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
192	0.08479	0.363	ct_293	accD	-5.01	0.360945	270 -- 276	79 -- 85	acetyl-CoA carboxylase carboxyltransferase subunit beta	_____________269_____277\n_____________\|_______\|\n5'-GUA...GUGGC_______AAUGU...UGA-3'\n______________UGGCUAA\n______________:\|\|\|\|\|\|\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	270 -- 276	79 -- 85	-7.87376 kcal/mol	1.76808 kcal/mol	1.09751 kcal/mol	269 277@LB@ \| \|@LB@5'-GUA...GUGGC AAUGU...UGA-3'@LB@ UGGCUAA@LB@ :\|\|\|\|\|\|@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -5.01 kcal/mol@LB@Hybridization Energy -7.87376 kcal/mol@LB@Unfolding Energy - mRNA 1.76808 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 270 -- 276@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 79 -- 85@LB@
198	0.08843	0.3671	ct_257	N/A	-6.39	0.194258	76 -- 83	79 -- 86		_____________75_______84\n_____________\|________\|\n5'-CUA...GGCGG________CAGAA...UCA-3'\n______________AUGGCUGA\n______________\|:\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	77 -- 83	79 -- 85	-9.5904 kcal/mol	2.10083 kcal/mol	1.09752 kcal/mol	75 84@LB@ \| \|@LB@5'-CUA...GGCGG CAGAA...UCA-3'@LB@ AUGGCUGA@LB@ \|:\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -6.39 kcal/mol@LB@Hybridization Energy -9.5904 kcal/mol@LB@Unfolding Energy - mRNA 2.10083 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 79 -- 85@LB@
200	0.0896	0.3683	ct_487	yhhF	-5.19	0.334580	14 -- 20	79 -- 85	methyltransferase	_____________13______21\n_____________\|_______\|\n5'-ACG...UCCUC_______UAAUG...UUA-3'\n______________CGGUUAG\n______________\|\|\|:\|\|:\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	14 -- 20	79 -- 85	-7.01592 kcal/mol	0.727938 kcal/mol	1.09751 kcal/mol	13 21@LB@ \| \|@LB@5'-ACG...UCCUC UAAUG...UUA-3'@LB@ CGGUUAG@LB@ \|\|\|:\|\|:@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -5.19 kcal/mol@LB@Hybridization Energy -7.01592 kcal/mol@LB@Unfolding Energy - mRNA 0.727938 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 14 -- 20@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 79 -- 85@LB@
15	0.003628	0.1836	ct_134	N/A	-6.77	0.161910	221 -- 229	80 -- 88		_____________220_______230\n_____________\|_________\|\n5'-CAA...UGUGU_________CGAUG...UUC-3'\n______________AUACGGUUA\n______________\|\|\|\|\|\|:\|\|\n______________UAUGCCGAU\n3'-UUU...GCCUC_________UGAGG...GAA-5'\n_____________\|_________\|\n_____________89________79\n	223 -- 229	80 -- 86	-9.99522 kcal/mol	2.13198 kcal/mol	1.09753 kcal/mol	220 230@LB@ \| \|@LB@5'-CAA...UGUGU CGAUG...UUC-3'@LB@ AUACGGUUA@LB@ \|\|\|\|\|\|:\|\|@LB@ UAUGCCGAU@LB@3'-UUU...GCCUC UGAGG...GAA-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -6.77 kcal/mol@LB@Hybridization Energy -9.99522 kcal/mol@LB@Unfolding Energy - mRNA 2.13198 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 221 -- 229@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 80 -- 86@LB@
32	0.009822	0.2518	ct_649	ygfA	-6.64	0.172247	22 -- 28	80 -- 86	5-formyltetrahydrofolate cyclo-ligase	_____________21______29\n_____________\|_______\|\n5'-UAC...AAGUG_______CCGAG...AGC-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	22 -- 28	80 -- 86	-8.81528 kcal/mol	1.11082 kcal/mol	1.06449 kcal/mol	21 29@LB@ \| \|@LB@5'-UAC...AAGUG CCGAG...AGC-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -8.81528 kcal/mol@LB@Unfolding Energy - mRNA 1.11082 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 22 -- 28@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 80 -- 86@LB@
42	0.01617	0.29	ct_610	N/A	-8.69	0.058803	15 -- 22	80 -- 87	virulence protein CADD	_____________14_______23\n_____________\|________\|\n5'-GAU...GCAGU________UUGUU...GGG-3'\n______________UGCGGCUG\n______________\|:\|\|\|\|\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	16 -- 22	80 -- 86	-11.8172 kcal/mol	2.02516 kcal/mol	1.09752 kcal/mol	14 23@LB@ \| \|@LB@5'-GAU...GCAGU UUGUU...GGG-3'@LB@ UGCGGCUG@LB@ \|:\|\|\|\|\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -11.8172 kcal/mol@LB@Unfolding Energy - mRNA 2.02516 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 15 -- 22@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 80 -- 86@LB@
49	0.01821	0.29	ct_733	N/A	-8.44	0.067485	96 -- 102	80 -- 86		_____________95______103\n_____________\|_______\|\n5'-AUG...UGCCA_______UUGAU...CUA-3'\n______________GCGGCUA\n______________:\|\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	96 -- 102	80 -- 86	-11.4095 kcal/mol	1.90152 kcal/mol	1.06449 kcal/mol	95 103@LB@ \| \|@LB@5'-AUG...UGCCA UUGAU...CUA-3'@LB@ GCGGCUA@LB@ :\|\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -11.4095 kcal/mol@LB@Unfolding Energy - mRNA 1.90152 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 96 -- 102@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 80 -- 86@LB@
52	0.01886	0.29	ct_784	rnpA	-5.05	0.354130	114 -- 120	80 -- 86	ribonuclease P protein component	_____________113_____121\n_____________\|_______\|\n5'-UCU...CUCGC_______CAAAA...UGA-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	114 -- 120	80 -- 86	-8.53572 kcal/mol	2.4168 kcal/mol	1.06449 kcal/mol	113 121@LB@ \| \|@LB@5'-UCU...CUCGC CAAAA...UGA-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.05 kcal/mol@LB@Hybridization Energy -8.53572 kcal/mol@LB@Unfolding Energy - mRNA 2.4168 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 114 -- 120@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 80 -- 86@LB@
55	0.02093	0.29	ct_785	rl34	-4.69	0.410747	264 -- 270	80 -- 86	50S ribosomal protein L34	_____________263_____271\n_____________\|_______\|\n5'-ACA...CUCGC_______CAAAA...GCC-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	264 -- 270	80 -- 86	-8.67787 kcal/mol	2.92801 kcal/mol	1.06449 kcal/mol	263 271@LB@ \| \|@LB@5'-ACA...CUCGC CAAAA...GCC-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -8.67787 kcal/mol@LB@Unfolding Energy - mRNA 2.92801 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 264 -- 270@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 80 -- 86@LB@
56	0.02215	0.29	ct_104	fabI	-6.34	0.199539	263 -- 271	80 -- 88	enoyl-(acyl carrier protein) reductase	_____________262_______272\n_____________\|_________\|\n5'-UUU...AACGG_________GGGCA...CAG-3'\n______________GUAUGGCUG\n______________:\|\|:\|\|\|\|:\n______________UAUGCCGAU\n3'-UUU...GCCUC_________UGAGG...GAA-5'\n_____________\|_________\|\n_____________89________79\n	265 -- 271	80 -- 86	-10.7973 kcal/mol	3.36368 kcal/mol	1.09753 kcal/mol	262 272@LB@ \| \|@LB@5'-UUU...AACGG GGGCA...CAG-3'@LB@ GUAUGGCUG@LB@ :\|\|:\|\|\|\|:@LB@ UAUGCCGAU@LB@3'-UUU...GCCUC UGAGG...GAA-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -6.34 kcal/mol@LB@Hybridization Energy -10.7973 kcal/mol@LB@Unfolding Energy - mRNA 3.36368 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 263 -- 271@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 80 -- 86@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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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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