Input and runtime details for job 6860187 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
134	0.01437	0.3575	b1798	leuE	-11.20	0.161096	19 -- 44	168 -- 191	leucine efflux protein	_____________18_________________________45\n_____________\|__________________________\|\n5'-UGC...AGAAU________________UGCCGA____UACCC...AAA-3'\n______________UUUUACGCCAGUAUUU______GCAC\n______________\|\|\|\|\|\|:\|\|\|:\|\|:\|:______:\|\|\|\n______________AAAAUGUGGUUAUGAG______UGUG\n3'-UUU...CCACU________________UCAG______UACUA...UAG-5'\n_____________\|__________________________\|\n_____________192________________________167\n	26 -- 32	178 -- 184	-22.4094 kcal/mol	4.02149 kcal/mol	4.92826 kcal/mol	18 45@LB@ \| \|@LB@5'-UGC...AGAAU UGCCGA UACCC...AAA-3'@LB@ UUUUACGCCAGUAUUU GCAC@LB@ \|\|\|\|\|\|:\|\|\|:\|\|:\|: :\|\|\|@LB@ AAAAUGUGGUUAUGAG UGUG@LB@3'-UUU...CCACU UCAG UACUA...UAG-5'@LB@ \| \|@LB@ 192 167@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -22.4094 kcal/mol@LB@Unfolding Energy - mRNA 4.02149 kcal/mol@LB@Unfolding Energy - sRNA 4.92826 kcal/mol@LB@@LB@Position - mRNA 19 -- 44@LB@Position - sRNA 168 -- 191@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 178 -- 184@LB@
132	0.0143	0.3575	b0147	ligT	-9.89	0.288456	69 -- 117	16 -- 69	2'-5' RNA ligase	_____________68__________________________________118\n_____________\|___________________________________\|\n5'-CCA...AAGUA______GUA_G___GCAGCAA_______C_A____ACAAA...CGG-3'\n______________AUUCAG___A_ACG_______CGGGCAA_G_CGAC\n______________\|:\|\|\|\|___\|_\|\|:_______\|:\|\|\|\|\|_\|_\|:\|\|\n______________UGAGUC___U_UGU_______GUCCGUU_C_GUUG\n3'-UUU...GGUUA______AG__G___ACUAC___________A____AAAGU...UAG-5'\n_____________\|___________________________________\|\n_____________70__________________________________15\n	112 -- 118	155 -- 161	-21.4956 kcal/mol	4.52534 kcal/mol	8.18567 kcal/mol	68 118@LB@ \| \|@LB@5'-CCA...AAGUA GUA G GCAGCAA C A ACAAA...CGG-3'@LB@ AUUCAG A ACG CGGGCAA G CGAC@LB@ \|:\|\|\|\| \| \|\|: \|:\|\|\|\|\| \| \|:\|\|@LB@ UGAGUC U UGU GUCCGUU C GUUG@LB@3'-UUU...GGUUA AG G ACUAC A AAAGU...UAG-5'@LB@ \| \|@LB@ 70 15@LB@@LB@@LB@Energy -9.89 kcal/mol@LB@Hybridization Energy -21.4956 kcal/mol@LB@Unfolding Energy - mRNA 4.52534 kcal/mol@LB@Unfolding Energy - sRNA 8.18567 kcal/mol@LB@@LB@Position - mRNA 69 -- 117@LB@Position - sRNA 16 -- 69@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 155 -- 161@LB@
32	0.002513	0.2642	b3456	livM	-11.89	0.117100	251 -- 271	186 -- 206	branched-chain amino acid ABC transporter permease	_____________250___________________________272\n_____________\|_____________________________\|\n5'-GCC...CUGCU______GCCG___________UG______CCGGA...CCA-3'\n______________GGUGAU_____ACCGGUAUUC__GGUCGC\n______________\|\|\|\|\|\|_____\|\|\|::\|\|:\|\|__:\|\|\|:\|\n______________CCACUA_____UGGUUAUGAG__UCAGUG\n3'-UUU...ACCGC______AAAUG__________________UGUAC...UAG-5'\n_____________\|_____________________________\|\n_____________207___________________________185\n	169 -- 175	176 -- 182	-27.5836 kcal/mol	14.0763 kcal/mol	5.03772 kcal/mol	250 272@LB@ \| \|@LB@5'-GCC...CUGCU GCCG UG CCGGA...CCA-3'@LB@ GGUGAU ACCGGUAUUC GGUCGC@LB@ \|\|\|\|\|\| \|\|\|::\|\|:\|\| :\|\|\|:\|@LB@ CCACUA UGGUUAUGAG UCAGUG@LB@3'-UUU...ACCGC AAAUG UGUAC...UAG-5'@LB@ \| \|@LB@ 207 185@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -27.5836 kcal/mol@LB@Unfolding Energy - mRNA 14.0763 kcal/mol@LB@Unfolding Energy - sRNA 5.03772 kcal/mol@LB@@LB@Position - mRNA 251 -- 271@LB@Position - sRNA 186 -- 206@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 176 -- 182@LB@
