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
76	0.007084	0.3087	b4214	cysQ	-5.34	0.578728	11 -- 17	26 -- 32	3'(2') 5'-bisphosphate nucleotidase	_____________10______18\n_____________\|_______\|\n5'-AAC...AAUCA_______CAUCC...ACA-3'\n______________UCAGGGA\n______________\|\|\|\|\|\|\|\n______________AGUCCCU\n3'-UUU...ACUUA_______ACUAC...AAG-5'\n_____________\|_______\|\n_____________33______25\n	11 -- 17	26 -- 32	-11.6237 kcal/mol	0.931861 kcal/mol	5.35475 kcal/mol	10 18@LB@ \| \|@LB@5'-AAC...AAUCA CAUCC...ACA-3'@LB@ UCAGGGA@LB@ \|\|\|\|\|\|\|@LB@ AGUCCCU@LB@3'-UUU...ACUUA ACUAC...AAG-5'@LB@ \| \|@LB@ 33 25@LB@@LB@@LB@Energy -5.34 kcal/mol@LB@Hybridization Energy -11.6237 kcal/mol@LB@Unfolding Energy - mRNA 0.931861 kcal/mol@LB@Unfolding Energy - sRNA 5.35475 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 26 -- 32@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 26 -- 32@LB@
181	0.01793	0.3104	b1594	mlc	-11.10	0.078496	11 -- 37	1 -- 18	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor	_____________10__________________________38\n_____________\|___________________________\|\n5'-AAA...UCAUG______GUCCGGC_______AA_____GUAUU...GUA-3'\n______________AACAAA_______UGCGCGU__CUUUC\n______________\|\|\|\|\|\|_______\|\|\|\|\|\|\|__\|\|\|\|\|\n______________UUGUUU_______ACGCGCA__GAAAG\n3'-UUU...UACUA___________________________-5'\n_____________\|__________________________\|\n_____________19_________________________1\n	24 -- 30	6 -- 12	-16.8416 kcal/mol	4.49753 kcal/mol	1.24077 kcal/mol	10 38@LB@ \| \|@LB@5'-AAA...UCAUG GUCCGGC AA GUAUU...GUA-3'@LB@ AACAAA UGCGCGU CUUUC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGUUU ACGCGCA GAAAG@LB@3'-UUU...UACUA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -16.8416 kcal/mol@LB@Unfolding Energy - mRNA 4.49753 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 11 -- 37@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 6 -- 12@LB@
131	0.01264	0.3104	b3412	bioH	-11.05	0.080071	12 -- 32	7 -- 31	pimeloyl-ACP methyl ester carboxylesterase	_____________11________________________33\n_____________\|_________________________\|\n5'-GGC...GACCG______A__________________GCGGG...ACG-3'\n______________CAGGGA_GAUGG____GAGUGUGUG\n______________\|\|\|\|\|\|_\|\|\|\|:____:\|:\|\|:\|:\|\n______________GUCCCU_CUACU____UUUACGCGC\n3'-UUU...CUUAA______A_____AUUG_________AGAAAG-5'\n_____________\|_________________________\|\n_____________32________________________6\n	26 -- 32	7 -- 13	-25.3011 kcal/mol	6.49654 kcal/mol	7.75103 kcal/mol	11 33@LB@ \| \|@LB@5'-GGC...GACCG A GCGGG...ACG-3'@LB@ CAGGGA GAUGG GAGUGUGUG@LB@ \|\|\|\|\|\| \|\|\|\|: :\|:\|\|:\|:\|@LB@ GUCCCU CUACU UUUACGCGC@LB@3'-UUU...CUUAA A AUUG AGAAAG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -11.05 kcal/mol@LB@Hybridization Energy -25.3011 kcal/mol@LB@Unfolding Energy - mRNA 6.49654 kcal/mol@LB@Unfolding Energy - sRNA 7.75103 kcal/mol@LB@@LB@Position - mRNA 12 -- 32@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 7 -- 13@LB@
