Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
167	0.02971	0.5559	b3062	ttdB	-9.65	0.121251	224 -- 260	75 -- 106	L-tartrate dehydratase beta subunit	_____________223___________________________________261\n_____________\|_____________________________________\|\n5'-GGA...ACCCC____AAAG___A____________UA_______C___GAUGU...GCG-3'\n______________GAUC____CUG_AGAUCUGCAAGA__UUCGCGU_GGC\n______________\|\|\|\|____\|\|\|_\|\|\|\|\|:\|\|\|\|:\|__\|\|\|:\|\|\|_\|\|\|\n______________CUAG____GAC_UCUAGGCGUUUU__AAGUGCA_CCG\n________3'-CGC___________C____________C________A___AAAUC...AAG-5'\n_____________\|_____________________________________\|\n_____________107___________________________________74\n	250 -- 256	79 -- 85	-36.8095 kcal/mol	15.2774 kcal/mol	11.8787 kcal/mol	223 261@LB@ \| \|@LB@5'-GGA...ACCCC AAAG A UA C GAUGU...GCG-3'@LB@ GAUC CUG AGAUCUGCAAGA UUCGCGU GGC@LB@ \|\|\|\| \|\|\| \|\|\|\|\|:\|\|\|\|:\| \|\|\|:\|\|\| \|\|\|@LB@ CUAG GAC UCUAGGCGUUUU AAGUGCA CCG@LB@ 3'-CGC C C A AAAUC...AAG-5'@LB@ \| \|@LB@ 107 74@LB@@LB@@LB@Energy -9.65 kcal/mol@LB@Hybridization Energy -36.8095 kcal/mol@LB@Unfolding Energy - mRNA 15.2774 kcal/mol@LB@Unfolding Energy - sRNA 11.8787 kcal/mol@LB@@LB@Position - mRNA 224 -- 260@LB@Position - sRNA 75 -- 106@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 79 -- 85@LB@
168	0.0298	0.5559	b0161	degP	-8.84	0.166335	239 -- 253	75 -- 88	serine endoprotease (protease Do) membrane-associated	_____________238_____________254\n_____________\|_______________\|\n5'-AUU...GCUCU_______G_U_____GUUAU...CGA-3'\n______________GAGUUUA_G_UUGGC\n______________:\|\|\|\|:\|_\|_\|\|\|\|\|\n______________UUCAAGU_C_AACCG\n3'-CGC...GCGUU_______G_______AAAUC...AAG-5'\n_____________\|_______________\|\n_____________89______________74\n	239 -- 245	82 -- 88	-14.9204 kcal/mol	5.56475 kcal/mol	0.515884 kcal/mol	238 254@LB@ \| \|@LB@5'-AUU...GCUCU G U GUUAU...CGA-3'@LB@ GAGUUUA G UUGGC@LB@ :\|\|\|\|:\| \| \|\|\|\|\|@LB@ UUCAAGU C AACCG@LB@3'-CGC...GCGUU G AAAUC...AAG-5'@LB@ \| \|@LB@ 89 74@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -14.9204 kcal/mol@LB@Unfolding Energy - mRNA 5.56475 kcal/mol@LB@Unfolding Energy - sRNA 0.515884 kcal/mol@LB@@LB@Position - mRNA 239 -- 253@LB@Position - sRNA 75 -- 88@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 82 -- 88@LB@
173	0.03066	0.5559	b2928	yggC	-11.87	0.049837	290 -- 298	75 -- 83	putative PanK family P-loop kinase	_____________289_______299\n_____________\|_________\|\n5'-GAA...CUGCA_________GG-3'\n______________CAUGUUGGC\n______________\|\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	292 -- 298	75 -- 81	-14.124 kcal/mol	1.76242 kcal/mol	0.492259 kcal/mol	289 299@LB@ \| \|@LB@5'-GAA...CUGCA GG-3'@LB@ CAUGUUGGC@LB@ \|\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -14.124 kcal/mol@LB@Unfolding Energy - mRNA 1.76242 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 290 -- 298@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 75 -- 81@LB@
