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
31	0.0004941	0.05357	b1272	sohB	-11.06	0.104388	188 -- 235	1 -- 51	inner membrane protein S49 peptidase family protein	_____________187__________________________________________________236\n_____________\|____________________________________________________\|\n5'-UGU...UAACC____U_____AC__G___A__U____U_UGAA_____UU_____________GAAAA...AAC-3'\n______________AAGG_GG_GG__UC_UGG_AU_GUUG_C____UAUGG____UGUUUUU_GGC\n______________\|\|\|\|_\|\|_\|\|__\|\|_\|\|\|_\|:_\|:\|:_\|____\|\|\|\|\|____\|\|\|\|\|\|\|_:\|\|\n______________UUCC_CC_CC__AG_ACC_UG_CGAU_G____AUACC____ACAAAAA_UCG\n3'-UUU...UCCGA____U__A__A___G___A__U____C_UAAA_____CAAU_______G___-5'\n_____________\|___________________________________________________\|\n_____________52__________________________________________________1\n	226 -- 232	5 -- 11	-30.2617 kcal/mol	14.5124 kcal/mol	4.69283 kcal/mol	187 236@LB@ \| \|@LB@5'-UGU...UAACC U AC G A U U UGAA UU GAAAA...AAC-3'@LB@ AAGG GG GG UC UGG AU GUUG C UAUGG UGUUUUU GGC@LB@ \|\|\|\| \|\| \|\| \|\| \|\|\| \|: \|:\|: \| \|\|\|\|\| \|\|\|\|\|\|\| :\|\|@LB@ UUCC CC CC AG ACC UG CGAU G AUACC ACAAAAA UCG@LB@3'-UUU...UCCGA U A A G A U C UAAA CAAU G -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -30.2617 kcal/mol@LB@Unfolding Energy - mRNA 14.5124 kcal/mol@LB@Unfolding Energy - sRNA 4.69283 kcal/mol@LB@@LB@Position - mRNA 188 -- 235@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 5 -- 11@LB@
32	0.0005297	0.05563	b3456	livM	-14.95	0.011565	245 -- 274	15 -- 42	branched-chain amino acid ABC transporter permease	_____________244____________________________275\n_____________\|______________________________\|\n5'-GCC...GCGAU______U____U___G_____C________CGUGC...CCA-3'\n______________GUUCUU_GUGC_GGC_GGCGU_UUUAUGGG\n______________\|\|\|\|:\|_\|\|:\|_:\|\|_:\|\|:\|_\|\|\|\|\|\|\|\|\n______________CAAGGA_CAUG_UCG_UCGUA_AAAUACCC\n3'-UUU...UCCAC______C________A______________AAUAC...UCG-5'\n_____________\|______________________________\|\n_____________43_____________________________14\n	268 -- 274	15 -- 21	-29.6256 kcal/mol	10.1077 kcal/mol	4.57031 kcal/mol	244 275@LB@ \| \|@LB@5'-GCC...GCGAU U U G C CGUGC...CCA-3'@LB@ GUUCUU GUGC GGC GGCGU UUUAUGGG@LB@ \|\|\|\|:\| \|\|:\| :\|\| :\|\|:\| \|\|\|\|\|\|\|\|@LB@ CAAGGA CAUG UCG UCGUA AAAUACCC@LB@3'-UUU...UCCAC C A AAUAC...UCG-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -14.95 kcal/mol@LB@Hybridization Energy -29.6256 kcal/mol@LB@Unfolding Energy - mRNA 10.1077 kcal/mol@LB@Unfolding Energy - sRNA 4.57031 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 15 -- 21@LB@
