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@
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@
5	0.0001064	0.07159	b1784	yeaH	-10.63	0.089613	150 -- 205	1 -- 57	UPF0229 family protein	_____________149________________________________________________________206\n_____________\|__________________________________________________________\|\n5'-UGU...UGAGA__C_____CA_______G_____UACAGUUGGCAAA___AGUACG_____________CUGGU...CGA-3'\n______________AG_GGCAA__CA__GGC_UAGCA_____________UGU______GGGGGCAUAUGAC\n______________\|\|_\|\|\|\|\|__\|\|__\|\|\|_:\|:\|\|_____________\|\|\|______:::\|\|\|\|\|\|\|:\|\|\n______________UC_CCGUU__GU__CCG_GUUGU_____________ACA______UUUCCGUAUAUUG\n3'-UUU...UUUAG__A_____AC__UA___G_____CUUUUAUUUUAG____CUGUUA_____________-5'\n_____________\|_________________________________________________________\|\n_____________58________________________________________________________1\n	198 -- 204	2 -- 8	-36.8439 kcal/mol	14.0882 kcal/mol	12.1233 kcal/mol	149 206@LB@ \| \|@LB@5'-UGU...UGAGA C CA G UACAGUUGGCAAA AGUACG CUGGU...CGA-3'@LB@ AG GGCAA CA GGC UAGCA UGU GGGGGCAUAUGAC@LB@ \|\| \|\|\|\|\| \|\| \|\|\| :\|:\|\| \|\|\| :::\|\|\|\|\|\|\|:\|\|@LB@ UC CCGUU GU CCG GUUGU ACA UUUCCGUAUAUUG@LB@3'-UUU...UUUAG A AC UA G CUUUUAUUUUAG CUGUUA -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -36.8439 kcal/mol@LB@Unfolding Energy - mRNA 14.0882 kcal/mol@LB@Unfolding Energy - sRNA 12.1233 kcal/mol@LB@@LB@Position - mRNA 150 -- 205@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 2 -- 8@LB@
6	0.0002023	0.1081	b1884	cheR	-8.31	0.257615	184 -- 205	1 -- 21	chemotaxis regulator protein-glutamate methyltransferase	_____________183____________________206\n_____________\|______________________\|\n5'-GCC...CUGAA_____UGA_______C______UUCAU...UGA-3'\n______________GUGAU___GAAGGCG_UAUGAC\n______________\|\|\|\|:___:\|\|\|\|\|:_\|\|\|:\|\|\n______________CACUG___UUUCCGU_AUAUUG\n3'-UUU...UUAGA_____UUA______________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	192 -- 198	7 -- 13	-19.9838 kcal/mol	7.26541 kcal/mol	4.41334 kcal/mol	183 206@LB@ \| \|@LB@5'-GCC...CUGAA UGA C UUCAU...UGA-3'@LB@ GUGAU GAAGGCG UAUGAC@LB@ \|\|\|\|: :\|\|\|\|\|: \|\|\|:\|\|@LB@ CACUG UUUCCGU AUAUUG@LB@3'-UUU...UUAGA UUA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -19.9838 kcal/mol@LB@Unfolding Energy - mRNA 7.26541 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 184 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 7 -- 13@LB@
12	0.0004505	0.1262	b3248	yhdE	-11.12	0.070056	184 -- 205	1 -- 21	dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase	_____________183_____________________206\n_____________\|_______________________\|\n5'-UUA...UUGCA______________UUC______UUCUC...AGC-3'\n______________GUG_CAAUAAAGGU___UAUGAC\n______________\|\|\|_\|\|\|\|\|\|\|\|\|:___\|\|\|:\|\|\n______________CAC_GUUAUUUCCG___AUAUUG\n3'-UUU...UUAGA___U__________U________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	190 -- 196	8 -- 14	-19.9684 kcal/mol	4.43203 kcal/mol	4.41334 kcal/mol	183 206@LB@ \| \|@LB@5'-UUA...UUGCA UUC UUCUC...AGC-3'@LB@ GUG CAAUAAAGGU UAUGAC@LB@ \|\|\| \|\|\|\|\|\|\|\|\|: \|\|\|:\|\|@LB@ CAC GUUAUUUCCG AUAUUG@LB@3'-UUU...UUAGA U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -19.9684 kcal/mol@LB@Unfolding Energy - mRNA 4.43203 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 184 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 8 -- 14@LB@
