Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
194	0.02335	0.3864	b4182	yjfJ	-9.08	0.030148	209 -- 238	10 -- 37	PspA/IM30 family protein		_____________208____________________________239\n_____________\|______________________________\|\n5'-GAA...GGAAU____________AU______UG________GUUUA...AGC-3'\n______________UUUAAAAAGUUU__UUACGC__GGGAAAUC\n______________:\|\|\|\|\|\|\|:\|\|:__\|\|\|\|:\|__:\|\|\|\|\|\|\|\n______________GAAUUUUUUAAG__AAUGUG__UCCUUUAG\n3'-UUU...UUCGU____________C_______G_________ACUAC...CAA-5'\n_____________\|______________________________\|\n_____________38_____________________________9\n	232 -- 238	10 -- 16	-23.4786 kcal/mol	5.49388 kcal/mol	8.90309 kcal/mol	208 239@LB@ \| \|@LB@5'-GAA...GGAAU AU UG GUUUA...AGC-3'@LB@ UUUAAAAAGUUU UUACGC GGGAAAUC@LB@ :\|\|\|\|\|\|\|:\|\|: \|\|\|\|:\| :\|\|\|\|\|\|\|@LB@ GAAUUUUUUAAG AAUGUG UCCUUUAG@LB@3'-UUU...UUCGU C G ACUAC...CAA-5'@LB@ \| \|@LB@ 38 9@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -23.4786 kcal/mol@LB@Unfolding Energy - mRNA 5.49388 kcal/mol@LB@Unfolding Energy - sRNA 8.90309 kcal/mol@LB@@LB@Position - mRNA 209 -- 238@LB@Position - sRNA 10 -- 37@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 10 -- 16@LB@
7	4.438e-05	0.02042	b0794	ybhF	-10.77	0.009494	150 -- 165	11 -- 26	putative ABC transporter ATPase		_____________149______________166\n_____________\|________________\|\n5'-UAC...UGAUG________________GCCAG...GUU-3'\n______________CGUUACGCCAGGGAAU\n______________\|\|\|\|\|\|:\|\|\|\|\|:\|\|\|\n______________GCAAUGUGGUCCUUUA\n3'-UUU...UUUAA________________GACUA...CAA-5'\n_____________\|________________\|\n_____________27_______________10\n	157 -- 163	13 -- 19	-25.1629 kcal/mol	6.0475 kcal/mol	8.34814 kcal/mol	149 166@LB@ \| \|@LB@5'-UAC...UGAUG GCCAG...GUU-3'@LB@ CGUUACGCCAGGGAAU@LB@ \|\|\|\|\|\|:\|\|\|\|\|:\|\|\|@LB@ GCAAUGUGGUCCUUUA@LB@3'-UUU...UUUAA GACUA...CAA-5'@LB@ \| \|@LB@ 27 10@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -25.1629 kcal/mol@LB@Unfolding Energy - mRNA 6.0475 kcal/mol@LB@Unfolding Energy - sRNA 8.34814 kcal/mol@LB@@LB@Position - mRNA 150 -- 165@LB@Position - sRNA 11 -- 26@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 13 -- 19@LB@
176	0.02022	0.37	b0495	ybbA	-5.55	0.244939	212 -- 247	24 -- 59	putative ABC transporter ATPase		_____________211___________________________________248\n_____________\|_____________________________________\|\n5'-GCC...GCGGA____A_____G____UCAUCAU___________C___CGGUC...UCA-3'\n______________AAAC_UUGUU_AAGU________CUUAAGAAGU_CGU\n______________\|\|\|\|_\|\|\|:\|_\|\|\|:________\|\|\|\|\|:\|\|:\|_\|\|\|\n______________UUUG_AACGA_UUCG________GAAUUUUUUA_GCA\n3'-UUU...CCUAC__________A____UUCUUCGU__________A___AUGUG...CAA-5'\n_____________\|_____________________________________\|\n_____________60____________________________________23\n	235 -- 241	30 -- 36	-18.4731 kcal/mol	6.64875 kcal/mol	6.27609 kcal/mol	211 248@LB@ \| \|@LB@5'-GCC...GCGGA A G UCAUCAU C CGGUC...UCA-3'@LB@ AAAC UUGUU AAGU CUUAAGAAGU CGU@LB@ \|\|\|\| \|\|\|:\| \|\|\|: \|\|\|\|\|:\|\|:\| \|\|\|@LB@ UUUG AACGA UUCG GAAUUUUUUA GCA@LB@3'-UUU...CCUAC A UUCUUCGU A AUGUG...CAA-5'@LB@ \| \|@LB@ 60 23@LB@@LB@@LB@Energy -5.55 kcal/mol@LB@Hybridization Energy -18.4731 kcal/mol@LB@Unfolding Energy - mRNA 6.64875 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 212 -- 247@LB@Position - sRNA 24 -- 59@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 30 -- 36@LB@
