Input and runtime details for job 7743500 (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 7743500 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:00 CET 2018
	CopraRNA Started		@ Fri Feb 16 21:27:12 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 06:56:30 CET 2018
	Post-Processing Finished		@ Sat Feb 17 06:56:38 CET 2018
	Job Completed		@ Sat Feb 17 06:57:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7743500&toolName=CopraRNA ( 30 days expiry )

Description of the job

PrrF1

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_002516 Pseudomonas aeruginosa PAO1

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
15	2.583e-05	0.007914	pa3049	rmf	-22.33	0.000014	230 -- 282	40 -- 88	ribosome modulation factor		_____________229____________________________________________________283\n_____________\|______________________________________________________\|\n5'-CGA...UUGGA________UU_U_______UUA__AGAA____AUA______AA___________UUUGU...AUC-3'\n______________AAGAG_CC__C_UGCGUGG___UC____CGGC___ACCGGU__AUCUCGUGAUC\n______________\|\|\|\|\|_\|\|__\|_\|\|\|\|\|\|\|___\|\|____\|:\|\|___\|\|\|\|\|:__\|\|\|\|\|\|:\|\|:\|\n______________UUCUC_GG__G_ACGCACC___AG____GUCG___UGGCCG__UAGAGCGCUGG\n3'-UUU...UAGAC_____A__CU_________CAG__A_______AA_______AC___________UCAAC...GUU-5'\n_____________\|______________________________________________________\|\n_____________89_____________________________________________________39\n	276 -- 282	40 -- 46	-52.7199 kcal/mol	11.3783 kcal/mol	19.0139 kcal/mol	229 283@LB@ \| \|@LB@5'-CGA...UUGGA UU U UUA AGAA AUA AA UUUGU...AUC-3'@LB@ AAGAG CC C UGCGUGG UC CGGC ACCGGU AUCUCGUGAUC@LB@ \|\|\|\|\| \|\| \| \|\|\|\|\|\|\| \|\| \|:\|\| \|\|\|\|\|: \|\|\|\|\|\|:\|\|:\|@LB@ UUCUC GG G ACGCACC AG GUCG UGGCCG UAGAGCGCUGG@LB@3'-UUU...UAGAC A CU CAG A AA AC UCAAC...GUU-5'@LB@ \| \|@LB@ 89 39@LB@@LB@@LB@Energy -22.33 kcal/mol@LB@Hybridization Energy -52.7199 kcal/mol@LB@Unfolding Energy - mRNA 11.3783 kcal/mol@LB@Unfolding Energy - sRNA 19.0139 kcal/mol@LB@@LB@Position - mRNA 230 -- 282@LB@Position - sRNA 40 -- 88@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 40 -- 46@LB@
100	0.001607	0.07384	pa0607	rpe	-12.76	0.041806	177 -- 194	99 -- 118	ribulose-phosphate 3-epimerase		_____________176__________________195\n_____________\|____________________\|\n5'-CCG...GCCUU_______CC____U______UGCGC...UUC-3'\n______________CCGUGAU___CCU__UGAGG\n______________\|\|\|\|\|\|\|___\|\|\|__\|\|\|\|\|\n______________GGCACUA___GGA__ACUCC\n3'-UUU...UUUUU_______AUC___CU_____UCUAU...GUU-5'\n_____________\|____________________\|\n_____________119__________________98\n	177 -- 183	112 -- 118	-19.2108 kcal/mol	4.20353 kcal/mol	2.24947 kcal/mol	176 195@LB@ \| \|@LB@5'-CCG...GCCUU CC U UGCGC...UUC-3'@LB@ CCGUGAU CCU UGAGG@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ GGCACUA GGA ACUCC@LB@3'-UUU...UUUUU AUC CU UCUAU...GUU-5'@LB@ \| \|@LB@ 119 98@LB@@LB@@LB@Energy -12.76 kcal/mol@LB@Hybridization Energy -19.2108 kcal/mol@LB@Unfolding Energy - mRNA 4.20353 kcal/mol@LB@Unfolding Energy - sRNA 2.24947 kcal/mol@LB@@LB@Position - mRNA 177 -- 194@LB@Position - sRNA 99 -- 118@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 112 -- 118@LB@
