Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
123	0.01951	0.5155	b0032	carA	-10.10	0.092857	258 -- 264	55 -- 61	carbamoyl phosphate synthetase small subunit glutamine amidotransferase	_____________257_____265\n_____________\|_______\|\n5'-UUG...GGGCC_______CAACA...AUA-3'\n______________AUAGGGG\n______________\|\|\|\|\|\|\|\n______________UAUCCCC\n3'-UUU...AACUU_______AUUUG...UCG-5'\n_____________\|_______\|\n_____________62______54\n	258 -- 264	55 -- 61	-10.8319 kcal/mol	0.710423 kcal/mol	0.0258473 kcal/mol	257 265@LB@ \| \|@LB@5'-UUG...GGGCC CAACA...AUA-3'@LB@ AUAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UAUCCCC@LB@3'-UUU...AACUU AUUUG...UCG-5'@LB@ \| \|@LB@ 62 54@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -10.8319 kcal/mol@LB@Unfolding Energy - mRNA 0.710423 kcal/mol@LB@Unfolding Energy - sRNA 0.0258473 kcal/mol@LB@@LB@Position - mRNA 258 -- 264@LB@Position - sRNA 55 -- 61@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 55 -- 61@LB@
134	0.02184	0.526	b0034	caiF	-11.03	0.059446	251 -- 259	1 -- 9	cai operon transcriptional activator	_____________250_______260\n_____________\|_________\|\n5'-UGA...GAAUG_________UGAAA...AUU-3'\n______________GAUGAUGGC\n______________\|\|\|\|\|\|:\|\|\n______________CUACUAUCG\n3'-UUU...AAUUA_________-5'\n_____________\|________\|\n_____________10_______1\n	253 -- 259	1 -- 7	-13.9707 kcal/mol	2.91573 kcal/mol	0.0200155 kcal/mol	250 260@LB@ \| \|@LB@5'-UGA...GAAUG UGAAA...AUU-3'@LB@ GAUGAUGGC@LB@ \|\|\|\|\|\|:\|\|@LB@ CUACUAUCG@LB@3'-UUU...AAUUA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -13.9707 kcal/mol@LB@Unfolding Energy - mRNA 2.91573 kcal/mol@LB@Unfolding Energy - sRNA 0.0200155 kcal/mol@LB@@LB@Position - mRNA 251 -- 259@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 1 -- 7@LB@
24	0.001422	0.1946	b0065	yabI	-15.22	0.006192	70 -- 99	1 -- 29	DedA family inner membrane protein	_____________69______________________________100\n_____________\|_______________________________\|\n5'-UGA...CGUGC____U_____GAA_____G____________CGUCA...GUU-3'\n______________CGGU_GUGAA___AAAGU_AAUGAUG_UAGC\n______________\|\|\|\|_:\|:\|\|___\|\|\|\|\|_\|\|\|\|\|\|\|_\|\|\|\|\n______________GCCA_UAUUU___UUUCA_UUACUAC_AUCG\n3'-UUU...UUACU____U_____A_______A_______U____-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	89 -- 95	6 -- 12	-22.6746 kcal/mol	5.32597 kcal/mol	2.12711 kcal/mol	69 100@LB@ \| \|@LB@5'-UGA...CGUGC U GAA G CGUCA...GUU-3'@LB@ CGGU GUGAA AAAGU AAUGAUG UAGC@LB@ \|\|\|\| :\|:\|\| \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ GCCA UAUUU UUUCA UUACUAC AUCG@LB@3'-UUU...UUACU U A A U -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.22 kcal/mol@LB@Hybridization Energy -22.6746 kcal/mol@LB@Unfolding Energy - mRNA 5.32597 kcal/mol@LB@Unfolding Energy - sRNA 2.12711 kcal/mol@LB@@LB@Position - mRNA 70 -- 99@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 6 -- 12@LB@
