Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
55	0.005043	0.3024	b1625	cnu	-10.91	0.084723	38 -- 57	1 -- 21	nucleoid-associated oriC-binding protein; H-NS and StpA stabilizing factor	_____________37____________________58\n_____________\|_____________________\|\n5'-UUU...UCAGG_________________AC__UUUUC...AUC-3'\n______________GAUAGUAAA_GCGCGUU__UC\n______________\|\|\|\|::\|\|\|_\|\|\|\|\|\|:__\|\|\n______________CUAUUGUUU_CGCGCAG__AG\n3'-UUU...UACUA_________A_______AA__-5'\n_____________\|____________________\|\n_____________22___________________1\n	47 -- 53	5 -- 11	-17.9355 kcal/mol	5.76636 kcal/mol	1.25763 kcal/mol	37 58@LB@ \| \|@LB@5'-UUU...UCAGG AC UUUUC...AUC-3'@LB@ GAUAGUAAA GCGCGUU UC@LB@ \|\|\|\|::\|\|\| \|\|\|\|\|\|: \|\|@LB@ CUAUUGUUU CGCGCAG AG@LB@3'-UUU...UACUA A AA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -17.9355 kcal/mol@LB@Unfolding Energy - mRNA 5.76636 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 38 -- 57@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 5 -- 11@LB@
60	0.00555	0.3084	b2062	wza	-10.85	0.086669	18 -- 25	4 -- 11	colanic acid export protein; outer membrane auxillary lipoprotein	_____________17_______26\n_____________\|________\|\n5'-AAA...CGGUA________GGAUG...GCA-3'\n______________GCGUGUCU\n______________\|\|\|:\|\|\|\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	19 -- 25	4 -- 10	-13.9362 kcal/mol	1.92535 kcal/mol	1.15639 kcal/mol	17 26@LB@ \| \|@LB@5'-AAA...CGGUA GGAUG...GCA-3'@LB@ GCGUGUCU@LB@ \|\|\|:\|\|\|\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -13.9362 kcal/mol@LB@Unfolding Energy - mRNA 1.92535 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 18 -- 25@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 4 -- 10@LB@
145	0.01404	0.3104	b0721	sdhC	-10.79	0.088833	202 -- 215	9 -- 22	succinate dehydrogenase membrane subunit binds cytochrome b556	_____________201____________216\n_____________\|______________\|\n5'-UCC...AUUCA______G_______AAAAA...CCG-3'\n______________UGAUAA_AAAUGUG\n______________\|\|\|\|\|\|_\|\|\|\|\|:\|\n______________ACUAUU_UUUACGC\n3'-UUU...CUACU______G_______GCAGAAAG-5'\n_____________\|______________\|\n_____________23_____________8\n	209 -- 215	9 -- 15	-14.1232 kcal/mol	2.09271 kcal/mol	1.23827 kcal/mol	201 216@LB@ \| \|@LB@5'-UCC...AUUCA G AAAAA...CCG-3'@LB@ UGAUAA AAAUGUG@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|@LB@ ACUAUU UUUACGC@LB@3'-UUU...CUACU G GCAGAAAG-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -14.1232 kcal/mol@LB@Unfolding Energy - mRNA 2.09271 kcal/mol@LB@Unfolding Energy - sRNA 1.23827 kcal/mol@LB@@LB@Position - mRNA 202 -- 215@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 9 -- 15@LB@
94	0.009498	0.3104	b4198	ulaF	-10.74	0.090813	136 -- 150	6 -- 20	L-ribulose 5-phosphate 4-epimerase	_____________135_____________151\n_____________\|_______________\|\n5'-GUC...CAGAA________A______GAUUG...GCG-3'\n______________GUGGCGAA_GCGCGU\n______________:\|::\|:\|\|_\|\|\|\|\|\|\n______________UAUUGUUU_CGCGCA\n3'-UUU...ACUAC________A______GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	137 -- 143	13 -- 19	-18.1084 kcal/mol	6.12954 kcal/mol	1.24244 kcal/mol	135 151@LB@ \| \|@LB@5'-GUC...CAGAA A GAUUG...GCG-3'@LB@ GUGGCGAA GCGCGU@LB@ :\|::\|:\|\| \|\|\|\|\|\|@LB@ UAUUGUUU CGCGCA@LB@3'-UUU...ACUAC A GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -18.1084 kcal/mol@LB@Unfolding Energy - mRNA 6.12954 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 136 -- 150@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 13 -- 19@LB@
97	0.009805	0.3104	b1306	pspC	-10.74	0.090670	128 -- 139	7 -- 18	psp operon transcription co-activator	_____________127__________140\n_____________\|____________\|\n5'-CCG...AGCAA____________AACGU...CGG-3'\n______________AACGGAUGCGCG\n______________\|\|\|::\|\|\|\|\|\|\|\n______________UUGUUUACGCGC\n3'-UUU...UACUA____________AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	133 -- 139	7 -- 13	-18.5075 kcal/mol	6.55818 kcal/mol	1.20891 kcal/mol	127 140@LB@ \| \|@LB@5'-CCG...AGCAA AACGU...CGG-3'@LB@ AACGGAUGCGCG@LB@ \|\|\|::\|\|\|\|\|\|\|@LB@ UUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -18.5075 kcal/mol@LB@Unfolding Energy - mRNA 6.55818 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 128 -- 139@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 7 -- 13@LB@
