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	Additional homologs
74	0.01569	0.6177	b3012	dkgA	-8.72	0.074604	189 -- 197	44 -- 52	2 5-diketo-D-gluconate reductase A		_____________188_______198\n_____________\|_________\|\n5'-CUG...AUAUA_________CGUAU...CCA-3'\n______________AAGGAGGAA\n______________\|\|:\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	191 -- 197	44 -- 50	-11.1725 kcal/mol	1.58724 kcal/mol	0.860683 kcal/mol	188 198@LB@ \| \|@LB@5'-CUG...AUAUA CGUAU...CCA-3'@LB@ AAGGAGGAA@LB@ \|\|:\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.1725 kcal/mol@LB@Unfolding Energy - mRNA 1.58724 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
77	0.01626	0.6177	b1414	ydcF	-7.59	0.125301	189 -- 198	44 -- 53	DUF218 superfamily protein SAM-binding		_____________188________199\n_____________\|__________\|\n5'-GGU...AACGA__________CCAUG...UGC-3'\n______________UAAGGAGGAA\n______________:\|\|:\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	192 -- 198	44 -- 50	-11.4771 kcal/mol	2.95852 kcal/mol	0.927997 kcal/mol	188 199@LB@ \| \|@LB@5'-GGU...AACGA CCAUG...UGC-3'@LB@ UAAGGAGGAA@LB@ :\|\|:\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -7.59 kcal/mol@LB@Hybridization Energy -11.4771 kcal/mol@LB@Unfolding Energy - mRNA 2.95852 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 189 -- 198@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@LB@
80	0.01709	0.6177	b2498	upp	-4.70	0.418803	173 -- 195	44 -- 70	uracil phosphoribosyltransferase		_____________172_________________________196\n_____________\|___________________________\|\n5'-GGC...UUUUU___G___________C_______A___AGAGU...CCG-3'\n______________UGU_GCU____GCCC_UCAAAGG_GAA\n______________\|:\|_\|\|\|____\|\|\|\|_\|\|\|\|\|\|:_\|\|\|\n______________AUA_CGA____CGGG_AGUUUCU_CUU\n3'-UUU...CGGUU___G___UAAC____C_______C___AAAGU...ACA-5'\n_____________\|___________________________\|\n_____________71__________________________43\n	185 -- 191	48 -- 54	-22.3772 kcal/mol	6.37003 kcal/mol	11.3101 kcal/mol	172 196@LB@ \| \|@LB@5'-GGC...UUUUU G C A AGAGU...CCG-3'@LB@ UGU GCU GCCC UCAAAGG GAA@LB@ \|:\| \|\|\| \|\|\|\| \|\|\|\|\|\|: \|\|\|@LB@ AUA CGA CGGG AGUUUCU CUU@LB@3'-UUU...CGGUU G UAAC C C AAAGU...ACA-5'@LB@ \| \|@LB@ 71 43@LB@@LB@@LB@Energy -4.70 kcal/mol@LB@Hybridization Energy -22.3772 kcal/mol@LB@Unfolding Energy - mRNA 6.37003 kcal/mol@LB@Unfolding Energy - sRNA 11.3101 kcal/mol@LB@@LB@Position - mRNA 173 -- 195@LB@Position - sRNA 44 -- 70@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 48 -- 54@LB@
81	0.01751	0.6177	b2741	rpoS	-9.52	0.051528	88 -- 101	44 -- 56	RNA polymerase sigma S (sigma 38) factor		_____________87_____________102\n_____________\|______________\|\n5'-CGG...AAAUU_____C________AUCCG...AGG-3'\n______________CGUUA_AAGGGGAA\n______________\|\|\|:\|_\|\|\|:\|\|\|\|\n______________GCAGU_UUCUCCUU\n3'-UUU...ACCGG______________AAAGU...ACA-5'\n_____________\|______________\|\n_____________57_____________43\n	95 -- 101	44 -- 50	-13.0318 kcal/mol	2.56318 kcal/mol	0.948902 kcal/mol	87 102@LB@ \| \|@LB@5'-CGG...AAAUU C AUCCG...AGG-3'@LB@ CGUUA AAGGGGAA@LB@ \|\|\|:\| \|\|\|:\|\|\|\|@LB@ GCAGU UUCUCCUU@LB@3'-UUU...ACCGG AAAGU...ACA-5'@LB@ \| \|@LB@ 57 43@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -13.0318 kcal/mol@LB@Unfolding Energy - mRNA 2.56318 kcal/mol@LB@Unfolding Energy - sRNA 0.948902 kcal/mol@LB@@LB@Position - mRNA 88 -- 101@LB@Position - sRNA 44 -- 56@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 44 -- 50@LB@
83	0.0176	0.6177	b2457	eutM	-9.48	0.052376	185 -- 194	44 -- 53	ethanolamine utilization protein putative carboxysome structural protein		_____________184________195\n_____________\|__________\|\n5'-UAU...CCUGA__________AGCAC...UUA-3'\n______________UAAAGAGGAA\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	188 -- 194	44 -- 50	-11.8586 kcal/mol	1.44575 kcal/mol	0.927997 kcal/mol	184 195@LB@ \| \|@LB@5'-UAU...CCUGA AGCAC...UUA-3'@LB@ UAAAGAGGAA@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -11.8586 kcal/mol@LB@Unfolding Energy - mRNA 1.44575 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