121	0.01924	0.5155	b0074	leuA	-11.43	0.049038	243 -- 261	39 -- 56	2-isopropylmalate synthase	_____________242_________________262\n_____________\|___________________\|\n5'-CAU...GCGAC______________A____CAAGC...UGG-3'\n______________GGUGAACAGGCGUU_CAGG\n______________\|\|\|:\|\|\|\|\|:\|:\|\|_\|\|\|:\n______________CCAUUUGUCUGUAA_GUCU\n3'-UUU...UAUCC___________________UUACU...UCG-5'\n_____________\|___________________\|\n_____________57__________________38\n	247 -- 253	46 -- 52	-24.0317 kcal/mol	6.35652 kcal/mol	6.24929 kcal/mol	242 262@LB@ \| \|@LB@5'-CAU...GCGAC A CAAGC...UGG-3'@LB@ GGUGAACAGGCGUU CAGG@LB@ \|\|\|:\|\|\|\|\|:\|:\|\| \|\|\|:@LB@ CCAUUUGUCUGUAA GUCU@LB@3'-UUU...UAUCC UUACU...UCG-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -24.0317 kcal/mol@LB@Unfolding Energy - mRNA 6.35652 kcal/mol@LB@Unfolding Energy - sRNA 6.24929 kcal/mol@LB@@LB@Position - mRNA 243 -- 261@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 46 -- 52@LB@
108	0.01698	0.5123	b0078	ilvH	-10.97	0.061484	141 -- 180	1 -- 51	acetolactate synthase 3 small subunit valine-sensitive	_____________140_________________________________________________181\n_____________\|___________________________________________________\|\n5'-GCC...CCGAU______UCG___________________________AU_______UA____AAAAC...UGA-3'\n______________GCAGAU___CGGG_______GGCGG_AAUGGAUGAA____GUGGU___AGC\n______________:\|\|\|\|:___\|:\|:_______\|:\|\|\|_\|\|\|::\|\|:\|\|____:\|\|:\|___\|\|\|\n______________UGUCUG___GUCU_______CUGCC_UUAUUUAUUU____UACUA___UCG\n3'-UUU...CCAUU______UAA____UUACUUA_____A__________CAAU_____CUA___-5'\n_____________\|__________________________________________________\|\n_____________52_________________________________________________1\n	162 -- 168	16 -- 22	-27.7823 kcal/mol	10.4814 kcal/mol	6.33528 kcal/mol	140 181@LB@ \| \|@LB@5'-GCC...CCGAU UCG AU UA AAAAC...UGA-3'@LB@ GCAGAU CGGG GGCGG AAUGGAUGAA GUGGU AGC@LB@ :\|\|\|\|: \|:\|: \|:\|\|\| \|\|\|::\|\|:\|\| :\|\|:\| \|\|\|@LB@ UGUCUG GUCU CUGCC UUAUUUAUUU UACUA UCG@LB@3'-UUU...CCAUU UAA UUACUUA A CAAU CUA -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -10.97 kcal/mol@LB@Hybridization Energy -27.7823 kcal/mol@LB@Unfolding Energy - mRNA 10.4814 kcal/mol@LB@Unfolding Energy - sRNA 6.33528 kcal/mol@LB@@LB@Position - mRNA 141 -- 180@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 16 -- 22@LB@
138	0.02287	0.526	b0081	mraZ	-12.90	0.022954	180 -- 193	52 -- 64	RsmH methytransferase inhibitor	_____________179____________194\n_____________\|______________\|\n5'-GAU...AAGUG_____A________GGCUG...AAA-3'\n______________GGAAU_AGGGGUGA\n______________\|:\|\|\|_\|\|\|\|\|\|:\|\n______________CUUUA_UCCCCAUU\n3'-UUU...GCCAA______________UGUCU...UCG-5'\n_____________\|______________\|\n_____________65_____________51\n	187 -- 193	52 -- 58	-14.7021 kcal/mol	1.72638 kcal/mol	0.0778991 kcal/mol	179 194@LB@ \| \|@LB@5'-GAU...AAGUG A GGCUG...AAA-3'@LB@ GGAAU AGGGGUGA@LB@ \|:\|\|\| \|\|\|\|\|\|:\|@LB@ CUUUA UCCCCAUU@LB@3'-UUU...GCCAA UGUCU...UCG-5'@LB@ \| \|@LB@ 65 51@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -14.7021 kcal/mol@LB@Unfolding Energy - mRNA 1.72638 kcal/mol@LB@Unfolding Energy - sRNA 0.0778991 kcal/mol@LB@@LB@Position - mRNA 180 -- 193@LB@Position - sRNA 52 -- 64@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 52 -- 58@LB@
