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
156	0.02672	0.5559	b0957	ompA	-9.60	0.124024	22 -- 30	81 -- 89	outer membrane protein A (3a;II*;G;d)		_____________21________31\n_____________\|_________\|\n5'-CUU...CUGAC_________ACUUG...AAC-3'\n______________GGAGUUCAC\n______________::\|\|\|\|\|\|\|\n______________UUUCAAGUG\n3'-CGC...GGCGU_________CAACC...AAG-5'\n_____________\|_________\|\n_____________90________80\n	24 -- 30	81 -- 87	-11.1644 kcal/mol	1.067 kcal/mol	0.501582 kcal/mol	21 31@LB@ \| \|@LB@5'-CUU...CUGAC ACUUG...AAC-3'@LB@ GGAGUUCAC@LB@ ::\|\|\|\|\|\|\|@LB@ UUUCAAGUG@LB@3'-CGC...GGCGU CAACC...AAG-5'@LB@ \| \|@LB@ 90 80@LB@@LB@@LB@Energy -9.60 kcal/mol@LB@Hybridization Energy -11.1644 kcal/mol@LB@Unfolding Energy - mRNA 1.067 kcal/mol@LB@Unfolding Energy - sRNA 0.501582 kcal/mol@LB@@LB@Position - mRNA 22 -- 30@LB@Position - sRNA 81 -- 89@LB@Position Seed - mRNA 24 -- 30@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@
45	0.009513	0.5385	b2513	yfgM	-9.58	0.124672	177 -- 189	15 -- 27	ancillary SecYEG translocon subunit; putative anti-RcsB factor		_____________176___________190\n_____________\|_____________\|\n5'-GGC...UUACU_________A___AGAAG...UUG-3'\n______________GGGUUAAGG_AGG\n______________\|\|\|\|\|\|\|::_\|\|\|\n______________CCCAAUUUU_UCC\n3'-CGC...AAGUU_________C___ACGGC...AAG-5'\n_____________\|_____________\|\n_____________28____________14\n	179 -- 185	19 -- 25	-14.0675 kcal/mol	1.24912 kcal/mol	3.23583 kcal/mol	176 190@LB@ \| \|@LB@5'-GGC...UUACU A AGAAG...UUG-3'@LB@ GGGUUAAGG AGG@LB@ \|\|\|\|\|\|\|:: \|\|\|@LB@ CCCAAUUUU UCC@LB@3'-CGC...AAGUU C ACGGC...AAG-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -9.58 kcal/mol@LB@Hybridization Energy -14.0675 kcal/mol@LB@Unfolding Energy - mRNA 1.24912 kcal/mol@LB@Unfolding Energy - sRNA 3.23583 kcal/mol@LB@@LB@Position - mRNA 177 -- 189@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 19 -- 25@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@
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@
67	0.01284	0.5385	b1294	sapA	-9.42	0.132690	25 -- 48	61 -- 86	antimicrobial peptide transport ABC transporter periplasmic binding protein		_____________24_________________________49\n_____________\|__________________________\|\n5'-UAC...AAGUU________GA___A_______A____AAAUC...ACA-3'\n______________GUUC_UGU__GUU_UAGUUAU__GAG\n______________\|\|\|\|_:\|\|__\|:\|_\|\|\|\|\|\|\|__\|\|\|\n______________CAAG_GCA__CGA_AUCAAUA__CUC\n3'-CGC...GUUUU____U___AC___A_______AG___AACUC...AAG-5'\n_____________\|__________________________\|\n_____________87_________________________60\n	38 -- 44	66 -- 72	-17.3513 kcal/mol	6.21881 kcal/mol	1.70915 kcal/mol	24 49@LB@ \| \|@LB@5'-UAC...AAGUU GA A A AAAUC...ACA-3'@LB@ GUUC UGU GUU UAGUUAU GAG@LB@ \|\|\|\| :\|\| \|:\| \|\|\|\|\|\|\| \|\|\|@LB@ CAAG GCA CGA AUCAAUA CUC@LB@3'-CGC...GUUUU U AC A AG AACUC...AAG-5'@LB@ \| \|@LB@ 87 60@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -17.3513 kcal/mol@LB@Unfolding Energy - mRNA 6.21881 kcal/mol@LB@Unfolding Energy - sRNA 1.70915 kcal/mol@LB@@LB@Position - mRNA 25 -- 48@LB@Position - sRNA 61 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 66 -- 72@LB@
