Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
13	0.000833	0.2153	b1531	marA	-8.74	0.292618	190 -- 205	38 -- 57	multiple antibiotic resistance transcriptional regulator	_____________189__________________206\n_____________\|____________________\|\n5'-AAG...AAAAA____________________CAGAC...AGC-3'\n______________GAGGUA___UGA_CGAUGUC\n______________\|\|:\|:\|___\|\|\|_\|:\|\|\|\|\|\n______________CUUCGU___ACU_GUUACAG\n3'-UUU...AUGAC______UAC___C_______CACGA...GCG-5'\n_____________\|____________________\|\n_____________58___________________37\n	199 -- 205	38 -- 44	-15.3925 kcal/mol	3.44101 kcal/mol	3.2161 kcal/mol	189 206@LB@ \| \|@LB@5'-AAG...AAAAA CAGAC...AGC-3'@LB@ GAGGUA UGA CGAUGUC@LB@ \|\|:\|:\| \|\|\| \|:\|\|\|\|\|@LB@ CUUCGU ACU GUUACAG@LB@3'-UUU...AUGAC UAC C CACGA...GCG-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -15.3925 kcal/mol@LB@Unfolding Energy - mRNA 3.44101 kcal/mol@LB@Unfolding Energy - sRNA 3.2161 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 38 -- 44@LB@
54	0.00511	0.2905	b0487	cueR	-8.71	0.294876	81 -- 102	6 -- 25	copper-responsive regulon transcriptional regulator	_____________80_____________________103\n_____________\|______________________\|\n5'-GUU...ACAUC________C_CA__A_______UAUUA...AAA-3'\n______________UCUCUGUG_G__GU_CUUCCUG\n______________\|\|\|\|:\|:\|_\|__\|\|_\|\|\|\|\|\|\|\n______________AGAGGCGC_C__CA_GAAGGAC\n3'-UUU...GUCCA________U_C___________UAGCG-5'\n_____________\|______________________\|\n_____________26_____________________5\n	96 -- 102	6 -- 12	-22.4921 kcal/mol	6.07455 kcal/mol	7.70509 kcal/mol	80 103@LB@ \| \|@LB@5'-GUU...ACAUC C CA A UAUUA...AAA-3'@LB@ UCUCUGUG G GU CUUCCUG@LB@ \|\|\|\|:\|:\| \| \|\| \|\|\|\|\|\|\|@LB@ AGAGGCGC C CA GAAGGAC@LB@3'-UUU...GUCCA U C UAGCG-5'@LB@ \| \|@LB@ 26 5@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -22.4921 kcal/mol@LB@Unfolding Energy - mRNA 6.07455 kcal/mol@LB@Unfolding Energy - sRNA 7.70509 kcal/mol@LB@@LB@Position - mRNA 81 -- 102@LB@Position - sRNA 6 -- 25@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 6 -- 12@LB@
152	0.0188	0.4072	b0950	pqiA	-8.64	0.302533	34 -- 75	1 -- 61	paraquat-inducible SoxRS-regulated inner membrane protein	_____________33_____________________________________________________________76\n_____________\|______________________________________________________________\|\n5'-CUG...UGAAC__________UCU__A______________________AAAAAAU_____GG__________AAAAU...GUC-3'\n______________GCUGGGAGUA___UG_AGC________________GUU_________GGU____CUGAUCGC\n______________:\|\|\|\|:\|\|:\|___\|\|_\|\|\|________________\|\|\|_________\|\|\|____\|\|\|\|\|\|\|\|\n______________UGACCUUCGU___AC_UCG________________CAA_________CCA____GACUAGCG\n3'-UUU...CAUUA__________UAC______UUACAGCACGAAAGUC___GAGGCGCUC___GAAG________-5'\n_____________\|_____________________________________________________________\|\n_____________62____________________________________________________________1\n	69 -- 75	1 -- 7	-32.0531 kcal/mol	9.29686 kcal/mol	14.1206 kcal/mol	33 76@LB@ \| \|@LB@5'-CUG...UGAAC UCU A AAAAAAU GG AAAAU...GUC-3'@LB@ GCUGGGAGUA UG AGC GUU GGU CUGAUCGC@LB@ :\|\|\|\|:\|\|:\| \|\| \|\|\| \|\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UGACCUUCGU AC UCG CAA CCA GACUAGCG@LB@3'-UUU...CAUUA UAC UUACAGCACGAAAGUC GAGGCGCUC GAAG -5'@LB@ \| \|@LB@ 62 1@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -32.0531 kcal/mol@LB@Unfolding Energy - mRNA 9.29686 kcal/mol@LB@Unfolding Energy - sRNA 14.1206 kcal/mol@LB@@LB@Position - mRNA 34 -- 75@LB@Position - sRNA 1 -- 61@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 1 -- 7@LB@
