLI CGTACG 6 2 0 1 5 0 0
PspN4I GGNNCC 6 2 1 3 3 0 0
PspOMI GGGCCC 6 2 0 1 5 0 0
PspOMII cgcccar 7 2 0 27 25 0 0
PspPI GGNCC 5 2 0 1 4 0 0
PspPPI RGGWCCY 7 2 0 2 5 0 0
PspPRI ccycag 6 2 0 21 19 0 0
PspXI VCTCGAGB 8 2 0 2 6 0 0
PsrI GAACNNNNNNTAC 13 4 0 -8 -13 25 20
PssI rggnccy 7 2 0 5 2 0 0
PstI CTGCAG 6 2 0 5 1 0 0
PsuI RGATCY 6 2 0 1 5 0 0
PsyI GACNNNGTC 9 2 0 4 5 0 0
PteI GCGCGC 6 2 0 1 5 0 0
PvuI CGATCG 6 2 0 4 2 0 0
PvuII CAGCTG 6 2 1 3 3 0 0
RcaI TCATGA 6 2 0 1 5 0 0
RceI catcgac 7 2 0 27 25 0 0
RgaI GCGATCGC 8 2 0 5 3 0 0
RigI GGCCGGCC 8 2 0 6 2 0 0
RleAI cccaca 6 2 0 18 15 0 0
RpaB5I cgrggac 7 2 0 27 25 0 0
RruI TCGCGA 6 2 1 3 3 0 0
RsaI GTAC 4 2 1 2 2 0 0
RsaNI GTAC 4 2 0 1 3 0 0
RseI CAYNNNNRTG 10 2 1 5 5 0 0
RsrII CGGWCCG 7 2 0 2 5 0 0
Rsr2I CGGWCCG 7 2 0 2 5 0 0
SacI GAGCTC 6 2 0 5 1 0 0
SacII CCGCGG 6 2 0 4 2 0 0
SalI GTCGAC 6 2 0 1 5 0 0
SanDI GGGWCCC 7 2 0 2 5 0 0
SapI GCTCTTC 7 2 0 8 11 0 0
SaqAI TTAA 4 2 0 1 3 0 0
SatI GCNGC 5 2 0 2 3 0 0
SauI cctnagg 7 2 0 2 5 0 0
Sau96I GGNCC 5 2 0 1 4 0 0
Sau3AI GATC 4 2 0 -1 4 0 0
SbfI CCTGCAGG 8 2 0 6 2 0 0
ScaI AGTACT 6 2 1 3 3 0 0
SchI GAGTC 5 2 1 10 10 0 0
SciI ctcgag 6 2 1 3 3 0 0
ScrFI CCNGG 5 2 0 2 3 0 0
SdaI CCTGCAGG 8 2 0 6 2 0 0
SdeAI cagrag 6 2 0 27 25 0 0
SdeOSI gacnnnnrtga 11 4 0 -12 -14 23 21
SduI GDGCHC 6 2 0 5 1 0 0
SecI ccnngg 6 2 0 1 5 0 0
SelI cgcg 4 2 0 -1 4 0 0
SetI ASST 4 2 0 4 -1 0 0
SexAI ACCWGGT 7 2 0 1 6 0 0
SfaAI GCGATCGC 8 2 0 5 3 0 0
SfaNI GCATC 5 2 0 10 14 0 0
SfcI CTRYAG 6 2 0 1 5 0 0
SfeI ctryag 6 2 0 1 5 0 0
SfiI GGCCNNNNNGGCC 13 2 0 8 5 0 0
SfoI GGCGCC 6 2 1 3 3 0 0
Sfr274I CTCGAG 6 2 0 1 5 0 0
Sfr303I CCGCGG 6 2 0 4 2 0 0
SfuI TTCGAA 6 2 0 2 4 0 0
SgfI GCGATCGC 8 2 0 5 3 0 0
SgrAI CRCCGGYG 8 2 0 2 6 0 0
SgrBI CCGCGG 6 2 0 4 2 0 0
SgrDI CGTCGACG 8 2 0 2 6 0 0
SgsI GGCGCGCC 8 2 0 2 6 0 0
SimI gggtc 5 2 0 2 5 0 0
SinI GGWCC 5 2 0 1 4 0 0
SlaI CTCGAG 6 2 0 1 5 0 0
SmaI CCCGGG 6 2 1 3 3 0 0
SmiI ATTTAAAT 8 2 1 4 4 0 0