121	0.02058	0.5385	b0796	ybiH	-9.41	0.133616	217 -- 230	24 -- 36	DUF1956 domain-containing tetR family putative transcriptional regulator		_____________216____________231\n_____________\|______________\|\n5'-CGG...UGCCA____AA________GAACA...CCA-3'\n______________UGAC__UCAAGGGU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\n______________ACUG__AGUUCCCA\n3'-CGC...CCGUC____A_________AUUUU...AAG-5'\n_____________\|______________\|\n_____________37_____________23\n	224 -- 230	24 -- 30	-15.9856 kcal/mol	3.24975 kcal/mol	3.33025 kcal/mol	216 231@LB@ \| \|@LB@5'-CGG...UGCCA AA GAACA...CCA-3'@LB@ UGAC UCAAGGGU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ ACUG AGUUCCCA@LB@3'-CGC...CCGUC A AUUUU...AAG-5'@LB@ \| \|@LB@ 37 23@LB@@LB@@LB@Energy -9.41 kcal/mol@LB@Hybridization Energy -15.9856 kcal/mol@LB@Unfolding Energy - mRNA 3.24975 kcal/mol@LB@Unfolding Energy - sRNA 3.33025 kcal/mol@LB@@LB@Position - mRNA 217 -- 230@LB@Position - sRNA 24 -- 36@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 24 -- 30@LB@
200	0.03481	0.5559	b1058	yceO	-9.40	0.133707	85 -- 100	70 -- 85	uncharacterized protein		_____________84_______________101\n_____________\|________________\|\n5'-CCU...UUAAA_______CA_______GGGAA...GAU-3'\n______________UUUGCGU__GUUUUAG\n______________\|\|::\|\|\|__\|:\|\|\|\|\|\n______________AAGUGCA__CGAAAUC\n3'-CGC...UUUUC_______AC_______AAUAA...AAG-5'\n_____________\|________________\|\n_____________86_______________69\n	94 -- 100	70 -- 76	-11.7699 kcal/mol	1.79867 kcal/mol	0.567379 kcal/mol	84 101@LB@ \| \|@LB@5'-CCU...UUAAA CA GGGAA...GAU-3'@LB@ UUUGCGU GUUUUAG@LB@ \|\|::\|\|\| \|:\|\|\|\|\|@LB@ AAGUGCA CGAAAUC@LB@3'-CGC...UUUUC AC AAUAA...AAG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -11.7699 kcal/mol@LB@Unfolding Energy - mRNA 1.79867 kcal/mol@LB@Unfolding Energy - sRNA 0.567379 kcal/mol@LB@@LB@Position - mRNA 85 -- 100@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 70 -- 76@LB@
43	0.009109	0.5385	b2531	iscR	-9.39	0.134324	275 -- 298	62 -- 87	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor		_____________274________________________299\n_____________\|__________________________\|\n5'-AUG...GGCCC___A__________GAUAUUUC____AC-3'\n______________GGU_C_CGUUGGCU_________CGA\n______________:\|\|_\|_\|\|\|\|\|\|\|\|_________\|\|\|\n______________UCA_G_GCAACCGA_________GCU\n3'-CGC...CGUUU___A_U________AAUCAAUAA___CAACU...AAG-5'\n_____________\|__________________________\|\n_____________88_________________________61\n	281 -- 287	74 -- 80	-16.3089 kcal/mol	5.20915 kcal/mol	1.70771 kcal/mol	274 299@LB@ \| \|@LB@5'-AUG...GGCCC A GAUAUUUC AC-3'@LB@ GGU C CGUUGGCU CGA@LB@ :\|\| \| \|\|\|\|\|\|\|\| \|\|\|@LB@ UCA G GCAACCGA GCU@LB@3'-CGC...CGUUU A U AAUCAAUAA CAACU...AAG-5'@LB@ \| \|@LB@ 88 61@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -16.3089 kcal/mol@LB@Unfolding Energy - mRNA 5.20915 kcal/mol@LB@Unfolding Energy - sRNA 1.70771 kcal/mol@LB@@LB@Position - mRNA 275 -- 298@LB@Position - sRNA 62 -- 87@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 74 -- 80@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)

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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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