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
136	0.05474	0.3262	ct_592	sdhA	-7.43	0.115894	38 -- 56	18 -- 34	succinate dehydrogenase flavoprotein subunit	_____________37__________________57\n_____________\|___________________\|\n5'-UCU...UGUUA___CU_____UU_______GUUUA...UGU-3'\n______________UAG__GCUGU__UCCAUGG\n______________:\|\|__\|\|\|:\|__\|\|\|\|\|\|\|\n______________GUC__CGAUA__AGGUACC\n3'-UUU...UCUCA___UU______________GCAAU...GAA-5'\n_____________\|___________________\|\n_____________35__________________17\n	50 -- 56	18 -- 24	-18.2308 kcal/mol	5.82664 kcal/mol	4.97803 kcal/mol	37 57@LB@ \| \|@LB@5'-UCU...UGUUA CU UU GUUUA...UGU-3'@LB@ UAG GCUGU UCCAUGG@LB@ :\|\| \|\|\|:\| \|\|\|\|\|\|\|@LB@ GUC CGAUA AGGUACC@LB@3'-UUU...UCUCA UU GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -7.43 kcal/mol@LB@Hybridization Energy -18.2308 kcal/mol@LB@Unfolding Energy - mRNA 5.82664 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 38 -- 56@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 18 -- 24@LB@
24	0.006504	0.2093	ct_534	cutE	-7.36	0.119875	40 -- 61	34 -- 57	apolipoprotein N-acyltransferase	_____________39_______________________62\n_____________\|________________________\|\n5'-CAG...CAAUU________GAAGUU__________AAUCC...GCG-3'\n______________CCCCUGUG______C_C_AGAGUU\n______________\|\|\|\|\|\|\|\|______\|_\|_\|\|\|\|\|:\n______________GGGGACAC______G_G_UCUCAG\n3'-UUU...GAAGG________AUGUUU_U_A______UCUUC...GAA-5'\n_____________\|________________________\|\n_____________58_______________________33\n	41 -- 47	50 -- 56	-22.0571 kcal/mol	6.72142 kcal/mol	7.97509 kcal/mol	39 62@LB@ \| \|@LB@5'-CAG...CAAUU GAAGUU AAUCC...GCG-3'@LB@ CCCCUGUG C C AGAGUU@LB@ \|\|\|\|\|\|\|\| \| \| \|\|\|\|\|:@LB@ GGGGACAC G G UCUCAG@LB@3'-UUU...GAAGG AUGUUU U A UCUUC...GAA-5'@LB@ \| \|@LB@ 58 33@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -22.0571 kcal/mol@LB@Unfolding Energy - mRNA 6.72142 kcal/mol@LB@Unfolding Energy - sRNA 7.97509 kcal/mol@LB@@LB@Position - mRNA 40 -- 61@LB@Position - sRNA 34 -- 57@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 50 -- 56@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@
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@
36	0.01184	0.2704	ct_030	gmk	-11.03	0.015227	49 -- 70	6 -- 34	guanylate kinase	_____________48____________________________71\n_____________\|_____________________________\|\n5'-AUA...UGAUG_____________________________CCGAG...CAC-3'\n______________CGGAAGCU___UCAUG____UAGAGUACC\n______________\|:\|\|\|\|\|\|___:\|\|\|\|____\|\|\|\|:\|\|\|\|\n______________GUCUUCGA___GGUAC____AUCUUAUGG\n3'-UUU...UCUCA________UAA_____CGCA_________UUGAA-5'\n_____________\|_____________________________\|\n_____________35____________________________5\n	64 -- 70	6 -- 12	-24.3478 kcal/mol	4.72233 kcal/mol	8.59183 kcal/mol	48 71@LB@ \| \|@LB@5'-AUA...UGAUG CCGAG...CAC-3'@LB@ CGGAAGCU UCAUG UAGAGUACC@LB@ \|:\|\|\|\|\|\| :\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ GUCUUCGA GGUAC AUCUUAUGG@LB@3'-UUU...UCUCA UAA CGCA UUGAA-5'@LB@ \| \|@LB@ 35 5@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -24.3478 kcal/mol@LB@Unfolding Energy - mRNA 4.72233 kcal/mol@LB@Unfolding Energy - sRNA 8.59183 kcal/mol@LB@@LB@Position - mRNA 49 -- 70@LB@Position - sRNA 6 -- 34@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 6 -- 12@LB@
77	0.02807	0.29	ct_309	N/A	-7.23	0.128520	50 -- 64	17 -- 33		_____________49________________65\n_____________\|_________________\|\n5'-AGA...GCUUA_________GU______UAAAU...UAA-3'\n______________AGGGGCUAU____UGGU\n______________\|\|::\|\|\|\|\|____\|\|\|:\n______________UCUUCGAUA____ACCG\n3'-UUU...CUCAG_________AGGU____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	52 -- 58	25 -- 31	-14.8286 kcal/mol	2.62564 kcal/mol	4.97804 kcal/mol	49 65@LB@ \| \|@LB@5'-AGA...GCUUA GU UAAAU...UAA-3'@LB@ AGGGGCUAU UGGU@LB@ \|\|::\|\|\|\|\| \|\|\|:@LB@ UCUUCGAUA ACCG@LB@3'-UUU...CUCAG AGGU CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -7.23 kcal/mol@LB@Hybridization Energy -14.8286 kcal/mol@LB@Unfolding Energy - mRNA 2.62564 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 50 -- 64@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 25 -- 31@LB@
134	0.05433	0.3262	ct_581	thrS	-7.17	0.132364	52 -- 64	21 -- 33	threonine--tRNA ligase	_____________51___________65\n_____________\|____________\|\n5'-AAA...CUAAA_______CC___GAACU...CAG-3'\n______________AGAAGCU__UCC\n______________\|\|\|\|\|\|\|__\|\|\|\n______________UCUUCGA__AGG\n3'-UUU...CUCAG_______UA___UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________20\n	52 -- 58	27 -- 33	-13.855 kcal/mol	1.83194 kcal/mol	4.72509 kcal/mol	51 65@LB@ \| \|@LB@5'-AAA...CUAAA CC GAACU...CAG-3'@LB@ AGAAGCU UCC@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ UCUUCGA AGG@LB@3'-UUU...CUCAG UA UACCG...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -13.855 kcal/mol@LB@Unfolding Energy - mRNA 1.83194 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 52 -- 64@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 27 -- 33@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@
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@
66	0.02511	0.29	ct_461	N/A	-5.44	0.300406	64 -- 70	79 -- 85	UDP-2 3-diacylglucosamine pyrophosphohydrolase	_____________63______71\n_____________\|_______\|\n5'-ACA...UAAAU_______AGUUU...UGA-3'\n______________UGGCUAA\n______________:\|\|\|\|\|\|\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	64 -- 70	79 -- 85	-7.83174 kcal/mol	1.29235 kcal/mol	1.09751 kcal/mol	63 71@LB@ \| \|@LB@5'-ACA...UAAAU AGUUU...UGA-3'@LB@ UGGCUAA@LB@ :\|\|\|\|\|\|@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -5.44 kcal/mol@LB@Hybridization Energy -7.83174 kcal/mol@LB@Unfolding Energy - mRNA 1.29235 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 64 -- 70@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 79 -- 85@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)

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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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