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
163	0.01202	0.2504	b1482	osmC	-10.53	0.225653	203 -- 226	1 -- 22	lipoyl-dependent Cys-based peroxidase hydroperoxide resistance; salt-shock inducible membrane protein; peroxiredoxin		_____________202_______________________227\n_____________\|_________________________\|\n5'-UAG...ACAAU___A___CAU_________CA____ACACU...CGU-3'\n______________GAC_AUC___AAGAAAGGU___GGC\n______________\|\|\|_\|\|\|___\|\|\|\|\|\|:\|:___\|\|\|\n______________CUG_UAG___UUCUUUUCG___CCG\n3'-UUU...UACCC_______U___________UCA___-5'\n_____________\|________________________\|\n_____________23_______________________1\n	215 -- 221	7 -- 13	-17.1921 kcal/mol	5.11752 kcal/mol	1.54023 kcal/mol	202 227@LB@ \| \|@LB@5'-UAG...ACAAU A CAU CA ACACU...CGU-3'@LB@ GAC AUC AAGAAAGGU GGC@LB@ \|\|\| \|\|\| \|\|\|\|\|\|:\|: \|\|\|@LB@ CUG UAG UUCUUUUCG CCG@LB@3'-UUU...UACCC U UCA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -17.1921 kcal/mol@LB@Unfolding Energy - mRNA 5.11752 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 7 -- 13@LB@
20	0.0007622	0.1243	b1507	hipA	-19.17	0.001718	1 -- 29	1 -- 31	inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase		______________1________________________________30\n______________\|________________________________\|\n___________5'-________CU___________C___________GAAAA...UAG-3'\n______________CAAAAUGG__GGACG_CAGAG__GAGC__UGGC\n______________\|\|\|\|\|\|\|\|__\|\|\|\|:_\|\|:\|\|__:\|\|\|__\|\|\|\|\n______________GUUUUACC__CCUGU_GUUUC__UUCG__ACCG\n3'-UUU...GAGGU_______________A_____UU____UC____-5'\n_____________\|________________________________\|\n_____________32_______________________________1\n	2 -- 8	24 -- 30	-30.0086 kcal/mol	8.29611 kcal/mol	2.53929 kcal/mol	1 30@LB@ \| \|@LB@ 5'- CU C GAAAA...UAG-3'@LB@ CAAAAUGG GGACG CAGAG GAGC UGGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|: \|\|:\|\| :\|\|\| \|\|\|\|@LB@ GUUUUACC CCUGU GUUUC UUCG ACCG@LB@3'-UUU...GAGGU A UU UC -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -19.17 kcal/mol@LB@Hybridization Energy -30.0086 kcal/mol@LB@Unfolding Energy - mRNA 8.29611 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 1 -- 29@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 2 -- 8@LB@Position Seed - sRNA 24 -- 30@LB@
19	0.000738	0.1243	b1508	hipB	-18.00	0.004180	266 -- 295	1 -- 32	antitoxin of HipAB toxin-antitoxin system	b1299 b1434	_____________265________________________________296\n_____________\|__________________________________\|\n5'-AUG...CGCCA_________CU___________C___________GAAAA-3'\n______________GCAAAAUGG__GGACG_CAGAG__GAGC__UGGC\n______________:\|\|\|\|\|\|\|\|__\|\|\|\|:_\|\|:\|\|__:\|\|\|__\|\|\|\|\n______________UGUUUUACC__CCUGU_GUUUC__UUCG__ACCG\n3'-UUU...CGAGG________________A_____UU____UC____-5'\n_____________\|_________________________________\|\n_____________33________________________________1\n	268 -- 274	24 -- 30	-30.0826 kcal/mol	9.54799 kcal/mol	2.53929 kcal/mol	265 296@LB@ \| \|@LB@5'-AUG...CGCCA CU C GAAAA-3'@LB@ GCAAAAUGG GGACG CAGAG GAGC UGGC@LB@ :\|\|\|\|\|\|\|\| \|\|\|\|: \|\|:\|\| :\|\|\| \|\|\|\|@LB@ UGUUUUACC CCUGU GUUUC UUCG ACCG@LB@3'-UUU...CGAGG A UU UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -30.0826 kcal/mol@LB@Unfolding Energy - mRNA 9.54799 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 266 -- 295@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 24 -- 30@LB@
