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
177	0.07605	0.3532	ct_428	ubiE	-3.67	0.587989	9 -- 17	20 -- 28	demethylmenaquinone methyltransferase	_____________8_________18\n_____________\|_________\|\n___5'-UUCUUCAA_________UUCAG...AUA-3'\n______________CUAUUUCAU\n______________\|\|\|\|\|:\|\|\|\n______________GAUAAGGUA\n3'-UUU...UCUUC_________CCGCA...GAA-5'\n_____________\|_________\|\n_____________29________19\n	10 -- 16	21 -- 27	-8.26525 kcal/mol	0.050804 kcal/mol	4.54807 kcal/mol	8 18@LB@ \| \|@LB@ 5'-UUCUUCAA UUCAG...AUA-3'@LB@ CUAUUUCAU@LB@ \|\|\|\|\|:\|\|\|@LB@ GAUAAGGUA@LB@3'-UUU...UCUUC CCGCA...GAA-5'@LB@ \| \|@LB@ 29 19@LB@@LB@@LB@Energy -3.67 kcal/mol@LB@Hybridization Energy -8.26525 kcal/mol@LB@Unfolding Energy - mRNA 0.050804 kcal/mol@LB@Unfolding Energy - sRNA 4.54807 kcal/mol@LB@@LB@Position - mRNA 9 -- 17@LB@Position - sRNA 20 -- 28@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 21 -- 27@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@
154	0.06467	0.3424	ct_517	rl24	-3.21	0.671117	143 -- 150	27 -- 34	50S ribosomal protein L24	_____________142______151\n_____________\|________\|\n5'-UAA...CGAGA________UUGUU...AGG-3'\n______________CAGAGGCU\n______________\|\|\|\|:\|\|\|\n______________GUCUUCGA\n3'-UUU...UCUCA________UAAGG...GAA-5'\n_____________\|________\|\n_____________35_______26\n	144 -- 150	27 -- 33	-11.3134 kcal/mol	3.50051 kcal/mol	4.59929 kcal/mol	142 151@LB@ \| \|@LB@5'-UAA...CGAGA UUGUU...AGG-3'@LB@ CAGAGGCU@LB@ \|\|\|\|:\|\|\|@LB@ GUCUUCGA@LB@3'-UUU...UCUCA UAAGG...GAA-5'@LB@ \| \|@LB@ 35 26@LB@@LB@@LB@Energy -3.21 kcal/mol@LB@Hybridization Energy -11.3134 kcal/mol@LB@Unfolding Energy - mRNA 3.50051 kcal/mol@LB@Unfolding Energy - sRNA 4.59929 kcal/mol@LB@@LB@Position - mRNA 143 -- 150@LB@Position - sRNA 27 -- 34@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 27 -- 33@LB@
168	0.07022	0.3436	ct_336	ptsI	-3.01	0.707290	114 -- 124	23 -- 33	phosphoenolpyruvate-protein phosphotransferase	_____________113_________125\n_____________\|___________\|\n5'-GUU...GGCGA__UU_______AUAUA...UGU-3'\n______________GG__GCUGUUC\n______________:\|__\|\|\|:\|\|\|\n______________UC__CGAUAAG\n3'-UUU...CUCAG__UU_______GUACC...GAA-5'\n_____________\|___________\|\n_____________34__________22\n	118 -- 124	23 -- 29	-10.9545 kcal/mol	3.2189 kcal/mol	4.72321 kcal/mol	113 125@LB@ \| \|@LB@5'-GUU...GGCGA UU AUAUA...UGU-3'@LB@ GG GCUGUUC@LB@ :\| \|\|\|:\|\|\|@LB@ UC CGAUAAG@LB@3'-UUU...CUCAG UU GUACC...GAA-5'@LB@ \| \|@LB@ 34 22@LB@@LB@@LB@Energy -3.01 kcal/mol@LB@Hybridization Energy -10.9545 kcal/mol@LB@Unfolding Energy - mRNA 3.2189 kcal/mol@LB@Unfolding Energy - sRNA 4.72321 kcal/mol@LB@@LB@Position - mRNA 114 -- 124@LB@Position - sRNA 23 -- 33@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 23 -- 29@LB@
191	0.08461	0.363	ct_112	pepF	-2.97	0.715117	121 -- 127	54 -- 60	oligoendopeptidase F	_____________120_____128\n_____________\|_______\|\n5'-UCU...UCUCU_______ACUGG...AAG-3'\n______________UCCCCUU\n______________\|\|\|\|\|::\n______________AGGGGGG\n3'-UUU...ACUGA_______ACACA...GAA-5'\n_____________\|_______\|\n_____________61______53\n	121 -- 127	54 -- 60	-10.8708 kcal/mol	1.46061 kcal/mol	6.44182 kcal/mol	120 128@LB@ \| \|@LB@5'-UCU...UCUCU ACUGG...AAG-3'@LB@ UCCCCUU@LB@ \|\|\|\|\|::@LB@ AGGGGGG@LB@3'-UUU...ACUGA ACACA...GAA-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -2.97 kcal/mol@LB@Hybridization Energy -10.8708 kcal/mol@LB@Unfolding Energy - mRNA 1.46061 kcal/mol@LB@Unfolding Energy - sRNA 6.44182 kcal/mol@LB@@LB@Position - mRNA 121 -- 127@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 54 -- 60@LB@
101	0.03758	0.3036	ct_457	N/A	-2.86	0.734073	54 -- 60	80 -- 86	transcriptional regulator	_____________53______61\n_____________\|_______\|\n5'-GGA...GUAAG_______GGUUA...UCU-3'\n______________AUGGUUG\n______________\|:\|\|:\|:\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	54 -- 60	80 -- 86	-6.17108 kcal/mol	2.2465 kcal/mol	1.06449 kcal/mol	53 61@LB@ \| \|@LB@5'-GGA...GUAAG GGUUA...UCU-3'@LB@ AUGGUUG@LB@ \|:\|\|:\|:@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -2.86 kcal/mol@LB@Hybridization Energy -6.17108 kcal/mol@LB@Unfolding Energy - mRNA 2.2465 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 54 -- 60@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 80 -- 86@LB@
163	0.06794	0.3424	ct_661	N/A	-2.85	0.735752	184 -- 191	21 -- 28	DNA topoisomerase IV subunit B	_____________183______192\n_____________\|________\|\n5'-AAA...UUGCC________CACAC...GCG-3'\n______________UUAUUCCA\n______________:\|\|\|\|\|\|\|\n______________GAUAAGGU\n3'-UUU...UCUUC________ACCGC...GAA-5'\n_____________\|________\|\n_____________29_______20\n	185 -- 191	21 -- 27	-7.6538 kcal/mol	0.450062 kcal/mol	4.35509 kcal/mol	183 192@LB@ \| \|@LB@5'-AAA...UUGCC CACAC...GCG-3'@LB@ UUAUUCCA@LB@ :\|\|\|\|\|\|\|@LB@ GAUAAGGU@LB@3'-UUU...UCUUC ACCGC...GAA-5'@LB@ \| \|@LB@ 29 20@LB@@LB@@LB@Energy -2.85 kcal/mol@LB@Hybridization Energy -7.6538 kcal/mol@LB@Unfolding Energy - mRNA 0.450062 kcal/mol@LB@Unfolding Energy - sRNA 4.35509 kcal/mol@LB@@LB@Position - mRNA 184 -- 191@LB@Position - sRNA 21 -- 28@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 21 -- 27@LB@
158	0.06677	0.3424	ct_770	fabF	-2.81	0.742017	6 -- 13	26 -- 33	3-oxoacyl-ACP synthase	_____________5________14\n_____________\|________\|\n______5'-UAUAG________AAAAA...GUG-3'\n______________AGGAGUUA\n______________\|\|:\|\|:\|\|\n______________UCUUCGAU\n3'-UUU...CUCAG________AAGGU...GAA-5'\n_____________\|________\|\n_____________34_______25\n	7 -- 13	26 -- 32	-8.27201 kcal/mol	0.759487 kcal/mol	4.69868 kcal/mol	5 14@LB@ \| \|@LB@ 5'-UAUAG AAAAA...GUG-3'@LB@ AGGAGUUA@LB@ \|\|:\|\|:\|\|@LB@ UCUUCGAU@LB@3'-UUU...CUCAG AAGGU...GAA-5'@LB@ \| \|@LB@ 34 25@LB@@LB@@LB@Energy -2.81 kcal/mol@LB@Hybridization Energy -8.27201 kcal/mol@LB@Unfolding Energy - mRNA 0.759487 kcal/mol@LB@Unfolding Energy - sRNA 4.69868 kcal/mol@LB@@LB@Position - mRNA 6 -- 13@LB@Position - sRNA 26 -- 33@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 26 -- 32@LB@
140	0.05617	0.3262	ct_759	nlpD	-2.72	0.757894	26 -- 32	51 -- 57	muramidase	_____________25______33\n_____________\|_______\|\n5'-GAG...AGAGU_______AACCG...AGU-3'\n______________UCCCUGU\n______________:\|\|\|\|\|\|\n______________GGGGACA\n3'-UUU...GAAGG_______CAUGU...GAA-5'\n_____________\|_______\|\n_____________58______50\n	26 -- 32	51 -- 57	-10.8083 kcal/mol	0.989353 kcal/mol	7.09845 kcal/mol	25 33@LB@ \| \|@LB@5'-GAG...AGAGU AACCG...AGU-3'@LB@ UCCCUGU@LB@ :\|\|\|\|\|\|@LB@ GGGGACA@LB@3'-UUU...GAAGG CAUGU...GAA-5'@LB@ \| \|@LB@ 58 50@LB@@LB@@LB@Energy -2.72 kcal/mol@LB@Hybridization Energy -10.8083 kcal/mol@LB@Unfolding Energy - mRNA 0.989353 kcal/mol@LB@Unfolding Energy - sRNA 7.09845 kcal/mol@LB@@LB@Position - mRNA 26 -- 32@LB@Position - sRNA 51 -- 57@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 51 -- 57@LB@
88	0.03104	0.29	ct_766	miaA	-2.38	0.813549	82 -- 88	27 -- 33	tRNA dimethylallyltransferase	_____________81______89\n_____________\|_______\|\n5'-AUA...UAAUG_______UUGUA...UGU-3'\n______________GGAAGCU\n______________:\|\|\|\|\|\|\n______________UCUUCGA\n3'-UUU...CUCAG_______UAAGG...GAA-5'\n_____________\|_______\|\n_____________34______26\n	82 -- 88	27 -- 33	-8.83329 kcal/mol	1.86027 kcal/mol	4.59825 kcal/mol	81 89@LB@ \| \|@LB@5'-AUA...UAAUG UUGUA...UGU-3'@LB@ GGAAGCU@LB@ :\|\|\|\|\|\|@LB@ UCUUCGA@LB@3'-UUU...CUCAG UAAGG...GAA-5'@LB@ \| \|@LB@ 34 26@LB@@LB@@LB@Energy -2.38 kcal/mol@LB@Hybridization Energy -8.83329 kcal/mol@LB@Unfolding Energy - mRNA 1.86027 kcal/mol@LB@Unfolding Energy - sRNA 4.59825 kcal/mol@LB@@LB@Position - mRNA 82 -- 88@LB@Position - sRNA 27 -- 33@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 27 -- 33@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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