Input and runtime details for job 6038639 (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 6038639 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:57 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:19:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:35:30 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:35:37 CET 2018
	Job Completed		@ Fri Feb 16 21:35:51 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6038639&toolName=CopraRNA ( 30 days expiry )

Description of the job

IhtA

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_000117 Chlamydia trachomatis D/UW-3/CX

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
65	0.02498	0.29	ct_846	N/A	-7.66	0.102535	215 -- 232	42 -- 57		_____________214________________233\n_____________\|__________________\|\n5'-GCG...AUCUU____GAUAA_________AACUC...CUC-3'\n______________CCCC_____GUACAAACA\n______________\|\|\|\|_____\|\|\|\|\|\|\|\|\|\n______________GGGG_____CAUGUUUGU\n3'-UUU...GAAGG____ACA___________GAUCU...GAA-5'\n_____________\|__________________\|\n_____________58_________________41\n	226 -- 232	42 -- 48	-18.5622 kcal/mol	3.08308 kcal/mol	7.81778 kcal/mol	214 233@LB@ \| \|@LB@5'-GCG...AUCUU GAUAA AACUC...CUC-3'@LB@ CCCC GUACAAACA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ GGGG CAUGUUUGU@LB@3'-UUU...GAAGG ACA GAUCU...GAA-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -18.5622 kcal/mol@LB@Unfolding Energy - mRNA 3.08308 kcal/mol@LB@Unfolding Energy - sRNA 7.81778 kcal/mol@LB@@LB@Position - mRNA 215 -- 232@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 42 -- 48@LB@
39	0.01357	0.2859	ct_401	gltT	-7.80	0.095127	36 -- 47	44 -- 55	sodium:dicarboxylate symport protein	_____________35___________48\n_____________\|____________\|\n5'-UGU...GGUAU____________AAAGG...AUA-3'\n______________CCUGUGUACAGA\n______________\|\|\|\|\|\|\|\|\|\|:\|\n______________GGACACAUGUUU\n3'-UUU...AGGGG____________GUGAU...GAA-5'\n_____________\|____________\|\n_____________56___________43\n	41 -- 47	44 -- 50	-17.8988 kcal/mol	2.58215 kcal/mol	7.51272 kcal/mol	35 48@LB@ \| \|@LB@5'-UGU...GGUAU AAAGG...AUA-3'@LB@ CCUGUGUACAGA@LB@ \|\|\|\|\|\|\|\|\|\|:\|@LB@ GGACACAUGUUU@LB@3'-UUU...AGGGG GUGAU...GAA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -17.8988 kcal/mol@LB@Unfolding Energy - mRNA 2.58215 kcal/mol@LB@Unfolding Energy - sRNA 7.51272 kcal/mol@LB@@LB@Position - mRNA 36 -- 47@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 44 -- 50@LB@
89	0.03269	0.2942	ct_269	murE	-8.94	0.051230	172 -- 183	46 -- 57	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2 6-diaminopimelate ligase	_____________171__________184\n_____________\|____________\|\n5'-AUC...UGAAG____________UGUCU...UUG-3'\n______________CCCUUGUGUGCG\n______________\|\|\|:\|\|\|\|\|:\|:\n______________GGGGACACAUGU\n3'-UUU...GAAGG____________UUGUG...GAA-5'\n_____________\|____________\|\n_____________58___________45\n	176 -- 182	47 -- 53	-19.7508 kcal/mol	3.51628 kcal/mol	7.29173 kcal/mol	171 184@LB@ \| \|@LB@5'-AUC...UGAAG UGUCU...UUG-3'@LB@ CCCUUGUGUGCG@LB@ \|\|\|:\|\|\|\|\|:\|:@LB@ GGGGACACAUGU@LB@3'-UUU...GAAGG UUGUG...GAA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -19.7508 kcal/mol@LB@Unfolding Energy - mRNA 3.51628 kcal/mol@LB@Unfolding Energy - sRNA 7.29173 kcal/mol@LB@@LB@Position - mRNA 172 -- 183@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 47 -- 53@LB@
99	0.03647	0.3007	ct_810	rl32	-4.11	0.507281	35 -- 46	46 -- 58	50S ribosomal protein L32	_____________34____________47\n_____________\|_____________\|\n5'-UUC...CAAGU_____________CGUUU...GCA-3'\n______________CUUCCUG_GUAUA\n______________\|::\|\|\|\|_\|\|\|:\|\n______________GGGGGAC_CAUGU\n3'-UUU...UGAAG_______A_____UUGUG...GAA-5'\n_____________\|_____________\|\n_____________59____________45\n	35 -- 41	52 -- 58	-13.0221 kcal/mol	1.6119 kcal/mol	7.29598 kcal/mol	34 47@LB@ \| \|@LB@5'-UUC...CAAGU CGUUU...GCA-3'@LB@ CUUCCUG GUAUA@LB@ \|::\|\|\|\| \|\|\|:\|@LB@ GGGGGAC CAUGU@LB@3'-UUU...UGAAG A UUGUG...GAA-5'@LB@ \| \|@LB@ 59 45@LB@@LB@@LB@Energy -4.11 kcal/mol@LB@Hybridization Energy -13.0221 kcal/mol@LB@Unfolding Energy - mRNA 1.6119 kcal/mol@LB@Unfolding Energy - sRNA 7.29598 kcal/mol@LB@@LB@Position - mRNA 35 -- 46@LB@Position - sRNA 46 -- 58@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 52 -- 58@LB@
123	0.04914	0.3262	ct_754	icc	-7.18	0.131374	254 -- 264	47 -- 57		_____________253_________265\n_____________\|___________\|\n5'-AUU...AUUCA___________UCCCU...GCU-3'\n______________CUUCUGUGUAC\n______________\|::\|\|\|\|\|\|\|\|\n______________GGGGACACAUG\n3'-UUU...GAAGG___________UUUGU...GAA-5'\n_____________\|___________\|\n_____________58__________46\n	258 -- 264	47 -- 53	-16.923 kcal/mol	2.45356 kcal/mol	7.2877 kcal/mol	253 265@LB@ \| \|@LB@5'-AUU...AUUCA UCCCU...GCU-3'@LB@ CUUCUGUGUAC@LB@ \|::\|\|\|\|\|\|\|\|@LB@ GGGGACACAUG@LB@3'-UUU...GAAGG UUUGU...GAA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -16.923 kcal/mol@LB@Unfolding Energy - mRNA 2.45356 kcal/mol@LB@Unfolding Energy - sRNA 7.2877 kcal/mol@LB@@LB@Position - mRNA 254 -- 264@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 47 -- 53@LB@
103	0.03832	0.3036	ct_382	aroG	-9.59	0.035559	138 -- 150	48 -- 60	3-deoxy-7-phosphoheptulonate synthase	_____________137___________151\n_____________\|_____________\|\n5'-UUU...UUUUC_____________UAUGA...CUA-3'\n______________UCUUCCCUGUGUG\n______________\|\|::\|\|\|\|\|\|\|\|:\n______________AGGGGGGACACAU\n3'-UUU...ACUGA_____________GUUUG...GAA-5'\n_____________\|_____________\|\n_____________61____________47\n	144 -- 150	48 -- 54	-20.2814 kcal/mol	1.44568 kcal/mol	9.24642 kcal/mol	137 151@LB@ \| \|@LB@5'-UUU...UUUUC UAUGA...CUA-3'@LB@ UCUUCCCUGUGUG@LB@ \|\|::\|\|\|\|\|\|\|\|:@LB@ AGGGGGGACACAU@LB@3'-UUU...ACUGA GUUUG...GAA-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -20.2814 kcal/mol@LB@Unfolding Energy - mRNA 1.44568 kcal/mol@LB@Unfolding Energy - sRNA 9.24642 kcal/mol@LB@@LB@Position - mRNA 138 -- 150@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 48 -- 54@LB@
146	0.05858	0.3298	ct_655	kdsA	-5.70	0.267824	236 -- 245	48 -- 57	2-dehydro-3-deoxyphosphooctonate aldolase	_____________235________246\n_____________\|__________\|\n5'-GCU...GCAGG__________AUUGA...CUC-3'\n______________CCCUUGUGUA\n______________\|\|\|:\|\|\|\|\|\|\n______________GGGGACACAU\n3'-UUU...GAAGG__________GUUUG...GAA-5'\n_____________\|__________\|\n_____________58_________47\n	237 -- 243	50 -- 56	-16.3498 kcal/mol	3.37377 kcal/mol	7.27486 kcal/mol	235 246@LB@ \| \|@LB@5'-GCU...GCAGG AUUGA...CUC-3'@LB@ CCCUUGUGUA@LB@ \|\|\|:\|\|\|\|\|\|@LB@ GGGGACACAU@LB@3'-UUU...GAAGG GUUUG...GAA-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -5.70 kcal/mol@LB@Hybridization Energy -16.3498 kcal/mol@LB@Unfolding Energy - mRNA 3.37377 kcal/mol@LB@Unfolding Energy - sRNA 7.27486 kcal/mol@LB@@LB@Position - mRNA 236 -- 245@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 50 -- 56@LB@
111	0.04436	0.3262	ct_405	ribC	-3.97	0.532190	3 -- 10	49 -- 56	riboflavin synthase	_____________2________11\n_____________\|________\|\n_________5'-AA________CUUGU...AUG-3'\n______________UCCUGUGU\n______________:\|\|\|\|\|\|\|\n______________GGGACACA\n3'-UUU...AAGGG________UGUUU...GAA-5'\n_____________\|________\|\n_____________57_______48\n	4 -- 10	49 -- 55	-11.4476 kcal/mol	0.227857 kcal/mol	7.24525 kcal/mol	2 11@LB@ \| \|@LB@ 5'-AA CUUGU...AUG-3'@LB@ UCCUGUGU@LB@ :\|\|\|\|\|\|\|@LB@ GGGACACA@LB@3'-UUU...AAGGG UGUUU...GAA-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -3.97 kcal/mol@LB@Hybridization Energy -11.4476 kcal/mol@LB@Unfolding Energy - mRNA 0.227857 kcal/mol@LB@Unfolding Energy - sRNA 7.24525 kcal/mol@LB@@LB@Position - mRNA 3 -- 10@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 49 -- 55@LB@
81	0.02893	0.29	ct_185	zwf	-6.95	0.147965	38 -- 47	51 -- 60	glucose-6-phosphate 1-dehydrogenase	_____________37_________48\n_____________\|__________\|\n5'-AAG...GCCUG__________AUCGU...UUU-3'\n______________UCCUCCCUGU\n______________\|\|\|:\|\|\|\|\|\|\n______________AGGGGGGACA\n3'-UUU...ACUGA__________CAUGU...GAA-5'\n_____________\|__________\|\n_____________61_________50\n	41 -- 47	51 -- 57	-17.9011 kcal/mol	1.87917 kcal/mol	9.07545 kcal/mol	37 48@LB@ \| \|@LB@5'-AAG...GCCUG AUCGU...UUU-3'@LB@ UCCUCCCUGU@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGGGGGGACA@LB@3'-UUU...ACUGA CAUGU...GAA-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -17.9011 kcal/mol@LB@Unfolding Energy - mRNA 1.87917 kcal/mol@LB@Unfolding Energy - sRNA 9.07545 kcal/mol@LB@@LB@Position - mRNA 38 -- 47@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 51 -- 57@LB@
128	0.05098	0.3262	ct_279	nqr3	-7.28	0.125274	283 -- 291	51 -- 59	Na(+)-translocating NADH-quinone reductase subunit C	_____________282_______292\n_____________\|_________\|\n5'-CCG...UGGUA_________CUUCU...UGU-3'\n______________CCCUCCUGU\n______________\|\|\|:\|\|\|\|\|\n______________GGGGGGACA\n3'-UUU...CUGAA_________CAUGU...GAA-5'\n_____________\|_________\|\n_____________60________50\n	285 -- 291	51 -- 57	-15.9842 kcal/mol	0.606269 kcal/mol	8.10291 kcal/mol	282 292@LB@ \| \|@LB@5'-CCG...UGGUA CUUCU...UGU-3'@LB@ CCCUCCUGU@LB@ \|\|\|:\|\|\|\|\|@LB@ GGGGGGACA@LB@3'-UUU...CUGAA CAUGU...GAA-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -7.28 kcal/mol@LB@Hybridization Energy -15.9842 kcal/mol@LB@Unfolding Energy - mRNA 0.606269 kcal/mol@LB@Unfolding Energy - sRNA 8.10291 kcal/mol@LB@@LB@Position - mRNA 283 -- 291@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 51 -- 57@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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service.

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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