47	0.0003012	0.02946	pa1776	sigX	-11.73	0.074706	90 -- 102	103 -- 115	RNA polymerase sigma factor SigX		_____________89____________103\n_____________\|_____________\|\n5'-CGU...CGAUA___C_________CUCAC...UGU-3'\n______________UGA_UGGCCUGAU\n______________\|\|\|_\|:\|\|\|\|\|\|\|\n______________ACU_AUCGGACUA\n3'-UUU...UUGGC___A_________CUCCU...GUU-5'\n_____________\|_____________\|\n_____________116___________102\n	96 -- 102	103 -- 109	-16.1519 kcal/mol	2.30076 kcal/mol	2.12156 kcal/mol	89 103@LB@ \| \|@LB@5'-CGU...CGAUA C CUCAC...UGU-3'@LB@ UGA UGGCCUGAU@LB@ \|\|\| \|:\|\|\|\|\|\|\|@LB@ ACU AUCGGACUA@LB@3'-UUU...UUGGC A CUCCU...GUU-5'@LB@ \| \|@LB@ 116 102@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -16.1519 kcal/mol@LB@Unfolding Energy - mRNA 2.30076 kcal/mol@LB@Unfolding Energy - sRNA 2.12156 kcal/mol@LB@@LB@Position - mRNA 90 -- 102@LB@Position - sRNA 103 -- 115@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 103 -- 109@LB@
5	7.253e-07	0.0006667	pa5351	rubA1	-17.51	0.001615	172 -- 222	71 -- 121	rubredoxin		_____________171___________________________________________________223\n_____________\|_____________________________________________________\|\n5'-CGG...GCGCU__________AAC__GCCC____UAAACAA_______AG_____AA_______UGUGU...UGC-3'\n______________GAACCGUGGU___CC____GAGG________UGAAGA___UGGC__UGCGUGG\n______________:\|\|\|\|\|\|\|:\|___\|\|____\|\|\|\|________\|\|\|\|\|\|___:\|:\|__\|\|\|\|\|\|\|\n______________UUUGGCACUA___GG____CUCC________ACUUCU___GCUG__ACGCACC\n3'-UUU...CAGUU__________AUC__ACUA____UCUAUUAG______CAG_____________CAGAG...GUU-5'\n_____________\|_____________________________________________________\|\n_____________122___________________________________________________70\n	216 -- 222	71 -- 77	-42.807 kcal/mol	11.4444 kcal/mol	13.8582 kcal/mol	171 223@LB@ \| \|@LB@5'-CGG...GCGCU AAC GCCC UAAACAA AG AA UGUGU...UGC-3'@LB@ GAACCGUGGU CC GAGG UGAAGA UGGC UGCGUGG@LB@ :\|\|\|\|\|\|\|:\| \|\| \|\|\|\| \|\|\|\|\|\| :\|:\| \|\|\|\|\|\|\|@LB@ UUUGGCACUA GG CUCC ACUUCU GCUG ACGCACC@LB@3'-UUU...CAGUU AUC ACUA UCUAUUAG CAG CAGAG...GUU-5'@LB@ \| \|@LB@ 122 70@LB@@LB@@LB@Energy -17.51 kcal/mol@LB@Hybridization Energy -42.807 kcal/mol@LB@Unfolding Energy - mRNA 11.4444 kcal/mol@LB@Unfolding Energy - sRNA 13.8582 kcal/mol@LB@@LB@Position - mRNA 172 -- 222@LB@Position - sRNA 71 -- 121@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 71 -- 77@LB@
164	0.004161	0.1159	pa4420	N/A	-11.64	0.078545	165 -- 187	40 -- 62	S-adenosyl-methyltransferase MraW		_____________164______________________188\n_____________\|________________________\|\n5'-GAC...GGUGG_________AC__A__A_______UGAUC...GAA-3'\n______________GC_UGCCGG__GA_CU_CGCGACC\n______________\|\|_\|:\|\|\|\|__\|\|_\|\|_\|\|\|\|\|\|\|\n______________CG_AUGGCC__CU_GA_GCGCUGG\n3'-UUU...AGAGU__A______GA__A__________UCAAC...GUU-5'\n_____________\|________________________\|\n_____________63_______________________39\n	181 -- 187	40 -- 46	-28.7872 kcal/mol	5.30942 kcal/mol	11.8411 kcal/mol	164 188@LB@ \| \|@LB@5'-GAC...GGUGG AC A A UGAUC...GAA-3'@LB@ GC UGCCGG GA CU CGCGACC@LB@ \|\| \|:\|\|\|\| \|\| \|\| \|\|\|\|\|\|\|@LB@ CG AUGGCC CU GA GCGCUGG@LB@3'-UUU...AGAGU A GA A UCAAC...GUU-5'@LB@ \| \|@LB@ 63 39@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -28.7872 kcal/mol@LB@Unfolding Energy - mRNA 5.30942 kcal/mol@LB@Unfolding Energy - sRNA 11.8411 kcal/mol@LB@@LB@Position - mRNA 165 -- 187@LB@Position - sRNA 40 -- 62@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 40 -- 46@LB@
121	0.002197	0.08331	pa2583	N/A	-13.54	0.026172	146 -- 169	69 -- 89	sensor/response regulator hybrid protein	pa3044 pa3946 pa4982 pa1611	_____________145______________________170\n_____________\|________________________\|\n5'-CCU...UGCCA___C____G_____AG________UCCUG...UGA-3'\n______________GAG_GAGU_UCGAC__GCGUGGGU\n______________\|\|:_\|\|\|\|_:\|\|\|\|__\|\|\|\|\|\|\|\|\n______________CUU_CUCA_GGCUG__CGCACCCA\n3'-UUU...UUAGA______________A_________GAGAG...GUU-5'\n_____________\|________________________\|\n_____________90_______________________68\n	163 -- 169	69 -- 75	-28.6669 kcal/mol	9.05998 kcal/mol	6.06593 kcal/mol	145 170@LB@ \| \|@LB@5'-CCU...UGCCA C G AG UCCUG...UGA-3'@LB@ GAG GAGU UCGAC GCGUGGGU@LB@ \|\|: \|\|\|\| :\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUU CUCA GGCUG CGCACCCA@LB@3'-UUU...UUAGA A GAGAG...GUU-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -13.54 kcal/mol@LB@Hybridization Energy -28.6669 kcal/mol@LB@Unfolding Energy - mRNA 9.05998 kcal/mol@LB@Unfolding Energy - sRNA 6.06593 kcal/mol@LB@@LB@Position - mRNA 146 -- 169@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 69 -- 75@LB@
167	0.004312	0.117	pa2583	N/A	-13.54	0.026172	146 -- 169	69 -- 89	sensor/response regulator hybrid protein	pa3044 pa3946 pa4982 pa1611	_____________145______________________170\n_____________\|________________________\|\n5'-CCU...UGCCA___C____G_____AG________UCCUG...UGA-3'\n______________GAG_GAGU_UCGAC__GCGUGGGU\n______________\|\|:_\|\|\|\|_:\|\|\|\|__\|\|\|\|\|\|\|\|\n______________CUU_CUCA_GGCUG__CGCACCCA\n3'-UUU...UUAGA______________A_________GAGAG...GUU-5'\n_____________\|________________________\|\n_____________90_______________________68\n	163 -- 169	69 -- 75	-28.6669 kcal/mol	9.05998 kcal/mol	6.06593 kcal/mol	145 170@LB@ \| \|@LB@5'-CCU...UGCCA C G AG UCCUG...UGA-3'@LB@ GAG GAGU UCGAC GCGUGGGU@LB@ \|\|: \|\|\|\| :\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUU CUCA GGCUG CGCACCCA@LB@3'-UUU...UUAGA A GAGAG...GUU-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -13.54 kcal/mol@LB@Hybridization Energy -28.6669 kcal/mol@LB@Unfolding Energy - mRNA 9.05998 kcal/mol@LB@Unfolding Energy - sRNA 6.06593 kcal/mol@LB@@LB@Position - mRNA 146 -- 169@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 69 -- 75@LB@
