Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
1	0	0	b2215	ompC	-25.52	0.000001	134 -- 186	1 -- 70	outer membrane porin protein C	_____________133____________________________________________________________________187\n_____________\|______________________________________________________________________\|\n5'-AUC...GAUUA___AG__UU_____________________________________AAGCA___________________AGAGG...AUC-3'\n______________AUG__GG__AAUCAGU____AUGCAGUGGC__________AUAAAA________AAUAAAGGCAUAUAAC\n______________\|\|\|__\|\|__\|\|\|\|\|\|\|____\|\|\|\|\|:\|\|\|\|__________\|\|\|\|\|\|________\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UAC__CC__UUAGUCA____UACGUUACCG__________UAUUUU________UUAUUUCCGUAUAUUG\n3'-UUU...AAAUA___AA__UU_______CCGU__________GGUUGUCUUU______AGACACUG________________-5'\n_____________\|_____________________________________________________________________\|\n_____________71____________________________________________________________________1\n	180 -- 186	1 -- 7	-48.3995 kcal/mol	10.7142 kcal/mol	12.1618 kcal/mol	133 187@LB@ \| \|@LB@5'-AUC...GAUUA AG UU AAGCA AGAGG...AUC-3'@LB@ AUG GG AAUCAGU AUGCAGUGGC AUAAAA AAUAAAGGCAUAUAAC@LB@ \|\|\| \|\| \|\|\|\|\|\|\| \|\|\|\|\|:\|\|\|\| \|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UAC CC UUAGUCA UACGUUACCG UAUUUU UUAUUUCCGUAUAUUG@LB@3'-UUU...AAAUA AA UU CCGU GGUUGUCUUU AGACACUG -5'@LB@ \| \|@LB@ 71 1@LB@@LB@@LB@Energy -25.52 kcal/mol@LB@Hybridization Energy -48.3995 kcal/mol@LB@Unfolding Energy - mRNA 10.7142 kcal/mol@LB@Unfolding Energy - sRNA 12.1618 kcal/mol@LB@@LB@Position - mRNA 134 -- 186@LB@Position - sRNA 1 -- 70@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 1 -- 7@LB@
97	0.009098	0.3118	b3221	yhcH	-21.73	0.000051	38 -- 71	30 -- 66	DUF386 family protein cupin superfamily	_____________37____________________________________72\n_____________\|_____________________________________\|\n5'-AUC...GUGCG___U_________________U_______________GUAUC...AAG-3'\n______________UGG__GGUCGGUGGCA__GCG_UGGUCUGGCAGAAGG\n______________\|\|\|__::\|\|:\|\|\|\|\|\|__\|\|:_\|\|\|:\|:::\|\|\|\|\|::\n______________ACC__UUAGUCACCGU__CGU_ACCGGGUUGUCUUUU\n3'-UUU...AUACA___UU___________UA___U_______________AUUUU...UUG-5'\n_____________\|_____________________________________\|\n_____________67____________________________________29\n	57 -- 63	38 -- 44	-43.4799 kcal/mol	10.7586 kcal/mol	10.9916 kcal/mol	37 72@LB@ \| \|@LB@5'-AUC...GUGCG U U GUAUC...AAG-3'@LB@ UGG GGUCGGUGGCA GCG UGGUCUGGCAGAAGG@LB@ \|\|\| ::\|\|:\|\|\|\|\|\| \|\|: \|\|\|:\|:::\|\|\|\|\|::@LB@ ACC UUAGUCACCGU CGU ACCGGGUUGUCUUUU@LB@3'-UUU...AUACA UU UA U AUUUU...UUG-5'@LB@ \| \|@LB@ 67 29@LB@@LB@@LB@Energy -21.73 kcal/mol@LB@Hybridization Energy -43.4799 kcal/mol@LB@Unfolding Energy - mRNA 10.7586 kcal/mol@LB@Unfolding Energy - sRNA 10.9916 kcal/mol@LB@@LB@Position - mRNA 38 -- 71@LB@Position - sRNA 30 -- 66@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 38 -- 44@LB@
