Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
12	0.0004023	0.1087	b3176	glmM	-16.74	0.009770	131 -- 153	1 -- 22	phosphoglucosamine mutase	_____________130_____________________154\n_____________\|_______________________\|\n5'-GUU...UUCAU_____________CC____AA__GAUGC...CGG-3'\n______________GACGUCAAAGAAA__GUAG__GC\n______________\|\|\|:\|\|\|\|\|\|\|\|\|__\|:\|\|__\|\|\n______________CUGUAGUUUCUUU__CGUC__CG\n3'-UUU...UACCC_____________U_____AC__-5'\n_____________\|______________________\|\n_____________23_____________________1\n	137 -- 143	10 -- 16	-21.6768 kcal/mol	3.39473 kcal/mol	1.54023 kcal/mol	130 154@LB@ \| \|@LB@5'-GUU...UUCAU CC AA GAUGC...CGG-3'@LB@ GACGUCAAAGAAA GUAG GC@LB@ \|\|\|:\|\|\|\|\|\|\|\|\| \|:\|\| \|\|@LB@ CUGUAGUUUCUUU CGUC CG@LB@3'-UUU...UACCC U AC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -16.74 kcal/mol@LB@Hybridization Energy -21.6768 kcal/mol@LB@Unfolding Energy - mRNA 3.39473 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 131 -- 153@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 10 -- 16@LB@
38	0.001836	0.1648	b3188	sfsB	-13.60	0.058336	253 -- 274	1 -- 32	malPQ operon transcriptional activator	_____________252______________________________275\n_____________\|________________________________\|\n5'-CGG...UUUGC______A___A_____________________GGCGG...UGA-3'\n______________GCAAGA_GGG_ACGUCAA__________UGGC\n______________:\|\|\|:\|_\|\|\|_\|\|:\|\|\|\|__________\|\|\|\|\n______________UGUUUU_CCC_UGUAGUU__________ACCG\n3'-UUU...CGAGG______A___C_______UCUUUUCGUC____-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	264 -- 270	15 -- 21	-21.5209 kcal/mol	5.38314 kcal/mol	2.53929 kcal/mol	252 275@LB@ \| \|@LB@5'-CGG...UUUGC A A GGCGG...UGA-3'@LB@ GCAAGA GGG ACGUCAA UGGC@LB@ :\|\|\|:\| \|\|\| \|\|:\|\|\|\| \|\|\|\|@LB@ UGUUUU CCC UGUAGUU ACCG@LB@3'-UUU...CGAGG A C UCUUUUCGUC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -13.60 kcal/mol@LB@Hybridization Energy -21.5209 kcal/mol@LB@Unfolding Energy - mRNA 5.38314 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 253 -- 274@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 15 -- 21@LB@
76	0.004413	0.2038	b3211	yhcC	-9.63	0.312909	148 -- 162	49 -- 62	putative Fe-S oxidoreductase Radical SAM superfamily protein	_____________147_____________163\n_____________\|_______________\|\n5'-UGC...CGAAU______AA_______AGGCU...GCC-3'\n______________UGAGCU__AAAUGGC\n______________\|\|\|:\|:__\|\|\|\|\|\|\|\n______________ACUUGG__UUUACCG\n3'-UUU...UUGGA______C________CCCCA...CCG-5'\n_____________\|_______________\|\n_____________63______________48\n	156 -- 162	49 -- 55	-15.5959 kcal/mol	2.00852 kcal/mol	3.95968 kcal/mol	147 163@LB@ \| \|@LB@5'-UGC...CGAAU AA AGGCU...GCC-3'@LB@ UGAGCU AAAUGGC@LB@ \|\|\|:\|: \|\|\|\|\|\|\|@LB@ ACUUGG UUUACCG@LB@3'-UUU...UUGGA C CCCCA...CCG-5'@LB@ \| \|@LB@ 63 48@LB@@LB@@LB@Energy -9.63 kcal/mol@LB@Hybridization Energy -15.5959 kcal/mol@LB@Unfolding Energy - mRNA 2.00852 kcal/mol@LB@Unfolding Energy - sRNA 3.95968 kcal/mol@LB@@LB@Position - mRNA 148 -- 162@LB@Position - sRNA 49 -- 62@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 49 -- 55@LB@
149	0.01096	0.2504	b3230	rpsI	-12.23	0.111717	165 -- 205	1 -- 34	30S ribosomal subunit protein S9	_____________164_______________________________________206\n_____________\|_________________________________________\|\n5'-GUG...AGCAA_______UUCUU______UAAUC____UUAU_____A____UGAAA...GUU-3'\n______________CCGCAAG_____GACAUC_____GGGA____AGGCA_UGGC\n______________\|\|:\|\|\|:_____\|\|\|\|\|\|_____:\|:\|____\|:\|\|\|_\|\|\|\|\n______________GGUGUUU_____CUGUAG_____UCUU____UUCGU_ACCG\n3'-UUU...CCCGA_______UACCC______UU________________C____-5'\n_____________\|________________________________________\|\n_____________35_______________________________________1\n	165 -- 171	28 -- 34	-26.3465 kcal/mol	9.84752 kcal/mol	4.26884 kcal/mol	164 206@LB@ \| \|@LB@5'-GUG...AGCAA UUCUU UAAUC UUAU A UGAAA...GUU-3'@LB@ CCGCAAG GACAUC GGGA AGGCA UGGC@LB@ \|\|:\|\|\|: \|\|\|\|\|\| :\|:\| \|:\|\|\| \|\|\|\|@LB@ GGUGUUU CUGUAG UCUU UUCGU ACCG@LB@3'-UUU...CCCGA UACCC UU C -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -26.3465 kcal/mol@LB@Unfolding Energy - mRNA 9.84752 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 165 -- 205@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 28 -- 34@LB@
123	0.008923	0.2491	b3243	aaeR	-15.21	0.024673	72 -- 99	1 -- 34	transcriptional regulator for aaeXAB operon	_____________71_________________________________100\n_____________\|__________________________________\|\n5'-AAC...UGUCG________AA__________________C_____GAGAG...UCA-3'\n______________CCGCAGAG___GGGCAU____GGAAAGC_G_GGC\n______________\|\|:\|\|:\|:___\|\|:\|\|\|____\|:\|\|\|\|\|_\|_\|\|\|\n______________GGUGUUUU___CCUGUA____CUUUUCG_C_CCG\n3'-UUU...CCCGA________ACC______GUUU_______U_A___-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	88 -- 94	7 -- 13	-28.4227 kcal/mol	8.94529 kcal/mol	4.26884 kcal/mol	71 100@LB@ \| \|@LB@5'-AAC...UGUCG AA C GAGAG...UCA-3'@LB@ CCGCAGAG GGGCAU GGAAAGC G GGC@LB@ \|\|:\|\|:\|: \|\|:\|\|\| \|:\|\|\|\|\| \| \|\|\|@LB@ GGUGUUUU CCUGUA CUUUUCG C CCG@LB@3'-UUU...CCCGA ACC GUUU U A -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -28.4227 kcal/mol@LB@Unfolding Energy - mRNA 8.94529 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 72 -- 99@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 7 -- 13@LB@
140	0.01029	0.2504	b3247	rng	-10.20	0.255190	49 -- 63	1 -- 14	ribonuclease G	_____________48______________64\n_____________\|_______________\|\n5'-GUU...CCGUU___U_______GU__AUACG...CGC-3'\n______________AGA_AAAGCAG__GC\n______________\|\|\|_\|\|\|\|\|\|\|__\|\|\n______________UCU_UUUCGUC__CG\n3'-UUU...UAGUU___________AC__-5'\n_____________\|______________\|\n_____________15_____________1\n	53 -- 59	5 -- 11	-13.7724 kcal/mol	2.22711 kcal/mol	1.34059 kcal/mol	48 64@LB@ \| \|@LB@5'-GUU...CCGUU U GU AUACG...CGC-3'@LB@ AGA AAAGCAG GC@LB@ \|\|\| \|\|\|\|\|\|\| \|\|@LB@ UCU UUUCGUC CG@LB@3'-UUU...UAGUU AC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -13.7724 kcal/mol@LB@Unfolding Energy - mRNA 2.22711 kcal/mol@LB@Unfolding Energy - sRNA 1.34059 kcal/mol@LB@@LB@Position - mRNA 49 -- 63@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@LB@
55	0.002823	0.1778	b3319	rplD	-12.54	0.096993	18 -- 45	1 -- 32	50S ribosomal subunit protein L4	_____________17________________________________46\n_____________\|_________________________________\|\n5'-UCA...UCCGG________U____________C___AAAA____AGGUC...UUG-3'\n______________GCAAAGUG______UCAAAGG_AAG____UGGC\n______________:\|\|\|\|:\|\|______\|\|\|\|\|\|:_\|\|\|____\|\|\|\|\n______________UGUUUUAC______AGUUUCU_UUC____ACCG\n3'-UUU...CGAGG________CCCUGU_______U___GUC_____-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	27 -- 33	12 -- 18	-19.13 kcal/mol	4.04955 kcal/mol	2.53929 kcal/mol	17 46@LB@ \| \|@LB@5'-UCA...UCCGG U C AAAA AGGUC...UUG-3'@LB@ GCAAAGUG UCAAAGG AAG UGGC@LB@ :\|\|\|\|:\|\| \|\|\|\|\|\|: \|\|\| \|\|\|\|@LB@ UGUUUUAC AGUUUCU UUC ACCG@LB@3'-UUU...CGAGG CCCUGU U GUC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.54 kcal/mol@LB@Hybridization Energy -19.13 kcal/mol@LB@Unfolding Energy - mRNA 4.04955 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 18 -- 45@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 12 -- 18@LB@
44	0.002166	0.1648	b3349	slyD	-19.18	0.001707	20 -- 41	5 -- 23	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)	_____________19_____________________42\n_____________\|______________________\|\n5'-UGU...AGUGC__________UGC_________ACAAA...ACU-3'\n______________GGACAUCAGA___GAGAAGCAG\n______________\|\|\|\|\|\|\|\|:\|___\|\|:\|\|\|\|\|\|\n______________CCUGUAGUUU___CUUUUCGUC\n3'-UUU...UUACC______________________ACCG-5'\n_____________\|______________________\|\n_____________24_____________________4\n	35 -- 41	5 -- 11	-25.7728 kcal/mol	5.01574 kcal/mol	1.57523 kcal/mol	19 42@LB@ \| \|@LB@5'-UGU...AGUGC UGC ACAAA...ACU-3'@LB@ GGACAUCAGA GAGAAGCAG@LB@ \|\|\|\|\|\|\|\|:\| \|\|:\|\|\|\|\|\|@LB@ CCUGUAGUUU CUUUUCGUC@LB@3'-UUU...UUACC ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -19.18 kcal/mol@LB@Hybridization Energy -25.7728 kcal/mol@LB@Unfolding Energy - mRNA 5.01574 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 20 -- 41@LB@Position - sRNA 5 -- 23@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 5 -- 11@LB@
56	0.002838	0.1778	b3371	frlB	-17.11	0.007704	196 -- 228	2 -- 32	fructoselysine-6-P-deglycase	_____________195________________________________229\n_____________\|__________________________________\|\n5'-ACU...AGAAA________UU_________U________CC____ACUUU...ACG-3'\n______________AUAAAAUG__GGAUAUUGA__AAAAGCA__GUGG\n______________\|:\|\|\|\|\|\|__\|\|\|:\|\|::\|__\|\|\|\|\|\|\|__\|\|\|\|\n______________UGUUUUAC__CCUGUAGUU__UUUUCGU__CACC\n3'-UUU...CGAGG________C__________UC_____________G-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	216 -- 222	6 -- 12	-25.2618 kcal/mol	5.61622 kcal/mol	2.53929 kcal/mol	195 229@LB@ \| \|@LB@5'-ACU...AGAAA UU U CC ACUUU...ACG-3'@LB@ AUAAAAUG GGAUAUUGA AAAAGCA GUGG@LB@ \|:\|\|\|\|\|\| \|\|\|:\|\|::\| \|\|\|\|\|\|\| \|\|\|\|@LB@ UGUUUUAC CCUGUAGUU UUUUCGU CACC@LB@3'-UUU...CGAGG C UC G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -17.11 kcal/mol@LB@Hybridization Energy -25.2618 kcal/mol@LB@Unfolding Energy - mRNA 5.61622 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 196 -- 228@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 6 -- 12@LB@
169	0.01228	0.2504	b3386	rpe	-13.36	0.065831	171 -- 203	3 -- 33	D-ribulose-5-phosphate 3-epimerase	_____________170_______________________________204\n_____________\|_________________________________\|\n5'-CGC...UCACC_______AAAUAAUUC______________A__AAACA...UGC-3'\n______________CGCGAAA_________UCAAGGAGAAGCGG_UG\n______________\|:\|:\|\|\|_________\|\|\|\|:\|\|:\|\|\|\|:\|_\|\|\n______________GUGUUUU_________AGUUUCUUUUCGUC_AC\n3'-UUU...CCGAG_______ACCCCUGU__________________CG-5'\n_____________\|_________________________________\|\n_____________34________________________________2\n	194 -- 200	5 -- 11	-23.2607 kcal/mol	6.82691 kcal/mol	3.0786 kcal/mol	170 204@LB@ \| \|@LB@5'-CGC...UCACC AAAUAAUUC A AAACA...UGC-3'@LB@ CGCGAAA UCAAGGAGAAGCGG UG@LB@ \|:\|:\|\|\| \|\|\|\|:\|\|:\|\|\|\|:\| \|\|@LB@ GUGUUUU AGUUUCUUUUCGUC AC@LB@3'-UUU...CCGAG ACCCCUGU CG-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -13.36 kcal/mol@LB@Hybridization Energy -23.2607 kcal/mol@LB@Unfolding Energy - mRNA 6.82691 kcal/mol@LB@Unfolding Energy - sRNA 3.0786 kcal/mol@LB@@LB@Position - mRNA 171 -- 203@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 194 -- 200@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