Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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	Additional homologs
195	0.04073	0.6177	b3166	truB	-9.24	0.058593	189 -- 197	45 -- 53	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase		_____________188_______198\n_____________\|_________\|\n5'-GGC...GACAG_________CUAAU...AAC-3'\n______________CAAGGAGGA\n______________\|\|\|:\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	191 -- 197	45 -- 51	-13.1895 kcal/mol	3.02734 kcal/mol	0.917553 kcal/mol	188 198@LB@ \| \|@LB@5'-GGC...GACAG CUAAU...AAC-3'@LB@ CAAGGAGGA@LB@ \|\|\|:\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.24 kcal/mol@LB@Hybridization Energy -13.1895 kcal/mol@LB@Unfolding Energy - mRNA 3.02734 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 45 -- 51@LB@
36	0.007218	0.6129	b3938	metJ	-9.22	0.059290	181 -- 189	45 -- 53	transcriptional repressor S-adenosylmethionine-binding		_____________180_______190\n_____________\|_________\|\n5'-UCU...AUUGA_________UUAAG...UGU-3'\n______________CGAAGAGGA\n______________\|:\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	183 -- 189	45 -- 51	-12.478 kcal/mol	2.34125 kcal/mol	0.917553 kcal/mol	180 190@LB@ \| \|@LB@5'-UCU...AUUGA UUAAG...UGU-3'@LB@ CGAAGAGGA@LB@ \|:\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -12.478 kcal/mol@LB@Unfolding Energy - mRNA 2.34125 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 181 -- 189@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 45 -- 51@LB@
105	0.0216	0.6177	b2962	yggX	-9.20	0.059738	186 -- 194	45 -- 53	oxidative damage protective factor for iron-sulfur proteins		_____________185_______195\n_____________\|_________\|\n5'-UCA...GUCGA_________UGAUU...AGA-3'\n______________UAAAGAGGA\n______________:\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	188 -- 194	45 -- 51	-10.7665 kcal/mol	0.645872 kcal/mol	0.917553 kcal/mol	185 195@LB@ \| \|@LB@5'-UCA...GUCGA UGAUU...AGA-3'@LB@ UAAAGAGGA@LB@ :\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -10.7665 kcal/mol@LB@Unfolding Energy - mRNA 0.645872 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 45 -- 51@LB@
76	0.01599	0.6177	b1849	purT	-9.18	0.060248	187 -- 212	25 -- 50	phosphoribosylglycinamide formyltransferase 2		_____________186________________________213\n_____________\|__________________________\|\n5'-UUU...UAAUC______UA______AUGAC_______GGCAC...GUC-3'\n______________AGGGGA__UUCGUU_____GUUAUUA\n______________\|\|:\|\|\|__\|\|\|:\|\|_____:\|\|\|\|\|\|\n______________UCUCCU__AAGUAA_____UAAUAAU\n3'-UUU...CAGUU______UA______AAAAA_______ACGGC...ACA-5'\n_____________\|__________________________\|\n_____________51_________________________24\n	206 -- 212	25 -- 31	-15.1619 kcal/mol	4.88468 kcal/mol	1.09239 kcal/mol	186 213@LB@ \| \|@LB@5'-UUU...UAAUC UA AUGAC GGCAC...GUC-3'@LB@ AGGGGA UUCGUU GUUAUUA@LB@ \|\|:\|\|\| \|\|\|:\|\| :\|\|\|\|\|\|@LB@ UCUCCU AAGUAA UAAUAAU@LB@3'-UUU...CAGUU UA AAAAA ACGGC...ACA-5'@LB@ \| \|@LB@ 51 24@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -15.1619 kcal/mol@LB@Unfolding Energy - mRNA 4.88468 kcal/mol@LB@Unfolding Energy - sRNA 1.09239 kcal/mol@LB@@LB@Position - mRNA 187 -- 212@LB@Position - sRNA 25 -- 50@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 25 -- 31@LB@
138	0.02658	0.6177	b2331	smrB	-9.17	0.060779	224 -- 232	45 -- 53	putative DNA endonuclease		_____________223_______233\n_____________\|_________\|\n5'-UCA...CUUAG_________CCAGG...GAC-3'\n______________CGAGGAGGA\n______________\|:\|:\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	226 -- 232	45 -- 51	-12.8038 kcal/mol	2.72026 kcal/mol	0.917553 kcal/mol	223 233@LB@ \| \|@LB@5'-UCA...CUUAG CCAGG...GAC-3'@LB@ CGAGGAGGA@LB@ \|:\|:\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -12.8038 kcal/mol@LB@Unfolding Energy - mRNA 2.72026 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 224 -- 232@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 45 -- 51@LB@
