Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
131	0.01428	0.3654	b2099	yegU	-10.27	0.106798	246 -- 258	42 -- 54	ADP-ribosylglycohydrolase family protein	_____________245___________259\n_____________\|_____________\|\n5'-GUG...CGUUA__G__________GGAUG...CAC-3'\n______________GG_GAUGCGAUGG\n______________\|\|_:\|\|\|\|:\|\|\|\|\n______________CC_UUACGUUACC\n3'-UUU...AGUCA__G__________GGGUU...UUG-5'\n_____________\|_____________\|\n_____________55____________41\n	252 -- 258	42 -- 48	-19.8763 kcal/mol	6.10373 kcal/mol	3.49932 kcal/mol	245 259@LB@ \| \|@LB@5'-GUG...CGUUA G GGAUG...CAC-3'@LB@ GG GAUGCGAUGG@LB@ \|\| :\|\|\|\|:\|\|\|\|@LB@ CC UUACGUUACC@LB@3'-UUU...AGUCA G GGGUU...UUG-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -19.8763 kcal/mol@LB@Unfolding Energy - mRNA 6.10373 kcal/mol@LB@Unfolding Energy - sRNA 3.49932 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 42 -- 48@LB@
132	0.0144	0.3654	b2381	ypdB	-7.98	0.293473	18 -- 39	11 -- 32	response regulator activating yhjX; pyruvate-responsive YpdAB two-component system	_____________17_____________________40\n_____________\|______________________\|\n5'-AUU...GAAGC_________GCCG_________AUUGG...ACG-3'\n______________GAAUGAAAU____GGCAAUAAA\n______________:\|\|\|:\|\|\|\|____\|:\|\|\|\|\|\|\|\n______________UUUAUUUUA____CUGUUAUUU\n3'-UUU...UGUCU_________GACA_________CCGUA...UUG-5'\n_____________\|______________________\|\n_____________33_____________________10\n	33 -- 39	11 -- 17	-14.9693 kcal/mol	2.07375 kcal/mol	4.91579 kcal/mol	17 40@LB@ \| \|@LB@5'-AUU...GAAGC GCCG AUUGG...ACG-3'@LB@ GAAUGAAAU GGCAAUAAA@LB@ :\|\|\|:\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ UUUAUUUUA CUGUUAUUU@LB@3'-UUU...UGUCU GACA CCGUA...UUG-5'@LB@ \| \|@LB@ 33 10@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -14.9693 kcal/mol@LB@Unfolding Energy - mRNA 2.07375 kcal/mol@LB@Unfolding Energy - sRNA 4.91579 kcal/mol@LB@@LB@Position - mRNA 18 -- 39@LB@Position - sRNA 11 -- 32@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 11 -- 17@LB@
133	0.01445	0.3654	b1260	trpA	-8.36	0.252100	71 -- 77	38 -- 44	tryptophan synthase alpha subunit	_____________70______78\n_____________\|_______\|\n5'-GCC...CGCCC_______UGCGU...CAU-3'\n______________UGGCCCA\n______________\|\|\|\|\|\|\|\n______________ACCGGGU\n3'-UUU...ACGUU_______UGUCU...UUG-5'\n_____________\|_______\|\n_____________45______37\n	71 -- 77	38 -- 44	-13.3519 kcal/mol	1.05946 kcal/mol	3.93445 kcal/mol	70 78@LB@ \| \|@LB@5'-GCC...CGCCC UGCGU...CAU-3'@LB@ UGGCCCA@LB@ \|\|\|\|\|\|\|@LB@ ACCGGGU@LB@3'-UUU...ACGUU UGUCU...UUG-5'@LB@ \| \|@LB@ 45 37@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -13.3519 kcal/mol@LB@Unfolding Energy - mRNA 1.05946 kcal/mol@LB@Unfolding Energy - sRNA 3.93445 kcal/mol@LB@@LB@Position - mRNA 71 -- 77@LB@Position - sRNA 38 -- 44@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 38 -- 44@LB@
134	0.01498	0.3759	b3388	damX	-9.22	0.174550	186 -- 204	42 -- 59	cell division protein that binds to the septal ring	_____________185__________________205\n_____________\|____________________\|\n5'-GGG...ACCUU_____________UA_____AUGAA...AAC-3'\n______________UUAGUGG_GGUGU__AAUGG\n______________\|:\|\|\|\|\|_::\|\|:__\|\|\|\|\|\n______________AGUCACC_UUACG__UUACC\n3'-UUU...CUUUU_______G____________GGGUU...UUG-5'\n_____________\|____________________\|\n_____________60___________________41\n	186 -- 192	53 -- 59	-16.4488 kcal/mol	3.53707 kcal/mol	3.69565 kcal/mol	185 205@LB@ \| \|@LB@5'-GGG...ACCUU UA AUGAA...AAC-3'@LB@ UUAGUGG GGUGU AAUGG@LB@ \|:\|\|\|\|\| ::\|\|: \|\|\|\|\|@LB@ AGUCACC UUACG UUACC@LB@3'-UUU...CUUUU G GGGUU...UUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -16.4488 kcal/mol@LB@Unfolding Energy - mRNA 3.53707 kcal/mol@LB@Unfolding Energy - sRNA 3.69565 kcal/mol@LB@@LB@Position - mRNA 186 -- 204@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 53 -- 59@LB@
135	0.01531	0.3774	b3224	nanT	-10.34	0.103537	56 -- 77	28 -- 54	sialic acid transporter	_____________55__________________________78\n_____________\|___________________________\|\n5'-CGC...CUGAA_____________________UU____CAAGA...GUU-3'\n______________GGC___GC__UGGCCCAGCAG__GAUG\n______________\|\|\|___\|\|__\|\|\|\|\|\|\|:\|\|\|__:\|\|:\n______________CCG___CG__ACCGGGUUGUC__UUAU\n3'-UUU...AGUCA___UUA__UU___________UU____UUUAG...UUG-5'\n_____________\|___________________________\|\n_____________55__________________________27\n	63 -- 69	36 -- 42	-28.0045 kcal/mol	8.68418 kcal/mol	8.98285 kcal/mol	55 78@LB@ \| \|@LB@5'-CGC...CUGAA UU CAAGA...GUU-3'@LB@ GGC GC UGGCCCAGCAG GAUG@LB@ \|\|\| \|\| \|\|\|\|\|\|\|:\|\|\| :\|\|:@LB@ CCG CG ACCGGGUUGUC UUAU@LB@3'-UUU...AGUCA UUA UU UU UUUAG...UUG-5'@LB@ \| \|@LB@ 55 27@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -28.0045 kcal/mol@LB@Unfolding Energy - mRNA 8.68418 kcal/mol@LB@Unfolding Energy - sRNA 8.98285 kcal/mol@LB@@LB@Position - mRNA 56 -- 77@LB@Position - sRNA 28 -- 54@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 36 -- 42@LB@
136	0.01532	0.3774	b3054	ygiF	-8.05	0.285135	192 -- 208	38 -- 53	inorganic triphosphatase	_____________191_______________209\n_____________\|_________________\|\n5'-GGC...GAUAA____AG__C________GGAAA...CCG-3'\n______________GUAA__GC_AUGGCUCA\n______________\|:\|\|__\|\|_\|\|\|\|\|:\|\|\n______________CGUU__CG_UACCGGGU\n3'-UUU...GUCAC____A___U________UGUCU...UUG-5'\n_____________\|_________________\|\n_____________54________________37\n	202 -- 208	38 -- 44	-16.8567 kcal/mol	4.04422 kcal/mol	4.7597 kcal/mol	191 209@LB@ \| \|@LB@5'-GGC...GAUAA AG C GGAAA...CCG-3'@LB@ GUAA GC AUGGCUCA@LB@ \|:\|\| \|\| \|\|\|\|\|:\|\|@LB@ CGUU CG UACCGGGU@LB@3'-UUU...GUCAC A U UGUCU...UUG-5'@LB@ \| \|@LB@ 54 37@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -16.8567 kcal/mol@LB@Unfolding Energy - mRNA 4.04422 kcal/mol@LB@Unfolding Energy - sRNA 4.7597 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 38 -- 53@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 38 -- 44@LB@
137	0.01537	0.3774	b0952	pqiC	-8.31	0.257066	203 -- 237	17 -- 64	DUF330 family putative lipoprotein	_____________202________________________________________________238\n_____________\|__________________________________________________\|\n5'-ACG...ACAAU_____________U____A_______G_______________________UGGCC...GCG-3'\n______________GAAAA__AGUGGC_AGUG_CGAU__U_CAGCA___________CUGUGGC\n______________\|\|\|\|\|__\|\|\|\|\|\|_\|:\|\|_\|:\|\|__:_\|\|:\|\|___________\|\|\|\|\|:\|\n______________CUUUU__UCACCG_UUAC_GUUA__G_GUUGU___________GACACUG\n3'-UUU...ACAAC_____AG________________CC_G_____CUUUUAUUUUA_______UUAUU...UUG-5'\n_____________\|__________________________________________________\|\n_____________65_________________________________________________16\n	231 -- 237	17 -- 23	-29.1693 kcal/mol	9.7543 kcal/mol	11.1047 kcal/mol	202 238@LB@ \| \|@LB@5'-ACG...ACAAU U A G UGGCC...GCG-3'@LB@ GAAAA AGUGGC AGUG CGAU U CAGCA CUGUGGC@LB@ \|\|\|\|\| \|\|\|\|\|\| \|:\|\| \|:\|\| : \|\|:\|\| \|\|\|\|\|:\|@LB@ CUUUU UCACCG UUAC GUUA G GUUGU GACACUG@LB@3'-UUU...ACAAC AG CC G CUUUUAUUUUA UUAUU...UUG-5'@LB@ \| \|@LB@ 65 16@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -29.1693 kcal/mol@LB@Unfolding Energy - mRNA 9.7543 kcal/mol@LB@Unfolding Energy - sRNA 11.1047 kcal/mol@LB@@LB@Position - mRNA 203 -- 237@LB@Position - sRNA 17 -- 64@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 17 -- 23@LB@
