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
135	0.01297	0.3104	b3409	feoB	-9.25	0.161231	74 -- 82	5 -- 13	ferrous iron transporter protein B and GTP-binding protein; membrane protein	_____________73________83\n_____________\|_________\|\n5'-CCG...AUGUG_________GCUCC...GGG-3'\n______________GUGCGCGUC\n______________:\|\|\|\|\|\|\|\|\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	76 -- 82	5 -- 11	-15.2985 kcal/mol	4.89519 kcal/mol	1.15134 kcal/mol	73 83@LB@ \| \|@LB@5'-CCG...AUGUG GCUCC...GGG-3'@LB@ GUGCGCGUC@LB@ :\|\|\|\|\|\|\|\|@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -15.2985 kcal/mol@LB@Unfolding Energy - mRNA 4.89519 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 74 -- 82@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 5 -- 11@LB@
69	0.006491	0.3087	b3347	fkpA	-11.66	0.062814	96 -- 113	4 -- 22	FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase)	_____________95__________________114\n_____________\|___________________\|\n5'-UGG...AUAGA___________________GUAUG...CAG-3'\n______________UGAUAAUAGG_GCGUGUCU\n______________\|\|\|\|\|\|:\|::_\|\|\|:\|\|\|\|\n______________ACUAUUGUUU_CGCGCAGA\n3'-UUU...CUACU__________A________AAG-5'\n_____________\|___________________\|\n_____________23__________________3\n	107 -- 113	4 -- 10	-21.7718 kcal/mol	8.85627 kcal/mol	1.2572 kcal/mol	95 114@LB@ \| \|@LB@5'-UGG...AUAGA GUAUG...CAG-3'@LB@ UGAUAAUAGG GCGUGUCU@LB@ \|\|\|\|\|\|:\|:: \|\|\|:\|\|\|\|@LB@ ACUAUUGUUU CGCGCAGA@LB@3'-UUU...CUACU A AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -21.7718 kcal/mol@LB@Unfolding Energy - mRNA 8.85627 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 96 -- 113@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 4 -- 10@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@
103	0.01026	0.3104	b1083	flgL	-8.46	0.215699	195 -- 209	5 -- 21	flagellar hook-filament junction protein	_____________194_______________210\n_____________\|_________________\|\n5'-UUG...GGGGA______________U__AGUAC...GUA-3'\n______________GAUAA__GAUGCGU_UC\n______________\|\|\|\|\|__:\|\|\|\|\|:_\|\|\n______________CUAUU__UUACGCG_AG\n3'-UUU...UACUA_____GU_______C__AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	200 -- 206	8 -- 14	-13.0743 kcal/mol	3.36074 kcal/mol	1.24955 kcal/mol	194 210@LB@ \| \|@LB@5'-UUG...GGGGA U AGUAC...GUA-3'@LB@ GAUAA GAUGCGU UC@LB@ \|\|\|\|\| :\|\|\|\|\|: \|\|@LB@ CUAUU UUACGCG AG@LB@3'-UUU...UACUA GU C AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -13.0743 kcal/mol@LB@Unfolding Energy - mRNA 3.36074 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 195 -- 209@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 200 -- 206@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@
90	0.009145	0.3104	b1079	flgH	-6.81	0.379144	179 -- 204	10 -- 38	flagellar protein of basal-body outer-membrane L ring	_____________178___________________________205\n_____________\|_____________________________\|\n5'-ACU...GUUUA____U___U____A_________C_____AAAAA...GGG-3'\n______________CUGA_UUU___GA_GAUGAUAGC__AUGC\n______________\|\|\|\|_\|\|:___\|\|_\|\|\|\|\|\|\|:\|__\|\|\|\|\n______________GACU_AAG___CU_CUACUAUUG__UACG\n3'-UUU...GUAGA____U___UCC__A_________UU____CGCAG...AAG-5'\n_____________\|_____________________________\|\n_____________39____________________________9\n	193 -- 199	16 -- 22	-21.1251 kcal/mol	4.97135 kcal/mol	9.34299 kcal/mol	178 205@LB@ \| \|@LB@5'-ACU...GUUUA U U A C AAAAA...GGG-3'@LB@ CUGA UUU GA GAUGAUAGC AUGC@LB@ \|\|\|\| \|\|: \|\| \|\|\|\|\|\|\|:\| \|\|\|\|@LB@ GACU AAG CU CUACUAUUG UACG@LB@3'-UUU...GUAGA U UCC A UU CGCAG...AAG-5'@LB@ \| \|@LB@ 39 9@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -21.1251 kcal/mol@LB@Unfolding Energy - mRNA 4.97135 kcal/mol@LB@Unfolding Energy - sRNA 9.34299 kcal/mol@LB@@LB@Position - mRNA 179 -- 204@LB@Position - sRNA 10 -- 38@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 16 -- 22@LB@