79	0.007292	0.3087	b0063	araB	-12.45	0.045578	14 -- 28	6 -- 20	L-ribulokinase	_____________13______________29\n_____________\|_______________\|\n5'-CGG...AAGCC________AA_____AACAA...GGU-3'\n______________AUGACAAA__CGCGU\n______________\|\|:\|\|\|\|\|__\|\|\|\|\|\n______________UAUUGUUU__GCGCA\n3'-UUU...ACUAC________AC_____GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	15 -- 21	13 -- 19	-14.5023 kcal/mol	0.813134 kcal/mol	1.24244 kcal/mol	13 29@LB@ \| \|@LB@5'-CGG...AAGCC AA AACAA...GGU-3'@LB@ AUGACAAA CGCGU@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ UAUUGUUU GCGCA@LB@3'-UUU...ACUAC AC GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -14.5023 kcal/mol@LB@Unfolding Energy - mRNA 0.813134 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 14 -- 28@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 13 -- 19@LB@
168	0.01645	0.3104	b3720	bglH	-8.64	0.202347	15 -- 28	9 -- 22	carbohydrate-specific outer membrane porin cryptic	_____________14_____________29\n_____________\|______________\|\n5'-AUU...GAUCG_________UG___AAGGA...GCC-3'\n______________UGAUGAUAA__GCG\n______________\|\|\|\|:\|:\|\|__\|\|\|\n______________ACUAUUGUU__CGC\n3'-UUU...CUACU_________UA___GCAGAAAG-5'\n_____________\|______________\|\n_____________23_____________8\n	17 -- 23	14 -- 20	-13.7208 kcal/mol	3.8428 kcal/mol	1.23827 kcal/mol	14 29@LB@ \| \|@LB@5'-AUU...GAUCG UG AAGGA...GCC-3'@LB@ UGAUGAUAA GCG@LB@ \|\|\|\|:\|:\|\| \|\|\|@LB@ ACUAUUGUU CGC@LB@3'-UUU...CUACU UA GCAGAAAG-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -13.7208 kcal/mol@LB@Unfolding Energy - mRNA 3.8428 kcal/mol@LB@Unfolding Energy - sRNA 1.23827 kcal/mol@LB@@LB@Position - mRNA 15 -- 28@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 14 -- 20@LB@
60	0.00555	0.3084	b2062	wza	-10.85	0.086669	18 -- 25	4 -- 11	colanic acid export protein; outer membrane auxillary lipoprotein	_____________17_______26\n_____________\|________\|\n5'-AAA...CGGUA________GGAUG...GCA-3'\n______________GCGUGUCU\n______________\|\|\|:\|\|\|\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	19 -- 25	4 -- 10	-13.9362 kcal/mol	1.92535 kcal/mol	1.15639 kcal/mol	17 26@LB@ \| \|@LB@5'-AAA...CGGUA GGAUG...GCA-3'@LB@ GCGUGUCU@LB@ \|\|\|:\|\|\|\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -13.9362 kcal/mol@LB@Unfolding Energy - mRNA 1.92535 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 18 -- 25@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 4 -- 10@LB@
78	0.007118	0.3087	b1118	lolE	-12.65	0.041861	19 -- 36	6 -- 21	lipoprotein-releasing system transmembrane protein	_____________18_________________37\n_____________\|__________________\|\n5'-CUG...CUACC______CUC_________AACGC...GCA-3'\n______________GGUAAC___GAUGCGCGU\n______________\|:\|\|\|\|___:\|\|\|\|\|\|\|\|\n______________CUAUUG___UUACGCGCA\n3'-UUU...UACUA______U___________GAAAG-5'\n_____________\|__________________\|\n_____________22_________________5\n	30 -- 36	6 -- 12	-20.2716 kcal/mol	6.37224 kcal/mol	1.24519 kcal/mol	18 37@LB@ \| \|@LB@5'-CUG...CUACC CUC AACGC...GCA-3'@LB@ GGUAAC GAUGCGCGU@LB@ \|:\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ CUAUUG UUACGCGCA@LB@3'-UUU...UACUA U GAAAG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -12.65 kcal/mol@LB@Hybridization Energy -20.2716 kcal/mol@LB@Unfolding Energy - mRNA 6.37224 kcal/mol@LB@Unfolding Energy - sRNA 1.24519 kcal/mol@LB@@LB@Position - mRNA 19 -- 36@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 6 -- 12@LB@
