Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
162	0.02632	0.526	b1886	tar	-10.00	0.096892	244 -- 251	53 -- 60	methyl-accepting chemotaxis protein II		_____________243______252\n_____________\|________\|\n5'-UGC...GGUGC________UUCGC...UUC-3'\n______________UGGGGGUA\n______________\|:\|\|\|\|\|\|\n______________AUCCCCAU\n3'-UUU...ACUUU________UUGUC...UCG-5'\n_____________\|________\|\n_____________61_______52\n	245 -- 251	53 -- 59	-12.2006 kcal/mol	2.12623 kcal/mol	0.0710089 kcal/mol	243 252@LB@ \| \|@LB@5'-UGC...GGUGC UUCGC...UUC-3'@LB@ UGGGGGUA@LB@ \|:\|\|\|\|\|\|@LB@ AUCCCCAU@LB@3'-UUU...ACUUU UUGUC...UCG-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -12.2006 kcal/mol@LB@Unfolding Energy - mRNA 2.12623 kcal/mol@LB@Unfolding Energy - sRNA 0.0710089 kcal/mol@LB@@LB@Position - mRNA 244 -- 251@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 53 -- 59@LB@
115	0.01846	0.5155	b4483	tatD	-10.31	0.084235	251 -- 265	1 -- 13	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase		_____________250_____________266\n_____________\|_______________\|\n5'-CUG...GACCG________UU_____GUGCG...UCA-3'\n______________UGAUGAUG__GUAGC\n______________\|:\|\|\|\|\|\|__:\|\|\|\|\n______________AUUACUAC__UAUCG\n3'-UUU...UUUCA_______________-5'\n_____________\|______________\|\n_____________14_____________1\n	252 -- 258	6 -- 12	-13.1693 kcal/mol	2.8194 kcal/mol	0.0446954 kcal/mol	250 266@LB@ \| \|@LB@5'-CUG...GACCG UU GUGCG...UCA-3'@LB@ UGAUGAUG GUAGC@LB@ \|:\|\|\|\|\|\| :\|\|\|\|@LB@ AUUACUAC UAUCG@LB@3'-UUU...UUUCA -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -13.1693 kcal/mol@LB@Unfolding Energy - mRNA 2.8194 kcal/mol@LB@Unfolding Energy - sRNA 0.0446954 kcal/mol@LB@@LB@Position - mRNA 251 -- 265@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 6 -- 12@LB@
179	0.02973	0.5424	b2812	tcdA	-11.60	0.044907	209 -- 228	1 -- 28	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA		_____________208___________________________229\n_____________\|_____________________________\|\n5'-GUG...UCUGU_______________________C_____GUCAG...UUU-3'\n______________GGUAAU_________UAGUGAUG_AUGGC\n______________\|\|\|\|\|\|_________\|\|:\|\|\|\|\|_\|\|:\|\|\n______________CCAUUA_________AUUACUAC_UAUCG\n3'-UUU...UACUG______UUUAUUUCA______________-5'\n_____________\|____________________________\|\n_____________29___________________________1\n	216 -- 222	6 -- 12	-16.3639 kcal/mol	3.995 kcal/mol	0.766821 kcal/mol	208 229@LB@ \| \|@LB@5'-GUG...UCUGU C GUCAG...UUU-3'@LB@ GGUAAU UAGUGAUG AUGGC@LB@ \|\|\|\|\|\| \|\|:\|\|\|\|\| \|\|:\|\|@LB@ CCAUUA AUUACUAC UAUCG@LB@3'-UUU...UACUG UUUAUUUCA -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -16.3639 kcal/mol@LB@Unfolding Energy - mRNA 3.995 kcal/mol@LB@Unfolding Energy - sRNA 0.766821 kcal/mol@LB@@LB@Position - mRNA 209 -- 228@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 6 -- 12@LB@
