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	Additional homologs
46	0.002205	0.1648	b1662	ribC	-17.71	0.005126	34 -- 61	2 -- 29	riboflavin synthase alpha subunit		_____________33_____________________________62\n_____________\|______________________________\|\n5'-UUU...CGCCU_______CA___A_____A___________GAAAU...UGG-3'\n______________GAAUGGG__GCA__AAAG_AGAAGCAG_GG\n______________:\|\|\|\|\|\|__:\|\|__\|\|\|\|_\|:\|\|\|\|\|\|_\|\|\n______________UUUACCC__UGU__UUUC_UUUUCGUC_CC\n3'-UUU...GGUGU_______C____AG_____________A__G-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	53 -- 59	5 -- 11	-25.8778 kcal/mol	5.65259 kcal/mol	2.51906 kcal/mol	33 62@LB@ \| \|@LB@5'-UUU...CGCCU CA A A GAAAU...UGG-3'@LB@ GAAUGGG GCA AAAG AGAAGCAG GG@LB@ :\|\|\|\|\|\| :\|\| \|\|\|\| \|:\|\|\|\|\|\| \|\|@LB@ UUUACCC UGU UUUC UUUUCGUC CC@LB@3'-UUU...GGUGU C AG A G-5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -17.71 kcal/mol@LB@Hybridization Energy -25.8778 kcal/mol@LB@Unfolding Energy - mRNA 5.65259 kcal/mol@LB@Unfolding Energy - sRNA 2.51906 kcal/mol@LB@@LB@Position - mRNA 34 -- 61@LB@Position - sRNA 2 -- 29@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@LB@
1	0	0	b3752	rbsK	-20.54	0.000534	137 -- 155	1 -- 21	ribokinase		_____________136___________________156\n_____________\|_____________________\|\n5'-GCA...GUGUA_____________________ACGCG...GUA-3'\n______________AUA_UAAAGAAAAGCAG_GGC\n______________\|:\|_:\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\n______________UGU_GUUUCUUUUCGUC_CCG\n3'-UUU...ACCCC___A_____________A___-5'\n_____________\|____________________\|\n_____________22___________________1\n	146 -- 152	5 -- 11	-23.5677 kcal/mol	1.51892 kcal/mol	1.51103 kcal/mol	136 156@LB@ \| \|@LB@5'-GCA...GUGUA ACGCG...GUA-3'@LB@ AUA UAAAGAAAAGCAG GGC@LB@ \|:\| :\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|@LB@ UGU GUUUCUUUUCGUC CCG@LB@3'-UUU...ACCCC A A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -20.54 kcal/mol@LB@Hybridization Energy -23.5677 kcal/mol@LB@Unfolding Energy - mRNA 1.51892 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 137 -- 155@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 5 -- 11@LB@
140	0.01029	0.2504	b3247	rng	-10.20	0.255190	49 -- 63	1 -- 14	ribonuclease G		_____________48______________64\n_____________\|_______________\|\n5'-GUU...CCGUU___U_______GU__AUACG...CGC-3'\n______________AGA_AAAGCAG__GC\n______________\|\|\|_\|\|\|\|\|\|\|__\|\|\n______________UCU_UUUCGUC__CG\n3'-UUU...UAGUU___________AC__-5'\n_____________\|______________\|\n_____________15_____________1\n	53 -- 59	5 -- 11	-13.7724 kcal/mol	2.22711 kcal/mol	1.34059 kcal/mol	48 64@LB@ \| \|@LB@5'-GUU...CCGUU U GU AUACG...CGC-3'@LB@ AGA AAAGCAG GC@LB@ \|\|\| \|\|\|\|\|\|\| \|\|@LB@ UCU UUUCGUC CG@LB@3'-UUU...UAGUU AC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -13.7724 kcal/mol@LB@Unfolding Energy - mRNA 2.22711 kcal/mol@LB@Unfolding Energy - sRNA 1.34059 kcal/mol@LB@@LB@Position - mRNA 49 -- 63@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@LB@
144	0.01052	0.2504	b1066	rimJ	-12.60	0.094480	174 -- 195	1 -- 22	ribosomal-protein-S5-alanine N-acetyltransferase		_____________173_____________________196\n_____________\|_______________________\|\n5'-AUU...UUAAA_______C___________A___AUAGA...AUU-3'\n______________GACGUUA_GGGAAGG_AGU_GGU\n______________\|\|\|:\|:\|_:\|:\|\|:\|_\|\|\|_\|\|:\n______________CUGUAGU_UCUUUUC_UCA_CCG\n3'-UUU...UACCC_______U_______G_______-5'\n_____________\|______________________\|\n_____________23_____________________1\n	182 -- 188	8 -- 14	-20.3318 kcal/mol	6.19349 kcal/mol	1.54023 kcal/mol	173 196@LB@ \| \|@LB@5'-AUU...UUAAA C A AUAGA...AUU-3'@LB@ GACGUUA GGGAAGG AGU GGU@LB@ \|\|\|:\|:\| :\|:\|\|:\| \|\|\| \|\|:@LB@ CUGUAGU UCUUUUC UCA CCG@LB@3'-UUU...UACCC U G -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -20.3318 kcal/mol@LB@Unfolding Energy - mRNA 6.19349 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 174 -- 195@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 8 -- 14@LB@
