Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
105	0.004683	0.1538	b3349	slyD	-10.61	0.192215	166 -- 197	39 -- 73	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)		_____________165_________________________________198\n_____________\|___________________________________\|\n5'-UGU...ACAAU___________U____UUCCCAU________A___AUCAU...ACU-3'\n______________CUGCGC_CA_C_AUUC________GCUCAGG_GAU\n______________\|\|:\|:\|_\|\|_\|_\|\|\|\|________:\|\|\|\|\|\|_\|\|\|\n______________GAUGUG_GU_G_UAAG________UGAGUCC_CUA\n3'-UUU...UUUCU______U__C_U____CAACAAAG_______C___AAGGU...GCA-5'\n_____________\|___________________________________\|\n_____________74__________________________________38\n	187 -- 193	43 -- 49	-23.2642 kcal/mol	7.88699 kcal/mol	4.77295 kcal/mol	165 198@LB@ \| \|@LB@5'-UGU...ACAAU U UUCCCAU A AUCAU...ACU-3'@LB@ CUGCGC CA C AUUC GCUCAGG GAU@LB@ \|\|:\|:\| \|\| \| \|\|\|\| :\|\|\|\|\|\| \|\|\|@LB@ GAUGUG GU G UAAG UGAGUCC CUA@LB@3'-UUU...UUUCU U C U CAACAAAG C AAGGU...GCA-5'@LB@ \| \|@LB@ 74 38@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -23.2642 kcal/mol@LB@Unfolding Energy - mRNA 7.88699 kcal/mol@LB@Unfolding Energy - sRNA 4.77295 kcal/mol@LB@@LB@Position - mRNA 166 -- 197@LB@Position - sRNA 39 -- 73@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
132	0.005915	0.1577	b3356	yhfA	-11.83	0.112173	273 -- 293	39 -- 71	OsmC family protein		_____________272_______________________________294\n_____________\|_________________________________\|\n5'-CUG...UUUUA___G_________________________C___AAAGCAC-3'\n______________AUG_ACGGCA____________ACUCAGG_GAU\n______________\|::_\|\|:\|\|\|____________\|\|\|\|\|\|\|_\|\|\|\n______________UGU_UGUCGU____________UGAGUCC_CUA\n3'-UUU...UCUGA___G______UAAGCAACAAAG_______C___AAGGU...GCA-5'\n_____________\|_________________________________\|\n_____________72________________________________38\n	283 -- 289	43 -- 49	-20.9729 kcal/mol	4.393 kcal/mol	4.74947 kcal/mol	272 294@LB@ \| \|@LB@5'-CUG...UUUUA G C AAAGCAC-3'@LB@ AUG ACGGCA ACUCAGG GAU@LB@ \|:: \|\|:\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UGU UGUCGU UGAGUCC CUA@LB@3'-UUU...UCUGA G UAAGCAACAAAG C AAGGU...GCA-5'@LB@ \| \|@LB@ 72 38@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -20.9729 kcal/mol@LB@Unfolding Energy - mRNA 4.393 kcal/mol@LB@Unfolding Energy - sRNA 4.74947 kcal/mol@LB@@LB@Position - mRNA 273 -- 293@LB@Position - sRNA 39 -- 71@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 43 -- 49@LB@
160	0.007693	0.1668	b1671	ydhX	-11.21	0.148807	210 -- 235	39 -- 74	putative 4Fe-4S ferridoxin-type protein; FNR Nar NarP-regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex	b4072	_____________209__________________________________236\n_____________\|____________________________________\|\n5'-CAC...CCUUC___CG________________________U______GGGAA...AGG-3'\n______________ACU__ACGCA__AAUUUGU________UC_GGGGAU\n______________\|\|\|__\|\|:\|\|__\|\|\|\|:\|\|________\|\|_\|\|\|\|\|\|\n______________UGA__UGUGU__UUAAGCA________AG_CCCCUA\n3'-UUU...GUUUC___UG_____CG_______ACAAAGUG__U______AAGGU...GCA-5'\n_____________\|____________________________________\|\n_____________75___________________________________38\n	220 -- 226	56 -- 62	-21.5478 kcal/mol	5.56457 kcal/mol	4.77831 kcal/mol	209 236@LB@ \| \|@LB@5'-CAC...CCUUC CG U GGGAA...AGG-3'@LB@ ACU ACGCA AAUUUGU UC GGGGAU@LB@ \|\|\| \|\|:\|\| \|\|\|\|:\|\| \|\| \|\|\|\|\|\|@LB@ UGA UGUGU UUAAGCA AG CCCCUA@LB@3'-UUU...GUUUC UG CG ACAAAGUG U AAGGU...GCA-5'@LB@ \| \|@LB@ 75 38@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -21.5478 kcal/mol@LB@Unfolding Energy - mRNA 5.56457 kcal/mol@LB@Unfolding Energy - sRNA 4.77831 kcal/mol@LB@@LB@Position - mRNA 210 -- 235@LB@Position - sRNA 39 -- 74@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 56 -- 62@LB@
