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
111	0.04436	0.3262	ct_405	ribC	-3.97	0.532190	3 -- 10	49 -- 56	riboflavin synthase	_____________2________11\n_____________\|________\|\n_________5'-AA________CUUGU...AUG-3'\n______________UCCUGUGU\n______________:\|\|\|\|\|\|\|\n______________GGGACACA\n3'-UUU...AAGGG________UGUUU...GAA-5'\n_____________\|________\|\n_____________57_______48\n	4 -- 10	49 -- 55	-11.4476 kcal/mol	0.227857 kcal/mol	7.24525 kcal/mol	2 11@LB@ \| \|@LB@ 5'-AA CUUGU...AUG-3'@LB@ UCCUGUGU@LB@ :\|\|\|\|\|\|\|@LB@ GGGACACA@LB@3'-UUU...AAGGG UGUUU...GAA-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -3.97 kcal/mol@LB@Hybridization Energy -11.4476 kcal/mol@LB@Unfolding Energy - mRNA 0.227857 kcal/mol@LB@Unfolding Energy - sRNA 7.24525 kcal/mol@LB@@LB@Position - mRNA 3 -- 10@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 49 -- 55@LB@
112	0.04461	0.3262	ct_089	lcrE	-7.82	0.094118	129 -- 157	3 -- 33	low calcium response protein E	_____________128_____________________________158\n_____________\|_______________________________\|\n5'-CGG...UACCA_______UUA_____AAA_____________CUUUG...UUA-3'\n______________AGAAGUU___CC_UG___UUAGAAU_CCAGC\n______________\|\|\|\|\|:\|___\|\|_\|\|___\|\|\|\|\|\|\|_\|\|\|:\|\n______________UCUUCGA___GG_AC___AAUCUUA_GGUUG\n3'-UUU...CUCAG_______UAA__U__CGC_______U_____AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	129 -- 135	27 -- 33	-21.9416 kcal/mol	5.52555 kcal/mol	8.59196 kcal/mol	128 158@LB@ \| \|@LB@5'-CGG...UACCA UUA AAA CUUUG...UUA-3'@LB@ AGAAGUU CC UG UUAGAAU CCAGC@LB@ \|\|\|\|\|:\| \|\| \|\| \|\|\|\|\|\|\| \|\|\|:\|@LB@ UCUUCGA GG AC AAUCUUA GGUUG@LB@3'-UUU...CUCAG UAA U CGC U AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -7.82 kcal/mol@LB@Hybridization Energy -21.9416 kcal/mol@LB@Unfolding Energy - mRNA 5.52555 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 129 -- 157@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 27 -- 33@LB@
113	0.04597	0.3262	ct_841	ftsH	-6.80	0.159029	200 -- 207	80 -- 87	ATP-dependent zinc metalloprotease FtsH	_____________199______208\n_____________\|________\|\n5'-GGU...AGUUU________AAGAU...UUC-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	200 -- 206	81 -- 87	-10.6438 kcal/mol	2.74436 kcal/mol	1.09752 kcal/mol	199 208@LB@ \| \|@LB@5'-GGU...AGUUU AAGAU...UUC-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.80 kcal/mol@LB@Hybridization Energy -10.6438 kcal/mol@LB@Unfolding Energy - mRNA 2.74436 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@
114	0.04665	0.3262	ct_848	N/A	-8.83	0.054442	279 -- 286	79 -- 86		_____________278______287\n_____________\|________\|\n5'-CAA...CUGCA________UGAGA...CAC-3'\n______________ACGGCUGA\n______________\|\|\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	280 -- 286	79 -- 85	-11.4013 kcal/mol	1.46996 kcal/mol	1.09752 kcal/mol	278 287@LB@ \| \|@LB@5'-CAA...CUGCA UGAGA...CAC-3'@LB@ ACGGCUGA@LB@ \|\|\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -8.83 kcal/mol@LB@Hybridization Energy -11.4013 kcal/mol@LB@Unfolding Energy - mRNA 1.46996 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 279 -- 286@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 79 -- 85@LB@
115	0.04794	0.3262	ct_778	priA	-6.05	0.227860	46 -- 52	54 -- 60	primosomal protein N'	_____________45______53\n_____________\|_______\|\n5'-CGC...GUCAU_______AUCCU...AAA-3'\n______________UCCCCUC\n______________\|\|\|\|\|:\|\n______________AGGGGGG\n3'-UUU...ACUGA_______ACACA...GAA-5'\n_____________\|_______\|\n_____________61______53\n	46 -- 52	54 -- 60	-12.5948 kcal/mol	0.0982726 kcal/mol	6.44182 kcal/mol	45 53@LB@ \| \|@LB@5'-CGC...GUCAU AUCCU...AAA-3'@LB@ UCCCCUC@LB@ \|\|\|\|\|:\|@LB@ AGGGGGG@LB@3'-UUU...ACUGA ACACA...GAA-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -6.05 kcal/mol@LB@Hybridization Energy -12.5948 kcal/mol@LB@Unfolding Energy - mRNA 0.0982726 kcal/mol@LB@Unfolding Energy - sRNA 6.44182 kcal/mol@LB@@LB@Position - mRNA 46 -- 52@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 54 -- 60@LB@
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@
117	0.04834	0.3262	ct_237	fabG	-8.76	0.056710	143 -- 164	34 -- 58	3-oxoacyl-[acyl-carrier-protein] reductase	_____________142________________________165\n_____________\|__________________________\|\n5'-CGU...GAGUU_________________U________UAUGG...AUG-3'\n______________CCCCUUGU____AAACA_UUAGGGUC\n______________\|\|\|\|:\|\|\|____\|\|\|\|\|_:\|\|\|:\|\|\|\n______________GGGGGACA____UUUGU_GAUCUCAG\n3'-UUU...UGAAG________CAUG______________UCUUC...GAA-5'\n_____________\|__________________________\|\n_____________59_________________________33\n	144 -- 150	51 -- 57	-24.3621 kcal/mol	7.62467 kcal/mol	7.97757 kcal/mol	142 165@LB@ \| \|@LB@5'-CGU...GAGUU U UAUGG...AUG-3'@LB@ CCCCUUGU AAACA UUAGGGUC@LB@ \|\|\|\|:\|\|\| \|\|\|\|\| :\|\|\|:\|\|\|@LB@ GGGGGACA UUUGU GAUCUCAG@LB@3'-UUU...UGAAG CAUG UCUUC...GAA-5'@LB@ \| \|@LB@ 59 33@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -24.3621 kcal/mol@LB@Unfolding Energy - mRNA 7.62467 kcal/mol@LB@Unfolding Energy - sRNA 7.97757 kcal/mol@LB@@LB@Position - mRNA 143 -- 164@LB@Position - sRNA 34 -- 58@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 51 -- 57@LB@
118	0.04846	0.3262	ct_515	rs8	-12.50	0.006183	13 -- 43	3 -- 33	30S ribosomal protein S8	_____________12_______________________________44\n_____________\|________________________________\|\n5'-GGA...GACGA___U________UU__________UG______AAAUC...UGC-3'\n______________GGA_GUUAUUCC__UGGU_UUAGA__AUCAGC\n______________:\|\|_\|:\|\|\|\|\|\|__\|\|\|:_\|\|\|\|\|__\|:\|\|:\|\n______________UCU_CGAUAAGG__ACCG_AAUCU__UGGUUG\n3'-UUU...CUCAG___U________U_____C_____UA______AA-5'\n_____________\|________________________________\|\n_____________34_______________________________2\n	18 -- 24	22 -- 28	-29.6343 kcal/mol	8.5463 kcal/mol	8.59196 kcal/mol	12 44@LB@ \| \|@LB@5'-GGA...GACGA U UU UG AAAUC...UGC-3'@LB@ GGA GUUAUUCC UGGU UUAGA AUCAGC@LB@ :\|\| \|:\|\|\|\|\|\| \|\|\|: \|\|\|\|\| \|:\|\|:\|@LB@ UCU CGAUAAGG ACCG AAUCU UGGUUG@LB@3'-UUU...CUCAG U U C UA AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -29.6343 kcal/mol@LB@Unfolding Energy - mRNA 8.5463 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 13 -- 43@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 22 -- 28@LB@
119	0.04857	0.3262	ct_706	clpP_2	-8.60	0.061801	14 -- 27	22 -- 35	ATP-dependent Clp protease proteolytic subunit	_____________13_____________28\n_____________\|______________\|\n5'-CGA...AAGAU______________UUCUU...GGC-3'\n______________UUAGAGGUUGUUCC\n______________\|:\|\|\|:\|:\|:\|\|\|\|\n______________AGUCUUCGAUAAGG\n3'-UUU...AUCUC______________UACCG...GAA-5'\n_____________\|______________\|\n_____________36_____________21\n	16 -- 22	27 -- 33	-17.9181 kcal/mol	4.58788 kcal/mol	4.72627 kcal/mol	13 28@LB@ \| \|@LB@5'-CGA...AAGAU UUCUU...GGC-3'@LB@ UUAGAGGUUGUUCC@LB@ \|:\|\|\|:\|:\|:\|\|\|\|@LB@ AGUCUUCGAUAAGG@LB@3'-UUU...AUCUC UACCG...GAA-5'@LB@ \| \|@LB@ 36 21@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -17.9181 kcal/mol@LB@Unfolding Energy - mRNA 4.58788 kcal/mol@LB@Unfolding Energy - sRNA 4.72627 kcal/mol@LB@@LB@Position - mRNA 14 -- 27@LB@Position - sRNA 22 -- 35@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 27 -- 33@LB@
120	0.04883	0.3262	ct_827	nrdA	-5.19	0.334730	7 -- 13	82 -- 88	ribonucleoside-diphosphate reductase subunit alpha	_____________6_______14\n_____________\|_______\|\n_____5'-UUCUAU_______AUACA...CUU-3'\n______________AUAUGGU\n______________\|\|\|:\|\|:\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	7 -- 13	82 -- 88	-6.89581 kcal/mol	0.608866 kcal/mol	1.09753 kcal/mol	6 14@LB@ \| \|@LB@ 5'-UUCUAU AUACA...CUU-3'@LB@ AUAUGGU@LB@ \|\|\|:\|\|:@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -5.19 kcal/mol@LB@Hybridization Energy -6.89581 kcal/mol@LB@Unfolding Energy - mRNA 0.608866 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 7 -- 13@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 82 -- 88@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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