Forward Primer:
Select a forward primer here ...
Arc-109f ACKGCTCAGTAACACGT
Arc-112f GCTCAGTAACACGTGG
CYA106f CGGACGGGTGAGTAACGCGTGA
CYA359f GGGGAATYTTCCGCAATGGG
CYA432f CCGCGTGAGGGAGGAAGG
Eub-1055f ATGGCTGTCGTCAGCT
Eub-341f CCTACGGGAGGCAGCAG
Eub-8f AGAGTTTGATCCTGGCTCAG
Eub-8fm AGAGTTTGATCMTGGCTCAG
Eub-968f AACGCGAAGAACCTTAC
Euk1A CTGGTTGATCCTGCCAG
Uni-519f CAGCAGCCGCGGTAATAC
Uni-519fm CAGCMGCCGCGGTAATWC
or enter here:
Reverse Primer:
Select a reverse primer here ...
1062r ACAGCCATGCAGCACCT
1387r CCCGGGAACGTATTCACCGC
1492r GYTACCTTGTTACGACTT
Arc-533r TTACCGCGGCGGCTGGCA
Arc-934r GTGCTCCCCCGCCAATTCCT
CYA781r(a) GACTACTGGGGTATCTAATCCCATT
CYA781r(b) GACTACAGGGGTATCTAATCCCTTT
CYA792r TCCCCTAGCTTTCGTCCC
Eub-1113r GGGTTGCGCTCGTTG
Eub-1401r CGGTGTGTACAAGGCCCGGGAACG
Eub-536r GWATTACCGCGGCKGCTG
Eub-539r ATCGTATTACCGCGGCTGCTGGCA
Eub-926r CCGTCAATTCCTTTRAGTTT
Euk516r ACCAGACTTGCCCTCC
Uni-1406r ACGGGCGGTGTGTRC
Uni-1513r GGGTACCTTGTTACG
or enter here:
Restriction Enzyme:
Select a restriction enzyme here ...
AccII CG^CG
AfaI GT^AC
AvaII G^GWCC
AflIII A^CRYGT
AluI AG^CT
BfaI C^TAG
BamHI G^GATCC
BcuI A^CTAGT
BfaI C^TAG
Bme1580I GKGCM^C
BseGI GGATGNN^
Bsh1236I CG^CG
Bsp106I ^GATC
BspTI C^TTAAG
BstUI CG^CG
Bsu36I CC^TNAGG
BsuRI GG^CC
CfoI GCG^C
CviRI TG^CA
CviQI G^ATC
DdeI C^TNAG
DpnI (methA) GA^TC
DpnII ^GATC
EcoRI G^AATTC
FnuDII CG^CG
HaeIII GG^CC
HapII C^CGG
HhaI GCG^C
HinP1I G^CGC
HinfI G^ANTC
HpaII C^CGG
Hpy1881 TCN^GA
Hpy188III TC^NNGA
HpyCH4III CAN^GT
HpyCH4IV A^CGT
HpyCH4V TG^CA
HpyAV CCTTCNNNNN^N
Hsp92II CATG^
MaeI C^TAG
MaeII A^CGT
MboI ^GATC
MlyI GAGTCNNNNN^
MseI T^TAA
MslI CAYNN^NNRTG
MspI C^CGG
MvnI CG^CG
NdeII ^GATC
NlaIII CATG^
PalI GG^CC
RsaI GT^AC
Sau3AI ^GATC
Sau96I G^GNCC
ScrFI CC^NGG
StuI AGG^CCT
TaqI T^CGA
ThaI CG^CG
Tru9I T^TAA
TsoI TARCCANNNNNNNNN^NN
Tsp509I ^AATT
TthHB8I T^CGA
or enter here:
Restriction Enzyme:
Select a restriction enzyme here ...
AccII CG^CG
AfaI GT^AC
AvaII G^GWCC
AflIII A^CRYGT
AluI AG^CT
BfaI C^TAG
BamHI G^GATCC
BcuI A^CTAGT
BfaI C^TAG
Bme1580I GKGCM^C
BseGI GGATGNN^
Bsh1236I CG^CG
Bsp106I ^GATC
BspTI C^TTAAG
BstUI CG^CG
Bsu36I CC^TNAGG
BsuRI GG^CC
CfoI GCG^C
CviRI TG^CA
CviQI G^ATC
DdeI C^TNAG
DpnI (methA) GA^TC
DpnII ^GATC
EcoRI G^AATTC
FnuDII CG^CG
HaeIII GG^CC
HapII C^CGG
HhaI GCG^C
HinP1I G^CGC
HinfI G^ANTC
HpaII C^CGG
Hpy1881 TCN^GA
Hpy188III TC^NNGA
HpyCH4III CAN^GT
HpyCH4IV A^CGT
HpyCH4V TG^CA
HpyAV CCTTCNNNNN^N
Hsp92II CATG^
MaeI C^TAG
MaeII A^CGT
MboI ^GATC
MlyI GAGTCNNNNN^
MseI T^TAA
MslI CAYNN^NNRTG
MspI C^CGG
MvnI CG^CG
NdeII ^GATC
NlaIII CATG^
PalI GG^CC
RsaI GT^AC
Sau3AI ^GATC
Sau96I G^GNCC
ScrFI CC^NGG
StuI AGG^CCT
TaqI T^CGA
ThaI CG^CG
Tru9I T^TAA
TsoI TARCCANNNNNNNNN^NN
Tsp509I ^AATT
TthHB8I T^CGA
or enter here:
Restriction Enzyme:
Select a restriction enzyme here ...
