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
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@
137	0.006165	0.1512	b1024	pgaA	-6.60	0.530802	267 -- 274	1 -- 8	biofilm adhesin polysaccharide PGA secretin; OM porin; poly-beta-1 6-N-acetyl-D-glucosamine export protein	_____________266______275\n_____________\|________\|\n5'-CUC...CCGCA________AGCGA...CUG-3'\n______________UUUUUAGC\n______________\|\|\|\|:\|\|\|\n______________AAAAGUCG\n3'-UUU...AUACA________-5'\n_____________\|_______\|\n_____________9_______1\n	268 -- 274	1 -- 7	-8.19691 kcal/mol	0.802454 kcal/mol	0.799201 kcal/mol	266 275@LB@ \| \|@LB@5'-CUC...CCGCA AGCGA...CUG-3'@LB@ UUUUUAGC@LB@ \|\|\|\|:\|\|\|@LB@ AAAAGUCG@LB@3'-UUU...AUACA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.60 kcal/mol@LB@Hybridization Energy -8.19691 kcal/mol@LB@Unfolding Energy - mRNA 0.802454 kcal/mol@LB@Unfolding Energy - sRNA 0.799201 kcal/mol@LB@@LB@Position - mRNA 267 -- 274@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 1 -- 7@LB@
92	0.00311	0.1126	b1042	csgA	-13.02	0.037954	257 -- 281	29 -- 49	curlin subunit amyloid curli fibers cryptic	_____________256_______________________282\n_____________\|_________________________\|\n5'-CAA...GCUCU__C_____UU______CA_______GGCGG...GUG-3'\n______________GG_AGGUG__GUUCCU__GUACGGC\n______________\|\|_\|\|\|\|\|__\|\|\|\|\|\|__\|\|\|\|:\|\|\n______________CC_UCCAC__CAAGGA__CAUGUCG\n3'-UUU...CGAUU________________C________AUCGU...UCG-5'\n_____________\|_________________________\|\n_____________50________________________28\n	275 -- 281	29 -- 35	-27.0821 kcal/mol	9.75964 kcal/mol	4.30143 kcal/mol	256 282@LB@ \| \|@LB@5'-CAA...GCUCU C UU CA GGCGG...GUG-3'@LB@ GG AGGUG GUUCCU GUACGGC@LB@ \|\| \|\|\|\|\| \|\|\|\|\|\| \|\|\|\|:\|\|@LB@ CC UCCAC CAAGGA CAUGUCG@LB@3'-UUU...CGAUU C AUCGU...UCG-5'@LB@ \| \|@LB@ 50 28@LB@@LB@@LB@Energy -13.02 kcal/mol@LB@Hybridization Energy -27.0821 kcal/mol@LB@Unfolding Energy - mRNA 9.75964 kcal/mol@LB@Unfolding Energy - sRNA 4.30143 kcal/mol@LB@@LB@Position - mRNA 257 -- 281@LB@Position - sRNA 29 -- 49@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 29 -- 35@LB@
138	0.006247	0.1521	b1063	yceB	-7.15	0.457702	84 -- 117	1 -- 32	lipoprotein DUF1439 family	_____________83__________________________________118\n_____________\|___________________________________\|\n5'-UGC...CGCGG____CU_____CGC_______CCGCCG________UUUUU...ACC-3'\n______________CAGC__GUAUU____GGGUUG______UUUUCAGU\n______________\|\|\|\|__\|:\|\|\|____\|\|\|\|\|:______\|\|\|\|\|\|\|:\n______________GUCG__CGUAA____CCCAAU______AAAAGUCG\n3'-UUU...ACCAU____AU_____AAUA______ACA___________-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	111 -- 117	1 -- 7	-22.6034 kcal/mol	13.9644 kcal/mol	1.49075 kcal/mol	83 118@LB@ \| \|@LB@5'-UGC...CGCGG CU CGC CCGCCG UUUUU...ACC-3'@LB@ CAGC GUAUU GGGUUG UUUUCAGU@LB@ \|\|\|\| \|:\|\|\| \|\|\|\|\|: \|\|\|\|\|\|\|:@LB@ GUCG CGUAA CCCAAU AAAAGUCG@LB@3'-UUU...ACCAU AU AAUA ACA -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -22.6034 kcal/mol@LB@Unfolding Energy - mRNA 13.9644 kcal/mol@LB@Unfolding Energy - sRNA 1.49075 kcal/mol@LB@@LB@Position - mRNA 84 -- 117@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 1 -- 7@LB@
