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
161	0.02632	0.526	b3670	ilvN	-9.27	0.134814	179 -- 196	49 -- 65	acetolactate synthase 1 small subunit	_____________178________________197\n_____________\|__________________\|\n5'-UCA...AAUAC________U___GG____AGCCA...CUU-3'\n______________UGAAAUGG_GGG__AAUA\n______________\|\|\|\|\|\|:\|_\|\|\|__\|\|:\|\n______________ACUUUAUC_CCC__UUGU\n3'-UUU...GGCCA____________AU____CUGUA...UCG-5'\n_____________\|__________________\|\n_____________66_________________48\n	180 -- 186	58 -- 64	-15.3061 kcal/mol	4.40463 kcal/mol	1.63404 kcal/mol	178 197@LB@ \| \|@LB@5'-UCA...AAUAC U GG AGCCA...CUU-3'@LB@ UGAAAUGG GGG AAUA@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|:\|@LB@ ACUUUAUC CCC UUGU@LB@3'-UUU...GGCCA AU CUGUA...UCG-5'@LB@ \| \|@LB@ 66 48@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.3061 kcal/mol@LB@Unfolding Energy - mRNA 4.40463 kcal/mol@LB@Unfolding Energy - sRNA 1.63404 kcal/mol@LB@@LB@Position - mRNA 179 -- 196@LB@Position - sRNA 49 -- 65@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 58 -- 64@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@
77	0.01108	0.4523	b2099	yegU	-9.55	0.118747	1 -- 10	2 -- 11	ADP-ribosylglycohydrolase family protein	______________1_________11\n______________\|_________\|\n___________5'-__________AAAAG...CAC-3'\n______________GUGAUGAUGG\n______________:\|\|\|\|\|\|\|:\|\n______________UACUACUAUC\n3'-UUU...UCAAU__________G-5'\n_____________\|__________\|\n_____________12_________1\n	4 -- 10	2 -- 8	-12.4903 kcal/mol	2.91076 kcal/mol	0.0252227 kcal/mol	1 11@LB@ \| \|@LB@ 5'- AAAAG...CAC-3'@LB@ GUGAUGAUGG@LB@ :\|\|\|\|\|\|\|:\|@LB@ UACUACUAUC@LB@3'-UUU...UCAAU G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -9.55 kcal/mol@LB@Hybridization Energy -12.4903 kcal/mol@LB@Unfolding Energy - mRNA 2.91076 kcal/mol@LB@Unfolding Energy - sRNA 0.0252227 kcal/mol@LB@@LB@Position - mRNA 1 -- 10@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 2 -- 8@LB@
132	0.0212	0.526	b2455	eutE	-9.17	0.140915	224 -- 235	1 -- 12	aldehyde oxidoreductase ethanolamine utilization protein	_____________223__________236\n_____________\|____________\|\n5'-GGU...GAACA________A___GGUAC...UCG-3'\n______________GGUGGUGA_AGC\n______________::\|\|:\|\|\|_\|\|\|\n______________UUACUACU_UCG\n3'-UUU...UUCAA________A___-5'\n_____________\|___________\|\n_____________13__________1\n	225 -- 231	5 -- 11	-12.5804 kcal/mol	3.3751 kcal/mol	0.0394463 kcal/mol	223 236@LB@ \| \|@LB@5'-GGU...GAACA A GGUAC...UCG-3'@LB@ GGUGGUGA AGC@LB@ ::\|\|:\|\|\| \|\|\|@LB@ UUACUACU UCG@LB@3'-UUU...UUCAA A -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -12.5804 kcal/mol@LB@Unfolding Energy - mRNA 3.3751 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 224 -- 235@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 5 -- 11@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@
144	0.02445	0.526	b3441	yhhY	-11.04	0.059403	187 -- 218	22 -- 53	aminoacyl nucleotide detoxifying acetyltransferase	_____________186________________________________219\n_____________\|__________________________________\|\n5'-CCC...CCCCA__GA_____A______________GAUA______CGCCA...UGC-3'\n______________AA__GGACA___AGGAAUGAGUGA____GUAAUA\n______________\|\|__:\|\|\|\|___\|\|:\|\|\|\|\|:\|\|\|____\|\|\|\|\|\|\n______________UU__UCUGU___UCUUUACUUACU____CAUUAU\n3'-UUU...CCCCA__UG_____AAG____________GC________UUAUU...UCG-5'\n_____________\|__________________________________\|\n_____________54_________________________________21\n	202 -- 208	30 -- 36	-22.9472 kcal/mol	5.59747 kcal/mol	6.31329 kcal/mol	186 219@LB@ \| \|@LB@5'-CCC...CCCCA GA A GAUA CGCCA...UGC-3'@LB@ AA GGACA AGGAAUGAGUGA GUAAUA@LB@ \|\| :\|\|\|\| \|\|:\|\|\|\|\|:\|\|\| \|\|\|\|\|\|@LB@ UU UCUGU UCUUUACUUACU CAUUAU@LB@3'-UUU...CCCCA UG AAG GC UUAUU...UCG-5'@LB@ \| \|@LB@ 54 21@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -22.9472 kcal/mol@LB@Unfolding Energy - mRNA 5.59747 kcal/mol@LB@Unfolding Energy - sRNA 6.31329 kcal/mol@LB@@LB@Position - mRNA 187 -- 218@LB@Position - sRNA 22 -- 53@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 30 -- 36@LB@
