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@
100	0.01591	0.5059	b0531	sfmC	-11.86	0.039421	211 -- 227	6 -- 22	putative periplasmic pilus chaperone	b4316	_____________210_______________228\n_____________\|_________________\|\n5'-AAU...GACUA___________U_____CUCAU...GUA-3'\n______________AAAUAAAGUUA_UGAUG\n______________\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UUUAUUUCAAU_ACUAC\n3'-UUU...CAUUA___________U_____UAUCG-5'\n_____________\|_________________\|\n_____________23________________5\n	215 -- 221	12 -- 18	-15.888 kcal/mol	3.9302 kcal/mol	0.0976382 kcal/mol	210 228@LB@ \| \|@LB@5'-AAU...GACUA U CUCAU...GUA-3'@LB@ AAAUAAAGUUA UGAUG@LB@ \|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUUAUUUCAAU ACUAC@LB@3'-UUU...CAUUA U UAUCG-5'@LB@ \| \|@LB@ 23 5@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -15.888 kcal/mol@LB@Unfolding Energy - mRNA 3.9302 kcal/mol@LB@Unfolding Energy - sRNA 0.0976382 kcal/mol@LB@@LB@Position - mRNA 211 -- 227@LB@Position - sRNA 6 -- 22@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 12 -- 18@LB@
7	0.0001529	0.07172	b0687	seqA	-15.48	0.005290	212 -- 226	5 -- 19	negative modulator of initiation of replication		_____________211_____________227\n_____________\|_______________\|\n5'-GGA...ACGAU_______________ACUCU...UGA-3'\n______________UGAAGUUGAUGAUGA\n______________\|:\|\|\|\|\|:\|\|\|\|\|\|\|\n______________AUUUCAAUUACUACU\n3'-UUU...UAUUU_______________AUCG-5'\n_____________\|_______________\|\n_____________20______________4\n	220 -- 226	5 -- 11	-18.3215 kcal/mol	2.77487 kcal/mol	0.0620344 kcal/mol	211 227@LB@ \| \|@LB@5'-GGA...ACGAU ACUCU...UGA-3'@LB@ UGAAGUUGAUGAUGA@LB@ \|:\|\|\|\|\|:\|\|\|\|\|\|\|@LB@ AUUUCAAUUACUACU@LB@3'-UUU...UAUUU AUCG-5'@LB@ \| \|@LB@ 20 4@LB@@LB@@LB@Energy -15.48 kcal/mol@LB@Hybridization Energy -18.3215 kcal/mol@LB@Unfolding Energy - mRNA 2.77487 kcal/mol@LB@Unfolding Energy - sRNA 0.0620344 kcal/mol@LB@@LB@Position - mRNA 212 -- 226@LB@Position - sRNA 5 -- 19@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 5 -- 11@LB@
53	0.006355	0.3902	b2916	argP	-17.11	0.001913	217 -- 267	1 -- 51	transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor		_____________216____________________________________________________268\n_____________\|______________________________________________________\|\n5'-GGC...GGACU____A_____A____CAC_______________C_____CGAG_____UUG___GCGCG...CAG-3'\n______________ACAG_ACAUU_CAGG___UGGAUG_CGGUGAUA_GUGAA______GAU___AGC\n______________\|\|\|\|_\|\|\|\|\|_\|\|\|:___\|\|:\|\|\|_\|\|\|\|:\|\|\|_:\|:\|\|______\|\|\|___\|\|\|\n______________UGUC_UGUAA_GUCU___ACUUAC_GCCAUUAU_UAUUU______CUA___UCG\n3'-UUU...CCAUU_______________UU_______U________U_____CAAUUA___CUA___-5'\n_____________\|_____________________________________________________\|\n_____________52____________________________________________________1\n	242 -- 248	22 -- 28	-33.3201 kcal/mol	9.87503 kcal/mol	6.33528 kcal/mol	216 268@LB@ \| \|@LB@5'-GGC...GGACU A A CAC C CGAG UUG GCGCG...CAG-3'@LB@ ACAG ACAUU CAGG UGGAUG CGGUGAUA GUGAA GAU AGC@LB@ \|\|\|\| \|\|\|\|\| \|\|\|: \|\|:\|\|\| \|\|\|\|:\|\|\| :\|:\|\| \|\|\| \|\|\|@LB@ UGUC UGUAA GUCU ACUUAC GCCAUUAU UAUUU CUA UCG@LB@3'-UUU...CCAUU UU U U CAAUUA CUA -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -17.11 kcal/mol@LB@Hybridization Energy -33.3201 kcal/mol@LB@Unfolding Energy - mRNA 9.87503 kcal/mol@LB@Unfolding Energy - sRNA 6.33528 kcal/mol@LB@@LB@Position - mRNA 217 -- 267@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 22 -- 28@LB@
48	0.005342	0.3653	b3380	yhfW	-15.20	0.006283	218 -- 233	1 -- 15	phosphopentomutase-related metalloenzyme superfamily protein		_____________217______________234\n_____________\|________________\|\n5'-CUC...GUGGU________U_______UUUGG...GUG-3'\n______________GUUAGUGA_UGAUAGC\n______________\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|\n______________CAAUUACU_ACUAUCG\n3'-UUU...UAUUU________________-5'\n_____________\|_______________\|\n_____________16______________1\n	227 -- 233	1 -- 7	-17.7091 kcal/mol	2.46465 kcal/mol	0.0474282 kcal/mol	217 234@LB@ \| \|@LB@5'-CUC...GUGGU U UUUGG...GUG-3'@LB@ GUUAGUGA UGAUAGC@LB@ \|\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ CAAUUACU ACUAUCG@LB@3'-UUU...UAUUU -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -15.20 kcal/mol@LB@Hybridization Energy -17.7091 kcal/mol@LB@Unfolding Energy - mRNA 2.46465 kcal/mol@LB@Unfolding Energy - sRNA 0.0474282 kcal/mol@LB@@LB@Position - mRNA 218 -- 233@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 1 -- 7@LB@
