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	Additional homologs
84	0.01785	0.6177	b4318	fimF	-9.06	0.063721	96 -- 107	44 -- 55	minor component of type 1 fimbriae	b1504 b0943	_____________95___________108\n_____________\|____________\|\n5'-CAU...AAUGG_GA_________AAUGC...UCA-3'\n______________G__GAAGAGGAA\n______________\|__:\|\|\|\|\|\|\|\|\n______________C__UUUCUCCUU\n3'-UUU...CCGGG_AG_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	101 -- 107	44 -- 50	-12.9705 kcal/mol	2.96464 kcal/mol	0.941432 kcal/mol	95 108@LB@ \| \|@LB@5'-CAU...AAUGG GA AAUGC...UCA-3'@LB@ G GAAGAGGAA@LB@ \| :\|\|\|\|\|\|\|\|@LB@ C UUUCUCCUU@LB@3'-UUU...CCGGG AG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -12.9705 kcal/mol@LB@Unfolding Energy - mRNA 2.96464 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 96 -- 107@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 44 -- 50@LB@
43	0.008509	0.6129	b4322	uxuA	-11.91	0.016653	184 -- 195	44 -- 55	mannonate hydrolase		_____________183__________196\n_____________\|____________\|\n5'-CAU...ACUAU__G_________AAAUC...AUA-3'\n______________GU_AAAGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\|\|\n______________CA_UUUCUCCUU\n3'-UUU...CCGGG__G_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	189 -- 195	44 -- 50	-15.5118 kcal/mol	2.65561 kcal/mol	0.941432 kcal/mol	183 196@LB@ \| \|@LB@5'-CAU...ACUAU G AAAUC...AUA-3'@LB@ GU AAAGAGGAA@LB@ \|\| \|\|\|\|\|\|\|\|\|@LB@ CA UUUCUCCUU@LB@3'-UUU...CCGGG G AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -15.5118 kcal/mol@LB@Unfolding Energy - mRNA 2.65561 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
191	0.0398	0.6177	b4335	yjiM	-5.72	0.281824	283 -- 290	47 -- 54	putative 2-hydroxyglutaryl-CoA dehydratase		_____________282______291\n_____________\|________\|\n5'-CGG...GGAUC________CGCGG...UUC-3'\n______________UCAAGGAG\n______________\|\|\|\|:\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	284 -- 290	47 -- 53	-8.85878 kcal/mol	2.24401 kcal/mol	0.897871 kcal/mol	282 291@LB@ \| \|@LB@5'-CGG...GGAUC CGCGG...UUC-3'@LB@ UCAAGGAG@LB@ \|\|\|\|:\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -5.72 kcal/mol@LB@Hybridization Energy -8.85878 kcal/mol@LB@Unfolding Energy - mRNA 2.24401 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 283 -- 290@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 47 -- 53@LB@
126	0.02445	0.6177	b4364	yjjP	-5.95	0.256190	188 -- 200	42 -- 53	DUF1212 family inner membrane protein		_____________187___________201\n_____________\|_____________\|\n5'-UCA...UAUGA_______C_____AUGCA...UUU-3'\n______________CAAAGGG_GAGUU\n______________\|\|\|\|\|:\|_\|\|:\|\|\n______________GUUUCUC_CUUAA\n3'-UUU...GGGCA_____________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________54____________41\n	188 -- 194	47 -- 53	-11.6429 kcal/mol	4.76073 kcal/mol	0.933904 kcal/mol	187 201@LB@ \| \|@LB@5'-UCA...UAUGA C AUGCA...UUU-3'@LB@ CAAAGGG GAGUU@LB@ \|\|\|\|\|:\| \|\|:\|\|@LB@ GUUUCUC CUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -5.95 kcal/mol@LB@Hybridization Energy -11.6429 kcal/mol@LB@Unfolding Energy - mRNA 4.76073 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 188 -- 200@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
130	0.02541	0.6177	b4365	yjjQ	-8.08	0.100207	263 -- 277	38 -- 55	putative transcriptional regulator		_____________262_________________278\n_____________\|___________________\|\n5'-AGG...GCAGG___A_______________GAGGA...AUG-3'\n______________GUU_AAAGAGG____UCAU\n______________\|\|:_\|\|\|\|\|\|\|____\|\|\|\|\n______________CAG_UUUCUCC____AGUA\n3'-UUU...CCGGG___________UUAA____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	267 -- 273	46 -- 52	-10.7142 kcal/mol	1.46087 kcal/mol	1.17036 kcal/mol	262 278@LB@ \| \|@LB@5'-AGG...GCAGG A GAGGA...AUG-3'@LB@ GUU AAAGAGG UCAU@LB@ \|\|: \|\|\|\|\|\|\| \|\|\|\|@LB@ CAG UUUCUCC AGUA@LB@3'-UUU...CCGGG UUAA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -10.7142 kcal/mol@LB@Unfolding Energy - mRNA 1.46087 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 46 -- 52@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@
