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
95	0.01635	0.5385	b2287	nuoB	-8.27	0.206762	33 -- 42	71 -- 80	NADH:ubiquinone oxidoreductase chain B	_____________32_________43\n_____________\|__________\|\n5'-CAU...GCUGG__A_______UGGAA...UUA-3'\n______________GU_GGCUUUG\n______________\|\|_\|\|\|\|\|\|:\n______________CA_CCGAAAU\n3'-CGC...AAGUG__A_______CAAUA...AAG-5'\n_____________\|__________\|\n_____________81_________70\n	36 -- 42	71 -- 77	-10.0496 kcal/mol	1.54713 kcal/mol	0.236872 kcal/mol	32 43@LB@ \| \|@LB@5'-CAU...GCUGG A UGGAA...UUA-3'@LB@ GU GGCUUUG@LB@ \|\| \|\|\|\|\|\|:@LB@ CA CCGAAAU@LB@3'-CGC...AAGUG A CAAUA...AAG-5'@LB@ \| \|@LB@ 81 70@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -10.0496 kcal/mol@LB@Unfolding Energy - mRNA 1.54713 kcal/mol@LB@Unfolding Energy - sRNA 0.236872 kcal/mol@LB@@LB@Position - mRNA 33 -- 42@LB@Position - sRNA 71 -- 80@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 71 -- 77@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@
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@
198	0.03475	0.5559	b1249	clsA	-8.08	0.221640	216 -- 230	57 -- 82	cardiolipin synthase 1	_____________215________________________231\n_____________\|__________________________\|\n5'-GUC...UUUAU__________________________UUGGC...CAG-3'\n______________ACGUUGGU___________GAGUUGG\n______________\|\|\|\|\|\|\|:___________\|\|\|\|\|\|:\n______________UGCAACCG___________CUCAACU\n3'-CGC...UCAAG________AAAUCAAUAAG_______CUUUG...AAG-5'\n_____________\|__________________________\|\n_____________83_________________________56\n	224 -- 230	57 -- 63	-16.5635 kcal/mol	7.18735 kcal/mol	1.29708 kcal/mol	215 231@LB@ \| \|@LB@5'-GUC...UUUAU UUGGC...CAG-3'@LB@ ACGUUGGU GAGUUGG@LB@ \|\|\|\|\|\|\|: \|\|\|\|\|\|:@LB@ UGCAACCG CUCAACU@LB@3'-CGC...UCAAG AAAUCAAUAAG CUUUG...AAG-5'@LB@ \| \|@LB@ 83 56@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -16.5635 kcal/mol@LB@Unfolding Energy - mRNA 7.18735 kcal/mol@LB@Unfolding Energy - sRNA 1.29708 kcal/mol@LB@@LB@Position - mRNA 216 -- 230@LB@Position - sRNA 57 -- 82@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 57 -- 63@LB@
134	0.0229	0.5385	b3729	glmS	-8.05	0.223933	255 -- 266	79 -- 90	L-glutamine:D-fructose-6-phosphate aminotransferase	_____________254__________267\n_____________\|____________\|\n5'-CAG...UUCUU____________CGUCU...GUC-3'\n______________GAAGGUUUACGU\n______________:\|\|:\|\|\|:\|\|\|\|\n______________UUUUCAAGUGCA\n3'-CGC...AGGCG____________ACCGA...AAG-5'\n_____________\|____________\|\n_____________91___________78\n	260 -- 266	79 -- 85	-12.2414 kcal/mol	3.68327 kcal/mol	0.506924 kcal/mol	254 267@LB@ \| \|@LB@5'-CAG...UUCUU CGUCU...GUC-3'@LB@ GAAGGUUUACGU@LB@ :\|\|:\|\|\|:\|\|\|\|@LB@ UUUUCAAGUGCA@LB@3'-CGC...AGGCG ACCGA...AAG-5'@LB@ \| \|@LB@ 91 78@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -12.2414 kcal/mol@LB@Unfolding Energy - mRNA 3.68327 kcal/mol@LB@Unfolding Energy - sRNA 0.506924 kcal/mol@LB@@LB@Position - mRNA 255 -- 266@LB@Position - sRNA 79 -- 90@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 79 -- 85@LB@
