Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
106	0.0109	0.3104	b2510	yfgJ	-10.53	0.098521	243 -- 261	5 -- 21	DUF1407 family protein	_____________242_________________262\n_____________\|___________________\|\n5'-UAA...AUCAG________CC_________GCCGA...UUU-3'\n______________GAUAACGG__AUGCGCGUU\n______________\|\|\|\|\|\|::__\|\|\|\|\|\|\|\|:\n______________CUAUUGUU__UACGCGCAG\n3'-UUU...UACUA___________________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	255 -- 261	5 -- 11	-20.9599 kcal/mol	9.18032 kcal/mol	1.24955 kcal/mol	242 262@LB@ \| \|@LB@5'-UAA...AUCAG CC GCCGA...UUU-3'@LB@ GAUAACGG AUGCGCGUU@LB@ \|\|\|\|\|\|:: \|\|\|\|\|\|\|\|:@LB@ CUAUUGUU UACGCGCAG@LB@3'-UUU...UACUA AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -20.9599 kcal/mol@LB@Unfolding Energy - mRNA 9.18032 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 243 -- 261@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 5 -- 11@LB@
91	0.009339	0.3104	b2562	yfhL	-11.62	0.063873	146 -- 160	6 -- 20	putative 4Fe-4S cluster-containing protein	_____________145_____________161\n_____________\|_______________\|\n5'-AGC...UCUGA____A__________AUAAU...UUA-3'\n______________GUAA_GAAUGCGCGU\n______________:\|\|\|_:\|\|\|\|\|\|\|\|\|\n______________UAUU_UUUACGCGCA\n3'-UUU...ACUAC____G__________GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	154 -- 160	6 -- 12	-16.8242 kcal/mol	3.96482 kcal/mol	1.24244 kcal/mol	145 161@LB@ \| \|@LB@5'-AGC...UCUGA A AUAAU...UUA-3'@LB@ GUAA GAAUGCGCGU@LB@ :\|\|\| :\|\|\|\|\|\|\|\|\|@LB@ UAUU UUUACGCGCA@LB@3'-UUU...ACUAC G GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -16.8242 kcal/mol@LB@Unfolding Energy - mRNA 3.96482 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 146 -- 160@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 6 -- 12@LB@
72	0.006739	0.3087	b2520	yfhM	-8.19	0.237735	190 -- 217	6 -- 30	bacterial alpha2-macroglobulin colonization factor ECAM; anti-host protease defense factor; periplasmic inner membrane-anchored lipoprotein	_____________189__________________________218\n_____________\|____________________________\|\n5'-CUC...GUGGC________AAA____AA____UA_____AGCCG...CUU-3'\n______________AGGGAUGA___AUGA__AAGU__CGCGU\n______________\|\|\|\|\|\|\|\|___\|\|:\|__\|\|:\|__\|\|\|\|\|\n______________UCCCUACU___UAUU__UUUA__GCGCA\n3'-UUU...UUAAG________AC_____G_____C______GAAAG-5'\n_____________\|____________________________\|\n_____________31___________________________5\n	191 -- 197	23 -- 29	-19.496 kcal/mol	3.87755 kcal/mol	7.4255 kcal/mol	189 218@LB@ \| \|@LB@5'-CUC...GUGGC AAA AA UA AGCCG...CUU-3'@LB@ AGGGAUGA AUGA AAGU CGCGU@LB@ \|\|\|\|\|\|\|\| \|\|:\| \|\|:\| \|\|\|\|\|@LB@ UCCCUACU UAUU UUUA GCGCA@LB@3'-UUU...UUAAG AC G C GAAAG-5'@LB@ \| \|@LB@ 31 5@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -19.496 kcal/mol@LB@Unfolding Energy - mRNA 3.87755 kcal/mol@LB@Unfolding Energy - sRNA 7.4255 kcal/mol@LB@@LB@Position - mRNA 190 -- 217@LB@Position - sRNA 6 -- 30@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 23 -- 29@LB@