138	0.01562	0.3807	b1735	chbR	-9.56	0.149643	62 -- 73	41 -- 54	repressor of chb operon for N N'-diacetylchitobiose utilization	_____________61_____________74\n_____________\|______________\|\n5'-GAU...UUGAA______________GAAGG...CUG-3'\n______________GGCGAUGCG__GGC\n______________\|\|\|:\|\|\|\|:__\|\|\|\n______________CCGUUACGU__CCG\n3'-UUU...AGUCA_________UA___GGUUG...UUG-5'\n_____________\|______________\|\n_____________55_____________40\n	64 -- 70	46 -- 52	-18.6965 kcal/mol	5.24959 kcal/mol	3.89026 kcal/mol	61 74@LB@ \| \|@LB@5'-GAU...UUGAA GAAGG...CUG-3'@LB@ GGCGAUGCG GGC@LB@ \|\|\|:\|\|\|\|: \|\|\|@LB@ CCGUUACGU CCG@LB@3'-UUU...AGUCA UA GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -18.6965 kcal/mol@LB@Unfolding Energy - mRNA 5.24959 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 62 -- 73@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 46 -- 52@LB@
139	0.0159	0.3828	b2108	yehA	-9.84	0.131393	50 -- 60	55 -- 65	putative fimbrial-like adhesin protein	_____________49__________61\n_____________\|___________\|\n5'-GUU...GGCCA___________UAUUU...UUG-3'\n______________GGGAAGUCAGU\n______________\|\|:\|\|:\|\|\|\|\|\n______________CCUUUUAGUCA\n3'-UUU...UACAA___________CCGUU...UUG-5'\n_____________\|___________\|\n_____________66__________54\n	54 -- 60	55 -- 61	-13.8721 kcal/mol	3.08221 kcal/mol	0.952476 kcal/mol	49 61@LB@ \| \|@LB@5'-GUU...GGCCA UAUUU...UUG-3'@LB@ GGGAAGUCAGU@LB@ \|\|:\|\|:\|\|\|\|\|@LB@ CCUUUUAGUCA@LB@3'-UUU...UACAA CCGUU...UUG-5'@LB@ \| \|@LB@ 66 54@LB@@LB@@LB@Energy -9.84 kcal/mol@LB@Hybridization Energy -13.8721 kcal/mol@LB@Unfolding Energy - mRNA 3.08221 kcal/mol@LB@Unfolding Energy - sRNA 0.952476 kcal/mol@LB@@LB@Position - mRNA 50 -- 60@LB@Position - sRNA 55 -- 65@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 55 -- 61@LB@
140	0.01599	0.3828	b0119	yacL	-11.32	0.063485	266 -- 299	25 -- 57	UPF0231 family protein	_____________265_________________________________300\n_____________\|___________________________________\|\n5'-GGU...CAUGA______CGG___C_________GA___________G-3'\n______________AGUGGU___GCA_UGGUUUAAU__AGA_GGUGAAA\n______________\|\|\|\|\|:___\|\|\|_\|\|\|:::\|\|:__\|\|\|_::\|:\|\|\|\n______________UCACCG___CGU_ACCGGGUUG__UCU_UUAUUUU\n3'-UUU...UUUAG______UUA___U______________U_______AGACA...UUG-5'\n_____________\|___________________________________\|\n_____________58__________________________________24\n	293 -- 299	25 -- 31	-25.5028 kcal/mol	4.248 kcal/mol	9.93955 kcal/mol	265 300@LB@ \| \|@LB@5'-GGU...CAUGA CGG C GA G-3'@LB@ AGUGGU GCA UGGUUUAAU AGA GGUGAAA@LB@ \|\|\|\|\|: \|\|\| \|\|\|:::\|\|: \|\|\| ::\|:\|\|\|@LB@ UCACCG CGU ACCGGGUUG UCU UUAUUUU@LB@3'-UUU...UUUAG UUA U U AGACA...UUG-5'@LB@ \| \|@LB@ 58 24@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -25.5028 kcal/mol@LB@Unfolding Energy - mRNA 4.248 kcal/mol@LB@Unfolding Energy - sRNA 9.93955 kcal/mol@LB@@LB@Position - mRNA 266 -- 299@LB@Position - sRNA 25 -- 57@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 25 -- 31@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