186	0.03285	0.5559	b1003	yccJ	-7.53	0.270746	41 -- 54	75 -- 88	uncharacterized protein	_____________40_____________55\n_____________\|______________\|\n5'-CCU...UUCAC_________GC___ACGCC...GGU-3'\n______________AGGUUCGCG__GGU\n______________\|:\|\|\|\|:\|\|__\|\|:\n______________UUCAAGUGC__CCG\n3'-CGC...GCGUU_________AA___AAAUC...AAG-5'\n_____________\|______________\|\n_____________89_____________74\n	43 -- 49	80 -- 86	-16.6206 kcal/mol	8.57413 kcal/mol	0.515884 kcal/mol	40 55@LB@ \| \|@LB@5'-CCU...UUCAC GC ACGCC...GGU-3'@LB@ AGGUUCGCG GGU@LB@ \|:\|\|\|\|:\|\| \|\|:@LB@ UUCAAGUGC CCG@LB@3'-CGC...GCGUU AA AAAUC...AAG-5'@LB@ \| \|@LB@ 89 74@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -16.6206 kcal/mol@LB@Unfolding Energy - mRNA 8.57413 kcal/mol@LB@Unfolding Energy - sRNA 0.515884 kcal/mol@LB@@LB@Position - mRNA 41 -- 54@LB@Position - sRNA 75 -- 88@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 80 -- 86@LB@
157	0.02703	0.5559	b3221	yhcH	-9.14	0.148013	119 -- 127	77 -- 85	DUF386 family protein cupin superfamily	_____________118_______128\n_____________\|_________\|\n5'-AUC...GGCAU_________AUUUA...AAG-3'\n______________UUCAUGUUG\n______________\|\|\|\|:\|\|\|\|\n______________AAGUGCAAC\n3'-CGC...UUUUC_________CGAAA...AAG-5'\n_____________\|_________\|\n_____________86________76\n	121 -- 127	77 -- 83	-10.7393 kcal/mol	1.16925 kcal/mol	0.427568 kcal/mol	118 128@LB@ \| \|@LB@5'-AUC...GGCAU AUUUA...AAG-3'@LB@ UUCAUGUUG@LB@ \|\|\|\|:\|\|\|\|@LB@ AAGUGCAAC@LB@3'-CGC...UUUUC CGAAA...AAG-5'@LB@ \| \|@LB@ 86 76@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.16925 kcal/mol@LB@Unfolding Energy - sRNA 0.427568 kcal/mol@LB@@LB@Position - mRNA 119 -- 127@LB@Position - sRNA 77 -- 85@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 77 -- 83@LB@
194	0.03409	0.5559	b1836	yebV	-7.98	0.229830	12 -- 23	77 -- 87	uncharacterized protein	_____________11___________24\n_____________\|____________\|\n5'-CCA...GGAUU________A___AAAAA...CUG-3'\n______________GGUUCGCG_UUG\n______________:\|\|\|\|:\|\|_\|\|\|\n______________UCAAGUGC_AAC\n3'-CGC...CGUUU____________CGAAA...AAG-5'\n_____________\|____________\|\n_____________88___________76\n	13 -- 19	80 -- 86	-12.5297 kcal/mol	4.04369 kcal/mol	0.505155 kcal/mol	11 24@LB@ \| \|@LB@5'-CCA...GGAUU A AAAAA...CUG-3'@LB@ GGUUCGCG UUG@LB@ :\|\|\|\|:\|\| \|\|\|@LB@ UCAAGUGC AAC@LB@3'-CGC...CGUUU CGAAA...AAG-5'@LB@ \| \|@LB@ 88 76@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -12.5297 kcal/mol@LB@Unfolding Energy - mRNA 4.04369 kcal/mol@LB@Unfolding Energy - sRNA 0.505155 kcal/mol@LB@@LB@Position - mRNA 12 -- 23@LB@Position - sRNA 77 -- 87@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 80 -- 86@LB@
197	0.0346	0.5559	b2829	ptsP	-9.94	0.108120	103 -- 113	80 -- 90	PEP-protein phosphotransferase enzyme I; GAF domain containing protein	_____________102_________114\n_____________\|___________\|\n5'-CCA...AAUGA___________AGUGU...UGG-3'\n______________AAGAGUUCGCG\n______________\|\|:\|\|\|\|\|:\|\|\n______________UUUUCAAGUGC\n3'-CGC...AGGCG___________AACCG...AAG-5'\n_____________\|___________\|\n_____________91__________79\n	107 -- 113	80 -- 86	-13.2227 kcal/mol	2.77203 kcal/mol	0.506776 kcal/mol	102 114@LB@ \| \|@LB@5'-CCA...AAUGA AGUGU...UGG-3'@LB@ AAGAGUUCGCG@LB@ \|\|:\|\|\|\|\|:\|\|@LB@ UUUUCAAGUGC@LB@3'-CGC...AGGCG AACCG...AAG-5'@LB@ \| \|@LB@ 91 79@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -13.2227 kcal/mol@LB@Unfolding Energy - mRNA 2.77203 kcal/mol@LB@Unfolding Energy - sRNA 0.506776 kcal/mol@LB@@LB@Position - mRNA 103 -- 113@LB@Position - sRNA 80 -- 90@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 80 -- 86@LB@