19	0.0006629	0.1181	b2909	ygfB	-11.13	0.077732	186 -- 206	4 -- 22	UPF0149 family protein	_____________185___________________207\n_____________\|_____________________\|\n5'-AAA...CCCUU___C_________UUA_____AUACA...UCA-3'\n______________UGA_GACGAAUGC___UGUCU\n______________\|\|\|_:\|\|:\|\|\|\|\|___:\|\|\|\|\n______________ACU_UUGUUUACG___GCAGA\n3'-UUU...CUACU___A_________C_______AAG-5'\n_____________\|_____________________\|\n_____________23____________________3\n	192 -- 198	10 -- 16	-17.2827 kcal/mol	4.89762 kcal/mol	1.2572 kcal/mol	185 207@LB@ \| \|@LB@5'-AAA...CCCUU C UUA AUACA...UCA-3'@LB@ UGA GACGAAUGC UGUCU@LB@ \|\|\| :\|\|:\|\|\|\|\| :\|\|\|\|@LB@ ACU UUGUUUACG GCAGA@LB@3'-UUU...CUACU A C AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -17.2827 kcal/mol@LB@Unfolding Energy - mRNA 4.89762 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 186 -- 206@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 10 -- 16@LB@
32	0.001981	0.2094	b3110	yhaO	-10.61	0.095420	268 -- 283	7 -- 23	putative transporter	_____________267_______________284\n_____________\|_________________\|\n5'-AAU...AAUGA____G____________AGAAG...UCG-3'\n______________GUGA_AGCGAGUG_GCG\n______________:\|\|\|_\|:\|:\|:\|\|_\|\|\|\n______________UACU_UUGUUUAC_CGC\n3'-UUU...CCUAC____A________G___AGAAAG-5'\n_____________\|_________________\|\n_____________24________________6\n	274 -- 280	11 -- 17	-15.5882 kcal/mol	2.45682 kcal/mol	2.52012 kcal/mol	267 284@LB@ \| \|@LB@5'-AAU...AAUGA G AGAAG...UCG-3'@LB@ GUGA AGCGAGUG GCG@LB@ :\|\|\| \|:\|:\|:\|\| \|\|\|@LB@ UACU UUGUUUAC CGC@LB@3'-UUU...CCUAC A G AGAAAG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -15.5882 kcal/mol@LB@Unfolding Energy - mRNA 2.45682 kcal/mol@LB@Unfolding Energy - sRNA 2.52012 kcal/mol@LB@@LB@Position - mRNA 268 -- 283@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 11 -- 17@LB@
186	0.01836	0.3104	b3521	yhjC	-9.62	0.140197	158 -- 166	5 -- 13	LysR family putative transcriptional regulator	_____________157_______167\n_____________\|_________\|\n5'-UUU...GCGAU_________ACUGU...UUU-3'\n______________AUGCGCGUU\n______________\|\|\|\|\|\|\|\|:\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	160 -- 166	5 -- 11	-14.2497 kcal/mol	3.47777 kcal/mol	1.15134 kcal/mol	157 167@LB@ \| \|@LB@5'-UUU...GCGAU ACUGU...UUU-3'@LB@ AUGCGCGUU@LB@ \|\|\|\|\|\|\|\|:@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -9.62 kcal/mol@LB@Hybridization Energy -14.2497 kcal/mol@LB@Unfolding Energy - mRNA 3.47777 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 158 -- 166@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 5 -- 11@LB@
51	0.004574	0.3024	b3529	yhjK	-9.99	0.121635	195 -- 213	1 -- 18	cyclic-di-GMP phosphodiesterase	_____________194_________________214\n_____________\|___________________\|\n5'-AGC...GGGGA_____UU_______AAG__GCUCG...AUC-3'\n______________GACAA__UGCGCGU___UC\n______________:\|\|\|\|__\|\|\|\|\|\|\|___\|\|\n______________UUGUU__ACGCGCA___AG\n3'-UUU...UACUA_____U________GAA__-5'\n_____________\|__________________\|\n_____________19_________________1\n	202 -- 208	6 -- 12	-16.8324 kcal/mol	5.6017 kcal/mol	1.24077 kcal/mol	194 214@LB@ \| \|@LB@5'-AGC...GGGGA UU AAG GCUCG...AUC-3'@LB@ GACAA UGCGCGU UC@LB@ :\|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ UUGUU ACGCGCA AG@LB@3'-UUU...UACUA U GAA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -9.99 kcal/mol@LB@Hybridization Energy -16.8324 kcal/mol@LB@Unfolding Energy - mRNA 5.6017 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 195 -- 213@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 6 -- 12@LB@
