Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
46	0.009803	0.5385	b1418	cybB	-9.32	0.138160	281 -- 295	73 -- 89	cytochrome b561	_____________280_______________296\n_____________\|_________________\|\n5'-AAC...GCAAU_________________CUUCC-3'\n______________GGAGUUU_CG_UGGUUU\n______________::\|\|\|\|:_\|\|_\|\|\|:\|\|\n______________UUUCAAG_GC_ACCGAA\n3'-CGC...GGCGU_______U__A______AUCAA...AAG-5'\n_____________\|_________________\|\n_____________90________________72\n	281 -- 287	83 -- 89	-12.2046 kcal/mol	2.36714 kcal/mol	0.517627 kcal/mol	280 296@LB@ \| \|@LB@5'-AAC...GCAAU CUUCC-3'@LB@ GGAGUUU CG UGGUUU@LB@ ::\|\|\|\|: \|\| \|\|\|:\|\|@LB@ UUUCAAG GC ACCGAA@LB@3'-CGC...GGCGU U A AUCAA...AAG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -12.2046 kcal/mol@LB@Unfolding Energy - mRNA 2.36714 kcal/mol@LB@Unfolding Energy - sRNA 0.517627 kcal/mol@LB@@LB@Position - mRNA 281 -- 295@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 83 -- 89@LB@
120	0.02045	0.5385	b0979	cbdB	-12.05	0.046235	177 -- 194	16 -- 34	cytochrome bd-II oxidase subunit II	_____________176_________________195\n_____________\|___________________\|\n5'-AUA...ACGCA__AA_______________AAAAU...GCU-3'\n______________GC__CAGGGG_UAAAGGAG\n______________:\|__\|\|:\|\|\|_\|\|\|\|:\|\|\|\n______________UG__GUUCCC_AUUUUCUC\n3'-CGC...GUCAC__AA______A________CACGG...AAG-5'\n_____________\|___________________\|\n_____________35__________________15\n	188 -- 194	16 -- 22	-18.7902 kcal/mol	3.40633 kcal/mol	3.33043 kcal/mol	176 195@LB@ \| \|@LB@5'-AUA...ACGCA AA AAAAU...GCU-3'@LB@ GC CAGGGG UAAAGGAG@LB@ :\| \|\|:\|\|\| \|\|\|\|:\|\|\|@LB@ UG GUUCCC AUUUUCUC@LB@3'-CGC...GUCAC AA A CACGG...AAG-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -18.7902 kcal/mol@LB@Unfolding Energy - mRNA 3.40633 kcal/mol@LB@Unfolding Energy - sRNA 3.33043 kcal/mol@LB@@LB@Position - mRNA 177 -- 194@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 16 -- 22@LB@
61	0.01179	0.5385	b3748	rbsD	-10.58	0.083988	129 -- 141	72 -- 84	D-ribose pyranase	_____________128___________142\n_____________\|_____________\|\n5'-GGU...UAACG_____A_______CCCAA...UCC-3'\n______________UCACG_UGGUUUU\n______________\|\|\|\|\|_\|\|\|:\|\|\|\n______________AGUGC_ACCGAAA\n3'-CGC...UUUCA_____A_______UCAAU...AAG-5'\n_____________\|_____________\|\n_____________85____________71\n	135 -- 141	72 -- 78	-14.1499 kcal/mol	3.06287 kcal/mol	0.509125 kcal/mol	128 142@LB@ \| \|@LB@5'-GGU...UAACG A CCCAA...UCC-3'@LB@ UCACG UGGUUUU@LB@ \|\|\|\|\| \|\|\|:\|\|\|@LB@ AGUGC ACCGAAA@LB@3'-CGC...UUUCA A UCAAU...AAG-5'@LB@ \| \|@LB@ 85 71@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -14.1499 kcal/mol@LB@Unfolding Energy - mRNA 3.06287 kcal/mol@LB@Unfolding Energy - sRNA 0.509125 kcal/mol@LB@@LB@Position - mRNA 129 -- 141@LB@Position - sRNA 72 -- 84@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 72 -- 78@LB@