123	0.02427	0.6177	b4485	ytfR	-5.89	0.261942	32 -- 42	44 -- 54	putative sugar ABC transporter ATPase		_____________31__________43\n_____________\|___________\|\n5'-CCU...AAGAA_______A___GAAAA...GCC-3'\n______________UUAGAGA_GAA\n______________\|:\|:\|\|\|_\|\|\|\n______________AGUUUCU_CUU\n3'-UUU...CGGGC_______C___AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	32 -- 38	48 -- 54	-7.06152 kcal/mol	0.22708 kcal/mol	0.939671 kcal/mol	31 43@LB@ \| \|@LB@5'-CCU...AAGAA A GAAAA...GCC-3'@LB@ UUAGAGA GAA@LB@ \|:\|:\|\|\| \|\|\|@LB@ AGUUUCU CUU@LB@3'-UUU...CGGGC C AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -5.89 kcal/mol@LB@Hybridization Energy -7.06152 kcal/mol@LB@Unfolding Energy - mRNA 0.22708 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 32 -- 42@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 48 -- 54@LB@
156	0.03128	0.6177	b4512	ybdD	-7.87	0.110479	26 -- 38	43 -- 55	DUF466 family protein		_____________25____________39\n_____________\|_____________\|\n5'-GCA...UCAGA__G__________GUUGG...GGG-3'\n______________GU_AGGGGGGGAU\n______________\|\|_\|::\|:\|\|:\|\|\n______________CA_UUUCUCCUUA\n3'-UUU...CCGGG__G__________AAGUA...ACA-5'\n_____________\|_____________\|\n_____________56____________42\n	32 -- 38	43 -- 49	-14.3671 kcal/mol	5.55181 kcal/mol	0.946481 kcal/mol	25 39@LB@ \| \|@LB@5'-GCA...UCAGA G GUUGG...GGG-3'@LB@ GU AGGGGGGGAU@LB@ \|\| \|::\|:\|\|:\|\|@LB@ CA UUUCUCCUUA@LB@3'-UUU...CCGGG G AAGUA...ACA-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -7.87 kcal/mol@LB@Hybridization Energy -14.3671 kcal/mol@LB@Unfolding Energy - mRNA 5.55181 kcal/mol@LB@Unfolding Energy - sRNA 0.946481 kcal/mol@LB@@LB@Position - mRNA 26 -- 38@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 43 -- 49@LB@
13	0.003065	0.593	b4529	ydbJ	-10.82	0.027981	161 -- 194	44 -- 78	DUF333 family putative lipoprotein		_____________160___________________________________195\n_____________\|_____________________________________\|\n5'-GCA...UAUUU________________________AA__UC_______GAAAA...GUU-3'\n______________AUGG_CGGUGUCGU__UUGGCUUG__GA__AGAGGAA\n______________\|\|\|\|_\|::\|:\|\|\|:__\|\|\|\|\|::\|__:\|__\|\|\|\|\|\|\|\n______________UACC_GUUAUAGCG__AACCGGGC__UU__UCUCCUU\n_____3'-UUUUUU____G_________AU________AG___________AAAGU...ACA-5'\n_____________\|_____________________________________\|\n_____________79____________________________________43\n	188 -- 194	44 -- 50	-34.9495 kcal/mol	10.5981 kcal/mol	13.5333 kcal/mol	160 195@LB@ \| \|@LB@5'-GCA...UAUUU AA UC GAAAA...GUU-3'@LB@ AUGG CGGUGUCGU UUGGCUUG GA AGAGGAA@LB@ \|\|\|\| \|::\|:\|\|\|: \|\|\|\|\|::\| :\| \|\|\|\|\|\|\|@LB@ UACC GUUAUAGCG AACCGGGC UU UCUCCUU@LB@ 3'-UUUUUU G AU AG AAAGU...ACA-5'@LB@ \| \|@LB@ 79 43@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -34.9495 kcal/mol@LB@Unfolding Energy - mRNA 10.5981 kcal/mol@LB@Unfolding Energy - sRNA 13.5333 kcal/mol@LB@@LB@Position - mRNA 161 -- 194@LB@Position - sRNA 44 -- 78@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
188	0.03926	0.6177	b4547	ypfN	-8.44	0.084930	187 -- 194	44 -- 51	putative membrane protein UPF0370 family		_____________186______195\n_____________\|________\|\n5'-UGA...UCUGC________AUAAG...AGA-3'\n______________AAGAGGAA\n______________\|\|\|\|\|\|\|\|\n______________UUCUCCUU\n3'-UUU...GCAGU________AAAGU...ACA-5'\n_____________\|________\|\n_____________52_______43\n	188 -- 194	44 -- 50	-10.245 kcal/mol	0.953219 kcal/mol	0.848077 kcal/mol	186 195@LB@ \| \|@LB@5'-UGA...UCUGC AUAAG...AGA-3'@LB@ AAGAGGAA@LB@ \|\|\|\|\|\|\|\|@LB@ UUCUCCUU@LB@3'-UUU...GCAGU AAAGU...ACA-5'@LB@ \| \|@LB@ 52 43@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -10.245 kcal/mol@LB@Unfolding Energy - mRNA 0.953219 kcal/mol@LB@Unfolding Energy - sRNA 0.848077 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 44 -- 51@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@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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