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
132	0.0144	0.3654	b2381	ypdB	-7.98	0.293473	18 -- 39	11 -- 32	response regulator activating yhjX; pyruvate-responsive YpdAB two-component system	_____________17_____________________40\n_____________\|______________________\|\n5'-AUU...GAAGC_________GCCG_________AUUGG...ACG-3'\n______________GAAUGAAAU____GGCAAUAAA\n______________:\|\|\|:\|\|\|\|____\|:\|\|\|\|\|\|\|\n______________UUUAUUUUA____CUGUUAUUU\n3'-UUU...UGUCU_________GACA_________CCGUA...UUG-5'\n_____________\|______________________\|\n_____________33_____________________10\n	33 -- 39	11 -- 17	-14.9693 kcal/mol	2.07375 kcal/mol	4.91579 kcal/mol	17 40@LB@ \| \|@LB@5'-AUU...GAAGC GCCG AUUGG...ACG-3'@LB@ GAAUGAAAU GGCAAUAAA@LB@ :\|\|\|:\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ UUUAUUUUA CUGUUAUUU@LB@3'-UUU...UGUCU GACA CCGUA...UUG-5'@LB@ \| \|@LB@ 33 10@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -14.9693 kcal/mol@LB@Unfolding Energy - mRNA 2.07375 kcal/mol@LB@Unfolding Energy - sRNA 4.91579 kcal/mol@LB@@LB@Position - mRNA 18 -- 39@LB@Position - sRNA 11 -- 32@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 11 -- 17@LB@
57	0.004077	0.237	b4198	ulaF	-9.90	0.127727	21 -- 37	42 -- 55	L-ribulose 5-phosphate 4-epimerase	_____________20________________38\n_____________\|_________________\|\n5'-GUC...CCGUU_____AAG_________AUUUC...GCG-3'\n______________UGGCG___GUGUAGUGG\n______________\|\|\|\|:___:\|\|:\|:\|\|\|\n______________ACCGU___UACGUUACC\n3'-UUU...UAGUC_________________GGGUU...UUG-5'\n_____________\|_________________\|\n_____________56________________41\n	31 -- 37	42 -- 48	-17.0201 kcal/mol	3.6214 kcal/mol	3.50097 kcal/mol	20 38@LB@ \| \|@LB@5'-GUC...CCGUU AAG AUUUC...GCG-3'@LB@ UGGCG GUGUAGUGG@LB@ \|\|\|\|: :\|\|:\|:\|\|\|@LB@ ACCGU UACGUUACC@LB@3'-UUU...UAGUC GGGUU...UUG-5'@LB@ \| \|@LB@ 56 41@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -17.0201 kcal/mol@LB@Unfolding Energy - mRNA 3.6214 kcal/mol@LB@Unfolding Energy - sRNA 3.50097 kcal/mol@LB@@LB@Position - mRNA 21 -- 37@LB@Position - sRNA 42 -- 55@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 42 -- 48@LB@
199	0.02539	0.4256	b2094	gatA	-8.91	0.199733	27 -- 47	1 -- 21	galactitol-specific enzyme IIA component of PTS	_____________26_____________________48\n_____________\|______________________\|\n5'-UUA...UGAUG____AUCU______________AUCCC...AUG-3'\n______________GUGA____UGAAGGCGUG_GAC\n______________\|\|\|\|____\|:\|\|\|\|\|:\|:_:\|\|\n______________CACU____AUUUCCGUAU_UUG\n3'-UUU...UUAGA____GUU___________A___-5'\n_____________\|_____________________\|\n_____________22____________________1\n	38 -- 44	5 -- 11	-17.7737 kcal/mol	4.45083 kcal/mol	4.41334 kcal/mol	26 48@LB@ \| \|@LB@5'-UUA...UGAUG AUCU AUCCC...AUG-3'@LB@ GUGA UGAAGGCGUG GAC@LB@ \|\|\|\| \|:\|\|\|\|\|:\|: :\|\|@LB@ CACU AUUUCCGUAU UUG@LB@3'-UUU...UUAGA GUU A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -17.7737 kcal/mol@LB@Unfolding Energy - mRNA 4.45083 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 27 -- 47@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 5 -- 11@LB@
194	0.0246	0.4256	b0211	mltD	-5.59	0.639593	30 -- 36	59 -- 65	putative membrane-bound lytic murein transglycosylase D	_____________29______37\n_____________\|_______\|\n5'-GAG...AGAAC_______AUUGA...GUC-3'\n______________GGAAGAU\n______________\|\|\|\|:\|\|\n______________CCUUUUA\n3'-UUU...UACAA_______GUCAC...UUG-5'\n_____________\|_______\|\n_____________66______58\n	30 -- 36	59 -- 65	-7.35578 kcal/mol	0.945124 kcal/mol	0.81955 kcal/mol	29 37@LB@ \| \|@LB@5'-GAG...AGAAC AUUGA...GUC-3'@LB@ GGAAGAU@LB@ \|\|\|\|:\|\|@LB@ CCUUUUA@LB@3'-UUU...UACAA GUCAC...UUG-5'@LB@ \| \|@LB@ 66 58@LB@@LB@@LB@Energy -5.59 kcal/mol@LB@Hybridization Energy -7.35578 kcal/mol@LB@Unfolding Energy - mRNA 0.945124 kcal/mol@LB@Unfolding Energy - sRNA 0.81955 kcal/mol@LB@@LB@Position - mRNA 30 -- 36@LB@Position - sRNA 59 -- 65@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 59 -- 65@LB@