101	0.01605	0.5059	b3360	pabA	-8.89	0.158482	100 -- 107	55 -- 62	aminodeoxychorismate synthase subunit II	_____________99_______108\n_____________\|________\|\n5'-GCG...GGGGC________AUCUC...CGU-3'\n______________AAUGGGGG\n______________\|\|\|:\|\|\|\|\n______________UUAUCCCC\n3'-UUU...CAACU________AUUUG...UCG-5'\n_____________\|________\|\n_____________63_______54\n	101 -- 107	55 -- 61	-11.7531 kcal/mol	2.8331 kcal/mol	0.0270923 kcal/mol	99 108@LB@ \| \|@LB@5'-GCG...GGGGC AUCUC...CGU-3'@LB@ AAUGGGGG@LB@ \|\|\|:\|\|\|\|@LB@ UUAUCCCC@LB@3'-UUU...CAACU AUUUG...UCG-5'@LB@ \| \|@LB@ 63 54@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -11.7531 kcal/mol@LB@Unfolding Energy - mRNA 2.8331 kcal/mol@LB@Unfolding Energy - sRNA 0.0270923 kcal/mol@LB@@LB@Position - mRNA 100 -- 107@LB@Position - sRNA 55 -- 62@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 55 -- 61@LB@
86	0.013	0.4962	b0451	amtB	-9.48	0.122870	5 -- 23	1 -- 22	ammonium transporter	_____________4______________________24\n_____________\|______________________\|\n_______5'-CCAA_______AAU____________GAUUG...CGU-3'\n______________AAGUAAA_____UGAUG_UGGC\n______________\|\|:\|\|\|\|_____\|\|\|\|\|_\|:\|\|\n______________UUUAUUU_____ACUAC_AUCG\n3'-UUU...CAUUA_______CAAUU_____U____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	5 -- 11	16 -- 22	-11.4865 kcal/mol	1.90989 kcal/mol	0.0989066 kcal/mol	4 24@LB@ \| \|@LB@ 5'-CCAA AAU GAUUG...CGU-3'@LB@ AAGUAAA UGAUG UGGC@LB@ \|\|:\|\|\|\| \|\|\|\|\| \|:\|\|@LB@ UUUAUUU ACUAC AUCG@LB@3'-UUU...CAUUA CAAUU U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -11.4865 kcal/mol@LB@Unfolding Energy - mRNA 1.90989 kcal/mol@LB@Unfolding Energy - sRNA 0.0989066 kcal/mol@LB@@LB@Position - mRNA 5 -- 23@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 16 -- 22@LB@
193	0.03268	0.5507	b2513	yfgM	-8.78	0.166450	282 -- 288	52 -- 58	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________281_____289\n_____________\|_______\|\n5'-GGC...CUGUU_______UUUUG...UUG-3'\n______________GGGGUGA\n______________\|\|\|\|\|:\|\n______________CCCCAUU\n3'-UUU...UUUAU_______UGUCU...UCG-5'\n_____________\|_______\|\n_____________59______51\n	282 -- 288	52 -- 58	-10.2706 kcal/mol	1.44003 kcal/mol	0.0533 kcal/mol	281 289@LB@ \| \|@LB@5'-GGC...CUGUU UUUUG...UUG-3'@LB@ GGGGUGA@LB@ \|\|\|\|\|:\|@LB@ CCCCAUU@LB@3'-UUU...UUUAU UGUCU...UCG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -10.2706 kcal/mol@LB@Unfolding Energy - mRNA 1.44003 kcal/mol@LB@Unfolding Energy - sRNA 0.0533 kcal/mol@LB@@LB@Position - mRNA 282 -- 288@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 52 -- 58@LB@
159	0.02583	0.526	b2572	rseA	-12.83	0.023837	184 -- 236	1 -- 63	anti-sigma factor	_____________183_____________________________________________________________237\n_____________\|_______________________________________________________________\|\n5'-UCC...AUACU_____A_____U________G__________CA__UUUCCGCU____________________GAAAC...GGG-3'\n______________GGAUA_GGGUA__UAGGCAU_CAGAAA_GAA__AC______________UUAAUGG__AUGGC\n______________::\|\|\|_\|\|\|\|\|__:\|\|:\|\|\|_\|\|\|\|\|\|_\|\|\|__\|\|______________\|\|\|\|\|\|:__\|\|:\|\|\n______________UUUAU_CCCAU__GUCUGUA_GUCUUU_CUU__UG______________AAUUACU__UAUCG\n3'-UUU...CCAAC_____C_____UU_______A______A___AC__CCAUUAUUUAUUUC_______AC_____-5'\n_____________\|______________________________________________________________\|\n_____________64_____________________________________________________________1\n	225 -- 231	8 -- 14	-31.1691 kcal/mol	11.9981 kcal/mol	6.344 kcal/mol	183 237@LB@ \| \|@LB@5'-UCC...AUACU A U G CA UUUCCGCU GAAAC...GGG-3'@LB@ GGAUA GGGUA UAGGCAU CAGAAA GAA AC UUAAUGG AUGGC@LB@ ::\|\|\| \|\|\|\|\| :\|\|:\|\|\| \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\|\|: \|\|:\|\|@LB@ UUUAU CCCAU GUCUGUA GUCUUU CUU UG AAUUACU UAUCG@LB@3'-UUU...CCAAC C UU A A AC CCAUUAUUUAUUUC AC -5'@LB@ \| \|@LB@ 64 1@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -31.1691 kcal/mol@LB@Unfolding Energy - mRNA 11.9981 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 184 -- 236@LB@Position - sRNA 1 -- 63@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 8 -- 14@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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