145	0.01667	0.3828	b1835	rsmF	-17.85	0.001164	186 -- 211	35 -- 58	16S rRNA m(5)C1407 methyltransferase SAM-dependent	_____________185________________________212\n_____________\|__________________________\|\n5'-CGC...UUUGC________C____UC___________CACCG...GUC-3'\n______________CAGUGGUA_AUGC__GUGGCCCAACA\n______________\|\|\|\|\|\|:\|_\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|\n______________GUCACCGU_UACG__UACCGGGUUGU\n3'-UUU...UUUUA_____________U____________CUUUU...UUG-5'\n_____________\|__________________________\|\n_____________59_________________________34\n	205 -- 211	35 -- 41	-37.9392 kcal/mol	9.33395 kcal/mol	10.7541 kcal/mol	185 212@LB@ \| \|@LB@5'-CGC...UUUGC C UC CACCG...GUC-3'@LB@ CAGUGGUA AUGC GUGGCCCAACA@LB@ \|\|\|\|\|\|:\| \|\|\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ GUCACCGU UACG UACCGGGUUGU@LB@3'-UUU...UUUUA U CUUUU...UUG-5'@LB@ \| \|@LB@ 59 34@LB@@LB@@LB@Energy -17.85 kcal/mol@LB@Hybridization Energy -37.9392 kcal/mol@LB@Unfolding Energy - mRNA 9.33395 kcal/mol@LB@Unfolding Energy - sRNA 10.7541 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 35 -- 58@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 35 -- 41@LB@
190	0.0237	0.4194	b0428	cyoE	-16.93	0.002220	1 -- 26	41 -- 65	protoheme IX farnesyltransferase	______________1__________________________27\n______________\|__________________________\|\n___________5'-____C____C________G________ACAGG...GCA-3'\n______________GGAA_AAUC__UGGCAAU_GCAGUGGU\n______________\|\|\|\|_\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|:\|\|\|:\n______________CCUU_UUAG__ACCGUUA_CGUUACCG\n3'-UUU...UACAA_________UC________________GGUUG...UUG-5'\n_____________\|___________________________\|\n_____________66__________________________40\n	20 -- 26	41 -- 47	-29.3415 kcal/mol	6.59984 kcal/mol	5.80973 kcal/mol	1 27@LB@ \| \|@LB@ 5'- C C G ACAGG...GCA-3'@LB@ GGAA AAUC UGGCAAU GCAGUGGU@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|\| \|\|\|:\|\|\|:@LB@ CCUU UUAG ACCGUUA CGUUACCG@LB@3'-UUU...UACAA UC GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -16.93 kcal/mol@LB@Hybridization Energy -29.3415 kcal/mol@LB@Unfolding Energy - mRNA 6.59984 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 1 -- 26@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 41 -- 47@LB@
47	0.003222	0.2306	b1667	ydhR	-16.61	0.002759	245 -- 266	34 -- 55	putative monooxygenase	_____________244____________________267\n_____________\|______________________\|\n5'-UUG...CCAUU______C_________G_____CUUAA...AAC-3'\n______________UGGCGA_GCAAUGGCU_AGCAG\n______________\|\|\|\|:\|_\|\|\|\|\|\|\|\|:_\|:\|\|\|\n______________ACCGUU_CGUUACCGG_UUGUC\n3'-UUU...UAGUC______A_________G_____UUUUA...UUG-5'\n_____________\|______________________\|\n_____________56_____________________33\n	254 -- 260	40 -- 46	-33.2096 kcal/mol	7.64311 kcal/mol	8.95438 kcal/mol	244 267@LB@ \| \|@LB@5'-UUG...CCAUU C G CUUAA...AAC-3'@LB@ UGGCGA GCAAUGGCU AGCAG@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|\|: \|:\|\|\|@LB@ ACCGUU CGUUACCGG UUGUC@LB@3'-UUU...UAGUC A G UUUUA...UUG-5'@LB@ \| \|@LB@ 56 33@LB@@LB@@LB@Energy -16.61 kcal/mol@LB@Hybridization Energy -33.2096 kcal/mol@LB@Unfolding Energy - mRNA 7.64311 kcal/mol@LB@Unfolding Energy - sRNA 8.95438 kcal/mol@LB@@LB@Position - mRNA 245 -- 266@LB@Position - sRNA 34 -- 55@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 40 -- 46@LB@
