Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
61	0.006025	0.3261	b4330	yjiH	-10.68	0.204041	214 -- 227	80 -- 92	nucleoside recognition pore and gate family putative inner membrane transporter	_____________213______228\n_____________\|________\|\n5'-ACU...ACAAG________GUAGC...CCG-3'\n______________GGGAUGCU\n______________\|\|\|\|:\|\|\|\n______________CCCUGCGA\n3'-UUU...CAACA________AUUGG...UAG-5'\n_____________\|________\|\n_____________93_______79\n	215 -- 221	85 -- 91	-14.2816 kcal/mol	2.08889 kcal/mol	5.76908 kcal/mol	213 228@LB@ \| \|@LB@5'-ACU...ACAAG GUAGC...CCG-3'@LB@ GGGAUGCU@LB@ \|\|\|\|:\|\|\|@LB@ CCCUGCGA@LB@3'-UUU...CAACA AUUGG...UAG-5'@LB@ \| \|@LB@ 93 79@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -14.2816 kcal/mol@LB@Unfolding Energy - mRNA 2.08889 kcal/mol@LB@Unfolding Energy - sRNA 5.76908 kcal/mol@LB@@LB@Position - mRNA 214 -- 227@LB@Position - sRNA 80 -- 92@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 85 -- 91@LB@
62	0.006126	0.3261	b3824	rhtB	-10.68	0.204362	7 -- 23	171 -- 187	homoserine homoserine lactone and S-methyl-methionine efflux pump	_____________6_________________24\n_____________\|_________________\|\n_____5'-ACGCUG_______AAA_______GCGGU...ACC-3'\n______________ACGCCAG___UCAGUCA\n______________\|\|:\|\|\|:___\|\|\|\|\|\|\|\n______________UGUGGUU___AGUCAGU\n3'-UUU...UAAAA_______AUG_______GUGUA...UAG-5'\n_____________\|_________________\|\n_____________188_______________170\n	17 -- 23	171 -- 177	-18.1223 kcal/mol	1.9449 kcal/mol	4.7016 kcal/mol	6 24@LB@ \| \|@LB@ 5'-ACGCUG AAA GCGGU...ACC-3'@LB@ ACGCCAG UCAGUCA@LB@ \|\|:\|\|\|: \|\|\|\|\|\|\|@LB@ UGUGGUU AGUCAGU@LB@3'-UUU...UAAAA AUG GUGUA...UAG-5'@LB@ \| \|@LB@ 188 170@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -18.1223 kcal/mol@LB@Unfolding Energy - mRNA 1.9449 kcal/mol@LB@Unfolding Energy - sRNA 4.7016 kcal/mol@LB@@LB@Position - mRNA 7 -- 23@LB@Position - sRNA 171 -- 187@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 171 -- 177@LB@
148	0.01584	0.3602	b1822	rlmA	-10.68	0.203557	148 -- 239	111 -- 186	23S rRNA m(1)G745 methyltransferase SAM-dependent	_____________147___________240\n_____________\|_____________\|\n5'-AAG...GCGUG_____C_______UUGCG...GGU-3'\n______________AUUCG_GUUACAC\n______________\|:\|\|:_\|\|:\|\|\|\|\n______________UGAGU_CAGUGUG\n3'-UUU...GGUUA_____________UACUA...UAG-5'\n_____________\|_____________\|\n_____________187___________110\n	163 -- 169	168 -- 174	-12.5288 kcal/mol	1.89227 kcal/mol	0.283892 kcal/mol	147 240@LB@ \| \|@LB@5'-AAG...GCGUG C UUGCG...GGU-3'@LB@ AUUCG GUUACAC@LB@ \|:\|\|: \|\|:\|\|\|\|@LB@ UGAGU CAGUGUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 187 110@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -12.5288 kcal/mol@LB@Unfolding Energy - mRNA 1.89227 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 148 -- 239@LB@Position - sRNA 111 -- 186@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 168 -- 174@LB@
