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
114	0.01806	0.5155	b3033	yqiB	-9.53	0.119911	174 -- 206	15 -- 50	DUF1249 protein YqiB	_____________173__________________________________207\n_____________\|____________________________________\|\n5'-UGG...AUCAU__A_____AAA_____________C___________CGUUA...GCG-3'\n______________CA_GCGUU___AAAUGAGUG__GG__AUAAAUGAAG\n______________\|\|_:\|:\|\|___\|\|\|\|\|\|:\|\|__\|\|__\|\|\|\|\|\|:\|\|\|\n______________GU_UGUAA___UUUACUUAC__CC__UAUUUAUUUC\n3'-UUU...CAUUU__C_____GUC_________UG__AU__________AAUUA...UCG-5'\n_____________\|____________________________________\|\n_____________51___________________________________14\n	200 -- 206	15 -- 21	-20.8588 kcal/mol	5.00376 kcal/mol	6.32253 kcal/mol	173 207@LB@ \| \|@LB@5'-UGG...AUCAU A AAA C CGUUA...GCG-3'@LB@ CA GCGUU AAAUGAGUG GG AUAAAUGAAG@LB@ \|\| :\|:\|\| \|\|\|\|\|\|:\|\| \|\| \|\|\|\|\|\|:\|\|\|@LB@ GU UGUAA UUUACUUAC CC UAUUUAUUUC@LB@3'-UUU...CAUUU C GUC UG AU AAUUA...UCG-5'@LB@ \| \|@LB@ 51 14@LB@@LB@@LB@Energy -9.53 kcal/mol@LB@Hybridization Energy -20.8588 kcal/mol@LB@Unfolding Energy - mRNA 5.00376 kcal/mol@LB@Unfolding Energy - sRNA 6.32253 kcal/mol@LB@@LB@Position - mRNA 174 -- 206@LB@Position - sRNA 15 -- 50@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 15 -- 21@LB@
115	0.01846	0.5155	b4483	tatD	-10.31	0.084235	251 -- 265	1 -- 13	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase	_____________250_____________266\n_____________\|_______________\|\n5'-CUG...GACCG________UU_____GUGCG...UCA-3'\n______________UGAUGAUG__GUAGC\n______________\|:\|\|\|\|\|\|__:\|\|\|\|\n______________AUUACUAC__UAUCG\n3'-UUU...UUUCA_______________-5'\n_____________\|______________\|\n_____________14_____________1\n	252 -- 258	6 -- 12	-13.1693 kcal/mol	2.8194 kcal/mol	0.0446954 kcal/mol	250 266@LB@ \| \|@LB@5'-CUG...GACCG UU GUGCG...UCA-3'@LB@ UGAUGAUG GUAGC@LB@ \|:\|\|\|\|\|\| :\|\|\|\|@LB@ AUUACUAC UAUCG@LB@3'-UUU...UUUCA -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -13.1693 kcal/mol@LB@Unfolding Energy - mRNA 2.8194 kcal/mol@LB@Unfolding Energy - sRNA 0.0446954 kcal/mol@LB@@LB@Position - mRNA 251 -- 265@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 6 -- 12@LB@
116	0.01846	0.5155	b3349	slyD	-11.19	0.055067	245 -- 274	8 -- 47	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)	_____________244______________________________________275\n_____________\|________________________________________\|\n5'-UGU...CAGGU____A__________________UGUU_____________GUCUC...ACU-3'\n______________ACGU_CAGAA______GACGGUG________GGUUGAUGA\n______________\|\|:\|_\|\|\|\|\|______\|\|\|\|\|\|:________:\|\|\|:\|\|\|\|\n______________UGUA_GUCUU______CUGCCAU________UCAAUUACU\n3'-UUU...UUGUC____A_____UACUUA_______UAUUUAUU_________ACUAUCG-5'\n_____________\|________________________________________\|\n_____________48_______________________________________7\n	268 -- 274	8 -- 14	-23.1983 kcal/mol	5.6913 kcal/mol	6.31565 kcal/mol	244 