173	0.008582	0.1745	b0060	polB	-11.19	0.150164	8 -- 23	39 -- 51	DNA polymerase II		_____________7________________24\n_____________\|________________\|\n____5'-GAAGAGG_______UAU______AUUCU...AGG-3'\n______________UCGCUUA___GGGGAU\n______________\|\|:\|\|:\|___\|\|\|\|\|\|\n______________AGUGAGU___CCCCUA\n3'-UUU...AACAA________________AAGGU...GCA-5'\n_____________\|________________\|\n_____________52_______________38\n	8 -- 14	45 -- 51	-16.4647 kcal/mol	3.48224 kcal/mol	1.79807 kcal/mol	7 24@LB@ \| \|@LB@ 5'-GAAGAGG UAU AUUCU...AGG-3'@LB@ UCGCUUA GGGGAU@LB@ \|\|:\|\|:\| \|\|\|\|\|\|@LB@ AGUGAGU CCCCUA@LB@3'-UUU...AACAA AAGGU...GCA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -16.4647 kcal/mol@LB@Unfolding Energy - mRNA 3.48224 kcal/mol@LB@Unfolding Energy - sRNA 1.79807 kcal/mol@LB@@LB@Position - mRNA 8 -- 23@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 45 -- 51@LB@
20	0.0001757	0.02926	b4175	hflC	-15.67	0.013919	175 -- 193	40 -- 75	HflB protease modulator specific for phage lambda cII repressor		_____________174__________________________________194\n_____________\|____________________________________\|\n5'-UUA...GUAAC____________________________________AAUAA...GUU-3'\n______________GACUAC___CAGCG______________UCAGGGGG\n______________\|\|\|\|\|\|___\|\|\|\|:______________\|\|\|\|\|\|\|:\n______________CUGAUG___GUCGU______________AGUCCCCU\n3'-UUU...CGUUU______UGU_____UAAGCAACAAAGUG________AAAGG...GCA-5'\n_____________\|____________________________________\|\n_____________76___________________________________39\n	187 -- 193	40 -- 46	-24.7611 kcal/mol	4.31935 kcal/mol	4.77786 kcal/mol	174 194@LB@ \| \|@LB@5'-UUA...GUAAC AAUAA...GUU-3'@LB@ GACUAC CAGCG UCAGGGGG@LB@ \|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|\|\|:@LB@ CUGAUG GUCGU AGUCCCCU@LB@3'-UUU...CGUUU UGU UAAGCAACAAAGUG AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -15.67 kcal/mol@LB@Hybridization Energy -24.7611 kcal/mol@LB@Unfolding Energy - mRNA 4.31935 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
46	0.001357	0.1038	b1235	rssB	-13.33	0.053430	184 -- 194	40 -- 50	PcnB-degradosome interaction factor; response regulator		_____________183_________195\n_____________\|___________\|\n5'-AAU...AAAGC__G________GAGAA...CAA-3'\n______________CA_UCAGGGGA\n______________\|\|_\|\|\|\|\|\|\|\|\n______________GU_AGUCCCCU\n3'-UUU...ACAAA__G________AAAGG...GCA-5'\n_____________\|___________\|\n_____________51__________39\n	188 -- 194	40 -- 46	-19.1981 kcal/mol	4.11697 kcal/mol	1.75243 kcal/mol	183 195@LB@ \| \|@LB@5'-AAU...AAAGC G GAGAA...CAA-3'@LB@ CA UCAGGGGA@LB@ \|\| \|\|\|\|\|\|\|\|@LB@ GU AGUCCCCU@LB@3'-UUU...ACAAA G AAAGG...GCA-5'@LB@ \| \|@LB@ 51 39@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -19.1981 kcal/mol@LB@Unfolding Energy - mRNA 4.11697 kcal/mol@LB@Unfolding Energy - sRNA 1.75243 kcal/mol@LB@@LB@Position - mRNA 184 -- 194@LB@Position - sRNA 40 -- 50@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 40 -- 46@LB@
56	0.001982	0.1223	b2304	yfcH	-16.49	0.008143	193 -- 225	40 -- 77	putative NAD-dependent nucleotide-sugar epimerase		_____________192_________________________________________226\n_____________\|___________________________________________\|\n5'-AAA...AUCGG________AUGA__________________________A____CAGGA...ACC-3'\n______________GAGGCUGC____ACAUAGUGA_________UCAC_CGG_GGGA\n______________:\|\|:\|\|:\|____\|\|\|:\|\|::\|_________\|\|\|\|_\|:\|_\|\|\|\|\n______________UUCUGAUG____UGUGUCGUU_________AGUG_GUC_CCCU\n3'-UUU...CCCGU_____________________AAGCAACAA____A________AAAGG...GCA-5'\n_____________\|___________________________________________\|\n_____________78__________________________________________39\n	206 -- 212	62 -- 68	-29.217 kcal/mol	7.9505 kcal/mol	4.77871 kcal/mol	192 226@LB@ \| \|@LB@5'-AAA...AUCGG AUGA A CAGGA...ACC-3'@LB@ GAGGCUGC ACAUAGUGA UCAC CGG GGGA@LB@ :\|\|:\|\|:\| \|\|\|:\|\|::\| \|\|\|\| \|:\| \|\|\|\|@LB@ UUCUGAUG UGUGUCGUU AGUG GUC CCCU@LB@3'-UUU...CCCGU AAGCAACAA A AAAGG...GCA-5'@LB@ \| \|@LB@ 78 39@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -29.217 kcal/mol@LB@Unfolding Energy - mRNA 7.9505 kcal/mol@LB@Unfolding Energy - sRNA 4.77871 kcal/mol@LB@@LB@Position - mRNA 193 -- 225@LB@Position - sRNA 40 -- 77@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 62 -- 68@LB@
