Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
108	0.01118	0.3104	b2565	recO	-9.71	0.135448	294 -- 300	5 -- 11	gap repair protein		_____________293____300\n_____________\|______\|\n5'-GAA...GGCGC_______-3'\n______________GUGCGUC\n______________\|:\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	294 -- 300	5 -- 11	-11.8762 kcal/mol	1.05403 kcal/mol	1.11145 kcal/mol	293 300@LB@ \| \|@LB@5'-GAA...GGCGC -3'@LB@ GUGCGUC@LB@ \|:\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -11.8762 kcal/mol@LB@Unfolding Energy - mRNA 1.05403 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 294 -- 300@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 5 -- 11@LB@
186	0.01836	0.3104	b3521	yhjC	-9.62	0.140197	158 -- 166	5 -- 13	LysR family putative transcriptional regulator		_____________157_______167\n_____________\|_________\|\n5'-UUU...GCGAU_________ACUGU...UUU-3'\n______________AUGCGCGUU\n______________\|\|\|\|\|\|\|\|:\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	160 -- 166	5 -- 11	-14.2497 kcal/mol	3.47777 kcal/mol	1.15134 kcal/mol	157 167@LB@ \| \|@LB@5'-UUU...GCGAU ACUGU...UUU-3'@LB@ AUGCGCGUU@LB@ \|\|\|\|\|\|\|\|:@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -9.62 kcal/mol@LB@Hybridization Energy -14.2497 kcal/mol@LB@Unfolding Energy - mRNA 3.47777 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 158 -- 166@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 5 -- 11@LB@
167	0.01599	0.3104	b4220	tamA	-9.57	0.142740	193 -- 207	4 -- 21	translocation and assembly module for autotransporter export outer membrane subunit		_____________192________________208\n_____________\|__________________\|\n5'-CGC...UUCAG__GA______________AUAUC...GAC-3'\n______________GA____AAAUGUGCG_CU\n______________\|\|____\|\|\|\|\|:\|\|\|_\|\|\n______________CU____UUUACGCGC_GA\n3'-UUU...UACUA__AUUG_________A__AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	199 -- 205	7 -- 13	-13.0971 kcal/mol	2.26836 kcal/mol	1.2552 kcal/mol	192 208@LB@ \| \|@LB@5'-CGC...UUCAG GA AUAUC...GAC-3'@LB@ GA AAAUGUGCG CU@LB@ \|\| \|\|\|\|\|:\|\|\| \|\|@LB@ CU UUUACGCGC GA@LB@3'-UUU...UACUA AUUG A AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -13.0971 kcal/mol@LB@Unfolding Energy - mRNA 2.26836 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 193 -- 207@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 7 -- 13@LB@
80	0.007305	0.3087	b2392	mntH	-9.52	0.145914	200 -- 218	5 -- 21	manganese/divalent cation transporter		_____________199_________________219\n_____________\|___________________\|\n5'-GCU...CACAA_________CUAU______GAGAG...UCG-3'\n______________GAUGACGAA____CGCGUU\n______________\|\|\|:\|\|:\|\|____\|\|\|\|\|:\n______________CUAUUGUUU____GCGCAG\n3'-UUU...UACUA_________AC________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	202 -- 208	13 -- 19	-16.4824 kcal/mol	5.71706 kcal/mol	1.24955 kcal/mol	199 219@LB@ \| \|@LB@5'-GCU...CACAA CUAU GAGAG...UCG-3'@LB@ GAUGACGAA CGCGUU@LB@ \|\|\|:\|\|:\|\| \|\|\|\|\|:@LB@ CUAUUGUUU GCGCAG@LB@3'-UUU...UACUA AC AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -16.4824 kcal/mol@LB@Unfolding Energy - mRNA 5.71706 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 200 -- 218@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 13 -- 19@LB@
179	0.01766	0.3104	b0377	sbmA	-9.49	0.147268	6 -- 15	3 -- 12	peptide antibiotic transporter	b1496	_____________5__________16\n_____________\|__________\|\n______5'-GAUCC_______G__AAUCC...ACU-3'\n______________UGCGCGU_UU\n______________\|\|\|\|\|\|\|_\|\|\n______________ACGCGCA_AA\n3'-UUU...UGUUU_______G__AG-5'\n_____________\|__________\|\n_____________13_________2\n	6 -- 12	6 -- 12	-14.1156 kcal/mol	3.45883 kcal/mol	1.16529 kcal/mol	5 16@LB@ \| \|@LB@ 5'-GAUCC G AAUCC...ACU-3'@LB@ UGCGCGU UU@LB@ \|\|\|\|\|\|\| \|\|@LB@ ACGCGCA AA@LB@3'-UUU...UGUUU G AG-5'@LB@ \| \|@LB@ 13 2@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -14.1156 kcal/mol@LB@Unfolding Energy - mRNA 3.45883 kcal/mol@LB@Unfolding Energy - sRNA 1.16529 kcal/mol@LB@@LB@Position - mRNA 6 -- 15@LB@Position - sRNA 3 -- 12@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 6 -- 12@LB@