152	0.0171	0.3749	b3605	lldD	-10.23	0.248595	212 -- 221	68 -- 77	L-lactate dehydrogenase FMN-linked	_____________211_______222\n_____________\|_________\|\n5'-UUU...GAAAA_________UAUUU...ACA-3'\n______________ACGCAUGAU\n______________\|\|:\|\|\|\|\|\|\n______________UGUGUACUA\n3'-UUU...GUCAG_________CGUCC...UAG-5'\n_____________\|_________\|\n_____________78________67\n	199 -- 205	163 -- 169	-11.1438 kcal/mol	1.00002 kcal/mol	4.14962 kcal/mol	211 222@LB@ \| \|@LB@5'-UUU...GAAAA UAUUU...ACA-3'@LB@ ACGCAUGAU@LB@ \|\|:\|\|\|\|\|\|@LB@ UGUGUACUA@LB@3'-UUU...GUCAG CGUCC...UAG-5'@LB@ \| \|@LB@ 78 67@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -11.1438 kcal/mol@LB@Unfolding Energy - mRNA 1.00002 kcal/mol@LB@Unfolding Energy - sRNA 4.14962 kcal/mol@LB@@LB@Position - mRNA 212 -- 221@LB@Position - sRNA 68 -- 77@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 163 -- 169@LB@
105	0.01118	0.3575	b0439	lon	-14.09	0.041610	272 -- 293	1 -- 24	DNA-binding ATP-dependent protease La	_____________271_______294\n_____________\|_________\|\n5'-AUC...CACAU_________CUUAU...GGG-3'\n______________GGUCAUCCC\n______________\|\|\|\|\|\|\|\|\|\n______________CCAGUAGGG\n3'-UUU...UAACG_________UGACG...UAG-5'\n_____________\|_________\|\n_____________25________0\n	277 -- 283	128 -- 134	-16.7868 kcal/mol	1.03204 kcal/mol	4.55487 kcal/mol	271 294@LB@ \| \|@LB@5'-AUC...CACAU CUUAU...GGG-3'@LB@ GGUCAUCCC@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCAGUAGGG@LB@3'-UUU...UAACG UGACG...UAG-5'@LB@ \| \|@LB@ 25 0@LB@@LB@@LB@Energy -14.09 kcal/mol@LB@Hybridization Energy -16.7868 kcal/mol@LB@Unfolding Energy - mRNA 1.03204 kcal/mol@LB@Unfolding Energy - sRNA 4.55487 kcal/mol@LB@@LB@Position - mRNA 272 -- 293@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 128 -- 134@LB@
76	0.007832	0.3458	b1054	lpxL	-10.56	0.214918	224 -- 240	1 -- 17	lauryl-acyl carrier protein (ACP)-dependent acyltransferase	_____________223_______241\n_____________\|_________\|\n5'-AAA...CGCAC_________CGCGU...CCU-3'\n______________UGCUUCAUC\n______________\|\|\|\|\|\|\|\|\|\n______________ACGAAGUAG\n3'-UUU...GGGGA_________-5'\n_____________\|________\|\n_____________18_______1\n	234 -- 240	1 -- 7	-13.5925 kcal/mol	1.26369 kcal/mol	0.710349 kcal/mol	223 241@LB@ \| \|@LB@5'-AAA...CGCAC CGCGU...CCU-3'@LB@ UGCUUCAUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGAAGUAG@LB@3'-UUU...GGGGA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -13.5925 kcal/mol@LB@Unfolding Energy - mRNA 1.26369 kcal/mol@LB@Unfolding Energy - sRNA 0.710349 kcal/mol@LB@@LB@Position - mRNA 224 -- 240@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
189	0.02188	0.3833	b4033	malF	-11.66	0.130598	273 -- 284	194 -- 205	maltose transporter subunit	_____________272__________285\n_____________\|____________\|\n5'-CUG...UCGGC____________UACCU...UAA-3'\n______________CUGCUGGUGGGU\n______________\|\|\|\|\|\|\|:\|\|\|\|\n______________GACGACCGCCCA\n3'-UUU...UAUUA____________CUAAA...UAG-5'\n_____________\|____________\|\n_____________206__________193\n	278 -- 284	194 -- 200	-24.1506 kcal/mol	7.59361 kcal/mol	9.05892 kcal/mol	272 285@LB@ \| \|@LB@5'-CUG...UCGGC UACCU...UAA-3'@LB@ CUGCUGGUGGGU@LB@ \|\|\|\|\|\|\|:\|\|\|\|@LB@ GACGACCGCCCA@LB@3'-UUU...UAUUA CUAAA...UAG-5'@LB@ \| \|@LB@ 206 193@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -24.1506 kcal/mol@LB@Unfolding Energy - mRNA 7.59361 kcal/mol@LB@Unfolding Energy - sRNA 9.05892 kcal/mol@LB@@LB@Position - mRNA 273 -- 284@LB@Position - sRNA 194 -- 205@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 194 -- 200@LB@