13	0.0005138	0.1268	b0055	djlA	-16.40	0.003186	213 -- 240	39 -- 65	membrane-anchored DnaK co-chaperone DNA-binding protein	_____________212__________________________241\n_____________\|____________________________\|\n5'-GAC...AUUGG__A_______U_____UG__C_______UACUG...UUG-3'\n______________GG_AAAAUCA_UGGCG__GC_GUGGCCU\n______________\|\|_\|\|\|\|\|\|\|_\|\|\|\|:__\|\|_:\|\|\|\|\|:\n______________CC_UUUUAGU_ACCGU__CG_UACCGGG\n3'-UUU...UACAA__________C_____UA__U_______UUGUC...UUG-5'\n_____________\|____________________________\|\n_____________66___________________________38\n	234 -- 240	39 -- 45	-30.8595 kcal/mol	7.7929 kcal/mol	6.66922 kcal/mol	212 241@LB@ \| \|@LB@5'-GAC...AUUGG A U UG C UACUG...UUG-3'@LB@ GG AAAAUCA UGGCG GC GUGGCCU@LB@ \|\| \|\|\|\|\|\|\| \|\|\|\|: \|\| :\|\|\|\|\|:@LB@ CC UUUUAGU ACCGU CG UACCGGG@LB@3'-UUU...UACAA C UA U UUGUC...UUG-5'@LB@ \| \|@LB@ 66 38@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -30.8595 kcal/mol@LB@Unfolding Energy - mRNA 7.7929 kcal/mol@LB@Unfolding Energy - sRNA 6.66922 kcal/mol@LB@@LB@Position - mRNA 213 -- 240@LB@Position - sRNA 39 -- 65@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 39 -- 45@LB@
7	0.0002249	0.1081	b4032	malG	-16.06	0.003987	187 -- 221	31 -- 65	maltose transporter subunit	_____________186_________________________________222\n_____________\|___________________________________\|\n5'-CGU...AUUAA_______AACAAAAAUG_____________C____UCGCA...UGG-3'\n______________GGGAGAU__________GCAAUGGUCCAAC_GAAA\n______________\|\|:\|:\|\|__________\|\|\|\|\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CCUUUUA__________CGUUACCGGGUUG_CUUU\n3'-UUU...UACAA_______GUCACCGUUA_____________U____UAUUU...UUG-5'\n_____________\|___________________________________\|\n_____________66__________________________________30\n	210 -- 216	36 -- 42	-33.4232 kcal/mol	6.39587 kcal/mol	10.9697 kcal/mol	186 222@LB@ \| \|@LB@5'-CGU...AUUAA AACAAAAAUG C UCGCA...UGG-3'@LB@ GGGAGAU GCAAUGGUCCAAC GAAA@LB@ \|\|:\|:\|\| \|\|\|\|\|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CCUUUUA CGUUACCGGGUUG CUUU@LB@3'-UUU...UACAA GUCACCGUUA U UAUUU...UUG-5'@LB@ \| \|@LB@ 66 30@LB@@LB@@LB@Energy -16.06 kcal/mol@LB@Hybridization Energy -33.4232 kcal/mol@LB@Unfolding Energy - mRNA 6.39587 kcal/mol@LB@Unfolding Energy - sRNA 10.9697 kcal/mol@LB@@LB@Position - mRNA 187 -- 221@LB@Position - sRNA 31 -- 65@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 36 -- 42@LB@
2	3.183e-05	0.03921	b0889	lrp	-15.78	0.004789	150 -- 212	1 -- 70	leucine-responsive global transcriptional regulator	_____________149__________________________________________________________________________213\n_____________\|____________________________________________________________________________\|\n5'-GUG...CAGUG_____UC________ACA______A_G__A__AAU___________________________UAAU____G_____AAGAA...AGC-3'\n______________AUGUU__AGGGUCAG___GG_AGU_G_GA_GG____ACAGAGA___________GACAAUAA____GGUA_AUAGC\n______________\|\|\|\|\|__\|:::\|\|\|\|___\|\|_\|:\|_\|_:\|_\|\|____\|\|\|\|\|:\|___________\|\|\|\|\|\|\|\|____\|\|:\|_\|\|\|:\|\n______________UACAA__UUUUAGUC___CC_UUA_C_UU_CC____UGUCUUU___________CUGUUAUU____CCGU_UAUUG\n3'-UUU...AAAUA_____CC________A____G_____G__A__GGGU_______UAUUUUAGACA________U_______A_____-5'\n_____________\|___________________________________________________________________________\|\n_____________71__________________________________________________________________________1\n	