84	0.01785	0.6177	b4318	fimF	-9.06	0.063721	96 -- 107	44 -- 55	minor component of type 1 fimbriae	b1504 b0943	_____________95___________108\n_____________\|____________\|\n5'-CAU...AAUGG_GA_________AAUGC...UCA-3'\n______________G__GAAGAGGAA\n______________\|__:\|\|\|\|\|\|\|\|\n______________C__UUUCUCCUU\n3'-UUU...CCGGG_AG_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	101 -- 107	44 -- 50	-12.9705 kcal/mol	2.96464 kcal/mol	0.941432 kcal/mol	95 108@LB@ \| \|@LB@5'-CAU...AAUGG GA AAUGC...UCA-3'@LB@ G GAAGAGGAA@LB@ \| :\|\|\|\|\|\|\|\|@LB@ C UUUCUCCUU@LB@3'-UUU...CCGGG AG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -12.9705 kcal/mol@LB@Unfolding Energy - mRNA 2.96464 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 96 -- 107@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 44 -- 50@LB@
97	0.01904	0.6177	b3102	yqjG	-9.04	0.064335	159 -- 168	44 -- 53	putative S-transferase		_____________158________169\n_____________\|__________\|\n5'-GCA...AAAAA__________GCUCC...GGC-3'\n______________CGAGGAGGAA\n______________\|:\|:\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	162 -- 168	44 -- 50	-13.5343 kcal/mol	3.56251 kcal/mol	0.927997 kcal/mol	158 169@LB@ \| \|@LB@5'-GCA...AAAAA GCUCC...GGC-3'@LB@ CGAGGAGGAA@LB@ \|:\|:\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -13.5343 kcal/mol@LB@Unfolding Energy - mRNA 3.56251 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 159 -- 168@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 44 -- 50@LB@
99	0.01953	0.6177	b2473	ypfH	-12.09	0.015349	8 -- 40	44 -- 76	palmitoyl-CoA esterase activity uncertain physiological substrate		_____________7__________________________________41\n_____________\|__________________________________\|\n____5'-ACUUUCA_____CAAGA_____C___________C______GAGGC...GGG-3'\n______________GGCCG_____UGUUA_UGGUCCGUCAG_G_GGAA\n______________\|\|\|\|:_____:\|:\|\|_\|\|\|:\|\|\|\|\|\|:_\|_\|\|\|\|\n______________CCGGU_____GCGAU_ACCGGGCAGUU_C_CCUU\n___3'-UUUUUUUA_____UAUA______A___________U_U____AAAGU...ACA-5'\n_____________\|__________________________________\|\n_____________77_________________________________43\n	28 -- 34	51 -- 57	-34.8713 kcal/mol	9.35151 kcal/mol	13.433 kcal/mol	7 41@LB@ \| \|@LB@ 5'-ACUUUCA CAAGA C C GAGGC...GGG-3'@LB@ GGCCG UGUUA UGGUCCGUCAG G GGAA@LB@ \|\|\|\|: :\|:\|\| \|\|\|:\|\|\|\|\|\|: \| \|\|\|\|@LB@ CCGGU GCGAU ACCGGGCAGUU C CCUU@LB@ 3'-UUUUUUUA UAUA A U U AAAGU...ACA-5'@LB@ \| \|@LB@ 77 43@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -34.8713 kcal/mol@LB@Unfolding Energy - mRNA 9.35151 kcal/mol@LB@Unfolding Energy - sRNA 13.433 kcal/mol@LB@@LB@Position - mRNA 8 -- 40@LB@Position - sRNA 44 -- 76@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 51 -- 57@LB@
101	0.01972	0.6177	b3636	rpmG	-7.41	0.136064	187 -- 193	44 -- 50	50S ribosomal subunit protein L33		_____________186_____194\n_____________\|_______\|\n5'-CAC...UACUU_______AUAAA...AAC-3'\n______________AGAGGAA\n______________\|\|\|\|\|\|\|\n______________UCUCCUU\n3'-UUU...CAGUU_______AAAGU...ACA-5'\n_____________\|_______\|\n_____________51______43\n	187 -- 193	44 -- 50	-8.97978 kcal/mol	0.747566 kcal/mol	0.825028 kcal/mol	186 194@LB@ \| \|@LB@5'-CAC...UACUU AUAAA...AAC-3'@LB@ AGAGGAA@LB@ \|\|\|\|\|\|\|@LB@ UCUCCUU@LB@3'-UUU...CAGUU AAAGU...ACA-5'@LB@ \| \|@LB@ 51 43@LB@@LB@@LB@Energy -7.41 kcal/mol@LB@Hybridization Energy -8.97978 kcal/mol@LB@Unfolding Energy - mRNA 0.747566 kcal/mol@LB@Unfolding Energy - sRNA 0.825028 kcal/mol@LB@@LB@Position - mRNA 187 -- 193@LB@Position - sRNA 44 -- 50@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 44 -- 50@LB@
102	0.02032	0.6177	b1267	yciO	-10.56	0.031637	188 -- 197	44 -- 53	putative RNA binding protein		_____________187________198\n_____________\|__________\|\n5'-GCG...CACCA__________AUUAU...CAA-3'\n______________CAGAGAGGGA\n______________\|\|:\|\|\|\|\|:\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	46 -- 52	-13.8947 kcal/mol	2.40877 kcal/mol	0.927997 kcal/mol	187 198@LB@ \| \|@LB@5'-GCG...CACCA AUUAU...CAA-3'@LB@ CAGAGAGGGA@LB@ \|\|:\|\|\|\|\|:\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -13.8947 kcal/mol@LB@Unfolding Energy - mRNA 2.40877 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 188 -- 197@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 46 -- 52@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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