Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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	0.01184	0.4627	b3101	yqjF	-11.66	0.043663	211 -- 235	1 -- 23	putative quinol oxidase subunit		_____________210_______________________236\n_____________\|_________________________\|\n5'-CAG...AAAAU____A__U_______UAC_______GCGCA...GUA-3'\n______________UAGA_GA_GUUGGUG___UGGUAGC\n______________\|\|:\|_:\|_\|\|\|::\|\|___\|\|:\|\|\|\|\n______________AUUU_UU_CAAUUAC___ACUAUCG\n3'-UUU...CCAUU____A__U_______U_________-5'\n_____________\|________________________\|\n_____________24_______________________1\n	229 -- 235	1 -- 7	-15.9826 kcal/mol	4.21954 kcal/mol	0.105066 kcal/mol	210 236@LB@ \| \|@LB@5'-CAG...AAAAU A U UAC GCGCA...GUA-3'@LB@ UAGA GA GUUGGUG UGGUAGC@LB@ \|\|:\| :\| \|\|\|::\|\| \|\|:\|\|\|\|@LB@ AUUU UU CAAUUAC ACUAUCG@LB@3'-UUU...CCAUU A U U -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -15.9826 kcal/mol@LB@Unfolding Energy - mRNA 4.21954 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 211 -- 235@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
44	0.004782	0.3568	b3243	aaeR	-11.65	0.043804	4 -- 44	1 -- 57	transcriptional regulator for aaeXAB operon		_____________3_________________________________________________________45\n_____________\|_________________________________________________________\|\n________5'-AAC_________________UGU____CCU_____U_____G__________________AGGCG...UCA-3'\n______________GGG_AAACAGAC__UCA____UGA____UGGU_GUAAA_AGAG___________AGC\n______________\|\|\|_\|\|\|\|\|\|\|\|__\|\|\|____\|\|\|____:\|\|\|_:\|\|\|\|_\|:\|\|___________\|\|\|\n______________CCC_UUUGUCUG__AGU____ACU____GCCA_UAUUU_UUUC___________UCG\n3'-UUU...UUAUC___A________UA___CUUU___UACU____U_____A____AAUUACUACUA___-5'\n_____________\|________________________________________________________\|\n_____________58_______________________________________________________1\n	8 -- 14	46 -- 52	-26.9604 kcal/mol	8.9713 kcal/mol	6.33758 kcal/mol	3 45@LB@ \| \|@LB@ 5'-AAC UGU CCU U G AGGCG...UCA-3'@LB@ GGG AAACAGAC UCA UGA UGGU GUAAA AGAG AGC@LB@ \|\|\| \|\|\|\|\|\|\|\| \|\|\| \|\|\| :\|\|\| :\|\|\|\| \|:\|\| \|\|\|@LB@ CCC UUUGUCUG AGU ACU GCCA UAUUU UUUC UCG@LB@3'-UUU...UUAUC A UA CUUU UACU U A AAUUACUACUA -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -11.65 kcal/mol@LB@Hybridization Energy -26.9604 kcal/mol@LB@Unfolding Energy - mRNA 8.9713 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 4 -- 44@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 46 -- 52@LB@
18	0.0008759	0.1482	b3626	waaR	-11.62	0.044565	224 -- 238	11 -- 25	lipopolysaccharide 1 2-glucosyltransferase; UDP-glucose:(glucosyl)LPS alpha-1 2-glucosyltransferase		_____________223_____________239\n_____________\|_______________\|\n5'-UGG...AUAGA_______________AGCCU...GUG-3'\n______________GAUAGAUAAAGUUAA\n______________:\|\|\|:\|\|\|\|\|\|\|\|\|\|\n______________UUAUUUAUUUCAAUU\n3'-UUU...UGCCA_______________ACUAC...UCG-5'\n_____________\|_______________\|\n_____________26______________10\n	232 -- 238	11 -- 17	-12.9968 kcal/mol	1.27318 kcal/mol	0.10636 kcal/mol	223 239@LB@ \| \|@LB@5'-UGG...AUAGA AGCCU...GUG-3'@LB@ GAUAGAUAAAGUUAA@LB@ :\|\|\|:\|\|\|\|\|\|\|\|\|\|@LB@ UUAUUUAUUUCAAUU@LB@3'-UUU...UGCCA ACUAC...UCG-5'@LB@ \| \|@LB@ 26 10@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -12.9968 kcal/mol@LB@Unfolding Energy - mRNA 1.27318 kcal/mol@LB@Unfolding Energy - sRNA 0.10636 kcal/mol@LB@@LB@Position - mRNA 224 -- 238@LB@Position - sRNA 11 -- 25@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 11 -- 17@LB@
179	0.02973	0.5424	b2812	tcdA	-11.60	0.044907	209 -- 228	1 -- 28	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA		_____________208___________________________229\n_____________\|_____________________________\|\n5'-GUG...UCUGU_______________________C_____GUCAG...UUU-3'\n______________GGUAAU_________UAGUGAUG_AUGGC\n______________\|\|\|\|\|\|_________\|\|:\|\|\|\|\|_\|\|:\|\|\n______________CCAUUA_________AUUACUAC_UAUCG\n3'-UUU...UACUG______UUUAUUUCA______________-5'\n_____________\|____________________________\|\n_____________29___________________________1\n	216 -- 222	6 -- 12	-16.3639 kcal/mol	3.995 kcal/mol	0.766821 kcal/mol	208 229@LB@ \| \|@LB@5'-GUG...UCUGU C GUCAG...UUU-3'@LB@ GGUAAU UAGUGAUG AUGGC@LB@ \|\|\|\|\|\| \|\|:\|\|\|\|\| \|\|:\|\|@LB@ CCAUUA AUUACUAC UAUCG@LB@3'-UUU...UACUG UUUAUUUCA -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -16.3639 kcal/mol@LB@Unfolding Energy - mRNA 3.995 kcal/mol@LB@Unfolding Energy - sRNA 0.766821 kcal/mol@LB@@LB@Position - mRNA 209 -- 228@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 6 -- 12@LB@
181	0.02995	0.5424	b0601	ybdM	-11.52	0.046768	198 -- 207	55 -- 64	Spo0J family protein ParB-like nuclease domain		_____________197________208\n_____________\|__________\|\n5'-UUG...CGUCA__________AUACU...GCA-3'\n______________GGAAUGGGGG\n______________\|:\|\|\|:\|\|\|\|\n______________CUUUAUCCCC\n3'-UUU...GCCAA__________AUUUG...UCG-5'\n_____________\|__________\|\n_____________65_________54\n	201 -- 207	55 -- 61	-14.9628 kcal/mol	3.4127 kcal/mol	0.0291912 kcal/mol	197 208@LB@ \| \|@LB@5'-UUG...CGUCA AUACU...GCA-3'@LB@ GGAAUGGGGG@LB@ \|:\|\|\|:\|\|\|\|@LB@ CUUUAUCCCC@LB@3'-UUU...GCCAA AUUUG...UCG-5'@LB@ \| \|@LB@ 65 54@LB@@LB@@LB@Energy -11.52 kcal/mol@LB@Hybridization Energy -14.9628 kcal/mol@LB@Unfolding Energy - mRNA 3.4127 kcal/mol@LB@Unfolding Energy - sRNA 0.0291912 kcal/mol@LB@@LB@Position - mRNA 198 -- 207@LB@Position - sRNA 55 -- 64@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 55 -- 61@LB@
164	0.02654	0.526	b3993	thiE	-11.45	0.048376	123 -- 151	37 -- 65	thiamine phosphate synthase (thiamine phosphate pyrophosphorylase)		_____________122____________________________152\n_____________\|______________________________\|\n5'-CAC...ACUAU_________AAU__________G_______ACUUC...UAC-3'\n______________UGAAAUGGG____GGCGGAUAU_UCGGAGA\n______________\|\|\|\|\|\|:\|\|____::\|:\|\|:\|\|_\|\|:\|\|:\|\n______________ACUUUAUCC____UUGUCUGUA_AGUCUUU\n3'-UUU...GGCCA_________CCAU_________________ACUUA...UCG-5'\n_____________\|______________________________\|\n_____________66_____________________________36\n	125 -- 131	57 -- 63	-26.5084 kcal/mol	7.89908 kcal/mol	7.1561 kcal/mol	122 152@LB@ \| \|@LB@5'-CAC...ACUAU AAU G ACUUC...UAC-3'@LB@ UGAAAUGGG GGCGGAUAU UCGGAGA@LB@ \|\|\|\|\|\|:\|\| ::\|:\|\|:\|\| \|\|:\|\|:\|@LB@ ACUUUAUCC UUGUCUGUA AGUCUUU@LB@3'-UUU...GGCCA CCAU ACUUA...UCG-5'@LB@ \| \|@LB@ 66 36@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -26.5084 kcal/mol@LB@Unfolding Energy - mRNA 7.89908 kcal/mol@LB@Unfolding Energy - sRNA 7.1561 kcal/mol@LB@@LB@Position - mRNA 123 -- 151@LB@Position - sRNA 37 -- 65@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 57 -- 63@LB@
121	0.01924	0.5155	b0074	leuA	-11.43	0.049038	243 -- 261	39 -- 56	2-isopropylmalate synthase		_____________242_________________262\n_____________\|___________________\|\n5'-CAU...GCGAC______________A____CAAGC...UGG-3'\n______________GGUGAACAGGCGUU_CAGG\n______________\|\|\|:\|\|\|\|\|:\|:\|\|_\|\|\|:\n______________CCAUUUGUCUGUAA_GUCU\n3'-UUU...UAUCC___________________UUACU...UCG-5'\n_____________\|___________________\|\n_____________57__________________38\n	247 -- 253	46 -- 52	-24.0317 kcal/mol	6.35652 kcal/mol	6.24929 kcal/mol	242 262@LB@ \| \|@LB@5'-CAU...GCGAC A CAAGC...UGG-3'@LB@ GGUGAACAGGCGUU CAGG@LB@ \|\|\|:\|\|\|\|\|:\|:\|\| \|\|\|:@LB@ CCAUUUGUCUGUAA GUCU@LB@3'-UUU...UAUCC UUACU...UCG-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -24.0317 kcal/mol@LB@Unfolding Energy - mRNA 6.35652 kcal/mol@LB@Unfolding Energy - sRNA 6.24929 kcal/mol@LB@@LB@Position - mRNA 243 -- 261@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 46 -- 52@LB@
