Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
193	0.01107	0.1919	b3532	bcsB	-10.24	0.150531	226 -- 241	15 -- 35	regulator of cellulose synthase cyclic di-GMP binding	_____________225___________________242\n_____________\|_____________________\|\n5'-AAG...GAUUU_______G_____________GAUGA...UCA-3'\n______________GUGCAGU__GC____UAUGGG\n______________\|\|:\|\|\|:__\|\|____\|\|\|\|\|\|\n______________CAUGUCG__CG____AUACCC\n3'-UUU...AGGAC_______AU__UAAA______AAUAC...UCG-5'\n_____________\|_____________________\|\n_____________36____________________14\n	226 -- 232	29 -- 35	-18.7324 kcal/mol	7.03896 kcal/mol	1.4496 kcal/mol	225 242@LB@ \| \|@LB@5'-AAG...GAUUU G GAUGA...UCA-3'@LB@ GUGCAGU GC UAUGGG@LB@ \|\|:\|\|\|: \|\| \|\|\|\|\|\|@LB@ CAUGUCG CG AUACCC@LB@3'-UUU...AGGAC AU UAAA AAUAC...UCG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -18.7324 kcal/mol@LB@Unfolding Energy - mRNA 7.03896 kcal/mol@LB@Unfolding Energy - sRNA 1.4496 kcal/mol@LB@@LB@Position - mRNA 226 -- 241@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 29 -- 35@LB@
17	0.0001135	0.02244	b3531	bcsZ	-11.80	0.072553	125 -- 136	14 -- 30	endo-1 4-D-glucanase	_____________124_______________137\n_____________\|_________________\|\n5'-UCA...AUAUU_________________ACUGU...AGG-3'\n______________GCUGGCA_____UGGGU\n______________\|\|\|:\|\|\|_____\|\|\|\|\|\n______________CGAUCGU_____ACCCA\n3'-UUU...CAUGU_______AAAAU_____AUACA...UCG-5'\n_____________\|_________________\|\n_____________31________________13\n	125 -- 131	24 -- 30	-17.2227 kcal/mol	4.01076 kcal/mol	1.40705 kcal/mol	124 137@LB@ \| \|@LB@5'-UCA...AUAUU ACUGU...AGG-3'@LB@ GCUGGCA UGGGU@LB@ \|\|\|:\|\|\| \|\|\|\|\|@LB@ CGAUCGU ACCCA@LB@3'-UUU...CAUGU AAAAU AUACA...UCG-5'@LB@ \| \|@LB@ 31 13@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -17.2227 kcal/mol@LB@Unfolding Energy - mRNA 4.01076 kcal/mol@LB@Unfolding Energy - sRNA 1.40705 kcal/mol@LB@@LB@Position - mRNA 125 -- 136@LB@Position - sRNA 14 -- 30@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 24 -- 30@LB@
29	0.0004753	0.05348	b3412	bioH	-14.38	0.016792	146 -- 163	23 -- 40	pimeloyl-ACP methyl ester carboxylesterase	_____________145________________164\n_____________\|__________________\|\n5'-GGC...CAUAA___C_____U________AUGUU...ACG-3'\n______________UCC_GGUAC_GUUAGCAU\n______________\|\|\|_\|\|\|\|\|_\|:\|\|\|\|\|\|\n______________AGG_CCAUG_CGAUCGUA\n3'-UUU...CACCA___A_____U________AAAUA...UCG-5'\n_____________\|__________________\|\n_____________41_________________22\n	157 -- 163	23 -- 29	-23.5076 kcal/mol	4.57199 kcal/mol	4.55554 kcal/mol	145 164@LB@ \| \|@LB@5'-GGC...CAUAA C U AUGUU...ACG-3'@LB@ UCC GGUAC GUUAGCAU@LB@ \|\|\| \|\|\|\|\| \|:\|\|\|\|\|\|@LB@ AGG CCAUG CGAUCGUA@LB@3'-UUU...CACCA A U AAAUA...UCG-5'@LB@ \| \|@LB@ 41 22@LB@@LB@@LB@Energy -14.38 kcal/mol@LB@Hybridization Energy -23.5076 kcal/mol@LB@Unfolding Energy - mRNA 4.57199 kcal/mol@LB@Unfolding Energy - sRNA 4.55554 kcal/mol@LB@@LB@Position - mRNA 146 -- 163@LB@Position - sRNA 23 -- 40@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 23 -- 29@LB@
9	2.519e-05	0.009407	b0435	bolA	-15.32	0.008970	138 -- 163	15 -- 36	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________137________________________164\n_____________\|__________________________\|\n5'-UGA...GAAAC___AAAA_____________AAA___AUGGA...CCG-3'\n______________GGU____GCGGCUAGUAUUU___GGG\n______________\|\|\|____:\|:\|\|\|\|\|:\|\|\|\|___\|\|\|\n______________CCA____UGUCGAUCGUAAA___CCC\n3'-UUU...AAGGA____________________AUA___AAUAC...UCG-5'\n_____________\|__________________________\|\n_____________37_________________________14\n	