3	3.826e-06	0.004187	b0090	murG	-16.88	0.002220	177 -- 235	1 -- 51	N-acetylglucosaminyl transferase	_____________176_________________________________________________________236\n_____________\|___________________________________________________________\|\n5'-AUU...AAAGC___________UAC_____UCAC____A_____C___G____CGA______________AGGCG...GUU-3'\n______________GCAGGCGUUUG___GAGGU____GAUG_GUGGU_AAG_AAAG___UUAAUGGUGAUGGC\n______________:\|\|\|:\|:\|\|::___\|\|::\|____\|\|:\|_\|\|::\|_\|\|:_\|\|\|\|___\|\|\|\|\|\|:\|\|\|\|:\|\|\n______________UGUCUGUAAGU___CUUUA____CUGC_CAUUA_UUU_UUUC___AAUUACUACUAUCG\n3'-UUU...CCAUU___________________CUUA______________A_____________________-5'\n_____________\|__________________________________________________________\|\n_____________52_________________________________________________________1\n	229 -- 235	1 -- 7	-39.4015 kcal/mol	16.1862 kcal/mol	6.33528 kcal/mol	176 236@LB@ \| \|@LB@5'-AUU...AAAGC UAC UCAC A C G CGA AGGCG...GUU-3'@LB@ GCAGGCGUUUG GAGGU GAUG GUGGU AAG AAAG UUAAUGGUGAUGGC@LB@ :\|\|\|:\|:\|\|:: \|\|::\| \|\|:\| \|\|::\| \|\|: \|\|\|\| \|\|\|\|\|\|:\|\|\|\|:\|\|@LB@ UGUCUGUAAGU CUUUA CUGC CAUUA UUU UUUC AAUUACUACUAUCG@LB@3'-UUU...CCAUU CUUA A -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -16.88 kcal/mol@LB@Hybridization Energy -39.4015 kcal/mol@LB@Unfolding Energy - mRNA 16.1862 kcal/mol@LB@Unfolding Energy - sRNA 6.33528 kcal/mol@LB@@LB@Position - mRNA 177 -- 235@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
26	0.001686	0.211	b0091	murC	-10.53	0.075719	174 -- 220	1 -- 48	UDP-N-acetylmuramate:L-alanine ligase	_____________173______________________________________________221\n_____________\|________________________________________________\|\n5'-CAG...CGUAU__AUUUA______U___________A_______UACACAACAAU____AAAAC...GCG-3'\n______________GA_____AGAAGU_AAUGGC_GUAA_GAAUGAA___________UGGC\n______________\|\|_____\|\|\|\|:\|_\|\|\|\|:\|_\|\|\|\|_:\|\|\|:\|\|___________\|:\|\|\n______________CU_____UCUUUA_UUACUG_CAUU_UUUAUUU___________AUCG\n3'-UUU...UUUGU__GUAAG______C______C____A_______CAAUUACUACU____-5'\n_____________\|_______________________________________________\|\n_____________49______________________________________________1\n	199 -- 205	16 -- 22	-22.2946 kcal/mol	5.44296 kcal/mol	6.32011 kcal/mol	173 221@LB@ \| \|@LB@5'-CAG...CGUAU AUUUA U A UACACAACAAU AAAAC...GCG-3'@LB@ GA AGAAGU AAUGGC GUAA GAAUGAA UGGC@LB@ \|\| \|\|\|\|:\| \|\|\|\|:\| \|\|\|\| :\|\|\|:\|\| \|:\|\|@LB@ CU UCUUUA UUACUG CAUU UUUAUUU AUCG@LB@3'-UUU...UUUGU GUAAG C C A CAAUUACUACU -5'@LB@ \| \|@LB@ 49 1@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -22.2946 kcal/mol@LB@Unfolding Energy - mRNA 5.44296 kcal/mol@LB@Unfolding Energy - sRNA 6.32011 kcal/mol@LB@@LB@Position - mRNA 174 -- 220@LB@Position - sRNA 1 -- 48@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 16 -- 22@LB@