87	0.01323	0.4992	b1951	rcsA	-11.40	0.049597	149 -- 196	25 -- 65	transcriptional regulator of colanic acid capsular biosynthesis		_____________148______________________________________________197\n_____________\|________________________________________________\|\n5'-GUU...CAUGA_______UUCA______G___AUUAU____ACGCAU_______G____UGCCA...UUG-3'\n______________UGAAAUA____GGUAAG_GGA_____CGUU______UGAGUGA_GGUA\n______________\|\|\|\|\|\|\|____\|\|\|\|\|:_:\|\|_____\|:\|\|______\|\|\|:\|\|\|_\|\|\|\|\n______________ACUUUAU____CCAUUU_UCU_____GUAA______ACUUACU_CCAU\n3'-UUU...GGCCA_______CC________G____________GUCUUU_______G____UAUUU...UCG-5'\n_____________\|________________________________________________\|\n_____________66_______________________________________________24\n	149 -- 155	59 -- 65	-29.5865 kcal/mol	10.9819 kcal/mol	7.2015 kcal/mol	148 197@LB@ \| \|@LB@5'-GUU...CAUGA UUCA G AUUAU ACGCAU G UGCCA...UUG-3'@LB@ UGAAAUA GGUAAG GGA CGUU UGAGUGA GGUA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|: :\|\| \|:\|\| \|\|\|:\|\|\| \|\|\|\|@LB@ ACUUUAU CCAUUU UCU GUAA ACUUACU CCAU@LB@3'-UUU...GGCCA CC G GUCUUU G UAUUU...UCG-5'@LB@ \| \|@LB@ 66 24@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -29.5865 kcal/mol@LB@Unfolding Energy - mRNA 10.9819 kcal/mol@LB@Unfolding Energy - sRNA 7.2015 kcal/mol@LB@@LB@Position - mRNA 149 -- 196@LB@Position - sRNA 25 -- 65@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 59 -- 65@LB@
176	0.02871	0.5353	b0518	fdrA	-11.39	0.049925	288 -- 297	6 -- 15	putative NAD(P)-binding acyl-CoA synthetase	b0320	_____________287________298\n_____________\|__________\|\n5'-CGC...AAAAU__________UUU-3'\n______________GUUGAUGAUG\n______________\|\|\|:\|\|\|\|\|\|\n______________CAAUUACUAC\n3'-UUU...UAUUU__________UAUCG-5'\n_____________\|__________\|\n_____________16_________5\n	291 -- 297	6 -- 12	-11.8608 kcal/mol	0.426728 kcal/mol	0.0442104 kcal/mol	287 298@LB@ \| \|@LB@5'-CGC...AAAAU UUU-3'@LB@ GUUGAUGAUG@LB@ \|\|\|:\|\|\|\|\|\|@LB@ CAAUUACUAC@LB@3'-UUU...UAUUU UAUCG-5'@LB@ \| \|@LB@ 16 5@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -11.8608 kcal/mol@LB@Unfolding Energy - mRNA 0.426728 kcal/mol@LB@Unfolding Energy - sRNA 0.0442104 kcal/mol@LB@@LB@Position - mRNA 288 -- 297@LB@Position - sRNA 6 -- 15@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 6 -- 12@LB@
158	0.0258	0.526	b3738	atpB	-11.34	0.051140	75 -- 89	1 -- 15	F0 sector of membrane-bound ATP synthase subunit a		_____________74______________90\n_____________\|_______________\|\n5'-CAU...UUGGU____C__________GUUGG...ACC-3'\n______________GUUA_UGGUGGUGGC\n______________\|\|\|\|_\|\|:\|\|:\|:\|\|\n______________CAAU_ACUACUAUCG\n3'-UUU...UAUUU____U__________-5'\n_____________\|______________\|\n_____________16_____________1\n	83 -- 89	1 -- 7	-16.9836 kcal/mol	5.59496 kcal/mol	0.0474282 kcal/mol	74 90@LB@ \| \|@LB@5'-CAU...UUGGU C GUUGG...ACC-3'@LB@ GUUA UGGUGGUGGC@LB@ \|\|\|\| \|\|:\|\|:\|:\|\|@LB@ CAAU ACUACUAUCG@LB@3'-UUU...UAUUU U -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -16.9836 kcal/mol@LB@Unfolding Energy - mRNA 5.59496 kcal/mol@LB@Unfolding Energy - sRNA 0.0474282 kcal/mol@LB@@LB@Position - mRNA 75 -- 89@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 1 -- 7@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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service.

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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