SmiMI CAYNNNNRTG 10 2 1 5 5 0 0
SmlI CTYRAG 6 2 0 1 5 0 0
SmoI CTYRAG 6 2 0 1 5 0 0
SmuI CCCGC 5 2 0 9 11 0 0
SnaI gtatac 6 0 0 0 0 0 0
SnaBI TACGTA 6 2 1 3 3 0 0
SpeI ACTAGT 6 2 0 1 5 0 0
SphI GCATGC 6 2 0 5 1 0 0
SplI cgtacg 6 2 0 1 5 0 0
SpoDI gcggrag 7 0 0 0 0 0 0
SrfI GCCCGGGC 8 2 1 4 4 0 0
Sse9I AATT 4 2 0 -1 4 0 0
Sse232I cgccggcg 8 2 0 2 6 0 0
Sse8387I CCTGCAGG 8 2 0 6 2 0 0
Sse8647I aggwcct 7 2 0 2 5 0 0
SseBI AGGCCT 6 2 1 3 3 0 0
SsiI CCGC 4 2 0 1 3 0 0
SspI AATATT 6 2 1 3 3 0 0
SspDI GGCGCC 6 2 0 1 5 0 0
SspD5I ggtga 5 2 1 13 13 0 0
SstI GAGCTC 6 2 0 5 1 0 0
SstII CCGCGG 6 2 0 4 2 0 0
Sth132I cccg 4 2 0 8 12 0 0
Sth302II ccgg 4 2 1 2 2 0 0
StrI CTCGAG 6 2 0 1 5 0 0
StsI ggatg 5 2 0 15 19 0 0
StuI AGGCCT 6 2 1 3 3 0 0
StyI CCWWGG 6 2 0 1 5 0 0
StyD4I CCNGG 5 2 0 -1 5 0 0
SwaI ATTTAAAT 8 2 1 4 4 0 0
TaaI ACNGT 5 2 0 3 2 0 0
TaiI ACGT 4 2 0 4 -1 0 0
TaqI TCGA 4 2 0 1 3 0 0
TaqII GACCGA 6 2 0 17 15 0 0
TaqII CACCCA 6 2 0 17 15 0 0
TasI AATT 4 2 0 -1 4 0 0
TatI WGTACW 6 2 0 1 5 0 0
TauI GCSGC 5 2 0 4 1 0 0
TfiI GAWTC 5 2 0 1 4 0 0
TliI CTCGAG 6 2 0 1 5 0 0
Tru1I TTAA 4 2 0 1 3 0 0
Tru9I TTAA 4 2 0 1 3 0 0
TscAI CASTG 5 2 0 7 -3 0 0
TseI GCWGC 5 2 0 1 4 0 0
TsoI TARCCA 6 2 0 17 15 0 0
Tsp45I GTSAC 5 2 0 -1 5 0 0
Tsp509I AATT 4 2 0 -1 4 0 0
Tsp4CI acngt 5 2 0 3 2 0 0
TspDTI ATGAA 5 2 0 16 14 0 0
TspEI AATT 4 2 0 -1 4 0 0
TspGWI ACGGA 5 2 0 16 14 0 0
TspMI CCCGGG 6 2 0 1 5 0 0
TspRI CASTG 5 2 0 7 -3 0 0
TssI gagnnnctc 9 0 0 0 0 0 0
TstI CACNNNNNNTCC 12 4 0 -9 -14 24 19
TsuI gcgac 5 0 0 0 0 0 0
Tth111I GACNNNGTC 9 2 0 4 5 0 0
Tth111II caarca 6 2 0 17 15 0 0
UbaF9I tacnnnnnrtgt 12 0 0 0 0 0 0
UbaF11I tcgta 5 0 0 0 0 0 0
UbaF12I ctacnnngtc 10 0 0 0 0 0 0
UbaF13I gagnnnnnnctgg 13 0 0 0 0 0 0
UbaF14I ccannnnntcg 11 0 0 0 0 0 0
UbaPI cgaacg 6 0 0 0 0 0 0
UnbI ggncc 5 2 0 -1 5 0 0
Van91I CCANNNNNTGG 11 2 0 7 4 0 0
Vha464I CTTAAG 6 2 0 1 5 0 0
VneI GTGCAC 6 2 0 1 5 0 0
VpaK11AI ggwcc 5 2 0 -1 5 0 0
