Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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	Additional homologs
161	0.009429	0.2062	b1372	stfR	-7.17	0.431291	283 -- 297	69 -- 83	Rac prophage; putative tail fiber protein	b1547	_____________282_____________298\n_____________\|_______________\|\n5'-CAC...AAAAC__AA________C__UGG-3'\n______________GU__CAGCACCA_GG\n______________\|:__\|\|:\|\|\|\|\|_\|\|\n______________CG__GUUGUGGU_CC\n3'-UUU...UAUGA__CG________C__UUUAG...GUG-5'\n_____________\|_______________\|\n_____________84______________68\n	288 -- 294	72 -- 78	-17.3245 kcal/mol	2.81769 kcal/mol	7.33837 kcal/mol	282 298@LB@ \| \|@LB@5'-CAC...AAAAC AA C UGG-3'@LB@ GU CAGCACCA GG@LB@ \|: \|\|:\|\|\|\|\| \|\|@LB@ CG GUUGUGGU CC@LB@3'-UUU...UAUGA CG C UUUAG...GUG-5'@LB@ \| \|@LB@ 84 68@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -17.3245 kcal/mol@LB@Unfolding Energy - mRNA 2.81769 kcal/mol@LB@Unfolding Energy - sRNA 7.33837 kcal/mol@LB@@LB@Position - mRNA 283 -- 297@LB@Position - sRNA 69 -- 83@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 72 -- 78@LB@
38	0.002093	0.1727	b1174	minE	-11.55	0.070176	37 -- 55	69 -- 87	cell division topological specificity factor		_____________36___________________56\n_____________\|____________________\|\n5'-AAC...AGUAU_________UCUA_______UGAAC...AUG-3'\n______________UGC_GCGCC____ACCAGGG\n______________\|:\|_\|\|\|\|\|____\|\|\|\|\|\|\|\n______________AUG_CGCGG____UGGUCCC\n3'-UUU...CGCUU___A_____UUG________UUUAG...GUG-5'\n_____________\|____________________\|\n_____________88___________________68\n	49 -- 55	69 -- 75	-25.7186 kcal/mol	6.79304 kcal/mol	7.3743 kcal/mol	36 56@LB@ \| \|@LB@5'-AAC...AGUAU UCUA UGAAC...AUG-3'@LB@ UGC GCGCC ACCAGGG@LB@ \|:\| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ AUG CGCGG UGGUCCC@LB@3'-UUU...CGCUU A UUG UUUAG...GUG-5'@LB@ \| \|@LB@ 88 68@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -25.7186 kcal/mol@LB@Unfolding Energy - mRNA 6.79304 kcal/mol@LB@Unfolding Energy - sRNA 7.3743 kcal/mol@LB@@LB@Position - mRNA 37 -- 55@LB@Position - sRNA 69 -- 87@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 69 -- 75@LB@
176	0.01044	0.208	b0933	ssuB	-9.69	0.158756	203 -- 226	69 -- 90	aliphatic sulfonate ABC transporter ATPase		_____________202______________________227\n_____________\|________________________\|\n5'-AUU...GGUAU_________UC___UGA_______CACGC...AUA-3'\n______________GAAUACUGC__GUC___ACCAGGG\n______________\|\|\|\|\|\|\|\|\|__\|:\|___\|\|\|\|\|\|\|\n______________CUUAUGACG__CGG___UGGUCCC\n3'-UUU...ACGCG______________UUG_______UUUAG...GUG-5'\n_____________\|________________________\|\n_____________91_______________________68\n	220 -- 226	69 -- 75	-28.101 kcal/mol	8.24441 kcal/mol	10.1628 kcal/mol	202 227@LB@ \| \|@LB@5'-AUU...GGUAU UC UGA CACGC...AUA-3'@LB@ GAAUACUGC GUC ACCAGGG@LB@ \|\|\|\|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|@LB@ CUUAUGACG CGG UGGUCCC@LB@3'-UUU...ACGCG UUG UUUAG...GUG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -28.101 kcal/mol@LB@Unfolding Energy - mRNA 8.24441 kcal/mol@LB@Unfolding Energy - sRNA 10.1628 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 69 -- 75@LB@