151 -- 157	21 -- 27	-22.9811 kcal/mol	6.21269 kcal/mol	1.45166 kcal/mol	137 164@LB@ \| \|@LB@5'-UGA...GAAAC AAAA AAA AUGGA...CCG-3'@LB@ GGU GCGGCUAGUAUUU GGG@LB@ \|\|\| :\|:\|\|\|\|\|:\|\|\|\| \|\|\|@LB@ CCA UGUCGAUCGUAAA CCC@LB@3'-UUU...AAGGA AUA AAUAC...UCG-5'@LB@ \| \|@LB@ 37 14@LB@@LB@@LB@Energy -15.32 kcal/mol@LB@Hybridization Energy -22.9811 kcal/mol@LB@Unfolding Energy - mRNA 6.21269 kcal/mol@LB@Unfolding Energy - sRNA 1.45166 kcal/mol@LB@@LB@Position - mRNA 138 -- 163@LB@Position - sRNA 15 -- 36@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 21 -- 27@LB@
41	0.0008276	0.06626	b1218	chaC	-8.54	0.293650	119 -- 139	24 -- 45	cation transport regulator	_____________118____________________140\n_____________\|______________________\|\n5'-AUA...CGUUA________AAAAUG________AAAAU...CGC-3'\n______________GUGGUUUC______AGC_AGUA\n______________\|\|\|\|\|\|:\|______\|\|\|_\|\|:\|\n______________CACCAAGG______UCG_UCGU\n3'-UUU...UCCUC________ACCAUG___A____AAAAU...UCG-5'\n_____________\|______________________\|\n_____________46_____________________23\n	120 -- 126	38 -- 44	-17.6586 kcal/mol	4.55792 kcal/mol	4.55794 kcal/mol	118 140@LB@ \| \|@LB@5'-AUA...CGUUA AAAAUG AAAAU...CGC-3'@LB@ GUGGUUUC AGC AGUA@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|:\|@LB@ CACCAAGG UCG UCGU@LB@3'-UUU...UCCUC ACCAUG A AAAAU...UCG-5'@LB@ \| \|@LB@ 46 23@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -17.6586 kcal/mol@LB@Unfolding Energy - mRNA 4.55792 kcal/mol@LB@Unfolding Energy - sRNA 4.55794 kcal/mol@LB@@LB@Position - mRNA 119 -- 139@LB@Position - sRNA 24 -- 45@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 38 -- 44@LB@
121	0.005123	0.1413	b1735	chbR	-8.25	0.324466	38 -- 46	30 -- 38	repressor of chb operon for N N'-diacetylchitobiose utilization	_____________37________47\n_____________\|_________\|\n5'-GAU...CGCAU_________ACGAA...CUG-3'\n______________CUGGUACAG\n______________\|\|\|\|\|\|\|\|\|\n______________GACCAUGUC\n3'-UUU...CCAAG_________GAUCG...UCG-5'\n_____________\|_________\|\n_____________39________29\n	40 -- 46	30 -- 36	-15.5432 kcal/mol	3.07825 kcal/mol	4.2107 kcal/mol	37 47@LB@ \| \|@LB@5'-GAU...CGCAU ACGAA...CUG-3'@LB@ CUGGUACAG@LB@ \|\|\|\|\|\|\|\|\|@LB@ GACCAUGUC@LB@3'-UUU...CCAAG GAUCG...UCG-5'@LB@ \| \|@LB@ 39 29@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -15.5432 kcal/mol@LB@Unfolding Energy - mRNA 3.07825 kcal/mol@LB@Unfolding Energy - sRNA 4.2107 kcal/mol@LB@@LB@Position - mRNA 38 -- 46@LB@Position - sRNA 30 -- 38@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 30 -- 36@LB@
179	0.01003	0.1882	b0619	citA	-9.15	0.235039	224 -- 237	20 -- 33	sensory histidine kinase in two-component regulatory system with CitB	_____________223____________238\n_____________\|______________\|\n5'-CAU...AAUAA______U_______UCCAA...UCA-3'\n______________ACAGUU_GCAUUUU\n______________\|\|\|\|:\|_\|\|\|\|\|\|\|\n______________UGUCGA_CGUAAAA\n3'-UUU...GACCA______U_______UACCC...UCG-5'\n_____________\|______________\|\n_____________34_____________19\n	231 -- 237	20 -- 26	-13.7934 kcal/mol	3.21006 kcal/mol	1.43447 kcal/mol	223 238@LB@ \| \|@LB@5'-CAU...AAUAA U UCCAA...UCA-3'@LB@ ACAGUU GCAUUUU@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|@LB@ UGUCGA CGUAAAA@LB@3'-UUU...GACCA U UACCC...UCG-5'@LB@ \| \|@LB@ 34 19@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -13.7934 kcal/mol@LB@Unfolding Energy - mRNA 3.21006 kcal/mol@LB@Unfolding Energy - sRNA 1.43447 kcal/mol@LB@@LB@Position - mRNA 224 -- 237@LB@Position - sRNA 20 -- 33@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 20 -- 26@LB@