33	0.0006117	0.0623	b1795	yeaQ	-12.41	0.053010	276 -- 283	42 -- 49	UPF0410 family protein	_____________275______284\n_____________\|________\|\n5'-AUA...AAGAU________AUUCU...UCC-3'\n______________GGAGGUGG\n______________\|\|\|\|\|\|\|\|\n______________CCUCCACC\n3'-UUU...CGAUU________AAGGA...UCG-5'\n_____________\|________\|\n_____________50_______41\n	277 -- 283	42 -- 48	-16.41 kcal/mol	1.22894 kcal/mol	2.77009 kcal/mol	275 284@LB@ \| \|@LB@5'-AUA...AAGAU AUUCU...UCC-3'@LB@ GGAGGUGG@LB@ \|\|\|\|\|\|\|\|@LB@ CCUCCACC@LB@3'-UUU...CGAUU AAGGA...UCG-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -12.41 kcal/mol@LB@Hybridization Energy -16.41 kcal/mol@LB@Unfolding Energy - mRNA 1.22894 kcal/mol@LB@Unfolding Energy - sRNA 2.77009 kcal/mol@LB@@LB@Position - mRNA 276 -- 283@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 42 -- 48@LB@
34	0.0006341	0.06268	b3312	rpmC	-15.21	0.009642	105 -- 128	25 -- 49	50S ribosomal subunit protein L29	_____________104________________________129\n_____________\|__________________________\|\n5'-AAA...GAAAU___C____________A_G_______CCGUG...CAA-3'\n______________GGA_GGU_GUUCC_GG_A_AGCUGGC\n______________\|\|\|_\|\|\|_\|\|\|\|\|_\|\|_\|_\|\|\|\|:\|\|\n______________CCU_CCA_CAAGG_CC_U_UCGAUCG\n3'-UUU...CGAUU_______C_____A__A_G_______UAAAA...UCG-5'\n_____________\|__________________________\|\n_____________50_________________________24\n	122 -- 128	25 -- 31	-29.6215 kcal/mol	9.85059 kcal/mol	4.5577 kcal/mol	104 129@LB@ \| \|@LB@5'-AAA...GAAAU C A G CCGUG...CAA-3'@LB@ GGA GGU GUUCC GG A AGCUGGC@LB@ \|\|\| \|\|\| \|\|\|\|\| \|\| \| \|\|\|\|:\|\|@LB@ CCU CCA CAAGG CC U UCGAUCG@LB@3'-UUU...CGAUU C A A G UAAAA...UCG-5'@LB@ \| \|@LB@ 50 24@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -29.6215 kcal/mol@LB@Unfolding Energy - mRNA 9.85059 kcal/mol@LB@Unfolding Energy - sRNA 4.5577 kcal/mol@LB@@LB@Position - mRNA 105 -- 128@LB@Position - sRNA 25 -- 49@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 25 -- 31@LB@
35	0.0006725	0.06313	b3455	livG	-12.92	0.040223	97 -- 112	32 -- 46	branched-chain amino acid ABC transporter ATPase	_____________96_______________113\n_____________\|________________\|\n5'-AUG...UGCUC________GA______UGAUG...UCG-3'\n______________GGUGGUUU__UGGUGC\n______________\|\|\|\|\|\|\|:__\|\|\|\|:\|\n______________CCACCAAG__ACCAUG\n3'-UUU...UUCCU________G_______UCGAU...UCG-5'\n_____________\|________________\|\n_____________47_______________31\n	98 -- 104	39 -- 45	-21.8288 kcal/mol	5.65514 kcal/mol	3.25632 kcal/mol	96 113@LB@ \| \|@LB@5'-AUG...UGCUC GA UGAUG...UCG-3'@LB@ GGUGGUUU UGGUGC@LB@ \|\|\|\|\|\|\|: \|\|\|\|:\|@LB@ CCACCAAG ACCAUG@LB@3'-UUU...UUCCU G UCGAU...UCG-5'@LB@ \| \|@LB@ 47 31@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -21.8288 kcal/mol@LB@Unfolding Energy - mRNA 5.65514 kcal/mol@LB@Unfolding Energy - sRNA 3.25632 kcal/mol@LB@@LB@Position - mRNA 97 -- 112@LB@Position - sRNA 32 -- 46@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 39 -- 45@LB@