78	0.004634	0.2062	b1601	tqsA	-18.27	0.003423	191 -- 205	1 -- 25	pheromone AI-2 transporter		_____________190_______________________206\n_____________\|_________________________\|\n5'-AUU...AAAAC_________________________AAAGC...UCA-3'\n______________GGGGACA_________AGCA_UGGC\n______________\|\|\|\|\|\|\|_________\|\|\|\|_\|\|\|\|\n______________CCCCUGU_________UCGU_ACCG\n3'-UUU...UUUUA_______AGUUUCUUU____C____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	191 -- 197	19 -- 25	-23.2822 kcal/mol	2.49324 kcal/mol	2.51748 kcal/mol	190 206@LB@ \| \|@LB@5'-AUU...AAAAC AAAGC...UCA-3'@LB@ GGGGACA AGCA UGGC@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|\|\|@LB@ CCCCUGU UCGU ACCG@LB@3'-UUU...UUUUA AGUUUCUUU C -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -18.27 kcal/mol@LB@Hybridization Energy -23.2822 kcal/mol@LB@Unfolding Energy - mRNA 2.49324 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 19 -- 25@LB@
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@
104	0.006761	0.2281	b1671	ydhX	-13.25	0.069212	145 -- 167	2 -- 25	putative 4Fe-4S ferridoxin-type protein; FNR Nar NarP-regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex	b4072	_____________144_______________________168\n_____________\|_________________________\|\n5'-CAC...UUUCA___A_______U___U_________ACAGU...AGG-3'\n______________GGG_GAUGUCA_GGA__AG_GGUGG\n______________\|\|\|_\|\|::\|\|\|_:\|\|__\|\|_:\|\|\|\|\n______________CCC_CUGUAGU_UCU__UC_UCACC\n3'-UUU...UUUUA___________U___UU__G_____G-5'\n_____________\|_________________________\|\n_____________26________________________1\n	149 -- 155	16 -- 22	-23.0825 kcal/mol	7.31216 kcal/mol	2.51746 kcal/mol	144 168@LB@ \| \|@LB@5'-CAC...UUUCA A U U ACAGU...AGG-3'@LB@ GGG GAUGUCA GGA AG GGUGG@LB@ \|\|\| \|\|::\|\|\| :\|\| \|\| :\|\|\|\|@LB@ CCC CUGUAGU UCU UC UCACC@LB@3'-UUU...UUUUA U UU G G-5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -13.25 kcal/mol@LB@Hybridization Energy -23.0825 kcal/mol@LB@Unfolding Energy - mRNA 7.31216 kcal/mol@LB@Unfolding Energy - sRNA 2.51746 kcal/mol@LB@@LB@Position - mRNA 145 -- 167@LB@Position - sRNA 2 -- 25@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 16 -- 22@LB@
108	0.007234	0.2348	b1725	yniA	-14.77	0.031588	182 -- 211	1 -- 32	fructosamine kinase family protein		_____________181_________________________________212\n_____________\|___________________________________\|\n5'-GAG...GGCAG____C_____AGA_______UGU____________AAUCA...GGC-3'\n______________ACAA_AUGGG___GACAUCA______GGCA__GGC\n______________\|\|\|\|_\|\|\|\|\|___\|\|\|\|\|\|\|______:\|\|\|__\|\|\|\n______________UGUU_UACCC___CUGUAGU______UCGU__CCG\n3'-UUU...CGAGG____U_______________UUCUUU____CA___-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	195 -- 201	16 -- 22	-26.2676 kcal/mol	8.96188 kcal/mol	2.53929 kcal/mol	181 212@LB@ \| \|@LB@5'-GAG...GGCAG C AGA UGU AAUCA...GGC-3'@LB@ ACAA AUGGG GACAUCA GGCA GGC@LB@ \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| :\|\|\| \|\|\|@LB@ UGUU UACCC CUGUAGU UCGU CCG@LB@3'-UUU...CGAGG U UUCUUU CA -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -14.77 kcal/mol@LB@Hybridization Energy -26.2676 kcal/mol@LB@Unfolding Energy - mRNA 8.96188 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 182 -- 211@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 16 -- 22@LB@