122	0.005134	0.1413	b0437	clpP	-11.97	0.066798	162 -- 180	3 -- 36	proteolytic subunit of ClpA-ClpP and ClpX-ClpP ATP-dependent serine proteases	_____________161________________________________181\n_____________\|__________________________________\|\n5'-CCA...CAAUC________A_________________________AUUUU...UCU-3'\n______________GGUACAGC_GGU_______________UUUUUCA\n______________\|\|\|\|\|\|\|\|_:\|:_______________\|\|\|\|\|\|\|\n______________CCAUGUCG_UCG_______________AAAAAGU\n3'-UUU...AAGGA________A___UAAAAUACCCAAUAC_______CG-5'\n_____________\|__________________________________\|\n_____________37_________________________________2\n	174 -- 180	3 -- 9	-16.9285 kcal/mol	3.46571 kcal/mol	1.49503 kcal/mol	161 181@LB@ \| \|@LB@5'-CCA...CAAUC A AUUUU...UCU-3'@LB@ GGUACAGC GGU UUUUUCA@LB@ \|\|\|\|\|\|\|\| :\|: \|\|\|\|\|\|\|@LB@ CCAUGUCG UCG AAAAAGU@LB@3'-UUU...AAGGA A UAAAAUACCCAAUAC CG-5'@LB@ \| \|@LB@ 37 2@LB@@LB@@LB@Energy -11.97 kcal/mol@LB@Hybridization Energy -16.9285 kcal/mol@LB@Unfolding Energy - mRNA 3.46571 kcal/mol@LB@Unfolding Energy - sRNA 1.49503 kcal/mol@LB@@LB@Position - mRNA 162 -- 180@LB@Position - sRNA 3 -- 36@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 3 -- 9@LB@
110	0.004262	0.1302	b1871	cmoB	-11.44	0.086999	165 -- 182	22 -- 44	tRNA (cmo5U34)-carboxymethyltransferase carboxy-SAM-dependent	_____________164______________________183\n_____________\|________________________\|\n5'-CAC...AACUU______A_________________AAAAG...AGC-3'\n______________UGGUUC_CUGG______UGGCAUU\n______________\|\|\|\|\|\|_\|\|\|\|______\|:\|\|\|\|\|\n______________ACCAAG_GACC______AUCGUAA\n3'-UUU...CCUCC___________AUGUCG_______AAUAC...UCG-5'\n_____________\|________________________\|\n_____________45_______________________21\n	176 -- 182	22 -- 28	-20.1895 kcal/mol	4.19283 kcal/mol	4.55859 kcal/mol	164 183@LB@ \| \|@LB@5'-CAC...AACUU A AAAAG...AGC-3'@LB@ UGGUUC CUGG UGGCAUU@LB@ \|\|\|\|\|\| \|\|\|\| \|:\|\|\|\|\|@LB@ ACCAAG GACC AUCGUAA@LB@3'-UUU...CCUCC AUGUCG AAUAC...UCG-5'@LB@ \| \|@LB@ 45 21@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -20.1895 kcal/mol@LB@Unfolding Energy - mRNA 4.19283 kcal/mol@LB@Unfolding Energy - sRNA 4.55859 kcal/mol@LB@@LB@Position - mRNA 165 -- 182@LB@Position - sRNA 22 -- 44@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 22 -- 28@LB@
141	0.006623	0.1579	b1992	cobS	-16.13	0.004945	167 -- 192	24 -- 49	cobalamin synthase	_____________166_________________________193\n_____________\|___________________________\|\n5'-GAG...AGUAU__CU_________G_____UGG_____AAAAU...GUA-3'\n______________GG__GGUGGUUUC_GGUAU____AGUA\n______________\|\|__\|\|\|\|\|\|\|:\|_\|\|\|\|:____\|\|:\|\n______________CC__CCACCAAGG_CCAUG____UCGU\n3'-UUU...CGAUU__U__________A_____UCGA____AAAAU...UCG-5'\n_____________\|___________________________\|\n_____________50__________________________23\n	173 -- 179	38 -- 44	-26.3933 kcal/mol	5.70356 kcal/mol	4.5591 kcal/mol	166 193@LB@ \| \|@LB@5'-GAG...AGUAU CU G UGG AAAAU...GUA-3'@LB@ GG GGUGGUUUC GGUAU AGUA@LB@ \|\| \|\|\|\|\|\|\|:\| \|\|\|\|: \|\|:\|@LB@ CC CCACCAAGG CCAUG UCGU@LB@3'-UUU...CGAUU U A UCGA AAAAU...UCG-5'@LB@ \| \|@LB@ 50 23@LB@@LB@@LB@Energy -16.13 kcal/mol@LB@Hybridization Energy -26.3933 kcal/mol@LB@Unfolding Energy - mRNA 5.70356 kcal/mol@LB@Unfolding Energy - sRNA 4.5591 kcal/mol@LB@@LB@Position - mRNA 167 -- 192@LB@Position - sRNA 24 -- 49@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 38 -- 44@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)

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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

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