134	0.01479	0.3709	b1930	yedF	-8.51	0.315187	12 -- 23	55 -- 66	putative TusA family sulfurtransferase	_____________11___________24\n_____________\|____________\|\n5'-ACG...CUGGC___U________UGAUU...AAG-3'\n______________GUA_UACUGGGA\n______________\|\|\|_\|\|\|\|\|\|:\|\n______________CAU_AUGACCUU\n3'-UUU...CGAUU___U________CGUUA...GCG-5'\n_____________\|____________\|\n_____________67___________54\n	17 -- 23	55 -- 61	-12.6769 kcal/mol	2.14533 kcal/mol	2.01956 kcal/mol	11 24@LB@ \| \|@LB@5'-ACG...CUGGC U UGAUU...AAG-3'@LB@ GUA UACUGGGA@LB@ \|\|\| \|\|\|\|\|\|:\|@LB@ CAU AUGACCUU@LB@3'-UUU...CGAUU U CGUUA...GCG-5'@LB@ \| \|@LB@ 67 54@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -12.6769 kcal/mol@LB@Unfolding Energy - mRNA 2.14533 kcal/mol@LB@Unfolding Energy - sRNA 2.01956 kcal/mol@LB@@LB@Position - mRNA 12 -- 23@LB@Position - sRNA 55 -- 66@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 55 -- 61@LB@
194	0.02479	0.4226	b1260	trpA	-8.29	0.338830	290 -- 297	41 -- 48	tryptophan synthase alpha subunit	_____________289______298\n_____________\|________\|\n5'-GCC...GGCAU________CAU-3'\n______________UGAGCAGU\n______________\|\|\|\|\|\|:\|\n______________ACUCGUUA\n3'-UUU...GUUAC________CAGCA...GCG-5'\n_____________\|________\|\n_____________49_______40\n	291 -- 297	41 -- 47	-10.1831 kcal/mol	0.772851 kcal/mol	1.11967 kcal/mol	289 298@LB@ \| \|@LB@5'-GCC...GGCAU CAU-3'@LB@ UGAGCAGU@LB@ \|\|\|\|\|\|:\|@LB@ ACUCGUUA@LB@3'-UUU...GUUAC CAGCA...GCG-5'@LB@ \| \|@LB@ 49 40@LB@@LB@@LB@Energy -8.29 kcal/mol@LB@Hybridization Energy -10.1831 kcal/mol@LB@Unfolding Energy - mRNA 0.772851 kcal/mol@LB@Unfolding Energy - sRNA 1.11967 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 41 -- 48@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 41 -- 47@LB@
118	0.01263	0.3585	b0890	ftsK	-8.12	0.357469	20 -- 46	38 -- 59	DNA translocase at septal ring sorting daughter chromsomes	_____________19__________________________47\n_____________\|___________________________\|\n5'-ACA...UGUUA______AAGU___GCA_______C___UGGUU...UUG-3'\n______________UGGAAG____CAA___GAGUAAU_GUC\n______________\|\|\|\|\|\|____\|\|\|___\|\|\|:\|\|\|_\|\|\|\n______________ACCUUC____GUU___CUCGUUA_CAG\n3'-UUU...UUAUG_____________ACA___________CACGA...GCG-5'\n_____________\|___________________________\|\n_____________60__________________________37\n	36 -- 42	41 -- 47	-18.6025 kcal/mol	7.19996 kcal/mol	3.27871 kcal/mol	19 47@LB@ \| \|@LB@5'-ACA...UGUUA AAGU GCA C UGGUU...UUG-3'@LB@ UGGAAG CAA GAGUAAU GUC@LB@ \|\|\|\|\|\| \|\|\| \|\|\|:\|\|\| \|\|\|@LB@ ACCUUC GUU CUCGUUA CAG@LB@3'-UUU...UUAUG ACA CACGA...GCG-5'@LB@ \| \|@LB@ 60 37@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -18.6025 kcal/mol@LB@Unfolding Energy - mRNA 7.19996 kcal/mol@LB@Unfolding Energy - sRNA 3.27871 kcal/mol@LB@@LB@Position - mRNA 20 -- 46@LB@Position - sRNA 38 -- 59@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 41 -- 47@LB@
102	0.01034	0.3393	b3128	garD	-8.06	0.364232	93 -- 113	5 -- 25	D-galactarate dehydrogenase	_____________92____________________114\n_____________\|_____________________\|\n5'-AUA...UCACA________UUUAAAC______CAUUC...UGA-3'\n______________UUUCUGCG_______UCCUGA\n______________\|:\|\|:\|\|\|_______\|\|\|\|\|\|\n______________AGAGGCGC_______AGGACU\n3'-UUU...GUCCA________UCCCAGA______AGCG-5'\n_____________\|_____________________\|\n_____________26____________________4\n	94 -- 100	18 -- 24	-19.1191 kcal/mol	3.34271 kcal/mol	7.71155 kcal/mol	92 114@LB@ \| \|@LB@5'-AUA...UCACA UUUAAAC CAUUC...UGA-3'@LB@ UUUCUGCG UCCUGA@LB@ \|:\|\|:\|\|\| \|\|\|\|\|\|@LB@ AGAGGCGC AGGACU@LB@3'-UUU...GUCCA UCCCAGA AGCG-5'@LB@ \| \|@LB@ 26 4@LB@@LB@@LB@Energy -8.06 kcal/mol@LB@Hybridization Energy -19.1191 kcal/mol@LB@Unfolding Energy - mRNA 3.34271 kcal/mol@LB@Unfolding Energy - sRNA 7.71155 kcal/mol@LB@@LB@Position - mRNA 93 -- 113@LB@Position - sRNA 5 -- 25@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 18 -- 24@LB@