7	0.0001218	0.05555	b1811	yoaH	-21.30	0.000256	259 -- 293	1 -- 35	UPF0181 family protein		_____________258__________________________________294\n_____________\|____________________________________\|\n5'-ACG...GCGGA____G___C__AU____________U______C___CAGGCAA-3'\n______________UCCA_GAA_UG__GGCA_CAAGGGA_GAGCAG_GGC\n______________\|\|\|\|_:\|\|_\|\|__\|:\|\|_\|\|\|:\|:\|_:\|\|\|\|\|_\|\|\|\n______________AGGU_UUU_AC__CUGU_GUUUCUU_UUCGUC_CCG\n3'-UUU...ACCCG____G___U__CC____A______________A___-5'\n_____________\|___________________________________\|\n_____________36__________________________________1\n	276 -- 282	11 -- 17	-33.9537 kcal/mol	7.61738 kcal/mol	5.03645 kcal/mol	258 294@LB@ \| \|@LB@5'-ACG...GCGGA G C AU U C CAGGCAA-3'@LB@ UCCA GAA UG GGCA CAAGGGA GAGCAG GGC@LB@ \|\|\|\| :\|\| \|\| \|:\|\| \|\|\|:\|:\| :\|\|\|\|\| \|\|\|@LB@ AGGU UUU AC CUGU GUUUCUU UUCGUC CCG@LB@3'-UUU...ACCCG G U CC A A -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -21.30 kcal/mol@LB@Hybridization Energy -33.9537 kcal/mol@LB@Unfolding Energy - mRNA 7.61738 kcal/mol@LB@Unfolding Energy - sRNA 5.03645 kcal/mol@LB@@LB@Position - mRNA 259 -- 293@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 11 -- 17@LB@
40	0.001973	0.1648	b1823	cspC	-10.89	0.196769	199 -- 231	1 -- 29	stress protein member of the CspA-family		_____________198_______________________________232\n_____________\|_________________________________\|\n5'-UAU...UUUUC______CAA_G________UC____UA______UCAAC...UCU-3'\n______________AAAUGG___A_AUUAAAGG__AGGU__AGUGGU\n______________\|\|\|\|\|\|___\|_\|\|:\|\|\|\|:__\|:\|:__\|\|\|\|\|:\n______________UUUACC___U_UAGUUUCU__UUCG__UCACCG\n3'-UUU...GGUGU______CC__G________U_____________-5'\n_____________\|________________________________\|\n_____________30_______________________________1\n	210 -- 216	13 -- 19	-20.1954 kcal/mol	6.78842 kcal/mol	2.51907 kcal/mol	198 232@LB@ \| \|@LB@5'-UAU...UUUUC CAA G UC UA UCAAC...UCU-3'@LB@ AAAUGG A AUUAAAGG AGGU AGUGGU@LB@ \|\|\|\|\|\| \| \|\|:\|\|\|\|: \|:\|: \|\|\|\|\|:@LB@ UUUACC U UAGUUUCU UUCG UCACCG@LB@3'-UUU...GGUGU CC G U -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -10.89 kcal/mol@LB@Hybridization Energy -20.1954 kcal/mol@LB@Unfolding Energy - mRNA 6.78842 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 199 -- 231@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 13 -- 19@LB@
168	0.01219	0.2504	b1830	prc	-10.01	0.273454	1 -- 12	6 -- 17	carboxy-terminal protease for penicillin-binding protein 3		______________1___________13\n______________\|___________\|\n___________5'-_______C____CACCC...CGG-3'\n______________CGAAGAA_AGCA\n______________\|:\|\|\|\|\|_\|\|\|\|\n______________GUUUCUU_UCGU\n3'-UUU...CUGUA_______U____CACCG-5'\n_____________\|____________\|\n_____________18___________5\n	1 -- 7	11 -- 17	-11.3077 kcal/mol	0.751361 kcal/mol	0.542636 kcal/mol	1 13@LB@ \| \|@LB@ 5'- C CACCC...CGG-3'@LB@ CGAAGAA AGCA@LB@ \|:\|\|\|\|\| \|\|\|\|@LB@ GUUUCUU UCGU@LB@3'-UUU...CUGUA U CACCG-5'@LB@ \| \|@LB@ 18 5@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -11.3077 kcal/mol@LB@Unfolding Energy - mRNA 0.751361 kcal/mol@LB@Unfolding Energy - sRNA 0.542636 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 6 -- 17@LB@Position Seed - mRNA 1 -- 7@LB@Position Seed - sRNA 11 -- 17@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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