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	Additional homologs
181	0.03179	0.5559	b3240	aaeB	-9.50	0.128739	275 -- 287	72 -- 86	p-hydroxybenzoic acid efflux system component		_____________274_____________288\n_____________\|_______________\|\n5'-ACU...GCGCU_______________CACUU...UGG-3'\n______________GUUU__GUUGGCUUU\n______________\|\|\|:__\|\|\|\|\|\|\|\|\|\n______________CAAG__CAACCGAAA\n3'-CGC...GUUUU____UG_________UCAAU...AAG-5'\n_____________\|_______________\|\n_____________87______________71\n	281 -- 287	72 -- 78	-13.8127 kcal/mol	3.79774 kcal/mol	0.514266 kcal/mol	274 288@LB@ \| \|@LB@5'-ACU...GCGCU CACUU...UGG-3'@LB@ GUUU GUUGGCUUU@LB@ \|\|\|: \|\|\|\|\|\|\|\|\|@LB@ CAAG CAACCGAAA@LB@3'-CGC...GUUUU UG UCAAU...AAG-5'@LB@ \| \|@LB@ 87 71@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -13.8127 kcal/mol@LB@Unfolding Energy - mRNA 3.79774 kcal/mol@LB@Unfolding Energy - sRNA 0.514266 kcal/mol@LB@@LB@Position - mRNA 275 -- 287@LB@Position - sRNA 72 -- 86@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 72 -- 78@LB@
115	0.01932	0.5385	b3475	acpT	-9.48	0.130030	187 -- 194	75 -- 82	4'-phosphopantetheinyl transferase		_____________186______195\n_____________\|________\|\n5'-GGG...AUUAA________CCUGA...GCU-3'\n______________ACGUUGGC\n______________\|\|\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	188 -- 194	75 -- 81	-13.2305 kcal/mol	3.41608 kcal/mol	0.339284 kcal/mol	186 195@LB@ \| \|@LB@5'-GGG...AUUAA CCUGA...GCU-3'@LB@ ACGUUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -13.2305 kcal/mol@LB@Unfolding Energy - mRNA 3.41608 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 75 -- 81@LB@
22	0.004141	0.5385	b0462	acrB	-13.08	0.030428	256 -- 265	75 -- 84	multidrug efflux system protein		_____________255________266\n_____________\|__________\|\n5'-AAG...UAUCA__________AGGGG...CGC-3'\n______________UCAUGUUGGC\n______________\|\|\|:\|\|\|\|\|\|\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	259 -- 265	75 -- 81	-16.8887 kcal/mol	3.30616 kcal/mol	0.505918 kcal/mol	255 266@LB@ \| \|@LB@5'-AAG...UAUCA AGGGG...CGC-3'@LB@ UCAUGUUGGC@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -16.8887 kcal/mol@LB@Unfolding Energy - mRNA 3.30616 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 256 -- 265@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 75 -- 81@LB@
107	0.01867	0.5385	b1478	adhP	-13.80	0.022588	200 -- 222	62 -- 83	ethanol-active dehydrogenase/acetaldehyde-active reductase		_____________199_____________________223\n_____________\|_______________________\|\n5'-GCA...GGAAC____AA____GC_______A___AGGAU...GUU-3'\n______________UAUG__GGCU__AGUUGUU_CGA\n______________:\|:\|__\|\|\|\|__\|\|\|\|:\|\|_\|\|\|\n______________GUGC__CCGA__UCAAUAA_GCU\n3'-CGC...UUCAA____AA____AA___________CAACU...AAG-5'\n_____________\|_______________________\|\n_____________84______________________61\n	212 -- 218	65 -- 71	-18.0685 kcal/mol	2.64248 kcal/mol	1.62352 kcal/mol	199 223@LB@ \| \|@LB@5'-GCA...GGAAC AA GC A AGGAU...GUU-3'@LB@ UAUG GGCU AGUUGUU CGA@LB@ :\|:\| \|\|\|\| \|\|\|\|:\|\| \|\|\|@LB@ GUGC CCGA UCAAUAA GCU@LB@3'-CGC...UUCAA AA AA CAACU...AAG-5'@LB@ \| \|@LB@ 84 61@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -18.0685 kcal/mol@LB@Unfolding Energy - mRNA 2.64248 kcal/mol@LB@Unfolding Energy - sRNA 1.62352 kcal/mol@LB@@LB@Position - mRNA 200 -- 222@LB@Position - sRNA 62 -- 83@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 65 -- 71@LB@