168	0.004312	0.117	pa2583	N/A	-13.54	0.026172	146 -- 169	69 -- 89	sensor/response regulator hybrid protein	pa3044 pa3946 pa4982 pa1611	_____________145______________________170\n_____________\|________________________\|\n5'-CCU...UGCCA___C____G_____AG________UCCUG...UGA-3'\n______________GAG_GAGU_UCGAC__GCGUGGGU\n______________\|\|:_\|\|\|\|_:\|\|\|\|__\|\|\|\|\|\|\|\|\n______________CUU_CUCA_GGCUG__CGCACCCA\n3'-UUU...UUAGA______________A_________GAGAG...GUU-5'\n_____________\|________________________\|\n_____________90_______________________68\n	163 -- 169	69 -- 75	-28.6669 kcal/mol	9.05998 kcal/mol	6.06593 kcal/mol	145 170@LB@ \| \|@LB@5'-CCU...UGCCA C G AG UCCUG...UGA-3'@LB@ GAG GAGU UCGAC GCGUGGGU@LB@ \|\|: \|\|\|\| :\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUU CUCA GGCUG CGCACCCA@LB@3'-UUU...UUAGA A GAGAG...GUU-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -13.54 kcal/mol@LB@Hybridization Energy -28.6669 kcal/mol@LB@Unfolding Energy - mRNA 9.05998 kcal/mol@LB@Unfolding Energy - sRNA 6.06593 kcal/mol@LB@@LB@Position - mRNA 146 -- 169@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 69 -- 75@LB@
193	0.005243	0.1243	pa3725	recJ	-10.65	0.130688	184 -- 203	102 -- 119	single-stranded-DNA-specific exonuclease RecJ		_____________183__________________204\n_____________\|____________________\|\n5'-CGU...GUCGA____AAC__GUGA_______CGUAU...GCG-3'\n______________GCCG___GA____CCUGAUG\n______________:\|\|\|___\|\|____\|\|\|\|\|\|\|\n______________UGGC___CU____GGACUAC\n3'-UUU...GUUUU____A____AAUC_______UCCUC...GUU-5'\n_____________\|____________________\|\n_____________120__________________101\n	197 -- 203	102 -- 108	-15.7224 kcal/mol	2.82992 kcal/mol	2.24274 kcal/mol	183 204@LB@ \| \|@LB@5'-CGU...GUCGA AAC GUGA CGUAU...GCG-3'@LB@ GCCG GA CCUGAUG@LB@ :\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UGGC CU GGACUAC@LB@3'-UUU...GUUUU A AAUC UCCUC...GUU-5'@LB@ \| \|@LB@ 120 101@LB@@LB@@LB@Energy -10.65 kcal/mol@LB@Hybridization Energy -15.7224 kcal/mol@LB@Unfolding Energy - mRNA 2.82992 kcal/mol@LB@Unfolding Energy - sRNA 2.24274 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 102 -- 119@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 102 -- 108@LB@
143	0.003113	0.1001	pa1811	N/A	-11.02	0.108661	233 -- 245	105 -- 120	solute-binding protein		_____________232______________246\n_____________\|________________\|\n5'-GAG...GGCCU________________CCCAG...UCA-3'\n______________GGCCGUGA___GCCUG\n______________::\|\|\|\|\|\|___\|\|\|\|\|\n______________UUGGCACU___CGGAC\n3'-UUU...AGUUU________AAU_____UACUC...GUU-5'\n_____________\|________________\|\n_____________121______________104\n	234 -- 240	113 -- 119	-18.7383 kcal/mol	5.48096 kcal/mol	2.24173 kcal/mol	232 246@LB@ \| \|@LB@5'-GAG...GGCCU CCCAG...UCA-3'@LB@ GGCCGUGA GCCUG@LB@ ::\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGGCACU CGGAC@LB@3'-UUU...AGUUU AAU UACUC...GUU-5'@LB@ \| \|@LB@ 121 104@LB@@LB@@LB@Energy -11.02 kcal/mol@LB@Hybridization Energy -18.7383 kcal/mol@LB@Unfolding Energy - mRNA 5.48096 kcal/mol@LB@Unfolding Energy - sRNA 2.24173 kcal/mol@LB@@LB@Position - mRNA 233 -- 245@LB@Position - sRNA 105 -- 120@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 113 -- 119@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