Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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	Additional homologs
95	0.002866	0.1063	b1338	abgA	-10.09	0.104797	206 -- 225	73 -- 94	p-aminobenzoyl-glutamate hydrolase A subunit		_____________205____________________226\n_____________\|______________________\|\n5'-GAU...AUGGA___UU_________________AUUCG...UCC-3'\n______________GUC___UGAAUCAAUU_UGUUA\n______________\|\|\|___:\|\|\|\|\|\|\|\|\|_\|\|:\|\|\n______________CAG___GCUUAGUUAA_ACGAU\n3'-UUU...AGCCG___CAU__________C_____ACGUC...ACG-5'\n_____________\|______________________\|\n_____________95_____________________72\n	214 -- 220	79 -- 85	-14.4971 kcal/mol	2.01447 kcal/mol	2.39569 kcal/mol	205 226@LB@ \| \|@LB@5'-GAU...AUGGA UU AUUCG...UCC-3'@LB@ GUC UGAAUCAAUU UGUUA@LB@ \|\|\| :\|\|\|\|\|\|\|\|\| \|\|:\|\|@LB@ CAG GCUUAGUUAA ACGAU@LB@3'-UUU...AGCCG CAU C ACGUC...ACG-5'@LB@ \| \|@LB@ 95 72@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -14.4971 kcal/mol@LB@Unfolding Energy - mRNA 2.01447 kcal/mol@LB@Unfolding Energy - sRNA 2.39569 kcal/mol@LB@@LB@Position - mRNA 206 -- 225@LB@Position - sRNA 73 -- 94@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 79 -- 85@LB@
162	0.006351	0.1377	b1869	yecN	-10.06	0.106335	266 -- 273	1 -- 8	MAPEG family inner membrane protein		_____________265______274\n_____________\|________\|\n5'-UCA...GUCGU________GAAUG...GCG-3'\n______________UCGCCUGC\n______________\|\|:\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	267 -- 273	1 -- 7	-14.5941 kcal/mol	2.17055 kcal/mol	2.36381 kcal/mol	265 274@LB@ \| \|@LB@5'-UCA...GUCGU GAAUG...GCG-3'@LB@ UCGCCUGC@LB@ \|\|:\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.06 kcal/mol@LB@Hybridization Energy -14.5941 kcal/mol@LB@Unfolding Energy - mRNA 2.17055 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 266 -- 273@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@LB@
66	0.001137	0.05992	b0076	leuO	-9.90	0.116504	167 -- 195	35 -- 60	global transcription factor		_____________166_____________________________196\n_____________\|_______________________________\|\n5'-UAU...AUAAG___________UAAGUGU_____________UAAGU...UGA-3'\n______________GGAAAGGGAGU_______GACA__GUGGAGU\n______________::\|\|\|\|\|:\|\|\|_______\|\|\|\|__:\|\|\|\|\|:\n______________UUUUUCCUUCA_______CUGU__UACCUCG\n3'-UUU...UAAGU___________UU_________UA_______CGUUG...ACG-5'\n_____________\|_______________________________\|\n_____________61______________________________34\n	189 -- 195	35 -- 41	-23.1584 kcal/mol	8.98888 kcal/mol	4.23745 kcal/mol	166 196@LB@ \| \|@LB@5'-UAU...AUAAG UAAGUGU UAAGU...UGA-3'@LB@ GGAAAGGGAGU GACA GUGGAGU@LB@ ::\|\|\|\|\|:\|\|\| \|\|\|\| :\|\|\|\|\|:@LB@ UUUUUCCUUCA CUGU UACCUCG@LB@3'-UUU...UAAGU UU UA CGUUG...ACG-5'@LB@ \| \|@LB@ 61 34@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -23.1584 kcal/mol@LB@Unfolding Energy - mRNA 8.98888 kcal/mol@LB@Unfolding Energy - sRNA 4.23745 kcal/mol@LB@@LB@Position - mRNA 167 -- 195@LB@Position - sRNA 35 -- 60@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 35 -- 41@LB@
