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
200	0.04173	0.6177	b3155	yhbQ	-7.74	0.117248	9 -- 16	50 -- 57	GIY-YIG nuclease superfamily protein	_____________8________17\n_____________\|________\|\n___5'-UUUUUCUU________AUGUA...GCG-3'\n______________CCGUCAAA\n______________\|\|\|\|\|\|\|\|\n______________GGCAGUUU\n3'-UUU...AACCG________CUCCU...ACA-5'\n_____________\|________\|\n_____________58_______49\n	10 -- 16	50 -- 56	-10.5697 kcal/mol	0.110673 kcal/mol	2.72137 kcal/mol	8 17@LB@ \| \|@LB@ 5'-UUUUUCUU AUGUA...GCG-3'@LB@ CCGUCAAA@LB@ \|\|\|\|\|\|\|\|@LB@ GGCAGUUU@LB@3'-UUU...AACCG CUCCU...ACA-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -10.5697 kcal/mol@LB@Unfolding Energy - mRNA 0.110673 kcal/mol@LB@Unfolding Energy - sRNA 2.72137 kcal/mol@LB@@LB@Position - mRNA 9 -- 16@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 50 -- 56@LB@
195	0.04073	0.6177	b3166	truB	-9.24	0.058593	189 -- 197	45 -- 53	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase	_____________188_______198\n_____________\|_________\|\n5'-GGC...GACAG_________CUAAU...AAC-3'\n______________CAAGGAGGA\n______________\|\|\|:\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	191 -- 197	45 -- 51	-13.1895 kcal/mol	3.02734 kcal/mol	0.917553 kcal/mol	188 198@LB@ \| \|@LB@5'-GGC...GACAG CUAAU...AAC-3'@LB@ CAAGGAGGA@LB@ \|\|\|:\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.24 kcal/mol@LB@Hybridization Energy -13.1895 kcal/mol@LB@Unfolding Energy - mRNA 3.02734 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 45 -- 51@LB@
65	0.01408	0.6177	b3176	glmM	-9.74	0.046438	133 -- 141	48 -- 56	phosphoglucosamine mutase	_____________132_______142\n_____________\|_________\|\n5'-GUU...CAUGA_________AACCG...CGG-3'\n______________CGUCAAAGA\n______________\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCU\n3'-UUU...ACCGG_________CCUUA...ACA-5'\n_____________\|_________\|\n_____________57________47\n	135 -- 141	48 -- 54	-11.8395 kcal/mol	1.20122 kcal/mol	0.896433 kcal/mol	132 142@LB@ \| \|@LB@5'-GUU...CAUGA AACCG...CGG-3'@LB@ CGUCAAAGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCU@LB@3'-UUU...ACCGG CCUUA...ACA-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -11.8395 kcal/mol@LB@Unfolding Energy - mRNA 1.20122 kcal/mol@LB@Unfolding Energy - sRNA 0.896433 kcal/mol@LB@@LB@Position - mRNA 133 -- 141@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 48 -- 54@LB@
132	0.02588	0.6177	b3180	yhbY	-5.98	0.252347	290 -- 297	46 -- 53	RNA binding protein associated with pre-50S ribosomal subunits	_____________289______298\n_____________\|________\|\n5'-CUG...UUGAC________UGC-3'\n______________CGAAGGGG\n______________\|:\|\|\|:\|\|\n______________GUUUCUCC\n3'-UUU...GGGCA________UUAAA...ACA-5'\n_____________\|________\|\n_____________54_______45\n	291 -- 297	46 -- 52	-10.2464 kcal/mol	3.35117 kcal/mol	0.910679 kcal/mol	289 298@LB@ \| \|@LB@5'-CUG...UUGAC UGC-3'@LB@ CGAAGGGG@LB@ \|:\|\|\|:\|\|@LB@ GUUUCUCC@LB@3'-UUU...GGGCA UUAAA...ACA-5'@LB@ \| \|@LB@ 54 45@LB@@LB@@LB@Energy -5.98 kcal/mol@LB@Hybridization Energy -10.2464 kcal/mol@LB@Unfolding Energy - mRNA 3.35117 kcal/mol@LB@Unfolding Energy - sRNA 0.910679 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 46 -- 53@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 46 -- 52@LB@
125	0.02442	0.6177	b3181	greA	-6.11	0.239901	243 -- 260	40 -- 56	transcript cleavage factor	_____________242_________________261\n_____________\|___________________\|\n5'-CGC...AAUUA__________CU_______CUGAA...UCG-3'\n______________CG_CGAAGAG__GGAUUUU\n______________\|\|_\|:\|\|\|\|\|__\|:\|\|\|\|:\n______________GC_GUUUCUC__CUUAAAG\n3'-UUU...ACCGG__A________________UAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________39\n	245 -- 251	47 -- 53	-12.1125 kcal/mol	4.98158 kcal/mol	1.02557 kcal/mol	242 261@LB@ \| \|@LB@5'-CGC...AAUUA CU CUGAA...UCG-3'@LB@ CG CGAAGAG GGAUUUU@LB@ \|\| \|:\|\|\|\|\| \|:\|\|\|\|:@LB@ GC GUUUCUC CUUAAAG@LB@3'-UUU...ACCGG A UAAAA...ACA-5'@LB@ \| \|@LB@ 57 39@LB@@LB@@LB@Energy -6.11 kcal/mol@LB@Hybridization Energy -12.1125 kcal/mol@LB@Unfolding Energy - mRNA 4.98158 kcal/mol@LB@Unfolding Energy - sRNA 1.02557 kcal/mol@LB@@LB@Position - mRNA 243 -- 260@LB@Position - sRNA 40 -- 56@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 47 -- 53@LB@
158	0.03174	0.6177	b3185	rpmA	-9.10	0.062717	186 -- 199	39 -- 52	50S ribosomal subunit protein L27	_____________185____________200\n_____________\|______________\|\n5'-GAA...GACCU______A_______AAUGG...CGG-3'\n______________GAGGAG_GAUUUCA\n______________:\|:\|\|\|_:\|\|\|\|\|\|\n______________UUUCUC_UUAAAGU\n3'-UUU...GGCAG______C_______AAAAA...ACA-5'\n_____________\|______________\|\n_____________53_____________38\n	193 -- 199	39 -- 45	-11.8509 kcal/mol	1.7019 kcal/mol	1.05043 kcal/mol	185 200@LB@ \| \|@LB@5'-GAA...GACCU A AAUGG...CGG-3'@LB@ GAGGAG GAUUUCA@LB@ :\|:\|\|\| :\|\|\|\|\|\|@LB@ UUUCUC UUAAAGU@LB@3'-UUU...GGCAG C AAAAA...ACA-5'@LB@ \| \|@LB@ 53 38@LB@@LB@@LB@Energy -9.10 kcal/mol@LB@Hybridization Energy -11.8509 kcal/mol@LB@Unfolding Energy - mRNA 1.7019 kcal/mol@LB@Unfolding Energy - sRNA 1.05043 kcal/mol@LB@@LB@Position - mRNA 186 -- 199@LB@Position - sRNA 39 -- 52@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 39 -- 45@LB@
142	0.02758	0.6177	b3186	rplU	-10.01	0.040887	186 -- 200	38 -- 52	50S ribosomal subunit protein L21	_____________185_____________201\n_____________\|_______________\|\n5'-UUA...GCGCG____C__________AUGUA...UUG-3'\n______________GAAG_GGAGUUUUAU\n______________:\|\|\|_\|\|\|:\|\|\|:\|\|\n______________UUUC_CCUUAAAGUA\n3'-UUU...GGCAG____U__________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	194 -- 200	38 -- 44	-13.3778 kcal/mol	2.29537 kcal/mol	1.0693 kcal/mol	185 201@LB@ \| \|@LB@5'-UUA...GCGCG C AUGUA...UUG-3'@LB@ GAAG GGAGUUUUAU@LB@ :\|\|\| \|\|\|:\|\|\|:\|\|@LB@ UUUC CCUUAAAGUA@LB@3'-UUU...GGCAG U AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -13.3778 kcal/mol@LB@Unfolding Energy - mRNA 2.29537 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 186 -- 200@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 38 -- 44@LB@
141	0.02753	0.6177	b3215	yhcA	-6.30	0.221284	185 -- 194	39 -- 48	putative periplasmic chaperone protein	_____________184________195\n_____________\|__________\|\n5'-ACG...AUUAC__________AUUUA...AAA-3'\n______________AGGAGUUUUA\n______________\|\|\|\|:\|\|\|:\|\n______________UCCUUAAAGU\n3'-UUU...GUUUC__________AAAAA...ACA-5'\n_____________\|__________\|\n_____________49_________38\n	187 -- 193	40 -- 46	-10.0044 kcal/mol	2.68942 kcal/mol	1.01866 kcal/mol	184 195@LB@ \| \|@LB@5'-ACG...AUUAC AUUUA...AAA-3'@LB@ AGGAGUUUUA@LB@ \|\|\|\|:\|\|\|:\|@LB@ UCCUUAAAGU@LB@3'-UUU...GUUUC AAAAA...ACA-5'@LB@ \| \|@LB@ 49 38@LB@@LB@@LB@Energy -6.30 kcal/mol@LB@Hybridization Energy -10.0044 kcal/mol@LB@Unfolding Energy - mRNA 2.68942 kcal/mol@LB@Unfolding Energy - sRNA 1.01866 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 39 -- 48@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
64	0.01382	0.6177	b3250	mreC	-10.24	0.036759	206 -- 229	53 -- 75	cell wall structural complex MreBCD transmembrane component MreC	_____________205_______________________230\n_____________\|_________________________\|\n5'-GAC...AUGAA______UUUUA__CG__________GCUAC...GGA-3'\n______________GCCAAU_____GC___UGGCCCGUC\n______________\|\|\|\|\|\|_____\|\|___\|\|\|\|\|\|\|\|\|\n______________CGGUUA_____CG___ACCGGGCAG\n3'-UUU...UUUAC______UAG____AUA_________UUUCU...ACA-5'\n_____________\|_________________________\|\n_____________76________________________52\n	223 -- 229	53 -- 59	-27.5071 kcal/mol	5.94491 kcal/mol	11.3228 kcal/mol	205 230@LB@ \| \|@LB@5'-GAC...AUGAA UUUUA CG GCUAC...GGA-3'@LB@ GCCAAU GC UGGCCCGUC@LB@ \|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ CGGUUA CG ACCGGGCAG@LB@3'-UUU...UUUAC UAG AUA UUUCU...ACA-5'@LB@ \| \|@LB@ 76 52@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -27.5071 kcal/mol@LB@Unfolding Energy - mRNA 5.94491 kcal/mol@LB@Unfolding Energy - sRNA 11.3228 kcal/mol@LB@@LB@Position - mRNA 206 -- 229@LB@Position - sRNA 53 -- 75@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 53 -- 59@LB@
86	0.01794	0.6177	b3260	dusB	-7.53	0.128932	119 -- 138	38 -- 55	tRNA-dihydrouridine synthase B	_____________118__________________139\n_____________\|____________________\|\n5'-ACU...GAUUG_______UUU__CC______CUCGU...GAG-3'\n______________GUCAAAG___GG__UUUCAU\n______________\|\|\|\|\|\|\|___\|\|__\|\|\|\|\|\|\n______________CAGUUUC___CC__AAAGUA\n3'-UUU...CCGGG_______U____UU______AAAAA...ACA-5'\n_____________\|____________________\|\n_____________56___________________37\n	119 -- 125	49 -- 55	-13.3869 kcal/mol	4.6894 kcal/mol	1.17036 kcal/mol	118 139@LB@ \| \|@LB@5'-ACU...GAUUG UUU CC CUCGU...GAG-3'@LB@ GUCAAAG GG UUUCAU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ CAGUUUC CC AAAGUA@LB@3'-UUU...CCGGG U UU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -13.3869 kcal/mol@LB@Unfolding Energy - mRNA 4.6894 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 119 -- 138@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 49 -- 55@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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