164	0.02654	0.526	b3993	thiE	-11.45	0.048376	123 -- 151	37 -- 65	thiamine phosphate synthase (thiamine phosphate pyrophosphorylase)		_____________122____________________________152\n_____________\|______________________________\|\n5'-CAC...ACUAU_________AAU__________G_______ACUUC...UAC-3'\n______________UGAAAUGGG____GGCGGAUAU_UCGGAGA\n______________\|\|\|\|\|\|:\|\|____::\|:\|\|:\|\|_\|\|:\|\|:\|\n______________ACUUUAUCC____UUGUCUGUA_AGUCUUU\n3'-UUU...GGCCA_________CCAU_________________ACUUA...UCG-5'\n_____________\|______________________________\|\n_____________66_____________________________36\n	125 -- 131	57 -- 63	-26.5084 kcal/mol	7.89908 kcal/mol	7.1561 kcal/mol	122 152@LB@ \| \|@LB@5'-CAC...ACUAU AAU G ACUUC...UAC-3'@LB@ UGAAAUGGG GGCGGAUAU UCGGAGA@LB@ \|\|\|\|\|\|:\|\| ::\|:\|\|:\|\| \|\|:\|\|:\|@LB@ ACUUUAUCC UUGUCUGUA AGUCUUU@LB@3'-UUU...GGCCA CCAU ACUUA...UCG-5'@LB@ \| \|@LB@ 66 36@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -26.5084 kcal/mol@LB@Unfolding Energy - mRNA 7.89908 kcal/mol@LB@Unfolding Energy - sRNA 7.1561 kcal/mol@LB@@LB@Position - mRNA 123 -- 151@LB@Position - sRNA 37 -- 65@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 57 -- 63@LB@
76	0.01084	0.4523	b3990	thiH	-9.70	0.111440	16 -- 25	55 -- 64	tyrosine lyase involved in thiamine-thiazole moiety synthesis		_____________15_________26\n_____________\|__________\|\n5'-GCC...CGCUG__________CCGAC...AUG-3'\n______________GAAAUGGGGG\n______________\|\|\|\|\|:\|\|\|\|\n______________CUUUAUCCCC\n3'-UUU...GCCAA__________AUUUG...UCG-5'\n_____________\|__________\|\n_____________65_________54\n	19 -- 25	55 -- 61	-15.2995 kcal/mol	5.57445 kcal/mol	0.0291912 kcal/mol	15 26@LB@ \| \|@LB@5'-GCC...CGCUG CCGAC...AUG-3'@LB@ GAAAUGGGGG@LB@ \|\|\|\|\|:\|\|\|\|@LB@ CUUUAUCCCC@LB@3'-UUU...GCCAA AUUUG...UCG-5'@LB@ \| \|@LB@ 65 54@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -15.2995 kcal/mol@LB@Unfolding Energy - mRNA 5.57445 kcal/mol@LB@Unfolding Energy - sRNA 0.0291912 kcal/mol@LB@@LB@Position - mRNA 16 -- 25@LB@Position - sRNA 55 -- 64@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 55 -- 61@LB@
90	0.01478	0.5059	b0740	tolB	-11.20	0.054749	186 -- 207	1 -- 21	periplasmic protein		_____________185_____________________208\n_____________\|_______________________\|\n5'-UCC...GUCCA_______GAGAU___________AGGCA...CCG-3'\n______________GAUAAGG_____AUGAUGA_AGC\n______________:\|\|\|\|:\|_____\|\|\|\|\|\|\|_\|\|\|\n______________UUAUUUC_____UACUACU_UCG\n3'-UUU...AUUAU_______AAU_________A___-5'\n_____________\|______________________\|\n_____________22_____________________1\n	198 -- 204	5 -- 11	-16.1118 kcal/mol	4.84175 kcal/mol	0.0669945 kcal/mol	185 208@LB@ \| \|@LB@5'-UCC...GUCCA GAGAU AGGCA...CCG-3'@LB@ GAUAAGG AUGAUGA AGC@LB@ :\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|@LB@ UUAUUUC UACUACU UCG@LB@3'-UUU...AUUAU AAU A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -16.1118 kcal/mol@LB@Unfolding Energy - mRNA 4.84175 kcal/mol@LB@Unfolding Energy - sRNA 0.0669945 kcal/mol@LB@@LB@Position - mRNA 186 -- 207@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
118	0.01863	0.5155	b0738	tolR	-11.80	0.040697	190 -- 199	50 -- 59	membrane spanning protein in TolA-TolQ-TolR complex		_____________189________200\n_____________\|__________\|\n5'-UGG...CAACA__________CAUGG...UGG-3'\n______________AGGGGUAAGC\n______________\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	193 -- 199	50 -- 56	-16.6396 kcal/mol	4.1136 kcal/mol	0.728772 kcal/mol	189 200@LB@ \| \|@LB@5'-UGG...CAACA CAUGG...UGG-3'@LB@ AGGGGUAAGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -16.6396 kcal/mol@LB@Unfolding Energy - mRNA 4.1136 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 190 -- 199@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 50 -- 56@LB@
