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
16	0.003859	0.1836	ct_666	N/A	-9.59	0.035525	190 -- 206	16 -- 33		_____________189________________207\n_____________\|__________________\|\n5'-GAU...AAAAG_____G____________AGCGG...AAA-3'\n______________AGAGG_UA_UCUAUGGCG\n______________\|\|\|:\|_\|\|_\|\|:\|\|\|\|\|\|\n______________UCUUC_AU_AGGUACCGC\n3'-UUU...CUCAG_____G__A_________AAUCU...GAA-5'\n_____________\|__________________\|\n_____________34_________________15\n	200 -- 206	16 -- 22	-21.7302 kcal/mol	4.22495 kcal/mol	7.91433 kcal/mol	189 207@LB@ \| \|@LB@5'-GAU...AAAAG G AGCGG...AAA-3'@LB@ AGAGG UA UCUAUGGCG@LB@ \|\|\|:\| \|\| \|\|:\|\|\|\|\|\|@LB@ UCUUC AU AGGUACCGC@LB@3'-UUU...CUCAG G A AAUCU...GAA-5'@LB@ \| \|@LB@ 34 15@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -21.7302 kcal/mol@LB@Unfolding Energy - mRNA 4.22495 kcal/mol@LB@Unfolding Energy - sRNA 7.91433 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 16 -- 33@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 16 -- 22@LB@
23	0.006311	0.2093	ct_671	N/A	-7.19	0.130787	265 -- 279	17 -- 34		_____________264_________________280\n_____________\|___________________\|\n5'-CAA...ACGUA________________A__CUAGA...UCC-3'\n______________CAGAGGCU____CAUG_GC\n______________\|\|\|\|:\|\|\|____\|\|\|\|_\|\|\n______________GUCUUCGA____GUAC_CG\n3'-UUU...UCUCA________UAAG_______CAAUC...GAA-5'\n_____________\|___________________\|\n_____________35__________________16\n	266 -- 272	27 -- 33	-15.8996 kcal/mol	3.73088 kcal/mol	4.97809 kcal/mol	264 280@LB@ \| \|@LB@5'-CAA...ACGUA A CUAGA...UCC-3'@LB@ CAGAGGCU CAUG GC@LB@ \|\|\|\|:\|\|\| \|\|\|\| \|\|@LB@ GUCUUCGA GUAC CG@LB@3'-UUU...UCUCA UAAG CAAUC...GAA-5'@LB@ \| \|@LB@ 35 16@LB@@LB@@LB@Energy -7.19 kcal/mol@LB@Hybridization Energy -15.8996 kcal/mol@LB@Unfolding Energy - mRNA 3.73088 kcal/mol@LB@Unfolding Energy - sRNA 4.97809 kcal/mol@LB@@LB@Position - mRNA 265 -- 279@LB@Position - sRNA 17 -- 34@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 27 -- 33@LB@
25	0.00654	0.2093	ct_672	N/A	-9.75	0.032384	176 -- 205	17 -- 33	type III secretion system protein	_____________175____________________________206\n_____________\|______________________________\|\n5'-AUC...GUAGA_______CAUAUAUAAGGU___C_______AGUUG...CUG-3'\n______________AGAAGCU____________AUU_CCAUGGC\n______________\|\|\|\|\|\|\|____________\|\|\|_\|\|\|\|\|\|\|\n______________UCUUCGA____________UAA_GGUACCG\n3'-UUU...CUCAG______________________________CAAUC...GAA-5'\n_____________\|______________________________\|\n_____________34_____________________________16\n	199 -- 205	17 -- 23	-19.3096 kcal/mol	4.57941 kcal/mol	4.97804 kcal/mol	175 206@LB@ \| \|@LB@5'-AUC...GUAGA CAUAUAUAAGGU C AGUUG...CUG-3'@LB@ AGAAGCU AUU CCAUGGC@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCUUCGA UAA GGUACCG@LB@3'-UUU...CUCAG CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -9.75 kcal/mol@LB@Hybridization Energy -19.3096 kcal/mol@LB@Unfolding Energy - mRNA 4.57941 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 176 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
91	0.03287	0.2942	ct_674	yscC	-7.61	0.105180	32 -- 46	36 -- 57	type II secretion system protein	_____________31_____________________47\n_____________\|______________________\|\n5'-UGG...ACACA______________G_______AUUUG...CGG-3'\n______________CCCC_______AAA_GCUAGAG\n______________\|\|\|\|_______\|\|\|_:\|\|\|\|\|\|\n______________GGGG_______UUU_UGAUCUC\n3'-UUU...GAAGG____ACACAUG___G_______AGUCU...GAA-5'\n_____________\|______________________\|\n_____________58_____________________35\n	40 -- 46	36 -- 42	-18.3 kcal/mol	2.71277 kcal/mol	7.97448 kcal/mol	31 47@LB@ \| \|@LB@5'-UGG...ACACA G AUUUG...CGG-3'@LB@ CCCC AAA GCUAGAG@LB@ \|\|\|\| \|\|\| :\|\|\|\|\|\|@LB@ GGGG UUU UGAUCUC@LB@3'-UUU...GAAGG ACACAUG G AGUCU...GAA-5'@LB@ \| \|@LB@ 58 35@LB@@LB@@LB@Energy -7.61 kcal/mol@LB@Hybridization Energy -18.3 kcal/mol@LB@Unfolding Energy - mRNA 2.71277 kcal/mol@LB@Unfolding Energy - sRNA 7.97448 kcal/mol@LB@@LB@Position - mRNA 32 -- 46@LB@Position - sRNA 36 -- 57@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 36 -- 42@LB@
98	0.03528	0.2959	ct_676	N/A	-6.99	0.144558	38 -- 44	80 -- 86	protein-arginine kinase activator protein	_____________37______45\n_____________\|_______\|\n5'-GGG...GCUCA_______GAGCA...GUU-3'\n______________GCGGUUA\n______________:\|\|\|:\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	38 -- 44	80 -- 86	-8.44953 kcal/mol	0.39201 kcal/mol	1.06449 kcal/mol	37 45@LB@ \| \|@LB@5'-GGG...GCUCA GAGCA...GUU-3'@LB@ GCGGUUA@LB@ :\|\|\|:\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -8.44953 kcal/mol@LB@Unfolding Energy - mRNA 0.39201 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 38 -- 44@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 38 -- 44@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@
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@
196	0.08741	0.3657	ct_698	N/A	-4.23	0.486304	280 -- 292	22 -- 34	tRNA modification GTPase	_____________279___________293\n_____________\|_____________\|\n5'-AAA...CGGAC____U________UAUUUCUG-3'\n______________CGGA_GCUAUUUC\n______________\|:\|\|_\|\|\|\|\|\|:\|\n______________GUCU_CGAUAAGG\n3'-UUU...UCUCA____U________UACCG...GAA-5'\n_____________\|_____________\|\n_____________35____________21\n	285 -- 291	23 -- 29	-13.8571 kcal/mol	4.89721 kcal/mol	4.72608 kcal/mol	279 293@LB@ \| \|@LB@5'-AAA...CGGAC U UAUUUCUG-3'@LB@ CGGA GCUAUUUC@LB@ \|:\|\| \|\|\|\|\|\|:\|@LB@ GUCU CGAUAAGG@LB@3'-UUU...UCUCA U UACCG...GAA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -4.23 kcal/mol@LB@Hybridization Energy -13.8571 kcal/mol@LB@Unfolding Energy - mRNA 4.89721 kcal/mol@LB@Unfolding Energy - sRNA 4.72608 kcal/mol@LB@@LB@Position - mRNA 280 -- 292@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 23 -- 29@LB@
166	0.06935	0.3427	ct_700	N/A	-9.45	0.038462	185 -- 207	17 -- 35		_____________184_____________________208\n_____________\|_______________________\|\n5'-UGG...AAAAC___________GCAUUA______UAAUC...AUC-3'\n______________UCAGAAGUUGU______UGUGGC\n______________\|\|\|\|\|\|\|:\|:\|______::\|\|\|\|\n______________AGUCUUCGAUA______GUACCG\n3'-UUU...AUCUC___________AG__________CAAUC...GAA-5'\n_____________\|_______________________\|\n_____________36______________________16\n	187 -- 193	27 -- 33	-18.7157 kcal/mol	4.28595 kcal/mol	4.9781 kcal/mol	184 208@LB@ \| \|@LB@5'-UGG...AAAAC GCAUUA UAAUC...AUC-3'@LB@ UCAGAAGUUGU UGUGGC@LB@ \|\|\|\|\|\|\|:\|:\| ::\|\|\|\|@LB@ AGUCUUCGAUA GUACCG@LB@3'-UUU...AUCUC AG CAAUC...GAA-5'@LB@ \| \|@LB@ 36 16@LB@@LB@@LB@Energy -9.45 kcal/mol@LB@Hybridization Energy -18.7157 kcal/mol@LB@Unfolding Energy - mRNA 4.28595 kcal/mol@LB@Unfolding Energy - sRNA 4.9781 kcal/mol@LB@@LB@Position - mRNA 185 -- 207@LB@Position - sRNA 17 -- 35@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 27 -- 33@LB@
195	0.08712	0.3657	ct_704	pcnB_2	-3.31	0.654425	101 -- 107	28 -- 34	poly A polymerase	_____________100_____108\n_____________\|_______\|\n5'-CAA...UACGG_______CAUCC...UGC-3'\n______________UAGAAGC\n______________:\|\|\|\|\|\|\n______________GUCUUCG\n3'-UUU...UCUCA_______AUAAG...GAA-5'\n_____________\|_______\|\n_____________35______27\n	101 -- 107	28 -- 34	-7.75845 kcal/mol	0.338622 kcal/mol	4.11458 kcal/mol	100 108@LB@ \| \|@LB@5'-CAA...UACGG CAUCC...UGC-3'@LB@ UAGAAGC@LB@ :\|\|\|\|\|\|@LB@ GUCUUCG@LB@3'-UUU...UCUCA AUAAG...GAA-5'@LB@ \| \|@LB@ 35 27@LB@@LB@@LB@Energy -3.31 kcal/mol@LB@Hybridization Energy -7.75845 kcal/mol@LB@Unfolding Energy - mRNA 0.338622 kcal/mol@LB@Unfolding Energy - sRNA 4.11458 kcal/mol@LB@@LB@Position - mRNA 101 -- 107@LB@Position - sRNA 28 -- 34@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 28 -- 34@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