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
94	0.009498	0.3104	b4198	ulaF	-10.74	0.090813	136 -- 150	6 -- 20	L-ribulose 5-phosphate 4-epimerase	_____________135_____________151\n_____________\|_______________\|\n5'-GUC...CAGAA________A______GAUUG...GCG-3'\n______________GUGGCGAA_GCGCGU\n______________:\|::\|:\|\|_\|\|\|\|\|\|\n______________UAUUGUUU_CGCGCA\n3'-UUU...ACUAC________A______GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	137 -- 143	13 -- 19	-18.1084 kcal/mol	6.12954 kcal/mol	1.24244 kcal/mol	135 151@LB@ \| \|@LB@5'-GUC...CAGAA A GAUUG...GCG-3'@LB@ GUGGCGAA GCGCGU@LB@ :\|::\|:\|\| \|\|\|\|\|\|@LB@ UAUUGUUU CGCGCA@LB@3'-UUU...ACUAC A GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -18.1084 kcal/mol@LB@Unfolding Energy - mRNA 6.12954 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 136 -- 150@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 13 -- 19@LB@
114	0.01161	0.3104	b3392	hofP	-8.60	0.204995	138 -- 147	1 -- 11	DNA catabolic protein	_____________137_________148\n_____________\|___________\|\n5'-ACU...CGUGA___________GUUAA...GCG-3'\n______________GC_CGUUUUUC\n______________\|\|_\|\|\|:\|\|\|\|\n______________CG_GCAGAAAG\n3'-UUU...GUUUA__C________-5'\n_____________\|__________\|\n_____________12_________1\n	141 -- 147	1 -- 7	-12.6405 kcal/mol	2.86562 kcal/mol	1.17076 kcal/mol	137 148@LB@ \| \|@LB@5'-ACU...CGUGA GUUAA...GCG-3'@LB@ GC CGUUUUUC@LB@ \|\| \|\|\|:\|\|\|\|@LB@ CG GCAGAAAG@LB@3'-UUU...GUUUA C -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.6405 kcal/mol@LB@Unfolding Energy - mRNA 2.86562 kcal/mol@LB@Unfolding Energy - sRNA 1.17076 kcal/mol@LB@@LB@Position - mRNA 138 -- 147@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 1 -- 7@LB@
164	0.0157	0.3104	b1735	chbR	-6.99	0.357617	139 -- 145	6 -- 12	repressor of chb operon for N N'-diacetylchitobiose utilization	_____________138_____146\n_____________\|_______\|\n5'-GAU...AUGCU_______GAACU...CUG-3'\n______________UGCGCGU\n______________\|\|\|\|\|\|\|\n______________ACGCGCA\n3'-UUU...UGUUU_______GAAAG-5'\n_____________\|_______\|\n_____________13______5\n	139 -- 145	6 -- 12	-12.5358 kcal/mol	4.43858 kcal/mol	1.10371 kcal/mol	138 146@LB@ \| \|@LB@5'-GAU...AUGCU GAACU...CUG-3'@LB@ UGCGCGU@LB@ \|\|\|\|\|\|\|@LB@ ACGCGCA@LB@3'-UUU...UGUUU GAAAG-5'@LB@ \| \|@LB@ 13 5@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -12.5358 kcal/mol@LB@Unfolding Energy - mRNA 4.43858 kcal/mol@LB@Unfolding Energy - sRNA 1.10371 kcal/mol@LB@@LB@Position - mRNA 139 -- 145@LB@Position - sRNA 6 -- 12@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 6 -- 12@LB@
141	0.01345	0.3104	b3311	rpsQ	-8.13	0.242987	140 -- 150	8 -- 18	30S ribosomal subunit protein S17	_____________139_________151\n_____________\|___________\|\n5'-GGU...GUUGA___________CGCGA...UCU-3'\n______________AGCAAGUGCGU\n______________\|:\|\|\|:\|\|\|\|:\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	144 -- 150	8 -- 14	-14.6725 kcal/mol	5.33741 kcal/mol	1.20363 kcal/mol	139 151@LB@ \| \|@LB@5'-GGU...GUUGA CGCGA...UCU-3'@LB@ AGCAAGUGCGU@LB@ \|:\|\|\|:\|\|\|\|:@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -8.13 kcal/mol@LB@Hybridization Energy -14.6725 kcal/mol@LB@Unfolding Energy - mRNA 5.33741 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 140 -- 150@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 8 -- 14@LB@
