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
193	0.01107	0.1919	b3532	bcsB	-10.24	0.150531	226 -- 241	15 -- 35	regulator of cellulose synthase cyclic di-GMP binding	_____________225___________________242\n_____________\|_____________________\|\n5'-AAG...GAUUU_______G_____________GAUGA...UCA-3'\n______________GUGCAGU__GC____UAUGGG\n______________\|\|:\|\|\|:__\|\|____\|\|\|\|\|\|\n______________CAUGUCG__CG____AUACCC\n3'-UUU...AGGAC_______AU__UAAA______AAUAC...UCG-5'\n_____________\|_____________________\|\n_____________36____________________14\n	226 -- 232	29 -- 35	-18.7324 kcal/mol	7.03896 kcal/mol	1.4496 kcal/mol	225 242@LB@ \| \|@LB@5'-AAG...GAUUU G GAUGA...UCA-3'@LB@ GUGCAGU GC UAUGGG@LB@ \|\|:\|\|\|: \|\| \|\|\|\|\|\|@LB@ CAUGUCG CG AUACCC@LB@3'-UUU...AGGAC AU UAAA AAUAC...UCG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -18.7324 kcal/mol@LB@Unfolding Energy - mRNA 7.03896 kcal/mol@LB@Unfolding Energy - sRNA 1.4496 kcal/mol@LB@@LB@Position - mRNA 226 -- 241@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 29 -- 35@LB@
197	0.01153	0.1967	b0610	rnk	-10.49	0.135367	130 -- 162	7 -- 39	regulator of nucleoside diphosphate kinase	_____________129__________________________________163\n_____________\|____________________________________\|\n5'-UCU...CGCCG___________G__G_____CUUU____________AUCUG...CGU-3'\n______________CCUG__ACGGU_AG_GUUUU____UGGG_UAUGUUU\n______________\|\|\|\|__\|\|:\|:_\|\|_:\|\|\|\|____\|\|\|\|_\|\|\|\|\|\|\|\n______________GGAC__UGUCG_UC_UAAAA____ACCC_AUACAAA\n3'-UUU...ACCAA____CA_____A__G_____U_______A_______AAGUCG-5'\n_____________\|____________________________________\|\n_____________40___________________________________6\n	156 -- 162	7 -- 13	-25.6411 kcal/mol	10.5512 kcal/mol	4.60345 kcal/mol	129 163@LB@ \| \|@LB@5'-UCU...CGCCG G G CUUU AUCUG...CGU-3'@LB@ CCUG ACGGU AG GUUUU UGGG UAUGUUU@LB@ \|\|\|\| \|\|:\|: \|\| :\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ GGAC UGUCG UC UAAAA ACCC AUACAAA@LB@3'-UUU...ACCAA CA A G U A AAGUCG-5'@LB@ \| \|@LB@ 40 6@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -25.6411 kcal/mol@LB@Unfolding Energy - mRNA 10.5512 kcal/mol@LB@Unfolding Energy - sRNA 4.60345 kcal/mol@LB@@LB@Position - mRNA 130 -- 162@LB@Position - sRNA 7 -- 39@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 7 -- 13@LB@
121	0.005123	0.1413	b1735	chbR	-8.25	0.324466	38 -- 46	30 -- 38	repressor of chb operon for N N'-diacetylchitobiose utilization	_____________37________47\n_____________\|_________\|\n5'-GAU...CGCAU_________ACGAA...CUG-3'\n______________CUGGUACAG\n______________\|\|\|\|\|\|\|\|\|\n______________GACCAUGUC\n3'-UUU...CCAAG_________GAUCG...UCG-5'\n_____________\|_________\|\n_____________39________29\n	40 -- 46	30 -- 36	-15.5432 kcal/mol	3.07825 kcal/mol	4.2107 kcal/mol	37 47@LB@ \| \|@LB@5'-GAU...CGCAU ACGAA...CUG-3'@LB@ CUGGUACAG@LB@ \|\|\|\|\|\|\|\|\|@LB@ GACCAUGUC@LB@3'-UUU...CCAAG GAUCG...UCG-5'@LB@ \| \|@LB@ 39 29@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -15.5432 kcal/mol@LB@Unfolding Energy - mRNA 3.07825 kcal/mol@LB@Unfolding Energy - sRNA 4.2107 kcal/mol@LB@@LB@Position - mRNA 38 -- 46@LB@Position - sRNA 30 -- 38@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 30 -- 36@LB@
