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
84	0.03042	0.29	ct_726	N/A	-6.32	0.200732	30 -- 36	81 -- 87	cell division protein	_____________29______37\n_____________\|_______\|\n5'-AGG...CCCCC_______UGCUG...AUC-3'\n______________UAUGGCU\n______________\|\|:\|\|\|\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	30 -- 36	81 -- 87	-8.84564 kcal/mol	1.42457 kcal/mol	1.09752 kcal/mol	29 37@LB@ \| \|@LB@5'-AGG...CCCCC UGCUG...AUC-3'@LB@ UAUGGCU@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 -8.84564 kcal/mol@LB@Unfolding Energy - mRNA 1.42457 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 30 -- 36@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 81 -- 87@LB@
72	0.02709	0.29	ct_530	fmt	-6.32	0.201483	239 -- 246	80 -- 87	methionyl-tRNA formyltransferase	_____________238______247\n_____________\|________\|\n5'-UAA...CAAUU________CUGUU...CGC-3'\n______________UGCGGCUA\n______________\|:\|\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	240 -- 246	80 -- 86	-12.3749 kcal/mol	4.96164 kcal/mol	1.09752 kcal/mol	238 247@LB@ \| \|@LB@5'-UAA...CAAUU CUGUU...CGC-3'@LB@ UGCGGCUA@LB@ \|:\|\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -12.3749 kcal/mol@LB@Unfolding Energy - mRNA 4.96164 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 239 -- 246@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 80 -- 86@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@
108	0.04117	0.3134	ct_817	tyrP_1	-6.29	0.204127	20 -- 34	17 -- 30	tyrosine-specific transport protein	_____________19______________35\n_____________\|_______________\|\n5'-CGA...AUCAU____UACA_______UUUAC...UCC-3'\n______________GGCU____CCAUGGC\n______________:\|\|\|____\|\|\|\|\|\|\|\n______________UCGA____GGUACCG\n3'-UUU...AGUCU____UAA________CAAUC...GAA-5'\n_____________\|_______________\|\n_____________31______________16\n	28 -- 34	17 -- 23	-15.6862 kcal/mol	4.66372 kcal/mol	4.73426 kcal/mol	19 35@LB@ \| \|@LB@5'-CGA...AUCAU UACA UUUAC...UCC-3'@LB@ GGCU CCAUGGC@LB@ :\|\|\| \|\|\|\|\|\|\|@LB@ UCGA GGUACCG@LB@3'-UUU...AGUCU UAA CAAUC...GAA-5'@LB@ \| \|@LB@ 31 16@LB@@LB@@LB@Energy -6.29 kcal/mol@LB@Hybridization Energy -15.6862 kcal/mol@LB@Unfolding Energy - mRNA 4.66372 kcal/mol@LB@Unfolding Energy - sRNA 4.73426 kcal/mol@LB@@LB@Position - mRNA 20 -- 34@LB@Position - sRNA 17 -- 30@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 17 -- 23@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@
153	0.06453	0.3424	ct_729	serS	-6.28	0.205305	1 -- 23	3 -- 33	serine--tRNA ligase	______________1______________________________24\n______________\|______________________________\|\n___________5'-____C_G_____U__________________CCUCA...UGG-3'\n______________AGAA_C_AUUCC_UG________AUGCCAAC\n______________\|\|\|\|_\|_\|\|\|\|\|_\|\|________\|\|:\|\|\|\|\|\n______________UCUU_G_UAAGG_AC________UAUGGUUG\n3'-UUU...CUCAG____C_A_____U__CGCAAUCU________AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	17 -- 23	3 -- 9	-16.9997 kcal/mol	2.1318 kcal/mol	8.59196 kcal/mol	1 24@LB@ \| \|@LB@ 5'- C G U CCUCA...UGG-3'@LB@ AGAA C AUUCC UG AUGCCAAC@LB@ \|\|\|\| \| \|\|\|\|\| \|\| \|\|:\|\|\|\|\|@LB@ UCUU G UAAGG AC UAUGGUUG@LB@3'-UUU...CUCAG C A U CGCAAUCU AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -6.28 kcal/mol@LB@Hybridization Energy -16.9997 kcal/mol@LB@Unfolding Energy - mRNA 2.1318 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 1 -- 23@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 3 -- 9@LB@
155	0.06493	0.3424	ct_355	N/A	-6.27	0.205473	16 -- 22	80 -- 86		_____________15______23\n_____________\|_______\|\n5'-GUU...UUCUG_______GGUCC...CCU-3'\n______________ACGGCUG\n______________\|\|\|\|\|\|:\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	16 -- 22	80 -- 86	-10.68 kcal/mol	3.341 kcal/mol	1.06449 kcal/mol	15 23@LB@ \| \|@LB@5'-GUU...UUCUG GGUCC...CCU-3'@LB@ ACGGCUG@LB@ \|\|\|\|\|\|:@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -10.68 kcal/mol@LB@Unfolding Energy - mRNA 3.341 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 16 -- 22@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 80 -- 86@LB@
176	0.07518	0.3511	ct_481	N/A	-6.18	0.214715	76 -- 94	18 -- 35		_____________75__________________95\n_____________\|___________________\|\n5'-AUA...CCAUU__U___AU___________AAACA...AUU-3'\n______________UC_GAA__CUGUUCUAUGG\n______________\|\|_\|\|\|__\|\|:\|\|\|:\|\|\|\|\n______________AG_CUU__GAUAAGGUACC\n3'-UUU...AUCUC__U___C____________GCAAU...GAA-5'\n_____________\|___________________\|\n_____________36__________________17\n	88 -- 94	18 -- 24	-16.4052 kcal/mol	5.24588 kcal/mol	4.97803 kcal/mol	75 95@LB@ \| \|@LB@5'-AUA...CCAUU U AU AAACA...AUU-3'@LB@ UC GAA CUGUUCUAUGG@LB@ \|\| \|\|\| \|\|:\|\|\|:\|\|\|\|@LB@ AG CUU GAUAAGGUACC@LB@3'-UUU...AUCUC U C GCAAU...GAA-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -6.18 kcal/mol@LB@Hybridization Energy -16.4052 kcal/mol@LB@Unfolding Energy - mRNA 5.24588 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 76 -- 94@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 18 -- 24@LB@
190	0.08414	0.363	ct_503	N/A	-6.17	0.215667	244 -- 250	81 -- 87		_____________243_____251\n_____________\|_______\|\n5'-UGG...UUUGU_______UCGCA...CUC-3'\n______________UACGGUU\n______________\|\|\|\|\|:\|\n______________AUGCCGA\n3'-UUU...CCUCU_______UUGAG...GAA-5'\n_____________\|_______\|\n_____________88______80\n	244 -- 250	81 -- 87	-7.94334 kcal/mol	0.67364 kcal/mol	1.09752 kcal/mol	243 251@LB@ \| \|@LB@5'-UGG...UUUGU UCGCA...CUC-3'@LB@ UACGGUU@LB@ \|\|\|\|\|:\|@LB@ AUGCCGA@LB@3'-UUU...CCUCU UUGAG...GAA-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -7.94334 kcal/mol@LB@Unfolding Energy - mRNA 0.67364 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 244 -- 250@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 81 -- 87@LB@
115	0.04794	0.3262	ct_778	priA	-6.05	0.227860	46 -- 52	54 -- 60	primosomal protein N'	_____________45______53\n_____________\|_______\|\n5'-CGC...GUCAU_______AUCCU...AAA-3'\n______________UCCCCUC\n______________\|\|\|\|\|:\|\n______________AGGGGGG\n3'-UUU...ACUGA_______ACACA...GAA-5'\n_____________\|_______\|\n_____________61______53\n	46 -- 52	54 -- 60	-12.5948 kcal/mol	0.0982726 kcal/mol	6.44182 kcal/mol	45 53@LB@ \| \|@LB@5'-CGC...GUCAU AUCCU...AAA-3'@LB@ UCCCCUC@LB@ \|\|\|\|\|:\|@LB@ AGGGGGG@LB@3'-UUU...ACUGA ACACA...GAA-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -6.05 kcal/mol@LB@Hybridization Energy -12.5948 kcal/mol@LB@Unfolding Energy - mRNA 0.0982726 kcal/mol@LB@Unfolding Energy - sRNA 6.44182 kcal/mol@LB@@LB@Position - mRNA 46 -- 52@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 54 -- 60@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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