86	0.01521	0.5385	b0605	ahpC	-11.47	0.058587	74 -- 93	73 -- 89	alkyl hydroperoxide reductase C22 subunit		_____________73___________________94\n_____________\|____________________\|\n5'-ACC...GGUGC_________AAA____U___ACGAA...GGA-3'\n______________AAAGUUCAC___GUUG_CUU\n______________\|\|\|\|\|\|\|\|\|___\|\|\|\|_\|\|\|\n______________UUUCAAGUG___CAAC_GAA\n3'-CGC...GGCGU________________C___AUCAA...AAG-5'\n_____________\|____________________\|\n_____________90___________________72\n	76 -- 82	81 -- 87	-14.6327 kcal/mol	2.64398 kcal/mol	0.517627 kcal/mol	73 94@LB@ \| \|@LB@5'-ACC...GGUGC AAA U ACGAA...GGA-3'@LB@ AAAGUUCAC GUUG CUU@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|@LB@ UUUCAAGUG CAAC GAA@LB@3'-CGC...GGCGU C AUCAA...AAG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -14.6327 kcal/mol@LB@Unfolding Energy - mRNA 2.64398 kcal/mol@LB@Unfolding Energy - sRNA 0.517627 kcal/mol@LB@@LB@Position - mRNA 74 -- 93@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 81 -- 87@LB@
96	0.0164	0.5385	b2670	alaE	-9.59	0.124335	245 -- 257	74 -- 86	alanine exporter alanine-inducible stress-responsive		_____________244___________258\n_____________\|_____________\|\n5'-CGG...GAUAC_______A_____GUUUA...UCU-3'\n______________GUUCGCG_UGGUU\n______________\|\|\|\|:\|\|_\|\|\|:\|\n______________CAAGUGC_ACCGA\n3'-CGC...GUUUU_______A_____AAUCA...AAG-5'\n_____________\|_____________\|\n_____________87____________73\n	245 -- 251	80 -- 86	-15.4589 kcal/mol	5.35611 kcal/mol	0.513318 kcal/mol	244 258@LB@ \| \|@LB@5'-CGG...GAUAC A GUUUA...UCU-3'@LB@ GUUCGCG UGGUU@LB@ \|\|\|\|:\|\| \|\|\|:\|@LB@ CAAGUGC ACCGA@LB@3'-CGC...GUUUU A AAUCA...AAG-5'@LB@ \| \|@LB@ 87 73@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -15.4589 kcal/mol@LB@Unfolding Energy - mRNA 5.35611 kcal/mol@LB@Unfolding Energy - sRNA 0.513318 kcal/mol@LB@@LB@Position - mRNA 245 -- 257@LB@Position - sRNA 74 -- 86@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 80 -- 86@LB@
162	0.02861	0.5559	b0564	appY	-9.53	0.127084	148 -- 162	62 -- 79	global transcriptional activator; DLP12 prophage	b1499 b3515 b4116 b0566 b3516	_____________147________________163\n_____________\|__________________\|\n5'-AAA...UUUAA__________________CUACU...UAA-3'\n______________UUGGUU___GUUAUUUGA\n______________\|\|\|\|:\|___\|\|\|\|\|\|:\|\|\n______________AACCGA___CAAUAAGCU\n3'-CGC...AGUGC______AAU_________CAACU...AAG-5'\n_____________\|__________________\|\n_____________80_________________61\n	156 -- 162	62 -- 68	-13.1987 kcal/mol	2.92728 kcal/mol	0.737706 kcal/mol	147 163@LB@ \| \|@LB@5'-AAA...UUUAA CUACU...UAA-3'@LB@ UUGGUU GUUAUUUGA@LB@ \|\|\|\|:\| \|\|\|\|\|\|:\|\|@LB@ AACCGA CAAUAAGCU@LB@3'-CGC...AGUGC AAU CAACU...AAG-5'@LB@ \| \|@LB@ 80 61@LB@@LB@@LB@Energy -9.53 kcal/mol@LB@Hybridization Energy -13.1987 kcal/mol@LB@Unfolding Energy - mRNA 2.92728 kcal/mol@LB@Unfolding Energy - sRNA 0.737706 kcal/mol@LB@@LB@Position - mRNA 148 -- 162@LB@Position - sRNA 62 -- 79@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 62 -- 68@LB@
