Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
109	0.007372	0.2348	b3701	dnaN	-13.44	0.063163	149 -- 162	9 -- 22	DNA polymerase III beta subunit		_____________148____________163\n_____________\|______________\|\n5'-GGC...GCCAC______________UUUUU...UGC-3'\n______________GAUAUCAAAGAAGA\n______________\|\|:\|\|\|\|\|\|\|\|\|:\|\n______________CUGUAGUUUCUUUU\n3'-UUU...UACCC______________CGUCACCG-5'\n_____________\|______________\|\n_____________23_____________8\n	156 -- 162	9 -- 15	-16.0152 kcal/mol	2.0875 kcal/mol	0.488786 kcal/mol	148 163@LB@ \| \|@LB@5'-GGC...GCCAC UUUUU...UGC-3'@LB@ GAUAUCAAAGAAGA@LB@ \|\|:\|\|\|\|\|\|\|\|\|:\|@LB@ CUGUAGUUUCUUUU@LB@3'-UUU...UACCC CGUCACCG-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -13.44 kcal/mol@LB@Hybridization Energy -16.0152 kcal/mol@LB@Unfolding Energy - mRNA 2.0875 kcal/mol@LB@Unfolding Energy - sRNA 0.488786 kcal/mol@LB@@LB@Position - mRNA 149 -- 162@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 9 -- 15@LB@
160	0.0118	0.2504	b0078	ilvH	-13.58	0.059018	151 -- 175	1 -- 25	acetolactate synthase 3 small subunit valine-sensitive		_____________150_______________________176\n_____________\|_________________________\|\n5'-GCC...UUCGC_______GAAU___UGAAAU_____UAAGC...UGA-3'\n______________GGGGGCG____GGA______GUGGU\n______________\|\|\|\|:\|:____:\|\|______\|\|\|\|:\n______________CCCCUGU____UCU______CACCG\n3'-UUU...UUUUA_______AGUU___UUUCGU_____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	151 -- 157	19 -- 25	-21.9405 kcal/mol	5.84786 kcal/mol	2.51748 kcal/mol	150 176@LB@ \| \|@LB@5'-GCC...UUCGC GAAU UGAAAU UAAGC...UGA-3'@LB@ GGGGGCG GGA GUGGU@LB@ \|\|\|\|:\|: :\|\| \|\|\|\|:@LB@ CCCCUGU UCU CACCG@LB@3'-UUU...UUUUA AGUU UUUCGU -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -21.9405 kcal/mol@LB@Unfolding Energy - mRNA 5.84786 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 151 -- 175@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 19 -- 25@LB@
112	0.007494	0.2348	b2529	iscU	-11.51	0.152972	152 -- 183	2 -- 33	iron-sulfur cluster assembly scaffold protein		_____________151______________________________184\n_____________\|________________________________\|\n5'-UGG...AACAG___C_______CU_____UUAAUC____UC__AAUCA...GGG-3'\n______________CAU_GAAUGGG__CAUCA______GGUA__GG\n______________\|\|:_:\|\|\|\|\|\|__\|\|\|\|\|______:\|:\|__\|\|\n______________GUG_UUUACCC__GUAGU______UCGU__CC\n3'-UUU...CCGAG___U_______CU_____UUCUUU____CA__G-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	156 -- 162	23 -- 29	-21.7 kcal/mol	7.11537 kcal/mol	3.07861 kcal/mol	151 184@LB@ \| \|@LB@5'-UGG...AACAG C CU UUAAUC UC AAUCA...GGG-3'@LB@ CAU GAAUGGG CAUCA GGUA GG@LB@ \|\|: :\|\|\|\|\|\| \|\|\|\|\| :\|:\| \|\|@LB@ GUG UUUACCC GUAGU UCGU CC@LB@3'-UUU...CCGAG U CU UUCUUU CA G-5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -21.7 kcal/mol@LB@Unfolding Energy - mRNA 7.11537 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 152 -- 183@LB@Position - sRNA 2 -- 33@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 23 -- 29@LB@
