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
105	0.03879	0.3036	ct_546	N/A	-8.76	0.056849	221 -- 228	80 -- 87	contains leader (17) peptide	_____________220______229\n_____________\|________\|\n5'-CGC...UUUAU________UUUUU...ACG-3'\n______________UGCGGCUA\n______________\|:\|\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	222 -- 228	80 -- 86	-12.4581 kcal/mol	2.60487 kcal/mol	1.09752 kcal/mol	220 229@LB@ \| \|@LB@5'-CGC...UUUAU UUUUU...ACG-3'@LB@ UGCGGCUA@LB@ \|:\|\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -12.4581 kcal/mol@LB@Unfolding Energy - mRNA 2.60487 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 221 -- 228@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 80 -- 86@LB@
42	0.01617	0.29	ct_610	N/A	-8.69	0.058803	15 -- 22	80 -- 87	virulence protein CADD	_____________14_______23\n_____________\|________\|\n5'-GAU...GCAGU________UUGUU...GGG-3'\n______________UGCGGCUG\n______________\|:\|\|\|\|\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	16 -- 22	80 -- 86	-11.8172 kcal/mol	2.02516 kcal/mol	1.09752 kcal/mol	14 23@LB@ \| \|@LB@5'-GAU...GCAGU UUGUU...GGG-3'@LB@ UGCGGCUG@LB@ \|:\|\|\|\|\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -8.69 kcal/mol@LB@Hybridization Energy -11.8172 kcal/mol@LB@Unfolding Energy - mRNA 2.02516 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 15 -- 22@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 80 -- 86@LB@
119	0.04857	0.3262	ct_706	clpP_2	-8.60	0.061801	14 -- 27	22 -- 35	ATP-dependent Clp protease proteolytic subunit	_____________13_____________28\n_____________\|______________\|\n5'-CGA...AAGAU______________UUCUU...GGC-3'\n______________UUAGAGGUUGUUCC\n______________\|:\|\|\|:\|:\|:\|\|\|\|\n______________AGUCUUCGAUAAGG\n3'-UUU...AUCUC______________UACCG...GAA-5'\n_____________\|______________\|\n_____________36_____________21\n	16 -- 22	27 -- 33	-17.9181 kcal/mol	4.58788 kcal/mol	4.72627 kcal/mol	13 28@LB@ \| \|@LB@5'-CGA...AAGAU UUCUU...GGC-3'@LB@ UUAGAGGUUGUUCC@LB@ \|:\|\|\|:\|:\|:\|\|\|\|@LB@ AGUCUUCGAUAAGG@LB@3'-UUU...AUCUC UACCG...GAA-5'@LB@ \| \|@LB@ 36 21@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -17.9181 kcal/mol@LB@Unfolding Energy - mRNA 4.58788 kcal/mol@LB@Unfolding Energy - sRNA 4.72627 kcal/mol@LB@@LB@Position - mRNA 14 -- 27@LB@Position - sRNA 22 -- 35@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 27 -- 33@LB@
1	6.997e-05	0.03358	ct_198	oppA_3	-8.59	0.062291	189 -- 206	17 -- 33	oligopeptide ABC transporter substrate-binding protein	_____________188________________207\n_____________\|__________________\|\n5'-AAA...UCUAA______C________C__AAGAU...CUC-3'\n______________GGAGGU_AUUCCAUG_GC\n______________:\|\|:\|:_\|\|\|\|\|\|\|\|_\|\|\n______________UCUUCG_UAAGGUAC_CG\n3'-UUU...CUCAG______A___________CAAUC...GAA-5'\n_____________\|__________________\|\n_____________34_________________16\n	197 -- 203	19 -- 25	-19.6111 kcal/mol	6.04348 kcal/mol	4.97804 kcal/mol	188 207@LB@ \| \|@LB@5'-AAA...UCUAA C C AAGAU...CUC-3'@LB@ GGAGGU AUUCCAUG GC@LB@ :\|\|:\|: \|\|\|\|\|\|\|\| \|\|@LB@ UCUUCG UAAGGUAC CG@LB@3'-UUU...CUCAG A CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -19.6111 kcal/mol@LB@Unfolding Energy - mRNA 6.04348 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 189 -- 206@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 19 -- 25@LB@