135	0.02294	0.5385	b4254	argI	-11.70	0.053356	4 -- 33	59 -- 85	ornithine carbamoyltransferase 1	b0273	_____________3______________________________34\n_____________\|______________________________\|\n________5'-UUC______C__UU___CC________C_____UGCCA...AUA-3'\n______________UUCACG_UG__CUU__AGUUGUUC_GGGUU\n______________\|\|\|\|\|\|_\|\|__\|\|\|__\|\|\|\|:\|\|\|_\|:\|\|\|\n______________AAGUGC_AC__GAA__UCAAUAAG_CUCAA\n3'-CGC...UUUUC______A__C____A_______________CUCUU...AAG-5'\n_____________\|______________________________\|\n_____________86_____________________________58\n	21 -- 27	64 -- 70	-19.7051 kcal/mol	6.29613 kcal/mol	1.70749 kcal/mol	3 34@LB@ \| \|@LB@ 5'-UUC C UU CC C UGCCA...AUA-3'@LB@ UUCACG UG CUU AGUUGUUC GGGUU@LB@ \|\|\|\|\|\| \|\| \|\|\| \|\|\|\|:\|\|\| \|:\|\|\|@LB@ AAGUGC AC GAA UCAAUAAG CUCAA@LB@3'-CGC...UUUUC A C A CUCUU...AAG-5'@LB@ \| \|@LB@ 86 58@LB@@LB@@LB@Energy -11.70 kcal/mol@LB@Hybridization Energy -19.7051 kcal/mol@LB@Unfolding Energy - mRNA 6.29613 kcal/mol@LB@Unfolding Energy - sRNA 1.70749 kcal/mol@LB@@LB@Position - mRNA 4 -- 33@LB@Position - sRNA 59 -- 85@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 64 -- 70@LB@
29	0.005218	0.5385	b3433	asd	-11.22	0.064904	208 -- 219	71 -- 82	aspartate-semialdehyde dehydrogenase NAD(P)-binding		_____________207__________220\n_____________\|____________\|\n5'-UCA...GAAAA____________UCGGC...UCU-3'\n______________AUGUUGGUUUUA\n______________\|:\|\|\|\|\|:\|\|\|\|\n______________UGCAACCGAAAU\n3'-CGC...UCAAG____________CAAUA...AAG-5'\n_____________\|____________\|\n_____________83___________70\n	213 -- 219	71 -- 77	-13.9075 kcal/mol	2.30708 kcal/mol	0.38228 kcal/mol	207 220@LB@ \| \|@LB@5'-UCA...GAAAA UCGGC...UCU-3'@LB@ AUGUUGGUUUUA@LB@ \|:\|\|\|\|\|:\|\|\|\|@LB@ UGCAACCGAAAU@LB@3'-CGC...UCAAG CAAUA...AAG-5'@LB@ \| \|@LB@ 83 70@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -13.9075 kcal/mol@LB@Unfolding Energy - mRNA 2.30708 kcal/mol@LB@Unfolding Energy - sRNA 0.38228 kcal/mol@LB@@LB@Position - mRNA 208 -- 219@LB@Position - sRNA 71 -- 82@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 71 -- 77@LB@
38	0.006978	0.5385	b3738	atpB	-10.53	0.085759	128 -- 143	69 -- 84	F0 sector of membrane-bound ATP synthase subunit a		_____________127______________144\n_____________\|________________\|\n5'-CAU...GAUCG______G_________GCUGG...ACC-3'\n______________UUACGU_GGUUUUGGU\n______________\|:\|\|\|\|_\|\|:\|\|\|:\|\|\n______________AGUGCA_CCGAAAUCA\n3'-CGC...UUUCA______A_________AUAAG...AAG-5'\n_____________\|________________\|\n_____________85_______________68\n	137 -- 143	69 -- 75	-16.8893 kcal/mol	5.79988 kcal/mol	0.563592 kcal/mol	127 144@LB@ \| \|@LB@5'-CAU...GAUCG G GCUGG...ACC-3'@LB@ UUACGU GGUUUUGGU@LB@ \|:\|\|\|\| \|\|:\|\|\|:\|\|@LB@ AGUGCA CCGAAAUCA@LB@3'-CGC...UUUCA A AUAAG...AAG-5'@LB@ \| \|@LB@ 85 68@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -16.8893 kcal/mol@LB@Unfolding Energy - mRNA 5.79988 kcal/mol@LB@Unfolding Energy - sRNA 0.563592 kcal/mol@LB@@LB@Position - mRNA 128 -- 143@LB@Position - sRNA 69 -- 84@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 69 -- 75@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

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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

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