Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
141	0.02753	0.6177	b3215	yhcA	-6.30	0.221284	185 -- 194	39 -- 48	putative periplasmic chaperone protein	_____________184________195\n_____________\|__________\|\n5'-ACG...AUUAC__________AUUUA...AAA-3'\n______________AGGAGUUUUA\n______________\|\|\|\|:\|\|\|:\|\n______________UCCUUAAAGU\n3'-UUU...GUUUC__________AAAAA...ACA-5'\n_____________\|__________\|\n_____________49_________38\n	187 -- 193	40 -- 46	-10.0044 kcal/mol	2.68942 kcal/mol	1.01866 kcal/mol	184 195@LB@ \| \|@LB@5'-ACG...AUUAC AUUUA...AAA-3'@LB@ AGGAGUUUUA@LB@ \|\|\|\|:\|\|\|:\|@LB@ UCCUUAAAGU@LB@3'-UUU...GUUUC AAAAA...ACA-5'@LB@ \| \|@LB@ 49 38@LB@@LB@@LB@Energy -6.30 kcal/mol@LB@Hybridization Energy -10.0044 kcal/mol@LB@Unfolding Energy - mRNA 2.68942 kcal/mol@LB@Unfolding Energy - sRNA 1.01866 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 39 -- 48@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
142	0.02758	0.6177	b3186	rplU	-10.01	0.040887	186 -- 200	38 -- 52	50S ribosomal subunit protein L21	_____________185_____________201\n_____________\|_______________\|\n5'-UUA...GCGCG____C__________AUGUA...UUG-3'\n______________GAAG_GGAGUUUUAU\n______________:\|\|\|_\|\|\|:\|\|\|:\|\|\n______________UUUC_CCUUAAAGUA\n3'-UUU...GGCAG____U__________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	194 -- 200	38 -- 44	-13.3778 kcal/mol	2.29537 kcal/mol	1.0693 kcal/mol	185 201@LB@ \| \|@LB@5'-UUA...GCGCG C AUGUA...UUG-3'@LB@ GAAG GGAGUUUUAU@LB@ :\|\|\| \|\|\|:\|\|\|:\|\|@LB@ UUUC CCUUAAAGUA@LB@3'-UUU...GGCAG U AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -13.3778 kcal/mol@LB@Unfolding Energy - mRNA 2.29537 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 186 -- 200@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 38 -- 44@LB@
143	0.02773	0.6177	b0409	secF	-7.84	0.111773	181 -- 195	43 -- 55	SecYEG protein translocase auxillary subunit	_____________180_____________196\n_____________\|_______________\|\n5'-CUU...AAGCU_____UCU_______GCGAU...UGU-3'\n______________GUCAA___GAGGAGU\n______________\|\|\|\|\|___\|\|\|\|\|:\|\n______________CAGUU___CUCCUUA\n3'-UUU...CCGGG_____U_________AAGUA...ACA-5'\n_____________\|_______________\|\n_____________56______________42\n	189 -- 195	43 -- 49	-13.7308 kcal/mol	4.94116 kcal/mol	0.946481 kcal/mol	180 196@LB@ \| \|@LB@5'-CUU...AAGCU UCU GCGAU...UGU-3'@LB@ GUCAA GAGGAGU@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ CAGUU CUCCUUA@LB@3'-UUU...CCGGG U AAGUA...ACA-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -13.7308 kcal/mol@LB@Unfolding Energy - mRNA 4.94116 kcal/mol@LB@Unfolding Energy - sRNA 0.946481 kcal/mol@LB@@LB@Position - mRNA 181 -- 195@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 43 -- 49@LB@
144	0.02798	0.6177	b0682	chiQ	-9.70	0.047426	184 -- 197	41 -- 56	chitosugar-induced verified lipoprotein	_____________183______________198\n_____________\|________________\|\n5'-CGG...CCGCA____U___________GCUAU...ACA-3'\n______________CGUU___GAGGAAUUU\n______________\|\|\|:___\|\|\|\|\|\|\|\|\|\n______________GCAG___CUCCUUAAA\n3'-UUU...ACCGG____UUU_________GUAAA...ACA-5'\n_____________\|________________\|\n_____________57_______________40\n	191 -- 197	41 -- 47	-13.1137 kcal/mol	2.46147 kcal/mol	0.955312 kcal/mol	183 198@LB@ \| \|@LB@5'-CGG...CCGCA U GCUAU...ACA-3'@LB@ CGUU GAGGAAUUU@LB@ \|\|\|: \|\|\|\|\|\|\|\|\|@LB@ GCAG CUCCUUAAA@LB@3'-UUU...ACCGG UUU GUAAA...ACA-5'@LB@ \| \|@LB@ 57 40@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -13.1137 kcal/mol@LB@Unfolding Energy - mRNA 2.46147 kcal/mol@LB@Unfolding Energy - sRNA 0.955312 kcal/mol@LB@@LB@Position - mRNA 184 -- 197@LB@Position - sRNA 41 -- 56@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 41 -- 47@LB@
145	0.02855	0.6177	b2252	ais	-5.71	0.282709	182 -- 202	38 -- 55	putative LPS core heptose(II)-phosphate phosphatase	_____________181___________________203\n_____________\|_____________________\|\n5'-ACC...CGCUU___UAU___U_______A___GUUAG...GGA-3'\n______________GUC___AGG_GGAGUUU_CGU\n______________\|\|\|___\|:\|_\|\|\|:\|\|\|_\|:\|\n______________CAG___UUC_CCUUAAA_GUA\n3'-UUU...CCGGG___U_____U___________AAAAA...ACA-5'\n_____________\|_____________________\|\n_____________56____________________37\n	192 -- 198	41 -- 47	-12.7294 kcal/mol	5.84979 kcal/mol	1.17036 kcal/mol	181 203@LB@ \| \|@LB@5'-ACC...CGCUU UAU U A GUUAG...GGA-3'@LB@ GUC AGG GGAGUUU CGU@LB@ \|\|\| \|:\| \|\|\|:\|\|\| \|:\|@LB@ CAG UUC CCUUAAA GUA@LB@3'-UUU...CCGGG U U AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -5.71 kcal/mol@LB@Hybridization Energy -12.7294 kcal/mol@LB@Unfolding Energy - mRNA 5.84979 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 182 -- 202@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 41 -- 47@LB@