86	0.002806	0.1082	b1107	nagZ	-13.13	0.035629	98 -- 119	25 -- 47	beta N-acetyl-glucosaminidase	_____________97______________________120\n_____________\|_______________________\|\n5'-AUU...AAGCA_________GA_____C______GACAA...CGC-3'\n______________GGGUGGUUU___GUAC_GCUGGC\n______________:\|\|\|\|\|\|\|:___\|\|\|\|_\|\|\|:\|\|\n______________UCCACCAAG___CAUG_CGAUCG\n3'-UUU...AUUCC_________GAC____U______UAAAA...UCG-5'\n_____________\|_______________________\|\n_____________48______________________24\n	100 -- 106	39 -- 45	-29.3426 kcal/mol	11.6523 kcal/mol	4.55753 kcal/mol	97 120@LB@ \| \|@LB@5'-AUU...AAGCA GA C GACAA...CGC-3'@LB@ GGGUGGUUU GUAC GCUGGC@LB@ :\|\|\|\|\|\|\|: \|\|\|\| \|\|\|:\|\|@LB@ UCCACCAAG CAUG CGAUCG@LB@3'-UUU...AUUCC GAC U UAAAA...UCG-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -29.3426 kcal/mol@LB@Unfolding Energy - mRNA 11.6523 kcal/mol@LB@Unfolding Energy - sRNA 4.55753 kcal/mol@LB@@LB@Position - mRNA 98 -- 119@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 39 -- 45@LB@
118	0.00496	0.1407	b1128	roxA	-15.27	0.009267	80 -- 105	22 -- 49	50S ribosomal protein L16 arginine hydroxylase; 2-oxoglutarate oxygenase	_____________79___________________________106\n_____________\|____________________________\|\n5'-UGG...CGGAU_______A_____________C______CUGCG...ACC-3'\n______________GGAGGUG_UUUUUGGU_C_GC_AGCAUU\n______________\|\|\|\|\|\|\|_\|\|::\|\|\|\|_\|_\|\|_\|\|\|\|\|\|\n______________CCUCCAC_AAGGACCA_G_CG_UCGUAA\n3'-UUU...CGAUU_______C________U_U__A______AAUAC...UCG-5'\n_____________\|____________________________\|\n_____________50___________________________21\n	80 -- 86	43 -- 49	-30.554 kcal/mol	10.7239 kcal/mol	4.55979 kcal/mol	79 106@LB@ \| \|@LB@5'-UGG...CGGAU A C CUGCG...ACC-3'@LB@ GGAGGUG UUUUUGGU C GC AGCAUU@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\| \| \|\| \|\|\|\|\|\|@LB@ CCUCCAC AAGGACCA G CG UCGUAA@LB@3'-UUU...CGAUU C U U A AAUAC...UCG-5'@LB@ \| \|@LB@ 50 21@LB@@LB@@LB@Energy -15.27 kcal/mol@LB@Hybridization Energy -30.554 kcal/mol@LB@Unfolding Energy - mRNA 10.7239 kcal/mol@LB@Unfolding Energy - sRNA 4.55979 kcal/mol@LB@@LB@Position - mRNA 80 -- 105@LB@Position - sRNA 22 -- 49@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 43 -- 49@LB@
14	9.306e-05	0.02121	b1205	ychH	-11.92	0.068307	242 -- 277	15 -- 49	DUF2583 family putative inner membrane protein	_____________241____________________________________278\n_____________\|______________________________________\|\n5'-CAA...CUCAU____U___G________GUAAU_G____CGGC______GUAUU...UAC-3'\n______________GGGG_UGG__UCUGGUG_____G_UGGU_____GUGGG\n______________\|\|:\|_\|\|\|__:\|\|\|\|\|:_____\|_\|:\|:_____:\|\|\|\|\n______________CCUC_ACC__GGACCAU_____C_AUCG_____UACCC\n3'-UUU...CGAUU____C___AA_______GU____G____UAAAA_____AAUAC...UCG-5'\n_____________\|______________________________________\|\n_____________50_____________________________________14\n	