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
22	0.005311	0.1984	ct_111	groES	-5.40	0.305537	269 -- 283	17 -- 33	co-chaperonin GroES	_____________268_______________284\n_____________\|_________________\|\n5'-AGC...GAAGA_____________CU__AAGAG...UUC-3'\n______________AGAAGCU__UCCA__GC\n______________\|\|\|\|\|\|\|__\|\|\|\|__\|\|\n______________UCUUCGA__AGGU__CG\n3'-UUU...CUCAG_______UA____AC__CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	269 -- 275	27 -- 33	-15.094 kcal/mol	4.71335 kcal/mol	4.97804 kcal/mol	268 284@LB@ \| \|@LB@5'-AGC...GAAGA CU AAGAG...UUC-3'@LB@ AGAAGCU UCCA GC@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|@LB@ UCUUCGA AGGU CG@LB@3'-UUU...CUCAG UA AC CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -5.40 kcal/mol@LB@Hybridization Energy -15.094 kcal/mol@LB@Unfolding Energy - mRNA 4.71335 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 269 -- 283@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 27 -- 33@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@
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@
76	0.02744	0.29	ct_510	secY	-5.37	0.309530	200 -- 207	80 -- 87	preprotein translocase subunit SecY	_____________199______208\n_____________\|________\|\n5'-GAU...AAGUU________CAUUG...UCC-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	201 -- 207	80 -- 86	-9.93483 kcal/mol	3.46443 kcal/mol	1.09752 kcal/mol	199 208@LB@ \| \|@LB@5'-GAU...AAGUU CAUUG...UCC-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -5.37 kcal/mol@LB@Hybridization Energy -9.93483 kcal/mol@LB@Unfolding Energy - mRNA 3.46443 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 201 -- 207@LB@Position Seed - sRNA 80 -- 86@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@
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@
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@
161	0.06753	0.3424	ct_656	N/A	-5.22	0.330968	193 -- 236	21 -- 57		_____________192_____________________________________________237\n_____________\|_______________________________________________\|\n5'-AUG...GGGAG_________________GCAAUUCAUAGC_______U________G_AACCA...UGA-3'\n______________UCUCU_UGUAUGGACAC____________GAGUCAG___CUGUUC_A\n______________:\|:\|\|_\|\|\|\|:::\|\|\|\|____________\|\|\|\|\|\|\|___\|\|:\|\|\|_\|\n______________GGGGA_ACAUGUUUGUG____________CUCAGUC___GAUAAG_U\n3'-UUU...GAAGG_____C___________AU_________________UUC______G_ACCGC...GAA-5'\n_____________\|_______________________________________________\|\n_____________58______________________________________________20\n	221 -- 227	32 -- 38	-30.4155 kcal/mol	12.5085 kcal/mol	12.6912 kcal/mol	192 237@LB@ \| \|@LB@5'-AUG...GGGAG GCAAUUCAUAGC U G AACCA...UGA-3'@LB@ UCUCU UGUAUGGACAC GAGUCAG CUGUUC A@LB@ :\|:\|\| \|\|\|\|:::\|\|\|\| \|\|\|\|\|\|\| \|\|:\|\|\| \|@LB@ GGGGA ACAUGUUUGUG CUCAGUC GAUAAG U@LB@3'-UUU...GAAGG C AU UUC G ACCGC...GAA-5'@LB@ \| \|@LB@ 58 20@LB@@LB@@LB@Energy -5.22 kcal/mol@LB@Hybridization Energy -30.4155 kcal/mol@LB@Unfolding Energy - mRNA 12.5085 kcal/mol@LB@Unfolding Energy - sRNA 12.6912 kcal/mol@LB@@LB@Position - mRNA 193 -- 236@LB@Position - sRNA 21 -- 57@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 32 -- 38@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@
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

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

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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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