Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
87	0.005508	0.2147	b0083	ftsL	-13.20	0.070894	129 -- 146	1 -- 23	membrane bound cell division leucine zipper septum protein	_____________128_____________________147\n_____________\|_______________________\|\n5'-CGU...AUGCC_______________________UGAGA...UGC-3'\n______________GGGC___GAAGAAGAG__GUGGC\n______________\|\|:\|___:\|\|\|\|\|:\|\|__\|\|\|\|\|\n______________CCUG___UUUCUUUUC__CACCG\n3'-UUU...UUACC____UAG_________GU_____-5'\n_____________\|______________________\|\n_____________24_____________________1\n	135 -- 141	8 -- 14	-20.4792 kcal/mol	5.69631 kcal/mol	1.57928 kcal/mol	128 147@LB@ \| \|@LB@5'-CGU...AUGCC UGAGA...UGC-3'@LB@ GGGC GAAGAAGAG GUGGC@LB@ \|\|:\| :\|\|\|\|\|:\|\| \|\|\|\|\|@LB@ CCUG UUUCUUUUC CACCG@LB@3'-UUU...UUACC UAG GU -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -20.4792 kcal/mol@LB@Unfolding Energy - mRNA 5.69631 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 129 -- 146@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 8 -- 14@LB@
89	0.005593	0.2147	b3398	yrfF	-14.72	0.032340	186 -- 206	1 -- 31	putative RcsCDB-response attenuator inner membrane protein	_____________185______________________________207\n_____________\|________________________________\|\n5'-UUA...CUAAG_____________________________A__ACCAU...GGA-3'\n______________UAAGAUGGGGA__________AAGCA_UG_GC\n______________:\|\|:\|\|\|\|\|\|\|__________\|\|\|\|\|_\|\|_\|\|\n______________GUUUUACCCCU__________UUCGU_AC_CG\n3'-UUU...GAGGU___________GUAGUUUCUU_____C_____-5'\n_____________\|_______________________________\|\n_____________32______________________________1\n	190 -- 196	21 -- 27	-21.8606 kcal/mol	4.59782 kcal/mol	2.53929 kcal/mol	185 207@LB@ \| \|@LB@5'-UUA...CUAAG A ACCAU...GGA-3'@LB@ UAAGAUGGGGA AAGCA UG GC@LB@ :\|\|:\|\|\|\|\|\|\| \|\|\|\|\| \|\| \|\|@LB@ GUUUUACCCCU UUCGU AC CG@LB@3'-UUU...GAGGU GUAGUUUCUU C -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -14.72 kcal/mol@LB@Hybridization Energy -21.8606 kcal/mol@LB@Unfolding Energy - mRNA 4.59782 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 186 -- 206@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 21 -- 27@LB@
90	0.005632	0.2147	b1234	rssA	-9.83	0.291555	191 -- 222	1 -- 26	putative patatin-like family phospholipase	_____________190_______________________________223\n_____________\|_________________________________\|\n5'-GAU...AAUCU__C____AUAAU_______AUAAAAA_______UGGCG...AAA-3'\n______________UG_GGGA_____GAGAAAG_______UAG_GGC\n______________\|\|_\|\|\|\|_____:\|\|\|\|\|:_______:\|\|_\|\|\|\n______________AC_CCCU_____UUCUUUU_______GUC_CCG\n3'-UUU...GUUUU_______GUAGU_______C_________A___-5'\n_____________\|________________________________\|\n_____________27_______________________________1\n	203 -- 209	9 -- 15	-16.1024 kcal/mol	3.75149 kcal/mol	2.51842 kcal/mol	190 223@LB@ \| \|@LB@5'-GAU...AAUCU C AUAAU AUAAAAA UGGCG...AAA-3'@LB@ UG GGGA GAGAAAG UAG GGC@LB@ \|\| \|\|\|\| :\|\|\|\|\|: :\|\| \|\|\|@LB@ AC CCCU UUCUUUU GUC CCG@LB@3'-UUU...GUUUU GUAGU C A -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -16.1024 kcal/mol@LB@Unfolding Energy - mRNA 3.75149 kcal/mol@LB@Unfolding Energy - sRNA 2.51842 kcal/mol@LB@@LB@Position - mRNA 191 -- 222@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 9 -- 15@LB@
