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
66	0.003537	0.1858	b0411	tsx	-15.28	0.023631	170 -- 194	1 -- 34	nucleoside channel receptor of phage T6 and colicin K		_____________169_________________________________195\n_____________\|___________________________________\|\n5'-AGG...CACUC_______________UU__________________AUACA...ACU-3'\n______________CCGCAA____GGGAU__UCAAA______CAGUGGC\n______________\|\|:\|\|\|____\|\|\|\|:__\|\|\|\|\|______\|\|\|\|\|\|\|\n______________GGUGUU____CCCUG__AGUUU______GUCACCG\n3'-UUU...CCCGA______UUAC_____U______CUUUUC_______-5'\n_____________\|__________________________________\|\n_____________35_________________________________1\n	188 -- 194	1 -- 7	-27.9509 kcal/mol	8.39787 kcal/mol	4.26884 kcal/mol	169 195@LB@ \| \|@LB@5'-AGG...CACUC UU AUACA...ACU-3'@LB@ CCGCAA GGGAU UCAAA CAGUGGC@LB@ \|\|:\|\|\| \|\|\|\|: \|\|\|\|\| \|\|\|\|\|\|\|@LB@ GGUGUU CCCUG AGUUU GUCACCG@LB@3'-UUU...CCCGA UUAC U CUUUUC -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -15.28 kcal/mol@LB@Hybridization Energy -27.9509 kcal/mol@LB@Unfolding Energy - mRNA 8.39787 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 170 -- 194@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 1 -- 7@LB@
187	0.01374	0.2529	b1344	ttcA	-15.51	0.020761	46 -- 73	1 -- 29	tRNA s(2)C32 thioltransferase iron sulfur cluster protein		_____________45_____________________________74\n_____________\|______________________________\|\n5'-GCU...CAGCC____________G___CUGC_____A____GUAUG...UCA-3'\n______________AAAUGGGG_CAU_AAA_____GCAG_UGGU\n______________\|\|\|\|\|\|\|\|_\|\|\|_\|\|\|_____\|\|\|\|_\|\|\|:\n______________UUUACCCC_GUA_UUU_____CGUC_ACCG\n3'-UUU...GGUGU________U___G___CUUUU_________-5'\n_____________\|_____________________________\|\n_____________30____________________________1\n	47 -- 53	22 -- 28	-26.0543 kcal/mol	8.02666 kcal/mol	2.51907 kcal/mol	45 74@LB@ \| \|@LB@5'-GCU...CAGCC G CUGC A GUAUG...UCA-3'@LB@ AAAUGGGG CAU AAA GCAG UGGU@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|\|\|:@LB@ UUUACCCC GUA UUU CGUC ACCG@LB@3'-UUU...GGUGU U G CUUUU -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.51 kcal/mol@LB@Hybridization Energy -26.0543 kcal/mol@LB@Unfolding Energy - mRNA 8.02666 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 46 -- 73@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 22 -- 28@LB@
176	0.01279	0.2504	b3980	tufB	-13.59	0.058494	200 -- 216	7 -- 22	translation elongation factor EF-Tu 2	b3339	_____________199_______________217\n_____________\|_________________\|\n5'-UCC...CAAUC______U__________UUGAA...CUA-3'\n______________GAUGUC_AAAGAAAAGU\n______________\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________CUGUAG_UUUCUUUUCG\n3'-UUU...UACCC_________________UCACCG-5'\n_____________\|_________________\|\n_____________23________________6\n	210 -- 216	7 -- 13	-16.0105 kcal/mol	1.82662 kcal/mol	0.590875 kcal/mol	199 217@LB@ \| \|@LB@5'-UCC...CAAUC U UUGAA...CUA-3'@LB@ GAUGUC AAAGAAAAGU@LB@ \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ CUGUAG UUUCUUUUCG@LB@3'-UUU...UACCC UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -13.59 kcal/mol@LB@Hybridization Energy -16.0105 kcal/mol@LB@Unfolding Energy - mRNA 1.82662 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 200 -- 216@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 7 -- 13@LB@
157	0.0114	0.2504	b3833	ubiE	-14.57	0.035245	198 -- 236	1 -- 30	bifunctional 2-octaprenyl-6-methoxy-1 4-benzoquinone methylase/ S-adenosylmethionine:2-DMK methyltransferase		_____________197_____________________________________237\n_____________\|_______________________________________\|\n5'-ACA...GCAUU_______U____AA____C______CGAC___CUU____UUUCA...CAU-3'\n______________GAGAUGG_GGAU__GUCA_AAGAAA____GCA___UGGU\n______________:\|:\|\|\|\|_\|\|\|:__:\|\|\|_\|\|\|\|\|\|____\|\|\|___\|\|\|:\n______________UUUUACC_CCUG__UAGU_UUCUUU____CGU___ACCG\n3'-UUU...AGGUG_________________________U______C______-5'\n_____________\|______________________________________\|\n_____________31_____________________________________1\n	198 -- 204	24 -- 30	-23.6374 kcal/mol	6.55293 kcal/mol	2.51911 kcal/mol	197 237@LB@ \| \|@LB@5'-ACA...GCAUU U AA C CGAC CUU UUUCA...CAU-3'@LB@ GAGAUGG GGAU GUCA AAGAAA GCA UGGU@LB@ :\|:\|\|\|\| \|\|\|: :\|\|\| \|\|\|\|\|\| \|\|\| \|\|\|:@LB@ UUUUACC CCUG UAGU UUCUUU CGU ACCG@LB@3'-UUU...AGGUG U C -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -23.6374 kcal/mol@LB@Unfolding Energy - mRNA 6.55293 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 198 -- 236@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 24 -- 30@LB@
95	0.005813	0.2147	b3450	ugpC	-12.76	0.087557	84 -- 111	1 -- 34	sn-glycerol-3-phosphate ABC transporter ATPase		_____________83_________________________________112\n_____________\|__________________________________\|\n5'-GUG...AGGCA___________A________U_____________GAUGU...UCG-3'\n______________CCACGGAAUGG__AC_UCAG_GA____UGGUGGC\n______________\|\|\|\|::\|\|\|\|\|__\|\|_\|\|\|:_\|\|____::\|\|\|\|\|\n______________GGUGUUUUACC__UG_AGUU_CU____GUCACCG\n3'-UUU...CCCGA___________CC__U____U__UUUC_______-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	105 -- 111	1 -- 7	-27.9886 kcal/mol	10.9582 kcal/mol	4.26884 kcal/mol	83 112@LB@ \| \|@LB@5'-GUG...AGGCA A U GAUGU...UCG-3'@LB@ CCACGGAAUGG AC UCAG GA UGGUGGC@LB@ \|\|\|\|::\|\|\|\|\| \|\| \|\|\|: \|\| ::\|\|\|\|\|@LB@ GGUGUUUUACC UG AGUU CU GUCACCG@LB@3'-UUU...CCCGA CC U U UUUC -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -12.76 kcal/mol@LB@Hybridization Energy -27.9886 kcal/mol@LB@Unfolding Energy - mRNA 10.9582 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 84 -- 111@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 1 -- 7@LB@
188	0.01388	0.2529	b4198	ulaF	-10.93	0.193396	24 -- 37	2 -- 17	L-ribulose 5-phosphate 4-epimerase		_____________23_______________38\n_____________\|________________\|\n5'-GUC...UUUGG______U_________AUUUC...GCG-3'\n______________CGAAGG___GUAGUGG\n______________\|:\|\|\|:___\|:\|\|\|\|\|\n______________GUUUCU___CGUCACC\n3'-UUU...CUGUA______UUU_______G-5'\n_____________\|________________\|\n_____________18_______________1\n	31 -- 37	2 -- 8	-15.3961 kcal/mol	3.02615 kcal/mol	1.43836 kcal/mol	23 38@LB@ \| \|@LB@5'-GUC...UUUGG U AUUUC...GCG-3'@LB@ CGAAGG GUAGUGG@LB@ \|:\|\|\|: \|:\|\|\|\|\|@LB@ GUUUCU CGUCACC@LB@3'-UUU...CUGUA UUU G-5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -10.93 kcal/mol@LB@Hybridization Energy -15.3961 kcal/mol@LB@Unfolding Energy - mRNA 3.02615 kcal/mol@LB@Unfolding Energy - sRNA 1.43836 kcal/mol@LB@@LB@Position - mRNA 24 -- 37@LB@Position - sRNA 2 -- 17@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 2 -- 8@LB@
