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
171	0.01954	0.3812	b3687	ibpA	-6.40	0.875621	11 -- 20	10 -- 18	heat shock chaperone	_____________10____________21\n_____________\|_____________\|\n5'-AAC...GCCCC_______U_____AUAGA...GCU-3'\n______________CUCAGUC_AUGCA\n______________\|\|\|\|\|\|\|_\|::\|\|\n______________GAGUCAG_UGUGU\n3'-UUU...GUUAU_____________ACUAC...UAG-5'\n_____________\|_____________\|\n_____________19____________9\n	19 -- 25	172 -- 178	-14.2159 kcal/mol	5.36362 kcal/mol	0.433674 kcal/mol	10 21@LB@ \| \|@LB@5'-AAC...GCCCC U AUAGA...GCU-3'@LB@ CUCAGUC AUGCA@LB@ \|\|\|\|\|\|\| \|::\|\|@LB@ GAGUCAG UGUGU@LB@3'-UUU...GUUAU ACUAC...UAG-5'@LB@ \| \|@LB@ 19 9@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -14.2159 kcal/mol@LB@Unfolding Energy - mRNA 5.36362 kcal/mol@LB@Unfolding Energy - sRNA 0.433674 kcal/mol@LB@@LB@Position - mRNA 11 -- 20@LB@Position - sRNA 10 -- 18@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 172 -- 178@LB@
172	0.01969	0.3812	b0213	yafS	-9.47	0.344290	95 -- 113	1 -- 19	putative S-adenosyl-L-methionine-dependent methyltransferase	_____________94________114\n_____________\|_________\|\n5'-UGG...UCAAA_________CUCCU...UCA-3'\n______________CUGUCGUGG\n______________\|\|\|\|\|\|:\|\|\n______________GACAGCGCC\n3'-UUU...GAAGC_________AUUUU...UAG-5'\n_____________\|_________\|\n_____________20________0\n	228 -- 234	50 -- 56	-16.2917 kcal/mol	2.78861 kcal/mol	4.02 kcal/mol	94 114@LB@ \| \|@LB@5'-UGG...UCAAA CUCCU...UCA-3'@LB@ CUGUCGUGG@LB@ \|\|\|\|\|\|:\|\|@LB@ GACAGCGCC@LB@3'-UUU...GAAGC AUUUU...UAG-5'@LB@ \| \|@LB@ 20 0@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -16.2917 kcal/mol@LB@Unfolding Energy - mRNA 2.78861 kcal/mol@LB@Unfolding Energy - sRNA 4.02 kcal/mol@LB@@LB@Position - mRNA 95 -- 113@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 50 -- 56@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@
174	0.01972	0.3812	b0478	ybaL	-7.90	0.612018	5 -- 14	166 -- 176	inner membrane putative NAD(P)-binding transporter	_____________4___________15\n_____________\|___________\|\n_______5'-UUUA___________AAGCC...UGG-3'\n______________CAGUCGC_CAU\n______________\|\|\|\|\|:\|_\|\|\|\n______________GUCAGUG_GUA\n3'-UUU...UAUGA_______U___CUACG...UAG-5'\n_____________\|___________\|\n_____________177_________165\n	5 -- 11	170 -- 176	-11.743 kcal/mol	0.493889 kcal/mol	0.598087 kcal/mol	4 15@LB@ \| \|@LB@ 5'-UUUA AAGCC...UGG-3'@LB@ CAGUCGC CAU@LB@ \|\|\|\|\|:\| \|\|\|@LB@ GUCAGUG GUA@LB@3'-UUU...UAUGA U CUACG...UAG-5'@LB@ \| \|@LB@ 177 165@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -11.743 kcal/mol@LB@Unfolding Energy - mRNA 0.493889 kcal/mol@LB@Unfolding Energy - sRNA 0.598087 kcal/mol@LB@@LB@Position - mRNA 5 -- 14@LB@Position - sRNA 166 -- 176@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 170 -- 176@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@
176	0.01994	0.3812	b2170	setB	-11.80	0.122017	181 -- 237	58 -- 116	lactose/glucose efflux system	_____________180____________238\n_____________\|______________\|\n5'-GCU...GAUCG______________AACUC...UGC-3'\n______________AC_CAG_CAUGCAU\n______________\|\|_\|\|\|_\|\|::\|\|\|\n______________UG_GUC_GUGUGUA\n3'-UUU...GGUUA__A___A_______CUACG...UAG-5'\n_____________\|______________\|\n_____________117____________57\n	200 -- 206	166 -- 172	-10.2756 kcal/mol	1.89616 kcal/mol	0.604817 kcal/mol	180 238@LB@ \| \|@LB@5'-GCU...GAUCG AACUC...UGC-3'@LB@ AC CAG CAUGCAU@LB@ \|\| \|\|\| \|\|::\|\|\|@LB@ UG GUC GUGUGUA@LB@3'-UUU...GGUUA A A CUACG...UAG-5'@LB@ \| \|@LB@ 117 57@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -10.2756 kcal/mol@LB@Unfolding Energy - mRNA 1.89616 kcal/mol@LB@Unfolding Energy - sRNA 0.604817 kcal/mol@LB@@LB@Position - mRNA 181 -- 237@LB@Position - sRNA 58 -- 116@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 166 -- 172@LB@