275@LB@ \| \|@LB@5'-UGU...CAGGU A UGUU GUCUC...ACU-3'@LB@ ACGU CAGAA GACGGUG GGUUGAUGA@LB@ \|\|:\| \|\|\|\|\| \|\|\|\|\|\|: :\|\|\|:\|\|\|\|@LB@ UGUA GUCUU CUGCCAU UCAAUUACU@LB@3'-UUU...UUGUC A UACUUA UAUUUAUU ACUAUCG-5'@LB@ \| \|@LB@ 48 7@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -23.1983 kcal/mol@LB@Unfolding Energy - mRNA 5.6913 kcal/mol@LB@Unfolding Energy - sRNA 6.31565 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 8 -- 47@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 8 -- 14@LB@
117	0.01855	0.5155	b3011	yqhD	-12.43	0.029448	82 -- 109	34 -- 64	aldehyde reductase NADPH-dependent	_____________81________________________________110\n_____________\|_________________________________\|\n5'-GUU...CUGGA________CA____________GG_________GCAUU...UGA-3'\n______________GAAAUAGG_______AGACAUU__CAGAAAUGA\n______________\|\|\|\|\|\|\|\|_______\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\|\|\n______________CUUUAUCC_______UCUGUAA__GUCUUUACU\n3'-UUU...GCCAA________CCAUUUG__________________UACUG...UCG-5'\n_____________\|_________________________________\|\n_____________65________________________________33\n	83 -- 89	57 -- 63	-24.9555 kcal/mol	6.2587 kcal/mol	6.27071 kcal/mol	81 110@LB@ \| \|@LB@5'-GUU...CUGGA CA GG GCAUU...UGA-3'@LB@ GAAAUAGG AGACAUU CAGAAAUGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CUUUAUCC UCUGUAA GUCUUUACU@LB@3'-UUU...GCCAA CCAUUUG UACUG...UCG-5'@LB@ \| \|@LB@ 65 33@LB@@LB@@LB@Energy -12.43 kcal/mol@LB@Hybridization Energy -24.9555 kcal/mol@LB@Unfolding Energy - mRNA 6.2587 kcal/mol@LB@Unfolding Energy - sRNA 6.27071 kcal/mol@LB@@LB@Position - mRNA 82 -- 109@LB@Position - sRNA 34 -- 64@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 57 -- 63@LB@
118	0.01863	0.5155	b0738	tolR	-11.80	0.040697	190 -- 199	50 -- 59	membrane spanning protein in TolA-TolQ-TolR complex	_____________189________200\n_____________\|__________\|\n5'-UGG...CAACA__________CAUGG...UGG-3'\n______________AGGGGUAAGC\n______________\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	193 -- 199	50 -- 56	-16.6396 kcal/mol	4.1136 kcal/mol	0.728772 kcal/mol	189 200@LB@ \| \|@LB@5'-UGG...CAACA CAUGG...UGG-3'@LB@ AGGGGUAAGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -16.6396 kcal/mol@LB@Unfolding Energy - mRNA 4.1136 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 190 -- 199@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 50 -- 56@LB@
119	0.019	0.5155	b0904	focA	-10.20	0.088413	192 -- 208	1 -- 18	formate channel	_____________191________________209\n_____________\|__________________\|\n5'-GAG...AAGAG______________A___UGACA...AGA-3'\n______________AGAGUUAGUG_UGA_AGC\n______________\|:\|\|\|\|\|:\|\|_\|\|\|_\|\|\|\n______________UUUCAAUUAC_ACU_UCG\n3'-UUU...AUUUA__________U___A___-5'\n_____________\|_________________\|\n_____________19________________1\n	195 -- 201	9 -- 15	-16.1977 kcal/mol	5.93514 kcal/mol	0.0611543 kcal/mol	191 209@LB@ \| \|@LB@5'-GAG...AAGAG A UGACA...AGA-3'@LB@ AGAGUUAGUG UGA AGC@LB@ \|:\|\|\|\|\|:\|\| \|\|\| \|\|\|@LB@ UUUCAAUUAC ACU UCG@LB@3'-UUU...AUUUA U A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -16.1977 kcal/mol@LB@Unfolding Energy - mRNA 5.93514 kcal/mol@LB@Unfolding Energy - sRNA 0.0611543 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 9 -- 15@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@