170	0.01232	0.2504	b2580	ung	-11.45	0.156876	183 -- 205	1 -- 22	uracil-DNA-glycosylase		_____________182______________________206\n_____________\|________________________\|\n5'-UCU...UUGAA_______C________G__A____UAACG...CCG-3'\n______________GAU_UCG_AGGAGAGC_AG_UGGC\n______________\|\|:_\|\|:_\|\|:\|:\|\|\|_\|\|_\|\|\|\|\n______________CUG_AGU_UCUUUUCG_UC_ACCG\n3'-UUU...UACCC___U___U________________-5'\n_____________\|_______________________\|\n_____________23______________________1\n	191 -- 197	7 -- 13	-20.4372 kcal/mol	7.45123 kcal/mol	1.54023 kcal/mol	182 206@LB@ \| \|@LB@5'-UCU...UUGAA C G A UAACG...CCG-3'@LB@ GAU UCG AGGAGAGC AG UGGC@LB@ \|\|: \|\|: \|\|:\|:\|\|\| \|\| \|\|\|\|@LB@ CUG AGU UCUUUUCG UC ACCG@LB@3'-UUU...UACCC U U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -20.4372 kcal/mol@LB@Unfolding Energy - mRNA 7.45123 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 183 -- 205@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 7 -- 13@LB@
178	0.01293	0.2504	b4258	valS	-13.78	0.053235	248 -- 266	1 -- 21	valyl-tRNA synthetase		_____________247___________________267\n_____________\|_____________________\|\n5'-AUC...UACGA_____U_______________UACUU...AAA-3'\n______________GCA_C_GGGAAAAGCAG_GGC\n______________:\|\|_\|_::\|\|\|\|\|\|\|\|\|_\|\|\|\n______________UGU_G_UUCUUUUCGUC_CCG\n3'-UUU...ACCCC___A_U___________A___-5'\n_____________\|____________________\|\n_____________22___________________1\n	257 -- 263	5 -- 11	-22.196 kcal/mol	6.90555 kcal/mol	1.51103 kcal/mol	247 267@LB@ \| \|@LB@5'-AUC...UACGA U UACUU...AAA-3'@LB@ GCA C GGGAAAAGCAG GGC@LB@ :\|\| \| ::\|\|\|\|\|\|\|\|\| \|\|\|@LB@ UGU G UUCUUUUCGUC CCG@LB@3'-UUU...ACCCC A U A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.78 kcal/mol@LB@Hybridization Energy -22.196 kcal/mol@LB@Unfolding Energy - mRNA 6.90555 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 248 -- 266@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 5 -- 11@LB@
14	0.0006392	0.1243	b3745	viaA	-13.90	0.050132	246 -- 264	10 -- 25	stimulator of RavA ATPase activity; von Willebrand factor domain protein		_____________245_________________265\n_____________\|___________________\|\n5'-ACG...GCGAA_A_____UG__________UGAUC...CGG-3'\n______________G_GGGAU__AUCGAAGAGA\n______________\|_\|\|\|\|:__\|\|\|:\|\|\|\|:\|\n______________C_CCCUG__UAGUUUCUUU\n3'-UUU...UUUUA___________________UCGUC...CCG-5'\n_____________\|___________________\|\n_____________26__________________9\n	258 -- 264	10 -- 16	-16.9183 kcal/mol	2.35086 kcal/mol	0.670388 kcal/mol	245 265@LB@ \| \|@LB@5'-ACG...GCGAA A UG UGAUC...CGG-3'@LB@ G GGGAU AUCGAAGAGA@LB@ \| \|\|\|\|: \|\|\|:\|\|\|\|:\|@LB@ C CCCUG UAGUUUCUUU@LB@3'-UUU...UUUUA UCGUC...CCG-5'@LB@ \| \|@LB@ 26 9@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -16.9183 kcal/mol@LB@Unfolding Energy - mRNA 2.35086 kcal/mol@LB@Unfolding Energy - sRNA 0.670388 kcal/mol@LB@@LB@Position - mRNA 246 -- 264@LB@Position - sRNA 10 -- 25@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 10 -- 16@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@

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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