Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
87	0.00233	0.09349	b2522	sseB	-8.85	0.094489	280 -- 288	1 -- 9	rhodanase-like enzyme sulfur transfer from thiosulfate		_____________279_______289\n_____________\|_________\|\n5'-GGU...UUUCC_________UGGAA...CCG-3'\n______________GUACUCUAC\n______________\|\|\|\|:\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	282 -- 288	1 -- 7	-12.3435 kcal/mol	1.38525 kcal/mol	2.12872 kcal/mol	279 289@LB@ \| \|@LB@5'-GGU...UUUCC UGGAA...CCG-3'@LB@ GUACUCUAC@LB@ \|\|\|\|:\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -12.3435 kcal/mol@LB@Unfolding Energy - mRNA 1.38525 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 280 -- 288@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 1 -- 7@LB@
88	0.002339	0.09349	b3878	yihQ	-11.00	0.022508	260 -- 267	1 -- 8	putative sulpholipid alpha-glucosidase; alpha-glucosyl fluoride glucosidase	b3656	_____________259______268\n_____________\|________\|\n5'-AAC...AGUUU________AUUUU...GCA-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	261 -- 267	1 -- 7	-13.427 kcal/mol	0.33456 kcal/mol	2.11603 kcal/mol	259 268@LB@ \| \|@LB@5'-AAC...AGUUU AUUUU...GCA-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -13.427 kcal/mol@LB@Unfolding Energy - mRNA 0.33456 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 260 -- 267@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 1 -- 7@LB@
89	0.002377	0.09395	b4136	dsbD	-10.47	0.032769	211 -- 231	1 -- 22	thiol:disulfide interchange protein and activator of DsbC		_____________210____________________232\n_____________\|______________________\|\n5'-UGC...UCAAC_______UA_G___________UACUU...CGG-3'\n______________GCAUCUU__C_CUG_AUCCUGC\n______________:\|\|\|\|\|\|__\|_\|\|\|_\|:\|\|\|:\|\n______________UGUAGAA__G_GAC_UGGGAUG\n3'-AUU...UAUCU_______UG_A___A_______-5'\n_____________\|_____________________\|\n_____________23____________________1\n	225 -- 231	1 -- 7	-23.5098 kcal/mol	5.0672 kcal/mol	7.99236 kcal/mol	210 232@LB@ \| \|@LB@5'-UGC...UCAAC UA G UACUU...CGG-3'@LB@ GCAUCUU C CUG AUCCUGC@LB@ :\|\|\|\|\|\| \| \|\|\| \|:\|\|\|:\|@LB@ UGUAGAA G GAC UGGGAUG@LB@3'-AUU...UAUCU UG A A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.47 kcal/mol@LB@Hybridization Energy -23.5098 kcal/mol@LB@Unfolding Energy - mRNA 5.0672 kcal/mol@LB@Unfolding Energy - sRNA 7.99236 kcal/mol@LB@@LB@Position - mRNA 211 -- 231@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 1 -- 7@LB@
92	0.002567	0.09816	b4120	melB	-8.04	0.151444	195 -- 202	1 -- 8	melibiose:sodium symporter		_____________194______203\n_____________\|________\|\n5'-AUA...CCCGA________GAGCA...ACA-3'\n______________UACCCUAU\n______________\|\|\|\|\|\|\|:\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	196 -- 202	1 -- 7	-10.9179 kcal/mol	0.779946 kcal/mol	2.11603 kcal/mol	194 203@LB@ \| \|@LB@5'-AUA...CCCGA GAGCA...ACA-3'@LB@ UACCCUAU@LB@ \|\|\|\|\|\|\|:@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -10.9179 kcal/mol@LB@Unfolding Energy - mRNA 0.779946 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 195 -- 202@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 1 -- 7@LB@
94	0.002669	0.09947	b2659	csiD	-13.62	0.002680	28 -- 48	1 -- 21	carbon starvation protein		_____________27____________________49\n_____________\|_____________________\|\n5'-GUU...UGUCU__C________AA________GUUAA...UGG-3'\n______________CA_UUUGCCUU__UACCCUAC\n______________\|\|_:\|\|:\|\|\|:__\|\|\|\|\|\|\|\|\n______________GU_GAAUGGAG__AUGGGAUG\n3'-AUU...AUCUU__A________AC________-5'\n_____________\|____________________\|\n_____________22___________________1\n	42 -- 48	1 -- 7	-22.7197 kcal/mol	1.13457 kcal/mol	7.99195 kcal/mol	27 49@LB@ \| \|@LB@5'-GUU...UGUCU C AA GUUAA...UGG-3'@LB@ CA UUUGCCUU UACCCUAC@LB@ \|\| :\|\|:\|\|\|: \|\|\|\|\|\|\|\|@LB@ GU GAAUGGAG AUGGGAUG@LB@3'-AUU...AUCUU A AC -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -22.7197 kcal/mol@LB@Unfolding Energy - mRNA 1.13457 kcal/mol@LB@Unfolding Energy - sRNA 7.99195 kcal/mol@LB@@LB@Position - mRNA 28 -- 48@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 1 -- 7@LB@