58	0.002015	0.1223	b0189	rof	-8.06	0.473679	29 -- 61	40 -- 71	modulator of Rho-dependent transcription termination		_____________28_________________________________62\n_____________\|__________________________________\|\n5'-AGG...AGUUA_______A_____A__CG_AAA________C___GACUU...GCG-3'\n______________AUACGCA_GCGGU_CG__G___UCGC_CAG_GGA\n______________\|:\|\|:\|\|_\|\|::\|_\|\|__\|___\|\|:\|_\|\|\|_\|\|\|\n______________UGUGUGU_CGUUA_GC__C___AGUG_GUC_CCU\n3'-UUU...UCUGA_____________A__AA_AA_____A___C___AAAGG...GCA-5'\n_____________\|__________________________________\|\n_____________72_________________________________39\n	29 -- 35	65 -- 71	-25.5885 kcal/mol	12.7864 kcal/mol	4.74818 kcal/mol	28 62@LB@ \| \|@LB@5'-AGG...AGUUA A A CG AAA C GACUU...GCG-3'@LB@ AUACGCA GCGGU CG G UCGC CAG GGA@LB@ \|:\|\|:\|\| \|\|::\| \|\| \| \|\|:\| \|\|\| \|\|\|@LB@ UGUGUGU CGUUA GC C AGUG GUC CCU@LB@3'-UUU...UCUGA A AA AA A C AAAGG...GCA-5'@LB@ \| \|@LB@ 72 39@LB@@LB@@LB@Energy -8.06 kcal/mol@LB@Hybridization Energy -25.5885 kcal/mol@LB@Unfolding Energy - mRNA 12.7864 kcal/mol@LB@Unfolding Energy - sRNA 4.74818 kcal/mol@LB@@LB@Position - mRNA 29 -- 61@LB@Position - sRNA 40 -- 71@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 65 -- 71@LB@
60	0.002324	0.1363	b0881	clpS	-11.74	0.117068	9 -- 15	40 -- 46	regulatory protein for ClpA substrate specificity		_____________8_______16\n_____________\|_______\|\n___5'-GCAUUUGA_______CAAGG...UCA-3'\n______________CAGGGGA\n______________\|\|\|\|\|\|\|\n______________GUCCCCU\n3'-UUU...AGUGA_______AAAGG...GCA-5'\n_____________\|_______\|\n_____________47______39\n	9 -- 15	40 -- 46	-13.2936 kcal/mol	0.199257 kcal/mol	1.35582 kcal/mol	8 16@LB@ \| \|@LB@ 5'-GCAUUUGA CAAGG...UCA-3'@LB@ CAGGGGA@LB@ \|\|\|\|\|\|\|@LB@ GUCCCCU@LB@3'-UUU...AGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 47 39@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -13.2936 kcal/mol@LB@Unfolding Energy - mRNA 0.199257 kcal/mol@LB@Unfolding Energy - sRNA 1.35582 kcal/mol@LB@@LB@Position - mRNA 9 -- 15@LB@Position - sRNA 40 -- 46@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 40 -- 46@LB@
67	0.002719	0.1417	b3454	livF	-11.67	0.120634	106 -- 122	40 -- 58	branched-chain amino acid ABC transporter ATPase		_____________105_________________123\n_____________\|___________________\|\n5'-AGA...AUUUA___GG_____A________CGCCG...UUG-3'\n______________CGU____UCA_UCAGGGGA\n______________\|\|\|____\|\|\|_\|\|\|\|\|\|\|\|\n______________GCA____AGU_AGUCCCCU\n3'-UUU...GUUAA___ACAA___G________AAAGG...GCA-5'\n_____________\|___________________\|\n_____________59__________________39\n	116 -- 122	40 -- 46	-19.8465 kcal/mol	5.75116 kcal/mol	2.42241 kcal/mol	105 123@LB@ \| \|@LB@5'-AGA...AUUUA GG A CGCCG...UUG-3'@LB@ CGU UCA UCAGGGGA@LB@ \|\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GCA AGU AGUCCCCU@LB@3'-UUU...GUUAA ACAA G AAAGG...GCA-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -19.8465 kcal/mol@LB@Unfolding Energy - mRNA 5.75116 kcal/mol@LB@Unfolding Energy - sRNA 2.42241 kcal/mol@LB@@LB@Position - mRNA 106 -- 122@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 40 -- 46@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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