145	0.006858	0.158	b2079	baeR	-14.59	0.014658	61 -- 107	1 -- 46	response regulator in two-component regulatory system with BaeS	_____________60________________________________________________108\n_____________\|_________________________________________________\|\n5'-CAG...CCAGC__C______G__C__G________A____CC__AACAU____GA_____ACAUA...CGA-3'\n______________GG_GGUUCC_GG_UG_GGCUGGCG_UUUG__UG_____UGUU____AGC\n______________\|\|_\|\|\|\|\|\|_\|\|_\|:_:\|\|\|:\|\|:_\|\|\|:__\|\|_____\|\|\|\|____\|\|\|\n______________CC_CCAAGG_CC_AU_UCGAUCGU_AAAU__AC_____ACAA____UCG\n3'-UUU...UUCCU__A______A_____G________A________CCAAU____AAAG___-5'\n_____________\|________________________________________________\|\n_____________47_______________________________________________1\n	78 -- 84	24 -- 30	-36.7072 kcal/mol	17.5074 kcal/mol	4.60935 kcal/mol	60 108@LB@ \| \|@LB@5'-CAG...CCAGC C G C G A CC AACAU GA ACAUA...CGA-3'@LB@ GG GGUUCC GG UG GGCUGGCG UUUG UG UGUU AGC@LB@ \|\| \|\|\|\|\|\| \|\| \|: :\|\|\|:\|\|: \|\|\|: \|\| \|\|\|\| \|\|\|@LB@ CC CCAAGG CC AU UCGAUCGU AAAU AC ACAA UCG@LB@3'-UUU...UUCCU A A G A CCAAU AAAG -5'@LB@ \| \|@LB@ 47 1@LB@@LB@@LB@Energy -14.59 kcal/mol@LB@Hybridization Energy -36.7072 kcal/mol@LB@Unfolding Energy - mRNA 17.5074 kcal/mol@LB@Unfolding Energy - sRNA 4.60935 kcal/mol@LB@@LB@Position - mRNA 61 -- 107@LB@Position - sRNA 1 -- 46@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 24 -- 30@LB@
52	0.001222	0.07744	b2217	rcsB	-14.74	0.013297	68 -- 91	9 -- 38	response regulator in two-component regulatory system with RcsC and YojN	_____________67_______________________________92\n_____________\|________________________________\|\n5'-AAC...UAAAU_______CC___A___________________GAAAC...GCG-3'\n______________CUGGUAC__GGC_AGCA________GUUAUGU\n______________\|\|\|\|\|\|\|__:\|\|_\|\|\|\|________\|\|\|\|\|\|\|\n______________GACCAUG__UCG_UCGU________CAAUACA\n3'-UUU...CCAAG____________A____AAAAUACC_______AAAAGUCG-5'\n_____________\|________________________________\|\n_____________39_______________________________8\n	85 -- 91	9 -- 15	-24.0406 kcal/mol	4.76673 kcal/mol	4.53501 kcal/mol	67 92@LB@ \| \|@LB@5'-AAC...UAAAU CC A GAAAC...GCG-3'@LB@ CUGGUAC GGC AGCA GUUAUGU@LB@ \|\|\|\|\|\|\| :\|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ GACCAUG UCG UCGU CAAUACA@LB@3'-UUU...CCAAG A AAAAUACC AAAAGUCG-5'@LB@ \| \|@LB@ 39 8@LB@@LB@@LB@Energy -14.74 kcal/mol@LB@Hybridization Energy -24.0406 kcal/mol@LB@Unfolding Energy - mRNA 4.76673 kcal/mol@LB@Unfolding Energy - sRNA 4.53501 kcal/mol@LB@@LB@Position - mRNA 68 -- 91@LB@Position - sRNA 9 -- 38@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 9 -- 15@LB@