36	0.0006761	0.06313	b0759	galE	-8.98	0.250354	205 -- 236	22 -- 48	UDP-galactose-4-epimerase	_____________204_______________________________237\n_____________\|_________________________________\|\n5'-GCA...UAUGA___UUC_____A__GG____A____________GGAAG...UCU-3'\n______________GAG___UGGUU_CC__UGGU_GCGGUUA_CAUU\n______________\|\|\|___\|\|\|\|\|_\|\|__\|\|\|\|_:\|:\|:\|\|_\|\|\|\|\n______________CUC___ACCAA_GG__ACCA_UGUCGAU_GUAA\n3'-UUU...GAUUC___C________________________C____AAUAC...UCG-5'\n_____________\|_________________________________\|\n_____________49________________________________21\n	226 -- 232	27 -- 33	-23.3933 kcal/mol	9.85191 kcal/mol	4.55969 kcal/mol	204 237@LB@ \| \|@LB@5'-GCA...UAUGA UUC A GG A GGAAG...UCU-3'@LB@ GAG UGGUU CC UGGU GCGGUUA CAUU@LB@ \|\|\| \|\|\|\|\| \|\| \|\|\|\| :\|:\|:\|\| \|\|\|\|@LB@ CUC ACCAA GG ACCA UGUCGAU GUAA@LB@3'-UUU...GAUUC C C AAUAC...UCG-5'@LB@ \| \|@LB@ 49 21@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -23.3933 kcal/mol@LB@Unfolding Energy - mRNA 9.85191 kcal/mol@LB@Unfolding Energy - sRNA 4.55969 kcal/mol@LB@@LB@Position - mRNA 205 -- 236@LB@Position - sRNA 22 -- 48@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 27 -- 33@LB@
37	0.0006972	0.06333	b1594	mlc	-9.54	0.201866	190 -- 226	24 -- 50	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor	_____________189___________________________________227\n_____________\|_____________________________________\|\n5'-AAA...AUAUA____GUAUGC_______G___AAAAC____CUG____CAUUG...GUA-3'\n______________GGGA______GGUGGUU_CUG_____CAGC___GGCA\n______________:\|\|\|______\|\|\|\|\|\|\|_\|\|\|_____\|\|\|\|___:\|\|\|\n______________UCCU______CCACCAA_GAC_____GUCG___UCGU\n3'-UUU...CCGAU_________________G___CAU______A______AAAAU...UCG-5'\n_____________\|_____________________________________\|\n_____________51____________________________________23\n	200 -- 206	40 -- 46	-27.1319 kcal/mol	12.9802 kcal/mol	4.6134 kcal/mol	189 227@LB@ \| \|@LB@5'-AAA...AUAUA GUAUGC G AAAAC CUG CAUUG...GUA-3'@LB@ GGGA GGUGGUU CUG CAGC GGCA@LB@ :\|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\|\| :\|\|\|@LB@ UCCU CCACCAA GAC GUCG UCGU@LB@3'-UUU...CCGAU G CAU A AAAAU...UCG-5'@LB@ \| \|@LB@ 51 23@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -27.1319 kcal/mol@LB@Unfolding Energy - mRNA 12.9802 kcal/mol@LB@Unfolding Energy - sRNA 4.6134 kcal/mol@LB@@LB@Position - mRNA 190 -- 226@LB@Position - sRNA 24 -- 50@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 40 -- 46@LB@
38	0.0007298	0.06455	b3196	yrbG	-13.22	0.033821	90 -- 115	1 -- 31	putative calcium/sodium:proton antiporter	_____________89______________________________116\n_____________\|_______________________________\|\n5'-UUC...GCGAA___________________UUAC________CGCAU...UUG-3'\n______________AGCUGGCAUUU_____GUU____UUUUUAGC\n______________\|\|\|\|:\|\|\|\|\|\|_____\|\|\|____\|\|\|\|:\|\|\|\n______________UCGAUCGUAAA_____CAA____AAAAGUCG\n3'-UUU...CCAUG___________AUACC___UACA________-5'\n_____________\|______________________________\|\n_____________32_____________________________1\n	109 -- 115	1 -- 7	-21.7779 kcal/mol	7.06678 kcal/mol	1.48722 kcal/mol	89 116@LB@ \| \|@LB@5'-UUC...GCGAA UUAC CGCAU...UUG-3'@LB@ AGCUGGCAUUU GUU UUUUUAGC@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\| \|\|\|\|:\|\|\|@LB@ UCGAUCGUAAA CAA AAAAGUCG@LB@3'-UUU...CCAUG AUACC UACA -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -21.7779 kcal/mol@LB@Unfolding Energy - mRNA 7.06678 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 90 -- 115@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 1 -- 7@LB@