177	0.02028	0.3833	b1732	katE	-12.45	0.090323	227 -- 246	168 -- 187	catalase HPII heme d-containing	_____________226___________________247\n_____________\|_____________________\|\n5'-UGG...AACCC_______C__________C__UACAC...ACG-3'\n______________ACAUCAG_AC_CAGUCAC_AC\n______________\|\|\|:\|\|:_\|\|_\|\|\|\|\|\|\|_\|\|\n______________UGUGGUU_UG_GUCAGUG_UG\n3'-UUU...UAAAA_______A__A__________UACUA...UAG-5'\n_____________\|_____________________\|\n_____________188___________________167\n	237 -- 243	170 -- 176	-19.9766 kcal/mol	1.23864 kcal/mol	4.88067 kcal/mol	226 247@LB@ \| \|@LB@5'-UGG...AACCC C C UACAC...ACG-3'@LB@ ACAUCAG AC CAGUCAC AC@LB@ \|\|\|:\|\|: \|\| \|\|\|\|\|\|\| \|\|@LB@ UGUGGUU UG GUCAGUG UG@LB@3'-UUU...UAAAA A A UACUA...UAG-5'@LB@ \| \|@LB@ 188 167@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -19.9766 kcal/mol@LB@Unfolding Energy - mRNA 1.23864 kcal/mol@LB@Unfolding Energy - sRNA 4.88067 kcal/mol@LB@@LB@Position - mRNA 227 -- 246@LB@Position - sRNA 168 -- 187@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 170 -- 176@LB@
178	0.02044	0.3833	b3433	asd	-8.72	0.462346	170 -- 185	58 -- 71	aspartate-semialdehyde dehydrogenase NAD(P)-binding	_____________169__________________186\n_____________\|____________________\|\n5'-UCA...UUAUA___________CUU______AAAAA...UCU-3'\n______________CAG_CACACAU___UGCAGG\n______________\|\|\|_\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________GUC_GUGUGUA___ACGUCC\n3'-UUU...UAUGA___A_______CU_______GUUCA...UAG-5'\n_____________\|____________________\|\n_____________72___________________57\n	173 -- 179	166 -- 172	-22.5694 kcal/mol	4.04779 kcal/mol	7.34152 kcal/mol	169 186@LB@ \| \|@LB@5'-UCA...UUAUA CUU AAAAA...UCU-3'@LB@ CAG CACACAU UGCAGG@LB@ \|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUC GUGUGUA ACGUCC@LB@3'-UUU...UAUGA A CU GUUCA...UAG-5'@LB@ \| \|@LB@ 72 57@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -22.5694 kcal/mol@LB@Unfolding Energy - mRNA 4.04779 kcal/mol@LB@Unfolding Energy - sRNA 7.34152 kcal/mol@LB@@LB@Position - mRNA 170 -- 185@LB@Position - sRNA 58 -- 71@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 166 -- 172@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@
180	0.02081	0.3833	b3728	pstS	-9.23	0.378852	18 -- 25	128 -- 135	phosphate ABC transporter periplasmic binding protein	_____________17___________26\n_____________\|____________\|\n5'-AGA...UCCUA____________GUAGC...GUG-3'\n______________UUUUGCUUC_UC\n______________::\|\|\|\|\|\|\|_\|\|\n______________GGAACGAAG_AG\n3'-UUU...GUGGG_________U__-5'\n_____________\|___________\|\n_____________136_________128\n	149 -- 155	4 -- 10	-10.5275 kcal/mol	1.71006 kcal/mol	1.04836 kcal/mol	17 26@LB@ \| \|@LB@5'-AGA...UCCUA GUAGC...GUG-3'@LB@ UUUUGCUUC UC@LB@ ::\|\|\|\|\|\|\| \|\|@LB@ GGAACGAAG AG@LB@3'-UUU...GUGGG U -5'@LB@ \| \|@LB@ 136 128@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -10.5275 kcal/mol@LB@Unfolding Energy - mRNA 1.71006 kcal/mol@LB@Unfolding Energy - sRNA 1.04836 kcal/mol@LB@@LB@Position - mRNA 18 -- 25@LB@Position - sRNA 128 -- 135@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 4 -- 10@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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