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	Additional homologs
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@
40	0.002726	0.2279	b1799	dmlR	-13.48	0.029707	223 -- 239	2 -- 20	transcriptional activator of dmlA	b3060	_____________222_________________240\n_____________\|___________________\|\n5'-CGC...GCUGA_____U_____________AUGCU...CGG-3'\n______________AUGAU___UGCGCGUCUUU\n______________\|\|:\|:___\|\|\|\|\|\|\|\|\|\|\|\n______________UAUUG___ACGCGCAGAAA\n3'-UUU...ACUAC_____UUU___________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	233 -- 239	2 -- 8	-19.9945 kcal/mol	5.2543 kcal/mol	1.25604 kcal/mol	222 240@LB@ \| \|@LB@5'-CGC...GCUGA U AUGCU...CGG-3'@LB@ AUGAU UGCGCGUCUUU@LB@ \|\|:\|: \|\|\|\|\|\|\|\|\|\|\|@LB@ UAUUG ACGCGCAGAAA@LB@3'-UUU...ACUAC UUU G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -19.9945 kcal/mol@LB@Unfolding Energy - mRNA 5.2543 kcal/mol@LB@Unfolding Energy - sRNA 1.25604 kcal/mol@LB@@LB@Position - mRNA 223 -- 239@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 2 -- 8@LB@
9	0.000195	0.07335	b1830	prc	-15.09	0.015143	131 -- 161	7 -- 38	carboxy-terminal protease for penicillin-binding protein 3		_____________130______________________________162\n_____________\|________________________________\|\n5'-CGA...UCCAG___________U___UCUU____U________CAGAA...CGG-3'\n______________CUGAAUUCGGG_AUG____UGAU__GUGCGCG\n______________\|\|\|\|\|\|\|\|:\|\|_\|\|\|____\|:\|:__:\|\|\|\|\|\|\n______________GACUUAAGUCC_UAC____AUUG__UACGCGC\n3'-UUU...GUAGA___________C___UACU____UU_______AGAAAG-5'\n_____________\|________________________________\|\n_____________39_______________________________6\n	155 -- 161	7 -- 13	-31.7028 kcal/mol	7.25259 kcal/mol	9.35859 kcal/mol	130 162@LB@ \| \|@LB@5'-CGA...UCCAG U UCUU U CAGAA...CGG-3'@LB@ CUGAAUUCGGG AUG UGAU GUGCGCG@LB@ \|\|\|\|\|\|\|\|:\|\| \|\|\| \|:\|: :\|\|\|\|\|\|@LB@ GACUUAAGUCC UAC AUUG UACGCGC@LB@3'-UUU...GUAGA C UACU UU AGAAAG-5'@LB@ \| \|@LB@ 39 6@LB@@LB@@LB@Energy -15.09 kcal/mol@LB@Hybridization Energy -31.7028 kcal/mol@LB@Unfolding Energy - mRNA 7.25259 kcal/mol@LB@Unfolding Energy - sRNA 9.35859 kcal/mol@LB@@LB@Position - mRNA 131 -- 161@LB@Position - sRNA 7 -- 38@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 7 -- 13@LB@
124	0.0124	0.3104	b1860	ruvB	-8.20	0.236824	252 -- 265	8 -- 20	ATP-dependent DNA helicase component of RuvABC resolvasome		_____________251____________266\n_____________\|______________\|\n5'-ACG...AAGAU_________C____CAUUC...GUC-3'\n______________GUAGCAGAU_GCGC\n______________:\|\|:\|\|:\|\|_\|\|\|\|\n______________UAUUGUUUA_CGCG\n3'-UUU...ACUAC______________CAGAAAG-5'\n_____________\|______________\|\n_____________21_____________7\n	252 -- 258	14 -- 20	-14.7986 kcal/mol	5.36112 kcal/mol	1.23367 kcal/mol	251 266@LB@ \| \|@LB@5'-ACG...AAGAU C CAUUC...GUC-3'@LB@ GUAGCAGAU GCGC@LB@ :\|\|:\|\|:\|\| \|\|\|\|@LB@ UAUUGUUUA CGCG@LB@3'-UUU...ACUAC CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -8.20 kcal/mol@LB@Hybridization Energy -14.7986 kcal/mol@LB@Unfolding Energy - mRNA 5.36112 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 252 -- 265@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 14 -- 20@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@
54	0.004897	0.3024	b1949	fliQ	-8.93	0.181731	208 -- 239	7 -- 38	flagellar biosynthesis protein		_____________207_______________________________240\n_____________\|_________________________________\|\n5'-UUC...GACAC__________UC__________G__C__AA___AUGAA...UUA-3'\n______________CUGAA_UCGG__AUGAUGAUGG_GA_UG__GCG\n______________\|\|\|\|\|_\|\|:\|__\|\|\|\|\|\|\|\|::_:\|_\|\|__\|\|\|\n______________GACUU_AGUC__UACUACUAUU_UU_AC__CGC\n3'-UUU...GUAGA_____A____CC__________G__U__G____AGAAAG-5'\n_____________\|_________________________________\|\n_____________39________________________________6\n	222 -- 228	17 -- 23	-27.1148 kcal/mol	8.82457 kcal/mol	9.35859 kcal/mol	207 240@LB@ \| \|@LB@5'-UUC...GACAC UC G C AA AUGAA...UUA-3'@LB@ CUGAA UCGG AUGAUGAUGG GA UG GCG@LB@ \|\|\|\|\| \|\|:\| \|\|\|\|\|\|\|\|:: :\| \|\| \|\|\|@LB@ GACUU AGUC UACUACUAUU UU AC CGC@LB@3'-UUU...GUAGA A CC G U G AGAAAG-5'@LB@ \| \|@LB@ 39 6@LB@@LB@@LB@Energy -8.93 kcal/mol@LB@Hybridization Energy -27.1148 kcal/mol@LB@Unfolding Energy - mRNA 8.82457 kcal/mol@LB@Unfolding Energy - sRNA 9.35859 kcal/mol@LB@@LB@Position - mRNA 208 -- 239@LB@Position - sRNA 7 -- 38@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 17 -- 23@LB@