193	0.00868	0.1548	b4226	ppa	-9.88	0.117380	102 -- 122	43 -- 61	inorganic pyrophosphatase		_____________101___________________123\n_____________\|_____________________\|\n5'-AUA...CUGGU__________AAUG_______AAACA...UCG-3'\n______________GAAAAAGGAA____AAGACGA\n______________:\|\|\|\|\|\|\|\|\|____\|\|\|\|\|:\|\n______________UUUUUUCCUU____UUCUGUU\n3'-UUU...UUAAG__________CA_________AUACC...ACG-5'\n_____________\|_____________________\|\n_____________62____________________42\n	116 -- 122	43 -- 49	-15.2744 kcal/mol	3.19261 kcal/mol	2.19883 kcal/mol	101 123@LB@ \| \|@LB@5'-AUA...CUGGU AAUG AAACA...UCG-3'@LB@ GAAAAAGGAA AAGACGA@LB@ :\|\|\|\|\|\|\|\|\| \|\|\|\|\|:\|@LB@ UUUUUUCCUU UUCUGUU@LB@3'-UUU...UUAAG CA AUACC...ACG-5'@LB@ \| \|@LB@ 62 42@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -15.2744 kcal/mol@LB@Unfolding Energy - mRNA 3.19261 kcal/mol@LB@Unfolding Energy - sRNA 2.19883 kcal/mol@LB@@LB@Position - mRNA 102 -- 122@LB@Position - sRNA 43 -- 61@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 43 -- 49@LB@
103	0.003335	0.1114	b3494	uspB	-9.88	0.117554	193 -- 207	43 -- 57	universal stress (ethanol tolerance) protein B		_____________192_____________208\n_____________\|_______________\|\n5'-AAU...CCGGG_________U_____GCACC...UGC-3'\n______________GAGGAGGUA_GAUAA\n______________:\|\|\|\|:\|\|\|_\|\|:\|\|\n______________UUCCUUCAU_CUGUU\n3'-UUU...GUUUU_________U_____AUACC...ACG-5'\n_____________\|_______________\|\n_____________58______________42\n	195 -- 201	49 -- 55	-16.0492 kcal/mol	4.41466 kcal/mol	1.75421 kcal/mol	192 208@LB@ \| \|@LB@5'-AAU...CCGGG U GCACC...UGC-3'@LB@ GAGGAGGUA GAUAA@LB@ :\|\|\|\|:\|\|\| \|\|:\|\|@LB@ UUCCUUCAU CUGUU@LB@3'-UUU...GUUUU U AUACC...ACG-5'@LB@ \| \|@LB@ 58 42@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -16.0492 kcal/mol@LB@Unfolding Energy - mRNA 4.41466 kcal/mol@LB@Unfolding Energy - sRNA 1.75421 kcal/mol@LB@@LB@Position - mRNA 193 -- 207@LB@Position - sRNA 43 -- 57@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 49 -- 55@LB@
80	0.001886	0.08273	b3205	yhbJ	-9.88	0.117656	21 -- 27	1 -- 7	adaptor protein for GlmZ/GlmY sRNA decay glucosamine-6-phosphate-regulated; NTPase		_____________20______28\n_____________\|_______\|\n5'-CGG...AAACG_______AUACU...CCG-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	21 -- 27	1 -- 7	-13.6981 kcal/mol	1.48735 kcal/mol	2.34039 kcal/mol	20 28@LB@ \| \|@LB@5'-CGG...AAACG AUACU...CCG-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -13.6981 kcal/mol@LB@Unfolding Energy - mRNA 1.48735 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 21 -- 27@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 1 -- 7@LB@
45	0.0004696	0.03623	b4035	malK	-9.83	0.120497	188 -- 201	44 -- 57	maltose ABC transportor ATPase		_____________187____________202\n_____________\|______________\|\n5'-CGC...UUACA_______A______UGGCG...UGU-3'\n______________AAGGGAG_AGGGCA\n______________\|\|\|\|:\|\|_\|:\|:\|\|\n______________UUCCUUC_UUCUGU\n3'-UUU...GUUUU_______A______UAUAC...ACG-5'\n_____________\|______________\|\n_____________58_____________43\n	188 -- 194	51 -- 57	-14.5332 kcal/mol	2.95068 kcal/mol	1.74831 kcal/mol	187 202@LB@ \| \|@LB@5'-CGC...UUACA A UGGCG...UGU-3'@LB@ AAGGGAG AGGGCA@LB@ \|\|\|\|:\|\| \|:\|:\|\|@LB@ UUCCUUC UUCUGU@LB@3'-UUU...GUUUU A UAUAC...ACG-5'@LB@ \| \|@LB@ 58 43@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -14.5332 kcal/mol@LB@Unfolding Energy - mRNA 2.95068 kcal/mol@LB@Unfolding Energy - sRNA 1.74831 kcal/mol@LB@@LB@Position - mRNA 188 -- 201@LB@Position - sRNA 44 -- 57@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 51 -- 57@LB@