62	0.005646	0.3084	b1242	ychE	-13.92	0.024785	141 -- 151	1 -- 11	UPF0056 family inner membrane protein	_____________140_________152\n_____________\|___________\|\n5'-CAU...UGUCA___________CAACC...GCA-3'\n______________GCGCGUCUUUU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________CGCGCAGAAAG\n3'-UUU...GUUUA___________-5'\n_____________\|__________\|\n_____________12_________1\n	145 -- 151	1 -- 7	-17.9236 kcal/mol	2.83374 kcal/mol	1.17076 kcal/mol	140 152@LB@ \| \|@LB@5'-CAU...UGUCA CAACC...GCA-3'@LB@ GCGCGUCUUUU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ CGCGCAGAAAG@LB@3'-UUU...GUUUA -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -17.9236 kcal/mol@LB@Unfolding Energy - mRNA 2.83374 kcal/mol@LB@Unfolding Energy - sRNA 1.17076 kcal/mol@LB@@LB@Position - mRNA 141 -- 151@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 1 -- 7@LB@
129	0.01261	0.3104	b3025	qseB	-10.92	0.084347	141 -- 152	5 -- 17	quorum sensing DNA-binding response regulator in two-component regulatory system with QseC	_____________140___________153\n_____________\|_____________\|\n5'-GUG...GCUGU_____________ACAAC...GUC-3'\n______________ACAGA_GCGCGUU\n______________\|\|\|:\|_\|\|\|\|\|\|:\n______________UGUUU_CGCGCAG\n3'-UUU...ACUAU_____A_______AAAG-5'\n_____________\|_____________\|\n_____________18____________4\n	146 -- 152	5 -- 11	-15.7823 kcal/mol	3.63703 kcal/mol	1.22241 kcal/mol	140 153@LB@ \| \|@LB@5'-GUG...GCUGU ACAAC...GUC-3'@LB@ ACAGA GCGCGUU@LB@ \|\|\|:\| \|\|\|\|\|\|:@LB@ UGUUU CGCGCAG@LB@3'-UUU...ACUAU A AAAG-5'@LB@ \| \|@LB@ 18 4@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -15.7823 kcal/mol@LB@Unfolding Energy - mRNA 3.63703 kcal/mol@LB@Unfolding Energy - sRNA 1.22241 kcal/mol@LB@@LB@Position - mRNA 141 -- 152@LB@Position - sRNA 5 -- 17@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 5 -- 11@LB@
44	0.003062	0.2325	b3847	pepQ	-9.98	0.122201	144 -- 157	8 -- 21	proline dipeptidase	_____________143____________158\n_____________\|______________\|\n5'-UUG...CUCUG_____AC_______UAAGA...UUC-3'\n______________GAUGA__GAUGUGC\n______________\|\|\|:\|__:\|\|\|:\|\|\n______________CUAUU__UUACGCG\n3'-UUU...UACUA_____GU_______CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	151 -- 157	8 -- 14	-13.3112 kcal/mol	2.09686 kcal/mol	1.23638 kcal/mol	143 158@LB@ \| \|@LB@5'-UUG...CUCUG AC UAAGA...UUC-3'@LB@ GAUGA GAUGUGC@LB@ \|\|\|:\| :\|\|\|:\|\|@LB@ CUAUU UUACGCG@LB@3'-UUU...UACUA GU CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -9.98 kcal/mol@LB@Hybridization Energy -13.3112 kcal/mol@LB@Unfolding Energy - mRNA 2.09686 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 144 -- 157@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 8 -- 14@LB@
34	0.002145	0.2094	b1939	fliG	-13.29	0.032191	145 -- 162	6 -- 22	flagellar motor switching and energizing component	_____________144________________163\n_____________\|__________________\|\n5'-AGC...AUGUC_________UCC______GGUGG...AAG-3'\n______________UGAUAACGA___GCGCGU\n______________\|\|\|\|\|\|\|:\|___\|\|\|\|\|\|\n______________ACUAUUGUU___CGCGCA\n3'-UUU...CUACU_________UA_______GAAAG-5'\n_____________\|__________________\|\n_____________23_________________5\n	147 -- 153	14 -- 20	-19.5862 kcal/mol	5.04831 kcal/mol	1.24718 kcal/mol	144 163@LB@ \| \|@LB@5'-AGC...AUGUC UCC GGUGG...AAG-3'@LB@ UGAUAACGA GCGCGU@LB@ \|\|\|\|\|\|\|:\| \|\|\|\|\|\|@LB@ ACUAUUGUU CGCGCA@LB@3'-UUU...CUACU UA GAAAG-5'@LB@ \| \|@LB@ 23 5@LB@@LB@@LB@Energy -13.29 kcal/mol@LB@Hybridization Energy -19.5862 kcal/mol@LB@Unfolding Energy - mRNA 5.04831 kcal/mol@LB@Unfolding Energy - sRNA 1.24718 kcal/mol@LB@@LB@Position - mRNA 145 -- 162@LB@Position - sRNA 6 -- 22@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 14 -- 20@LB@
91	0.009339	0.3104	b2562	yfhL	-11.62	0.063873	146 -- 160	6 -- 20	putative 4Fe-4S cluster-containing protein	_____________145_____________161\n_____________\|_______________\|\n5'-AGC...UCUGA____A__________AUAAU...UUA-3'\n______________GUAA_GAAUGCGCGU\n______________:\|\|\|_:\|\|\|\|\|\|\|\|\|\n______________UAUU_UUUACGCGCA\n3'-UUU...ACUAC____G__________GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	154 -- 160	6 -- 12	-16.8242 kcal/mol	3.96482 kcal/mol	1.24244 kcal/mol	145 161@LB@ \| \|@LB@5'-AGC...UCUGA A AUAAU...UUA-3'@LB@ GUAA GAAUGCGCGU@LB@ :\|\|\| :\|\|\|\|\|\|\|\|\|@LB@ UAUU UUUACGCGCA@LB@3'-UUU...ACUAC G GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -16.8242 kcal/mol@LB@Unfolding Energy - mRNA 3.96482 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 146 -- 160@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 6 -- 12@LB@
175	0.01743	0.3104	b0921	smtA	-12.81	0.039244	146 -- 164	2 -- 20	putative S-adenosyl-L-methionine-dependent methyltransferase	_____________145_________________165\n_____________\|___________________\|\n5'-AUC...UGGCU________AUA________AUCAG...AUC-3'\n______________GUGACAAA___GCGUCUUU\n______________:\|:\|\|\|\|\|___\|\|\|\|\|\|\|\|\n______________UAUUGUUU___CGCAGAAA\n3'-UUU...ACUAC________ACG________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	158 -- 164	2 -- 8	-18.7664 kcal/mol	4.69909 kcal/mol	1.25604 kcal/mol	145 165@LB@ \| \|@LB@5'-AUC...UGGCU AUA AUCAG...AUC-3'@LB@ GUGACAAA GCGUCUUU@LB@ :\|:\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UAUUGUUU CGCAGAAA@LB@3'-UUU...ACUAC ACG G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -12.81 kcal/mol@LB@Hybridization Energy -18.7664 kcal/mol@LB@Unfolding Energy - mRNA 4.69909 kcal/mol@LB@Unfolding Energy - sRNA 1.25604 kcal/mol@LB@@LB@Position - mRNA 146 -- 164@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 2 -- 8@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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