93	0.00579	0.2147	b1256	ompW	-13.14	0.073154	206 -- 220	1 -- 16	outer membrane protein W	_____________205______________221\n_____________\|________________\|\n5'-GAC...AUGAA____UU__________GGCUU...CUG-3'\n______________AAAG__AA_CAGUGGC\n______________\|\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________UUUC__UU_GUCACCG\n3'-UUU...UGUAG____UU__C_______-5'\n_____________\|_______________\|\n_____________17______________1\n	214 -- 220	1 -- 7	-16.0357 kcal/mol	1.55126 kcal/mol	1.34555 kcal/mol	205 221@LB@ \| \|@LB@5'-GAC...AUGAA UU GGCUU...CUG-3'@LB@ AAAG AA CAGUGGC@LB@ \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUC UU GUCACCG@LB@3'-UUU...UGUAG UU C -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -16.0357 kcal/mol@LB@Unfolding Energy - mRNA 1.55126 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 206 -- 220@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 1 -- 7@LB@
94	0.005808	0.2147	b0652	gltL	-13.33	0.066498	266 -- 292	1 -- 31	glutamate/aspartate ABC transporter ATPase	_____________265_____________________________293\n_____________\|_______________________________\|\n5'-CUC...UCAAC_______AAAA________C___________GGUUUGCG-3'\n______________CGAAGUG________AAGG_GAAGUGGUGGU\n______________\|:\|\|:\|\|________\|\|:\|_:\|\|\|::\|\|\|\|:\n______________GUUUUAC________UUUC_UUUCGUCACCG\n3'-UUU...GAGGU_______CCCUGUAG____U___________-5'\n_____________\|______________________________\|\n_____________32_____________________________1\n	286 -- 292	1 -- 7	-20.9442 kcal/mol	5.07032 kcal/mol	2.53929 kcal/mol	265 293@LB@ \| \|@LB@5'-CUC...UCAAC AAAA C GGUUUGCG-3'@LB@ CGAAGUG AAGG GAAGUGGUGGU@LB@ \|:\|\|:\|\| \|\|:\| :\|\|\|::\|\|\|\|:@LB@ GUUUUAC UUUC UUUCGUCACCG@LB@3'-UUU...GAGGU CCCUGUAG U -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -20.9442 kcal/mol@LB@Unfolding Energy - mRNA 5.07032 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 266 -- 292@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 1 -- 7@LB@
95	0.005813	0.2147	b3450	ugpC	-12.76	0.087557	84 -- 111	1 -- 34	sn-glycerol-3-phosphate ABC transporter ATPase	_____________83_________________________________112\n_____________\|__________________________________\|\n5'-GUG...AGGCA___________A________U_____________GAUGU...UCG-3'\n______________CCACGGAAUGG__AC_UCAG_GA____UGGUGGC\n______________\|\|\|\|::\|\|\|\|\|__\|\|_\|\|\|:_\|\|____::\|\|\|\|\|\n______________GGUGUUUUACC__UG_AGUU_CU____GUCACCG\n3'-UUU...CCCGA___________CC__U____U__UUUC_______-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	105 -- 111	1 -- 7	-27.9886 kcal/mol	10.9582 kcal/mol	4.26884 kcal/mol	83 112@LB@ \| \|@LB@5'-GUG...AGGCA A U GAUGU...UCG-3'@LB@ CCACGGAAUGG AC UCAG GA UGGUGGC@LB@ \|\|\|\|::\|\|\|\|\| \|\| \|\|\|: \|\| ::\|\|\|\|\|@LB@ GGUGUUUUACC UG AGUU CU GUCACCG@LB@3'-UUU...CCCGA CC U U UUUC -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -12.76 kcal/mol@LB@Hybridization Energy -27.9886 kcal/mol@LB@Unfolding Energy - mRNA 10.9582 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 84 -- 111@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 1 -- 7@LB@
96	0.005909	0.216	b0511	ybbW	-13.57	0.059054	201 -- 236	1 -- 27	putative allantoin transporter	_____________200___________________________________237\n_____________\|_____________________________________\|\n5'-UGG...GAUUU____A_____________ACUAUUCC____AC_C___UAUAG...UUA-3'\n______________AUGG__ACAUCAGAGAAA________AGCA__G_GGC\n______________\|\|\|\|__\|\|\|\|\|\|:\|\|\|\|\|________\|\|\|\|__\|_\|\|\|\n______________UACC__UGUAGUUUCUUU________UCGU__C_CCG\n3'-UUU...UGUUU____CC___________________________A___-5'\n_____________\|____________________________________\|\n_____________28___________________________________1\n	211 -- 217	10 -- 16	-23.7564 kcal/mol	7.66376 kcal/mol	2.51867 kcal/mol	200 237@LB@ \| \|@LB@5'-UGG...GAUUU A ACUAUUCC AC C UAUAG...UUA-3'@LB@ AUGG ACAUCAGAGAAA AGCA G GGC@LB@ \|\|\|\| \|\|\|\|\|\|:\|\|\|\|\| \|\|\|\| \| \|\|\|@LB@ UACC UGUAGUUUCUUU UCGU C CCG@LB@3'-UUU...UGUUU CC A -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -23.7564 kcal/mol@LB@Unfolding Energy - mRNA 7.66376 kcal/mol@LB@Unfolding Energy - sRNA 2.51867 kcal/mol@LB@@LB@Position - mRNA 201 -- 236@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 10 -- 16@LB@