138	0.01331	0.3104	b2897	sdhE	-11.73	0.060976	261 -- 284	1 -- 21	flavinator of succinate dehydrogenase; antitoxin of CptAB toxin-antitoxin pair	_____________260_______________________285\n_____________\|_________________________\|\n5'-GUA...AACUC____UUU___UC_____________GAACA...ACA-3'\n______________GAUA___CAA__AUGC_CGUUUUUC\n______________\|\|\|\|___\|\|\|__\|\|\|\|_\|\|\|:\|\|\|\|\n______________CUAU___GUU__UACG_GCAGAAAG\n3'-UUU...UACUA____U___________C________-5'\n_____________\|________________________\|\n_____________22_______________________1\n	278 -- 284	1 -- 7	-16.4732 kcal/mol	3.48371 kcal/mol	1.25763 kcal/mol	260 285@LB@ \| \|@LB@5'-GUA...AACUC UUU UC GAACA...ACA-3'@LB@ GAUA CAA AUGC CGUUUUUC@LB@ \|\|\|\| \|\|\| \|\|\|\| \|\|\|:\|\|\|\|@LB@ CUAU GUU UACG GCAGAAAG@LB@3'-UUU...UACUA U C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -16.4732 kcal/mol@LB@Unfolding Energy - mRNA 3.48371 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 261 -- 284@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 1 -- 7@LB@
111	0.01125	0.3104	b0102	zapD	-10.07	0.117779	99 -- 113	8 -- 22	FtsZ stabilizer	_____________98______________114\n_____________\|_______________\|\n5'-ACC...GUCAU_________CG____ACCGG...CCA-3'\n______________UGAUAAUAA__GCGC\n______________\|\|\|\|\|\|:\|\|__\|\|\|\|\n______________ACUAUUGUU__CGCG\n3'-UUU...CUACU_________UA____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	101 -- 107	14 -- 20	-15.8633 kcal/mol	4.55182 kcal/mol	1.23838 kcal/mol	98 114@LB@ \| \|@LB@5'-ACC...GUCAU CG ACCGG...CCA-3'@LB@ UGAUAAUAA GCGC@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|@LB@ ACUAUUGUU CGCG@LB@3'-UUU...CUACU UA CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -10.07 kcal/mol@LB@Hybridization Energy -15.8633 kcal/mol@LB@Unfolding Energy - mRNA 4.55182 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 99 -- 113@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 14 -- 20@LB@
196	0.01921	0.3104	b2167	fruA	-9.92	0.125082	150 -- 163	5 -- 22	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________149________________164\n_____________\|__________________\|\n5'-CGC...CGCAA__________________GACUU...AAA-3'\n______________UGAUGGC____GCGCGUC\n______________\|\|\|\|::\|____\|\|\|\|\|\|\|\n______________ACUAUUG____CGCGCAG\n3'-UUU...CUACU_______UUUA_______AAAG-5'\n_____________\|__________________\|\n_____________23_________________4\n	157 -- 163	5 -- 11	-18.2874 kcal/mol	7.11819 kcal/mol	1.25155 kcal/mol	149 164@LB@ \| \|@LB@5'-CGC...CGCAA GACUU...AAA-3'@LB@ UGAUGGC GCGCGUC@LB@ \|\|\|\|::\| \|\|\|\|\|\|\|@LB@ ACUAUUG CGCGCAG@LB@3'-UUU...CUACU UUUA AAAG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -18.2874 kcal/mol@LB@Unfolding Energy - mRNA 7.11819 kcal/mol@LB@Unfolding Energy - sRNA 1.25155 kcal/mol@LB@@LB@Position - mRNA 150 -- 163@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 5 -- 11@LB@
187	0.01837	0.3104	b2151	galS	-10.59	0.096282	222 -- 228	5 -- 11	galactose- and fucose-inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor	_____________221_____229\n_____________\|_______\|\n5'-UCU...AUGUA_______AGGCU...GUG-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	222 -- 228	5 -- 11	-14.6299 kcal/mol	2.93004 kcal/mol	1.11145 kcal/mol	221 229@LB@ \| \|@LB@5'-UCU...AUGUA AGGCU...GUG-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -14.6299 kcal/mol@LB@Unfolding Energy - mRNA 2.93004 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 222 -- 228@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 5 -- 11@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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