Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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	Additional homologs
143	0.006558	0.1605	b0161	degP	-10.78	0.178564	159 -- 170	58 -- 69	serine endoprotease (protease Do) membrane-associated		_____________158__________171\n_____________\|____________\|\n5'-AUU...GAAGA____________UGCGU...CGA-3'\n______________ACACAGCAAUUU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UGUGUCGUUAAG\n3'-UUU...UGAUG____________CAACA...GCA-5'\n_____________\|____________\|\n_____________70___________57\n	164 -- 170	58 -- 64	-16.5275 kcal/mol	2.62124 kcal/mol	3.12494 kcal/mol	158 171@LB@ \| \|@LB@5'-AUU...GAAGA UGCGU...CGA-3'@LB@ ACACAGCAAUUU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UGUGUCGUUAAG@LB@3'-UUU...UGAUG CAACA...GCA-5'@LB@ \| \|@LB@ 70 57@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -16.5275 kcal/mol@LB@Unfolding Energy - mRNA 2.62124 kcal/mol@LB@Unfolding Energy - sRNA 3.12494 kcal/mol@LB@@LB@Position - mRNA 159 -- 170@LB@Position - sRNA 58 -- 69@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 58 -- 64@LB@
148	0.006951	0.1638	b3995	rsd	-9.56	0.289012	16 -- 28	58 -- 70	stationary phase protein binds sigma 70 RNA polymerase subunit		_____________15____________29\n_____________\|_____________\|\n5'-AAU...UUCGC_____________UCCCU...ACU-3'\n______________CAUAUGGCAAUUC\n______________\|\|:\|::\|\|\|\|\|\|\|\n______________GUGUGUCGUUAAG\n3'-UUU...CUGAU_____________CAACA...GCA-5'\n_____________\|_____________\|\n_____________71____________57\n	22 -- 28	58 -- 64	-15.8606 kcal/mol	3.09015 kcal/mol	3.21169 kcal/mol	15 29@LB@ \| \|@LB@5'-AAU...UUCGC UCCCU...ACU-3'@LB@ CAUAUGGCAAUUC@LB@ \|\|:\|::\|\|\|\|\|\|\|@LB@ GUGUGUCGUUAAG@LB@3'-UUU...CUGAU CAACA...GCA-5'@LB@ \| \|@LB@ 71 57@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -15.8606 kcal/mol@LB@Unfolding Energy - mRNA 3.09015 kcal/mol@LB@Unfolding Energy - sRNA 3.21169 kcal/mol@LB@@LB@Position - mRNA 16 -- 28@LB@Position - sRNA 58 -- 70@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 58 -- 64@LB@
177	0.008834	0.1747	b0932	pepN	-9.31	0.316043	123 -- 145	58 -- 78	aminopeptidase N		_____________122_____________________146\n_____________\|_______________________\|\n5'-GUA...AAGAU_____UU_______GC_______ACGCA...AGA-3'\n______________GAAGA__CUGCAUA__GCGAUUU\n______________:\|\|\|\|__\|\|:\|\|:\|__\|\|:\|\|\|:\n______________UUUCU__GAUGUGU__CGUUAAG\n3'-UUU...ACCCG______________GU_______CAACA...GCA-5'\n_____________\|_______________________\|\n_____________79______________________57\n	139 -- 145	58 -- 64	-18.0038 kcal/mol	5.38317 kcal/mol	3.31018 kcal/mol	122 146@LB@ \| \|@LB@5'-GUA...AAGAU UU GC ACGCA...AGA-3'@LB@ GAAGA CUGCAUA GCGAUUU@LB@ :\|\|\|\| \|\|:\|\|:\| \|\|:\|\|\|:@LB@ UUUCU GAUGUGU CGUUAAG@LB@3'-UUU...ACCCG GU CAACA...GCA-5'@LB@ \| \|@LB@ 79 57@LB@@LB@@LB@Energy -9.31 kcal/mol@LB@Hybridization Energy -18.0038 kcal/mol@LB@Unfolding Energy - mRNA 5.38317 kcal/mol@LB@Unfolding Energy - sRNA 3.31018 kcal/mol@LB@@LB@Position - mRNA 123 -- 145@LB@Position - sRNA 58 -- 78@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 58 -- 64@LB@
197	0.01006	0.1776	b0069	sgrR	-8.41	0.425671	7 -- 22	58 -- 74	transcriptional DNA-binding transcriptional activator of sgrS sRNA		_____________6_________________23\n_____________\|_________________\|\n_____5'-CAUCCC____________CC___AAGCA...UGA-3'\n______________ACUGCAU_CAGU__UUC\n______________\|\|\|:\|\|:_\|\|\|:__\|\|\|\n______________UGAUGUG_GUCG__AAG\n3'-UUU...GUUUC_______U____UU___CAACA...GCA-5'\n_____________\|_________________\|\n_____________75________________57\n	7 -- 13	68 -- 74	-13.3461 kcal/mol	1.63335 kcal/mol	3.3008 kcal/mol	6 23@LB@ \| \|@LB@ 5'-CAUCCC CC AAGCA...UGA-3'@LB@ ACUGCAU CAGU UUC@LB@ \|\|\|:\|\|: \|\|\|: \|\|\|@LB@ UGAUGUG GUCG AAG@LB@3'-UUU...GUUUC U UU CAACA...GCA-5'@LB@ \| \|@LB@ 75 57@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.3461 kcal/mol@LB@Unfolding Energy - mRNA 1.63335 kcal/mol@LB@Unfolding Energy - sRNA 3.3008 kcal/mol@LB@@LB@Position - mRNA 7 -- 22@LB@Position - sRNA 58 -- 74@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 68 -- 74@LB@
19	0.0001526	0.02826	b1040	csgD	-18.47	0.001904	103 -- 117	60 -- 74	csgBAC operon transcriptional regulator	b3520	_____________102_____________118\n_____________\|_______________\|\n5'-UUA...UUAUU_______________GCAAC...CGC-3'\n______________ACUACACACAGCAGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UGAUGUGUGUCGUUA\n3'-UUU...GUUUC_______________AGCAA...GCA-5'\n_____________\|_______________\|\n_____________75______________59\n	111 -- 117	60 -- 66	-23.4761 kcal/mol	1.72592 kcal/mol	3.27997 kcal/mol	102 118@LB@ \| \|@LB@5'-UUA...UUAUU GCAAC...CGC-3'@LB@ ACUACACACAGCAGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UGAUGUGUGUCGUUA@LB@3'-UUU...GUUUC AGCAA...GCA-5'@LB@ \| \|@LB@ 75 59@LB@@LB@@LB@Energy -18.47 kcal/mol@LB@Hybridization Energy -23.4761 kcal/mol@LB@Unfolding Energy - mRNA 1.72592 kcal/mol@LB@Unfolding Energy - sRNA 3.27997 kcal/mol@LB@@LB@Position - mRNA 103 -- 117@LB@Position - sRNA 60 -- 74@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 60 -- 66@LB@
34	0.0005364	0.05552	b4244	pyrI	-10.55	0.196904	198 -- 215	60 -- 77	aspartate carbamoyltransferase regulatory subunit		_____________197________________216\n_____________\|__________________\|\n5'-UUC...AAAUA_____G_______A____AAAUU...UCA-3'\n______________GAGAU_ACACACG_UAAU\n______________:\|\|\|:_\|\|\|\|\|\|:_:\|\|\|\n______________UUCUG_UGUGUGU_GUUA\n3'-UUU...CCCGU_____A_______C____AGCAA...GCA-5'\n_____________\|__________________\|\n_____________78_________________59\n	204 -- 210	65 -- 71	-15.1619 kcal/mol	1.32522 kcal/mol	3.29036 kcal/mol	197 216@LB@ \| \|@LB@5'-UUC...AAAUA G A AAAUU...UCA-3'@LB@ GAGAU ACACACG UAAU@LB@ :\|\|\|: \|\|\|\|\|\|: :\|\|\|@LB@ UUCUG UGUGUGU GUUA@LB@3'-UUU...CCCGU A C AGCAA...GCA-5'@LB@ \| \|@LB@ 78 59@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -15.1619 kcal/mol@LB@Unfolding Energy - mRNA 1.32522 kcal/mol@LB@Unfolding Energy - sRNA 3.29036 kcal/mol@LB@@LB@Position - mRNA 198 -- 215@LB@Position - sRNA 60 -- 77@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 65 -- 71@LB@
55	0.001955	0.1223	b0840	deoR	-10.34	0.214583	216 -- 260	60 -- 103	deoxyribose-5-phosphate-inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx		_____________215____________________________________________261\n_____________\|______________________________________________\|\n5'-GUG...GUCGC_______G________C__C__CU_____A____AA__________AAGUU...UUU-3'\n______________GAAGAGC_UAUCG_GG_AG_UG__GCAAG_AUUA__ACGCAGCGAU\n______________:\|\|:\|\|\|_:\|\|\|\|_\|\|_\|\|_\|\|__\|\|\|\|:_\|:\|\|__\|\|:\|\|\|\|:\|\|\n______________UUUUUCG_GUAGC_CC_UC_AC__CGUUU_UGAU__UGUGUCGUUA\n_________3'-UU_______G_____A__C__U__C______C____G___________AGCAA...GCA-5'\n_____________\|______________________________________________\|\n_____________104____________________________________________59\n	254 -- 260	60 -- 66	-39.4084 kcal/mol	12.9673 kcal/mol	16.1071 kcal/mol	215 261@LB@ \| \|@LB@5'-GUG...GUCGC G C C CU A AA AAGUU...UUU-3'@LB@ GAAGAGC UAUCG GG AG UG GCAAG AUUA ACGCAGCGAU@LB@ :\|\|:\|\|\| :\|\|\|\| \|\| \|\| \|\| \|\|\|\|: \|:\|\| \|\|:\|\|\|\|:\|\|@LB@ UUUUUCG GUAGC CC UC AC CGUUU UGAU UGUGUCGUUA@LB@ 3'-UU G A C U C C G AGCAA...GCA-5'@LB@ \| \|@LB@ 104 59@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -39.4084 kcal/mol@LB@Unfolding Energy - mRNA 12.9673 kcal/mol@LB@Unfolding Energy - sRNA 16.1071 kcal/mol@LB@@LB@Position - mRNA 216 -- 260@LB@Position - sRNA 60 -- 103@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 60 -- 66@LB@
116	0.005119	0.155	b2513	yfgM	-8.84	0.371642	84 -- 101	60 -- 75	ancillary SecYEG translocon subunit; putative anti-RcsB factor		_____________83_________________102\n_____________\|__________________\|\n5'-GGC...GAAGU_____ACG__________AGUGA...UUG-3'\n______________GGCUA___GCACAGCAGU\n______________\|:\|\|\|___:\|\|\|\|\|\|\|:\|\n______________CUGAU___UGUGUCGUUA\n3'-UUU...CGUUU_____G____________AGCAA...GCA-5'\n_____________\|__________________\|\n_____________76_________________59\n	95 -- 101	60 -- 66	-19.484 kcal/mol	7.35825 kcal/mol	3.28851 kcal/mol	83 102@LB@ \| \|@LB@5'-GGC...GAAGU ACG AGUGA...UUG-3'@LB@ GGCUA GCACAGCAGU@LB@ \|:\|\|\| :\|\|\|\|\|\|\|:\|@LB@ CUGAU UGUGUCGUUA@LB@3'-UUU...CGUUU G AGCAA...GCA-5'@LB@ \| \|@LB@ 76 59@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -19.484 kcal/mol@LB@Unfolding Energy - mRNA 7.35825 kcal/mol@LB@Unfolding Energy - sRNA 3.28851 kcal/mol@LB@@LB@Position - mRNA 84 -- 101@LB@Position - sRNA 60 -- 75@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 60 -- 66@LB@
190	0.009703	0.1776	b4125	dcuS	-9.98	0.246838	251 -- 265	60 -- 75	sensory histidine kinase in two-component regulatory system with DcuR regulator of anaerobic fumarate respiration		_____________250______________266\n_____________\|________________\|\n5'-UCC...AAAUU__G_____________CUUAA...UAU-3'\n______________GA_UAC_CACAGUGAU\n______________\|\|_\|\|\|_\|\|\|\|\|::\|\|\n______________CU_AUG_GUGUCGUUA\n3'-UUU...CGUUU__G___U_________AGCAA...GCA-5'\n_____________\|________________\|\n_____________76_______________59\n	259 -- 265	60 -- 66	-16.3548 kcal/mol	3.08747 kcal/mol	3.28851 kcal/mol	250 266@LB@ \| \|@LB@5'-UCC...AAAUU G CUUAA...UAU-3'@LB@ GA UAC CACAGUGAU@LB@ \|\| \|\|\| \|\|\|\|\|::\|\|@LB@ CU AUG GUGUCGUUA@LB@3'-UUU...CGUUU G U AGCAA...GCA-5'@LB@ \| \|@LB@ 76 59@LB@@LB@@LB@Energy -9.98 kcal/mol@LB@Hybridization Energy -16.3548 kcal/mol@LB@Unfolding Energy - mRNA 3.08747 kcal/mol@LB@Unfolding Energy - sRNA 3.28851 kcal/mol@LB@@LB@Position - mRNA 251 -- 265@LB@Position - sRNA 60 -- 75@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 60 -- 66@LB@
40	0.0008945	0.07693	b0525	ppiB	-7.31	0.578113	284 -- 298	61 -- 76	peptidyl-prolyl cis-trans isomerase B (rotamase B)		_____________283______________299\n_____________\|________________\|\n5'-UGU...UUCCU___________C____AG-3'\n______________GGACUAC_UGC_GCGA\n______________:\|\|\|\|\|\|_::\|_\|\|:\|\n______________UCUGAUG_GUG_CGUU\n3'-UUU...CCGUU_______U___U____AAGCA...GCA-5'\n_____________\|________________\|\n_____________77_______________60\n	284 -- 290	70 -- 76	-14.2171 kcal/mol	3.65067 kcal/mol	3.25604 kcal/mol	283 299@LB@ \| \|@LB@5'-UGU...UUCCU C AG-3'@LB@ GGACUAC UGC GCGA@LB@ :\|\|\|\|\|\| ::\| \|\|:\|@LB@ UCUGAUG GUG CGUU@LB@3'-UUU...CCGUU U U AAGCA...GCA-5'@LB@ \| \|@LB@ 77 60@LB@@LB@@LB@Energy -7.31 kcal/mol@LB@Hybridization Energy -14.2171 kcal/mol@LB@Unfolding Energy - mRNA 3.65067 kcal/mol@LB@Unfolding Energy - sRNA 3.25604 kcal/mol@LB@@LB@Position - mRNA 284 -- 298@LB@Position - sRNA 61 -- 76@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 70 -- 76@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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