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
2	5.107e-11	8.961e-08	b2314	dedD	-25.37	0.000001	176 -- 205	1 -- 30	membrane-anchored periplasmic protein involved in septation	_____________175_____________________________206\n_____________\|_______________________________\|\n5'-UUG...UCAUG______AUU______________________AAGUA...AUU-3'\n______________GAAGUG___GACG_CGAGGAGAAGCGGUGGC\n______________:\|\|:\|\|___\|\|\|:_\|:\|:\|\|:\|\|\|\|:\|\|\|\|\|\n______________UUUUAC___CUGU_GUUUCUUUUCGUCACCG\n3'-UUU...AGGUG______CC_____A_________________-5'\n_____________\|______________________________\|\n_____________31_____________________________1\n	199 -- 205	1 -- 7	-36.5756 kcal/mol	8.68219 kcal/mol	2.51911 kcal/mol	175 206@LB@ \| \|@LB@5'-UUG...UCAUG AUU AAGUA...AUU-3'@LB@ GAAGUG GACG CGAGGAGAAGCGGUGGC@LB@ :\|\|:\|\| \|\|\|: \|:\|:\|\|:\|\|\|\|:\|\|\|\|\|@LB@ UUUUAC CUGU GUUUCUUUUCGUCACCG@LB@3'-UUU...AGGUG CC A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -25.37 kcal/mol@LB@Hybridization Energy -36.5756 kcal/mol@LB@Unfolding Energy - mRNA 8.68219 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 176 -- 205@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 1 -- 7@LB@
71	0.003993	0.1953	b2347	yfdC	-11.68	0.141997	251 -- 269	1 -- 17	putative inner membrane protein	_____________250__________________270\n_____________\|____________________\|\n5'-GCA...GAGAG_______AAA______C___AAAAA...UCC-3'\n______________CGAAGAA___GAGC_G_GGC\n______________\|:\|\|\|\|\|___:\|\|\|_\|_\|\|\|\n______________GUUUCUU___UUCG_C_CCG\n3'-UUU...CUGUA______________U_A___-5'\n_____________\|___________________\|\n_____________18__________________1\n	251 -- 257	11 -- 17	-16.1242 kcal/mol	3.00377 kcal/mol	1.43853 kcal/mol	250 270@LB@ \| \|@LB@5'-GCA...GAGAG AAA C AAAAA...UCC-3'@LB@ CGAAGAA GAGC G GGC@LB@ \|:\|\|\|\|\| :\|\|\| \| \|\|\|@LB@ GUUUCUU UUCG C CCG@LB@3'-UUU...CUGUA U A -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -16.1242 kcal/mol@LB@Unfolding Energy - mRNA 3.00377 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 251 -- 269@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 11 -- 17@LB@
146	0.01079	0.2504	b2453	eutG	-16.22	0.013596	18 -- 37	1 -- 22	ethanol dehydrogenase involved in ethanolamine utilization; aldehyde reductase	_____________17_____________________38\n_____________\|______________________\|\n5'-GGC...CGCCC_____AUU______________AUUAC...GUC-3'\n______________GGCAU____GAAGGGCAG_GGC\n______________\|:\|\|\|____\|\|\|::\|\|\|\|_\|\|\|\n______________CUGUA____CUUUUCGUC_CCG\n3'-UUU...UACCC_____GUUU_________A___-5'\n_____________\|_____________________\|\n_____________23____________________1\n	28 -- 34	5 -- 11	-23.1742 kcal/mol	5.41796 kcal/mol	1.54023 kcal/mol	17 38@LB@ \| \|@LB@5'-GGC...CGCCC AUU AUUAC...GUC-3'@LB@ GGCAU GAAGGGCAG GGC@LB@ \|:\|\|\| \|\|\|::\|\|\|\| \|\|\|@LB@ CUGUA CUUUUCGUC CCG@LB@3'-UUU...UACCC GUUU A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -23.1742 kcal/mol@LB@Unfolding Energy - mRNA 5.41796 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 18 -- 37@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 5 -- 11@LB@
190	0.01401	0.2529	b2478	dapA	-10.08	0.266807	73 -- 98	6 -- 25	dihydrodipicolinate synthase	_____________72_________________________99\n_____________\|__________________________\|\n5'-GGC...UUUAA____UGA____UUCUU__________UAAAA...CCA-3'\n______________GGGG___GUUG_____AAGGAAAGCA\n______________\|\|\|\|___:\|::_____\|\|\|:\|\|\|\|\|\|\n______________CCCC___UAGU_____UUCUUUUCGU\n3'-UUU...UUUUA____UG____________________CACCG-5'\n_____________\|__________________________\|\n_____________26_________________________5\n	92 -- 98	6 -- 12	-17.2074 kcal/mol	6.41889 kcal/mol	0.70636 kcal/mol	72 99@LB@ \| \|@LB@5'-GGC...UUUAA UGA UUCUU UAAAA...CCA-3'@LB@ GGGG GUUG AAGGAAAGCA@LB@ \|\|\|\| :\|:: \|\|\|:\|\|\|\|\|\|@LB@ CCCC UAGU UUCUUUUCGU@LB@3'-UUU...UUUUA UG CACCG-5'@LB@ \| \|@LB@ 26 5@LB@@LB@@LB@Energy -10.08 kcal/mol@LB@Hybridization Energy -17.2074 kcal/mol@LB@Unfolding Energy - mRNA 6.41889 kcal/mol@LB@Unfolding Energy - sRNA 0.70636 kcal/mol@LB@@LB@Position - mRNA 73 -- 98@LB@Position - sRNA 6 -- 25@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 6 -- 12@LB@
29	0.00125	0.1512	b2499	purM	-15.92	0.016248	173 -- 203	3 -- 34	phosphoribosylaminoimidazole synthetase	_____________172____________________________________204\n_____________\|______________________________________\|\n5'-UAU...UUCUA_______UAACGC________CC_______________ACCGA...CGC-3'\n______________CCGCAAG______GUGGGGAC_________AAGCAGUG\n______________\|\|:\|\|\|:______:\|\|\|\|\|\|\|_________\|\|\|\|\|\|\|\|\n______________GGUGUUU______UACCCCUG_________UUCGUCAC\n3'-UUU...CCCGA_____________________UAGUUUCUU________CG-5'\n_____________\|______________________________________\|\n_____________35_____________________________________2\n	197 -- 203	3 -- 9	-29.7141 kcal/mol	9.52212 kcal/mol	4.26884 kcal/mol	172 204@LB@ \| \|@LB@5'-UAU...UUCUA UAACGC CC ACCGA...CGC-3'@LB@ CCGCAAG GUGGGGAC AAGCAGUG@LB@ \|\|:\|\|\|: :\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GGUGUUU UACCCCUG UUCGUCAC@LB@3'-UUU...CCCGA UAGUUUCUU CG-5'@LB@ \| \|@LB@ 35 2@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -29.7141 kcal/mol@LB@Unfolding Energy - mRNA 9.52212 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 173 -- 203@LB@Position - sRNA 3 -- 34@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
84	0.005241	0.2147	b2513	yfgM	-12.13	0.116945	176 -- 204	2 -- 26	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________175___________________________205\n_____________\|_____________________________\|\n5'-GGC...GUUAC____UUAAGG_________G_CAGC____AAAUU...UUG-3'\n______________UGGG______AAGGAGAAG_A____GUGG\n______________\|\|\|\|______\|\|:\|\|:\|\|\|_\|____\|\|\|\|\n______________ACCC______UUUCUUUUC_U____CACC\n3'-UUU...GUUUU____CUGUAG_________G_________G-5'\n_____________\|_____________________________\|\n_____________27____________________________1\n	188 -- 194	8 -- 14	-19.1762 kcal/mol	4.53021 kcal/mol	2.5184 kcal/mol	175 205@LB@ \| \|@LB@5'-GGC...GUUAC UUAAGG G CAGC AAAUU...UUG-3'@LB@ UGGG AAGGAGAAG A GUGG@LB@ \|\|\|\| \|\|:\|\|:\|\|\| \| \|\|\|\|@LB@ ACCC UUUCUUUUC U CACC@LB@3'-UUU...GUUUU CUGUAG G G-5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -19.1762 kcal/mol@LB@Unfolding Energy - mRNA 4.53021 kcal/mol@LB@Unfolding Energy - sRNA 2.5184 kcal/mol@LB@@LB@Position - mRNA 176 -- 204@LB@Position - sRNA 2 -- 26@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 8 -- 14@LB@
195	0.01413	0.2529	b2527	hscB	-14.38	0.038945	62 -- 81	1 -- 21	HscA co-chaperone J domain-containing protein Hsc56; IscU-specific chaperone HscAB	_____________61____________________82\n_____________\|_____________________\|\n5'-GGU...CCCGA__________U__________UGCGG...CUG-3'\n______________ACGUCAAAGA_GAGU_GUGGU\n______________\|\|:\|\|\|\|\|\|\|_:\|\|:_\|\|\|\|:\n______________UGUAGUUUCU_UUCG_CACCG\n3'-UUU...ACCCC__________U____U_____-5'\n_____________\|____________________\|\n_____________22___________________1\n	65 -- 71	12 -- 18	-23.3701 kcal/mol	7.47956 kcal/mol	1.51103 kcal/mol	61 82@LB@ \| \|@LB@5'-GGU...CCCGA U UGCGG...CUG-3'@LB@ ACGUCAAAGA GAGU GUGGU@LB@ \|\|:\|\|\|\|\|\|\| :\|\|: \|\|\|\|:@LB@ UGUAGUUUCU UUCG CACCG@LB@3'-UUU...ACCCC U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.38 kcal/mol@LB@Hybridization Energy -23.3701 kcal/mol@LB@Unfolding Energy - mRNA 7.47956 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 62 -- 81@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 12 -- 18@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@
39	0.001912	0.1648	b2532	trmJ	-14.54	0.035636	97 -- 121	1 -- 23	tRNA mC32 mU32 2'-O-methyltransferase SAM-dependent	_____________96________________________122\n_____________\|_________________________\|\n5'-CGU...UCACU_____________C__G_AAAC___GCAGA...UGU-3'\n______________GGAUGUUAAAGAA_GG_A____GGC\n______________\|\|\|::\|:\|\|\|\|\|\|_:\|_\|____\|\|\|\n______________CCUGUAGUUUCUU_UC_U____CCG\n3'-UUU...UUACC_____________U__G_CA_____-5'\n_____________\|________________________\|\n_____________24_______________________1\n	103 -- 109	11 -- 17	-19.8008 kcal/mol	3.67656 kcal/mol	1.57928 kcal/mol	96 122@LB@ \| \|@LB@5'-CGU...UCACU C G AAAC GCAGA...UGU-3'@LB@ GGAUGUUAAAGAA GG A GGC@LB@ \|\|\|::\|:\|\|\|\|\|\| :\| \| \|\|\|@LB@ CCUGUAGUUUCUU UC U CCG@LB@3'-UUU...UUACC U G CA -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -14.54 kcal/mol@LB@Hybridization Energy -19.8008 kcal/mol@LB@Unfolding Energy - mRNA 3.67656 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 97 -- 121@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 11 -- 17@LB@
133	0.009634	0.2504	b2551	glyA	-13.83	0.051752	272 -- 286	6 -- 21	serine hydroxymethyltransferase	_____________271______________287\n_____________\|________________\|\n5'-CAA...AAAGU________________CAUCG...UCG-3'\n______________ACGUC_AGGAAGAGCA\n______________\|\|:\|\|_\|:\|\|\|:\|\|\|\|\n______________UGUAG_UUCUUUUCGU\n3'-UUU...ACCCC_____U__________CACCG-5'\n_____________\|________________\|\n_____________22_______________5\n	280 -- 286	6 -- 12	-16.7043 kcal/mol	2.28484 kcal/mol	0.584589 kcal/mol	271 287@LB@ \| \|@LB@5'-CAA...AAAGU CAUCG...UCG-3'@LB@ ACGUC AGGAAGAGCA@LB@ \|\|:\|\| \|:\|\|\|:\|\|\|\|@LB@ UGUAG UUCUUUUCGU@LB@3'-UUU...ACCCC U CACCG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -16.7043 kcal/mol@LB@Unfolding Energy - mRNA 2.28484 kcal/mol@LB@Unfolding Energy - sRNA 0.584589 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 6 -- 12@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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