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
83	0.0294	0.29	ct_767	N/A	-5.43	0.301596	255 -- 261	54 -- 60		_____________254_____262\n_____________\|_______\|\n5'-CUC...UUUAU_______UGGAA...AAC-3'\n______________UCCCCCU\n______________\|\|\|\|\|\|:\n______________AGGGGGG\n3'-UUU...ACUGA_______ACACA...GAA-5'\n_____________\|_______\|\n_____________61______53\n	255 -- 261	54 -- 60	-13.2051 kcal/mol	1.33057 kcal/mol	6.44182 kcal/mol	254 262@LB@ \| \|@LB@5'-CUC...UUUAU UGGAA...AAC-3'@LB@ UCCCCCU@LB@ \|\|\|\|\|\|:@LB@ AGGGGGG@LB@3'-UUU...ACUGA ACACA...GAA-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -5.43 kcal/mol@LB@Hybridization Energy -13.2051 kcal/mol@LB@Unfolding Energy - mRNA 1.33057 kcal/mol@LB@Unfolding Energy - sRNA 6.44182 kcal/mol@LB@@LB@Position - mRNA 255 -- 261@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 54 -- 60@LB@
109	0.04235	0.3194	ct_002	gatC	-8.76	0.056639	255 -- 282	18 -- 44	aspartyl/glutamyl-tRNA amidotransferase subunit C	_____________254__________________________283\n_____________\|____________________________\|\n5'-GAC...AUGCU________________AUGCCCA_____AAGAG...CUA-3'\n______________GCAUUGGAGUUGGAAG_______CGUGG\n______________:\|\|:\|:\|\|\|\|::\|\|\|\|_______\|:\|\|\|\n______________UGUGAUCUCAGUCUUC_______GUACC\n3'-UUU...AUGUU________________GAUAAG______GCAAU...GAA-5'\n_____________\|____________________________\|\n_____________45___________________________17\n	261 -- 267	32 -- 38	-28.0671 kcal/mol	6.54471 kcal/mol	12.7603 kcal/mol	254 283@LB@ \| \|@LB@5'-GAC...AUGCU AUGCCCA AAGAG...CUA-3'@LB@ GCAUUGGAGUUGGAAG CGUGG@LB@ :\|\|:\|:\|\|\|\|::\|\|\|\| \|:\|\|\|@LB@ UGUGAUCUCAGUCUUC GUACC@LB@3'-UUU...AUGUU GAUAAG GCAAU...GAA-5'@LB@ \| \|@LB@ 45 17@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -28.0671 kcal/mol@LB@Unfolding Energy - mRNA 6.54471 kcal/mol@LB@Unfolding Energy - sRNA 12.7603 kcal/mol@LB@@LB@Position - mRNA 255 -- 282@LB@Position - sRNA 18 -- 44@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 32 -- 38@LB@
125	0.05005	0.3262	ct_644	yohI	-5.25	0.326074	256 -- 262	53 -- 59	tRNA-dihydrouridine synthase	_____________255_____263\n_____________\|_______\|\n5'-CUG...CUACG_______AGCGG...CGG-3'\n______________CCCCCUU\n______________\|\|\|\|\|:\|\n______________GGGGGGA\n3'-UUU...CUGAA_______CACAU...GAA-5'\n_____________\|_______\|\n_____________60______52\n	256 -- 262	53 -- 59	-11.5527 kcal/mol	0.822659 kcal/mol	5.47887 kcal/mol	255 263@LB@ \| \|@LB@5'-CUG...CUACG AGCGG...CGG-3'@LB@ CCCCCUU@LB@ \|\|\|\|\|:\|@LB@ GGGGGGA@LB@3'-UUU...CUGAA CACAU...GAA-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -5.25 kcal/mol@LB@Hybridization Energy -11.5527 kcal/mol@LB@Unfolding Energy - mRNA 0.822659 kcal/mol@LB@Unfolding Energy - sRNA 5.47887 kcal/mol@LB@@LB@Position - mRNA 256 -- 262@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 53 -- 59@LB@
71	0.027	0.29	ct_712	N/A	-6.32	0.201489	257 -- 263	81 -- 87	type III secretion system effector protein	_____________256_____264\n_____________\|_______\|\n5'-CAG...GAGAC_______CCUCG...CAG-3'\n______________UGCGGCU\n______________\|:\|\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	257 -- 263	81 -- 87	-10.8048 kcal/mol	3.3916 kcal/mol	1.09752 kcal/mol	256 264@LB@ \| \|@LB@5'-CAG...GAGAC CCUCG...CAG-3'@LB@ UGCGGCU@LB@ \|:\|\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -10.8048 kcal/mol@LB@Unfolding Energy - mRNA 3.3916 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 257 -- 263@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 81 -- 87@LB@
80	0.02888	0.29	ct_821	sucC	-7.97	0.087313	257 -- 264	53 -- 60	succinyl-CoA ligase subunit beta	_____________256______265\n_____________\|________\|\n5'-UCG...CCUAU________AUCAC...CAG-3'\n______________UCCCCCCU\n______________\|\|\|\|\|\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	258 -- 264	53 -- 59	-16.0066 kcal/mol	1.58949 kcal/mol	6.45136 kcal/mol	256 265@LB@ \| \|@LB@5'-UCG...CCUAU AUCAC...CAG-3'@LB@ UCCCCCCU@LB@ \|\|\|\|\|\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -16.0066 kcal/mol@LB@Unfolding Energy - mRNA 1.58949 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 257 -- 264@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 53 -- 59@LB@
46	0.01681	0.29	ct_425	N/A	-8.97	0.050526	259 -- 284	2 -- 23		_____________258_________________________285\n_____________\|___________________________\|\n5'-CUU...UUCUA__________UC_____UUCU______AAUUU...AAG-3'\n______________CC_UGGCGUU__GAAUA____UCAGCU\n______________\|\|_\|\|\|\|\|\|\|__\|\|\|\|\|____:\|\|:\|\|\n______________GG_ACCGCAA__CUUAU____GGUUGA\n3'-UUU...GAUAA__U_______U________________A-5'\n_____________\|___________________________\|\n_____________24__________________________1\n	261 -- 267	14 -- 20	-21.0816 kcal/mol	4.01638 kcal/mol	8.09761 kcal/mol	258 285@LB@ \| \|@LB@5'-CUU...UUCUA UC UUCU AAUUU...AAG-3'@LB@ CC UGGCGUU GAAUA UCAGCU@LB@ \|\| \|\|\|\|\|\|\| \|\|\|\|\| :\|\|:\|\|@LB@ GG ACCGCAA CUUAU GGUUGA@LB@3'-UUU...GAUAA U U A-5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -21.0816 kcal/mol@LB@Unfolding Energy - mRNA 4.01638 kcal/mol@LB@Unfolding Energy - sRNA 8.09761 kcal/mol@LB@@LB@Position - mRNA 259 -- 284@LB@Position - sRNA 2 -- 23@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 14 -- 20@LB@
62	0.02417	0.29	ct_705	clpX	-8.32	0.072096	259 -- 275	17 -- 33	ATP-dependent Clp protease ATP-binding subunit ClpX	_____________258_______________276\n_____________\|_________________\|\n5'-CUG...UGUUG________A__GC____CCAUC...AUU-3'\n______________AGAAGCUA_UC__UGGU\n______________\|\|\|\|\|\|\|\|_\|\|__\|\|\|:\n______________UCUUCGAU_AG__ACCG\n3'-UUU...CUCAG________A__GU____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	260 -- 266	26 -- 32	-18.4351 kcal/mol	5.13531 kcal/mol	4.97804 kcal/mol	258 276@LB@ \| \|@LB@5'-CUG...UGUUG A GC CCAUC...AUU-3'@LB@ AGAAGCUA UC UGGU@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|:@LB@ UCUUCGAU AG ACCG@LB@3'-UUU...CUCAG A GU CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -18.4351 kcal/mol@LB@Unfolding Energy - mRNA 5.13531 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 259 -- 275@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 26 -- 32@LB@
95	0.03456	0.2959	ct_073	N/A	-12.13	0.007785	261 -- 279	41 -- 58	contains leader (19) peptide	_____________260_________________280\n_____________\|___________________\|\n5'-GAC...CUGAU_________AUU_______UGACA...GGG-3'\n______________CCCUCUGUG___CAAACAU\n______________\|\|\|:\|\|\|\|\|___\|\|\|\|\|\|:\n______________GGGGGACAC___GUUUGUG\n3'-UUU...UGAAG_________AU________AUCUC...GAA-5'\n_____________\|___________________\|\n_____________59__________________40\n	263 -- 269	50 -- 56	-22.185 kcal/mol	2.22773 kcal/mol	7.82865 kcal/mol	260 280@LB@ \| \|@LB@5'-GAC...CUGAU AUU UGACA...GGG-3'@LB@ CCCUCUGUG CAAACAU@LB@ \|\|\|:\|\|\|\|\| \|\|\|\|\|\|:@LB@ GGGGGACAC GUUUGUG@LB@3'-UUU...UGAAG AU AUCUC...GAA-5'@LB@ \| \|@LB@ 59 40@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -22.185 kcal/mol@LB@Unfolding Energy - mRNA 2.22773 kcal/mol@LB@Unfolding Energy - sRNA 7.82865 kcal/mol@LB@@LB@Position - mRNA 261 -- 279@LB@Position - sRNA 41 -- 58@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 50 -- 56@LB@
135	0.05472	0.3262	ct_283	N/A	-6.89	0.152000	262 -- 284	14 -- 35		_____________261______________________285\n_____________\|________________________\|\n5'-UAC...GUUUA_____CU________GC_______UGUUU...UUG-3'\n______________UCGGA__AGUUA_UC__UGGCGUU\n______________\|\|:\|\|__\|\|:\|\|_\|\|__\|\|\|\|\|\|\|\n______________AGUCU__UCGAU_AG__ACCGCAA\n3'-UUU...AUCUC____________A__GU_______UCUUA...GAA-5'\n_____________\|________________________\|\n_____________36_______________________13\n	278 -- 284	14 -- 20	-19.9844 kcal/mol	4.64246 kcal/mol	8.44936 kcal/mol	261 285@LB@ \| \|@LB@5'-UAC...GUUUA CU GC UGUUU...UUG-3'@LB@ UCGGA AGUUA UC UGGCGUU@LB@ \|\|:\|\| \|\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ AGUCU UCGAU AG ACCGCAA@LB@3'-UUU...AUCUC A GU UCUUA...GAA-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -6.89 kcal/mol@LB@Hybridization Energy -19.9844 kcal/mol@LB@Unfolding Energy - mRNA 4.64246 kcal/mol@LB@Unfolding Energy - sRNA 8.44936 kcal/mol@LB@@LB@Position - mRNA 262 -- 284@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 14 -- 20@LB@
56	0.02215	0.29	ct_104	fabI	-6.34	0.199539	263 -- 271	80 -- 88	enoyl-(acyl carrier protein) reductase	_____________262_______272\n_____________\|_________\|\n5'-UUU...AACGG_________GGGCA...CAG-3'\n______________GUAUGGCUG\n______________:\|\|:\|\|\|\|:\n______________UAUGCCGAU\n3'-UUU...GCCUC_________UGAGG...GAA-5'\n_____________\|_________\|\n_____________89________79\n	265 -- 271	80 -- 86	-10.7973 kcal/mol	3.36368 kcal/mol	1.09753 kcal/mol	262 272@LB@ \| \|@LB@5'-UUU...AACGG GGGCA...CAG-3'@LB@ GUAUGGCUG@LB@ :\|\|:\|\|\|\|:@LB@ UAUGCCGAU@LB@3'-UUU...GCCUC UGAGG...GAA-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -6.34 kcal/mol@LB@Hybridization Energy -10.7973 kcal/mol@LB@Unfolding Energy - mRNA 3.36368 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 263 -- 271@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 80 -- 86@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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