158	0.03174	0.6177	b3185	rpmA	-9.10	0.062717	186 -- 199	39 -- 52	50S ribosomal subunit protein L27		_____________185____________200\n_____________\|______________\|\n5'-GAA...GACCU______A_______AAUGG...CGG-3'\n______________GAGGAG_GAUUUCA\n______________:\|:\|\|\|_:\|\|\|\|\|\|\n______________UUUCUC_UUAAAGU\n3'-UUU...GGCAG______C_______AAAAA...ACA-5'\n_____________\|______________\|\n_____________53_____________38\n	193 -- 199	39 -- 45	-11.8509 kcal/mol	1.7019 kcal/mol	1.05043 kcal/mol	185 200@LB@ \| \|@LB@5'-GAA...GACCU A AAUGG...CGG-3'@LB@ GAGGAG GAUUUCA@LB@ :\|:\|\|\| :\|\|\|\|\|\|@LB@ UUUCUC UUAAAGU@LB@3'-UUU...GGCAG C AAAAA...ACA-5'@LB@ \| \|@LB@ 53 38@LB@@LB@@LB@Energy -9.10 kcal/mol@LB@Hybridization Energy -11.8509 kcal/mol@LB@Unfolding Energy - mRNA 1.7019 kcal/mol@LB@Unfolding Energy - sRNA 1.05043 kcal/mol@LB@@LB@Position - mRNA 186 -- 199@LB@Position - sRNA 39 -- 52@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 39 -- 45@LB@
51	0.009714	0.6129	b1736	chbA	-9.09	0.063099	186 -- 194	44 -- 52	N N'-diacetylchitobiose-specific enzyme IIA component of PTS		_____________185_______195\n_____________\|_________\|\n5'-GGU...AGAAA_________CGAUG...GCC-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	188 -- 194	44 -- 50	-11.469 kcal/mol	1.52278 kcal/mol	0.860683 kcal/mol	185 195@LB@ \| \|@LB@5'-GGU...AGAAA CGAUG...GCC-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -9.09 kcal/mol@LB@Hybridization Energy -11.469 kcal/mol@LB@Unfolding Energy - mRNA 1.52278 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
84	0.01785	0.6177	b4318	fimF	-9.06	0.063721	96 -- 107	44 -- 55	minor component of type 1 fimbriae	b1504 b0943	_____________95___________108\n_____________\|____________\|\n5'-CAU...AAUGG_GA_________AAUGC...UCA-3'\n______________G__GAAGAGGAA\n______________\|__:\|\|\|\|\|\|\|\|\n______________C__UUUCUCCUU\n3'-UUU...CCGGG_AG_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	101 -- 107	44 -- 50	-12.9705 kcal/mol	2.96464 kcal/mol	0.941432 kcal/mol	95 108@LB@ \| \|@LB@5'-CAU...AAUGG GA AAUGC...UCA-3'@LB@ G GAAGAGGAA@LB@ \| :\|\|\|\|\|\|\|\|@LB@ C UUUCUCCUU@LB@3'-UUU...CCGGG AG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -12.9705 kcal/mol@LB@Unfolding Energy - mRNA 2.96464 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 96 -- 107@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 44 -- 50@LB@
97	0.01904	0.6177	b3102	yqjG	-9.04	0.064335	159 -- 168	44 -- 53	putative S-transferase		_____________158________169\n_____________\|__________\|\n5'-GCA...AAAAA__________GCUCC...GGC-3'\n______________CGAGGAGGAA\n______________\|:\|:\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	162 -- 168	44 -- 50	-13.5343 kcal/mol	3.56251 kcal/mol	0.927997 kcal/mol	158 169@LB@ \| \|@LB@5'-GCA...AAAAA GCUCC...GGC-3'@LB@ CGAGGAGGAA@LB@ \|:\|:\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -13.5343 kcal/mol@LB@Unfolding Energy - mRNA 3.56251 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 159 -- 168@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 44 -- 50@LB@
150	0.03022	0.6177	b1285	gmr	-9.04	0.064446	208 -- 218	47 -- 57	cyclic-di-GMP phosphodiesterase; csgD regulator; modulator of RNase II stability		_____________207_________219\n_____________\|___________\|\n5'-UUU...GAAAA___________UCCAC...CUA-3'\n______________CCGUUAGGGAG\n______________\|\|\|\|:\|::\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	212 -- 218	47 -- 53	-14.7452 kcal/mol	2.96952 kcal/mol	2.73556 kcal/mol	207 219@LB@ \| \|@LB@5'-UUU...GAAAA UCCAC...CUA-3'@LB@ CCGUUAGGGAG@LB@ \|\|\|\|:\|::\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -14.7452 kcal/mol@LB@Unfolding Energy - mRNA 2.96952 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 208 -- 218@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 47 -- 53@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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