173	0.0197	0.3812	b3210	arcB	-10.66	0.206219	214 -- 224	197 -- 207	aerobic respiration control sensor histidine protein kinase cognate to two-component response regulators ArcA and RssB	_____________213_________________225\n_____________\|___________________\|\n5'-UGC...UAACG_____G_____________AUUAU...UUC-3'\n______________UAACU_UCAGAAUUG_GGU\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|\|_\|\|\|\n______________GUUGA_AGUCUUAAC_CCA\n3'-UUU...GUUCA_____A_________G___GUAGG...UAG-5'\n_____________\|___________________\|\n_____________208_________________196\n	156 -- 162	138 -- 144	-19.5528 kcal/mol	4.59493 kcal/mol	5.63708 kcal/mol	213 225@LB@ \| \|@LB@5'-UGC...UAACG G AUUAU...UUC-3'@LB@ UAACU UCAGAAUUG GGU@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|@LB@ GUUGA AGUCUUAAC CCA@LB@3'-UUU...GUUCA A G GUAGG...UAG-5'@LB@ \| \|@LB@ 208 196@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -19.5528 kcal/mol@LB@Unfolding Energy - mRNA 4.59493 kcal/mol@LB@Unfolding Energy - sRNA 5.63708 kcal/mol@LB@@LB@Position - mRNA 214 -- 224@LB@Position - sRNA 197 -- 207@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 138 -- 144@LB@
153	0.01719	0.3749	b2997	hybO	-10.59	0.212773	44 -- 57	176 -- 189	hydrogenase 2 small subunit	_____________43_________________58\n_____________\|__________________\|\n5'-CUC...AUUAA______________CU__CCUUC...GCA-3'\n______________UUACACUAAUGCUU__UC\n______________\|\|\|\|\|\|:\|\|\|:\|\|:__\|\|\n______________AAUGUGGUUAUGAG__AG\n3'-UUU...ACUAA______________UC__UGUGU...UAG-5'\n_____________\|__________________\|\n_____________190________________175\n	51 -- 57	176 -- 182	-17.3647 kcal/mol	0.828093 kcal/mol	4.66778 kcal/mol	43 58@LB@ \| \|@LB@5'-CUC...AUUAA CU CCUUC...GCA-3'@LB@ UUACACUAAUGCUU UC@LB@ \|\|\|\|\|\|:\|\|\|:\|\|: \|\|@LB@ AAUGUGGUUAUGAG AG@LB@3'-UUU...ACUAA UC UGUGU...UAG-5'@LB@ \| \|@LB@ 190 175@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -17.3647 kcal/mol@LB@Unfolding Energy - mRNA 0.828093 kcal/mol@LB@Unfolding Energy - sRNA 4.66778 kcal/mol@LB@@LB@Position - mRNA 44 -- 57@LB@Position - sRNA 176 -- 189@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 176 -- 182@LB@
64	0.006252	0.3261	b3195	mlaF	-10.58	0.212925	52 -- 62	81 -- 91	ABC transporter maintaining OM lipid asymmetry ATP-binding protein	_____________51____________________________________63\n_____________\|_____________________________________\|\n5'-UUU...UUCAA___UAA___GA______________AAAA__A_____AGACG...GAG-3'\n______________GGU___AUU__GCGCC_AUGCUUAG____UC_ACGCA\n______________\|\|\|___\|\|\|__:\|:\|\|_\|\|:\|\|:\|\|____\|\|_\|\|:\|\|\n______________CCA___UAA__UGUGG_UAUGAGUC____AG_UGUGU\n3'-UUU...ACCGC___C_____AA_____U____________________ACUAC...UAG-5'\n_____________\|_____________________________________\|\n_____________92____________________________________80\n	166 -- 172	174 -- 180	-23.2269 kcal/mol	9.4943 kcal/mol	5.22711 kcal/mol	51 63@LB@ \| \|@LB@5'-UUU...UUCAA UAA GA AAAA A AGACG...GAG-3'@LB@ GGU AUU GCGCC AUGCUUAG UC ACGCA@LB@ \|\|\| \|\|\| :\|:\|\| \|\|:\|\|:\|\| \|\| \|\|:\|\|@LB@ CCA UAA UGUGG UAUGAGUC AG UGUGU@LB@3'-UUU...ACCGC C AA U ACUAC...UAG-5'@LB@ \| \|@LB@ 92 80@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -23.2269 kcal/mol@LB@Unfolding Energy - mRNA 9.4943 kcal/mol@LB@Unfolding Energy - sRNA 5.22711 kcal/mol@LB@@LB@Position - mRNA 52 -- 62@LB@Position - sRNA 81 -- 91@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 174 -- 180@LB@
76	0.007832	0.3458	b1054	lpxL	-10.56	0.214918	224 -- 240	1 -- 17	lauryl-acyl carrier protein (ACP)-dependent acyltransferase	_____________223_______241\n_____________\|_________\|\n5'-AAA...CGCAC_________CGCGU...CCU-3'\n______________UGCUUCAUC\n______________\|\|\|\|\|\|\|\|\|\n______________ACGAAGUAG\n3'-UUU...GGGGA_________-5'\n_____________\|________\|\n_____________18_______1\n	234 -- 240	1 -- 7	-13.5925 kcal/mol	1.26369 kcal/mol	0.710349 kcal/mol	223 241@LB@ \| \|@LB@5'-AAA...CGCAC CGCGU...CCU-3'@LB@ UGCUUCAUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGAAGUAG@LB@3'-UUU...GGGGA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -13.5925 kcal/mol@LB@Unfolding Energy - mRNA 1.26369 kcal/mol@LB@Unfolding Energy - sRNA 0.710349 kcal/mol@LB@@LB@Position - mRNA 224 -- 240@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