33	0.001071	0.1045	b2058	wcaB	-10.41	0.012241	46 -- 64	25 -- 42	putative acyl transferase		_____________45__________________65\n_____________\|___________________\|\n5'-ACC...ACCGC______AA___C_______ACCGC...AGA-3'\n______________AAGCAC__AGA_AAAUUCG\n______________\|\|\|\|\|\|__\|:\|_\|\|\|\|\|\|\|\n______________UUCGUG__UUU_UUUAAGC\n3'-UUU...CGUUC______AA___________AAUGU...CAA-5'\n_____________\|___________________\|\n_____________43__________________24\n	58 -- 64	25 -- 31	-12.8013 kcal/mol	0.745291 kcal/mol	1.64855 kcal/mol	45 65@LB@ \| \|@LB@5'-ACC...ACCGC AA C ACCGC...AGA-3'@LB@ AAGCAC AGA AAAUUCG@LB@ \|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|@LB@ UUCGUG UUU UUUAAGC@LB@3'-UUU...CGUUC AA AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -12.8013 kcal/mol@LB@Unfolding Energy - mRNA 0.745291 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 46 -- 64@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 25 -- 31@LB@
170	0.01916	0.363	b1202	ycgV	-6.78	0.125661	82 -- 88	39 -- 45	putative adhesin	b2647	_____________81______89\n_____________\|_______\|\n5'-ACU...UCUCU_______UCAUC...UUG-3'\n______________GAGAAGC\n______________:\|\|\|\|\|\|\n______________UUCUUCG\n3'-UUU...AUUCG_______UGAAU...CAA-5'\n_____________\|_______\|\n_____________46______38\n	82 -- 88	39 -- 45	-7.60605 kcal/mol	0.31609 kcal/mol	0.514773 kcal/mol	81 89@LB@ \| \|@LB@5'-ACU...UCUCU UCAUC...UUG-3'@LB@ GAGAAGC@LB@ :\|\|\|\|\|\|@LB@ UUCUUCG@LB@3'-UUU...AUUCG UGAAU...CAA-5'@LB@ \| \|@LB@ 46 38@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -7.60605 kcal/mol@LB@Unfolding Energy - mRNA 0.31609 kcal/mol@LB@Unfolding Energy - sRNA 0.514773 kcal/mol@LB@@LB@Position - mRNA 82 -- 88@LB@Position - sRNA 39 -- 45@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 39 -- 45@LB@
84	0.005596	0.2146	b4065	yjcE	-5.39	0.265673	197 -- 210	9 -- 22	putative cation/proton antiporter		_____________196____________211\n_____________\|______________\|\n5'-UAU...AGGGA____AU________UCUUC...UGC-3'\n______________ACGC__GGAAAUCU\n______________\|\|:\|__\|\|\|\|\|\|\|\|\n______________UGUG__CCUUUAGA\n3'-UUU...AGCAA____GU________CUACACAA-5'\n_____________\|______________\|\n_____________23_____________8\n	203 -- 209	10 -- 16	-15.8377 kcal/mol	2.89158 kcal/mol	7.5588 kcal/mol	196 211@LB@ \| \|@LB@5'-UAU...AGGGA AU UCUUC...UGC-3'@LB@ ACGC GGAAAUCU@LB@ \|\|:\| \|\|\|\|\|\|\|\|@LB@ UGUG CCUUUAGA@LB@3'-UUU...AGCAA GU CUACACAA-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -15.8377 kcal/mol@LB@Unfolding Energy - mRNA 2.89158 kcal/mol@LB@Unfolding Energy - sRNA 7.5588 kcal/mol@LB@@LB@Position - mRNA 197 -- 210@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 10 -- 16@LB@
59	0.003153	0.1645	b1220	ychO	-8.71	0.038404	242 -- 262	37 -- 56	putative invasin		_____________241___________________263\n_____________\|_____________________\|\n5'-UCA...UUACU________U______C_____AGCUA...CAA-3'\n______________CUUGCUUG_AGCAGG_GGUAC\n______________\|\|\|\|\|\|\|:_\|\|\|\|:\|_:\|:\|\|\n______________GAACGAAU_UCGUUC_UCGUG\n3'-UUU...ACUUU_______________U_____AAUUU...CAA-5'\n_____________\|_____________________\|\n_____________57____________________36\n	242 -- 248	50 -- 56	-24.8668 kcal/mol	9.95535 kcal/mol	6.20049 kcal/mol	241 263@LB@ \| \|@LB@5'-UCA...UUACU U C AGCUA...CAA-3'@LB@ CUUGCUUG AGCAGG GGUAC@LB@ \|\|\|\|\|\|\|: \|\|\|\|:\| :\|:\|\|@LB@ GAACGAAU UCGUUC UCGUG@LB@3'-UUU...ACUUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -24.8668 kcal/mol@LB@Unfolding Energy - mRNA 9.95535 kcal/mol@LB@Unfolding Energy - sRNA 6.20049 kcal/mol@LB@@LB@Position - mRNA 242 -- 262@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 50 -- 56@LB@
160	0.01746	0.3504	b4542	yohO	-11.65	0.004993	133 -- 150	23 -- 41	putative membrane protein		_____________132_________________151\n_____________\|___________________\|\n5'-UCG...CACUC_________U_________AACAA...GUG-3'\n______________GGCAUUUAA__GAUUCGUU\n______________:\|\|\|:\|\|\|\|__:\|\|\|\|\|\|\|\n______________UCGUGAAUU__UUAAGCAA\n3'-UUU...GUUCU_________UU________UGUGG...CAA-5'\n_____________\|___________________\|\n_____________42__________________22\n	144 -- 150	23 -- 29	-16.4387 kcal/mol	3.13759 kcal/mol	1.64896 kcal/mol	132 151@LB@ \| \|@LB@5'-UCG...CACUC U AACAA...GUG-3'@LB@ GGCAUUUAA GAUUCGUU@LB@ :\|\|\|:\|\|\|\| :\|\|\|\|\|\|\|@LB@ UCGUGAAUU UUAAGCAA@LB@3'-UUU...GUUCU UU UGUGG...CAA-5'@LB@ \| \|@LB@ 42 22@LB@@LB@@LB@Energy -11.65 kcal/mol@LB@Hybridization Energy -16.4387 kcal/mol@LB@Unfolding Energy - mRNA 3.13759 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 133 -- 150@LB@Position - sRNA 23 -- 41@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 23 -- 29@LB@
52	0.002466	0.1527	b3527	yhjJ	-8.40	0.046956	207 -- 220	25 -- 41	putative periplasmic M16 family chaperone		_____________206_______________221\n_____________\|_________________\|\n5'-CUC...UGCAG_________________ACUUU...GGC-3'\n______________GGCAC___AAAAAUUCG\n______________:\|\|\|\|___\|\|\|\|\|\|\|\|\|\n______________UCGUG___UUUUUAAGC\n3'-UUU...GUUCU_____AAU_________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	214 -- 220	25 -- 31	-13.4116 kcal/mol	3.36563 kcal/mol	1.64839 kcal/mol	206 221@LB@ \| \|@LB@5'-CUC...UGCAG ACUUU...GGC-3'@LB@ GGCAC AAAAAUUCG@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCGUG UUUUUAAGC@LB@3'-UUU...GUUCU AAU AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -13.4116 kcal/mol@LB@Unfolding Energy - mRNA 3.36563 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 207 -- 220@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 25 -- 31@LB@
144	0.01453	0.3231	b3614	yibQ	-4.49	0.404320	261 -- 267	34 -- 40	putative polysaccharide deacetylase		_____________260_____268\n_____________\|_______\|\n5'-UGG...CCCCC_______CUGGC...UUG-3'\n______________GUACUUG\n______________\|:\|\|\|\|:\n______________CGUGAAU\n3'-UUU...UUCUU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________41______33\n	261 -- 267	34 -- 40	-7.10274 kcal/mol	0.998159 kcal/mol	1.61352 kcal/mol	260 268@LB@ \| \|@LB@5'-UGG...CCCCC CUGGC...UUG-3'@LB@ GUACUUG@LB@ \|:\|\|\|\|:@LB@ CGUGAAU@LB@3'-UUU...UUCUU UUUUU...CAA-5'@LB@ \| \|@LB@ 41 33@LB@@LB@@LB@Energy -4.49 kcal/mol@LB@Hybridization Energy -7.10274 kcal/mol@LB@Unfolding Energy - mRNA 0.998159 kcal/mol@LB@Unfolding Energy - sRNA 1.61352 kcal/mol@LB@@LB@Position - mRNA 261 -- 267@LB@Position - sRNA 34 -- 40@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 34 -- 40@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching