Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
130	0.02541	0.6177	b4365	yjjQ	-8.08	0.100207	263 -- 277	38 -- 55	putative transcriptional regulator	_____________262_________________278\n_____________\|___________________\|\n5'-AGG...GCAGG___A_______________GAGGA...AUG-3'\n______________GUU_AAAGAGG____UCAU\n______________\|\|:_\|\|\|\|\|\|\|____\|\|\|\|\n______________CAG_UUUCUCC____AGUA\n3'-UUU...CCGGG___________UUAA____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	267 -- 273	46 -- 52	-10.7142 kcal/mol	1.46087 kcal/mol	1.17036 kcal/mol	262 278@LB@ \| \|@LB@5'-AGG...GCAGG A GAGGA...AUG-3'@LB@ GUU AAAGAGG UCAU@LB@ \|\|: \|\|\|\|\|\|\| \|\|\|\|@LB@ CAG UUUCUCC AGUA@LB@3'-UUU...CCGGG UUAA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -10.7142 kcal/mol@LB@Unfolding Energy - mRNA 1.46087 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 46 -- 52@LB@
137	0.02646	0.6177	b3807	cyaY	-4.99	0.375460	213 -- 221	38 -- 46	iron-dependent inhibitor of iron-sulfur cluster formation; frataxin; iron-binding and oxidizing protein	_____________212_______222\n_____________\|_________\|\n5'-UGA...ACAGU_________CGCCU...AAA-3'\n______________GAAUUUCAU\n______________\|\|\|\|\|\|\|\|\|\n______________CUUAAAGUA\n3'-UUU...UUCUC_________AAAAA...ACA-5'\n_____________\|_________\|\n_____________47________37\n	215 -- 221	38 -- 44	-7.89908 kcal/mol	1.90809 kcal/mol	1.00074 kcal/mol	212 222@LB@ \| \|@LB@5'-UGA...ACAGU CGCCU...AAA-3'@LB@ GAAUUUCAU@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUUAAAGUA@LB@3'-UUU...UUCUC AAAAA...ACA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -4.99 kcal/mol@LB@Hybridization Energy -7.89908 kcal/mol@LB@Unfolding Energy - mRNA 1.90809 kcal/mol@LB@Unfolding Energy - sRNA 1.00074 kcal/mol@LB@@LB@Position - mRNA 213 -- 221@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
140	0.02703	0.6177	b3447	ggt	-5.41	0.319095	66 -- 81	38 -- 54	gamma-glutamyltranspeptidase	_____________65________________82\n_____________\|_________________\|\n5'-GUU...AAGAA________UC_______CGCGU...CGU-3'\n______________UCAGA_AG__GUUUCAU\n______________\|\|\|:\|_\|\|__:\|\|\|\|\|\|\n______________AGUUU_UC__UAAAGUA\n3'-UUU...CGGGC_____C__CU_______AAAAA...ACA-5'\n_____________\|_________________\|\n_____________55________________37\n	75 -- 81	38 -- 44	-8.61894 kcal/mol	2.03989 kcal/mol	1.17036 kcal/mol	65 82@LB@ \| \|@LB@5'-GUU...AAGAA UC CGCGU...CGU-3'@LB@ UCAGA AG GUUUCAU@LB@ \|\|\|:\| \|\| :\|\|\|\|\|\|@LB@ AGUUU UC UAAAGUA@LB@3'-UUU...CGGGC C CU AAAAA...ACA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -5.41 kcal/mol@LB@Hybridization Energy -8.61894 kcal/mol@LB@Unfolding Energy - mRNA 2.03989 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 66 -- 81@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 38 -- 44@LB@
142	0.02758	0.6177	b3186	rplU	-10.01	0.040887	186 -- 200	38 -- 52	50S ribosomal subunit protein L21	_____________185_____________201\n_____________\|_______________\|\n5'-UUA...GCGCG____C__________AUGUA...UUG-3'\n______________GAAG_GGAGUUUUAU\n______________:\|\|\|_\|\|\|:\|\|\|:\|\|\n______________UUUC_CCUUAAAGUA\n3'-UUU...GGCAG____U__________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	194 -- 200	38 -- 44	-13.3778 kcal/mol	2.29537 kcal/mol	1.0693 kcal/mol	185 201@LB@ \| \|@LB@5'-UUA...GCGCG C AUGUA...UUG-3'@LB@ GAAG GGAGUUUUAU@LB@ :\|\|\| \|\|\|:\|\|\|:\|\|@LB@ UUUC CCUUAAAGUA@LB@3'-UUU...GGCAG U AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -13.3778 kcal/mol@LB@Unfolding Energy - mRNA 2.29537 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 186 -- 200@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 38 -- 44@LB@
145	0.02855	0.6177	b2252	ais	-5.71	0.282709	182 -- 202	38 -- 55	putative LPS core heptose(II)-phosphate phosphatase	_____________181___________________203\n_____________\|_____________________\|\n5'-ACC...CGCUU___UAU___U_______A___GUUAG...GGA-3'\n______________GUC___AGG_GGAGUUU_CGU\n______________\|\|\|___\|:\|_\|\|\|:\|\|\|_\|:\|\n______________CAG___UUC_CCUUAAA_GUA\n3'-UUU...CCGGG___U_____U___________AAAAA...ACA-5'\n_____________\|_____________________\|\n_____________56____________________37\n	192 -- 198	41 -- 47	-12.7294 kcal/mol	5.84979 kcal/mol	1.17036 kcal/mol	181 203@LB@ \| \|@LB@5'-ACC...CGCUU UAU U A GUUAG...GGA-3'@LB@ GUC AGG GGAGUUU CGU@LB@ \|\|\| \|:\| \|\|\|:\|\|\| \|:\|@LB@ CAG UUC CCUUAAA GUA@LB@3'-UUU...CCGGG U U AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -5.71 kcal/mol@LB@Hybridization Energy -12.7294 kcal/mol@LB@Unfolding Energy - mRNA 5.84979 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 182 -- 202@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 41 -- 47@LB@
169	0.03425	0.6177	b0336	codB	-12.15	0.014930	188 -- 202	38 -- 52	cytosine transporter	_____________187_____________203\n_____________\|_______________\|\n5'-CCA...GCAAA_______________GUCGC...UUU-3'\n______________AAGGGGGAAUUUCGU\n______________\|\|:\|:\|\|\|\|\|\|\|\|:\|\n______________UUUCUCCUUAAAGUA\n3'-UUU...GGCAG_______________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	196 -- 202	38 -- 44	-18.3448 kcal/mol	5.13025 kcal/mol	1.0693 kcal/mol	187 203@LB@ \| \|@LB@5'-CCA...GCAAA GUCGC...UUU-3'@LB@ AAGGGGGAAUUUCGU@LB@ \|\|:\|:\|\|\|\|\|\|\|\|:\|@LB@ UUUCUCCUUAAAGUA@LB@3'-UUU...GGCAG AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -18.3448 kcal/mol@LB@Unfolding Energy - mRNA 5.13025 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 188 -- 202@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
174	0.03548	0.6177	b2437	eutR	-7.66	0.121193	279 -- 299	38 -- 55	eut operon transcriptional activator AraC family	_____________278___________________300\n_____________\|_____________________\|\n5'-CGC...CGAAG_______U___UAAUG_____C-3'\n______________GUCGAAG_GGA_____UUCAU\n______________\|\|\|:\|\|\|_\|\|\|_____\|\|\|\|\|\n______________CAGUUUC_CCU_____AAGUA\n3'-UUU...CCGGG_______U___UA________AAAAA...ACA-5'\n_____________\|_____________________\|\n_____________56____________________37\n	279 -- 285	49 -- 55	-15.2982 kcal/mol	6.46344 kcal/mol	1.17036 kcal/mol	278 300@LB@ \| \|@LB@5'-CGC...CGAAG U UAAUG C-3'@LB@ GUCGAAG GGA UUCAU@LB@ \|\|\|:\|\|\| \|\|\| \|\|\|\|\|@LB@ CAGUUUC CCU AAGUA@LB@3'-UUU...CCGGG U UA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -15.2982 kcal/mol@LB@Unfolding Energy - mRNA 6.46344 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 279 -- 299@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 49 -- 55@LB@