124	0.00526	0.1416	b3170	rimP	-10.72	0.121991	191 -- 217	24 -- 49	ribosome maturation factor for 30S subunits	_____________190__________________________218\n_____________\|____________________________\|\n5'-CUU...GUCUU________G_____UCC___UUAG____AAAAU...CAU-3'\n______________GGGGGUGG__CUUG___ACA____AGCA\n______________\|\|:\|\|\|\|\|__\|:\|\|___\|\|\|____\|\|\|\|\n______________CCUCCACC__GGAC___UGU____UCGU\n3'-UUU...CGAUU________AA____CA____CGA_____AAAAU...UCG-5'\n_____________\|____________________________\|\n_____________50___________________________23\n	192 -- 198	42 -- 48	-23.9554 kcal/mol	8.6777 kcal/mol	4.5591 kcal/mol	190 218@LB@ \| \|@LB@5'-CUU...GUCUU G UCC UUAG AAAAU...CAU-3'@LB@ GGGGGUGG CUUG ACA AGCA@LB@ \|\|:\|\|\|\|\| \|:\|\| \|\|\| \|\|\|\|@LB@ CCUCCACC GGAC UGU UCGU@LB@3'-UUU...CGAUU AA CA CGA AAAAU...UCG-5'@LB@ \| \|@LB@ 50 23@LB@@LB@@LB@Energy -10.72 kcal/mol@LB@Hybridization Energy -23.9554 kcal/mol@LB@Unfolding Energy - mRNA 8.6777 kcal/mol@LB@Unfolding Energy - sRNA 4.5591 kcal/mol@LB@@LB@Position - mRNA 191 -- 217@LB@Position - sRNA 24 -- 49@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 42 -- 48@LB@
133	0.005817	0.146	b3461	rpoH	-7.67	0.391921	235 -- 243	24 -- 32	RNA polymerase sigma 32 (sigma H) factor	_____________234_______244\n_____________\|_________\|\n5'-GGA...AGCCC_________ACCUG...AGG-3'\n______________CAGUUGGCA\n______________\|\|\|:\|:\|\|\|\n______________GUCGAUCGU\n3'-UUU...ACCAU_________AAAAU...UCG-5'\n_____________\|_________\|\n_____________33________23\n	237 -- 243	24 -- 30	-13.04 kcal/mol	3.94405 kcal/mol	1.424 kcal/mol	234 244@LB@ \| \|@LB@5'-GGA...AGCCC ACCUG...AGG-3'@LB@ CAGUUGGCA@LB@ \|\|\|:\|:\|\|\|@LB@ GUCGAUCGU@LB@3'-UUU...ACCAU AAAAU...UCG-5'@LB@ \| \|@LB@ 33 23@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -13.04 kcal/mol@LB@Unfolding Energy - mRNA 3.94405 kcal/mol@LB@Unfolding Energy - sRNA 1.424 kcal/mol@LB@@LB@Position - mRNA 235 -- 243@LB@Position - sRNA 24 -- 32@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 24 -- 30@LB@
104	0.003825	0.1236	b0081	mraZ	-12.90	0.040525	169 -- 210	15 -- 49	RsmH methytransferase inhibitor	_____________168________________________________________211\n_____________\|__________________________________________\|\n5'-GAU...AUUGU____CAAA____GAAUAAGG____A_________GUUCC___GAGCA...AAA-3'\n______________GGGG____GUGG________GGUG_GGCUGGCAU_____GGG\n______________\|\|:\|____\|\|\|\|________\|\|\|:_:\|\|\|:\|\|\|\|_____\|\|\|\n______________CCUC____CACC________CCAU_UCGAUCGUA_____CCC\n3'-UUU...CGAUU____________AAGGA_______G_________AAAUA___AAUAC...UCG-5'\n_____________\|__________________________________________\|\n_____________50_________________________________________14\n	196 -- 202	23 -- 29	-32.8076 kcal/mol	15.3299 kcal/mol	4.57366 kcal/mol	168 211@LB@ \| \|@LB@5'-GAU...AUUGU CAAA GAAUAAGG A GUUCC GAGCA...AAA-3'@LB@ GGGG GUGG GGUG GGCUGGCAU GGG@LB@ \|\|:\| \|\|\|\| \|\|\|: :\|\|\|:\|\|\|\| \|\|\|@LB@ CCUC CACC CCAU UCGAUCGUA CCC@LB@3'-UUU...CGAUU AAGGA G AAAUA AAUAC...UCG-5'@LB@ \| \|@LB@ 50 14@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -32.8076 kcal/mol@LB@Unfolding Energy - mRNA 15.3299 kcal/mol@LB@Unfolding Energy - sRNA 4.57366 kcal/mol@LB@@LB@Position - mRNA 169 -- 210@LB@Position - sRNA 15 -- 49@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 23 -- 29@LB@
94	0.003268	0.1162	b2687	luxS	-10.18	0.155002	189 -- 196	42 -- 49	S-ribosylhomocysteine lyase	_____________188______197\n_____________\|________\|\n5'-GAA...UUACC________CUAAA...UCA-3'\n______________GGAGGUGG\n______________\|\|\|\|\|\|\|\|\n______________CCUCCACC\n3'-UUU...CGAUU________AAGGA...UCG-5'\n_____________\|________\|\n_____________50_______41\n	190 -- 196	42 -- 48	-16.7111 kcal/mol	3.76521 kcal/mol	2.77009 kcal/mol	188 197@LB@ \| \|@LB@5'-GAA...UUACC CUAAA...UCA-3'@LB@ GGAGGUGG@LB@ \|\|\|\|\|\|\|\|@LB@ CCUCCACC@LB@3'-UUU...CGAUU AAGGA...UCG-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -10.18 kcal/mol@LB@Hybridization Energy -16.7111 kcal/mol@LB@Unfolding Energy - mRNA 3.76521 kcal/mol@LB@Unfolding Energy - sRNA 2.77009 kcal/mol@LB@@LB@Position - mRNA 189 -- 196@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 42 -- 48@LB@
79	0.002261	0.09621	b2556	glrK	-15.72	0.006745	240 -- 258	20 -- 38	sensor protein kinase regulating glmY sRNA in two-component system with response regulator GlrR	_____________239_________________259\n_____________\|___________________\|\n5'-CUA...GACAA______AU___________UGCUG...CCU-3'\n______________CUGGUA__GCUGGCAUUUU\n______________\|\|\|\|\|\|__\|\|\|:\|\|\|\|\|\|\|\n______________GACCAU__CGAUCGUAAAA\n3'-UUU...CCAAG______GU___________UACCC...UCG-5'\n_____________\|___________________\|\n_____________39__________________19\n	252 -- 258	20 -- 26	-25.6316 kcal/mol	5.4283 kcal/mol	4.48821 kcal/mol	239 259@LB@ \| \|@LB@5'-CUA...GACAA AU UGCUG...CCU-3'@LB@ CUGGUA GCUGGCAUUUU@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|\|@LB@ GACCAU CGAUCGUAAAA@LB@3'-UUU...CCAAG GU UACCC...UCG-5'@LB@ \| \|@LB@ 39 19@LB@@LB@@LB@Energy -15.72 kcal/mol@LB@Hybridization Energy -25.6316 kcal/mol@LB@Unfolding Energy - mRNA 5.4283 kcal/mol@LB@Unfolding Energy - sRNA 4.48821 kcal/mol@LB@@LB@Position - mRNA 240 -- 258@LB@Position - sRNA 20 -- 38@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 20 -- 26@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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