98	0.006107	0.2179	b3822	recQ	-9.35	0.343777	185 -- 205	1 -- 22	ATP-dependent DNA helicase	_____________184_____________________206\n_____________\|_______________________\|\n5'-CGC...UUUCA___A_______U___U_______GCAGG...UUA-3'\n______________GGC_AUCGGGG_GAA___GUGGC\n______________\|:\|_\|\|\|:::\|_:\|\|___\|\|\|\|\|\n______________CUG_UAGUUUC_UUU___CACCG\n3'-UUU...UACCC___________U___CGU_____-5'\n_____________\|______________________\|\n_____________23_____________________1\n	189 -- 195	13 -- 19	-17.8698 kcal/mol	6.98341 kcal/mol	1.54023 kcal/mol	184 206@LB@ \| \|@LB@5'-CGC...UUUCA A U U GCAGG...UUA-3'@LB@ GGC AUCGGGG GAA GUGGC@LB@ \|:\| \|\|\|:::\| :\|\| \|\|\|\|\|@LB@ CUG UAGUUUC UUU CACCG@LB@3'-UUU...UACCC U CGU -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -17.8698 kcal/mol@LB@Unfolding Energy - mRNA 6.98341 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 185 -- 205@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 13 -- 19@LB@
99	0.006147	0.2179	b4477	dgoA	-14.15	0.044006	176 -- 210	1 -- 31	2-oxo-3-deoxygalactonate 6-phosphate aldolase	_____________175___________________________________211\n_____________\|_____________________________________\|\n5'-CAG...CAUUU____C___UAUAA___G_____CUCAU__________AAACU...UCG-3'\n______________CAGG_UGG_____GGA_CAUCG_______GCAGUGGC\n______________\|\|::_\|\|\|_____\|\|\|_\|\|\|\|:_______\|\|\|\|\|\|\|\|\n______________GUUU_ACC_____CCU_GUAGU_______CGUCACCG\n3'-UUU...GAGGU____U_________________UUCUUUU________-5'\n_____________\|____________________________________\|\n_____________32___________________________________1\n	204 -- 210	1 -- 7	-26.5297 kcal/mol	9.84206 kcal/mol	2.53929 kcal/mol	175 211@LB@ \| \|@LB@5'-CAG...CAUUU C UAUAA G CUCAU AAACU...UCG-3'@LB@ CAGG UGG GGA CAUCG GCAGUGGC@LB@ \|\|:: \|\|\| \|\|\| \|\|\|\|: \|\|\|\|\|\|\|\|@LB@ GUUU ACC CCU GUAGU CGUCACCG@LB@3'-UUU...GAGGU U UUCUUUU -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -26.5297 kcal/mol@LB@Unfolding Energy - mRNA 9.84206 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 176 -- 210@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 1 -- 7@LB@
102	0.006464	0.2224	b3785	wzzE	-10.51	0.228012	146 -- 168	1 -- 22	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein	_____________145_____________________169\n_____________\|_______________________\|\n5'-GCU...ACGCA___UG__U_____UC________AGCCC...UUA-3'\n______________GAC__CG_AGAAA__GUGGUGGC\n______________\|\|\|__\|:_\|\|\|\|\|__\|::\|\|\|\|\|\n______________CUG__GU_UCUUU__CGUCACCG\n3'-UUU...UACCC___UA__U_____U_________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	162 -- 168	1 -- 7	-19.8866 kcal/mol	7.83936 kcal/mol	1.54023 kcal/mol	145 169@LB@ \| \|@LB@5'-GCU...ACGCA UG U UC AGCCC...UUA-3'@LB@ GAC CG AGAAA GUGGUGGC@LB@ \|\|\| \|: \|\|\|\|\| \|::\|\|\|\|\|@LB@ CUG GU UCUUU CGUCACCG@LB@3'-UUU...UACCC UA U U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -19.8866 kcal/mol@LB@Unfolding Energy - mRNA 7.83936 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 146 -- 168@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 1 -- 7@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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