VpaK11BI GGWCC 5 2 0 1 4 0 0
VspI ATTAAT 6 2 0 2 4 0 0
XagI CCTNNNNNAGG 11 2 0 5 6 0 0
XapI RAATTY 6 2 0 1 5 0 0
XbaI TCTAGA 6 2 0 1 5 0 0
XceI RCATGY 6 2 0 5 1 0 0
XcmI CCANNNNNNNNNTGG 15 2 0 8 7 0 0
XhoI CTCGAG 6 2 0 1 5 0 0
XhoII RGATCY 6 2 0 1 5 0 0
XmaI CCCGGG 6 2 0 1 5 0 0
XmaIII cggccg 6 2 0 1 5 0 0
XmaCI CCCGGG 6 2 0 1 5 0 0
XmaJI CCTAGG 6 2 0 1 5 0 0
XmiI GTMKAC 6 2 0 2 4 0 0
XmnI GAANNNNTTC 10 2 1 5 5 0 0
XspI CTAG 4 2 0 1 3 0 0
ZraI GACGTC 6 2 1 3 3 0 0
ZrmI AGTACT 6 2 1 3 3 0 0
Zsp2I ATGCAT 6 2 0 5 1 0 0
... | rescan_seq [options]
[-? | --help] # Print full usage description.
[-r <list> | --res_enz] # List of restriction enzyme names.
[-R <file!> | --res_enz_in] # Path to file with restriction enzyme names - one per line.
[-o | --res_enz_only] # Only output restriction enzyme information without upstream records.
[-M | --no_matches] # Don't output MATCHES.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following example sequence in the file test.fna:
ggatctggagcgcaGGATCCtcgcggcagcgcttgtcggcGGATCCgcgggcacgctgaa
That contains two BamHI sites (in uppercase) which can be located like this:
read_fasta -i test.fna | rescan_seq -r BamHI
RE: BamHI
RE_COUNT: 2
SEQ: ggatctggagcgcaGGATCCtcgcggcagcgcttgtcggcGGATCCgcgggcacgctgaa
RE_MATCHES: 14;40
SEQ_LEN: 60
SEQ_NAME: test
---
It is also possible to specify a file, using the -R switch, with one RE per line and use that as input:
read_fasta -i test.fna | rescan_seq -R RE.txt
RE: BamHI
RE_COUNT: 2
SEQ: ggatctggagcgcaGGATCCtcgcggcagcgcttgtcggcGGATCCgcgggcacgctgaa
RE_MATCHES: 14;40
SEQ_LEN: 60
SEQ_NAME: test
---
And it is possible to suppress the upstream records and only output the RE info using the -o switch:
read_fasta -i test.fna | rescan_seq -r BamHI
RE: BamHI
RE_COUNT: 2
RE_MATCHES: 14;40
---
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2009
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
rescan_seq is part of the Biopieces framework.