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
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@
162	0.06757	0.3424	ct_083	N/A	-6.28	0.205297	111 -- 125	18 -- 33		_____________110______________126\n_____________\|________________\|\n5'-GCU...CAAGA________CAG_____AAAUC...UUU-3'\n______________AGAAGCUG____GUGG\n______________\|\|\|\|\|\|\|:____:\|\|\|\n______________UCUUCGAU____UACC\n3'-UUU...CUCAG________AAGG____GCAAU...GAA-5'\n_____________\|________________\|\n_____________34_______________17\n	112 -- 118	26 -- 32	-15.1014 kcal/mol	3.84734 kcal/mol	4.97798 kcal/mol	110 126@LB@ \| \|@LB@5'-GCU...CAAGA CAG AAAUC...UUU-3'@LB@ AGAAGCUG GUGG@LB@ \|\|\|\|\|\|\|: :\|\|\|@LB@ UCUUCGAU UACC@LB@3'-UUU...CUCAG AAGG GCAAU...GAA-5'@LB@ \| \|@LB@ 34 17@LB@@LB@@LB@Energy -6.28 kcal/mol@LB@Hybridization Energy -15.1014 kcal/mol@LB@Unfolding Energy - mRNA 3.84734 kcal/mol@LB@Unfolding Energy - sRNA 4.97798 kcal/mol@LB@@LB@Position - mRNA 111 -- 125@LB@Position - sRNA 18 -- 33@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 26 -- 32@LB@
163	0.06794	0.3424	ct_661	N/A	-2.85	0.735752	184 -- 191	21 -- 28	DNA topoisomerase IV subunit B	_____________183______192\n_____________\|________\|\n5'-AAA...UUGCC________CACAC...GCG-3'\n______________UUAUUCCA\n______________:\|\|\|\|\|\|\|\n______________GAUAAGGU\n3'-UUU...UCUUC________ACCGC...GAA-5'\n_____________\|________\|\n_____________29_______20\n	185 -- 191	21 -- 27	-7.6538 kcal/mol	0.450062 kcal/mol	4.35509 kcal/mol	183 192@LB@ \| \|@LB@5'-AAA...UUGCC CACAC...GCG-3'@LB@ UUAUUCCA@LB@ :\|\|\|\|\|\|\|@LB@ GAUAAGGU@LB@3'-UUU...UCUUC ACCGC...GAA-5'@LB@ \| \|@LB@ 29 20@LB@@LB@@LB@Energy -2.85 kcal/mol@LB@Hybridization Energy -7.6538 kcal/mol@LB@Unfolding Energy - mRNA 0.450062 kcal/mol@LB@Unfolding Energy - sRNA 4.35509 kcal/mol@LB@@LB@Position - mRNA 184 -- 191@LB@Position - sRNA 21 -- 28@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 21 -- 27@LB@
164	0.06834	0.3424	ct_716	N/A	-9.26	0.042990	10 -- 57	2 -- 60		_____________9____________________________________________________________58\n_____________\|____________________________________________________________\|\n5'-UCA...GAGCU________UACU_____GC_________U_________GAUAUCAU______________AGGAG...UAG-3'\n______________UCUCUCCU_____CAAA__CUA___UCA_GAAGCUAUU________________CCAACU\n______________\|\|:\|:\|\|\|_____\|\|\|\|__\|\|\|___\|\|\|_\|\|\|\|\|\|\|\|\|________________\|\|\|\|\|\|\n______________AGGGGGGA_____GUUU__GAU___AGU_CUUCGAUAA________________GGUUGA\n3'-UUU...ACUGA________CACAU____GU___CUC_____________GGUACCGCAAUCUUAU______A-5'\n_____________\|____________________________________________________________\|\n_____________61___________________________________________________________1\n	37 -- 43	24 -- 30	-32.8059 kcal/mol	5.03112 kcal/mol	18.5194 kcal/mol	