68	0.001184	0.06134	b3188	sfsB	-9.82	0.121108	186 -- 205	37 -- 57	malPQ operon transcriptional activator		_____________185___________________206\n_____________\|_____________________\|\n5'-CGG...AACUU____________AAAA_____AAGUA...UGA-3'\n______________AAGG_AGUGAGG____AUGGA\n______________\|\|\|\|_\|\|\|:\|\|:____\|\|\|\|\|\n______________UUCC_UCAUUCU____UACCU\n3'-UUU...GUUUU____U_______GUUA_____CGCGU...ACG-5'\n_____________\|_____________________\|\n_____________58____________________36\n	190 -- 196	46 -- 52	-17.294 kcal/mol	3.7439 kcal/mol	3.68958 kcal/mol	185 206@LB@ \| \|@LB@5'-CGG...AACUU AAAA AAGUA...UGA-3'@LB@ AAGG AGUGAGG AUGGA@LB@ \|\|\|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ UUCC UCAUUCU UACCU@LB@3'-UUU...GUUUU U GUUA CGCGU...ACG-5'@LB@ \| \|@LB@ 58 36@LB@@LB@@LB@Energy -9.82 kcal/mol@LB@Hybridization Energy -17.294 kcal/mol@LB@Unfolding Energy - mRNA 3.7439 kcal/mol@LB@Unfolding Energy - sRNA 3.68958 kcal/mol@LB@@LB@Position - mRNA 186 -- 205@LB@Position - sRNA 37 -- 57@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 46 -- 52@LB@
83	0.001966	0.08273	b1584	speG	-9.79	0.123144	169 -- 214	25 -- 77	spermidine N(1)-acetyltransferase		_____________168_____________________________________________________215\n_____________\|_______________________________________________________\|\n5'-UCU...UAACC__________________________U____G____CGUUAU___CA________CAGUG...GGU-3'\n______________UGUUAU____UGAUUUA____AGGAA_GUAA_GACA_______GC__AGCGCCCA\n______________\|\|:\|\|\|____\|:\|\|\|:\|____\|\|\|\|\|_\|\|\|\|_\|\|\|\|_______\|\|__\|:\|\|\|\|\|\|\n______________ACGAUA____AUUAAGU____UCCUU_CAUU_CUGU_______CG__UUGCGGGU\n3'-UUU...UUAAC______CGUC_______UUUU_______________UAUACCU__CG________AGCGA...ACG-5'\n_____________\|_______________________________________________________\|\n_____________78______________________________________________________24\n	208 -- 214	25 -- 31	-32.6914 kcal/mol	9.23779 kcal/mol	13.6641 kcal/mol	168 215@LB@ \| \|@LB@5'-UCU...UAACC U G CGUUAU CA CAGUG...GGU-3'@LB@ UGUUAU UGAUUUA AGGAA GUAA GACA GC AGCGCCCA@LB@ \|\|:\|\|\| \|:\|\|\|:\| \|\|\|\|\| \|\|\|\| \|\|\|\| \|\| \|:\|\|\|\|\|\|@LB@ ACGAUA AUUAAGU UCCUU CAUU CUGU CG UUGCGGGU@LB@3'-UUU...UUAAC CGUC UUUU UAUACCU CG AGCGA...ACG-5'@LB@ \| \|@LB@ 78 24@LB@@LB@@LB@Energy -9.79 kcal/mol@LB@Hybridization Energy -32.6914 kcal/mol@LB@Unfolding Energy - mRNA 9.23779 kcal/mol@LB@Unfolding Energy - sRNA 13.6641 kcal/mol@LB@@LB@Position - mRNA 169 -- 214@LB@Position - sRNA 25 -- 77@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 25 -- 31@LB@
28	0.0001471	0.01851	b0997	torA	-9.78	0.123932	184 -- 203	41 -- 60	trimethylamine N-oxide (TMAO) reductase I catalytic subunit	b3551 b1872	_____________183__________________204\n_____________\|____________________\|\n5'-UAC...GCGAU__________A__A______AACAA...CGC-3'\n______________AAGAAGGAAG_AA_AUAAUG\n______________\|\|:\|\|\|\|\|\|\|_\|\|_\|:\|\|\|:\n______________UUUUUCCUUC_UU_UGUUAU\n3'-UUU...UAAGU__________A__C______ACCUC...ACG-5'\n_____________\|____________________\|\n_____________61___________________40\n	187 -- 193	51 -- 57	-13.1224 kcal/mol	1.37417 kcal/mol	1.96633 kcal/mol	183 204@LB@ \| \|@LB@5'-UAC...GCGAU A A AACAA...CGC-3'@LB@ AAGAAGGAAG AA AUAAUG@LB@ \|\|:\|\|\|\|\|\|\| \|\| \|:\|\|\|:@LB@ UUUUUCCUUC UU UGUUAU@LB@3'-UUU...UAAGU A C ACCUC...ACG-5'@LB@ \| \|@LB@ 61 40@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -13.1224 kcal/mol@LB@Unfolding Energy - mRNA 1.37417 kcal/mol@LB@Unfolding Energy - sRNA 1.96633 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 41 -- 60@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 51 -- 57@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