132	0.0226	0.5385	b2721	hycE	-8.05	0.224194	140 -- 148	71 -- 79	hydrogenase 3 large subunit	_____________139_______149\n_____________\|_________\|\n5'-UUC...UGGGU_________CAUUU...UGA-3'\n______________UUGGCUUUG\n______________\|\|\|\|\|\|\|\|:\n______________AACCGAAAU\n3'-CGC...AGUGC_________CAAUA...AAG-5'\n_____________\|_________\|\n_____________80________70\n	142 -- 148	71 -- 77	-10.5671 kcal/mol	2.29615 kcal/mol	0.222833 kcal/mol	139 149@LB@ \| \|@LB@5'-UUC...UGGGU CAUUU...UGA-3'@LB@ UUGGCUUUG@LB@ \|\|\|\|\|\|\|\|:@LB@ AACCGAAAU@LB@3'-CGC...AGUGC CAAUA...AAG-5'@LB@ \| \|@LB@ 80 70@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -10.5671 kcal/mol@LB@Unfolding Energy - mRNA 2.29615 kcal/mol@LB@Unfolding Energy - sRNA 0.222833 kcal/mol@LB@@LB@Position - mRNA 140 -- 148@LB@Position - sRNA 71 -- 79@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 71 -- 77@LB@
78	0.01399	0.5385	b3526	kdgK	-7.99	0.228654	189 -- 197	80 -- 88	2-dehydro-3-deoxygluconokinase	_____________188_______198\n_____________\|_________\|\n5'-CCC...AGAUC_________ACUAU...CUU-3'\n______________AGGUUCACG\n______________\|:\|\|\|\|\|\|\|\n______________UUCAAGUGC\n3'-CGC...GCGUU_________AACCG...AAG-5'\n_____________\|_________\|\n_____________89________79\n	191 -- 197	80 -- 86	-11.7911 kcal/mol	3.29177 kcal/mol	0.504555 kcal/mol	188 198@LB@ \| \|@LB@5'-CCC...AGAUC ACUAU...CUU-3'@LB@ AGGUUCACG@LB@ \|:\|\|\|\|\|\|\|@LB@ UUCAAGUGC@LB@3'-CGC...GCGUU AACCG...AAG-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -11.7911 kcal/mol@LB@Unfolding Energy - mRNA 3.29177 kcal/mol@LB@Unfolding Energy - sRNA 0.504555 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 80 -- 86@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@
160	0.02795	0.5559	b1475	fdnH	-7.98	0.230122	69 -- 80	24 -- 35	formate dehydrogenase-N Fe-S (beta) subunit nitrate-inducible	_____________68___________81\n_____________\|____________\|\n5'-CGC...ACUGG____________GUCGC...UUA-3'\n______________GGCUUUGAGGGU\n______________\|:\|\|\|::\|\|\|\|\|\n______________CUGAAGUUCCCA\n3'-CGC...CGUCA____________AUUUU...AAG-5'\n_____________\|____________\|\n_____________36___________23\n	74 -- 80	24 -- 30	-17.8377 kcal/mol	6.53052 kcal/mol	3.32971 kcal/mol	68 81@LB@ \| \|@LB@5'-CGC...ACUGG GUCGC...UUA-3'@LB@ GGCUUUGAGGGU@LB@ \|:\|\|\|::\|\|\|\|\|@LB@ CUGAAGUUCCCA@LB@3'-CGC...CGUCA AUUUU...AAG-5'@LB@ \| \|@LB@ 36 23@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -17.8377 kcal/mol@LB@Unfolding Energy - mRNA 6.53052 kcal/mol@LB@Unfolding Energy - sRNA 3.32971 kcal/mol@LB@@LB@Position - mRNA 69 -- 80@LB@Position - sRNA 24 -- 35@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 24 -- 30@LB@
182	0.03197	0.5559	b0212	gloB	-7.96	0.231442	50 -- 71	56 -- 75	hydroxyacylglutathione hydrolase	_____________49_____________________72\n_____________\|______________________\|\n5'-UUG...AUACA_______GAACCA_________CUGGC...AGC-3'\n______________UUUUAGU______CGGGUUGAG\n______________:\|\|\|\|\|\|______\|\|:\|\|\|\|\|\|\n______________GAAAUCA______GCUCAACUC\n3'-CGC...CAACC_______AUAA___________UUUGA...AAG-5'\n_____________\|______________________\|\n_____________76_____________________55\n	65 -- 71	56 -- 62	-16.3693 kcal/mol	6.6953 kcal/mol	1.71204 kcal/mol	49 72@LB@ \| \|@LB@5'-UUG...AUACA GAACCA CUGGC...AGC-3'@LB@ UUUUAGU CGGGUUGAG@LB@ :\|\|\|\|\|\| \|\|:\|\|\|\|\|\|@LB@ GAAAUCA GCUCAACUC@LB@3'-CGC...CAACC AUAA UUUGA...AAG-5'@LB@ \| \|@LB@ 76 55@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -16.3693 kcal/mol@LB@Unfolding Energy - mRNA 6.6953 kcal/mol@LB@Unfolding Energy - sRNA 1.71204 kcal/mol@LB@@LB@Position - mRNA 50 -- 71@LB@Position - sRNA 56 -- 75@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 56 -- 62@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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