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
80	0.007305	0.3087	b2392	mntH	-9.52	0.145914	200 -- 218	5 -- 21	manganese/divalent cation transporter	_____________199_________________219\n_____________\|___________________\|\n5'-GCU...CACAA_________CUAU______GAGAG...UCG-3'\n______________GAUGACGAA____CGCGUU\n______________\|\|\|:\|\|:\|\|____\|\|\|\|\|:\n______________CUAUUGUUU____GCGCAG\n3'-UUU...UACUA_________AC________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	202 -- 208	13 -- 19	-16.4824 kcal/mol	5.71706 kcal/mol	1.24955 kcal/mol	199 219@LB@ \| \|@LB@5'-GCU...CACAA CUAU GAGAG...UCG-3'@LB@ GAUGACGAA CGCGUU@LB@ \|\|\|:\|\|:\|\| \|\|\|\|\|:@LB@ CUAUUGUUU GCGCAG@LB@3'-UUU...UACUA AC AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -16.4824 kcal/mol@LB@Unfolding Energy - mRNA 5.71706 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 200 -- 218@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 13 -- 19@LB@
33	0.002096	0.2094	b0937	ssuE	-11.36	0.070700	201 -- 209	5 -- 13	NAD(P)H-dependent FMN reductase	_____________200_______210\n_____________\|_________\|\n5'-CUG...AGAGU_________AUCAC...AGG-3'\n______________AUGCGUGUC\n______________\|\|\|\|\|:\|\|\|\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	203 -- 209	5 -- 11	-14.6108 kcal/mol	2.09491 kcal/mol	1.15134 kcal/mol	200 210@LB@ \| \|@LB@5'-CUG...AGAGU AUCAC...AGG-3'@LB@ AUGCGUGUC@LB@ \|\|\|\|\|:\|\|\|@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -14.6108 kcal/mol@LB@Unfolding Energy - mRNA 2.09491 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 201 -- 209@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 5 -- 11@LB@
88	0.008928	0.3104	b0405	queA	-8.89	0.184414	201 -- 209	5 -- 13	S-adenosylmethionine:tRNA ribosyltransferase-isomerase	_____________200_______210\n_____________\|_________\|\n5'-GGG...GUGUC_________ACCGA...GGC-3'\n______________AUGCGCGUU\n______________\|\|\|\|\|\|\|\|:\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	203 -- 209	5 -- 11	-14.1161 kcal/mol	4.07268 kcal/mol	1.15134 kcal/mol	200 210@LB@ \| \|@LB@5'-GGG...GUGUC ACCGA...GGC-3'@LB@ AUGCGCGUU@LB@ \|\|\|\|\|\|\|\|:@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -14.1161 kcal/mol@LB@Unfolding Energy - mRNA 4.07268 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 201 -- 209@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 5 -- 11@LB@
140	0.01344	0.3104	b2388	glk	-4.25	0.738023	201 -- 214	10 -- 20	glucokinase	_____________200____________215\n_____________\|______________\|\n5'-CUA...GAAGA_______AGU____AUUAG...AUU-3'\n______________AUGACAA___AUGC\n______________\|\|:\|\|\|\|___\|\|\|\|\n______________UAUUGUU___UACG\n3'-UUU...ACUAC______________CGCAG...AAG-5'\n_____________\|______________\|\n_____________21_____________9\n	201 -- 207	14 -- 20	-8.41213 kcal/mol	2.93934 kcal/mol	1.22774 kcal/mol	200 215@LB@ \| \|@LB@5'-CUA...GAAGA AGU AUUAG...AUU-3'@LB@ AUGACAA AUGC@LB@ \|\|:\|\|\|\| \|\|\|\|@LB@ UAUUGUU UACG@LB@3'-UUU...ACUAC CGCAG...AAG-5'@LB@ \| \|@LB@ 21 9@LB@@LB@@LB@Energy -4.25 kcal/mol@LB@Hybridization Energy -8.41213 kcal/mol@LB@Unfolding Energy - mRNA 2.93934 kcal/mol@LB@Unfolding Energy - sRNA 1.22774 kcal/mol@LB@@LB@Position - mRNA 201 -- 214@LB@Position - sRNA 10 -- 20@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 14 -- 20@LB@
190	0.01867	0.3104	b0196	rcsF	-10.27	0.109081	201 -- 211	2 -- 13	putative outer membrane protein	_____________200__________212\n_____________\|____________\|\n5'-AAU...AUACU____________ACCGA...AGC-3'\n______________AUGCGUG_CUUU\n______________\|\|\|\|\|:\|_\|\|\|\|\n______________UACGCGC_GAAA\n3'-UUU...UUGUU_______A____G-5'\n_____________\|____________\|\n_____________14___________1\n	201 -- 207	7 -- 13	-12.8527 kcal/mol	1.40833 kcal/mol	1.17421 kcal/mol	200 212@LB@ \| \|@LB@5'-AAU...AUACU ACCGA...AGC-3'@LB@ AUGCGUG CUUU@LB@ \|\|\|\|\|:\| \|\|\|\|@LB@ UACGCGC GAAA@LB@3'-UUU...UUGUU A G-5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -12.8527 kcal/mol@LB@Unfolding Energy - mRNA 1.40833 kcal/mol@LB@Unfolding Energy - sRNA 1.17421 kcal/mol@LB@@LB@Position - mRNA 201 -- 211@LB@Position - sRNA 2 -- 13@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 7 -- 13@LB@
