Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
21	0.001192	0.1727	b2526	hscA	-14.48	0.018641	235 -- 259	63 -- 88	DnaK-like molecular chaperone specific for IscU	_____________234________________________260\n_____________\|__________________________\|\n5'-AGC...UUUGA__________________C_UC____GGCGG...UGG-3'\n______________GUGCUGCGCC_GCAUCAG_G__GUCU\n______________:\|:\|\|\|\|\|\|\|_:\|\|:\|\|\|_\|__:\|\|\|\n______________UAUGACGCGG_UGUGGUC_C__UAGA\n3'-UUU...GCGCU__________U_______C_UU____ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________89_________________________62\n	245 -- 251	71 -- 77	-31.0682 kcal/mol	9.20475 kcal/mol	7.38674 kcal/mol	234 260@LB@ \| \|@LB@5'-AGC...UUUGA C UC GGCGG...UGG-3'@LB@ GUGCUGCGCC GCAUCAG G GUCU@LB@ :\|:\|\|\|\|\|\|\| :\|\|:\|\|\| \| :\|\|\|@LB@ UAUGACGCGG UGUGGUC C UAGA@LB@3'-UUU...GCGCU U C UU ACCGA...GUG-5'@LB@ \| \|@LB@ 89 62@LB@@LB@@LB@Energy -14.48 kcal/mol@LB@Hybridization Energy -31.0682 kcal/mol@LB@Unfolding Energy - mRNA 9.20475 kcal/mol@LB@Unfolding Energy - sRNA 7.38674 kcal/mol@LB@@LB@Position - mRNA 235 -- 259@LB@Position - sRNA 63 -- 88@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 71 -- 77@LB@
22	0.001393	0.1727	b0794	ybhF	-14.07	0.022426	148 -- 164	67 -- 84	putative ABC transporter ATPase	_____________147________________165\n_____________\|__________________\|\n5'-UAC...GAUGA__________________UGCCA...GUU-3'\n______________UGCGUU_ACGCCAGGGAA\n______________\|\|\|\|::_\|\|:\|\|\|\|\|\|\|\|\n______________ACGCGG_UGUGGUCCCUU\n3'-UUU...UUAUG______U___________UAGAA...GUG-5'\n_____________\|__________________\|\n_____________85_________________66\n	158 -- 164	67 -- 73	-27.705 kcal/mol	6.27905 kcal/mol	7.35473 kcal/mol	147 165@LB@ \| \|@LB@5'-UAC...GAUGA UGCCA...GUU-3'@LB@ UGCGUU ACGCCAGGGAA@LB@ \|\|\|\|:: \|\|:\|\|\|\|\|\|\|\|@LB@ ACGCGG UGUGGUCCCUU@LB@3'-UUU...UUAUG U UAGAA...GUG-5'@LB@ \| \|@LB@ 85 66@LB@@LB@@LB@Energy -14.07 kcal/mol@LB@Hybridization Energy -27.705 kcal/mol@LB@Unfolding Energy - mRNA 6.27905 kcal/mol@LB@Unfolding Energy - sRNA 7.35473 kcal/mol@LB@@LB@Position - mRNA 148 -- 164@LB@Position - sRNA 67 -- 84@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 67 -- 73@LB@
23	0.001421	0.1727	b1234	rssA	-12.55	0.044848	179 -- 192	61 -- 74	putative patatin-like family phospholipase	_____________178____________193\n_____________\|______________\|\n5'-GAU...GCAUU______________CGGGA...AAA-3'\n______________CCAGGGGAAUCUUG\n______________\|\|\|\|\|\|:\|\|\|\|\|\|\|\n______________GGUCCCUUUAGAAC\n3'-UUU...GUUGU______________CGACG...GUG-5'\n_____________\|______________\|\n_____________75_____________60\n	186 -- 192	61 -- 67	-22.3239 kcal/mol	6.14875 kcal/mol	3.62869 kcal/mol	178 193@LB@ \| \|@LB@5'-GAU...GCAUU CGGGA...AAA-3'@LB@ CCAGGGGAAUCUUG@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|\|@LB@ GGUCCCUUUAGAAC@LB@3'-UUU...GUUGU CGACG...GUG-5'@LB@ \| \|@LB@ 75 60@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -22.3239 kcal/mol@LB@Unfolding Energy - mRNA 6.14875 kcal/mol@LB@Unfolding Energy - sRNA 3.62869 kcal/mol@LB@@LB@Position - mRNA 179 -- 192@LB@Position - sRNA 61 -- 74@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 61 -- 67@LB@