AccII CG^CG
AfaI GT^AC
AvaII G^GWCC
AflIII A^CRYGT
AluI AG^CT
BfaI C^TAG
BamHI G^GATCC
BcuI A^CTAGT
BfaI C^TAG
Bme1580I GKGCM^C
BseGI GGATGNN^
Bsh1236I CG^CG
Bsp106I ^GATC
BspTI C^TTAAG
BstUI CG^CG
Bsu36I CC^TNAGG
BsuRI GG^CC
CfoI GCG^C
CviRI TG^CA
CviQI G^ATC
DdeI C^TNAG
DpnI (methA) GA^TC
DpnII ^GATC
EcoRI G^AATTC
FnuDII CG^CG
HaeIII GG^CC
HapII C^CGG
HhaI GCG^C
HinP1I G^CGC
HinfI G^ANTC
HpaII C^CGG
Hpy1881 TCN^GA
Hpy188III TC^NNGA
HpyCH4III CAN^GT
HpyCH4IV A^CGT
HpyCH4V TG^CA
HpyAV CCTTCNNNNN^N
Hsp92II CATG^
MaeI C^TAG
MaeII A^CGT
MboI ^GATC
MlyI GAGTCNNNNN^
MseI T^TAA
MslI CAYNN^NNRTG
MspI C^CGG
MvnI CG^CG
NdeII ^GATC
NlaIII CATG^
PalI GG^CC
RsaI GT^AC
Sau3AI ^GATC
Sau96I G^GNCC
ScrFI CC^NGG
StuI AGG^CCT
TaqI T^CGA
ThaI CG^CG
Tru9I T^TAA
TsoI TARCCANNNNNNNNN^NN
Tsp509I ^AATT
TthHB8I T^CGA
or enter here:
Select Database:
RDP (R10, U27) 69,742 16S rRNA Archaeal
RDP (R10, U27) 10,346 Good Quality (>1200) Archaeal
RDP (R10, U27) 1,519,357 16S Bacterial rRNA
RDP (R10, U27) 700,829 Good Quality (>1200) Bacterial
Greengenes, 407,309 16S rDNA
SILVA (R106) 207,909 LSU (23S/28S) Parc
SILVA (R106) 18, 913 LSU (23S/28S) Ref
SILVA (R106) 1,471,257 SSU (16S/18S) Parc
SILVA (R106) 512,037 SSU (16S/18S) Ref
ITS fungal database (R.J. Cano)
Full length mcrA sequences (M. Poulsen)
Glomeromycota 18S rSSU (W. Taheri)
Custom Actinobacteria database provided by Ainsley Hamm
Custom database provided by E. Heinzel
Poultry 16s rDNA (S. Wei and A. Gutek)
Ruman associated 16S sequences (M. Poulsen)
Human oral 16S database based on http://www.homd.org
Soil database based on RDP r12u10 by Ru Li
Customized database submitted by D.F. Rodrigues
Customized database sumbitted by Y. Liu of SoMAS, SBU
Mammalian guts microbes 16S rRNA (Ley et al., 2008)
Protozoan 18S sequences (by M. Thomas)
Pathogenic bacterial sequences (by Soeltan-Kaersenhout)
16S Bacterial rRNA Sequences (by A. Hartman)
Methyl Coenzyme-M Reductase (mcrA) (by G.M. Nava)
Dissimilatory Sulfite Reductase A, B (by G.M. Nava)
Nitrous Oxide Reductase (nosZ) Gene Sequences
H.Q. 16S Gut Organisms (by S. Bhandari)
Pig Bacterial 16S rRNA (by Hojberg et al.)
Dr. Fouke's 16S Sequences (by Maalouf et al.)
Greengenes 16S rDNA data (http://greengenes.lbl.gov)
Sequences provided by Allison E. Murray (NR99_778)
Sequences provided by Michael Falk of U.C. Davis
18S sequences from yeasts (by A. Marcobal)
Sensitivity:
digest allows at most
0
1
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8
9
10
mismatches within
0
1
2
3
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5
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8
9
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14
15
bases from 5' end of primer
Report:
Only the shortest ones
All fragment lengths
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