166	0.01595	0.3104	b3560	glyQ	-10.24	0.110293	22 -- 29	7 -- 14	glycine tRNA synthetase alpha subunit	_____________21_______30\n_____________\|________\|\n5'-ACA...UAUGA________GUUAU...UGG-3'\n______________AAUGCGCG\n______________\|\|\|\|\|\|\|\|\n______________UUACGCGC\n3'-UUU...AUUGU________AGAAAG-5'\n_____________\|________\|\n_____________15_______6\n	23 -- 29	7 -- 13	-12.7168 kcal/mol	1.35517 kcal/mol	1.11978 kcal/mol	21 30@LB@ \| \|@LB@5'-ACA...UAUGA GUUAU...UGG-3'@LB@ AAUGCGCG@LB@ \|\|\|\|\|\|\|\|@LB@ UUACGCGC@LB@3'-UUU...AUUGU AGAAAG-5'@LB@ \| \|@LB@ 15 6@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -12.7168 kcal/mol@LB@Unfolding Energy - mRNA 1.35517 kcal/mol@LB@Unfolding Energy - sRNA 1.11978 kcal/mol@LB@@LB@Position - mRNA 22 -- 29@LB@Position - sRNA 7 -- 14@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 7 -- 13@LB@
198	0.0193	0.3104	b2961	mutY	-10.33	0.106403	22 -- 38	1 -- 15	adenine DNA glycosylase	_____________21________________39\n_____________\|_________________\|\n5'-CGU...CGGUG_____A__U________AUAAA...UAU-3'\n______________AAAUG_CG_CGUUUUUC\n______________\|\|\|\|\|_\|\|_\|\|\|:\|\|\|\|\n______________UUUAC_GC_GCAGAAAG\n3'-UUU...UAUUG_________________-5'\n_____________\|________________\|\n_____________16_______________1\n	32 -- 38	1 -- 7	-14.8981 kcal/mol	3.3462 kcal/mol	1.21803 kcal/mol	21 39@LB@ \| \|@LB@5'-CGU...CGGUG A U AUAAA...UAU-3'@LB@ AAAUG CG CGUUUUUC@LB@ \|\|\|\|\| \|\| \|\|\|:\|\|\|\|@LB@ UUUAC GC GCAGAAAG@LB@3'-UUU...UAUUG -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -14.8981 kcal/mol@LB@Unfolding Energy - mRNA 3.3462 kcal/mol@LB@Unfolding Energy - sRNA 1.21803 kcal/mol@LB@@LB@Position - mRNA 22 -- 38@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 1 -- 7@LB@
133	0.01287	0.3104	b3179	rlmE	-8.60	0.205247	24 -- 43	1 -- 17	23S rRNA U2552 2'-O-ribose methyltransferase SAM-dependent	_____________23___________________44\n_____________\|____________________\|\n5'-GCC...CUUGA__________CAGAC_____AGGUG...CCC-3'\n______________GCGGAUGUGC_____CUUUC\n______________:\|::\|\|\|:\|\|_____\|\|\|\|\|\n______________UGUUUACGCG_____GAAAG\n3'-UUU...ACUAU__________CA________-5'\n_____________\|___________________\|\n_____________18__________________1\n	27 -- 33	8 -- 14	-16.3409 kcal/mol	6.50016 kcal/mol	1.23994 kcal/mol	23 44@LB@ \| \|@LB@5'-GCC...CUUGA CAGAC AGGUG...CCC-3'@LB@ GCGGAUGUGC CUUUC@LB@ :\|::\|\|\|:\|\| \|\|\|\|\|@LB@ UGUUUACGCG GAAAG@LB@3'-UUU...ACUAU CA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -16.3409 kcal/mol@LB@Unfolding Energy - mRNA 6.50016 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 24 -- 43@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 8 -- 14@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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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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