179	0.02059	0.3833	b2535	csiE	-10.55	0.216292	103 -- 142	58 -- 90	stationary phase inducible protein	_____________102___________143\n_____________\|_____________\|\n5'-GCA...GAUUA__________C__CAUUU...UGG-3'\n______________GCAUUCCCUU_GC\n______________\|\|\|::\|\|\|\|\|_\|\|\n______________CGUGGGGGAA_CG\n3'-UUU...UACCC_____________AAGUAG-5'\n_____________\|_____________\|\n_____________91____________57\n	133 -- 139	9 -- 15	-16.9052 kcal/mol	2.85301 kcal/mol	6.64496 kcal/mol	102 143@LB@ \| \|@LB@5'-GCA...GAUUA C CAUUU...UGG-3'@LB@ GCAUUCCCUU GC@LB@ \|\|\|::\|\|\|\|\| \|\|@LB@ CGUGGGGGAA CG@LB@3'-UUU...UACCC AAGUAG-5'@LB@ \| \|@LB@ 91 57@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -16.9052 kcal/mol@LB@Unfolding Energy - mRNA 2.85301 kcal/mol@LB@Unfolding Energy - sRNA 6.64496 kcal/mol@LB@@LB@Position - mRNA 103 -- 142@LB@Position - sRNA 58 -- 90@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 9 -- 15@LB@
110	0.01217	0.3575	b1324	tpx	-10.54	0.217228	251 -- 258	126 -- 133	lipid hydroperoxide peroxidase	_____________250____________259\n_____________\|______________\|\n5'-GCG...ACUCC______________GUCUG...AAG-3'\n______________UUGUUGUCGCGGUG\n______________\|:\|:\|\|\|\|\|\|\|\|\|:\n______________AGCGACAGCGCCAU\n3'-UUU...GUUGA______________UUUAU...UAG-5'\n_____________\|______________\|\n_____________134____________125\n	99 -- 105	48 -- 54	-22.761 kcal/mol	7.03952 kcal/mol	5.88061 kcal/mol	250 259@LB@ \| \|@LB@5'-GCG...ACUCC GUCUG...AAG-3'@LB@ UUGUUGUCGCGGUG@LB@ \|:\|:\|\|\|\|\|\|\|\|\|:@LB@ AGCGACAGCGCCAU@LB@3'-UUU...GUUGA UUUAU...UAG-5'@LB@ \| \|@LB@ 134 125@LB@@LB@@LB@Energy -10.54 kcal/mol@LB@Hybridization Energy -22.761 kcal/mol@LB@Unfolding Energy - mRNA 7.03952 kcal/mol@LB@Unfolding Energy - sRNA 5.88061 kcal/mol@LB@@LB@Position - mRNA 251 -- 258@LB@Position - sRNA 126 -- 133@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 48 -- 54@LB@
175	0.0199	0.3812	b3085	ygjP	-10.42	0.228945	225 -- 233	128 -- 136	putative metal dependent hydrolase	_____________224_______234\n_____________\|_________\|\n5'-AAC...UUCAG_________GAGCA...AAC-3'\n______________GGUUAUCCC\n______________\|\|\|:\|\|\|\|\|\n______________CCAGUAGGG\n3'-UUU...UAACG_________UGACG...UAG-5'\n_____________\|_________\|\n_____________137_______127\n	227 -- 233	128 -- 134	-15.1258 kcal/mol	2.43348 kcal/mol	4.55487 kcal/mol	224 234@LB@ \| \|@LB@5'-AAC...UUCAG GAGCA...AAC-3'@LB@ GGUUAUCCC@LB@ \|\|\|:\|\|\|\|\|@LB@ CCAGUAGGG@LB@3'-UUU...UAACG UGACG...UAG-5'@LB@ \| \|@LB@ 137 127@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -15.1258 kcal/mol@LB@Unfolding Energy - mRNA 2.43348 kcal/mol@LB@Unfolding Energy - sRNA 4.55487 kcal/mol@LB@@LB@Position - mRNA 225 -- 233@LB@Position - sRNA 128 -- 136@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 128 -- 134@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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service.

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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