132	0.01454	0.37	b1083	flgL	-7.54	0.428067	272 -- 293	37 -- 57	flagellar hook-filament junction protein	_____________271____________________294\n_____________\|______________________\|\n5'-UUG...UGGAU______CG_C__ACA_______ACGGGUA-3'\n______________GAAGUA__G_GA___GAUGUCG\n______________\|\|\|\|:\|__\|_\|\|___:\|\|\|\|\|\|\n______________CUUCGU__C_CU___UUACAGC\n3'-UUU...AUGAC______UA_A__CG________ACGAA...GCG-5'\n_____________\|______________________\|\n_____________58_____________________36\n	287 -- 293	37 -- 43	-16.4529 kcal/mol	5.68525 kcal/mol	3.2267 kcal/mol	271 294@LB@ \| \|@LB@5'-UUG...UGGAU CG C ACA ACGGGUA-3'@LB@ GAAGUA G GA GAUGUCG@LB@ \|\|\|\|:\| \| \|\| :\|\|\|\|\|\|@LB@ CUUCGU C CU UUACAGC@LB@3'-UUU...AUGAC UA A CG ACGAA...GCG-5'@LB@ \| \|@LB@ 58 36@LB@@LB@@LB@Energy -7.54 kcal/mol@LB@Hybridization Energy -16.4529 kcal/mol@LB@Unfolding Energy - mRNA 5.68525 kcal/mol@LB@Unfolding Energy - sRNA 3.2267 kcal/mol@LB@@LB@Position - mRNA 272 -- 293@LB@Position - sRNA 37 -- 57@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 37 -- 43@LB@
146	0.01749	0.3998	b1611	fumC	-5.84	0.669018	232 -- 244	46 -- 59	fumarate hydratase (fumarase C) aerobic Class II	_____________231____________245\n_____________\|______________\|\n5'-AGG...UUCGA______________UGUCC...UCC-3'\n______________UGGGGGCGAU_UGA\n______________\|\|\|::\|\|:\|\|_\|\|\|\n______________ACCUUCGUUA_ACU\n3'-UUU...UUAUG__________C___CGUUA...GCG-5'\n_____________\|______________\|\n_____________60_____________45\n	233 -- 239	52 -- 58	-14.3864 kcal/mol	5.35896 kcal/mol	3.18972 kcal/mol	231 245@LB@ \| \|@LB@5'-AGG...UUCGA UGUCC...UCC-3'@LB@ UGGGGGCGAU UGA@LB@ \|\|\|::\|\|:\|\| \|\|\|@LB@ ACCUUCGUUA ACU@LB@3'-UUU...UUAUG C CGUUA...GCG-5'@LB@ \| \|@LB@ 60 45@LB@@LB@@LB@Energy -5.84 kcal/mol@LB@Hybridization Energy -14.3864 kcal/mol@LB@Unfolding Energy - mRNA 5.35896 kcal/mol@LB@Unfolding Energy - sRNA 3.18972 kcal/mol@LB@@LB@Position - mRNA 232 -- 244@LB@Position - sRNA 46 -- 59@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 52 -- 58@LB@
157	0.0194	0.4072	b2720	hycF	-4.41	0.858528	100 -- 115	42 -- 59	formate hydrogenlyase complex iron-sulfur protein	_____________99_________________116\n_____________\|__________________\|\n5'-CGA...GACCG___U_________C____GAAGA...CAG-3'\n______________UGG___CGAUGUG_GUAA\n______________\|\|\|___\|:\|\|\|\|\|_\|:\|\|\n______________ACC___GUUACAC_CGUU\n3'-UUU...UUAUG___UUC_______U____ACAGC...GCG-5'\n_____________\|__________________\|\n_____________60_________________41\n	104 -- 110	47 -- 53	-13.6757 kcal/mol	5.98921 kcal/mol	3.27185 kcal/mol	99 116@LB@ \| \|@LB@5'-CGA...GACCG U C GAAGA...CAG-3'@LB@ UGG CGAUGUG GUAA@LB@ \|\|\| \|:\|\|\|\|\| \|:\|\|@LB@ ACC GUUACAC CGUU@LB@3'-UUU...UUAUG UUC U ACAGC...GCG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -4.41 kcal/mol@LB@Hybridization Energy -13.6757 kcal/mol@LB@Unfolding Energy - mRNA 5.98921 kcal/mol@LB@Unfolding Energy - sRNA 3.27185 kcal/mol@LB@@LB@Position - mRNA 100 -- 115@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 47 -- 53@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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