130	0.01263	0.3104	b1952	dsrB	-7.17	0.338083	230 -- 240	7 -- 18	uncharacterized protein		_____________229__________241\n_____________\|____________\|\n5'-CGU...GUCAA____________GUCCG...ACC-3'\n______________AACGGAUG_GCG\n______________\|\|\|::\|\|\|_\|\|\|\n______________UUGUUUAC_CGC\n3'-UUU...UACUA________G___AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	231 -- 237	11 -- 17	-11.9456 kcal/mol	3.57064 kcal/mol	1.20891 kcal/mol	229 241@LB@ \| \|@LB@5'-CGU...GUCAA GUCCG...ACC-3'@LB@ AACGGAUG GCG@LB@ \|\|\|::\|\|\| \|\|\|@LB@ UUGUUUAC CGC@LB@3'-UUU...UACUA G AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -11.9456 kcal/mol@LB@Unfolding Energy - mRNA 3.57064 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 230 -- 240@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 11 -- 17@LB@
178	0.01756	0.3104	b2017	yefM	-12.99	0.036476	219 -- 231	5 -- 18	antitoxin of the YoeB-YefM toxin-antitoxin system		_____________218____________232\n_____________\|______________\|\n5'-AUU...GCUAC______________AGAAU...AUG-3'\n______________AGCGAA_GCGCGUC\n______________\|:\|:\|\|_\|\|\|\|\|\|\|\n______________UUGUUU_CGCGCAG\n3'-UUU...UACUA______A_______AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	225 -- 231	5 -- 11	-18.6086 kcal/mol	4.39571 kcal/mol	1.2243 kcal/mol	218 232@LB@ \| \|@LB@5'-AUU...GCUAC AGAAU...AUG-3'@LB@ AGCGAA GCGCGUC@LB@ \|:\|:\|\| \|\|\|\|\|\|\|@LB@ UUGUUU CGCGCAG@LB@3'-UUU...UACUA A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -12.99 kcal/mol@LB@Hybridization Energy -18.6086 kcal/mol@LB@Unfolding Energy - mRNA 4.39571 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 219 -- 231@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 5 -- 11@LB@
160	0.015	0.3104	b2022	hisB	-11.12	0.077869	165 -- 171	5 -- 11	histidinol-phosphatase and imidazoleglycerol-phosphate dehydratase		_____________164_____172\n_____________\|_______\|\n5'-CAG...AGCCA_______AUUGA...AAC-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	165 -- 171	5 -- 11	-14.7431 kcal/mol	2.50821 kcal/mol	1.11145 kcal/mol	164 172@LB@ \| \|@LB@5'-CAG...AGCCA AUUGA...AAC-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -14.7431 kcal/mol@LB@Unfolding Energy - mRNA 2.50821 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 165 -- 171@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 5 -- 11@LB@
29	0.001844	0.2094	b2047	wcaJ	-13.26	0.032615	200 -- 222	7 -- 21	colanic biosynthesis UDP-glucose lipid carrier transferase		_____________199_____________________223\n_____________\|_______________________\|\n5'-GCA...ACAAC__________CUAAAAAA_____AGCGA...UAU-3'\n______________GAUGACAAAU________GCGCG\n______________\|\|\|:\|\|\|\|\|\|________\|\|\|\|\|\n______________CUAUUGUUUA________CGCGC\n3'-UUU...UACUA_______________________AGAAAG-5'\n_____________\|_______________________\|\n_____________22______________________6\n	203 -- 209	12 -- 18	-17.5174 kcal/mol	3.01646 kcal/mol	1.24179 kcal/mol	199 223@LB@ \| \|@LB@5'-GCA...ACAAC CUAAAAAA AGCGA...UAU-3'@LB@ GAUGACAAAU GCGCG@LB@ \|\|\|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUUUA CGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -17.5174 kcal/mol@LB@Unfolding Energy - mRNA 3.01646 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 200 -- 222@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 12 -- 18@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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