180	0.02233	0.4143	b0435	bolA	-10.38	0.101210	35 -- 46	39 -- 51	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________34____________47\n_____________\|_____________\|\n5'-UGA...ACACU_____________GUGUU...CCG-3'\n______________GAUGCGA_GGCCU\n______________:\|\|\|\|:\|_\|\|\|\|:\n______________UUACGUU_CCGGG\n3'-UUU...CACCG_______A_____UUGUC...UUG-5'\n_____________\|_____________\|\n_____________52____________38\n	35 -- 41	45 -- 51	-16.689 kcal/mol	1.55914 kcal/mol	4.74571 kcal/mol	34 47@LB@ \| \|@LB@5'-UGA...ACACU GUGUU...CCG-3'@LB@ GAUGCGA GGCCU@LB@ :\|\|\|\|:\| \|\|\|\|:@LB@ UUACGUU CCGGG@LB@3'-UUU...CACCG A UUGUC...UUG-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.689 kcal/mol@LB@Unfolding Energy - mRNA 1.55914 kcal/mol@LB@Unfolding Energy - sRNA 4.74571 kcal/mol@LB@@LB@Position - mRNA 35 -- 46@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 45 -- 51@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@
32	0.002002	0.2088	b0423	thiI	-12.47	0.034301	40 -- 74	41 -- 65	tRNA s(4)U8 sulfurtransferase	_____________39_____________________________________75\n_____________\|______________________________________\|\n5'-AUG...GUAAC___C____________AUAGCAAAUAACGC________AAGGU...UUU-3'\n______________GGA___UCAG_GGCAA______________GCAAUGGU\n______________\|\|\|___\|\|\|\|_\|\|\|\|\|______________\|\|\|\|\|\|\|:\n______________CCU___AGUC_CCGUU______________CGUUACCG\n3'-UUU...UACAA___UUU____A_____A_____________________GGUUG...UUG-5'\n_____________\|______________________________________\|\n_____________66_____________________________________40\n	68 -- 74	41 -- 47	-23.8518 kcal/mol	5.56921 kcal/mol	5.80973 kcal/mol	39 75@LB@ \| \|@LB@5'-AUG...GUAAC C AUAGCAAAUAACGC AAGGU...UUU-3'@LB@ GGA UCAG GGCAA GCAAUGGU@LB@ \|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ CCU AGUC CCGUU CGUUACCG@LB@3'-UUU...UACAA UUU A A GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -12.47 kcal/mol@LB@Hybridization Energy -23.8518 kcal/mol@LB@Unfolding Energy - mRNA 5.56921 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 40 -- 74@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 41 -- 47@LB@
151	0.01786	0.3828	b0412	yajI	-11.20	0.067280	41 -- 55	41 -- 54	putative lipoprotein	_____________40______________56\n_____________\|_______________\|\n5'-CGA...GAAUG_________UAC___GUCCU...UCA-3'\n______________GGCAAUGCA___GGC\n______________\|\|\|\|\|\|\|\|\|___\|\|\|\n______________CCGUUACGU___CCG\n3'-UUU...AGUCA_________UA____GGUUG...UUG-5'\n_____________\|_______________\|\n_____________55______________40\n	43 -- 49	46 -- 52	-19.8433 kcal/mol	4.75092 kcal/mol	3.89026 kcal/mol	40 56@LB@ \| \|@LB@5'-CGA...GAAUG UAC GUCCU...UCA-3'@LB@ GGCAAUGCA GGC@LB@ \|\|\|\|\|\|\|\|\| \|\|\|@LB@ CCGUUACGU CCG@LB@3'-UUU...AGUCA UA GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -19.8433 kcal/mol@LB@Unfolding Energy - mRNA 4.75092 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 41 -- 55@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 46 -- 52@LB@
115	0.0114	0.3326	b2531	iscR	-8.61	0.227442	42 -- 64	8 -- 31	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________41_______________________65\n_____________\|________________________\|\n5'-AUG...GCCAC_______AAA______C_______UAAAU...AAC-3'\n______________GAUAAAA____UGGCA_UGAAGGU\n______________:\|\|\|\|\|\|____\|\|:\|\|_\|:\|\|\|\|:\n______________UUAUUUU____ACUGU_AUUUCCG\n3'-UUU...GUCUU_______AGAC_____U_______UAUAUUG-5'\n_____________\|________________________\|\n_____________32_______________________7\n	58 -- 64	8 -- 14	-15.5579 kcal/mol	1.96266 kcal/mol	4.98963 kcal/mol	41 65@LB@ \| \|@LB@5'-AUG...GCCAC AAA C UAAAU...AAC-3'@LB@ GAUAAAA UGGCA UGAAGGU@LB@ :\|\|\|\|\|\| \|\|:\|\| \|:\|\|\|\|:@LB@ UUAUUUU ACUGU AUUUCCG@LB@3'-UUU...GUCUU AGAC U UAUAUUG-5'@LB@ \| \|@LB@ 32 7@LB@@LB@@LB@Energy -8.61 kcal/mol@LB@Hybridization Energy -15.5579 kcal/mol@LB@Unfolding Energy - mRNA 1.96266 kcal/mol@LB@Unfolding Energy - sRNA 4.98963 kcal/mol@LB@@LB@Position - mRNA 42 -- 64@LB@Position - sRNA 8 -- 31@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 8 -- 14@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@

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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