153	0.02513	0.526	b2745	truD	-9.91	0.100940	94 -- 116	1 -- 24	tRNA(Glu) pseudouridine(13) synthase		_____________93_______________________117\n_____________\|________________________\|\n5'-AAC...GCCAU________U_____C_____A___CACUA...UGG-3'\n______________AUGGAUGA_GUUAA__GUGA_AGC\n______________\|\|::\|\|:\|_\|\|\|\|\|__:\|\|\|_\|\|\|\n______________UAUUUAUU_CAAUU__UACU_UCG\n3'-UUU...GCCAU________U_____AC____A___-5'\n_____________\|_______________________\|\n_____________25______________________1\n	95 -- 101	17 -- 23	-14.0384 kcal/mol	4.01581 kcal/mol	0.108605 kcal/mol	93 117@LB@ \| \|@LB@5'-AAC...GCCAU U C A CACUA...UGG-3'@LB@ AUGGAUGA GUUAA GUGA AGC@LB@ \|\|::\|\|:\| \|\|\|\|\| :\|\|\| \|\|\|@LB@ UAUUUAUU CAAUU UACU UCG@LB@3'-UUU...GCCAU U AC A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -14.0384 kcal/mol@LB@Unfolding Energy - mRNA 4.01581 kcal/mol@LB@Unfolding Energy - sRNA 0.108605 kcal/mol@LB@@LB@Position - mRNA 94 -- 116@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 17 -- 23@LB@
141	0.0236	0.526	b3339	tufA	-10.69	0.070202	69 -- 84	1 -- 19	translation elongation factor EF-Tu 1	b3980	_____________68__________________85\n_____________\|___________________\|\n5'-AAU...AUUCC___________________GCCGA...CCA-3'\n______________UGAAGU__AUGAUGA_AGC\n______________\|:\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|\n______________AUUUCA__UACUACU_UCG\n3'-UUU...UAUUU______AU_______A___-5'\n_____________\|__________________\|\n_____________20_________________1\n	75 -- 81	5 -- 11	-13.5879 kcal/mol	2.83361 kcal/mol	0.0638423 kcal/mol	68 85@LB@ \| \|@LB@5'-AAU...AUUCC GCCGA...CCA-3'@LB@ UGAAGU AUGAUGA AGC@LB@ \|:\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ AUUUCA UACUACU UCG@LB@3'-UUU...UAUUU AU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -13.5879 kcal/mol@LB@Unfolding Energy - mRNA 2.83361 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 69 -- 84@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 5 -- 11@LB@
140	0.02319	0.526	b3615	waaH	-10.58	0.073933	178 -- 212	1 -- 47	LPS(HepIII)-glucuronic acid glycosyltransferase		_____________177______________________________________________213\n_____________\|________________________________________________\|\n5'-GAU...GGAUA____________C____U_______UU________________AC___ACCAA...GGA-3'\n______________AC_UUCAGAGGU____G_CGGUAAU___________AUGAUGA__AGC\n______________\|\|_\|\|\|\|\|\|::\|____\|_\|\|\|\|\|\|\|___________\|\|\|\|\|\|\|__\|\|\|\n______________UG_AAGUCUUUA____C_GCCAUUA___________UACUACU__UCG\n3'-UUU...UUGUC__U_________CUUA_U_______UUUAUUUCAAU_______A____-5'\n_____________\|_______________________________________________\|\n_____________48______________________________________________1\n	201 -- 207	5 -- 11	-24.9941 kcal/mol	8.09222 kcal/mol	6.32011 kcal/mol	177 213@LB@ \| \|@LB@5'-GAU...GGAUA C U UU AC ACCAA...GGA-3'@LB@ AC UUCAGAGGU G CGGUAAU AUGAUGA AGC@LB@ \|\| \|\|\|\|\|\|::\| \| \|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UG AAGUCUUUA C GCCAUUA UACUACU UCG@LB@3'-UUU...UUGUC U CUUA U UUUAUUUCAAU A -5'@LB@ \| \|@LB@ 48 1@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -24.9941 kcal/mol@LB@Unfolding Energy - mRNA 8.09222 kcal/mol@LB@Unfolding Energy - sRNA 6.32011 kcal/mol@LB@@LB@Position - mRNA 178 -- 212@LB@Position - sRNA 1 -- 47@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 5 -- 11@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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