23	0.001281	0.182	b3541	dppD	-11.06	0.072175	116 -- 139	1 -- 23	dipeptide/heme ABC transporter ATPas	_____________115______________________140\n_____________\|________________________\|\n5'-UUU...CGAUC___C________CU_____U____CUGAU...GCG-3'\n______________CUG_UGACGGUG__GGCAU_UAAC\n______________\|\|\|_\|\|\|\|::\|:__\|\|\|\|\|_\|\|\|\|\n______________GAC_ACUGUUAU__CCGUA_AUUG\n3'-UUU...UUUUA____________UU_____U____-5'\n_____________\|_______________________\|\n_____________24______________________1\n	121 -- 127	13 -- 19	-21.9665 kcal/mol	6.28511 kcal/mol	4.61692 kcal/mol	115 140@LB@ \| \|@LB@5'-UUU...CGAUC C CU U CUGAU...GCG-3'@LB@ CUG UGACGGUG GGCAU UAAC@LB@ \|\|\| \|\|\|\|::\|: \|\|\|\|\| \|\|\|\|@LB@ GAC ACUGUUAU CCGUA AUUG@LB@3'-UUU...UUUUA UU U -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -21.9665 kcal/mol@LB@Unfolding Energy - mRNA 6.28511 kcal/mol@LB@Unfolding Energy - sRNA 4.61692 kcal/mol@LB@@LB@Position - mRNA 116 -- 139@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 13 -- 19@LB@
25	0.001369	0.1841	b2599	pheA	-10.09	0.116571	180 -- 205	1 -- 20	chorismate mutase and prephenate dehydratase P-protein	_____________179________________________206\n_____________\|__________________________\|\n5'-UGA...UUUAU______CAA_______ACAC______AUCGG...UCG-3'\n______________UGAUAA___AAAGGCA____UAUGAC\n______________\|\|\|:\|\|___\|\|\|\|\|\|\|____\|\|\|:\|\|\n______________ACUGUU___UUUCCGU____AUAUUG\n3'-UUU...UAGAC______A___________________-5'\n_____________\|_________________________\|\n_____________21________________________1\n	189 -- 195	7 -- 13	-16.49 kcal/mol	2.17136 kcal/mol	4.22784 kcal/mol	179 206@LB@ \| \|@LB@5'-UGA...UUUAU CAA ACAC AUCGG...UCG-3'@LB@ UGAUAA AAAGGCA UAUGAC@LB@ \|\|\|:\|\| \|\|\|\|\|\|\| \|\|\|:\|\|@LB@ ACUGUU UUUCCGU AUAUUG@LB@3'-UUU...UAGAC A -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -16.49 kcal/mol@LB@Unfolding Energy - mRNA 2.17136 kcal/mol@LB@Unfolding Energy - sRNA 4.22784 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 7 -- 13@LB@
27	0.001616	0.2012	b0085	murE	-13.53	0.018874	165 -- 198	1 -- 33	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso- diaminopimelate ligase	_____________164_________________________________199\n_____________\|___________________________________\|\n5'-UGC...CGAUA_________________U___C______AGGG___AGGUG...CGG-3'\n______________AAAAU_GAAUUUGUGAU_AAU_AAGGCG____GAC\n______________\|\|\|\|\|_:\|\|\|:\|\|\|\|\|:_\|\|\|_\|\|\|\|\|:____:\|\|\n______________UUUUA_UUUAGACACUG_UUA_UUCCGU____UUG\n3'-UUU...UUGUC_____U_______________U______AUA____-5'\n_____________\|__________________________________\|\n_____________34_________________________________1\n	174 -- 180	17 -- 23	-22.2929 kcal/mol	3.71145 kcal/mol	5.04823 kcal/mol	164 199@LB@ \| \|@LB@5'-UGC...CGAUA U C AGGG AGGUG...CGG-3'@LB@ AAAAU GAAUUUGUGAU AAU AAGGCG GAC@LB@ \|\|\|\|\| :\|\|\|:\|\|\|\|\|: \|\|\| \|\|\|\|\|: :\|\|@LB@ UUUUA UUUAGACACUG UUA UUCCGU UUG@LB@3'-UUU...UUGUC U U AUA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -22.2929 kcal/mol@LB@Unfolding Energy - mRNA 3.71145 kcal/mol@LB@Unfolding Energy - sRNA 5.04823 kcal/mol@LB@@LB@Position - mRNA 165 -- 198@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 17 -- 23@LB@