24	0.001457	0.1727	b0424	yajL	-16.26	0.008266	79 -- 97	64 -- 86	oxidative-stress-resistance chaperone	_____________78______________________98\n_____________\|_______________________\|\n5'-AGA...CGCGC_______________________GACUA...CCA-3'\n______________GCUGCGCCA_CACU___GAAAUC\n______________:\|\|\|\|\|\|\|\|_\|\|\|:___\|\|\|\|\|\|\n______________UGACGCGGU_GUGG___CUUUAG\n3'-UUU...GCUUA_________U____UCC______AACCG...GUG-5'\n_____________\|_______________________\|\n_____________87______________________63\n	81 -- 87	78 -- 84	-26.9283 kcal/mol	3.28429 kcal/mol	7.38435 kcal/mol	78 98@LB@ \| \|@LB@5'-AGA...CGCGC GACUA...CCA-3'@LB@ GCUGCGCCA CACU GAAAUC@LB@ :\|\|\|\|\|\|\|\| \|\|\|: \|\|\|\|\|\|@LB@ UGACGCGGU GUGG CUUUAG@LB@3'-UUU...GCUUA U UCC AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -16.26 kcal/mol@LB@Hybridization Energy -26.9283 kcal/mol@LB@Unfolding Energy - mRNA 3.28429 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 79 -- 97@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 78 -- 84@LB@
25	0.001541	0.1727	b1948	fliP	-12.25	0.051366	190 -- 216	44 -- 71	flagellar biosynthesis protein	_____________189__________________________217\n_____________\|____________________________\|\n5'-AUU...GUAGC________C__A_________UU_____CUGUC...GCG-3'\n______________GGGAGAUC_UG__UGCGUCGU__AUUGU\n______________\|\|\|\|:\|\|\|_\|\|__\|\|\|\|:\|\|\|__\|\|\|:\|\n______________CCCUUUAG_AC__ACGCGGCA__UAAUA\n3'-UUU...GUGGU________A__CG________UU_____AUACU...GUG-5'\n_____________\|____________________________\|\n_____________72___________________________43\n	203 -- 209	51 -- 57	-29.2591 kcal/mol	10.1171 kcal/mol	6.89657 kcal/mol	189 217@LB@ \| \|@LB@5'-AUU...GUAGC C A UU CUGUC...GCG-3'@LB@ GGGAGAUC UG UGCGUCGU AUUGU@LB@ \|\|\|\|:\|\|\| \|\| \|\|\|\|:\|\|\| \|\|\|:\|@LB@ CCCUUUAG AC ACGCGGCA UAAUA@LB@3'-UUU...GUGGU A CG UU AUACU...GUG-5'@LB@ \| \|@LB@ 72 43@LB@@LB@@LB@Energy -12.25 kcal/mol@LB@Hybridization Energy -29.2591 kcal/mol@LB@Unfolding Energy - mRNA 10.1171 kcal/mol@LB@Unfolding Energy - sRNA 6.89657 kcal/mol@LB@@LB@Position - mRNA 190 -- 216@LB@Position - sRNA 44 -- 71@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 51 -- 57@LB@
26	0.001553	0.1727	b0853	ybjN	-8.94	0.217650	161 -- 169	52 -- 60	negative regulator of motility; multicopy suppressor of coaA(Ts)	_____________160_______170\n_____________\|_________\|\n5'-CGC...CGUAA_________GUCUU...AUC-3'\n______________GCUGUGCCG\n______________\|\|\|\|:\|\|\|\|\n______________CGACGCGGC\n3'-UUU...AGAAC_________AUUUA...GUG-5'\n_____________\|_________\|\n_____________61________51\n	163 -- 169	52 -- 58	-18.9448 kcal/mol	5.13325 kcal/mol	4.86882 kcal/mol	160 170@LB@ \| \|@LB@5'-CGC...CGUAA GUCUU...AUC-3'@LB@ GCUGUGCCG@LB@ \|\|\|\|:\|\|\|\|@LB@ CGACGCGGC@LB@3'-UUU...AGAAC AUUUA...GUG-5'@LB@ \| \|@LB@ 61 51@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -18.9448 kcal/mol@LB@Unfolding Energy - mRNA 5.13325 kcal/mol@LB@Unfolding Energy - sRNA 4.86882 kcal/mol@LB@@LB@Position - mRNA 161 -- 169@LB@Position - sRNA 52 -- 60@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 52 -- 58@LB@
27	0.001577	0.1727	b1679	sufE	-9.94	0.142549	247 -- 262	68 -- 86	sulfur acceptor protein	_____________246_________________263\n_____________\|___________________\|\n5'-AUG...UUUAC___________U_______AGAGA...GUC-3'\n______________GCUGCGCCAAC____GGGA\n______________:\|\|\|\|\|\|\|\|\|\|____\|\|\|\|\n______________UGACGCGGUUG____CCCU\n3'-UUU...GCUUA___________UGGU____UUAGA...GUG-5'\n_____________\|___________________\|\n_____________87__________________67\n	251 -- 257	76 -- 82	-25.4399 kcal/mol	8.12138 kcal/mol	7.37523 kcal/mol	246 263@LB@ \| \|@LB@5'-AUG...UUUAC U AGAGA...GUC-3'@LB@ GCUGCGCCAAC GGGA@LB@ :\|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UGACGCGGUUG CCCU@LB@3'-UUU...GCUUA UGGU UUAGA...GUG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -25.4399 kcal/mol@LB@Unfolding Energy - mRNA 8.12138 kcal/mol@LB@Unfolding Energy - sRNA 7.37523 kcal/mol@LB@@LB@Position - mRNA 247 -- 262@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 76 -- 82@LB@