146	0.02871	0.6177	b1120	cobB	-8.56	0.080407	32 -- 40	43 -- 51	deacetylase of acs and cheY chemotaxis regulator	_____________31________41\n_____________\|_________\|\n5'-CGC...GAUGC_________GCGUG...AUC-3'\n______________GGGAGGAAU\n______________::\|\|\|\|\|\|\|\n______________UUCUCCUUA\n3'-UUU...GCAGU_________AAGUA...ACA-5'\n_____________\|_________\|\n_____________52________42\n	34 -- 40	43 -- 49	-11.3695 kcal/mol	1.94725 kcal/mol	0.859837 kcal/mol	31 41@LB@ \| \|@LB@5'-CGC...GAUGC GCGUG...AUC-3'@LB@ GGGAGGAAU@LB@ ::\|\|\|\|\|\|\|@LB@ UUCUCCUUA@LB@3'-UUU...GCAGU AAGUA...ACA-5'@LB@ \| \|@LB@ 52 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -11.3695 kcal/mol@LB@Unfolding Energy - mRNA 1.94725 kcal/mol@LB@Unfolding Energy - sRNA 0.859837 kcal/mol@LB@@LB@Position - mRNA 32 -- 40@LB@Position - sRNA 43 -- 51@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 43 -- 49@LB@
147	0.02922	0.6177	b3836	tatA	-6.91	0.169904	186 -- 195	44 -- 53	TatABCE protein translocation system subunit	_____________185________196\n_____________\|__________\|\n5'-CUA...UCUAC__C_______CAUGU...GUG-3'\n______________CA_AGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\n______________GU_UCUCCUU\n3'-UUU...GGGCA__U_______AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	44 -- 50	-10.6779 kcal/mol	2.84312 kcal/mol	0.927997 kcal/mol	185 196@LB@ \| \|@LB@5'-CUA...UCUAC C CAUGU...GUG-3'@LB@ CA AGAGGAA@LB@ \|\| \|\|\|\|\|\|\|@LB@ GU UCUCCUU@LB@3'-UUU...GGGCA U AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -10.6779 kcal/mol@LB@Unfolding Energy - mRNA 2.84312 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
148	0.02945	0.6177	b0692	potE	-8.42	0.085901	187 -- 195	44 -- 52	putrescine/proton symporter: putrescine/ornithine antiporter	_____________186_______196\n_____________\|_________\|\n5'-UGU...UGUUG_________AAAUU...AGC-3'\n______________AAAGGGGAA\n______________\|\|\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-10.6161 kcal/mol	1.33649 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-UGU...UGUUG AAAUU...AGC-3'@LB@ AAAGGGGAA@LB@ \|\|\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -10.6161 kcal/mol@LB@Unfolding Energy - mRNA 1.33649 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
149	0.03014	0.6177	b4470	yhaM	-8.71	0.074988	251 -- 260	44 -- 54	putative L-serine dehydratase alpha chain	_____________250_________261\n_____________\|___________\|\n5'-UGU...GCCGU___________GUAAA...UGG-3'\n______________UC_AGGAGGAA\n______________\|\|_\|:\|\|\|\|\|\|\n______________AG_UUCUCCUU\n3'-UUU...CGGGC__U________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	254 -- 260	44 -- 50	-10.8529 kcal/mol	1.19981 kcal/mol	0.939671 kcal/mol	250 261@LB@ \| \|@LB@5'-UGU...GCCGU GUAAA...UGG-3'@LB@ UC AGGAGGAA@LB@ \|\| \|:\|\|\|\|\|\|@LB@ AG UUCUCCUU@LB@3'-UUU...CGGGC U AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -10.8529 kcal/mol@LB@Unfolding Energy - mRNA 1.19981 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 251 -- 260@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 44 -- 50@LB@
150	0.03022	0.6177	b1285	gmr	-9.04	0.064446	208 -- 218	47 -- 57	cyclic-di-GMP phosphodiesterase; csgD regulator; modulator of RNase II stability	_____________207_________219\n_____________\|___________\|\n5'-UUU...GAAAA___________UCCAC...CUA-3'\n______________CCGUUAGGGAG\n______________\|\|\|\|:\|::\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	212 -- 218	47 -- 53	-14.7452 kcal/mol	2.96952 kcal/mol	2.73556 kcal/mol	207 219@LB@ \| \|@LB@5'-UUU...GAAAA UCCAC...CUA-3'@LB@ CCGUUAGGGAG@LB@ \|\|\|\|:\|::\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -14.7452 kcal/mol@LB@Unfolding Energy - mRNA 2.96952 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 208 -- 218@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 47 -- 53@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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