122	0.01943	0.5155	b1842	holE	-10.27	0.085496	209 -- 257	4 -- 63	DNA polymerase III theta subunit	_____________208____________________________________________________________258\n_____________\|______________________________________________________________\|\n5'-GUC...CUGAA____CU__C_____U___U__AA_____________________________G____UC___UUGGC...UGC-3'\n______________GAAU__GG_UAAAC_GGA_CA__CAGAAAUG_____________GAUAAAGU_AAUG__GAU\n______________:\|\|\|__\|\|_\|\|\|\|\|_:\|\|_\|\|__\|\|\|\|\|\|\|\|_____________:\|\|\|\|\|\|\|_\|\|\|\|__\|\|\|\n______________UUUA__CC_AUUUG_UCU_GU__GUCUUUAC_____________UUAUUUCA_UUAC__CUA\n3'-UUU...CCAAC____UC__C____________AA________UUACUGCCAUUAU________A____UA___UCG-5'\n_____________\|______________________________________________________________\|\n_____________64_____________________________________________________________3\n	241 -- 247	14 -- 20	-26.5551 kcal/mol	9.93779 kcal/mol	6.34398 kcal/mol	208 258@LB@ \| \|@LB@5'-GUC...CUGAA CU C U U AA G UC UUGGC...UGC-3'@LB@ GAAU GG UAAAC GGA CA CAGAAAUG GAUAAAGU AAUG GAU@LB@ :\|\|\| \|\| \|\|\|\|\| :\|\| \|\| \|\|\|\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|\| \|\|\|@LB@ UUUA CC AUUUG UCU GU GUCUUUAC UUAUUUCA UUAC CUA@LB@3'-UUU...CCAAC UC C AA UUACUGCCAUUAU A UA UCG-5'@LB@ \| \|@LB@ 64 3@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -26.5551 kcal/mol@LB@Unfolding Energy - mRNA 9.93779 kcal/mol@LB@Unfolding Energy - sRNA 6.34398 kcal/mol@LB@@LB@Position - mRNA 209 -- 257@LB@Position - sRNA 4 -- 63@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 14 -- 20@LB@
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@
124	0.01977	0.5155	b1920	fliY	-11.21	0.054671	192 -- 201	49 -- 58	cystine transporter subunit	_____________191________202\n_____________\|__________\|\n5'-CCA...CAUUC__________UGAAA...UGC-3'\n______________GGGGUGAAUA\n______________\|\|\|\|\|:\|\|:\|\n______________CCCCAUUUGU\n3'-UUU...UUUAU__________CUGUA...UCG-5'\n_____________\|__________\|\n_____________59_________48\n	195 -- 201	49 -- 55	-14.4557 kcal/mol	2.52037 kcal/mol	0.729386 kcal/mol	191 202@LB@ \| \|@LB@5'-CCA...CAUUC UGAAA...UGC-3'@LB@ GGGGUGAAUA@LB@ \|\|\|\|\|:\|\|:\|@LB@ CCCCAUUUGU@LB@3'-UUU...UUUAU CUGUA...UCG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -14.4557 kcal/mol@LB@Unfolding Energy - mRNA 2.52037 kcal/mol@LB@Unfolding Energy - sRNA 0.729386 kcal/mol@LB@@LB@Position - mRNA 192 -- 201@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 49 -- 55@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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