192 -- 198	12 -- 18	-35.9997 kcal/mol	8.06188 kcal/mol	12.1618 kcal/mol	149 213@LB@ \| \|@LB@5'-GUG...CAGUG UC ACA A G A AAU UAAU G AAGAA...AGC-3'@LB@ AUGUU AGGGUCAG GG AGU G GA GG ACAGAGA GACAAUAA GGUA AUAGC@LB@ \|\|\|\|\| \|:::\|\|\|\| \|\| \|:\| \| :\| \|\| \|\|\|\|\|:\| \|\|\|\|\|\|\|\| \|\|:\| \|\|\|:\|@LB@ UACAA UUUUAGUC CC UUA C UU CC UGUCUUU CUGUUAUU CCGU UAUUG@LB@3'-UUU...AAAUA CC A G G A GGGU UAUUUUAGACA U A -5'@LB@ \| \|@LB@ 71 1@LB@@LB@@LB@Energy -15.78 kcal/mol@LB@Hybridization Energy -35.9997 kcal/mol@LB@Unfolding Energy - mRNA 8.06188 kcal/mol@LB@Unfolding Energy - sRNA 12.1618 kcal/mol@LB@@LB@Position - mRNA 150 -- 212@LB@Position - sRNA 1 -- 70@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 12 -- 18@LB@
48	0.003417	0.237	b0002	thrA	-15.68	0.005086	222 -- 242	46 -- 65	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________221___________________243\n_____________\|_____________________\|\n5'-CCA...UCGGC__UAC___________A____GAACG...UGG-3'\n______________GG___AUCAGUGGCAA_UGCA\n______________\|\|___\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\n______________CC___UAGUCACCGUU_ACGU\n3'-UUU...UACAA__UUU________________UACCG...UUG-5'\n_____________\|_____________________\|\n_____________66____________________45\n	231 -- 237	50 -- 56	-24.9116 kcal/mol	5.14883 kcal/mol	4.07994 kcal/mol	221 243@LB@ \| \|@LB@5'-CCA...UCGGC UAC A GAACG...UGG-3'@LB@ GG AUCAGUGGCAA UGCA@LB@ \|\| \|\|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CC UAGUCACCGUU ACGU@LB@3'-UUU...UACAA UUU UACCG...UUG-5'@LB@ \| \|@LB@ 66 45@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -24.9116 kcal/mol@LB@Unfolding Energy - mRNA 5.14883 kcal/mol@LB@Unfolding Energy - sRNA 4.07994 kcal/mol@LB@@LB@Position - mRNA 222 -- 242@LB@Position - sRNA 46 -- 65@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 50 -- 56@LB@
129	0.01395	0.3636	b2314	dedD	-15.05	0.007607	192 -- 211	45 -- 65	membrane-anchored periplasmic protein involved in septation	_____________191___________________212\n_____________\|_____________________\|\n5'-UUG...CGCGA______G______________GUUUC...AUU-3'\n______________GGAGAA_CGGUGGCAA_GUAA\n______________\|\|\|:\|\|_\|:\|\|\|\|\|\|\|_\|:\|\|\n______________CCUUUU_GUCACCGUU_CGUU\n3'-UUU...UACAA______A_________A____ACCGG...UUG-5'\n_____________\|_____________________\|\n_____________66____________________44\n	201 -- 207	50 -- 56	-23.8601 kcal/mol	4.54883 kcal/mol	4.26469 kcal/mol	191 212@LB@ \| \|@LB@5'-UUG...CGCGA G GUUUC...AUU-3'@LB@ GGAGAA CGGUGGCAA GUAA@LB@ \|\|\|:\|\| \|:\|\|\|\|\|\|\| \|:\|\|@LB@ CCUUUU GUCACCGUU CGUU@LB@3'-UUU...UACAA A A ACCGG...UUG-5'@LB@ \| \|@LB@ 66 44@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -23.8601 kcal/mol@LB@Unfolding Energy - mRNA 4.54883 kcal/mol@LB@Unfolding Energy - sRNA 4.26469 kcal/mol@LB@@LB@Position - mRNA 192 -- 211@LB@Position - sRNA 45 -- 65@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 50 -- 56@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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