97	0.01584	0.5059	b0116	lpd	-10.63	0.072174	157 -- 204	5 -- 49	dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase	_____________156_______________________________________________205\n_____________\|_________________________________________________\|\n5'-CCG...CUGAA_____A_____U____CC_C___A________UAUA___GUC_______GUACU...UAA-3'\n______________AGACG__CGGG_AUGA__G_CGG_GAUAAAUA____GAG___AUGAUGA\n______________\|\|\|\|:__\|:\|:_\|\|\|\|__\|_\|\|\|_:\|\|\|\|\|\|\|____:\|\|___\|\|\|\|\|\|\|\n______________UCUGU__GUCU_UACU__C_GCC_UUAUUUAU____UUC___UACUACU\n3'-UUU...AUUUG_____AA____U____UA_U___A_______________AAU_______AUCG-5'\n_____________\|_________________________________________________\|\n_____________50________________________________________________4\n	198 -- 204	5 -- 11	-27.6335 kcal/mol	10.6788 kcal/mol	6.32229 kcal/mol	156 205@LB@ \| \|@LB@5'-CCG...CUGAA A U CC C A UAUA GUC GUACU...UAA-3'@LB@ AGACG CGGG AUGA G CGG GAUAAAUA GAG AUGAUGA@LB@ \|\|\|\|: \|:\|: \|\|\|\| \| \|\|\| :\|\|\|\|\|\|\| :\|\| \|\|\|\|\|\|\|@LB@ UCUGU GUCU UACU C GCC UUAUUUAU UUC UACUACU@LB@3'-UUU...AUUUG AA U UA U A AAU AUCG-5'@LB@ \| \|@LB@ 50 4@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -27.6335 kcal/mol@LB@Unfolding Energy - mRNA 10.6788 kcal/mol@LB@Unfolding Energy - sRNA 6.32229 kcal/mol@LB@@LB@Position - mRNA 157 -- 204@LB@Position - sRNA 5 -- 49@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
196	0.0332	0.554	b0128	yadH	-11.13	0.056665	104 -- 121	39 -- 55	putative ABC transporter permease	_____________103________________122\n_____________\|__________________\|\n5'-UUA...GUUAA_______G__________UAUUA...UCA-3'\n______________GUGAGCA_GGCAUUCAGG\n______________\|\|:\|:\|\|_\|:\|\|\|\|\|\|\|:\n______________CAUUUGU_CUGUAAGUCU\n3'-UUU...AUCCC__________________UUACU...UCG-5'\n_____________\|__________________\|\n_____________56_________________38\n	114 -- 120	40 -- 46	-20.6932 kcal/mol	3.311 kcal/mol	6.24918 kcal/mol	103 122@LB@ \| \|@LB@5'-UUA...GUUAA G UAUUA...UCA-3'@LB@ GUGAGCA GGCAUUCAGG@LB@ \|\|:\|:\|\| \|:\|\|\|\|\|\|\|:@LB@ CAUUUGU CUGUAAGUCU@LB@3'-UUU...AUCCC UUACU...UCG-5'@LB@ \| \|@LB@ 56 38@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -20.6932 kcal/mol@LB@Unfolding Energy - mRNA 3.311 kcal/mol@LB@Unfolding Energy - sRNA 6.24918 kcal/mol@LB@@LB@Position - mRNA 104 -- 121@LB@Position - sRNA 39 -- 55@LB@Position Seed - mRNA 114 -- 120@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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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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