8	0.000167	0.07068	b0814	ompX	-11.11	0.078421	202 -- 223	1 -- 22	outer membrane protein X	_____________201____________________224\n_____________\|______________________\|\n5'-CUG...GGUUA___AAAA__U___A________AGCAC...CAC-3'\n______________UGA____AA_UGC_UGUCUUUC\n______________\|\|\|____\|\|_\|\|\|_:\|\|\|\|\|\|\|\n______________ACU____UU_ACG_GCAGAAAG\n3'-UUU...CUACU___AUUG__U___C________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	217 -- 223	1 -- 7	-15.5509 kcal/mol	3.18554 kcal/mol	1.25963 kcal/mol	201 224@LB@ \| \|@LB@5'-CUG...GGUUA AAAA U A AGCAC...CAC-3'@LB@ UGA AA UGC UGUCUUUC@LB@ \|\|\| \|\| \|\|\| :\|\|\|\|\|\|\|@LB@ ACU UU ACG GCAGAAAG@LB@3'-UUU...CUACU AUUG U C -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -11.11 kcal/mol@LB@Hybridization Energy -15.5509 kcal/mol@LB@Unfolding Energy - mRNA 3.18554 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 202 -- 223@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 1 -- 7@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@
176	0.01748	0.3104	b0435	bolA	-9.78	0.131850	202 -- 220	4 -- 22	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________201_________________221\n_____________\|___________________\|\n5'-UGA...UUUCA________C___A___GA_AGAAG...CCG-3'\n______________UGAUGAUA_GUG_GCG__U\n______________\|\|\|\|:\|:\|_:\|\|_\|\|\|__\|\n______________ACUAUUGU_UAC_CGC__A\n3'-UUU...CUACU________U___G___AG_AAG-5'\n_____________\|___________________\|\n_____________23__________________3\n	203 -- 209	15 -- 21	-14.8727 kcal/mol	3.8346 kcal/mol	1.2572 kcal/mol	201 221@LB@ \| \|@LB@5'-UGA...UUUCA C A GA AGAAG...CCG-3'@LB@ UGAUGAUA GUG GCG U@LB@ \|\|\|\|:\|:\| :\|\| \|\|\| \|@LB@ ACUAUUGU UAC CGC A@LB@3'-UUU...CUACU U G AG AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -14.8727 kcal/mol@LB@Unfolding Energy - mRNA 3.8346 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 202 -- 220@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 15 -- 21@LB@
41	0.00276	0.2279	b0889	lrp	-10.49	0.100208	207 -- 221	8 -- 21	leucine-responsive global transcriptional regulator	_____________206_____________222\n_____________\|_______________\|\n5'-GUG...UGGUA_________AA____CCUGG...AGC-3'\n______________GAUAGCAAG__GCGC\n______________\|\|\|\|:\|\|\|:__\|\|\|\|\n______________CUAUUGUUU__CGCG\n3'-UUU...UACUA_________A_____CAGAAAG-5'\n_____________\|_______________\|\n_____________22______________7\n	209 -- 215	13 -- 19	-15.2704 kcal/mol	3.5472 kcal/mol	1.23638 kcal/mol	206 222@LB@ \| \|@LB@5'-GUG...UGGUA AA CCUGG...AGC-3'@LB@ GAUAGCAAG GCGC@LB@ \|\|\|\|:\|\|\|: \|\|\|\|@LB@ CUAUUGUUU CGCG@LB@3'-UUU...UACUA A CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -15.2704 kcal/mol@LB@Unfolding Energy - mRNA 3.5472 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 207 -- 221@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 13 -- 19@LB@
126	0.01241	0.3104	b4379	yjjW	-11.82	0.058804	207 -- 217	8 -- 18	putative pyruvate formate lyase activating enzyme	_____________206_________218\n_____________\|___________\|\n5'-CGG...UGAAC___________UUUAG...UGC-3'\n______________AGCAGAUGCGC\n______________\|:\|\|:\|\|\|\|\|\|\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	211 -- 217	8 -- 14	-16.9543 kcal/mol	3.92931 kcal/mol	1.20363 kcal/mol	206 218@LB@ \| \|@LB@5'-CGG...UGAAC UUUAG...UGC-3'@LB@ AGCAGAUGCGC@LB@ \|:\|\|:\|\|\|\|\|\|@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -16.9543 kcal/mol@LB@Unfolding Energy - mRNA 3.92931 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 207 -- 217@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 8 -- 14@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

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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

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