65	0.003263	0.1727	b2584	pka	-7.67	0.359085	49 -- 62	69 -- 82	protein lysine acetyltransferase		_____________48_____________63\n_____________\|______________\|\n5'-AGG...AUGGC__G___________CGGCG...GUA-3'\n______________CG_CGAUACCGGGG\n______________\|\|_\|:\|:\|\|\|:\|\|\|\n______________GC_GUUGUGGUCCC\n3'-UUU...AUGAC__G___________UUUAG...GUG-5'\n_____________\|______________\|\n_____________83_____________68\n	56 -- 62	69 -- 75	-21.7159 kcal/mol	7.18281 kcal/mol	6.85849 kcal/mol	48 63@LB@ \| \|@LB@5'-AGG...AUGGC G CGGCG...GUA-3'@LB@ CG CGAUACCGGGG@LB@ \|\| \|:\|:\|\|\|:\|\|\|@LB@ GC GUUGUGGUCCC@LB@3'-UUU...AUGAC G UUUAG...GUG-5'@LB@ \| \|@LB@ 83 68@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -21.7159 kcal/mol@LB@Unfolding Energy - mRNA 7.18281 kcal/mol@LB@Unfolding Energy - sRNA 6.85849 kcal/mol@LB@@LB@Position - mRNA 49 -- 62@LB@Position - sRNA 69 -- 82@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 69 -- 75@LB@
125	0.006795	0.1914	b3003	yghA	-11.52	0.071261	264 -- 274	70 -- 80	putative oxidoreductase	b2902	_____________263_________275\n_____________\|___________\|\n5'-AAC...AACAA___________CAUCC...UAC-3'\n______________CCGACGCCAGG\n______________\|\|:\|\|:\|\|\|\|\|\n______________GGUUGUGGUCC\n3'-UUU...GACGC___________CUUUA...GUG-5'\n_____________\|___________\|\n_____________81__________69\n	268 -- 274	70 -- 76	-20.3781 kcal/mol	2.1599 kcal/mol	6.70146 kcal/mol	263 275@LB@ \| \|@LB@5'-AAC...AACAA CAUCC...UAC-3'@LB@ CCGACGCCAGG@LB@ \|\|:\|\|:\|\|\|\|\|@LB@ GGUUGUGGUCC@LB@3'-UUU...GACGC CUUUA...GUG-5'@LB@ \| \|@LB@ 81 69@LB@@LB@@LB@Energy -11.52 kcal/mol@LB@Hybridization Energy -20.3781 kcal/mol@LB@Unfolding Energy - mRNA 2.1599 kcal/mol@LB@Unfolding Energy - sRNA 6.70146 kcal/mol@LB@@LB@Position - mRNA 264 -- 274@LB@Position - sRNA 70 -- 80@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 70 -- 76@LB@
17	0.0008046	0.1666	b0590	fepD	-14.87	0.015550	17 -- 43	70 -- 94	ferrienterobactin ABC transporter permease		_____________16__________________________44\n_____________\|___________________________\|\n5'-AAU...AACGA___AG___________GA_________UGCGU...AAU-3'\n______________GCG__GAAUACUGCGC__AACGCCGGG\n______________\|\|\|__\|\|\|\|\|\|\|\|\|\|\|__\|\|\|:\|\|:\|\|\n______________CGC__CUUAUGACGCG__UUGUGGUCC\n3'-UUU...CCCCA___G____________G__________CUUUA...GUG-5'\n_____________\|___________________________\|\n_____________95__________________________69\n	37 -- 43	70 -- 76	-38.1858 kcal/mol	10.2318 kcal/mol	13.036 kcal/mol	16 44@LB@ \| \|@LB@5'-AAU...AACGA AG GA UGCGU...AAU-3'@LB@ GCG GAAUACUGCGC AACGCCGGG@LB@ \|\|\| \|\|\|\|\|\|\|\|\|\|\| \|\|\|:\|\|:\|\|@LB@ CGC CUUAUGACGCG UUGUGGUCC@LB@3'-UUU...CCCCA G G CUUUA...GUG-5'@LB@ \| \|@LB@ 95 69@LB@@LB@@LB@Energy -14.87 kcal/mol@LB@Hybridization Energy -38.1858 kcal/mol@LB@Unfolding Energy - mRNA 10.2318 kcal/mol@LB@Unfolding Energy - sRNA 13.036 kcal/mol@LB@@LB@Position - mRNA 17 -- 43@LB@Position - sRNA 70 -- 94@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 70 -- 76@LB@
77	0.00398	0.182	b2411	ligA	-14.36	0.019662	79 -- 95	70 -- 86	DNA ligase NAD(+)-dependent		_____________78________________96\n_____________\|_________________\|\n5'-GCA...CAGAA_______G_________ACAUC...CUG-3'\n______________AUUGCGC_AGUACCAGG\n______________\|:\|\|\|\|\|_\|::\|\|\|\|\|\|\n______________UGACGCG_UUGUGGUCC\n3'-UUU...GCUUA_______G_________CUUUA...GUG-5'\n_____________\|_________________\|\n_____________87________________69\n	89 -- 95	70 -- 76	-25.4632 kcal/mol	3.82569 kcal/mol	7.27772 kcal/mol	78 96@LB@ \| \|@LB@5'-GCA...CAGAA G ACAUC...CUG-3'@LB@ AUUGCGC AGUACCAGG@LB@ \|:\|\|\|\|\| \|::\|\|\|\|\|\|@LB@ UGACGCG UUGUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -25.4632 kcal/mol@LB@Unfolding Energy - mRNA 3.82569 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 79 -- 95@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 70 -- 76@LB@
