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
47	0.01707	0.29	ct_577	N/A	-4.79	0.394783	124 -- 141	41 -- 59		_____________123_________________142\n_____________\|___________________\|\n5'-GAU...CAAGC_______CCUAA_______AAAAG...AAU-3'\n______________CUCCUCU______AAACAC\n______________\|:\|\|:\|\|______\|\|\|\|\|\|\n______________GGGGGGA______UUUGUG\n3'-UUU...CUGAA_______CACAUG______AUCUC...GAA-5'\n_____________\|___________________\|\n_____________60__________________40\n	124 -- 130	53 -- 59	-14.9438 kcal/mol	1.33474 kcal/mol	8.82318 kcal/mol	123 142@LB@ \| \|@LB@5'-GAU...CAAGC CCUAA AAAAG...AAU-3'@LB@ CUCCUCU AAACAC@LB@ \|:\|\|:\|\| \|\|\|\|\|\|@LB@ GGGGGGA UUUGUG@LB@3'-UUU...CUGAA CACAUG AUCUC...GAA-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -4.79 kcal/mol@LB@Hybridization Energy -14.9438 kcal/mol@LB@Unfolding Energy - mRNA 1.33474 kcal/mol@LB@Unfolding Energy - sRNA 8.82318 kcal/mol@LB@@LB@Position - mRNA 124 -- 141@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 53 -- 59@LB@
40	0.01393	0.2859	ct_695	N/A	-4.73	0.403172	160 -- 166	82 -- 88		_____________159_____167\n_____________\|_______\|\n5'-AUU...AAGGU_______GUUCG...AGG-3'\n______________AUGCGGU\n______________\|\|:\|\|\|:\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	160 -- 166	82 -- 88	-8.16543 kcal/mol	2.33498 kcal/mol	1.09753 kcal/mol	159 167@LB@ \| \|@LB@5'-AUU...AAGGU GUUCG...AGG-3'@LB@ AUGCGGU@LB@ \|\|:\|\|\|:@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -4.73 kcal/mol@LB@Hybridization Energy -8.16543 kcal/mol@LB@Unfolding Energy - mRNA 2.33498 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 160 -- 166@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 82 -- 88@LB@
170	0.07264	0.3448	ct_415	yebL	-4.69	0.409849	24 -- 30	22 -- 28	metal ABC transporter substrate-binding protein	_____________23______31\n_____________\|_______\|\n5'-AUU...AAAAA_______UCACC...CCU-3'\n______________CUGUUCC\n______________\|\|:\|\|\|\|\n______________GAUAAGG\n3'-UUU...UCUUC_______UACCG...GAA-5'\n_____________\|_______\|\n_____________29______21\n	24 -- 30	22 -- 28	-9.14166 kcal/mol	0.102316 kcal/mol	4.35007 kcal/mol	23 31@LB@ \| \|@LB@5'-AUU...AAAAA UCACC...CCU-3'@LB@ CUGUUCC@LB@ \|\|:\|\|\|\|@LB@ GAUAAGG@LB@3'-UUU...UCUUC UACCG...GAA-5'@LB@ \| \|@LB@ 29 21@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -9.14166 kcal/mol@LB@Unfolding Energy - mRNA 0.102316 kcal/mol@LB@Unfolding Energy - sRNA 4.35007 kcal/mol@LB@@LB@Position - mRNA 24 -- 30@LB@Position - sRNA 22 -- 28@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 22 -- 28@LB@
138	0.05554	0.3262	ct_806	ptr	-4.69	0.410459	54 -- 70	19 -- 33	insulinase/protease	_____________53________________71\n_____________\|_________________\|\n5'-GUU...UCCGA________AUAUA____AUAAA...UAA-3'\n______________AGAAGCUG_____CAUG\n______________\|\|\|\|\|\|\|:_____\|\|\|\|\n______________UCUUCGAU_____GUAC\n3'-UUU...CUCAG________AAG______CGCAA...GAA-5'\n_____________\|_________________\|\n_____________34________________18\n	55 -- 61	26 -- 32	-13.627 kcal/mol	3.96302 kcal/mol	4.97702 kcal/mol	53 71@LB@ \| \|@LB@5'-GUU...UCCGA AUAUA AUAAA...UAA-3'@LB@ AGAAGCUG CAUG@LB@ \|\|\|\|\|\|\|: \|\|\|\|@LB@ UCUUCGAU GUAC@LB@3'-UUU...CUCAG AAG CGCAA...GAA-5'@LB@ \| \|@LB@ 34 18@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -13.627 kcal/mol@LB@Unfolding Energy - mRNA 3.96302 kcal/mol@LB@Unfolding Energy - sRNA 4.97702 kcal/mol@LB@@LB@Position - mRNA 54 -- 70@LB@Position - sRNA 19 -- 33@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 26 -- 32@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@