39	0.0008004	0.06626	b1533	eamA	-12.23	0.058236	233 -- 264	16 -- 49	cysteine and O-acetyl-L-serine efflux system	_____________232_________________________________265\n_____________\|___________________________________\|\n5'-GUU...CUACU__UA_____CGUA___G_______A__________UCAUC...UGA-3'\n______________GG__GUGGU____UGG___GGCUA__AUUUUGUGG\n______________\|\|__\|\|\|\|\|____\|\|\|___:\|\|\|\|__\|\|\|\|\|:\|\|\|\n______________CC__CACCA____ACC___UCGAU__UAAAAUACC\n3'-UUU...CGAUU__UC_____AGG____AUG_____CG_________CAAUA...UCG-5'\n_____________\|___________________________________\|\n_____________50__________________________________15\n	258 -- 264	16 -- 22	-27.5137 kcal/mol	10.7081 kcal/mol	4.57266 kcal/mol	232 265@LB@ \| \|@LB@5'-GUU...CUACU UA CGUA G A UCAUC...UGA-3'@LB@ GG GUGGU UGG GGCUA AUUUUGUGG@LB@ \|\| \|\|\|\|\| \|\|\| :\|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CC CACCA ACC UCGAU UAAAAUACC@LB@3'-UUU...CGAUU UC AGG AUG CG CAAUA...UCG-5'@LB@ \| \|@LB@ 50 15@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -27.5137 kcal/mol@LB@Unfolding Energy - mRNA 10.7081 kcal/mol@LB@Unfolding Energy - sRNA 4.57266 kcal/mol@LB@@LB@Position - mRNA 233 -- 264@LB@Position - sRNA 16 -- 49@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 16 -- 22@LB@
40	0.0008246	0.06626	b4019	metH	-11.44	0.086775	244 -- 271	15 -- 42	homocysteine-N5-methyltetrahydrofolate transmethylase B12-dependent	_____________243____________________________272\n_____________\|______________________________\|\n5'-UGA...UGAAC__A_________U__AC____G________CACCA...ACG-3'\n______________GU_UUCUGGUGC_GG__GGCG___UAUGGG\n______________\|\|_\|:\|\|\|\|\|:\|_:\|__:\|\|:___\|\|\|\|\|\|\n______________CA_AGGACCAUG_UC__UCGU___AUACCC\n3'-UUU...UCCAC_______________GA____AAA______AAUAC...UCG-5'\n_____________\|______________________________\|\n_____________43_____________________________14\n	249 -- 255	32 -- 38	-26.1297 kcal/mol	10.116 kcal/mol	4.57031 kcal/mol	243 272@LB@ \| \|@LB@5'-UGA...UGAAC A U AC G CACCA...ACG-3'@LB@ GU UUCUGGUGC GG GGCG UAUGGG@LB@ \|\| \|:\|\|\|\|\|:\| :\| :\|\|: \|\|\|\|\|\|@LB@ CA AGGACCAUG UC UCGU AUACCC@LB@3'-UUU...UCCAC GA AAA AAUAC...UCG-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -26.1297 kcal/mol@LB@Unfolding Energy - mRNA 10.116 kcal/mol@LB@Unfolding Energy - sRNA 4.57031 kcal/mol@LB@@LB@Position - mRNA 244 -- 271@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 32 -- 38@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)

Job resubmission

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service.

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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