42	0.002147	0.1727	b0082	rsmH	-13.18	0.033634	23 -- 49	70 -- 94	16S rRNA m(4)C1402 methyltransferase SAM-dependent		_____________22__________________________50\n_____________\|___________________________\|\n5'-UGG...UAAUC____C_________G____AU______CUGAC...GUC-3'\n______________GCGC_AGUACUGCG_CAAC__GCCGGG\n______________\|\|\|\|_\|:\|\|\|\|\|\|\|_\|\|\|\|__:\|\|:\|\|\n______________CGCG_UUAUGACGC_GUUG__UGGUCC\n3'-UUU...CCCCA____C_________G____________CUUUA...GUG-5'\n_____________\|___________________________\|\n_____________95__________________________69\n	30 -- 36	81 -- 87	-36.7334 kcal/mol	10.4772 kcal/mol	13.036 kcal/mol	22 50@LB@ \| \|@LB@5'-UGG...UAAUC C G AU CUGAC...GUC-3'@LB@ GCGC AGUACUGCG CAAC GCCGGG@LB@ \|\|\|\| \|:\|\|\|\|\|\|\| \|\|\|\| :\|\|:\|\|@LB@ CGCG UUAUGACGC GUUG UGGUCC@LB@3'-UUU...CCCCA C G CUUUA...GUG-5'@LB@ \| \|@LB@ 95 69@LB@@LB@@LB@Energy -13.18 kcal/mol@LB@Hybridization Energy -36.7334 kcal/mol@LB@Unfolding Energy - mRNA 10.4772 kcal/mol@LB@Unfolding Energy - sRNA 13.036 kcal/mol@LB@@LB@Position - mRNA 23 -- 49@LB@Position - sRNA 70 -- 94@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 81 -- 87@LB@
89	0.004811	0.1855	b4336	yjiN	-13.14	0.034257	120 -- 134	70 -- 84	zinc-type alcohol dehydrogenase-like protein		_____________119_____________135\n_____________\|_______________\|\n5'-GGU...UCGCG_______________CAGCC...CCA-3'\n______________UGCGCCAGCAUCAGG\n______________\|\|\|\|\|\|\|:\|\|:\|\|\|\|\n______________ACGCGGUUGUGGUCC\n3'-UUU...UUAUG_______________CUUUA...GUG-5'\n_____________\|_______________\|\n_____________85______________69\n	128 -- 134	70 -- 76	-28.7852 kcal/mol	8.39668 kcal/mol	7.24859 kcal/mol	119 135@LB@ \| \|@LB@5'-GGU...UCGCG CAGCC...CCA-3'@LB@ UGCGCCAGCAUCAGG@LB@ \|\|\|\|\|\|\|:\|\|:\|\|\|\|@LB@ ACGCGGUUGUGGUCC@LB@3'-UUU...UUAUG CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -28.7852 kcal/mol@LB@Unfolding Energy - mRNA 8.39668 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 120 -- 134@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 70 -- 76@LB@
31	0.001682	0.1727	b1887	cheW	-12.93	0.037697	13 -- 28	70 -- 86	purine-binding chemotaxis protein		_____________12________________29\n_____________\|_________________\|\n5'-GUG...AAUUA_________________UUGUG...UCC-3'\n______________AUUG_GUCAACACCAGG\n______________\|:\|\|_\|:\|\|\|\|\|\|\|\|\|\|\n______________UGAC_CGGUUGUGGUCC\n3'-UUU...GCUUA____G____________CUUUA...GUG-5'\n_____________\|_________________\|\n_____________87________________69\n	22 -- 28	70 -- 76	-24.746 kcal/mol	4.53921 kcal/mol	7.27772 kcal/mol	12 29@LB@ \| \|@LB@5'-GUG...AAUUA UUGUG...UCC-3'@LB@ AUUG GUCAACACCAGG@LB@ \|:\|\| \|:\|\|\|\|\|\|\|\|\|\|@LB@ UGAC CGGUUGUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -12.93 kcal/mol@LB@Hybridization Energy -24.746 kcal/mol@LB@Unfolding Energy - mRNA 4.53921 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 13 -- 28@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 70 -- 76@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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