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
116	0.04833	0.3262	ct_570	gspF	-8.17	0.078365	199 -- 207	80 -- 88	type II secretion system protein F	_____________198_______208\n_____________\|_________\|\n5'-AUC...AGGGG_________GGUUU...CUG-3'\n______________AUAUGGCUA\n______________\|\|\|:\|\|\|\|\|\n______________UAUGCCGAU\n3'-UUU...GCCUC_________UGAGG...GAA-5'\n_____________\|_________\|\n_____________89________79\n	201 -- 207	80 -- 86	-11.0443 kcal/mol	1.77912 kcal/mol	1.09753 kcal/mol	198 208@LB@ \| \|@LB@5'-AUC...AGGGG GGUUU...CUG-3'@LB@ AUAUGGCUA@LB@ \|\|\|:\|\|\|\|\|@LB@ UAUGCCGAU@LB@3'-UUU...GCCUC UGAGG...GAA-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -11.0443 kcal/mol@LB@Unfolding Energy - mRNA 1.77912 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 199 -- 207@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 80 -- 86@LB@
121	0.04894	0.3262	ct_310	atpE	-7.64	0.103947	27 -- 34	80 -- 87	V-type ATP synthase subunit E	_____________26_______35\n_____________\|________\|\n5'-GCA...CCUUC________CCUUC...UUC-3'\n______________UACGGCUG\n______________\|\|\|\|\|\|\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	28 -- 34	80 -- 86	-11.9035 kcal/mol	3.17039 kcal/mol	1.09752 kcal/mol	26 35@LB@ \| \|@LB@5'-GCA...CCUUC CCUUC...UUC-3'@LB@ UACGGCUG@LB@ \|\|\|\|\|\|\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -11.9035 kcal/mol@LB@Unfolding Energy - mRNA 3.17039 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 27 -- 34@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 80 -- 86@LB@
122	0.04895	0.3262	ct_683	N/A	-8.21	0.076506	46 -- 53	80 -- 87		_____________45_______54\n_____________\|________\|\n5'-AAG...GUACU________GGAGA...AAG-3'\n______________UACGGCUA\n______________\|\|\|\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	47 -- 53	80 -- 86	-12.375 kcal/mol	3.06531 kcal/mol	1.09752 kcal/mol	45 54@LB@ \| \|@LB@5'-AAG...GUACU GGAGA...AAG-3'@LB@ UACGGCUA@LB@ \|\|\|\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -12.375 kcal/mol@LB@Unfolding Energy - mRNA 3.06531 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 46 -- 53@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 80 -- 86@LB@
133	0.05414	0.3262	ct_059	fer	-7.78	0.096344	200 -- 207	80 -- 87	ferredoxin	_____________199______208\n_____________\|________\|\n5'-UUC...AGUCC________AGCUC...CUU-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	200 -- 206	81 -- 87	-10.7757 kcal/mol	1.8981 kcal/mol	1.09752 kcal/mol	199 208@LB@ \| \|@LB@5'-UUC...AGUCC AGCUC...CUU-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -7.78 kcal/mol@LB@Hybridization Energy -10.7757 kcal/mol@LB@Unfolding Energy - mRNA 1.8981 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 200 -- 207@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 81 -- 87@LB@
137	0.05536	0.3262	ct_389	N/A	-5.69	0.269629	175 -- 181	80 -- 86		_____________174_____182\n_____________\|_______\|\n5'-GUU...AUAAC_______UCUCA...GCC-3'\n______________GCGGCUG\n______________:\|\|\|\|\|:\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	175 -- 181	80 -- 86	-10.4159 kcal/mol	3.66497 kcal/mol	1.06449 kcal/mol	174 182@LB@ \| \|@LB@5'-GUU...AUAAC UCUCA...GCC-3'@LB@ GCGGCUG@LB@ :\|\|\|\|\|:@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.69 kcal/mol@LB@Hybridization Energy -10.4159 kcal/mol@LB@Unfolding Energy - mRNA 3.66497 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 175 -- 181@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 80 -- 86@LB@
155	0.06493	0.3424	ct_355	N/A	-6.27	0.205473	16 -- 22	80 -- 86		_____________15______23\n_____________\|_______\|\n5'-GUU...UUCUG_______GGUCC...CCU-3'\n______________ACGGCUG\n______________\|\|\|\|\|\|:\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	16 -- 22	80 -- 86	-10.68 kcal/mol	3.341 kcal/mol	1.06449 kcal/mol	15 23@LB@ \| \|@LB@5'-GUU...UUCUG GGUCC...CCU-3'@LB@ ACGGCUG@LB@ \|\|\|\|\|\|:@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -10.68 kcal/mol@LB@Unfolding Energy - mRNA 3.341 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 16 -- 22@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 80 -- 86@LB@
156	0.06505	0.3424	ct_254	N/A	-6.97	0.146186	84 -- 91	80 -- 87		_____________83_______92\n_____________\|________\|\n5'-GUC...AUCGU________GCGUU...UAC-3'\n______________UAUGGCUG\n______________\|\|:\|\|\|\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	85 -- 91	80 -- 86	-9.90306 kcal/mol	1.8348 kcal/mol	1.09752 kcal/mol	83 92@LB@ \| \|@LB@5'-GUC...AUCGU GCGUU...UAC-3'@LB@ UAUGGCUG@LB@ \|\|:\|\|\|\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -9.90306 kcal/mol@LB@Unfolding Energy - mRNA 1.8348 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 84 -- 91@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 80 -- 86@LB@
181	0.07898	0.3587	ct_186	devB	-5.59	0.281766	201 -- 207	80 -- 86	6-phosphogluconolactonase	_____________200_____208\n_____________\|_______\|\n5'-GAA...UAUAC_______CCCUU...CAG-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	201 -- 207	80 -- 86	-9.11344 kcal/mol	2.46127 kcal/mol	1.06449 kcal/mol	200 208@LB@ \| \|@LB@5'-GAA...UAUAC CCCUU...CAG-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.59 kcal/mol@LB@Hybridization Energy -9.11344 kcal/mol@LB@Unfolding Energy - mRNA 2.46127 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 201 -- 207@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 80 -- 86@LB@
41	0.01426	0.2859	ct_458	YhhY	-4.46	0.446972	238 -- 245	81 -- 88	acetyltransferase	_____________237______246\n_____________\|________\|\n5'-UUA...UCGGU________CCUGA...GAG-3'\n______________AUACGGUU\n______________\|\|\|\|\|\|:\|\n______________UAUGCCGA\n3'-UUU...GCCUC________UUGAG...GAA-5'\n_____________\|________\|\n_____________89_______80\n	239 -- 245	81 -- 87	-8.66821 kcal/mol	3.10635 kcal/mol	1.09753 kcal/mol	237 246@LB@ \| \|@LB@5'-UUA...UCGGU CCUGA...GAG-3'@LB@ AUACGGUU@LB@ \|\|\|\|\|\|:\|@LB@ UAUGCCGA@LB@3'-UUU...GCCUC UUGAG...GAA-5'@LB@ \| \|@LB@ 89 80@LB@@LB@@LB@Energy -4.46 kcal/mol@LB@Hybridization Energy -8.66821 kcal/mol@LB@Unfolding Energy - mRNA 3.10635 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 238 -- 245@LB@Position - sRNA 81 -- 88@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 81 -- 87@LB@
71	0.027	0.29	ct_712	N/A	-6.32	0.201489	257 -- 263	81 -- 87	type III secretion system effector protein	_____________256_____264\n_____________\|_______\|\n5'-CAG...GAGAC_______CCUCG...CAG-3'\n______________UGCGGCU\n______________\|:\|\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	257 -- 263	81 -- 87	-10.8048 kcal/mol	3.3916 kcal/mol	1.09752 kcal/mol	256 264@LB@ \| \|@LB@5'-CAG...GAGAC CCUCG...CAG-3'@LB@ UGCGGCU@LB@ \|:\|\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -10.8048 kcal/mol@LB@Unfolding Energy - mRNA 3.3916 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 257 -- 263@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 81 -- 87@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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