155	0.02668	0.5559	b1625	cnu	-8.12	0.218326	240 -- 246	81 -- 87	nucleoid-associated oriC-binding protein; H-NS and StpA stabilizing factor	_____________239_____247\n_____________\|_______\|\n5'-UUU...AAAUC_______UCGAA...AUC-3'\n______________AGUUCAC\n______________\|\|\|\|\|\|\|\n______________UCAAGUG\n3'-CGC...CGUUU_______CAACC...AAG-5'\n_____________\|_______\|\n_____________88______80\n	240 -- 246	81 -- 87	-9.1905 kcal/mol	0.576286 kcal/mol	0.494577 kcal/mol	239 247@LB@ \| \|@LB@5'-UUU...AAAUC UCGAA...AUC-3'@LB@ AGUUCAC@LB@ \|\|\|\|\|\|\|@LB@ UCAAGUG@LB@3'-CGC...CGUUU CAACC...AAG-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -9.1905 kcal/mol@LB@Unfolding Energy - mRNA 0.576286 kcal/mol@LB@Unfolding Energy - sRNA 0.494577 kcal/mol@LB@@LB@Position - mRNA 240 -- 246@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 81 -- 87@LB@
156	0.02672	0.5559	b0957	ompA	-9.60	0.124024	22 -- 30	81 -- 89	outer membrane protein A (3a;II*;G;d)	_____________21________31\n_____________\|_________\|\n5'-CUU...CUGAC_________ACUUG...AAC-3'\n______________GGAGUUCAC\n______________::\|\|\|\|\|\|\|\n______________UUUCAAGUG\n3'-CGC...GGCGU_________CAACC...AAG-5'\n_____________\|_________\|\n_____________90________80\n	24 -- 30	81 -- 87	-11.1644 kcal/mol	1.067 kcal/mol	0.501582 kcal/mol	21 31@LB@ \| \|@LB@5'-CUU...CUGAC ACUUG...AAC-3'@LB@ GGAGUUCAC@LB@ ::\|\|\|\|\|\|\|@LB@ UUUCAAGUG@LB@3'-CGC...GGCGU CAACC...AAG-5'@LB@ \| \|@LB@ 90 80@LB@@LB@@LB@Energy -9.60 kcal/mol@LB@Hybridization Energy -11.1644 kcal/mol@LB@Unfolding Energy - mRNA 1.067 kcal/mol@LB@Unfolding Energy - sRNA 0.501582 kcal/mol@LB@@LB@Position - mRNA 22 -- 30@LB@Position - sRNA 81 -- 89@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 81 -- 87@LB@
161	0.02817	0.5559	b0852	rimK	-8.21	0.210781	44 -- 79	81 -- 107	ribosomal protein S6 modification protein	_____________43___________________________________80\n_____________\|____________________________________\|\n5'-AAC...CGCCG____A_______CGAUCAU______C___CAA____UAAAG...AUC-3'\n______________GGAU_CCUGGAG_______AUCCGC_GAA___UCAU\n______________\|\|\|\|_\|\|\|\|\|\|\|_______\|\|\|\|\|\|_:\|\|___\|\|\|:\n______________CCUA_GGACCUC_______UAGGCG_UUU___AGUG\n_________3'-CG_________________________U___CA_____CAACC...AAG-5'\n_____________\|____________________________________\|\n_____________108__________________________________80\n	49 -- 55	97 -- 103	-27.5385 kcal/mol	7.46513 kcal/mol	11.8593 kcal/mol	43 80@LB@ \| \|@LB@5'-AAC...CGCCG A CGAUCAU C CAA UAAAG...AUC-3'@LB@ GGAU CCUGGAG AUCCGC GAA UCAU@LB@ \|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\| :\|\| \|\|\|:@LB@ CCUA GGACCUC UAGGCG UUU AGUG@LB@ 3'-CG U CA CAACC...AAG-5'@LB@ \| \|@LB@ 108 80@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -27.5385 kcal/mol@LB@Unfolding Energy - mRNA 7.46513 kcal/mol@LB@Unfolding Energy - sRNA 11.8593 kcal/mol@LB@@LB@Position - mRNA 44 -- 79@LB@Position - sRNA 81 -- 107@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 97 -- 103@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)

Job resubmission

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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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