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
101	0.006298	0.2188	b3549	tag	-14.94	0.028658	147 -- 165	3 -- 21	3-methyl-adenine DNA glycosylase I constitutive		_____________146__________________166\n_____________\|____________________\|\n5'-GCA...CCGAU_________________C__AAAUU...AAA-3'\n______________GCGUC_AAGAAAAGCGG_UG\n______________:\|:\|\|_\|\|\|\|\|\|\|\|\|:\|_\|\|\n______________UGUAG_UUCUUUUCGUC_AC\n3'-UUU...ACCCC_____U______________CG-5'\n_____________\|____________________\|\n_____________22___________________2\n	156 -- 162	5 -- 11	-20.7072 kcal/mol	4.25403 kcal/mol	1.5107 kcal/mol	146 166@LB@ \| \|@LB@5'-GCA...CCGAU C AAAUU...AAA-3'@LB@ GCGUC AAGAAAAGCGG UG@LB@ :\|:\|\| \|\|\|\|\|\|\|\|\|:\| \|\|@LB@ UGUAG UUCUUUUCGUC AC@LB@3'-UUU...ACCCC U CG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -14.94 kcal/mol@LB@Hybridization Energy -20.7072 kcal/mol@LB@Unfolding Energy - mRNA 4.25403 kcal/mol@LB@Unfolding Energy - sRNA 1.5107 kcal/mol@LB@@LB@Position - mRNA 147 -- 165@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 5 -- 11@LB@
102	0.006464	0.2224	b3785	wzzE	-10.51	0.228012	146 -- 168	1 -- 22	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein		_____________145_____________________169\n_____________\|_______________________\|\n5'-GCU...ACGCA___UG__U_____UC________AGCCC...UUA-3'\n______________GAC__CG_AGAAA__GUGGUGGC\n______________\|\|\|__\|:_\|\|\|\|\|__\|::\|\|\|\|\|\n______________CUG__GU_UCUUU__CGUCACCG\n3'-UUU...UACCC___UA__U_____U_________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	162 -- 168	1 -- 7	-19.8866 kcal/mol	7.83936 kcal/mol	1.54023 kcal/mol	145 169@LB@ \| \|@LB@5'-GCU...ACGCA UG U UC AGCCC...UUA-3'@LB@ GAC CG AGAAA GUGGUGGC@LB@ \|\|\| \|: \|\|\|\|\| \|::\|\|\|\|\|@LB@ CUG GU UCUUU CGUCACCG@LB@3'-UUU...UACCC UA U U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -19.8866 kcal/mol@LB@Unfolding Energy - mRNA 7.83936 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 146 -- 168@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 1 -- 7@LB@
103	0.006657	0.2268	b3617	kbl	-13.19	0.071337	258 -- 276	7 -- 25	glycine C-acetyltransferase		_____________257_________________277\n_____________\|___________________\|\n5'-UUU...CGGAA___UUGU____________GCAUU...AAG-3'\n______________GGG____UUAAAGAAGAGC\n______________\|\|\|____\|:\|\|\|\|\|\|:\|\|\|\n______________CCC____AGUUUCUUUUCG\n3'-UUU...UUUUA___CUGU____________UCACCG-5'\n_____________\|___________________\|\n_____________26__________________6\n	270 -- 276	7 -- 13	-19.594 kcal/mol	5.69693 kcal/mol	0.70626 kcal/mol	257 277@LB@ \| \|@LB@5'-UUU...CGGAA UUGU GCAUU...AAG-3'@LB@ GGG UUAAAGAAGAGC@LB@ \|\|\| \|:\|\|\|\|\|\|:\|\|\|@LB@ CCC AGUUUCUUUUCG@LB@3'-UUU...UUUUA CUGU UCACCG-5'@LB@ \| \|@LB@ 26 6@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -19.594 kcal/mol@LB@Unfolding Energy - mRNA 5.69693 kcal/mol@LB@Unfolding Energy - sRNA 0.70626 kcal/mol@LB@@LB@Position - mRNA 258 -- 276@LB@Position - sRNA 7 -- 25@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 7 -- 13@LB@
104	0.006761	0.2281	b1671	ydhX	-13.25	0.069212	145 -- 167	2 -- 25	putative 4Fe-4S ferridoxin-type protein; FNR Nar NarP-regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex	b4072	_____________144_______________________168\n_____________\|_________________________\|\n5'-CAC...UUUCA___A_______U___U_________ACAGU...AGG-3'\n______________GGG_GAUGUCA_GGA__AG_GGUGG\n______________\|\|\|_\|\|::\|\|\|_:\|\|__\|\|_:\|\|\|\|\n______________CCC_CUGUAGU_UCU__UC_UCACC\n3'-UUU...UUUUA___________U___UU__G_____G-5'\n_____________\|_________________________\|\n_____________26________________________1\n	149 -- 155	16 -- 22	-23.0825 kcal/mol	7.31216 kcal/mol	2.51746 kcal/mol	144 168@LB@ \| \|@LB@5'-CAC...UUUCA A U U ACAGU...AGG-3'@LB@ GGG GAUGUCA GGA AG GGUGG@LB@ \|\|\| \|\|::\|\|\| :\|\| \|\| :\|\|\|\|@LB@ CCC CUGUAGU UCU UC UCACC@LB@3'-UUU...UUUUA U UU G G-5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -13.25 kcal/mol@LB@Hybridization Energy -23.0825 kcal/mol@LB@Unfolding Energy - mRNA 7.31216 kcal/mol@LB@Unfolding Energy - sRNA 2.51746 kcal/mol@LB@@LB@Position - mRNA 145 -- 167@LB@Position - sRNA 2 -- 25@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 16 -- 22@LB@
105	0.007004	0.2333	b4034	malE	-12.62	0.093531	92 -- 123	2 -- 32	maltose transporter subunit		_____________91_________________________________124\n_____________\|__________________________________\|\n5'-AGG...ACAAA____C_________________C___G__GA___AAAGA...UGG-3'\n______________GCGA_GGUGGGG_CGU_AGGGG_AAG_AG__UGG\n______________:\|:\|_::\|\|\|\|\|_\|:\|_\|::\|:_\|\|\|_\|\|__\|\|\|\n______________UGUU_UUACCCC_GUA_UUUCU_UUC_UC__ACC\n3'-UUU...CGAGG____________U___G_____U___G_______G-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	97 -- 103	22 -- 28	-24.1065 kcal/mol	8.94734 kcal/mol	2.53929 kcal/mol	91 124@LB@ \| \|@LB@5'-AGG...ACAAA C C G GA AAAGA...UGG-3'@LB@ GCGA GGUGGGG CGU AGGGG AAG AG UGG@LB@ :\|:\| ::\|\|\|\|\| \|:\| \|::\|: \|\|\| \|\| \|\|\|@LB@ UGUU UUACCCC GUA UUUCU UUC UC ACC@LB@3'-UUU...CGAGG U G U G G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -24.1065 kcal/mol@LB@Unfolding Energy - mRNA 8.94734 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 92 -- 123@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 22 -- 28@LB@
106	0.007048	0.2333	b4512	ybdD	-9.12	0.369799	33 -- 54	1 -- 25	DUF466 family protein	b4353	_____________32________________________55\n_____________\|_________________________\|\n5'-GCA...GAGGG___________C___U_________UUAGU...GGG-3'\n______________GGGGAUGUUGG_GAA__GU__UGGC\n______________\|\|\|\|\|::\|:::_\|\|\|__\|:__\|\|\|\|\n______________CCCCUGUAGUU_CUU__CG__ACCG\n3'-UUU...UUUUA___________U___UU__UC____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	36 -- 42	16 -- 22	-21.5624 kcal/mol	9.92515 kcal/mol	2.51748 kcal/mol	32 55@LB@ \| \|@LB@5'-GCA...GAGGG C U UUAGU...GGG-3'@LB@ GGGGAUGUUGG GAA GU UGGC@LB@ \|\|\|\|\|::\|::: \|\|\| \|: \|\|\|\|@LB@ CCCCUGUAGUU CUU CG ACCG@LB@3'-UUU...UUUUA U UU UC -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -9.12 kcal/mol@LB@Hybridization Energy -21.5624 kcal/mol@LB@Unfolding Energy - mRNA 9.92515 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 33 -- 54@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 16 -- 22@LB@
