Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
118	0.01176	0.3326	b3601	mtlR	-9.20	0.175568	190 -- 199	44 -- 53	mannitol operon repressor	_____________189________200\n_____________\|__________\|\n5'-UAU...AUAAA__________AAUGG...UUG-3'\n______________GCAAUGCAAU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGUUACGUUA\n3'-UUU...GUCAC__________CCGGG...UUG-5'\n_____________\|__________\|\n_____________54_________43\n	193 -- 199	44 -- 50	-14.2394 kcal/mol	1.82821 kcal/mol	3.20822 kcal/mol	189 200@LB@ \| \|@LB@5'-UAU...AUAAA AAUGG...UUG-3'@LB@ GCAAUGCAAU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGUUACGUUA@LB@3'-UUU...GUCAC CCGGG...UUG-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -14.2394 kcal/mol@LB@Unfolding Energy - mRNA 1.82821 kcal/mol@LB@Unfolding Energy - sRNA 3.20822 kcal/mol@LB@@LB@Position - mRNA 190 -- 199@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 44 -- 50@LB@
146	0.01679	0.3828	b2699	recA	-5.90	0.590167	190 -- 206	40 -- 58	DNA recombination and repair protein; ssDNA-dependent ATPase; synaptase; ssDNA and dsDNA binding protein; ATP-dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor	_____________189_________________207\n_____________\|___________________\|\n5'-UGC...CAUGA___GA____A_________AUCGA...ACC-3'\n______________CAG__GUAA___AAUGGCU\n______________\|\|\|__\|:\|\|___\|\|\|\|\|\|:\n______________GUC__CGUU___UUACCGG\n3'-UUU...UUUUA___AC____ACG_______GUUGU...UUG-5'\n_____________\|___________________\|\n_____________59__________________39\n	200 -- 206	40 -- 46	-15.424 kcal/mol	3.45581 kcal/mol	6.06808 kcal/mol	189 207@LB@ \| \|@LB@5'-UGC...CAUGA GA A AUCGA...ACC-3'@LB@ CAG GUAA AAUGGCU@LB@ \|\|\| \|:\|\| \|\|\|\|\|\|:@LB@ GUC CGUU UUACCGG@LB@3'-UUU...UUUUA AC ACG GUUGU...UUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -5.90 kcal/mol@LB@Hybridization Energy -15.424 kcal/mol@LB@Unfolding Energy - mRNA 3.45581 kcal/mol@LB@Unfolding Energy - sRNA 6.06808 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 40 -- 46@LB@
175	0.02099	0.4033	b2913	serA	-5.57	0.642321	190 -- 257	5 -- 65	D-3-phosphoglycerate dehydrogenase	_____________189_____________________________________________________________________258\n_____________\|_______________________________________________________________________\|\n5'-UGU...AGACA___UU____AAA______AG___UCGC___AGAAA________U____UU____C________________CACCA...CCA-3'\n______________GGA__GGGU___UGGCAA__GUA____UGG_____GACA_AGA_UAAG__UCUG_UGGUA__GAAGGCGUG\n______________\|\|\|__:::\|___\|\|\|\|\|\|__\|:\|____\|\|\|_____:\|\|\|_\|:\|_\|\|\|:__\|\|\|\|_\|\|::\|__:\|\|\|\|\|:\|:\n______________CCU__UUUA___ACCGUU__CGU____ACC_____UUGU_UUU_AUUU__AGAC_ACUGU__UUUCCGUAU\n3'-UUU...UACAA_________GUC______A____U______GGG______C___U____U___________UA_________AUUG-5'\n_____________\|_______________________________________________________________________\|\n_____________66______________________________________________________________________4\n	251 -- 257	5 -- 11	-32.5395 kcal/mol	14.8085 kcal/mol	12.157 kcal/mol	189 258@LB@ \| \|@LB@5'-UGU...AGACA UU AAA AG UCGC AGAAA U UU C CACCA...CCA-3'@LB@ GGA GGGU UGGCAA GUA UGG GACA AGA UAAG UCUG UGGUA GAAGGCGUG@LB@ \|\|\| :::\| \|\|\|\|\|\| \|:\| \|\|\| :\|\|\| \|:\| \|\|\|: \|\|\|\| \|\|::\| :\|\|\|\|\|:\|:@LB@ CCU UUUA ACCGUU CGU ACC UUGU UUU AUUU AGAC ACUGU UUUCCGUAU@LB@3'-UUU...UACAA GUC A U GGG C U U UA AUUG-5'@LB@ \| \|@LB@ 66 4@LB@@LB@@LB@Energy -5.57 kcal/mol@LB@Hybridization Energy -32.5395 kcal/mol@LB@Unfolding Energy - mRNA 14.8085 kcal/mol@LB@Unfolding Energy - sRNA 12.157 kcal/mol@LB@@LB@Position - mRNA 190 -- 257@LB@Position - sRNA 5 -- 65@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 5 -- 11@LB@