6	9.655e-05	0.04801	b4175	hflC	-9.47	0.148653	186 -- 211	5 -- 32	HflB protease modulator specific for phage lambda cII repressor		_____________185____________________________212\n_____________\|______________________________\|\n5'-UUA...CAGCG_________________________AA___AGUUA...GUU-3'\n______________UCAGGGG_GA__AUAAC_GAUGCGU__GUC\n______________\|\|\|\|\|\|:_\|\|__\|\|\|\|\|_:\|\|\|\|\|:__\|\|\|\n______________AGUCCCU_CU__UAUUG_UUACGCG__CAG\n3'-UUU...ACUUA_______A__AC_____U____________AAAG-5'\n_____________\|______________________________\|\n_____________33_____________________________4\n	200 -- 206	8 -- 14	-26.2754 kcal/mol	8.97237 kcal/mol	7.8362 kcal/mol	185 212@LB@ \| \|@LB@5'-UUA...CAGCG AA AGUUA...GUU-3'@LB@ UCAGGGG GA AUAAC GAUGCGU GUC@LB@ \|\|\|\|\|\|: \|\| \|\|\|\|\| :\|\|\|\|\|: \|\|\|@LB@ AGUCCCU CU UAUUG UUACGCG CAG@LB@3'-UUU...ACUUA A AC U AAAG-5'@LB@ \| \|@LB@ 33 4@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -26.2754 kcal/mol@LB@Unfolding Energy - mRNA 8.97237 kcal/mol@LB@Unfolding Energy - sRNA 7.8362 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 5 -- 32@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 8 -- 14@LB@
100	0.01004	0.3104	b3166	truB	-9.42	0.151044	113 -- 128	5 -- 18	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase		_____________112______________129\n_____________\|________________\|\n5'-GGC...GGUUG__G________AU___AAACC...AAC-3'\n______________AA_GGAUGCGC__GUC\n______________\|\|_::\|\|\|\|\|\|__\|\|\|\n______________UU_UUUACGCG__CAG\n3'-UUU...UACUA__G_____________AAAG-5'\n_____________\|________________\|\n_____________19_______________4\n	117 -- 123	8 -- 14	-15.4757 kcal/mol	4.82661 kcal/mol	1.2243 kcal/mol	112 129@LB@ \| \|@LB@5'-GGC...GGUUG G AU AAACC...AAC-3'@LB@ AA GGAUGCGC GUC@LB@ \|\| ::\|\|\|\|\|\| \|\|\|@LB@ UU UUUACGCG CAG@LB@3'-UUU...UACUA G AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -15.4757 kcal/mol@LB@Unfolding Energy - mRNA 4.82661 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 113 -- 128@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 8 -- 14@LB@
64	0.005939	0.3087	b3237	argR	-9.39	0.153279	85 -- 104	1 -- 19	l-arginine-responsive arginine metabolism regulon transcriptional regulator		_____________84____________________105\n_____________\|_____________________\|\n5'-ACA...AAAUU_______AUCC__________AUAAC...UGC-3'\n______________UGAUAAA____CGC_UCUUUC\n______________\|:\|:\|\|\|____\|\|\|_\|\|\|\|\|\|\n______________AUUGUUU____GCG_AGAAAG\n3'-UUU...CUACU_______AC_____C______-5'\n_____________\|____________________\|\n_____________20___________________1\n	85 -- 91	13 -- 19	-12.1021 kcal/mol	1.46458 kcal/mol	1.25156 kcal/mol	84 105@LB@ \| \|@LB@5'-ACA...AAAUU AUCC AUAAC...UGC-3'@LB@ UGAUAAA CGC UCUUUC@LB@ \|:\|:\|\|\| \|\|\| \|\|\|\|\|\|@LB@ AUUGUUU GCG AGAAAG@LB@3'-UUU...CUACU AC C -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -12.1021 kcal/mol@LB@Unfolding Energy - mRNA 1.46458 kcal/mol@LB@Unfolding Energy - sRNA 1.25156 kcal/mol@LB@@LB@Position - mRNA 85 -- 104@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 13 -- 19@LB@
120	0.01222	0.3104	b0916	ycaQ	-9.32	0.156865	225 -- 243	1 -- 17	DUF1006 family protein with C-terminal wHTH domain		_____________224_________________244\n_____________\|___________________\|\n5'-UGG...CCCUU__U_________AAUC___ACCUU...AUA-3'\n______________GC_GAUGCGCGU____UUC\n______________:\|_:\|\|\|\|\|\|\|\|____\|\|\|\n______________UG_UUACGCGCA____AAG\n3'-UUU...ACUAU__U_________GA_____-5'\n_____________\|__________________\|\n_____________18_________________1\n	230 -- 236	6 -- 12	-16.5738 kcal/mol	6.00902 kcal/mol	1.23994 kcal/mol	224 244@LB@ \| \|@LB@5'-UGG...CCCUU U AAUC ACCUU...AUA-3'@LB@ GC GAUGCGCGU UUC@LB@ :\| :\|\|\|\|\|\|\|\| \|\|\|@LB@ UG UUACGCGCA AAG@LB@3'-UUU...ACUAU U GA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -16.5738 kcal/mol@LB@Unfolding Energy - mRNA 6.00902 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 225 -- 243@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 6 -- 12@LB@
135	0.01297	0.3104	b3409	feoB	-9.25	0.161231	74 -- 82	5 -- 13	ferrous iron transporter protein B and GTP-binding protein; membrane protein		_____________73________83\n_____________\|_________\|\n5'-CCG...AUGUG_________GCUCC...GGG-3'\n______________GUGCGCGUC\n______________:\|\|\|\|\|\|\|\|\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	76 -- 82	5 -- 11	-15.2985 kcal/mol	4.89519 kcal/mol	1.15134 kcal/mol	73 83@LB@ \| \|@LB@5'-CCG...AUGUG GCUCC...GGG-3'@LB@ GUGCGCGUC@LB@ :\|\|\|\|\|\|\|\|@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -15.2985 kcal/mol@LB@Unfolding Energy - mRNA 4.89519 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 74 -- 82@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 5 -- 11@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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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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