Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
28	0.0008326	0.09021	b2563	acpS	-7.40	0.086911	170 -- 193	37 -- 61	holo-[acyl-carrier-protein] synthase 1	_____________169_______________________194\n_____________\|_________________________\|\n5'-GCC...AGAAA______GU___GAU__U________GUGGC...GCG-3'\n______________UGAAGC___CU___GC_GGAAGCGC\n______________\|\|\|\|:\|___\|\|___\|\|_:\|\|\|\|\|:\|\n______________ACUUUG___GA___CG_UCUUCGUG\n3'-UUU...GCCCU______AAC__AUU__U________AAUUU...CAA-5'\n_____________\|_________________________\|\n_____________62________________________36\n	187 -- 193	37 -- 43	-21.5547 kcal/mol	6.80255 kcal/mol	7.3495 kcal/mol	169 194@LB@ \| \|@LB@5'-GCC...AGAAA GU GAU U GUGGC...GCG-3'@LB@ UGAAGC CU GC GGAAGCGC@LB@ \|\|\|\|:\| \|\| \|\| :\|\|\|\|\|:\|@LB@ ACUUUG GA CG UCUUCGUG@LB@3'-UUU...GCCCU AAC AUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -7.40 kcal/mol@LB@Hybridization Energy -21.5547 kcal/mol@LB@Unfolding Energy - mRNA 6.80255 kcal/mol@LB@Unfolding Energy - sRNA 7.3495 kcal/mol@LB@@LB@Position - mRNA 170 -- 193@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 37 -- 43@LB@
95	0.007016	0.2379	b0464	acrR	-8.52	0.043413	219 -- 228	37 -- 46	transcriptional repressor	_____________218________229\n_____________\|__________\|\n5'-AAG...CCAAA__________AAGAA...CGC-3'\n______________CAAGAAGCGC\n______________\|\|\|\|\|\|\|\|:\|\n______________GUUCUUCGUG\n3'-UUU...AAUUC__________AAUUU...CAA-5'\n_____________\|__________\|\n_____________47_________36\n	222 -- 228	37 -- 43	-15.2794 kcal/mol	1.54243 kcal/mol	5.21654 kcal/mol	218 229@LB@ \| \|@LB@5'-AAG...CCAAA AAGAA...CGC-3'@LB@ CAAGAAGCGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ GUUCUUCGUG@LB@3'-UUU...AAUUC AAUUU...CAA-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -8.52 kcal/mol@LB@Hybridization Energy -15.2794 kcal/mol@LB@Unfolding Energy - mRNA 1.54243 kcal/mol@LB@Unfolding Energy - sRNA 5.21654 kcal/mol@LB@@LB@Position - mRNA 219 -- 228@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 37 -- 43@LB@
5	2.271e-05	0.01463	b0476	aes	-9.47	0.023317	2 -- 45	10 -- 53	acetyl esterase	_____________1______________________________________________46\n_____________\|______________________________________________\|\n__________5'-C_____CG_________AUGUUU_____UA_________________UCAUG...CAA-3'\n______________GUUUA___GGGAAGUA______GGAUU__CGUU_UACCGGGAAAUU\n______________\|:\|\|\|___::\|\|\|\|:\|______::\|\|\|__\|\|\|\|_:\|\|\|:\|\|\|\|\|\|:\n______________CGAAU___UUCUUCGU______UUUAA__GCAA_GUGGUCCUUUAG\n3'-UUU...UUGAA_____UCG________GAAUUU___________U____________ACUAC...CAA-5'\n_____________\|______________________________________________\|\n_____________54_____________________________________________9\n	39 -- 45	10 -- 16	-31.5647 kcal/mol	8.26599 kcal/mol	13.8307 kcal/mol	1 46@LB@ \| \|@LB@ 5'-C CG AUGUUU UA UCAUG...CAA-3'@LB@ GUUUA GGGAAGUA GGAUU CGUU UACCGGGAAAUU@LB@ \|:\|\|\| ::\|\|\|\|:\| ::\|\|\| \|\|\|\| :\|\|\|:\|\|\|\|\|\|:@LB@ CGAAU UUCUUCGU UUUAA GCAA GUGGUCCUUUAG@LB@3'-UUU...UUGAA UCG GAAUUU U ACUAC...CAA-5'@LB@ \| \|@LB@ 54 9@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -31.5647 kcal/mol@LB@Unfolding Energy - mRNA 8.26599 kcal/mol@LB@Unfolding Energy - sRNA 13.8307 kcal/mol@LB@@LB@Position - mRNA 2 -- 45@LB@Position - sRNA 10 -- 53@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 10 -- 16@LB@