251 -- 257	33 -- 39	-28.7764 kcal/mol	12.2787 kcal/mol	4.57366 kcal/mol	241 278@LB@ \| \|@LB@5'-CAA...CUCAU U G GUAAU G CGGC GUAUU...UAC-3'@LB@ GGGG UGG UCUGGUG G UGGU GUGGG@LB@ \|\|:\| \|\|\| :\|\|\|\|\|: \| \|:\|: :\|\|\|\|@LB@ CCUC ACC GGACCAU C AUCG UACCC@LB@3'-UUU...CGAUU C AA GU G UAAAA AAUAC...UCG-5'@LB@ \| \|@LB@ 50 14@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -28.7764 kcal/mol@LB@Unfolding Energy - mRNA 12.2787 kcal/mol@LB@Unfolding Energy - sRNA 4.57366 kcal/mol@LB@@LB@Position - mRNA 242 -- 277@LB@Position - sRNA 15 -- 49@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 33 -- 39@LB@
63	0.00172	0.09016	b1209	lolB	-15.80	0.006355	144 -- 167	11 -- 36	lipoprotein localization factor	_____________143________________________168\n_____________\|__________________________\|\n5'-AAU...CGGAC____AC_________AA_________AACUG...GCC-3'\n______________GGUA__GCUAGCAUU____GGGUUAU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\n______________CCAU__CGAUCGUAA____CCCAAUA\n3'-UUU...AAGGA____GU_________AAUA_______CAAAA...UCG-5'\n_____________\|__________________________\|\n_____________37_________________________10\n	161 -- 167	11 -- 17	-25.6291 kcal/mol	8.35909 kcal/mol	1.47376 kcal/mol	143 168@LB@ \| \|@LB@5'-AAU...CGGAC AC AA AACUG...GCC-3'@LB@ GGUA GCUAGCAUU GGGUUAU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CCAU CGAUCGUAA CCCAAUA@LB@3'-UUU...AAGGA GU AAUA CAAAA...UCG-5'@LB@ \| \|@LB@ 37 10@LB@@LB@@LB@Energy -15.80 kcal/mol@LB@Hybridization Energy -25.6291 kcal/mol@LB@Unfolding Energy - mRNA 8.35909 kcal/mol@LB@Unfolding Energy - sRNA 1.47376 kcal/mol@LB@@LB@Position - mRNA 144 -- 167@LB@Position - sRNA 11 -- 36@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 11 -- 17@LB@
6	7.051e-06	0.00395	b1213	ychQ	-11.22	0.096653	74 -- 98	15 -- 40	SIRB family inner membrane protein	_____________73___________________________99\n_____________\|____________________________\|\n5'-GAC...UCUGC______AAC__________GCA______CGAAG...AUC-3'\n______________UUCUGG___AUGGCUGGCA______GGG\n______________\|:\|\|\|\|___\|::\|\|\|:\|\|\|______\|\|\|\n______________AGGACC___UGUCGAUCGU______CCC\n3'-UUU...CACCA______A____________AAAAUA___AAUAC...UCG-5'\n_____________\|____________________________\|\n_____________41___________________________14\n	86 -- 92	24 -- 30	-24.2509 kcal/mol	8.46179 kcal/mol	4.56973 kcal/mol	73 99@LB@ \| \|@LB@5'-GAC...UCUGC AAC GCA CGAAG...AUC-3'@LB@ UUCUGG AUGGCUGGCA GGG@LB@ \|:\|\|\|\| \|::\|\|\|:\|\|\| \|\|\|@LB@ AGGACC UGUCGAUCGU CCC@LB@3'-UUU...CACCA A AAAAUA AAUAC...UCG-5'@LB@ \| \|@LB@ 41 14@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -24.2509 kcal/mol@LB@Unfolding Energy - mRNA 8.46179 kcal/mol@LB@Unfolding Energy - sRNA 4.56973 kcal/mol@LB@@LB@Position - mRNA 74 -- 98@LB@Position - sRNA 15 -- 40@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 24 -- 30@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@

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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