28	0.001577	0.1727	b0598	cstA	-11.00	0.089647	31 -- 48	28 -- 45	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein	_____________30__________________49\n_____________\|___________________\|\n5'-GUA...ACAGA___________A_______AAAAC...ACG-3'\n______________AUUA_GAUGAG_UUGCAGG\n______________\|\|\|\|_\|\|\|\|\|\|_\|\|:\|\|:\|\n______________UAAU_CUACUC_AAUGUUC\n3'-UUU...UUUAA____A______________CCGUG...GUG-5'\n_____________\|___________________\|\n_____________46__________________27\n	42 -- 48	28 -- 34	-16.2081 kcal/mol	3.25033 kcal/mol	1.95571 kcal/mol	30 49@LB@ \| \|@LB@5'-GUA...ACAGA A AAAAC...ACG-3'@LB@ AUUA GAUGAG UUGCAGG@LB@ \|\|\|\| \|\|\|\|\|\| \|\|:\|\|:\|@LB@ UAAU CUACUC AAUGUUC@LB@3'-UUU...UUUAA A CCGUG...GUG-5'@LB@ \| \|@LB@ 46 27@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -16.2081 kcal/mol@LB@Unfolding Energy - mRNA 3.25033 kcal/mol@LB@Unfolding Energy - sRNA 1.95571 kcal/mol@LB@@LB@Position - mRNA 31 -- 48@LB@Position - sRNA 28 -- 45@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 28 -- 34@LB@
29	0.001588	0.1727	b4371	rsmC	-11.43	0.073969	145 -- 160	74 -- 89	16S rRNA m(2)G1207 methyltransferase SAM-dependent	_____________144______________161\n_____________\|________________\|\n5'-AUC...UCGUC_____C__________AUGGC...UGC-3'\n______________GAUAC_GCGCCAACAU\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|\|:\n______________UUAUG_CGCGGUUGUG\n3'-UUU...CGCGC_____A__________GUCCC...GUG-5'\n_____________\|________________\|\n_____________90_______________73\n	154 -- 160	74 -- 80	-22.1753 kcal/mol	3.46317 kcal/mol	7.27848 kcal/mol	144 161@LB@ \| \|@LB@5'-AUC...UCGUC C AUGGC...UGC-3'@LB@ GAUAC GCGCCAACAU@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ UUAUG CGCGGUUGUG@LB@3'-UUU...CGCGC A GUCCC...GUG-5'@LB@ \| \|@LB@ 90 73@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -22.1753 kcal/mol@LB@Unfolding Energy - mRNA 3.46317 kcal/mol@LB@Unfolding Energy - sRNA 7.27848 kcal/mol@LB@@LB@Position - mRNA 145 -- 160@LB@Position - sRNA 74 -- 89@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 74 -- 80@LB@
30	0.001614	0.1727	b3607	cysE	-13.31	0.031682	13 -- 32	63 -- 81	serine acetyltransferase	_____________12___________________33\n_____________\|____________________\|\n5'-CGG...GAAAU______A____A________AUCAA...CGA-3'\n______________GCCAAU_ACCG_GGAAAUUU\n______________\|\|\|\|\|:_\|\|\|:_\|\|\|\|\|\|:\|\n______________CGGUUG_UGGU_CCUUUAGA\n3'-UUU...UGACG___________C________ACCGA...GUG-5'\n_____________\|____________________\|\n_____________82___________________62\n	26 -- 32	63 -- 69	-21.8966 kcal/mol	1.53041 kcal/mol	7.0543 kcal/mol	12 33@LB@ \| \|@LB@5'-CGG...GAAAU A A AUCAA...CGA-3'@LB@ GCCAAU ACCG GGAAAUUU@LB@ \|\|\|\|\|: \|\|\|: \|\|\|\|\|\|:\|@LB@ CGGUUG UGGU CCUUUAGA@LB@3'-UUU...UGACG C ACCGA...GUG-5'@LB@ \| \|@LB@ 82 62@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -21.8966 kcal/mol@LB@Unfolding Energy - mRNA 1.53041 kcal/mol@LB@Unfolding Energy - sRNA 7.0543 kcal/mol@LB@@LB@Position - mRNA 13 -- 32@LB@Position - sRNA 63 -- 81@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 63 -- 69@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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