169	0.01667	0.3104	b3575	yiaK	-9.90	0.125874	198 -- 219	8 -- 29	2 3-diketo-L-gulonate reductase NADH-dependent	_____________197____________________220\n_____________\|______________________\|\n5'-UUU...AGCCU_______AA______UU__A__AGUUA...UCG-3'\n______________GGGAUGA__GUGACA__UG_GC\n______________\|\|\|\|\|\|\|__:\|:\|\|\|__\|\|_\|\|\n______________CCCUACU__UAUUGU__AC_CG\n3'-UUU...UAAGU_______AC______UU__G__CAGAAAG-5'\n_____________\|______________________\|\n_____________30_____________________7\n	198 -- 204	23 -- 29	-23.0827 kcal/mol	5.7681 kcal/mol	7.41331 kcal/mol	197 220@LB@ \| \|@LB@5'-UUU...AGCCU AA UU A AGUUA...UCG-3'@LB@ GGGAUGA GUGACA UG GC@LB@ \|\|\|\|\|\|\| :\|:\|\|\| \|\| \|\|@LB@ CCCUACU UAUUGU AC CG@LB@3'-UUU...UAAGU AC UU G CAGAAAG-5'@LB@ \| \|@LB@ 30 7@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -23.0827 kcal/mol@LB@Unfolding Energy - mRNA 5.7681 kcal/mol@LB@Unfolding Energy - sRNA 7.41331 kcal/mol@LB@@LB@Position - mRNA 198 -- 219@LB@Position - sRNA 8 -- 29@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 23 -- 29@LB@
199	0.01944	0.3104	b3657	yicJ	-13.22	0.033173	129 -- 161	8 -- 45	putative transporter	_____________128_____________________________________162\n_____________\|_______________________________________\|\n5'-CAG...GAAUA_________CA_____________UU____A________UAUCG...UGU-3'\n______________UUCG_CUCU_____CAGGGAUGGU____AC_AAAUGCGU\n______________\|\|\|:_\|\|\|\|_____\|\|\|\|\|\|\|\|:\|____\|\|_\|\|\|\|\|\|\|:\n______________AAGU_GAGA_____GUCCCUACUA____UG_UUUACGCG\n3'-UUU...UUUUA____A____CUUAA__________CUAU___________CAGAAAG-5'\n_____________\|_______________________________________\|\n_____________46______________________________________7\n	155 -- 161	8 -- 14	-30.3918 kcal/mol	7.7216 kcal/mol	9.45195 kcal/mol	128 162@LB@ \| \|@LB@5'-CAG...GAAUA CA UU A UAUCG...UGU-3'@LB@ UUCG CUCU CAGGGAUGGU AC AAAUGCGU@LB@ \|\|\|: \|\|\|\| \|\|\|\|\|\|\|\|:\| \|\| \|\|\|\|\|\|\|:@LB@ AAGU GAGA GUCCCUACUA UG UUUACGCG@LB@3'-UUU...UUUUA A CUUAA CUAU CAGAAAG-5'@LB@ \| \|@LB@ 46 7@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -30.3918 kcal/mol@LB@Unfolding Energy - mRNA 7.7216 kcal/mol@LB@Unfolding Energy - sRNA 9.45195 kcal/mol@LB@@LB@Position - mRNA 129 -- 161@LB@Position - sRNA 8 -- 45@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 8 -- 14@LB@
137	0.01327	0.3104	b3858	yihD	-10.36	0.105347	5 -- 11	5 -- 11	DUF1040 protein YihD	_____________4_______12\n_____________\|_______\|\n_______5'-AUAA_______AGCGA...CGA-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	5 -- 11	5 -- 11	-14.974 kcal/mol	3.50324 kcal/mol	1.11145 kcal/mol	4 12@LB@ \| \|@LB@ 5'-AUAA AGCGA...CGA-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -14.974 kcal/mol@LB@Unfolding Energy - mRNA 3.50324 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 5 -- 11@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 5 -- 11@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)

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