107	0.007146	0.2343	b0085	murE	-14.50	0.036427	193 -- 205	1 -- 25	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso- diaminopimelate ligase		_____________192_______________________206\n_____________\|_________________________\|\n5'-UGC...GGCGA_________________________AGAUC...CGG-3'\n______________GGGGACA____________GGUGGC\n______________\|\|\|\|\|\|\|____________:\|\|\|\|\|\n______________CCCCUGU____________UCACCG\n3'-UUU...UUUUA_______AGUUUCUUUUCG______-5'\n_____________\|________________________\|\n_____________26_______________________1\n	193 -- 199	19 -- 25	-21.3886 kcal/mol	4.36682 kcal/mol	2.51748 kcal/mol	192 206@LB@ \| \|@LB@5'-UGC...GGCGA AGAUC...CGG-3'@LB@ GGGGACA GGUGGC@LB@ \|\|\|\|\|\|\| :\|\|\|\|\|@LB@ CCCCUGU UCACCG@LB@3'-UUU...UUUUA AGUUUCUUUUCG -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -14.50 kcal/mol@LB@Hybridization Energy -21.3886 kcal/mol@LB@Unfolding Energy - mRNA 4.36682 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 19 -- 25@LB@
108	0.007234	0.2348	b1725	yniA	-14.77	0.031588	182 -- 211	1 -- 32	fructosamine kinase family protein		_____________181_________________________________212\n_____________\|___________________________________\|\n5'-GAG...GGCAG____C_____AGA_______UGU____________AAUCA...GGC-3'\n______________ACAA_AUGGG___GACAUCA______GGCA__GGC\n______________\|\|\|\|_\|\|\|\|\|___\|\|\|\|\|\|\|______:\|\|\|__\|\|\|\n______________UGUU_UACCC___CUGUAGU______UCGU__CCG\n3'-UUU...CGAGG____U_______________UUCUUU____CA___-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	195 -- 201	16 -- 22	-26.2676 kcal/mol	8.96188 kcal/mol	2.53929 kcal/mol	181 212@LB@ \| \|@LB@5'-GAG...GGCAG C AGA UGU AAUCA...GGC-3'@LB@ ACAA AUGGG GACAUCA GGCA GGC@LB@ \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| :\|\|\| \|\|\|@LB@ UGUU UACCC CUGUAGU UCGU CCG@LB@3'-UUU...CGAGG U UUCUUU CA -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -14.77 kcal/mol@LB@Hybridization Energy -26.2676 kcal/mol@LB@Unfolding Energy - mRNA 8.96188 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 182 -- 211@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 16 -- 22@LB@
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@
110	0.007401	0.2348	b0784	moaD	-14.78	0.031320	178 -- 203	3 -- 25	molybdopterin synthase small subunit		_____________177________________________204\n_____________\|__________________________\|\n5'-GCA...AAGUC___U___U______U________A__AUUAA...AGC-3'\n______________GGG_GAC_UUAAGG_GGAAGCGG_UG\n______________\|\|\|_\|\|\|_\|:\|\|:\|_::\|\|\|\|:\|_\|\|\n______________CCC_CUG_AGUUUC_UUUUCGUC_AC\n3'-UUU...UUUUA_______U__________________CG-5'\n_____________\|__________________________\|\n_____________26_________________________2\n	194 -- 200	5 -- 11	-23.9822 kcal/mol	6.68375 kcal/mol	2.5166 kcal/mol	177 204@LB@ \| \|@LB@5'-GCA...AAGUC U U U A AUUAA...AGC-3'@LB@ GGG GAC UUAAGG GGAAGCGG UG@LB@ \|\|\| \|\|\| \|:\|\|:\| ::\|\|\|\|:\| \|\|@LB@ CCC CUG AGUUUC UUUUCGUC AC@LB@3'-UUU...UUUUA U CG-5'@LB@ \| \|@LB@ 26 2@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -23.9822 kcal/mol@LB@Unfolding Energy - mRNA 6.68375 kcal/mol@LB@Unfolding Energy - sRNA 2.5166 kcal/mol@LB@@LB@Position - mRNA 178 -- 203@LB@Position - sRNA 3 -- 25@LB@Position Seed - mRNA 194 -- 200@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)

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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