179	0.03684	0.6177	b0335	prpE	-7.81	0.113441	203 -- 221	38 -- 55	propionate--CoA ligase	_____________202_________________222\n_____________\|___________________\|\n5'-GCC...AUUAU___UUUU__C_________CAGCG...AAA-3'\n______________GUC____AG_GAAUUUUAU\n______________\|\|\|____\|\|_\|\|\|\|\|\|:\|\|\n______________CAG____UC_CUUAAAGUA\n3'-UUU...CCGGG___UUUC____________AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	215 -- 221	38 -- 44	-10.8576 kcal/mol	1.87676 kcal/mol	1.17036 kcal/mol	202 222@LB@ \| \|@LB@5'-GCC...AUUAU UUUU C CAGCG...AAA-3'@LB@ GUC AG GAAUUUUAU@LB@ \|\|\| \|\| \|\|\|\|\|\|:\|\|@LB@ CAG UC CUUAAAGUA@LB@3'-UUU...CCGGG UUUC AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -10.8576 kcal/mol@LB@Unfolding Energy - mRNA 1.87676 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
198	0.04148	0.6177	b1067	yceH	-6.24	0.226874	185 -- 202	38 -- 56	UPF0502 family protein	_____________184_________________203\n_____________\|___________________\|\n5'-GCA...CCGGC__C___________C____GAAAU...GUG-3'\n______________CG_UAAGGAG_AAU_UCAU\n______________\|\|_:\|\|:\|\|\|_\|\|\|_\|\|\|\|\n______________GC_GUUUCUC_UUA_AGUA\n3'-UUU...ACCGG__A_______C___A____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________37\n	188 -- 194	47 -- 53	-10.8881 kcal/mol	3.47135 kcal/mol	1.17918 kcal/mol	184 203@LB@ \| \|@LB@5'-GCA...CCGGC C C GAAAU...GUG-3'@LB@ CG UAAGGAG AAU UCAU@LB@ \|\| :\|\|:\|\|\| \|\|\| \|\|\|\|@LB@ GC GUUUCUC UUA AGUA@LB@3'-UUU...ACCGG A C A AAAAA...ACA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -6.24 kcal/mol@LB@Hybridization Energy -10.8881 kcal/mol@LB@Unfolding Energy - mRNA 3.47135 kcal/mol@LB@Unfolding Energy - sRNA 1.17918 kcal/mol@LB@@LB@Position - mRNA 185 -- 202@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
14	0.003078	0.593	b0886	cydC	-10.90	0.026971	183 -- 199	39 -- 56	glutathione/cysteine ABC transporter export permease/ATPase	_____________182________________200\n_____________\|__________________\|\n5'-GCG...CCCAU_____________A____AAUGC...UCG-3'\n______________CGUC_AGGAGGAG_UUUA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|:\|\n______________GCAG_UUCUCCUU_AAGU\n3'-UUU...ACCGG____U________A____AAAAA...ACA-5'\n_____________\|__________________\|\n_____________57_________________38\n	188 -- 194	44 -- 50	-16.2318 kcal/mol	4.17801 kcal/mol	1.15786 kcal/mol	182 200@LB@ \| \|@LB@5'-GCG...CCCAU A AAUGC...UCG-3'@LB@ CGUC AGGAGGAG UUUA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|:\|@LB@ GCAG UUCUCCUU AAGU@LB@3'-UUU...ACCGG U A AAAAA...ACA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -16.2318 kcal/mol@LB@Unfolding Energy - mRNA 4.17801 kcal/mol@LB@Unfolding Energy - sRNA 1.15786 kcal/mol@LB@@LB@Position - mRNA 183 -- 199@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@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