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
12	0.002873	0.1836	ct_040	ruvB	-8.58	0.062725	112 -- 136	36 -- 60	Holliday junction DNA helicase RuvB	_____________111_______________________137\n_____________\|_________________________\|\n5'-CAG...GGGAA_________ACUU___C________GAUGU...AAG-3'\n______________UCCCUCUUG____CAG_CGCUGGAG\n______________\|\|\|\|:\|:\|\|____\|\|:_\|:\|\|:\|\|\|\n______________AGGGGGGAC____GUU_GUGAUCUC\n3'-UUU...ACUGA_________ACAU___U________AGUCU...GAA-5'\n_____________\|_________________________\|\n_____________61________________________35\n	113 -- 119	53 -- 59	-26.2752 kcal/mol	7.75429 kcal/mol	9.944 kcal/mol	111 137@LB@ \| \|@LB@5'-CAG...GGGAA ACUU C GAUGU...AAG-3'@LB@ UCCCUCUUG CAG CGCUGGAG@LB@ \|\|\|\|:\|:\|\| \|\|: \|:\|\|:\|\|\|@LB@ AGGGGGGAC GUU GUGAUCUC@LB@3'-UUU...ACUGA ACAU U AGUCU...GAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -26.2752 kcal/mol@LB@Unfolding Energy - mRNA 7.75429 kcal/mol@LB@Unfolding Energy - sRNA 9.944 kcal/mol@LB@@LB@Position - mRNA 112 -- 136@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 53 -- 59@LB@
52	0.01886	0.29	ct_784	rnpA	-5.05	0.354130	114 -- 120	80 -- 86	ribonuclease P protein component	_____________113_____121\n_____________\|_______\|\n5'-UCU...CUCGC_______CAAAA...UGA-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	114 -- 120	80 -- 86	-8.53572 kcal/mol	2.4168 kcal/mol	1.06449 kcal/mol	113 121@LB@ \| \|@LB@5'-UCU...CUCGC CAAAA...UGA-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.05 kcal/mol@LB@Hybridization Energy -8.53572 kcal/mol@LB@Unfolding Energy - mRNA 2.4168 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 114 -- 120@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 80 -- 86@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@
74	0.02719	0.29	ct_114	N/A	-7.65	0.102976	115 -- 129	17 -- 32		_____________114______________130\n_____________\|________________\|\n5'-AGG...GCGGU______UA________AAAAG...AAA-3'\n______________GGAGCU___CUAUGGC\n______________\|:\|\|\|\|___\|:\|\|\|\|\|\n______________CUUCGA___GGUACCG\n3'-UUU...UCAGU______UAA_______CAAUC...GAA-5'\n_____________\|________________\|\n_____________33_______________16\n	123 -- 129	17 -- 23	-17.2748 kcal/mol	4.65579 kcal/mol	4.96575 kcal/mol	114 130@LB@ \| \|@LB@5'-AGG...GCGGU UA AAAAG...AAA-3'@LB@ GGAGCU CUAUGGC@LB@ \|:\|\|\|\| \|:\|\|\|\|\|@LB@ CUUCGA GGUACCG@LB@3'-UUU...UCAGU UAA CAAUC...GAA-5'@LB@ \| \|@LB@ 33 16@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -17.2748 kcal/mol@LB@Unfolding Energy - mRNA 4.65579 kcal/mol@LB@Unfolding Energy - sRNA 4.96575 kcal/mol@LB@@LB@Position - mRNA 115 -- 129@LB@Position - sRNA 17 -- 32@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 17 -- 23@LB@
82	0.02927	0.29	ct_342	rs21	-5.39	0.307662	118 -- 125	14 -- 21	30S ribosomal protein S21	_____________117______126\n_____________\|________\|\n5'-UUA...UAAAA________ACAAU...AGU-3'\n______________GUGGUGUU\n______________:\|\|\|:\|\|\|\n______________UACCGCAA\n3'-UUU...UAAGG________UCUUA...GAA-5'\n_____________\|________\|\n_____________22_______13\n	119 -- 125	14 -- 20	-8.72589 kcal/mol	2.15057 kcal/mol	1.18847 kcal/mol	117 126@LB@ \| \|@LB@5'-UUA...UAAAA ACAAU...AGU-3'@LB@ GUGGUGUU@LB@ :\|\|\|:\|\|\|@LB@ UACCGCAA@LB@3'-UUU...UAAGG UCUUA...GAA-5'@LB@ \| \|@LB@ 22 13@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -8.72589 kcal/mol@LB@Unfolding Energy - mRNA 2.15057 kcal/mol@LB@Unfolding Energy - sRNA 1.18847 kcal/mol@LB@@LB@Position - mRNA 118 -- 125@LB@Position - sRNA 14 -- 21@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 14 -- 20@LB@
87	0.03104	0.29	ct_437	fusA	-5.85	0.250219	118 -- 125	79 -- 86	elongation factor G	_____________117______126\n_____________\|________\|\n5'-AUC...AUCGC________AGCAA...UCU-3'\n______________AUGGCUGA\n______________\|:\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	119 -- 125	79 -- 85	-8.84241 kcal/mol	1.89322 kcal/mol	1.09752 kcal/mol	117 126@LB@ \| \|@LB@5'-AUC...AUCGC AGCAA...UCU-3'@LB@ AUGGCUGA@LB@ \|:\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -5.85 kcal/mol@LB@Hybridization Energy -8.84241 kcal/mol@LB@Unfolding Energy - mRNA 1.89322 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 118 -- 125@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 79 -- 85@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@
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@
73	0.02714	0.29	ct_211	N/A	-9.30	0.041995	126 -- 170	20 -- 59		_____________125____________________________________________171\n_____________\|______________________________________________\|\n5'-AGA...UCAAG_____AUUCU_______AAGUC____UUUGAU_________C____ACGAA...UUU-3'\n______________CCCCU_____CUGUGUG_____CAUU_______GAAGCUAU_CCAU\n______________\|\|\|\|:_____\|\|\|\|\|\|:_____\|\|:\|_______\|\|\|\|\|\|\|\|_\|\|\|\|\n______________GGGGG_____GACACAU_____GUGA_______CUUCGAUA_GGUA\n3'-UUU...CUGAA_________________GUUU_____UCUCAGU________A____CCGCA...GAA-5'\n_____________\|______________________________________________\|\n_____________60_____________________________________________19\n	159 -- 165	25 -- 31	-32.2967 kcal/mol	9.12092 kcal/mol	13.8789 kcal/mol	125 171@LB@ \| \|@LB@5'-AGA...UCAAG AUUCU AAGUC UUUGAU C ACGAA...UUU-3'@LB@ CCCCU CUGUGUG CAUU GAAGCUAU CCAU@LB@ \|\|\|\|: \|\|\|\|\|\|: \|\|:\| \|\|\|\|\|\|\|\| \|\|\|\|@LB@ GGGGG GACACAU GUGA CUUCGAUA GGUA@LB@3'-UUU...CUGAA GUUU UCUCAGU A CCGCA...GAA-5'@LB@ \| \|@LB@ 60 19@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -32.2967 kcal/mol@LB@Unfolding Energy - mRNA 9.12092 kcal/mol@LB@Unfolding Energy - sRNA 13.8789 kcal/mol@LB@@LB@Position - mRNA 126 -- 170@LB@Position - sRNA 20 -- 59@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 25 -- 31@LB@
130	0.05252	0.3262	ct_826	pssA	-5.40	0.306560	126 -- 136	23 -- 33	CDP-diacylglycerol--serine O-phosphatidyltransferase	_____________125_________137\n_____________\|___________\|\n5'-AUA...UAAAA_______UC__AACAA...UCA-3'\n______________AGAAGCU__UC\n______________\|\|\|\|\|\|\|__\|\|\n______________UCUUCGA__AG\n3'-UUU...CUCAG_______UA__GUACC...GAA-5'\n_____________\|___________\|\n_____________34__________22\n	126 -- 132	27 -- 33	-11.4676 kcal/mol	1.34949 kcal/mol	4.72321 kcal/mol	125 137@LB@ \| \|@LB@5'-AUA...UAAAA UC AACAA...UCA-3'@LB@ AGAAGCU UC@LB@ \|\|\|\|\|\|\| \|\|@LB@ UCUUCGA AG@LB@3'-UUU...CUCAG UA GUACC...GAA-5'@LB@ \| \|@LB@ 34 22@LB@@LB@@LB@Energy -5.40 kcal/mol@LB@Hybridization Energy -11.4676 kcal/mol@LB@Unfolding Energy - mRNA 1.34949 kcal/mol@LB@Unfolding Energy - sRNA 4.72321 kcal/mol@LB@@LB@Position - mRNA 126 -- 136@LB@Position - sRNA 23 -- 33@LB@Position Seed - mRNA 126 -- 132@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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