45	0.002879	0.2151	b3319	rplD	-8.41	0.246804	191 -- 204	42 -- 54	50S ribosomal subunit protein L4	_____________190____________205\n_____________\|______________\|\n5'-UCA...CGUAA__A___A_______AAUUA...UUG-3'\n______________GG_GAU_GCAAUGG\n______________\|\|_:\|\|_\|\|\|\|\|\|\|\n______________CC_UUA_CGUUACC\n3'-UUU...AGUCA__G___________GGGUU...UUG-5'\n_____________\|______________\|\n_____________55_____________41\n	198 -- 204	42 -- 48	-13.9027 kcal/mol	1.99374 kcal/mol	3.49932 kcal/mol	190 205@LB@ \| \|@LB@5'-UCA...CGUAA A A AAUUA...UUG-3'@LB@ GG GAU GCAAUGG@LB@ \|\| :\|\| \|\|\|\|\|\|\|@LB@ CC UUA CGUUACC@LB@3'-UUU...AGUCA G GGGUU...UUG-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.9027 kcal/mol@LB@Unfolding Energy - mRNA 1.99374 kcal/mol@LB@Unfolding Energy - sRNA 3.49932 kcal/mol@LB@@LB@Position - mRNA 191 -- 204@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 42 -- 48@LB@
90	0.007755	0.2889	b1852	zwf	-12.23	0.039232	191 -- 223	38 -- 65	glucose-6-phosphate 1-dehydrogenase	_____________190_______________________________224\n_____________\|_________________________________\|\n5'-UCA...CUUAA_______G_CA_______AAC____ACA_____GGCCU...UGG-3'\n______________GGAGAAU_A__UGGCGGU___GCAA___GCCCA\n______________\|\|\|:\|\|\|_\|__\|\|\|\|::\|___\|\|\|\|___\|\|\|\|\|\n______________CCUUUUA_U__ACCGUUA___CGUU___CGGGU\n3'-UUU...UACAA_______G_C_______________AC______UGUCU...UUG-5'\n_____________\|_________________________________\|\n_____________66________________________________37\n	202 -- 208	49 -- 55	-27.1425 kcal/mol	8.24293 kcal/mol	6.67322 kcal/mol	190 224@LB@ \| \|@LB@5'-UCA...CUUAA G CA AAC ACA GGCCU...UGG-3'@LB@ GGAGAAU A UGGCGGU GCAA GCCCA@LB@ \|\|\|:\|\|\| \| \|\|\|\|::\| \|\|\|\| \|\|\|\|\|@LB@ CCUUUUA U ACCGUUA CGUU CGGGU@LB@3'-UUU...UACAA G C AC UGUCU...UUG-5'@LB@ \| \|@LB@ 66 37@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -27.1425 kcal/mol@LB@Unfolding Energy - mRNA 8.24293 kcal/mol@LB@Unfolding Energy - sRNA 6.67322 kcal/mol@LB@@LB@Position - mRNA 191 -- 223@LB@Position - sRNA 38 -- 65@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 49 -- 55@LB@
129	0.01395	0.3636	b2314	dedD	-15.05	0.007607	192 -- 211	45 -- 65	membrane-anchored periplasmic protein involved in septation	_____________191___________________212\n_____________\|_____________________\|\n5'-UUG...CGCGA______G______________GUUUC...AUU-3'\n______________GGAGAA_CGGUGGCAA_GUAA\n______________\|\|\|:\|\|_\|:\|\|\|\|\|\|\|_\|:\|\|\n______________CCUUUU_GUCACCGUU_CGUU\n3'-UUU...UACAA______A_________A____ACCGG...UUG-5'\n_____________\|_____________________\|\n_____________66____________________44\n	201 -- 207	50 -- 56	-23.8601 kcal/mol	4.54883 kcal/mol	4.26469 kcal/mol	191 212@LB@ \| \|@LB@5'-UUG...CGCGA G GUUUC...AUU-3'@LB@ GGAGAA CGGUGGCAA GUAA@LB@ \|\|\|:\|\| \|:\|\|\|\|\|\|\| \|:\|\|@LB@ CCUUUU GUCACCGUU CGUU@LB@3'-UUU...UACAA A A ACCGG...UUG-5'@LB@ \| \|@LB@ 66 44@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -23.8601 kcal/mol@LB@Unfolding Energy - mRNA 4.54883 kcal/mol@LB@Unfolding Energy - sRNA 4.26469 kcal/mol@LB@@LB@Position - mRNA 192 -- 211@LB@Position - sRNA 45 -- 65@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 50 -- 56@LB@
