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
169	0.009174	0.1803	b1467	narY	-12.55	0.049142	183 -- 194	25 -- 36	nitrate reductase 2 (NRZ) beta subunit	_____________182__________195\n_____________\|____________\|\n5'-CGC...GAUCA_______GA___GAAAA...GCG-3'\n______________GGUACAG__GGC\n______________\|\|\|\|\|\|\|__:\|\|\n______________CCAUGUC__UCG\n3'-UUU...AAGGA_______GA___UAAAA...UCG-5'\n_____________\|____________\|\n_____________37___________24\n	183 -- 189	30 -- 36	-16.0252 kcal/mol	2.04549 kcal/mol	1.42738 kcal/mol	182 195@LB@ \| \|@LB@5'-CGC...GAUCA GA GAAAA...GCG-3'@LB@ GGUACAG GGC@LB@ \|\|\|\|\|\|\| :\|\|@LB@ CCAUGUC UCG@LB@3'-UUU...AAGGA GA UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -16.0252 kcal/mol@LB@Unfolding Energy - mRNA 2.04549 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 30 -- 36@LB@
76	0.002251	0.09621	b0020	nhaR	-13.73	0.025158	90 -- 112	25 -- 46	transcriptional activator of nhaA	_____________89______________________113\n_____________\|_______________________\|\n5'-AUC...UCUUC__C___AA____A__________UACGC...CUC-3'\n______________GG_GGU__UUGG_UACAGCUGGU\n______________\|\|_\|\|\|__:\|\|\|_\|\|\|\|\|\|\|:\|:\n______________CC_CCA__GACC_AUGUCGAUCG\n3'-UUU...UUCCU__A___AG_______________UAAAA...UCG-5'\n_____________\|_______________________\|\n_____________47______________________24\n	106 -- 112	25 -- 31	-27.2836 kcal/mol	8.99906 kcal/mol	4.55673 kcal/mol	89 113@LB@ \| \|@LB@5'-AUC...UCUUC C AA A UACGC...CUC-3'@LB@ GG GGU UUGG UACAGCUGGU@LB@ \|\| \|\|\| :\|\|\| \|\|\|\|\|\|\|:\|:@LB@ CC CCA GACC AUGUCGAUCG@LB@3'-UUU...UUCCU A AG UAAAA...UCG-5'@LB@ \| \|@LB@ 47 24@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -27.2836 kcal/mol@LB@Unfolding Energy - mRNA 8.99906 kcal/mol@LB@Unfolding Energy - sRNA 4.55673 kcal/mol@LB@@LB@Position - mRNA 90 -- 112@LB@Position - sRNA 25 -- 46@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 25 -- 31@LB@
96	0.003358	0.117	b3367	nirC	-13.97	0.021706	56 -- 81	6 -- 37	nitrite transporter	_____________55_________________________________82\n_____________\|__________________________________\|\n5'-AUG...CGGCG___________C______________A_______AACGG...UGG-3'\n______________UGGUGCAGCUG_GC________GGUU_AUGUUUU\n______________\|\|\|\|:\|\|\|\|\|:_\|\|________\|\|\|\|_\|\|\|\|\|\|\|\n______________ACCAUGUCGAU_CG________CCAA_UACAAAA\n3'-UUU...CAAGG______________UAAAAUAC____________AGUCG-5'\n_____________\|__________________________________\|\n_____________38_________________________________5\n	75 -- 81	6 -- 12	-26.6239 kcal/mol	9.95316 kcal/mol	2.70019 kcal/mol	55 82@LB@ \| \|@LB@5'-AUG...CGGCG C A AACGG...UGG-3'@LB@ UGGUGCAGCUG GC GGUU AUGUUUU@LB@ \|\|\|\|:\|\|\|\|\|: \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ ACCAUGUCGAU CG CCAA UACAAAA@LB@3'-UUU...CAAGG UAAAAUAC AGUCG-5'@LB@ \| \|@LB@ 38 5@LB@@LB@@LB@Energy -13.97 kcal/mol@LB@Hybridization Energy -26.6239 kcal/mol@LB@Unfolding Energy - mRNA 9.95316 kcal/mol@LB@Unfolding Energy - sRNA 2.70019 kcal/mol@LB@@LB@Position - mRNA 56 -- 81@LB@Position - sRNA 6 -- 37@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 6 -- 12@LB@