113	0.009602	0.2693	b3237	argR	-14.05	0.000763	205 -- 250	27 -- 60	l-arginine-responsive arginine metabolism regulon transcriptional regulator	_____________204_____________________________________________251\n_____________\|_______________________________________________\|\n5'-ACA...UAUGC______CG____________AGAACUAGUUAA___________C___ACUUA...UGC-3'\n______________GAAGCU__GC_UAAGCAAGA____________AGCAUUUAAAG_AUU\n______________\|\|\|:\|\|__\|\|_\|\|\|\|\|\|\|\|\|____________\|\|\|\|:\|\|\|\|\|:_\|\|\|\n______________CUUUGA__CG_AUUCGUUCU____________UCGUGAAUUUU_UAA\n3'-UUU...CCCUA______A___A________________________________U___GCAAU...CAA-5'\n_____________\|_______________________________________________\|\n_____________61______________________________________________26\n	238 -- 244	33 -- 39	-28.1986 kcal/mol	7.87477 kcal/mol	6.27096 kcal/mol	204 251@LB@ \| \|@LB@5'-ACA...UAUGC CG AGAACUAGUUAA C ACUUA...UGC-3'@LB@ GAAGCU GC UAAGCAAGA AGCAUUUAAAG AUU@LB@ \|\|\|:\|\| \|\| \|\|\|\|\|\|\|\|\| \|\|\|\|:\|\|\|\|\|: \|\|\|@LB@ CUUUGA CG AUUCGUUCU UCGUGAAUUUU UAA@LB@3'-UUU...CCCUA A A U GCAAU...CAA-5'@LB@ \| \|@LB@ 61 26@LB@@LB@@LB@Energy -14.05 kcal/mol@LB@Hybridization Energy -28.1986 kcal/mol@LB@Unfolding Energy - mRNA 7.87477 kcal/mol@LB@Unfolding Energy - sRNA 6.27096 kcal/mol@LB@@LB@Position - mRNA 205 -- 250@LB@Position - sRNA 27 -- 60@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 33 -- 39@LB@
53	0.002646	0.1597	b1704	aroH	-6.03	0.190589	111 -- 120	31 -- 40	3-deoxy-D-arabino-heptulosonate-7-phosphate synthase tryptophan repressible	_____________110________121\n_____________\|__________\|\n5'-CCA...ACCUC__________UCAGC...CCC-3'\n______________GCACUUGAAA\n______________\|\|\|\|\|\|:\|\|\|\n______________CGUGAAUUUU\n3'-UUU...UUCUU__________UUAAG...CAA-5'\n_____________\|__________\|\n_____________41_________30\n	114 -- 120	31 -- 37	-11.574 kcal/mol	3.92769 kcal/mol	1.61955 kcal/mol	110 121@LB@ \| \|@LB@5'-CCA...ACCUC UCAGC...CCC-3'@LB@ GCACUUGAAA@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CGUGAAUUUU@LB@3'-UUU...UUCUU UUAAG...CAA-5'@LB@ \| \|@LB@ 41 30@LB@@LB@@LB@Energy -6.03 kcal/mol@LB@Hybridization Energy -11.574 kcal/mol@LB@Unfolding Energy - mRNA 3.92769 kcal/mol@LB@Unfolding Energy - sRNA 1.61955 kcal/mol@LB@@LB@Position - mRNA 111 -- 120@LB@Position - sRNA 31 -- 40@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 31 -- 37@LB@
131	0.01234	0.3033	b4139	aspA	-5.03	0.315570	237 -- 252	26 -- 41	aspartate ammonia-lyase	_____________236______________253\n_____________\|________________\|\n5'-GAU...UGUUG_____CA_________CAGCU...ACU-3'\n______________GGUAC__GGGAAGUUC\n______________:\|:\|\|__:::\|\|:\|\|\|\n______________UCGUG__UUUUUUAAG\n3'-UUU...GUUCU_____AA_________CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	246 -- 252	26 -- 32	-10.8102 kcal/mol	4.127 kcal/mol	1.64829 kcal/mol	236 253@LB@ \| \|@LB@5'-GAU...UGUUG CA CAGCU...ACU-3'@LB@ GGUAC GGGAAGUUC@LB@ :\|:\|\| :::\|\|:\|\|\|@LB@ UCGUG UUUUUUAAG@LB@3'-UUU...GUUCU AA CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -5.03 kcal/mol@LB@Hybridization Energy -10.8102 kcal/mol@LB@Unfolding Energy - mRNA 4.127 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 237 -- 252@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 26 -- 32@LB@