52	0.003856	0.237	b2844	yqeF	-12.45	0.034706	43 -- 109	1 -- 67	short chain acyltransferase	_____________42______________________________________________________________________110\n_____________\|_______________________________________________________________________\|\n5'-CCA...CUCUA____U__________________A_____U___U_CC___UAU____C____UGCUGCUC________UU_CUUUG...UCG-3'\n______________UUGG_GGGUUAGUGGU__UGCAA___CCU_ACG_G__AGU___GUCU_UGAC________AGGCAUAU__C\n______________\|\|\|\|_:::\|:\|\|\|\|\|:__\|\|\|\|\|___\|\|:_\|\|:_\|__\|:\|___:\|\|\|_\|\|\|\|________\|\|\|\|\|\|\|\|__\|\n______________AACC_UUUAGUCACCG__ACGUU___GGG_UGU_C__UUA___UAGA_ACUG________UCCGUAUA__G\n3'-UUU...UAUAC____U___________UU_____ACC___U_____UU___UUU____C____UUAUU___________UU_-5'\n_____________\|______________________________________________________________________\|\n_____________68_____________________________________________________________________1\n	100 -- 106	4 -- 10	-44.1841 kcal/mol	19.5714 kcal/mol	12.1612 kcal/mol	42 110@LB@ \| \|@LB@5'-CCA...CUCUA U A U U CC UAU C UGCUGCUC UU CUUUG...UCG-3'@LB@ UUGG GGGUUAGUGGU UGCAA CCU ACG G AGU GUCU UGAC AGGCAUAU C@LB@ \|\|\|\| :::\|:\|\|\|\|\|: \|\|\|\|\| \|\|: \|\|: \| \|:\| :\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|@LB@ AACC UUUAGUCACCG ACGUU GGG UGU C UUA UAGA ACUG UCCGUAUA G@LB@3'-UUU...UAUAC U UU ACC U UU UUU C UUAUU UU -5'@LB@ \| \|@LB@ 68 1@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -44.1841 kcal/mol@LB@Unfolding Energy - mRNA 19.5714 kcal/mol@LB@Unfolding Energy - sRNA 12.1612 kcal/mol@LB@@LB@Position - mRNA 43 -- 109@LB@Position - sRNA 1 -- 67@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 4 -- 10@LB@
58	0.004088	0.237	b0998	torD	-12.26	0.038501	93 -- 144	1 -- 57	TorA-maturation chaperone	_____________92__________________________________________________________145\n_____________\|___________________________________________________________\|\n5'-GGU...ACGCU_____AAAU__AGAA___A________C_______CAG________________U____GGCCC...CCA-3'\n______________GGUGG____UG_____GU_CAACGGAA_AGUGGAG___GUGAC______GGCGU_UAAC\n______________:\|\|\|\|____\|\|_____\|:_\|\|\|\|:\|\|\|_\|:\|::\|:___\|\|\|\|\|______\|\|\|:\|_\|\|\|\|\n______________UCACC____AC_____CG_GUUGUCUU_UUAUUUU___CACUG______CCGUA_AUUG\n3'-UUU...UUUAG_____GUU___GUUAC__G________________AGA_____UUAUUU_____U____-5'\n_____________\|__________________________________________________________\|\n_____________58_________________________________________________________1\n	111 -- 117	33 -- 39	-35.8821 kcal/mol	11.4978 kcal/mol	12.1233 kcal/mol	92 145@LB@ \| \|@LB@5'-GGU...ACGCU AAAU AGAA A C CAG U GGCCC...CCA-3'@LB@ GGUGG UG GU CAACGGAA AGUGGAG GUGAC GGCGU UAAC@LB@ :\|\|\|\| \|\| \|: \|\|\|\|:\|\|\| \|:\|::\|: \|\|\|\|\| \|\|\|:\| \|\|\|\|@LB@ UCACC AC CG GUUGUCUU UUAUUUU CACUG CCGUA AUUG@LB@3'-UUU...UUUAG GUU GUUAC G AGA UUAUUU U -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -35.8821 kcal/mol@LB@Unfolding Energy - mRNA 11.4978 kcal/mol@LB@Unfolding Energy - sRNA 12.1233 kcal/mol@LB@@LB@Position - mRNA 93 -- 144@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 33 -- 39@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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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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