82	0.005087	0.2147	b2741	rpoS	-15.46	0.021295	2 -- 28	1 -- 25	RNA polymerase sigma S (sigma 38) factor		_____________1____________________________29\n_____________\|____________________________\|\n__________5'-C___A___ACAA____UU___________AAAAA...AGG-3'\n______________GGG_ACA____GAAG__AAGGCGG_GGC\n______________\|\|\|_\|\|\|____:\|\|\|__\|\|:\|\|:\|_\|\|\|\n______________CCC_UGU____UUUC__UUUCGUC_CCG\n3'-UUU...UUUUA___C___AG______U________A___-5'\n_____________\|___________________________\|\n_____________26__________________________1\n	19 -- 25	5 -- 11	-23.9329 kcal/mol	5.95047 kcal/mol	2.51748 kcal/mol	1 29@LB@ \| \|@LB@ 5'-C A ACAA UU AAAAA...AGG-3'@LB@ GGG ACA GAAG AAGGCGG GGC@LB@ \|\|\| \|\|\| :\|\|\| \|\|:\|\|:\| \|\|\|@LB@ CCC UGU UUUC UUUCGUC CCG@LB@3'-UUU...UUUUA C AG U A -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -15.46 kcal/mol@LB@Hybridization Energy -23.9329 kcal/mol@LB@Unfolding Energy - mRNA 5.95047 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 2 -- 28@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 5 -- 11@LB@
23	0.0008148	0.1243	b2573	rpoE	-12.22	0.112158	248 -- 284	1 -- 24	RNA polymerase sigma E factor		_____________247___________________________________285\n_____________\|_____________________________________\|\n5'-ACA...CAGAA____G______AAGCCUUUAACUUACU_______C__UAUCA...UGG-3'\n______________GGGA_AUCAGA________________GGUAGUG_GC\n______________\|\|\|\|_\|\|\|\|:\|________________:\|:\|\|\|\|_\|\|\n______________CCCU_UAGUUU________________UCGUCAC_CG\n3'-UUU...UUUAC____G______CUUU______________________-5'\n_____________\|____________________________________\|\n_____________25___________________________________1\n	275 -- 281	3 -- 9	-22.4239 kcal/mol	7.75978 kcal/mol	2.44282 kcal/mol	247 285@LB@ \| \|@LB@5'-ACA...CAGAA G AAGCCUUUAACUUACU C UAUCA...UGG-3'@LB@ GGGA AUCAGA GGUAGUG GC@LB@ \|\|\|\| \|\|\|\|:\| :\|:\|\|\|\| \|\|@LB@ CCCU UAGUUU UCGUCAC CG@LB@3'-UUU...UUUAC G CUUU -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -12.22 kcal/mol@LB@Hybridization Energy -22.4239 kcal/mol@LB@Unfolding Energy - mRNA 7.75978 kcal/mol@LB@Unfolding Energy - sRNA 2.44282 kcal/mol@LB@@LB@Position - mRNA 248 -- 284@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 3 -- 9@LB@
3	3.973e-07	0.0004647	b0081	mraZ	-16.47	0.011640	172 -- 200	1 -- 32	RsmH methytransferase inhibitor		_____________171______________________________201\n_____________\|________________________________\|\n5'-GAU...GUGGG__________A___A_____U___________AUGUU...AAA-3'\n______________GCAAAGUGGG_AUA__GGGG_GAGGC__UGGC\n______________:\|\|\|\|:\|\|\|\|_\|:\|__:::\|_:\|:\|\|__\|\|\|\|\n______________UGUUUUACCC_UGU__UUUC_UUUCG__ACCG\n3'-UUU...CGAGG__________C___AG____U_____UC____-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	175 -- 181	23 -- 29	-28.2943 kcal/mol	9.28897 kcal/mol	2.53929 kcal/mol	171 201@LB@ \| \|@LB@5'-GAU...GUGGG A A U AUGUU...AAA-3'@LB@ GCAAAGUGGG AUA GGGG GAGGC UGGC@LB@ :\|\|\|\|:\|\|\|\| \|:\| :::\| :\|:\|\| \|\|\|\|@LB@ UGUUUUACCC UGU UUUC UUUCG ACCG@LB@3'-UUU...CGAGG C AG U UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -16.47 kcal/mol@LB@Hybridization Energy -28.2943 kcal/mol@LB@Unfolding Energy - mRNA 9.28897 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 172 -- 200@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 23 -- 29@LB@