118	0.01199	0.3104	b2573	rpoE	-10.72	0.091300	77 -- 87	8 -- 18	RNA polymerase sigma E factor	_____________76__________88\n_____________\|___________\|\n5'-ACA...ACAAA___________UACGG...UGG-3'\n______________AACAGAUGCGU\n______________\|\|\|\|:\|\|\|\|\|:\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	81 -- 87	8 -- 14	-15.0531 kcal/mol	3.12642 kcal/mol	1.20363 kcal/mol	76 88@LB@ \| \|@LB@5'-ACA...ACAAA UACGG...UGG-3'@LB@ AACAGAUGCGU@LB@ \|\|\|\|:\|\|\|\|\|:@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -10.72 kcal/mol@LB@Hybridization Energy -15.0531 kcal/mol@LB@Unfolding Energy - mRNA 3.12642 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 77 -- 87@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 8 -- 14@LB@
32	0.001981	0.2094	b3110	yhaO	-10.61	0.095420	268 -- 283	7 -- 23	putative transporter	_____________267_______________284\n_____________\|_________________\|\n5'-AAU...AAUGA____G____________AGAAG...UCG-3'\n______________GUGA_AGCGAGUG_GCG\n______________:\|\|\|_\|:\|:\|:\|\|_\|\|\|\n______________UACU_UUGUUUAC_CGC\n3'-UUU...CCUAC____A________G___AGAAAG-5'\n_____________\|_________________\|\n_____________24________________6\n	274 -- 280	11 -- 17	-15.5882 kcal/mol	2.45682 kcal/mol	2.52012 kcal/mol	267 284@LB@ \| \|@LB@5'-AAU...AAUGA G AGAAG...UCG-3'@LB@ GUGA AGCGAGUG GCG@LB@ :\|\|\| \|:\|:\|:\|\| \|\|\|@LB@ UACU UUGUUUAC CGC@LB@3'-UUU...CCUAC A G AGAAAG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -15.5882 kcal/mol@LB@Unfolding Energy - mRNA 2.45682 kcal/mol@LB@Unfolding Energy - sRNA 2.52012 kcal/mol@LB@@LB@Position - mRNA 268 -- 283@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 11 -- 17@LB@
31	0.001974	0.2094	b1080	flgI	-10.59	0.096403	87 -- 101	7 -- 21	putative flagellar basal body protein	_____________86______________102\n_____________\|_______________\|\n5'-AUU...ACUCA_______________CAUUG...AAA-3'\n______________GGUGGCGGAUGCGCG\n______________\|:\|::\|::\|\|\|\|\|\|\|\n______________CUAUUGUUUACGCGC\n3'-UUU...UACUA_______________AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	95 -- 101	7 -- 13	-22.6939 kcal/mol	10.8668 kcal/mol	1.24179 kcal/mol	86 102@LB@ \| \|@LB@5'-AUU...ACUCA CAUUG...AAA-3'@LB@ GGUGGCGGAUGCGCG@LB@ \|:\|::\|::\|\|\|\|\|\|\|@LB@ CUAUUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -22.6939 kcal/mol@LB@Unfolding Energy - mRNA 10.8668 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 87 -- 101@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 7 -- 13@LB@
187	0.01837	0.3104	b2151	galS	-10.59	0.096282	222 -- 228	5 -- 11	galactose- and fucose-inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor	_____________221_____229\n_____________\|_______\|\n5'-UCU...AUGUA_______AGGCU...GUG-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	222 -- 228	5 -- 11	-14.6299 kcal/mol	2.93004 kcal/mol	1.11145 kcal/mol	221 229@LB@ \| \|@LB@5'-UCU...AUGUA AGGCU...GUG-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -14.6299 kcal/mol@LB@Unfolding Energy - mRNA 2.93004 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 222 -- 228@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 5 -- 11@LB@
106	0.0109	0.3104	b2510	yfgJ	-10.53	0.098521	243 -- 261	5 -- 21	DUF1407 family protein	_____________242_________________262\n_____________\|___________________\|\n5'-UAA...AUCAG________CC_________GCCGA...UUU-3'\n______________GAUAACGG__AUGCGCGUU\n______________\|\|\|\|\|\|::__\|\|\|\|\|\|\|\|:\n______________CUAUUGUU__UACGCGCAG\n3'-UUU...UACUA___________________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	255 -- 261	5 -- 11	-20.9599 kcal/mol	9.18032 kcal/mol	1.24955 kcal/mol	242 262@LB@ \| \|@LB@5'-UAA...AUCAG CC GCCGA...UUU-3'@LB@ GAUAACGG AUGCGCGUU@LB@ \|\|\|\|\|\|:: \|\|\|\|\|\|\|\|:@LB@ CUAUUGUU UACGCGCAG@LB@3'-UUU...UACUA AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -20.9599 kcal/mol@LB@Unfolding Energy - mRNA 9.18032 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 243 -- 261@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 5 -- 11@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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