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
142	0.0566	0.3262	ct_284	N/A	-6.95	0.147726	278 -- 292	18 -- 30	phospholipase D	_____________277_____________293\n_____________\|_______________\|\n5'-AUC...ACUAU_________GG____AGACAAAA-3'\n______________AGCUAUUCC__AUGG\n______________\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UCGAUAAGG__UACC\n3'-UUU...AGUCU_______________GCAAU...GAA-5'\n_____________\|_______________\|\n_____________31______________17\n	280 -- 286	22 -- 28	-16.5616 kcal/mol	4.87795 kcal/mol	4.73403 kcal/mol	277 293@LB@ \| \|@LB@5'-AUC...ACUAU GG AGACAAAA-3'@LB@ AGCUAUUCC AUGG@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UCGAUAAGG UACC@LB@3'-UUU...AGUCU GCAAU...GAA-5'@LB@ \| \|@LB@ 31 17@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -16.5616 kcal/mol@LB@Unfolding Energy - mRNA 4.87795 kcal/mol@LB@Unfolding Energy - sRNA 4.73403 kcal/mol@LB@@LB@Position - mRNA 278 -- 292@LB@Position - sRNA 18 -- 30@LB@Position Seed - mRNA 280 -- 286@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@
124	0.04963	0.3262	ct_290	ptsN_1	-8.82	0.054773	1 -- 15	18 -- 32	PTS fructose transporter subunit IIA	______________1______________16\n______________\|______________\|\n___________5'-____G__________GAUGC...UUA-3'\n______________GAGG_UAUUUUGUGG\n______________\|\|:\|_\|\|\|\|:::\|\|\|\n______________CUUC_AUAAGGUACC\n3'-UUU...UCAGU____G__________GCAAU...GAA-5'\n_____________\|_______________\|\n_____________33______________17\n	9 -- 15	18 -- 24	-16.4794 kcal/mol	2.69105 kcal/mol	4.96566 kcal/mol	1 16@LB@ \| \|@LB@ 5'- G GAUGC...UUA-3'@LB@ GAGG UAUUUUGUGG@LB@ \|\|:\| \|\|\|\|:::\|\|\|@LB@ CUUC AUAAGGUACC@LB@3'-UUU...UCAGU G GCAAU...GAA-5'@LB@ \| \|@LB@ 33 17@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -16.4794 kcal/mol@LB@Unfolding Energy - mRNA 2.69105 kcal/mol@LB@Unfolding Energy - sRNA 4.96566 kcal/mol@LB@@LB@Position - mRNA 1 -- 15@LB@Position - sRNA 18 -- 32@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 18 -- 24@LB@
139	0.05609	0.3262	ct_291	ptsN_2	-9.13	0.046270	268 -- 291	36 -- 59	PTS fructose transporter subunit IIA	_____________267______________________292\n_____________\|________________________\|\n5'-UGU...AAUCA_______ACAUU____________AAGAU...UCC-3'\n______________CUUUCUU_____CAGAUACUAGAG\n______________\|:::\|:\|_____\|\|:\|:\|\|\|\|\|\|\|\n______________GGGGGGA_____GUUUGUGAUCUC\n3'-UUU...CUGAA_______CACAU____________AGUCU...GAA-5'\n_____________\|________________________\|\n_____________60_______________________35\n	285 -- 291	36 -- 42	-20.1073 kcal/mol	2.01119 kcal/mol	8.97132 kcal/mol	267 292@LB@ \| \|@LB@5'-UGU...AAUCA ACAUU AAGAU...UCC-3'@LB@ CUUUCUU CAGAUACUAGAG@LB@ \|:::\|:\| \|\|:\|:\|\|\|\|\|\|\|@LB@ GGGGGGA GUUUGUGAUCUC@LB@3'-UUU...CUGAA CACAU AGUCU...GAA-5'@LB@ \| \|@LB@ 60 35@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -20.1073 kcal/mol@LB@Unfolding Energy - mRNA 2.01119 kcal/mol@LB@Unfolding Energy - sRNA 8.97132 kcal/mol@LB@@LB@Position - mRNA 268 -- 291@LB@Position - sRNA 36 -- 59@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 36 -- 42@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@
77	0.02807	0.29	ct_309	N/A	-7.23	0.128520	50 -- 64	17 -- 33		_____________49________________65\n_____________\|_________________\|\n5'-AGA...GCUUA_________GU______UAAAU...UAA-3'\n______________AGGGGCUAU____UGGU\n______________\|\|::\|\|\|\|\|____\|\|\|:\n______________UCUUCGAUA____ACCG\n3'-UUU...CUCAG_________AGGU____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	52 -- 58	25 -- 31	-14.8286 kcal/mol	2.62564 kcal/mol	4.97804 kcal/mol	49 65@LB@ \| \|@LB@5'-AGA...GCUUA GU UAAAU...UAA-3'@LB@ AGGGGCUAU UGGU@LB@ \|\|::\|\|\|\|\| \|\|\|:@LB@ UCUUCGAUA ACCG@LB@3'-UUU...CUCAG AGGU CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -7.23 kcal/mol@LB@Hybridization Energy -14.8286 kcal/mol@LB@Unfolding Energy - mRNA 2.62564 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 50 -- 64@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 25 -- 31@LB@
121	0.04894	0.3262	ct_310	atpE	-7.64	0.103947	27 -- 34	80 -- 87	V-type ATP synthase subunit E	_____________26_______35\n_____________\|________\|\n5'-GCA...CCUUC________CCUUC...UUC-3'\n______________UACGGCUG\n______________\|\|\|\|\|\|\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	28 -- 34	80 -- 86	-11.9035 kcal/mol	3.17039 kcal/mol	1.09752 kcal/mol	26 35@LB@ \| \|@LB@5'-GCA...CCUUC CCUUC...UUC-3'@LB@ UACGGCUG@LB@ \|\|\|\|\|\|\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -11.9035 kcal/mol@LB@Unfolding Energy - mRNA 3.17039 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 27 -- 34@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 80 -- 86@LB@
182	0.07944	0.3588	ct_320	nusG	-7.37	0.119406	230 -- 236	81 -- 87	transcription termination/antitermination protein NusG	_____________229_____237\n_____________\|_______\|\n5'-AAC...GUUUU_______CAAGA...UUA-3'\n______________UACGGCU\n______________\|\|\|\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	230 -- 236	81 -- 87	-10.814 kcal/mol	2.34788 kcal/mol	1.09752 kcal/mol	229 237@LB@ \| \|@LB@5'-AAC...GUUUU CAAGA...UUA-3'@LB@ UACGGCU@LB@ \|\|\|\|\|\|\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -7.37 kcal/mol@LB@Hybridization Energy -10.814 kcal/mol@LB@Unfolding Energy - mRNA 2.34788 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 230 -- 236@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 81 -- 87@LB@
160	0.06752	0.3424	ct_324	N/A	-4.86	0.383763	195 -- 205	17 -- 27		_____________194_________206\n_____________\|___________\|\n5'-ACA...GUAGA__GG_______CAAAG...UGC-3'\n______________UA__CCAUGGU\n______________\|\|__\|\|\|\|\|\|:\n______________AU__GGUACCG\n3'-UUU...CUUCG__AA_______CAAUC...GAA-5'\n_____________\|___________\|\n_____________28__________16\n	199 -- 205	17 -- 23	-11.7516 kcal/mol	2.4023 kcal/mol	4.49196 kcal/mol	194 206@LB@ \| \|@LB@5'-ACA...GUAGA GG CAAAG...UGC-3'@LB@ UA CCAUGGU@LB@ \|\| \|\|\|\|\|\|:@LB@ AU GGUACCG@LB@3'-UUU...CUUCG AA CAAUC...GAA-5'@LB@ \| \|@LB@ 28 16@LB@@LB@@LB@Energy -4.86 kcal/mol@LB@Hybridization Energy -11.7516 kcal/mol@LB@Unfolding Energy - mRNA 2.4023 kcal/mol@LB@Unfolding Energy - sRNA 4.49196 kcal/mol@LB@@LB@Position - mRNA 195 -- 205@LB@Position - sRNA 17 -- 27@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
90	0.03275	0.2942	ct_332	pykF	-4.34	0.468844	109 -- 116	80 -- 87	pyruvate kinase	_____________108______117\n_____________\|________\|\n5'-UUU...GCGAU________CUAAA...GCC-3'\n______________UGCGGUUG\n______________\|:\|\|\|:\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	110 -- 116	80 -- 86	-9.21836 kcal/mol	3.78563 kcal/mol	1.09752 kcal/mol	108 117@LB@ \| \|@LB@5'-UUU...GCGAU CUAAA...GCC-3'@LB@ UGCGGUUG@LB@ \|:\|\|\|:\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -4.34 kcal/mol@LB@Hybridization Energy -9.21836 kcal/mol@LB@Unfolding Energy - mRNA 3.78563 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 109 -- 116@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 110 -- 116@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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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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