26	0.006621	0.2093	ct_267	ihfA	-8.59	0.062448	193 -- 205	17 -- 31	DNA-binding protein HU	_____________192_____________206\n_____________\|_______________\|\n5'-UAA...GCAAC_______________AACGA...AUA-3'\n______________AAGCUA__CCAUGGC\n______________\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UUCGAU__GGUACCG\n3'-UUU...CAGUC______AA_______CAAUC...GAA-5'\n_____________\|_______________\|\n_____________32______________16\n	199 -- 205	17 -- 23	-17.4173 kcal/mol	3.97125 kcal/mol	4.86101 kcal/mol	192 206@LB@ \| \|@LB@5'-UAA...GCAAC AACGA...AUA-3'@LB@ AAGCUA CCAUGGC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUCGAU GGUACCG@LB@3'-UUU...CAGUC AA CAAUC...GAA-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -17.4173 kcal/mol@LB@Unfolding Energy - mRNA 3.97125 kcal/mol@LB@Unfolding Energy - sRNA 4.86101 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
12	0.002873	0.1836	ct_040	ruvB	-8.58	0.062725	112 -- 136	36 -- 60	Holliday junction DNA helicase RuvB	_____________111_______________________137\n_____________\|_________________________\|\n5'-CAG...GGGAA_________ACUU___C________GAUGU...AAG-3'\n______________UCCCUCUUG____CAG_CGCUGGAG\n______________\|\|\|\|:\|:\|\|____\|\|:_\|:\|\|:\|\|\|\n______________AGGGGGGAC____GUU_GUGAUCUC\n3'-UUU...ACUGA_________ACAU___U________AGUCU...GAA-5'\n_____________\|_________________________\|\n_____________61________________________35\n	113 -- 119	53 -- 59	-26.2752 kcal/mol	7.75429 kcal/mol	9.944 kcal/mol	111 137@LB@ \| \|@LB@5'-CAG...GGGAA ACUU C GAUGU...AAG-3'@LB@ UCCCUCUUG CAG CGCUGGAG@LB@ \|\|\|\|:\|:\|\| \|\|: \|:\|\|:\|\|\|@LB@ AGGGGGGAC GUU GUGAUCUC@LB@3'-UUU...ACUGA ACAU U AGUCU...GAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -26.2752 kcal/mol@LB@Unfolding Energy - mRNA 7.75429 kcal/mol@LB@Unfolding Energy - sRNA 9.944 kcal/mol@LB@@LB@Position - mRNA 112 -- 136@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 53 -- 59@LB@
51	0.01855	0.29	ct_758	murD	-8.46	0.066834	21 -- 39	25 -- 51	UDP-N-acetylmuramoylalanine--D-glutamate ligase	_____________20__________________________40\n_____________\|___________________________\|\n5'-CUG...GUGAU___________________________AAAUU...ACA-3'\n______________UGUACA________AGUCGGAAGUUAU\n______________\|\|\|\|\|\|________\|\|\|\|:\|\|\|\|:\|\|\|\n______________ACAUGU________UCAGUCUUCGAUA\n3'-UUU...GGGAC______UUGUGAUC_____________AGGUA...GAA-5'\n_____________\|___________________________\|\n_____________52__________________________24\n	33 -- 39	25 -- 31	-21.2974 kcal/mol	1.17475 kcal/mol	11.6617 kcal/mol	20 40@LB@ \| \|@LB@5'-CUG...GUGAU AAAUU...ACA-3'@LB@ UGUACA AGUCGGAAGUUAU@LB@ \|\|\|\|\|\| \|\|\|\|:\|\|\|\|:\|\|\|@LB@ ACAUGU UCAGUCUUCGAUA@LB@3'-UUU...GGGAC UUGUGAUC AGGUA...GAA-5'@LB@ \| \|@LB@ 52 24@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -21.2974 kcal/mol@LB@Unfolding Energy - mRNA 1.17475 kcal/mol@LB@Unfolding Energy - sRNA 11.6617 kcal/mol@LB@@LB@Position - mRNA 21 -- 39@LB@Position - sRNA 25 -- 51@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 25 -- 31@LB@
6	0.000543	0.07439	ct_280	nqr4	-8.45	0.067322	89 -- 131	2 -- 35	Na(+)-translocating NADH-quinone reductase subunit D	_____________88___________________________________________132\n_____________\|____________________________________________\|\n5'-GAC...GAAUU__________C___GACUUGUA_________CC_______UU__CUCAU...CGG-3'\n______________UCAGGAGCUA_UUU________AUGGUGUUA__GAAU_CC__CU\n______________\|\|\|\|:\|\|\|\|\|_\|::________\|\|\|\|:\|\|\|\|__\|\|\|\|_\|\|__\|\|\n______________AGUCUUCGAU_AGG________UACCGCAAU__CUUA_GG__GA\n3'-UUU...AUCUC__________A__________________________U__UU__A-5'\n_____________\|____________________________________________\|\n_____________36___________________________________________1\n	113 -- 119	13 -- 19	-28.603 kcal/mol	11.5634 kcal/mol	8.59199 kcal/mol	88 132@LB@ \| \|@LB@5'-GAC...GAAUU C GACUUGUA CC UU CUCAU...CGG-3'@LB@ UCAGGAGCUA UUU AUGGUGUUA GAAU CC CU@LB@ \|\|\|\|:\|\|\|\|\| \|:: \|\|\|\|:\|\|\|\| \|\|\|\| \|\| \|\|@LB@ AGUCUUCGAU AGG UACCGCAAU CUUA GG GA@LB@3'-UUU...AUCUC A U UU A-5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -28.603 kcal/mol@LB@Unfolding Energy - mRNA 11.5634 kcal/mol@LB@Unfolding Energy - sRNA 8.59199 kcal/mol@LB@@LB@Position - mRNA 89 -- 131@LB@Position - sRNA 2 -- 35@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 13 -- 19@LB@
49	0.01821	0.29	ct_733	N/A	-8.44	0.067485	96 -- 102	80 -- 86		_____________95______103\n_____________\|_______\|\n5'-AUG...UGCCA_______UUGAU...CUA-3'\n______________GCGGCUA\n______________:\|\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	96 -- 102	80 -- 86	-11.4095 kcal/mol	1.90152 kcal/mol	1.06449 kcal/mol	95 103@LB@ \| \|@LB@5'-AUG...UGCCA UUGAU...CUA-3'@LB@ GCGGCUA@LB@ :\|\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -11.4095 kcal/mol@LB@Unfolding Energy - mRNA 1.90152 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 96 -- 102@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 80 -- 86@LB@
62	0.02417	0.29	ct_705	clpX	-8.32	0.072096	259 -- 275	17 -- 33	ATP-dependent Clp protease ATP-binding subunit ClpX	_____________258_______________276\n_____________\|_________________\|\n5'-CUG...UGUUG________A__GC____CCAUC...AUU-3'\n______________AGAAGCUA_UC__UGGU\n______________\|\|\|\|\|\|\|\|_\|\|__\|\|\|:\n______________UCUUCGAU_AG__ACCG\n3'-UUU...CUCAG________A__GU____CAAUC...GAA-5'\n_____________\|_________________\|\n_____________34________________16\n	260 -- 266	26 -- 32	-18.4351 kcal/mol	5.13531 kcal/mol	4.97804 kcal/mol	258 276@LB@ \| \|@LB@5'-CUG...UGUUG A GC CCAUC...AUU-3'@LB@ AGAAGCUA UC UGGU@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|:@LB@ UCUUCGAU AG ACCG@LB@3'-UUU...CUCAG A GU CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -18.4351 kcal/mol@LB@Unfolding Energy - mRNA 5.13531 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 259 -- 275@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 26 -- 32@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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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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