60	0.008489	0.4523	b3912	cpxR	-10.34	0.082729	218 -- 229	5 -- 16	response regulator in two-component regulatory system with CpxA		_____________217__________230\n_____________\|____________\|\n5'-UGA...CUGUU____________CCGAG...AUG-3'\n______________AGUUGAUGAUGA\n______________\|\|\|\|:\|\|\|\|\|\|\|\n______________UCAAUUACUACU\n3'-UUU...UUAUU____________AUCG-5'\n_____________\|____________\|\n_____________17___________4\n	223 -- 229	5 -- 11	-14.1725 kcal/mol	3.78244 kcal/mol	0.0462955 kcal/mol	217 230@LB@ \| \|@LB@5'-UGA...CUGUU CCGAG...AUG-3'@LB@ AGUUGAUGAUGA@LB@ \|\|\|\|:\|\|\|\|\|\|\|@LB@ UCAAUUACUACU@LB@3'-UUU...UUAUU AUCG-5'@LB@ \| \|@LB@ 17 4@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -14.1725 kcal/mol@LB@Unfolding Energy - mRNA 3.78244 kcal/mol@LB@Unfolding Energy - sRNA 0.0462955 kcal/mol@LB@@LB@Position - mRNA 218 -- 229@LB@Position - sRNA 5 -- 16@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 5 -- 11@LB@
73	0.01069	0.4523	b1949	fliQ	-11.32	0.051762	219 -- 228	2 -- 11	flagellar biosynthesis protein		_____________218________229\n_____________\|__________\|\n5'-UUC...CGGUC__________GGACU...UUA-3'\n______________AUGAUGAUGG\n______________\|\|\|\|\|\|\|\|:\|\n______________UACUACUAUC\n3'-UUU...UCAAU__________G-5'\n_____________\|__________\|\n_____________12_________1\n	222 -- 228	2 -- 8	-12.2017 kcal/mol	0.859554 kcal/mol	0.0252227 kcal/mol	218 229@LB@ \| \|@LB@5'-UUC...CGGUC GGACU...UUA-3'@LB@ AUGAUGAUGG@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UACUACUAUC@LB@3'-UUU...UCAAU G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -12.2017 kcal/mol@LB@Unfolding Energy - mRNA 0.859554 kcal/mol@LB@Unfolding Energy - sRNA 0.0252227 kcal/mol@LB@@LB@Position - mRNA 219 -- 228@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 2 -- 8@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@
132	0.0212	0.526	b2455	eutE	-9.17	0.140915	224 -- 235	1 -- 12	aldehyde oxidoreductase ethanolamine utilization protein		_____________223__________236\n_____________\|____________\|\n5'-GGU...GAACA________A___GGUAC...UCG-3'\n______________GGUGGUGA_AGC\n______________::\|\|:\|\|\|_\|\|\|\n______________UUACUACU_UCG\n3'-UUU...UUCAA________A___-5'\n_____________\|___________\|\n_____________13__________1\n	225 -- 231	5 -- 11	-12.5804 kcal/mol	3.3751 kcal/mol	0.0394463 kcal/mol	223 236@LB@ \| \|@LB@5'-GGU...GAACA A GGUAC...UCG-3'@LB@ GGUGGUGA AGC@LB@ ::\|\|:\|\|\| \|\|\|@LB@ UUACUACU UCG@LB@3'-UUU...UUCAA A -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -12.5804 kcal/mol@LB@Unfolding Energy - mRNA 3.3751 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 224 -- 235@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 5 -- 11@LB@
94	0.01566	0.5059	b3918	cdh	-10.38	0.081442	225 -- 238	1 -- 14	CDP-diacylglycerol phosphotidylhydrolase		_____________224____________239\n_____________\|______________\|\n5'-AUU...UUUUU______________UAUCG...CAU-3'\n______________UUGGUGAUGAUAGU\n______________\|\|::\|\|\|\|\|\|\|\|\|:\n______________AAUUACUACUAUCG\n3'-UUU...AUUUC______________-5'\n_____________\|_____________\|\n_____________15____________1\n	232 -- 238	1 -- 7	-16.1883 kcal/mol	5.76383 kcal/mol	0.0473494 kcal/mol	224 239@LB@ \| \|@LB@5'-AUU...UUUUU UAUCG...CAU-3'@LB@ UUGGUGAUGAUAGU@LB@ \|\|::\|\|\|\|\|\|\|\|\|:@LB@ AAUUACUACUAUCG@LB@3'-UUU...AUUUC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.1883 kcal/mol@LB@Unfolding Energy - mRNA 5.76383 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 225 -- 238@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 232 -- 238@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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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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