153	0.01124	0.2504	b0414	ribD	-14.78	0.031370	153 -- 170	1 -- 22	fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5-amino-6-(5-phosphoribosylamino) uracil reductase		_____________152____________________171\n_____________\|______________________\|\n5'-AAA...UCGAA____________UU________GAAGA...AAG-3'\n______________GAUAUCAAAGAA______UGGC\n______________\|\|:\|\|\|\|\|\|\|\|\|______\|\|\|\|\n______________CUGUAGUUUCUU______ACCG\n3'-UUU...UACCC____________UUCGUC____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	158 -- 164	11 -- 17	-19.3666 kcal/mol	3.04735 kcal/mol	1.54023 kcal/mol	152 171@LB@ \| \|@LB@5'-AAA...UCGAA UU GAAGA...AAG-3'@LB@ GAUAUCAAAGAA UGGC@LB@ \|\|:\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUGUAGUUUCUU ACCG@LB@3'-UUU...UACCC UUCGUC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -19.3666 kcal/mol@LB@Unfolding Energy - mRNA 3.04735 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 153 -- 170@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 11 -- 17@LB@
199	0.01447	0.2552	b2790	yqcA	-9.70	0.305430	160 -- 205	1 -- 31	short-chain flavodoxin FMN-binding		_____________159_____________________________________________206\n_____________\|_______________________________________________\|\n5'-CUA...CGGGU________A__G__AAGUUCCUAAUC________AAAC_________GGAAA...CAA-3'\n______________CAGGAUGG_GA_AU____________CAGGGAGA____GGUA_UGGC\n______________\|\|::\|\|\|\|_\|\|_\|\|____________\|\|::\|\|:\|____:\|:\|_\|\|\|\|\n______________GUUUUACC_CU_UA____________GUUUCUUU____UCGU_ACCG\n3'-UUU...GAGGU________C__G______________________________C____-5'\n_____________\|______________________________________________\|\n_____________32_____________________________________________1\n	187 -- 193	10 -- 16	-23.6635 kcal/mol	11.4257 kcal/mol	2.53929 kcal/mol	159 206@LB@ \| \|@LB@5'-CUA...CGGGU A G AAGUUCCUAAUC AAAC GGAAA...CAA-3'@LB@ CAGGAUGG GA AU CAGGGAGA GGUA UGGC@LB@ \|\|::\|\|\|\| \|\| \|\| \|\|::\|\|:\| :\|:\| \|\|\|\|@LB@ GUUUUACC CU UA GUUUCUUU UCGU ACCG@LB@3'-UUU...GAGGU C G C -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -23.6635 kcal/mol@LB@Unfolding Energy - mRNA 11.4257 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 160 -- 205@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 10 -- 16@LB@
41	0.002071	0.1648	b0992	yccM	-9.88	0.287125	161 -- 167	1 -- 7	putative 4Fe-4S membrane protein		_____________160_____168\n_____________\|_______\|\n5'-AUC...UAGAA_______AUUUG...AAG-3'\n______________UAGUGGC\n______________:\|\|\|\|\|\|\n______________GUCACCG\n3'-UUU...UUUUC_______-5'\n_____________\|______\|\n_____________8______1\n	161 -- 167	1 -- 7	-11.7646 kcal/mol	0.660682 kcal/mol	1.22779 kcal/mol	160 168@LB@ \| \|@LB@5'-AUC...UAGAA AUUUG...AAG-3'@LB@ UAGUGGC@LB@ :\|\|\|\|\|\|@LB@ GUCACCG@LB@3'-UUU...UUUUC -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -11.7646 kcal/mol@LB@Unfolding Energy - mRNA 0.660682 kcal/mol@LB@Unfolding Energy - sRNA 1.22779 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@
115	0.007886	0.2401	b2890	lysS	-11.64	0.144658	161 -- 186	1 -- 20	lysine tRNA synthetase constitutive	b4129	_____________160_________________________187\n_____________\|___________________________\|\n5'-AAA...CAAUU________CAAGUUU____________UAUGA...GGA-3'\n______________UAUCGAAG_______GAAAGCAG_GGU\n______________:\|\|\|:\|\|\|_______:\|\|\|\|\|\|\|_\|\|:\n______________GUAGUUUC_______UUUUCGUC_CCG\n3'-UUU...CCCCU_______________________A___-5'\n_____________\|__________________________\|\n_____________21_________________________1\n	177 -- 183	5 -- 11	-18.6981 kcal/mol	5.60124 kcal/mol	1.45855 kcal/mol	160 187@LB@ \| \|@LB@5'-AAA...CAAUU CAAGUUU UAUGA...GGA-3'@LB@ UAUCGAAG GAAAGCAG GGU@LB@ :\|\|\|:\|\|\| :\|\|\|\|\|\|\| \|\|:@LB@ GUAGUUUC UUUUCGUC CCG@LB@3'-UUU...CCCCU A -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -18.6981 kcal/mol@LB@Unfolding Energy - mRNA 5.60124 kcal/mol@LB@Unfolding Energy - sRNA 1.45855 kcal/mol@LB@@LB@Position - mRNA 161 -- 186@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 5 -- 11@LB@
174	0.0127	0.2504	b1960	vsr	-15.05	0.027057	161 -- 177	1 -- 19	DNA mismatch endonuclease of very short patch repair		_____________160_________________178\n_____________\|___________________\|\n5'-UCG...CAAAA______C____________GUUGC...CCG-3'\n______________AUCAAA___AGGCGGUGGC\n______________\|\|\|\|\|\|___\|:\|\|:\|\|\|\|\|\n______________UAGUUU___UUCGUCACCG\n3'-UUU...CCCUG______CUU__________-5'\n_____________\|__________________\|\n_____________20_________________1\n	171 -- 177	1 -- 7	-22.0844 kcal/mol	5.58177 kcal/mol	1.45734 kcal/mol	160 178@LB@ \| \|@LB@5'-UCG...CAAAA C GUUGC...CCG-3'@LB@ AUCAAA AGGCGGUGGC@LB@ \|\|\|\|\|\| \|:\|\|:\|\|\|\|\|@LB@ UAGUUU UUCGUCACCG@LB@3'-UUU...CCCUG CUU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -22.0844 kcal/mol@LB@Unfolding Energy - mRNA 5.58177 kcal/mol@LB@Unfolding Energy - sRNA 1.45734 kcal/mol@LB@@LB@Position - mRNA 161 -- 177@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 1 -- 7@LB@
69	0.003755	0.191	b0889	lrp	-14.02	0.046951	165 -- 212	1 -- 32	leucine-responsive global transcriptional regulator		_____________164______________________________________________213\n_____________\|________________________________________________\|\n5'-GUG...GUCAG______GUA____AGGAAUA________CAAUAAUAAU_____AUA__AAGAA...AGC-3'\n______________ACAGGA___GGGA_______CAGAGAGA__________GGUAG___GC\n______________\|\|\|::\|___\|\|\|\|_______\|\|:\|\|\|:\|__________:\|:\|\|___\|\|\n______________UGUUUU___CCCU_______GUUUCUUU__________UCGUC___CG\n3'-UUU...CGAGG______AC_____GUA___________________________AC___-5'\n_____________\|_______________________________________________\|\n_____________33______________________________________________1\n	186 -- 192	10 -- 16	-19.2298 kcal/mol	2.66644 kcal/mol	2.53929 kcal/mol	164 213@LB@ \| \|@LB@5'-GUG...GUCAG GUA AGGAAUA CAAUAAUAAU AUA AAGAA...AGC-3'@LB@ ACAGGA GGGA CAGAGAGA GGUAG GC@LB@ \|\|\|::\| \|\|\|\| \|\|:\|\|\|:\| :\|:\|\| \|\|@LB@ UGUUUU CCCU GUUUCUUU UCGUC CG@LB@3'-UUU...CGAGG AC GUA AC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -14.02 kcal/mol@LB@Hybridization Energy -19.2298 kcal/mol@LB@Unfolding Energy - mRNA 2.66644 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 165 -- 212@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 10 -- 16@LB@
149	0.01096	0.2504	b3230	rpsI	-12.23	0.111717	165 -- 205	1 -- 34	30S ribosomal subunit protein S9		_____________164_______________________________________206\n_____________\|_________________________________________\|\n5'-GUG...AGCAA_______UUCUU______UAAUC____UUAU_____A____UGAAA...GUU-3'\n______________CCGCAAG_____GACAUC_____GGGA____AGGCA_UGGC\n______________\|\|:\|\|\|:_____\|\|\|\|\|\|_____:\|:\|____\|:\|\|\|_\|\|\|\|\n______________GGUGUUU_____CUGUAG_____UCUU____UUCGU_ACCG\n3'-UUU...CCCGA_______UACCC______UU________________C____-5'\n_____________\|________________________________________\|\n_____________35_______________________________________1\n	165 -- 171	28 -- 34	-26.3465 kcal/mol	9.84752 kcal/mol	4.26884 kcal/mol	164 206@LB@ \| \|@LB@5'-GUG...AGCAA UUCUU UAAUC UUAU A UGAAA...GUU-3'@LB@ CCGCAAG GACAUC GGGA AGGCA UGGC@LB@ \|\|:\|\|\|: \|\|\|\|\|\| :\|:\| \|:\|\|\| \|\|\|\|@LB@ GGUGUUU CUGUAG UCUU UUCGU ACCG@LB@3'-UUU...CCCGA UACCC UU C -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -26.3465 kcal/mol@LB@Unfolding Energy - mRNA 9.84752 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 165 -- 205@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 28 -- 34@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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