9 58@LB@ \| \|@LB@5'-UCA...GAGCU UACU GC U GAUAUCAU AGGAG...UAG-3'@LB@ UCUCUCCU CAAA CUA UCA GAAGCUAUU CCAACU@LB@ \|\|:\|:\|\|\| \|\|\|\| \|\|\| \|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ AGGGGGGA GUUU GAU AGU CUUCGAUAA GGUUGA@LB@3'-UUU...ACUGA CACAU GU CUC GGUACCGCAAUCUUAU A-5'@LB@ \| \|@LB@ 61 1@LB@@LB@@LB@Energy -9.26 kcal/mol@LB@Hybridization Energy -32.8059 kcal/mol@LB@Unfolding Energy - mRNA 5.03112 kcal/mol@LB@Unfolding Energy - sRNA 18.5194 kcal/mol@LB@@LB@Position - mRNA 10 -- 57@LB@Position - sRNA 2 -- 60@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 24 -- 30@LB@
165	0.06872	0.3424	ct_859	lytB	-7.21	0.129268	10 -- 22	19 -- 31	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	_____________9_____________23\n_____________\|_____________\|\n5'-UCG...UAUAA___________A_UAUCU...CUA-3'\n______________AGGCUAUUCCG_G\n______________\|:\|\|\|\|\|\|\|\|:_\|\n______________UUCGAUAAGGU_C\n3'-UUU...CAGUC___________A_CGCAA...GAA-5'\n_____________\|_____________\|\n_____________32____________18\n	14 -- 20	21 -- 27	-14.969 kcal/mol	2.89565 kcal/mol	4.85984 kcal/mol	9 23@LB@ \| \|@LB@5'-UCG...UAUAA A UAUCU...CUA-3'@LB@ AGGCUAUUCCG G@LB@ \|:\|\|\|\|\|\|\|\|: \|@LB@ UUCGAUAAGGU C@LB@3'-UUU...CAGUC A CGCAA...GAA-5'@LB@ \| \|@LB@ 32 18@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -14.969 kcal/mol@LB@Unfolding Energy - mRNA 2.89565 kcal/mol@LB@Unfolding Energy - sRNA 4.85984 kcal/mol@LB@@LB@Position - mRNA 10 -- 22@LB@Position - sRNA 19 -- 31@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 21 -- 27@LB@
166	0.06935	0.3427	ct_700	N/A	-9.45	0.038462	185 -- 207	17 -- 35		_____________184_____________________208\n_____________\|_______________________\|\n5'-UGG...AAAAC___________GCAUUA______UAAUC...AUC-3'\n______________UCAGAAGUUGU______UGUGGC\n______________\|\|\|\|\|\|\|:\|:\|______::\|\|\|\|\n______________AGUCUUCGAUA______GUACCG\n3'-UUU...AUCUC___________AG__________CAAUC...GAA-5'\n_____________\|_______________________\|\n_____________36______________________16\n	187 -- 193	27 -- 33	-18.7157 kcal/mol	4.28595 kcal/mol	4.9781 kcal/mol	184 208@LB@ \| \|@LB@5'-UGG...AAAAC GCAUUA UAAUC...AUC-3'@LB@ UCAGAAGUUGU UGUGGC@LB@ \|\|\|\|\|\|\|:\|:\| ::\|\|\|\|@LB@ AGUCUUCGAUA GUACCG@LB@3'-UUU...AUCUC AG CAAUC...GAA-5'@LB@ \| \|@LB@ 36 16@LB@@LB@@LB@Energy -9.45 kcal/mol@LB@Hybridization Energy -18.7157 kcal/mol@LB@Unfolding Energy - mRNA 4.28595 kcal/mol@LB@Unfolding Energy - sRNA 4.9781 kcal/mol@LB@@LB@Position - mRNA 185 -- 207@LB@Position - sRNA 17 -- 35@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 27 -- 33@LB@
167	0.06963	0.3427	ct_724	N/A	-5.10	0.346834	244 -- 255	24 -- 35		_____________243__________256\n_____________\|____________\|\n5'-ACC...GUUAU____________GUCGC...GAC-3'\n______________UCGGGGGUUAUU\n______________\|\|:\|::\|:\|\|\|\|\n______________AGUCUUCGAUAA\n3'-UUU...AUCUC____________GGUAC...GAA-5'\n_____________\|____________\|\n_____________36___________23\n	245 -- 251	28 -- 34	-12.4512 kcal/mol	2.62645 kcal/mol	4.72035 kcal/mol	243 256@LB@ \| \|@LB@5'-ACC...GUUAU GUCGC...GAC-3'@LB@ UCGGGGGUUAUU@LB@ \|\|:\|::\|:\|\|\|\|@LB@ AGUCUUCGAUAA@LB@3'-UUU...AUCUC GGUAC...GAA-5'@LB@ \| \|@LB@ 36 23@LB@@LB@@LB@Energy -5.10 kcal/mol@LB@Hybridization Energy -12.4512 kcal/mol@LB@Unfolding Energy - mRNA 2.62645 kcal/mol@LB@Unfolding Energy - sRNA 4.72035 kcal/mol@LB@@LB@Position - mRNA 244 -- 255@LB@Position - sRNA 24 -- 35@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 28 -- 34@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@
169	0.07086	0.3447	ct_615	sigA	-4.07	0.514760	248 -- 272	10 -- 33	RNA polymerase sigma factor	_____________247________________________273\n_____________\|__________________________\|\n5'-GGU...CAAGA_____AAA_____AAGAAA_______GAGUU...AAG-3'\n______________AGAAG____UCCA______GUUAGAA\n______________\|\|\|\|\|____\|\|\|\|______\|\|\|\|\|\|\|\n______________UCUUC____AGGU______CAAUCUU\n3'-UUU...CUCAG_____GAUA____ACCG_________AUGGU...GAA-5'\n_____________\|__________________________\|\n_____________34_________________________9\n	266 -- 272	10 -- 16	-15.5151 kcal/mol	2.85327 kcal/mol	8.5898 kcal/mol	247 273@LB@ \| \|@LB@5'-GGU...CAAGA AAA AAGAAA GAGUU...AAG-3'@LB@ AGAAG UCCA GUUAGAA@LB@ \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UCUUC AGGU CAAUCUU@LB@3'-UUU...CUCAG GAUA ACCG AUGGU...GAA-5'@LB@ \| \|@LB@ 34 9@LB@@LB@@LB@Energy -4.07 kcal/mol@LB@Hybridization Energy -15.5151 kcal/mol@LB@Unfolding Energy - mRNA 2.85327 kcal/mol@LB@Unfolding Energy - sRNA 8.5898 kcal/mol@LB@@LB@Position - mRNA 248 -- 272@LB@Position - sRNA 10 -- 33@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 10 -- 16@LB@
170	0.07264	0.3448	ct_415	yebL	-4.69	0.409849	24 -- 30	22 -- 28	metal ABC transporter substrate-binding protein	_____________23______31\n_____________\|_______\|\n5'-AUU...AAAAA_______UCACC...CCU-3'\n______________CUGUUCC\n______________\|\|:\|\|\|\|\n______________GAUAAGG\n3'-UUU...UCUUC_______UACCG...GAA-5'\n_____________\|_______\|\n_____________29______21\n	24 -- 30	22 -- 28	-9.14166 kcal/mol	0.102316 kcal/mol	4.35007 kcal/mol	23 31@LB@ \| \|@LB@5'-AUU...AAAAA UCACC...CCU-3'@LB@ CUGUUCC@LB@ \|\|:\|\|\|\|@LB@ GAUAAGG@LB@3'-UUU...UCUUC UACCG...GAA-5'@LB@ \| \|@LB@ 29 21@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -9.14166 kcal/mol@LB@Unfolding Energy - mRNA 0.102316 kcal/mol@LB@Unfolding Energy - sRNA 4.35007 kcal/mol@LB@@LB@Position - mRNA 24 -- 30@LB@Position - sRNA 22 -- 28@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 22 -- 28@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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