103	0.01739	0.5385	b0945	pyrD	-8.62	0.180746	193 -- 204	79 -- 90	dihydro-orotate oxidase FMN-linked	_____________192__________205\n_____________\|____________\|\n5'-UGU...UCCAG____________ACUAC...CGU-3'\n______________GAGAGUUCAUGU\n______________:\|:\|\|\|\|\|\|:\|\|\n______________UUUUCAAGUGCA\n3'-CGC...AGGCG____________ACCGA...AAG-5'\n_____________\|____________\|\n_____________91___________78\n	198 -- 204	79 -- 85	-13.8118 kcal/mol	4.6828 kcal/mol	0.506924 kcal/mol	192 205@LB@ \| \|@LB@5'-UGU...UCCAG ACUAC...CGU-3'@LB@ GAGAGUUCAUGU@LB@ :\|:\|\|\|\|\|\|:\|\|@LB@ UUUUCAAGUGCA@LB@3'-CGC...AGGCG ACCGA...AAG-5'@LB@ \| \|@LB@ 91 78@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -13.8118 kcal/mol@LB@Unfolding Energy - mRNA 4.6828 kcal/mol@LB@Unfolding Energy - sRNA 0.506924 kcal/mol@LB@@LB@Position - mRNA 193 -- 204@LB@Position - sRNA 79 -- 90@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 79 -- 85@LB@
188	0.03339	0.5559	b3232	zapE	-6.91	0.336884	267 -- 282	15 -- 35	divisome ATPase	_____________266____________________283\n_____________\|______________________\|\n5'-AGG...CCGAC___G__________________CCGUC...AAA-3'\n______________GAC_UUCA______AAAAGAGG\n______________\|\|\|_\|\|\|\|______\|\|\|\|\|\|\|\|\n______________CUG_AAGU______UUUUCUCC\n3'-CGC...CGUCA________UCCCAA________ACGGC...AAG-5'\n_____________\|______________________\|\n_____________36_____________________14\n	276 -- 282	15 -- 21	-13.3674 kcal/mol	3.12995 kcal/mol	3.33058 kcal/mol	266 283@LB@ \| \|@LB@5'-AGG...CCGAC G CCGUC...AAA-3'@LB@ GAC UUCA AAAAGAGG@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUG AAGU UUUUCUCC@LB@3'-CGC...CGUCA UCCCAA ACGGC...AAG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -13.3674 kcal/mol@LB@Unfolding Energy - mRNA 3.12995 kcal/mol@LB@Unfolding Energy - sRNA 3.33058 kcal/mol@LB@@LB@Position - mRNA 267 -- 282@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 15 -- 21@LB@
124	0.02124	0.5385	b0198	metI	-9.85	0.112177	270 -- 285	71 -- 87	DL-methionine transporter subunit	_____________269_______________286\n_____________\|_________________\|\n5'-UCA...UAUCC_____UU__________UGAUU...CGG-3'\n______________GGUUU___UUGGCUUUG\n______________:\|\|\|:___\|\|\|\|\|\|\|\|:\n______________UCAAG___AACCGAAAU\n3'-CGC...CGUUU_____UGC_________CAAUA...AAG-5'\n_____________\|_________________\|\n_____________88________________70\n	279 -- 285	71 -- 77	-13.0228 kcal/mol	2.60961 kcal/mol	0.562376 kcal/mol	269 286@LB@ \| \|@LB@5'-UCA...UAUCC UU UGAUU...CGG-3'@LB@ GGUUU UUGGCUUUG@LB@ :\|\|\|: \|\|\|\|\|\|\|\|:@LB@ UCAAG AACCGAAAU@LB@3'-CGC...CGUUU UGC CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -13.0228 kcal/mol@LB@Unfolding Energy - mRNA 2.60961 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 270 -- 285@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 71 -- 77@LB@
59	0.01163	0.5385	b1279	yciS	-7.12	0.313424	44 -- 60	74 -- 90	DUF1049 family inner membrane protein function unknown	_____________43________________61\n_____________\|_________________\|\n5'-ACC...AACAA_______A___C_____GAUUU...UGU-3'\n______________GAAAGUU_ACG_UGGUU\n______________:\|\|\|\|\|\|_\|\|\|_\|\|\|:\|\n______________UUUUCAA_UGC_ACCGA\n3'-CGC...AGGCG_______G___A_____AAUCA...AAG-5'\n_____________\|_________________\|\n_____________91________________73\n	44 -- 