136	0.01532	0.3774	b3054	ygiF	-8.05	0.285135	192 -- 208	38 -- 53	inorganic triphosphatase	_____________191_______________209\n_____________\|_________________\|\n5'-GGC...GAUAA____AG__C________GGAAA...CCG-3'\n______________GUAA__GC_AUGGCUCA\n______________\|:\|\|__\|\|_\|\|\|\|\|:\|\|\n______________CGUU__CG_UACCGGGU\n3'-UUU...GUCAC____A___U________UGUCU...UUG-5'\n_____________\|_________________\|\n_____________54________________37\n	202 -- 208	38 -- 44	-16.8567 kcal/mol	4.04422 kcal/mol	4.7597 kcal/mol	191 209@LB@ \| \|@LB@5'-GGC...GAUAA AG C GGAAA...CCG-3'@LB@ GUAA GC AUGGCUCA@LB@ \|:\|\| \|\| \|\|\|\|\|:\|\|@LB@ CGUU CG UACCGGGU@LB@3'-UUU...GUCAC A U UGUCU...UUG-5'@LB@ \| \|@LB@ 54 37@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -16.8567 kcal/mol@LB@Unfolding Energy - mRNA 4.04422 kcal/mol@LB@Unfolding Energy - sRNA 4.7597 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 38 -- 53@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 38 -- 44@LB@
143	0.01651	0.3828	b2793	syd	-11.91	0.046390	192 -- 225	39 -- 65	SecY-interacting protein	_____________191________________________________226\n_____________\|__________________________________\|\n5'-UCA...GAAGA_A___________A____UUGACC___CAA____UGAAA...UGU-3'\n______________G_GAAAUUAGUGG_CGAU______GCA___GCCC\n______________\|_:\|\|\|\|:\|\|\|\|\|_\|:\|\|______\|\|\|___\|\|\|\|\n______________C_UUUUAGUCACC_GUUA______CGU___CGGG\n3'-UUU...UACAA_C_________________________UAC____UUGUC...UUG-5'\n_____________\|__________________________________\|\n_____________66_________________________________38\n	198 -- 204	53 -- 59	-24.7129 kcal/mol	6.12952 kcal/mol	6.66922 kcal/mol	191 226@LB@ \| \|@LB@5'-UCA...GAAGA A A UUGACC CAA UGAAA...UGU-3'@LB@ G GAAAUUAGUGG CGAU GCA GCCC@LB@ \| :\|\|\|\|:\|\|\|\|\| \|:\|\| \|\|\| \|\|\|\|@LB@ C UUUUAGUCACC GUUA CGU CGGG@LB@3'-UUU...UACAA C UAC UUGUC...UUG-5'@LB@ \| \|@LB@ 66 38@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -24.7129 kcal/mol@LB@Unfolding Energy - mRNA 6.12952 kcal/mol@LB@Unfolding Energy - sRNA 6.66922 kcal/mol@LB@@LB@Position - mRNA 192 -- 225@LB@Position - sRNA 39 -- 65@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 53 -- 59@LB@
179	0.02223	0.4143	b2167	fruA	-7.15	0.399094	192 -- 200	5 -- 13	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________191_______201\n_____________\|_________\|\n5'-CGC...GCAGG_________AUGAA...AAA-3'\n______________AGAGGCAUA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCCGUAU\n3'-UUU...UGUUA_________AUUG-5'\n_____________\|_________\|\n_____________14________4\n	194 -- 200	5 -- 11	-11.8443 kcal/mol	1.8873 kcal/mol	2.80332 kcal/mol	191 201@LB@ \| \|@LB@5'-CGC...GCAGG AUGAA...AAA-3'@LB@ AGAGGCAUA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCCGUAU@LB@3'-UUU...UGUUA AUUG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -11.8443 kcal/mol@LB@Unfolding Energy - mRNA 1.8873 kcal/mol@LB@Unfolding Energy - sRNA 2.80332 kcal/mol@LB@@LB@Position - mRNA 192 -- 200@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
64	0.005005	0.2614	b3795	yifK	-6.27	0.531551	193 -- 206	51 -- 64	putative APC family amino acid transporter	_____________192____________207\n_____________\|______________\|\n5'-CAA...AACAC_______UA_____GAUAA...GGG-3'\n______________GAGGAUU__UGGCA\n______________\|\|::\|\|:__\|\|\|\|\|\n______________CUUUUAG__ACCGU\n3'-UUU...ACAAC_______UC_____UACGU...UUG-5'\n_____________\|______________\|\n_____________65_____________50\n	193 -- 199	58 -- 64	-12.618 kcal/mol	3.46106 kcal/mol	2.8882 kcal/mol	192 207@LB@ \| \|@LB@5'-CAA...AACAC UA GAUAA...GGG-3'@LB@ GAGGAUU UGGCA@LB@ \|\|::\|\|: \|\|\|\|\|@LB@ CUUUUAG ACCGU@LB@3'-UUU...ACAAC UC UACGU...UUG-5'@LB@ \| \|@LB@ 65 50@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -12.618 kcal/mol@LB@Unfolding Energy - mRNA 3.46106 kcal/mol@LB@Unfolding Energy - sRNA 2.8882 kcal/mol@LB@@LB@Position - mRNA 193 -- 206@LB@Position - sRNA 51 -- 64@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 58 -- 64@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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