Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
63	0.01324	0.6177	b3140	agaD	-9.33	0.056359	182 -- 192	45 -- 55	N-acetylgalactosamine-specific enzyme IID component of PTS	_____________181_________193\n_____________\|___________\|\n5'-GCG...AAAAU_AA________CUACA...GUU-3'\n______________G__GAAGAGGA\n______________\|__:\|\|\|\|\|\|\|\n______________C__UUUCUCCU\n3'-UUU...CCGGG_AG________UAAAG...ACA-5'\n_____________\|___________\|\n_____________56__________44\n	186 -- 192	45 -- 51	-11.186 kcal/mol	0.927202 kcal/mol	0.930875 kcal/mol	181 193@LB@ \| \|@LB@5'-GCG...AAAAU AA CUACA...GUU-3'@LB@ G GAAGAGGA@LB@ \| :\|\|\|\|\|\|\|@LB@ C UUUCUCCU@LB@3'-UUU...CCGGG AG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -11.186 kcal/mol@LB@Unfolding Energy - mRNA 0.927202 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 182 -- 192@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 45 -- 51@LB@
72	0.015	0.6177	b2513	yfgM	-10.40	0.034106	179 -- 190	45 -- 55	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________178__________191\n_____________\|____________\|\n5'-GGC...ACUGG________A___GAAGG...UUG-3'\n______________GUUAAGGA_GGA\n______________\|\|:\|\|:\|\|_\|\|\|\n______________CAGUUUCU_CCU\n3'-UUU...CCGGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________56___________44\n	180 -- 186	48 -- 54	-12.2699 kcal/mol	0.940443 kcal/mol	0.930875 kcal/mol	178 191@LB@ \| \|@LB@5'-GGC...ACUGG A GAAGG...UUG-3'@LB@ GUUAAGGA GGA@LB@ \|\|:\|\|:\|\| \|\|\|@LB@ CAGUUUCU CCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -10.40 kcal/mol@LB@Hybridization Energy -12.2699 kcal/mol@LB@Unfolding Energy - mRNA 0.940443 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 179 -- 190@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 48 -- 54@LB@
91	0.01869	0.6177	b3432	glgB	-9.43	0.053684	93 -- 103	45 -- 56	1 4-alpha-glucan branching enzyme	_____________92___________104\n_____________\|____________\|\n5'-CAU...GACGA____________UGCAC...GAC-3'\n______________CG_CAGAGAGGA\n______________\|\|_\|\|:\|\|\|\|\|\|\n______________GC_GUUUCUCCU\n3'-UUU...ACCGG__A_________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	97 -- 103	45 -- 51	-14.5586 kcal/mol	4.18817 kcal/mol	0.938337 kcal/mol	92 104@LB@ \| \|@LB@5'-CAU...GACGA UGCAC...GAC-3'@LB@ CG CAGAGAGGA@LB@ \|\| \|\|:\|\|\|\|\|\|@LB@ GC GUUUCUCCU@LB@3'-UUU...ACCGG A UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -14.5586 kcal/mol@LB@Unfolding Energy - mRNA 4.18817 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 93 -- 103@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 45 -- 51@LB@
94	0.01884	0.6177	b2048	cpsG	-10.80	0.028164	47 -- 56	45 -- 54	phosphomannomutase	_____________46_________57\n_____________\|__________\|\n5'-GGG...UUAUC__________UGAUG...GCG-3'\n______________UCGAAGAGGA\n______________\|\|:\|\|\|\|\|\|\|\n______________AGUUUCUCCU\n3'-UUU...CGGGC__________UAAAG...ACA-5'\n_____________\|__________\|\n_____________55_________44\n	50 -- 56	45 -- 51	-14.144 kcal/mol	2.41054 kcal/mol	0.929144 kcal/mol	46 57@LB@ \| \|@LB@5'-GGG...UUAUC UGAUG...GCG-3'@LB@ UCGAAGAGGA@LB@ \|\|:\|\|\|\|\|\|\|@LB@ AGUUUCUCCU@LB@3'-UUU...CGGGC UAAAG...ACA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -14.144 kcal/mol@LB@Unfolding Energy - mRNA 2.41054 kcal/mol@LB@Unfolding Energy - sRNA 0.929144 kcal/mol@LB@@LB@Position - mRNA 47 -- 56@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 45 -- 51@LB@
95	0.01894	0.6177	b0407	yajC	-8.94	0.067585	73 -- 105	45 -- 79	SecYEG protein translocase auxillary subunit	_____________72___________________________________106\n_____________\|____________________________________\|\n5'-UCU...CGUUU______G___U_A___AA______A___________UAAAU...UUU-3'\n______________GAUGGC_GGU_U_CGC____GGCU__UUGAAGAGGG\n______________:\|\|\|\|\|_::\|_\|_\|\|\|____\|\|\|:__\|::\|\|\|\|\|\|:\n______________UUACCG_UUA_A_GCG____CCGG__AGUUUCUCCU\n______3'-UUUUU______G___U_____AUAA____GC__________UAAAG...ACA-5'\n_____________\|____________________________________\|\n_____________80___________________________________44\n	99 -- 105	45 -- 51	-30.8043 kcal/mol	8.31146 kcal/mol	13.5551 kcal/mol	72 106@LB@ \| \|@LB@5'-UCU...CGUUU G U A AA A UAAAU...UUU-3'@LB@ GAUGGC GGU U CGC GGCU UUGAAGAGGG@LB@ :\|\|\|\|\| ::\| \| \|\|\| \|\|\|: \|::\|\|\|\|\|\|:@LB@ UUACCG UUA A GCG CCGG AGUUUCUCCU@LB@ 3'-UUUUU G U AUAA GC UAAAG...ACA-5'@LB@ \| \|@LB@ 80 44@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -30.8043 kcal/mol@LB@Unfolding Energy - mRNA 8.31146 kcal/mol@LB@Unfolding Energy - sRNA 13.5551 kcal/mol@LB@@LB@Position - mRNA 73 -- 105@LB@Position - sRNA 45 -- 79@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 45 -- 51@LB@