50	84 -- 90	-13.3715 kcal/mol	5.7376 kcal/mol	0.517587 kcal/mol	43 61@LB@ \| \|@LB@5'-ACC...AACAA A C GAUUU...UGU-3'@LB@ GAAAGUU ACG UGGUU@LB@ :\|\|\|\|\|\| \|\|\| \|\|\|:\|@LB@ UUUUCAA UGC ACCGA@LB@3'-CGC...AGGCG G A AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -7.12 kcal/mol@LB@Hybridization Energy -13.3715 kcal/mol@LB@Unfolding Energy - mRNA 5.7376 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 44 -- 60@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 84 -- 90@LB@
94	0.01616	0.5385	b4217	ytfK	-8.94	0.160287	283 -- 290	75 -- 82	DUF1107 family protein	_____________282______291\n_____________\|________\|\n5'-GAA...CAAGG________GCUUU...AAU-3'\n______________ACGUUGGC\n______________\|\|\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	284 -- 290	75 -- 81	-13.4875 kcal/mol	4.21202 kcal/mol	0.339284 kcal/mol	282 291@LB@ \| \|@LB@5'-GAA...CAAGG GCUUU...AAU-3'@LB@ ACGUUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -13.4875 kcal/mol@LB@Unfolding Energy - mRNA 4.21202 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 283 -- 290@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 75 -- 81@LB@
13	0.002299	0.5385	b3663	yicN	-11.49	0.058154	241 -- 256	60 -- 78	DUF1198 family protein	_____________240_________________257\n_____________\|___________________\|\n5'-CUU...GUUUG___________________GCUGA...AUC-3'\n______________UGGU__UGGUU_UUCGGGU\n______________\|\|\|:__\|:\|\|\|_\|\|\|\|:\|\|\n______________ACCG__AUCAA_AAGCUCA\n3'-CGC...GUGCA____AA_____U_______ACUCU...AAG-5'\n_____________\|___________________\|\n_____________79__________________59\n	250 -- 256	60 -- 66	-15.2298 kcal/mol	2.94333 kcal/mol	0.797083 kcal/mol	240 257@LB@ \| \|@LB@5'-CUU...GUUUG GCUGA...AUC-3'@LB@ UGGU UGGUU UUCGGGU@LB@ \|\|\|: \|:\|\|\| \|\|\|\|:\|\|@LB@ ACCG AUCAA AAGCUCA@LB@3'-CGC...GUGCA AA U ACUCU...AAG-5'@LB@ \| \|@LB@ 79 59@LB@@LB@@LB@Energy -11.49 kcal/mol@LB@Hybridization Energy -15.2298 kcal/mol@LB@Unfolding Energy - mRNA 2.94333 kcal/mol@LB@Unfolding Energy - sRNA 0.797083 kcal/mol@LB@@LB@Position - mRNA 241 -- 256@LB@Position - sRNA 60 -- 78@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 60 -- 66@LB@
26	0.00484	0.5385	b3033	yqiB	-11.20	0.065436	106 -- 117	15 -- 27	DUF1249 protein YqiB	_____________105___________118\n_____________\|_____________\|\n5'-UGG...CCAGU_____________GGAAA...GCG-3'\n______________GGG_UAGAAGAGG\n______________\|\|\|_\|\|:\|\|\|\|\|\|\n______________CCC_AUUUUCUCC\n3'-CGC...AAGUU___A_________ACGGC...AAG-5'\n_____________\|_____________\|\n_____________28____________14\n	111 -- 117	15 -- 21	-17.3581 kcal/mol	2.92425 kcal/mol	3.23583 kcal/mol	105 118@LB@ \| \|@LB@5'-UGG...CCAGU GGAAA...GCG-3'@LB@ GGG UAGAAGAGG@LB@ \|\|\| \|\|:\|\|\|\|\|\|@LB@ CCC AUUUUCUCC@LB@3'-CGC...AAGUU A ACGGC...AAG-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -17.3581 kcal/mol@LB@Unfolding Energy - mRNA 2.92425 kcal/mol@LB@Unfolding Energy - sRNA 3.23583 kcal/mol@LB@@LB@Position - mRNA 106 -- 117@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 15 -- 21@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