55	0.001331	0.08097	b2742	nlpD	-12.02	0.064935	253 -- 272	24 -- 44	activator of AmiC murein hydrolase activity lipoprotein	_____________252___________________273\n_____________\|_____________________\|\n5'-UAU...GUCAC_______GC____________GGCUG...CGG-3'\n______________UGGUUUC___UAUGGCUGGCA\n______________\|\|\|\|\|:\|___\|\|::\|\|\|:\|\|\|\n______________ACCAAGG___AUGUCGAUCGU\n3'-UUU...CCUCC_______ACC___________AAAAU...UCG-5'\n_____________\|_____________________\|\n_____________45____________________23\n	266 -- 272	24 -- 30	-23.7485 kcal/mol	7.16759 kcal/mol	4.55788 kcal/mol	252 273@LB@ \| \|@LB@5'-UAU...GUCAC GC GGCUG...CGG-3'@LB@ UGGUUUC UAUGGCUGGCA@LB@ \|\|\|\|\|:\| \|\|::\|\|\|:\|\|\|@LB@ ACCAAGG AUGUCGAUCGU@LB@3'-UUU...CCUCC ACC AAAAU...UCG-5'@LB@ \| \|@LB@ 45 23@LB@@LB@@LB@Energy -12.02 kcal/mol@LB@Hybridization Energy -23.7485 kcal/mol@LB@Unfolding Energy - mRNA 7.16759 kcal/mol@LB@Unfolding Energy - sRNA 4.55788 kcal/mol@LB@@LB@Position - mRNA 253 -- 272@LB@Position - sRNA 24 -- 44@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 24 -- 30@LB@
11	3.883e-05	0.01168	b4074	nrfE	-17.71	0.001322	131 -- 144	35 -- 48	heme lyase (NrfEFG) for insertion of heme into c552 subunit NrfE	_____________130____________145\n_____________\|______________\|\n5'-ACC...GAAAA______________ACGUA...UGC-3'\n______________GAGGUGGUUUCUGG\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\|\n______________CUCCACCAAGGACC\n3'-UUU...GAUUC______________AUGUC...UCG-5'\n_____________\|______________\|\n_____________49_____________34\n	138 -- 144	35 -- 41	-26.5218 kcal/mol	5.67902 kcal/mol	3.13693 kcal/mol	130 145@LB@ \| \|@LB@5'-ACC...GAAAA ACGUA...UGC-3'@LB@ GAGGUGGUUUCUGG@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|\|@LB@ CUCCACCAAGGACC@LB@3'-UUU...GAUUC AUGUC...UCG-5'@LB@ \| \|@LB@ 49 34@LB@@LB@@LB@Energy -17.71 kcal/mol@LB@Hybridization Energy -26.5218 kcal/mol@LB@Unfolding Energy - mRNA 5.67902 kcal/mol@LB@Unfolding Energy - sRNA 3.13693 kcal/mol@LB@@LB@Position - mRNA 131 -- 144@LB@Position - sRNA 35 -- 48@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 35 -- 41@LB@
165	0.008583	0.1748	b4075	nrfF	-7.99	0.354712	71 -- 77	63 -- 69	heme lyase (NrfEFG) for insertion of heme into c552 subunit NrfF	_____________70______78\n_____________\|_______\|\n5'-AGC...UCAUG_______AAACU...AAC-3'\n______________GGGGAGA\n______________:\|\|\|\|\|\|\n______________UCCCUCU\n3'-UUU...CACAU_______AAUGU...UCG-5'\n_____________\|_______\|\n_____________70______62\n	71 -- 77	63 -- 69	-11.2965 kcal/mol	2.37125 kcal/mol	0.939295 kcal/mol	70 78@LB@ \| \|@LB@5'-AGC...UCAUG AAACU...AAC-3'@LB@ GGGGAGA@LB@ :\|\|\|\|\|\|@LB@ UCCCUCU@LB@3'-UUU...CACAU AAUGU...UCG-5'@LB@ \| \|@LB@ 70 62@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -11.2965 kcal/mol@LB@Unfolding Energy - mRNA 2.37125 kcal/mol@LB@Unfolding Energy - sRNA 0.939295 kcal/mol@LB@@LB@Position - mRNA 71 -- 77@LB@Position - sRNA 63 -- 69@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 63 -- 69@LB@
23	0.0002818	0.04118	b1813	nudL	-13.86	0.023273	1 -- 17	22 -- 39	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase	______________1_________________18\n______________\|_________________\|\n___________5'-__________________GGCUA...CUG-3'\n______________CCUGGUGCGGC_AGCAUU\n______________\|\|\|\|\|\|:\|:\|\|_\|\|\|\|\|\|\n______________GGACCAUGUCG_UCGUAA\n3'-UUU...ACCAA___________A______AAUAC...UCG-5'\n_____________\|__________________\|\n_____________40_________________21\n	5 -- 11	29 -- 35	-27.845 kcal/mol	9.43444 kcal/mol	4.55392 kcal/mol	1 18@LB@ \| \|@LB@ 5'- GGCUA...CUG-3'@LB@ CCUGGUGCGGC AGCAUU@LB@ \|\|\|\|\|\|:\|:\|\| \|\|\|\|\|\|@LB@ GGACCAUGUCG UCGUAA@LB@3'-UUU...ACCAA A AAUAC...UCG-5'@LB@ \| \|@LB@ 40 21@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -27.845 kcal/mol@LB@Unfolding Energy - mRNA 9.43444 kcal/mol@LB@Unfolding Energy - sRNA 4.55392 kcal/mol@LB@@LB@Position - mRNA 1 -- 17@LB@Position - sRNA 22 -- 39@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 29 -- 35@LB@