105	0.0216	0.6177	b2962	yggX	-9.20	0.059738	186 -- 194	45 -- 53	oxidative damage protective factor for iron-sulfur proteins	_____________185_______195\n_____________\|_________\|\n5'-UCA...GUCGA_________UGAUU...AGA-3'\n______________UAAAGAGGA\n______________:\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	188 -- 194	45 -- 51	-10.7665 kcal/mol	0.645872 kcal/mol	0.917553 kcal/mol	185 195@LB@ \| \|@LB@5'-UCA...GUCGA UGAUU...AGA-3'@LB@ UAAAGAGGA@LB@ :\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -10.7665 kcal/mol@LB@Unfolding Energy - mRNA 0.645872 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 45 -- 51@LB@
117	0.02321	0.6177	b1712	ihfA	-8.91	0.068436	115 -- 126	45 -- 56	integration host factor (IHF) DNA-binding protein alpha subunit	_____________114__________127\n_____________\|____________\|\n5'-CGU...ACACU__AA________GAUUG...AGA-3'\n______________CG__GAAGAGGA\n______________\|\|__:\|\|\|\|\|\|\|\n______________GC__UUUCUCCU\n3'-UUU...ACCGG__AG________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	120 -- 126	45 -- 51	-12.2887 kcal/mol	2.43966 kcal/mol	0.938337 kcal/mol	114 127@LB@ \| \|@LB@5'-CGU...ACACU AA GAUUG...AGA-3'@LB@ CG GAAGAGGA@LB@ \|\| :\|\|\|\|\|\|\|@LB@ GC UUUCUCCU@LB@3'-UUU...ACCGG AG UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -12.2887 kcal/mol@LB@Unfolding Energy - mRNA 2.43966 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 115 -- 126@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 45 -- 51@LB@
124	0.02431	0.6177	b2044	wcaL	-7.42	0.135034	145 -- 156	45 -- 56	putative glycosyl transferase	_____________144__________157\n_____________\|____________\|\n5'-GGG...GUGAG_______C____AUGCA...AGA-3'\n______________CGUCAGA_AGGA\n______________\|\|\|\|\|:\|_\|\|\|\|\n______________GCAGUUU_UCCU\n3'-UUU...ACCGG_______C____UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	145 -- 151	50 -- 56	-12.5799 kcal/mol	4.21745 kcal/mol	0.938337 kcal/mol	144 157@LB@ \| \|@LB@5'-GGG...GUGAG C AUGCA...AGA-3'@LB@ CGUCAGA AGGA@LB@ \|\|\|\|\|:\| \|\|\|\|@LB@ GCAGUUU UCCU@LB@3'-UUU...ACCGG C UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -12.5799 kcal/mol@LB@Unfolding Energy - mRNA 4.21745 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 145 -- 156@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 50 -- 56@LB@
133	0.02604	0.6177	b0876	ybjD	-5.23	0.342712	179 -- 199	45 -- 55	putative OLD family ATP-dependent endonuclease; DUF2813 family protein	_____________178___________________200\n_____________\|_____________________\|\n5'-CGU...GAUAA____CAUAUUUCUG_______UAUGA...GGG-3'\n______________GUCA__________GAGGGGA\n______________\|\|\|\|__________:\|\|:\|\|\|\n______________CAGU__________UUCUCCU\n3'-UUU...CCGGG_____________________UAAAG...ACA-5'\n_____________\|_____________________\|\n_____________56____________________44\n	193 -- 199	45 -- 51	-10.7419 kcal/mol	4.58374 kcal/mol	0.930875 kcal/mol	178 200@LB@ \| \|@LB@5'-CGU...GAUAA CAUAUUUCUG UAUGA...GGG-3'@LB@ GUCA GAGGGGA@LB@ \|\|\|\| :\|\|:\|\|\|@LB@ CAGU UUCUCCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -5.23 kcal/mol@LB@Hybridization Energy -10.7419 kcal/mol@LB@Unfolding Energy - mRNA 4.58374 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 179 -- 199@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 45 -- 51@LB@
138	0.02658	0.6177	b2331	smrB	-9.17	0.060779	224 -- 232	45 -- 53	putative DNA endonuclease	_____________223_______233\n_____________\|_________\|\n5'-UCA...CUUAG_________CCAGG...GAC-3'\n______________CGAGGAGGA\n______________\|:\|:\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	226 -- 232	45 -- 51	-12.8038 kcal/mol	2.72026 kcal/mol	0.917553 kcal/mol	223 233@LB@ \| \|@LB@5'-UCA...CUUAG CCAGG...GAC-3'@LB@ CGAGGAGGA@LB@ \|:\|:\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -12.8038 kcal/mol@LB@Unfolding Energy - mRNA 2.72026 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 224 -- 232@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 45 -- 51@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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