167	0.01216	0.2504	b1013	rutR	-12.90	0.082087	181 -- 218	3 -- 35	rut operon transcriptional repressor for	b0796	_____________180________________________________________219\n_____________\|__________________________________________\|\n5'-CAA...GCCAA_______________GAGCGCAUGACG_____C_________AAAAC...AAU-3'\n______________UCUACAAGA_GGGGA____________CAAGG____GCAGUG\n______________\|\|:\|\|\|\|:\|_\|\|\|\|\|____________\|\|\|:\|____\|\|\|\|\|\|\n______________AGGUGUUUU_CCCCU____________GUUUC____CGUCAC\n3'-UUU...ACCCG_________A_____GUA______________UUUU______CG-5'\n_____________\|__________________________________________\|\n_____________36_________________________________________2\n	181 -- 187	29 -- 35	-29.1146 kcal/mol	11.1798 kcal/mol	5.03644 kcal/mol	180 219@LB@ \| \|@LB@5'-CAA...GCCAA GAGCGCAUGACG C AAAAC...AAU-3'@LB@ UCUACAAGA GGGGA CAAGG GCAGUG@LB@ \|\|:\|\|\|\|:\| \|\|\|\|\| \|\|\|:\| \|\|\|\|\|\|@LB@ AGGUGUUUU CCCCU GUUUC CGUCAC@LB@3'-UUU...ACCCG A GUA UUUU CG-5'@LB@ \| \|@LB@ 36 2@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -29.1146 kcal/mol@LB@Unfolding Energy - mRNA 11.1798 kcal/mol@LB@Unfolding Energy - sRNA 5.03644 kcal/mol@LB@@LB@Position - mRNA 181 -- 218@LB@Position - sRNA 3 -- 35@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 29 -- 35@LB@
133	0.009634	0.2504	b2551	glyA	-13.83	0.051752	272 -- 286	6 -- 21	serine hydroxymethyltransferase		_____________271______________287\n_____________\|________________\|\n5'-CAA...AAAGU________________CAUCG...UCG-3'\n______________ACGUC_AGGAAGAGCA\n______________\|\|:\|\|_\|:\|\|\|:\|\|\|\|\n______________UGUAG_UUCUUUUCGU\n3'-UUU...ACCCC_____U__________CACCG-5'\n_____________\|________________\|\n_____________22_______________5\n	280 -- 286	6 -- 12	-16.7043 kcal/mol	2.28484 kcal/mol	0.584589 kcal/mol	271 287@LB@ \| \|@LB@5'-CAA...AAAGU CAUCG...UCG-3'@LB@ ACGUC AGGAAGAGCA@LB@ \|\|:\|\| \|:\|\|\|:\|\|\|\|@LB@ UGUAG UUCUUUUCGU@LB@3'-UUU...ACCCC U CACCG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -16.7043 kcal/mol@LB@Unfolding Energy - mRNA 2.28484 kcal/mol@LB@Unfolding Energy - sRNA 0.584589 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 6 -- 12@LB@
21	0.0007937	0.1243	b3055	ygiM	-17.78	0.004866	75 -- 99	1 -- 23	SH3 domain protein		_____________74________________________100\n_____________\|_________________________\|\n5'-GGC...UUGAC______A____UUU___________AAGAC...AUA-3'\n______________GGGCGU_AAAG___GAAGCAGUGGC\n______________\|\|:\|:\|_\|\|\|\|___:\|\|\|\|\|\|\|\|\|\|\n______________CCUGUA_UUUC___UUUCGUCACCG\n3'-UUU...UUACC______G____U_____________-5'\n_____________\|________________________\|\n_____________24_______________________1\n	93 -- 99	1 -- 7	-29.8569 kcal/mol	10.4968 kcal/mol	1.57928 kcal/mol	74 100@LB@ \| \|@LB@5'-GGC...UUGAC A UUU AAGAC...AUA-3'@LB@ GGGCGU AAAG GAAGCAGUGGC@LB@ \|\|:\|:\| \|\|\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ CCUGUA UUUC UUUCGUCACCG@LB@3'-UUU...UUACC G U -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -17.78 kcal/mol@LB@Hybridization Energy -29.8569 kcal/mol@LB@Unfolding Energy - mRNA 10.4968 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 75 -- 99@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 93 -- 99@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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