200	0.02417	0.3893	b1747	astA	-6.36	0.159223	49 -- 56	39 -- 46	arginine succinyltransferase	_____________48_______57\n_____________\|________\|\n5'-GGC...UCUCU________GGCGA...AAG-3'\n______________CAGGAAGC\n______________\|\|:\|\|\|\|\|\n______________GUUCUUCG\n3'-UUU...AAUUC________UGAAU...CAA-5'\n_____________\|________\|\n_____________47_______38\n	50 -- 56	39 -- 45	-10.5455 kcal/mol	1.56403 kcal/mol	2.62555 kcal/mol	48 57@LB@ \| \|@LB@5'-GGC...UCUCU GGCGA...AAG-3'@LB@ CAGGAAGC@LB@ \|\|:\|\|\|\|\|@LB@ GUUCUUCG@LB@3'-UUU...AAUUC UGAAU...CAA-5'@LB@ \| \|@LB@ 47 38@LB@@LB@@LB@Energy -6.36 kcal/mol@LB@Hybridization Energy -10.5455 kcal/mol@LB@Unfolding Energy - mRNA 1.56403 kcal/mol@LB@Unfolding Energy - sRNA 2.62555 kcal/mol@LB@@LB@Position - mRNA 49 -- 56@LB@Position - sRNA 39 -- 46@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 39 -- 45@LB@
100	0.007523	0.2423	b1744	astE	-9.81	0.018546	117 -- 135	36 -- 53	succinylglutamate desuccinylase	_____________116_________________136\n_____________\|___________________\|\n5'-GGU...GCUGC__GAA______________GGAUG...UGC-3'\n______________GC___GGGCGGGAAGCACU\n______________\|\|___::\|\|::\|\|\|\|\|\|\|\|\n______________CG___UUCGUUCUUCGUGA\n3'-UUU...UUGAA__AA_______________AUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________35\n	129 -- 135	36 -- 42	-22.0517 kcal/mol	6.14291 kcal/mol	6.10238 kcal/mol	116 136@LB@ \| \|@LB@5'-GGU...GCUGC GAA GGAUG...UGC-3'@LB@ GC GGGCGGGAAGCACU@LB@ \|\| ::\|\|::\|\|\|\|\|\|\|\|@LB@ CG UUCGUUCUUCGUGA@LB@3'-UUU...UUGAA AA AUUUU...CAA-5'@LB@ \| \|@LB@ 54 35@LB@@LB@@LB@Energy -9.81 kcal/mol@LB@Hybridization Energy -22.0517 kcal/mol@LB@Unfolding Energy - mRNA 6.14291 kcal/mol@LB@Unfolding Energy - sRNA 6.10238 kcal/mol@LB@@LB@Position - mRNA 117 -- 135@LB@Position - sRNA 36 -- 53@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 36 -- 42@LB@
37	0.00139	0.121	b2222	atoA	-4.53	0.397320	265 -- 276	25 -- 38	acetyl-CoA:acetoacetyl-CoA transferase beta subunit	_____________264____________277\n_____________\|______________\|\n5'-CGC...CGUUA______________GUUUA...AUU-3'\n______________ACUUAGGGA__UCG\n______________\|\|\|\|\|:::\|__\|\|\|\n______________UGAAUUUUU__AGC\n3'-UUU...CUUCG_________UA___AAUGU...CAA-5'\n_____________\|______________\|\n_____________39_____________24\n	266 -- 272	31 -- 37	-7.73128 kcal/mol	1.76584 kcal/mol	1.4343 kcal/mol	264 277@LB@ \| \|@LB@5'-CGC...CGUUA GUUUA...AUU-3'@LB@ ACUUAGGGA UCG@LB@ \|\|\|\|\|:::\| \|\|\|@LB@ UGAAUUUUU AGC@LB@3'-UUU...CUUCG UA AAUGU...CAA-5'@LB@ \| \|@LB@ 39 24@LB@@LB@@LB@Energy -4.53 kcal/mol@LB@Hybridization Energy -7.73128 kcal/mol@LB@Unfolding Energy - mRNA 1.76584 kcal/mol@LB@Unfolding Energy - sRNA 1.4343 kcal/mol@LB@@LB@Position - mRNA 265 -- 276@LB@Position - sRNA 25 -- 38@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 31 -- 37@LB@
150	0.01547	0.3321	b3736	atpF	-5.86	0.208717	262 -- 272	37 -- 47	F0 sector of membrane-bound ATP synthase subunit b	_____________261_________273\n_____________\|___________\|\n5'-AUU...GUUCU___U_______GUAUG...UCG-3'\n______________GCA_GAAGUAC\n______________\|\|\|_\|\|\|\|:\|\|\n______________CGU_CUUCGUG\n3'-UUU...GAAUU___U_______AAUUU...CAA-5'\n_____________\|___________\|\n_____________48__________36\n	266 -- 272	37 -- 43	-12.6044 kcal/mol	1.50868 kcal/mol	5.23944 kcal/mol	261 273@LB@ \| \|@LB@5'-AUU...GUUCU U GUAUG...UCG-3'@LB@ GCA GAAGUAC@LB@ \|\|\| \|\|\|\|:\|\|@LB@ CGU CUUCGUG@LB@3'-UUU...GAAUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -5.86 kcal/mol@LB@Hybridization Energy -12.6044 kcal/mol@LB@Unfolding Energy - mRNA 1.50868 kcal/mol@LB@Unfolding Energy - sRNA 5.23944 kcal/mol@LB@@LB@Position - mRNA 262 -- 272@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 37 -- 43@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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