95	0.002686	0.09947	b2419	yfeK	-12.78	0.005552	57 -- 65	1 -- 9	uncharacterized protein		_____________56________66\n_____________\|_________\|\n5'-GUU...CUGCA_________UCUUA...UGG-3'\n______________GUGCCCUAC\n______________\|\|:\|\|\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	59 -- 65	1 -- 7	-16.152 kcal/mol	1.26264 kcal/mol	2.12872 kcal/mol	56 66@LB@ \| \|@LB@5'-GUU...CUGCA UCUUA...UGG-3'@LB@ GUGCCCUAC@LB@ \|\|:\|\|\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -16.152 kcal/mol@LB@Unfolding Energy - mRNA 1.26264 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 57 -- 65@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 1 -- 7@LB@
101	0.00315	0.1097	b1822	rlmA	-7.85	0.169074	182 -- 190	1 -- 9	23S rRNA m(1)G745 methyltransferase SAM-dependent		_____________181_______191\n_____________\|_________\|\n5'-AAG...CUUUA_________CGGAG...GGU-3'\n______________GUAUCCUGC\n______________\|\|\|:\|\|\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	184 -- 190	1 -- 7	-13.1594 kcal/mol	3.20778 kcal/mol	2.12872 kcal/mol	181 191@LB@ \| \|@LB@5'-AAG...CUUUA CGGAG...GGU-3'@LB@ GUAUCCUGC@LB@ \|\|\|:\|\|\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -13.1594 kcal/mol@LB@Unfolding Energy - mRNA 3.20778 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 182 -- 190@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 1 -- 7@LB@
105	0.003348	0.1101	b2218	rcsC	-11.03	0.021992	174 -- 214	1 -- 37	hybrid sensory kinase in two-component regulatory system with RcsB and YojN		_____________173_______________________________________215\n_____________\|_________________________________________\|\n5'-AGC...CCAUC____ACCU____C_____U__GCC______AAA________UUCUU...CCG-3'\n______________GGUC____GAGG_GGAGC_UC___CCUUUG___UACCUUGC\n______________\|\|\|\|____:\|\|:_:\|\|:\|_\|\|___\|\|\|:\|\|___\|\|\|\|:\|:\|\n______________CCAG____UUCU_UCUUG_AG___GGAGAC___AUGGGAUG\n3'-AUU...AUUUU____ACU_____A_____U__AAU_________________-5'\n_____________\|________________________________________\|\n_____________38_______________________________________1\n	208 -- 214	1 -- 7	-33.3544 kcal/mol	10.9963 kcal/mol	11.3499 kcal/mol	173 215@LB@ \| \|@LB@5'-AGC...CCAUC ACCU C U GCC AAA UUCUU...CCG-3'@LB@ GGUC GAGG GGAGC UC CCUUUG UACCUUGC@LB@ \|\|\|\| :\|\|: :\|\|:\| \|\| \|\|\|:\|\| \|\|\|\|:\|:\|@LB@ CCAG UUCU UCUUG AG GGAGAC AUGGGAUG@LB@3'-AUU...AUUUU ACU A U AAU -5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -33.3544 kcal/mol@LB@Unfolding Energy - mRNA 10.9963 kcal/mol@LB@Unfolding Energy - sRNA 11.3499 kcal/mol@LB@@LB@Position - mRNA 174 -- 214@LB@Position - sRNA 1 -- 37@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 1 -- 7@LB@
113	0.003703	0.1147	b1728	ydjM	-2.69	0.937889	161 -- 167	1 -- 7	inner membrane protein regulated by LexA		_____________160_____168\n_____________\|_______\|\n5'-CGC...UAAAA_______ACUGU...AUA-3'\n______________AUCCUAU\n______________\|:\|\|\|\|:\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	161 -- 167	1 -- 7	-7.15055 kcal/mol	2.44298 kcal/mol	2.03949 kcal/mol	160 168@LB@ \| \|@LB@5'-CGC...UAAAA ACUGU...AUA-3'@LB@ AUCCUAU@LB@ \|:\|\|\|\|:@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -2.69 kcal/mol@LB@Hybridization Energy -7.15055 kcal/mol@LB@Unfolding Energy - mRNA 2.44298 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 161 -- 167@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 1 -- 7@LB@
114	0.003723	0.1147	b2327	yfcA	-8.38	0.125082	22 -- 29	1 -- 8	TauE/TSUP family inner membrane protein		_____________21_______30\n_____________\|________\|\n5'-CAU...UACGU________CGAUA...GUG-3'\n______________UGCCCUGC\n______________\|:\|\|\|\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	23 -- 29	1 -- 7	-12.241 kcal/mol	1.76759 kcal/mol	2.11603 kcal/mol	21 30@LB@ \| \|@LB@5'-CAU...UACGU CGAUA...GUG-3'@LB@ UGCCCUGC@LB@ \|:\|\|\|\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -12.241 kcal/mol@LB@Unfolding Energy - mRNA 1.76759 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 22 -- 29@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 1 -- 7@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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