17	0.001014	0.2007	b4032	malG	-14.09	0.041561	127 -- 139	193 -- 205	maltose transporter subunit	_____________126___________140\n_____________\|_____________\|\n5'-CGU...UCUUC_____________CGCUG...UGG-3'\n______________CUGCUGGUGGGUG\n______________\|\|\|\|\|\|\|:\|\|\|\|\|\n______________GACGACCGCCCAC\n3'-UUU...UAUUA_____________UAAAA...UAG-5'\n_____________\|_____________\|\n_____________206___________192\n	132 -- 138	194 -- 200	-26.9183 kcal/mol	7.69341 kcal/mol	9.06058 kcal/mol	126 140@LB@ \| \|@LB@5'-CGU...UCUUC CGCUG...UGG-3'@LB@ CUGCUGGUGGGUG@LB@ \|\|\|\|\|\|\|:\|\|\|\|\|@LB@ GACGACCGCCCAC@LB@3'-UUU...UAUUA UAAAA...UAG-5'@LB@ \| \|@LB@ 206 192@LB@@LB@@LB@Energy -14.09 kcal/mol@LB@Hybridization Energy -26.9183 kcal/mol@LB@Unfolding Energy - mRNA 7.69341 kcal/mol@LB@Unfolding Energy - sRNA 9.06058 kcal/mol@LB@@LB@Position - mRNA 127 -- 139@LB@Position - sRNA 193 -- 205@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 194 -- 200@LB@
52	0.005023	0.3217	b0403	malZ	-9.64	0.320537	253 -- 286	155 -- 185	maltodextrin glucosidase	_____________252___________________________287\n_____________\|_____________________________\|\n5'-UUU...UCAAC_____________U____C__A_______AGACC...AGC-3'\n______________UGCUCA_UUACAC_GUGG_UG_CGGGCGA\n______________\|:\|\|\|\|_\|:\|\|\|\|_:\|\|:_\|\|_\|:\|\|\|:\|\n______________AUGAGU_AGUGUG_UACU_AC_GUCCGUU\n3'-UUU...UGGUU______C______________________CAGUU...UAG-5'\n_____________\|_____________________________\|\n_____________186___________________________154\n	280 -- 286	155 -- 161	-27.4446 kcal/mol	6.9929 kcal/mol	7.82707 kcal/mol	252 287@LB@ \| \|@LB@5'-UUU...UCAAC U C A AGACC...AGC-3'@LB@ UGCUCA UUACAC GUGG UG CGGGCGA@LB@ \|:\|\|\|\| \|:\|\|\|\| :\|\|: \|\| \|:\|\|\|:\|@LB@ AUGAGU AGUGUG UACU AC GUCCGUU@LB@3'-UUU...UGGUU C CAGUU...UAG-5'@LB@ \| \|@LB@ 186 154@LB@@LB@@LB@Energy -9.64 kcal/mol@LB@Hybridization Energy -27.4446 kcal/mol@LB@Unfolding Energy - mRNA 6.9929 kcal/mol@LB@Unfolding Energy - sRNA 7.82707 kcal/mol@LB@@LB@Position - mRNA 253 -- 286@LB@Position - sRNA 155 -- 185@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 155 -- 161@LB@
56	0.005619	0.3247	b2781	mazG	-9.54	0.334798	182 -- 193	141 -- 152	nucleoside triphosphate pyrophosphohydrolase	_____________181__________194\n_____________\|____________\|\n5'-UGA...ACCCG____________CAAUU...CGC-3'\n______________CAAUUUUCAGGA\n______________\|\|\|:\|\|\|\|\|\|:\|\n______________GUUGAAAGUCUU\n3'-UUU...GUUCA____________AACGC...UAG-5'\n_____________\|____________\|\n_____________153__________140\n	187 -- 193	141 -- 147	-13.182 kcal/mol	1.77322 kcal/mol	1.81388 kcal/mol	181 194@LB@ \| \|@LB@5'-UGA...ACCCG CAAUU...CGC-3'@LB@ CAAUUUUCAGGA@LB@ \|\|\|:\|\|\|\|\|\|:\|@LB@ GUUGAAAGUCUU@LB@3'-UUU...GUUCA AACGC...UAG-5'@LB@ \| \|@LB@ 153 140@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -13.182 kcal/mol@LB@Unfolding Energy - mRNA 1.77322 kcal/mol@LB@Unfolding Energy - sRNA 1.81388 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 141 -- 152@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 141 -- 147@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching