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
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@
192	0.08479	0.363	ct_293	accD	-5.01	0.360945	270 -- 276	79 -- 85	acetyl-CoA carboxylase carboxyltransferase subunit beta	_____________269_____277\n_____________\|_______\|\n5'-GUA...GUGGC_______AAUGU...UGA-3'\n______________UGGCUAA\n______________:\|\|\|\|\|\|\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	270 -- 276	79 -- 85	-7.87376 kcal/mol	1.76808 kcal/mol	1.09751 kcal/mol	269 277@LB@ \| \|@LB@5'-GUA...GUGGC AAUGU...UGA-3'@LB@ UGGCUAA@LB@ :\|\|\|\|\|\|@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -5.01 kcal/mol@LB@Hybridization Energy -7.87376 kcal/mol@LB@Unfolding Energy - mRNA 1.76808 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 270 -- 276@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 79 -- 85@LB@
193	0.08525	0.3631	ct_196	N/A	-5.32	0.316248	140 -- 149	20 -- 29	inclusion membrane protein	_____________139________150\n_____________\|__________\|\n5'-UUU...AUAAU__________UUCUU...AAC-3'\n______________GCUAUUUCAU\n______________\|\|\|\|\|\|:\|\|\|\n______________CGAUAAGGUA\n3'-UUU...GUCUU__________CCGCA...GAA-5'\n_____________\|__________\|\n_____________30_________19\n	141 -- 147	22 -- 28	-11.6207 kcal/mol	1.68905 kcal/mol	4.60882 kcal/mol	139 150@LB@ \| \|@LB@5'-UUU...AUAAU UUCUU...AAC-3'@LB@ GCUAUUUCAU@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CGAUAAGGUA@LB@3'-UUU...GUCUU CCGCA...GAA-5'@LB@ \| \|@LB@ 30 19@LB@@LB@@LB@Energy -5.32 kcal/mol@LB@Hybridization Energy -11.6207 kcal/mol@LB@Unfolding Energy - mRNA 1.68905 kcal/mol@LB@Unfolding Energy - sRNA 4.60882 kcal/mol@LB@@LB@Position - mRNA 140 -- 149@LB@Position - sRNA 20 -- 29@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 22 -- 28@LB@
194	0.08693	0.3657	ct_285	lplA_1	-4.48	0.444512	66 -- 74	27 -- 35	lipoate protein ligase	_____________65________75\n_____________\|_________\|\n5'-CUU...AAUUU_________UUUUU...UUC-3'\n______________UUAGAAGCU\n______________\|:\|\|\|\|\|\|\|\n______________AGUCUUCGA\n3'-UUU...AUCUC_________UAAGG...GAA-5'\n_____________\|_________\|\n_____________36________26\n	68 -- 74	27 -- 33	-10.5389 kcal/mol	1.46011 kcal/mol	4.60001 kcal/mol	65 75@LB@ \| \|@LB@5'-CUU...AAUUU UUUUU...UUC-3'@LB@ UUAGAAGCU@LB@ \|:\|\|\|\|\|\|\|@LB@ AGUCUUCGA@LB@3'-UUU...AUCUC UAAGG...GAA-5'@LB@ \| \|@LB@ 36 26@LB@@LB@@LB@Energy -4.48 kcal/mol@LB@Hybridization Energy -10.5389 kcal/mol@LB@Unfolding Energy - mRNA 1.46011 kcal/mol@LB@Unfolding Energy - sRNA 4.60001 kcal/mol@LB@@LB@Position - mRNA 66 -- 74@LB@Position - sRNA 27 -- 35@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 27 -- 33@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@
196	0.08741	0.3657	ct_698	N/A	-4.23	0.486304	280 -- 292	22 -- 34	tRNA modification GTPase	_____________279___________293\n_____________\|_____________\|\n5'-AAA...CGGAC____U________UAUUUCUG-3'\n______________CGGA_GCUAUUUC\n______________\|:\|\|_\|\|\|\|\|\|:\|\n______________GUCU_CGAUAAGG\n3'-UUU...UCUCA____U________UACCG...GAA-5'\n_____________\|_____________\|\n_____________35____________21\n	285 -- 291	23 -- 29	-13.8571 kcal/mol	4.89721 kcal/mol	4.72608 kcal/mol	279 293@LB@ \| \|@LB@5'-AAA...CGGAC U UAUUUCUG-3'@LB@ CGGA GCUAUUUC@LB@ \|:\|\| \|\|\|\|\|\|:\|@LB@ GUCU CGAUAAGG@LB@3'-UUU...UCUCA U UACCG...GAA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -4.23 kcal/mol@LB@Hybridization Energy -13.8571 kcal/mol@LB@Unfolding Energy - mRNA 4.89721 kcal/mol@LB@Unfolding Energy - sRNA 4.72608 kcal/mol@LB@@LB@Position - mRNA 280 -- 292@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 23 -- 29@LB@
197	0.08765	0.3657	ct_851	map	-5.60	0.279866	107 -- 113	81 -- 87	methionine aminopeptidase	_____________106_____114\n_____________\|_______\|\n5'-GCU...CUUUC_______UUCAA...AAC-3'\n______________UACGGCU\n______________\|\|\|\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	107 -- 113	81 -- 87	-10.6361 kcal/mol	3.93565 kcal/mol	1.09752 kcal/mol	106 114@LB@ \| \|@LB@5'-GCU...CUUUC UUCAA...AAC-3'@LB@ UACGGCU@LB@ \|\|\|\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -5.60 kcal/mol@LB@Hybridization Energy -10.6361 kcal/mol@LB@Unfolding Energy - mRNA 3.93565 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 107 -- 113@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 81 -- 87@LB@
198	0.08843	0.3671	ct_257	N/A	-6.39	0.194258	76 -- 83	79 -- 86		_____________75_______84\n_____________\|________\|\n5'-CUA...GGCGG________CAGAA...UCA-3'\n______________AUGGCUGA\n______________\|:\|\|\|\|:\|\n______________UGCCGAUU\n3'-UUU...CUCUA________GAGGU...GAA-5'\n_____________\|________\|\n_____________87_______78\n	77 -- 83	79 -- 85	-9.5904 kcal/mol	2.10083 kcal/mol	1.09752 kcal/mol	75 84@LB@ \| \|@LB@5'-CUA...GGCGG CAGAA...UCA-3'@LB@ AUGGCUGA@LB@ \|:\|\|\|\|:\|@LB@ UGCCGAUU@LB@3'-UUU...CUCUA GAGGU...GAA-5'@LB@ \| \|@LB@ 87 78@LB@@LB@@LB@Energy -6.39 kcal/mol@LB@Hybridization Energy -9.5904 kcal/mol@LB@Unfolding Energy - mRNA 2.10083 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 79 -- 86@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 79 -- 85@LB@
199	0.0896	0.3683	ct_774	cysQ	-5.35	0.311933	207 -- 214	53 -- 60	3'(2') 5'-bisphosphate nucleotidase	_____________206______215\n_____________\|________\|\n5'-UCA...UGUUC________CAAUG...UUC-3'\n______________UCCCUCCU\n______________\|\|\|\|:\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	208 -- 214	53 -- 59	-13.0073 kcal/mol	1.20108 kcal/mol	6.45136 kcal/mol	206 215@LB@ \| \|@LB@5'-UCA...UGUUC CAAUG...UUC-3'@LB@ UCCCUCCU@LB@ \|\|\|\|:\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -5.35 kcal/mol@LB@Hybridization Energy -13.0073 kcal/mol@LB@Unfolding Energy - mRNA 1.20108 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 207 -- 214@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 53 -- 59@LB@
200	0.0896	0.3683	ct_487	yhhF	-5.19	0.334580	14 -- 20	79 -- 85	methyltransferase	_____________13______21\n_____________\|_______\|\n5'-ACG...UCCUC_______UAAUG...UUA-3'\n______________CGGUUAG\n______________\|\|\|:\|\|:\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	14 -- 20	79 -- 85	-7.01592 kcal/mol	0.727938 kcal/mol	1.09751 kcal/mol	13 21@LB@ \| \|@LB@5'-ACG...UCCUC UAAUG...UUA-3'@LB@ CGGUUAG@LB@ \|\|\|:\|\|:@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -5.19 kcal/mol@LB@Hybridization Energy -7.01592 kcal/mol@LB@Unfolding Energy - mRNA 0.727938 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 14 -- 20@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 14 -- 20@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)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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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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