100	0.003656	0.1229	b2287	nuoB	-12.04	0.064387	31 -- 70	8 -- 47	NADH:ubiquinone oxidoreductase chain B	_____________30___________________________________________71\n_____________\|____________________________________________\|\n5'-CAU...CGGCU____A__C___G___A__________AU______UU________ACUGG...UUA-3'\n______________GGGU_GG_UUU_UGG___AGCU_GCA__UUUUAU___UUGUGUU\n______________:\|\|\|_\|\|_\|\|:_\|\|\|___\|\|\|\|_\|\|\|__\|\|\|\|\|\|___\|\|:\|\|\|\|\n______________UCCA_CC_AAG_ACC___UCGA_CGU__AAAAUA___AAUACAA\n3'-UUU...AUUCC___________G___AUG____U___________CCC_______AAAGUCG-5'\n_____________\|____________________________________________\|\n_____________48___________________________________________7\n	64 -- 70	8 -- 14	-25.7516 kcal/mol	9.10307 kcal/mol	4.60908 kcal/mol	30 71@LB@ \| \|@LB@5'-CAU...CGGCU A C G A AU UU ACUGG...UUA-3'@LB@ GGGU GG UUU UGG AGCU GCA UUUUAU UUGUGUU@LB@ :\|\|\| \|\| \|\|: \|\|\| \|\|\|\| \|\|\| \|\|\|\|\|\| \|\|:\|\|\|\|@LB@ UCCA CC AAG ACC UCGA CGU AAAAUA AAUACAA@LB@3'-UUU...AUUCC G AUG U CCC AAAGUCG-5'@LB@ \| \|@LB@ 48 7@LB@@LB@@LB@Energy -12.04 kcal/mol@LB@Hybridization Energy -25.7516 kcal/mol@LB@Unfolding Energy - mRNA 9.10307 kcal/mol@LB@Unfolding Energy - sRNA 4.60908 kcal/mol@LB@@LB@Position - mRNA 31 -- 70@LB@Position - sRNA 8 -- 47@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 8 -- 14@LB@
116	0.004845	0.1404	b2277	nuoM	-9.49	0.205960	1 -- 40	8 -- 43	NADH:ubiquinone oxidoreductase membrane subunit M	______________1___________________________________________41\n______________\|___________________________________________\|\n___________5'-_____G______________CUGUUG____UACUGC____A___AAGGA...UGA-3'\n______________GG_UC_UGGU___GCUGGCA______AUGG______GUUG_GUU\n______________\|\|_\|\|_\|\|\|\|___\|\|\|:\|\|\|______\|\|\|\|______\|\|\|:_\|\|\|\n______________CC_AG_ACCA___CGAUCGU______UACC______CAAU_CAA\n3'-UUU...CUCCA__A__G____UGU_______AAAA________________A___AAAGUCG-5'\n_____________\|____________________________________________\|\n_____________44___________________________________________7\n	10 -- 16	24 -- 30	-25.9982 kcal/mol	11.9029 kcal/mol	4.60748 kcal/mol	1 41@LB@ \| \|@LB@ 5'- G CUGUUG UACUGC A AAGGA...UGA-3'@LB@ GG UC UGGU GCUGGCA AUGG GUUG GUU@LB@ \|\| \|\| \|\|\|\| \|\|\|:\|\|\| \|\|\|\| \|\|\|: \|\|\|@LB@ CC AG ACCA CGAUCGU UACC CAAU CAA@LB@3'-UUU...CUCCA A G UGU AAAA A AAAGUCG-5'@LB@ \| \|@LB@ 44 7@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -25.9982 kcal/mol@LB@Unfolding Energy - mRNA 11.9029 kcal/mol@LB@Unfolding Energy - sRNA 4.60748 kcal/mol@LB@@LB@Position - mRNA 1 -- 40@LB@Position - sRNA 8 -- 43@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 24 -- 30@LB@
125	0.005266	0.1416	b0957	ompA	-12.88	0.041122	280 -- 293	25 -- 39	outer membrane protein A (3a;II*;G;d)	_____________279_____________294\n_____________\|_______________\|\n5'-CUU...UAACA_______________GCUAAAC-3'\n______________CCUGGUACA_CUGGU\n______________\|\|\|\|\|\|\|\|\|_\|\|:\|:\n______________GGACCAUGU_GAUCG\n3'-UUU...ACCAA_________C_____UAAAA...UCG-5'\n_____________\|_______________\|\n_____________40______________24\n	282 -- 288	31 -- 37	-21.2564 kcal/mol	3.82713 kcal/mol	4.55153 kcal/mol	279 294@LB@ \| \|@LB@5'-CUU...UAACA GCUAAAC-3'@LB@ CCUGGUACA CUGGU@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|:@LB@ GGACCAUGU GAUCG@LB@3'-UUU...ACCAA C UAAAA...UCG-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -21.2564 kcal/mol@LB@Unfolding Energy - mRNA 3.82713 kcal/mol@LB@Unfolding Energy - sRNA 4.55153 kcal/mol@LB@@LB@Position - mRNA 280 -- 293@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 31 -- 37@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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