152	0.064	0.3424	ct_749	alaS	-4.53	0.436714	274 -- 290	41 -- 57	alanine--tRNA ligase	_____________273_______________291\n_____________\|_________________\|\n5'-AAA...AUCUU_______UUUCCC____AAUGA...CUU-3'\n______________CUCCUGU______GCAU\n______________\|:\|\|\|\|\|______:\|\|:\n______________GGGGACA______UGUG\n3'-UUU...GAAGG_______CAUGUU____AUCUC...GAA-5'\n_____________\|_________________\|\n_____________58________________40\n	274 -- 280	51 -- 57	-13.0187 kcal/mol	0.670655 kcal/mol	7.82241 kcal/mol	273 291@LB@ \| \|@LB@5'-AAA...AUCUU UUUCCC AAUGA...CUU-3'@LB@ CUCCUGU GCAU@LB@ \|:\|\|\|\|\| :\|\|:@LB@ GGGGACA UGUG@LB@3'-UUU...GAAGG CAUGUU AUCUC...GAA-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -4.53 kcal/mol@LB@Hybridization Energy -13.0187 kcal/mol@LB@Unfolding Energy - mRNA 0.670655 kcal/mol@LB@Unfolding Energy - sRNA 7.82241 kcal/mol@LB@@LB@Position - mRNA 274 -- 290@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 51 -- 57@LB@
194	0.08693	0.3657	ct_285	lplA_1	-4.48	0.444512	66 -- 74	27 -- 35	lipoate protein ligase	_____________65________75\n_____________\|_________\|\n5'-CUU...AAUUU_________UUUUU...UUC-3'\n______________UUAGAAGCU\n______________\|:\|\|\|\|\|\|\|\n______________AGUCUUCGA\n3'-UUU...AUCUC_________UAAGG...GAA-5'\n_____________\|_________\|\n_____________36________26\n	68 -- 74	27 -- 33	-10.5389 kcal/mol	1.46011 kcal/mol	4.60001 kcal/mol	65 75@LB@ \| \|@LB@5'-CUU...AAUUU UUUUU...UUC-3'@LB@ UUAGAAGCU@LB@ \|:\|\|\|\|\|\|\|@LB@ AGUCUUCGA@LB@3'-UUU...AUCUC UAAGG...GAA-5'@LB@ \| \|@LB@ 36 26@LB@@LB@@LB@Energy -4.48 kcal/mol@LB@Hybridization Energy -10.5389 kcal/mol@LB@Unfolding Energy - mRNA 1.46011 kcal/mol@LB@Unfolding Energy - sRNA 4.60001 kcal/mol@LB@@LB@Position - mRNA 66 -- 74@LB@Position - sRNA 27 -- 35@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 27 -- 33@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@
57	0.02238	0.29	ct_132	N/A	-4.44	0.450895	20 -- 27	53 -- 60		_____________19_______28\n_____________\|________\|\n5'-GAU...AUGGA________AAAAA...ACA-3'\n______________UCUCCCCU\n______________\|\|:\|\|\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	21 -- 27	53 -- 59	-12.9803 kcal/mol	2.08802 kcal/mol	6.45136 kcal/mol	19 28@LB@ \| \|@LB@5'-GAU...AUGGA AAAAA...ACA-3'@LB@ UCUCCCCU@LB@ \|\|:\|\|\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -4.44 kcal/mol@LB@Hybridization Energy -12.9803 kcal/mol@LB@Unfolding Energy - mRNA 2.08802 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 20 -- 27@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 53 -- 59@LB@
150	0.06394	0.3424	ct_208	gseA	-4.42	0.454874	290 -- 300	19 -- 29	3-deoxy-D-manno-octulosonic acid transferase	_____________289________300\n_____________\|__________\|\n5'-UUG...AAAGU___U_______-3'\n______________GUU_UUCCAUG\n______________\|:\|_\|\|\|\|\|\|\|\n______________CGA_AAGGUAC\n3'-UUU...GUCUU___U_______CGCAA...GAA-5'\n_____________\|___________\|\n_____________30__________18\n	294 -- 300	19 -- 25	-10.2082 kcal/mol	1.1238 kcal/mol	4.66719 kcal/mol	289 300@LB@ \| \|@LB@5'-UUG...AAAGU U -3'@LB@ GUU UUCCAUG@LB@ \|:\| \|\|\|\|\|\|\|@LB@ CGA AAGGUAC@LB@3'-UUU...GUCUU U CGCAA...GAA-5'@LB@ \| \|@LB@ 30 18@LB@@LB@@LB@Energy -4.42 kcal/mol@LB@Hybridization Energy -10.2082 kcal/mol@LB@Unfolding Energy - mRNA 1.1238 kcal/mol@LB@Unfolding Energy - sRNA 4.66719 kcal/mol@LB@@LB@Position - mRNA 290 -- 300@LB@Position - sRNA 19 -- 29@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 19 -- 25@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

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching