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
131	0.05291	0.3262	ct_842	pnp	-7.97	0.086989	198 -- 205	17 -- 24	polyribonucleotide nucleotidyltransferase	_____________197______206\n_____________\|________\|\n5'-UGA...ACAAC________UUUUG...UCA-3'\n______________UCCAUGGC\n______________\|\|\|\|\|\|\|\|\n______________AGGUACCG\n3'-UUU...CGAUA________CAAUC...GAA-5'\n_____________\|________\|\n_____________25_______16\n	199 -- 205	17 -- 23	-14.0999 kcal/mol	1.64992 kcal/mol	4.47615 kcal/mol	197 206@LB@ \| \|@LB@5'-UGA...ACAAC UUUUG...UCA-3'@LB@ UCCAUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGGUACCG@LB@3'-UUU...CGAUA CAAUC...GAA-5'@LB@ \| \|@LB@ 25 16@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -14.0999 kcal/mol@LB@Unfolding Energy - mRNA 1.64992 kcal/mol@LB@Unfolding Energy - sRNA 4.47615 kcal/mol@LB@@LB@Position - mRNA 198 -- 205@LB@Position - sRNA 17 -- 24@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
132	0.05402	0.3262	ct_150	rl33	-5.54	0.287166	186 -- 205	17 -- 33	50S ribosomal protein L33	_____________185__________________206\n_____________\|____________________\|\n5'-CUC...UCUUG___AAA____CA________CAGCA...UAG-3'\n______________AGA___GGUU__UUCAUGGC\n______________\|\|\|___:\|:\|__\|:\|\|\|\|\|\|\n______________UCU___UCGA__AGGUACCG\n3'-UUU...CUCAG__________UA________CAAUC...GAA-5'\n_____________\|____________________\|\n_____________34___________________16\n	199 -- 205	17 -- 23	-14.3817 kcal/mol	3.85921 kcal/mol	4.97804 kcal/mol	185 206@LB@ \| \|@LB@5'-CUC...UCUUG AAA CA CAGCA...UAG-3'@LB@ AGA GGUU UUCAUGGC@LB@ \|\|\| :\|:\| \|:\|\|\|\|\|\|@LB@ UCU UCGA AGGUACCG@LB@3'-UUU...CUCAG UA CAAUC...GAA-5'@LB@ \| \|@LB@ 34 16@LB@@LB@@LB@Energy -5.54 kcal/mol@LB@Hybridization Energy -14.3817 kcal/mol@LB@Unfolding Energy - mRNA 3.85921 kcal/mol@LB@Unfolding Energy - sRNA 4.97804 kcal/mol@LB@@LB@Position - mRNA 186 -- 205@LB@Position - sRNA 17 -- 33@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 17 -- 23@LB@
133	0.05414	0.3262	ct_059	fer	-7.78	0.096344	200 -- 207	80 -- 87	ferredoxin	_____________199______208\n_____________\|________\|\n5'-UUC...AGUCC________AGCUC...CUU-3'\n______________UAUGGCUA\n______________\|\|:\|\|\|\|\|\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	200 -- 206	81 -- 87	-10.7757 kcal/mol	1.8981 kcal/mol	1.09752 kcal/mol	199 208@LB@ \| \|@LB@5'-UUC...AGUCC AGCUC...CUU-3'@LB@ UAUGGCUA@LB@ \|\|:\|\|\|\|\|@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -7.78 kcal/mol@LB@Hybridization Energy -10.7757 kcal/mol@LB@Unfolding Energy - mRNA 1.8981 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 200 -- 206@LB@Position Seed - sRNA 81 -- 87@LB@
134	0.05433	0.3262	ct_581	thrS	-7.17	0.132364	52 -- 64	21 -- 33	threonine--tRNA ligase	_____________51___________65\n_____________\|____________\|\n5'-AAA...CUAAA_______CC___GAACU...CAG-3'\n______________AGAAGCU__UCC\n______________\|\|\|\|\|\|\|__\|\|\|\n______________UCUUCGA__AGG\n3'-UUU...CUCAG_______UA___UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________20\n	52 -- 58	27 -- 33	-13.855 kcal/mol	1.83194 kcal/mol	4.72509 kcal/mol	51 65@LB@ \| \|@LB@5'-AAA...CUAAA CC GAACU...CAG-3'@LB@ AGAAGCU UCC@LB@ \|\|\|\|\|\|\| \|\|\|@LB@ UCUUCGA AGG@LB@3'-UUU...CUCAG UA UACCG...GAA-5'@LB@ \| \|@LB@ 34 20@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -13.855 kcal/mol@LB@Unfolding Energy - mRNA 1.83194 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 52 -- 64@LB@Position - sRNA 21 -- 33@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 27 -- 33@LB@
135	0.05472	0.3262	ct_283	N/A	-6.89	0.152000	262 -- 284	14 -- 35		_____________261______________________285\n_____________\|________________________\|\n5'-UAC...GUUUA_____CU________GC_______UGUUU...UUG-3'\n______________UCGGA__AGUUA_UC__UGGCGUU\n______________\|\|:\|\|__\|\|:\|\|_\|\|__\|\|\|\|\|\|\|\n______________AGUCU__UCGAU_AG__ACCGCAA\n3'-UUU...AUCUC____________A__GU_______UCUUA...GAA-5'\n_____________\|________________________\|\n_____________36_______________________13\n	278 -- 284	14 -- 20	-19.9844 kcal/mol	4.64246 kcal/mol	8.44936 kcal/mol	261 285@LB@ \| \|@LB@5'-UAC...GUUUA CU GC UGUUU...UUG-3'@LB@ UCGGA AGUUA UC UGGCGUU@LB@ \|\|:\|\| \|\|:\|\| \|\| \|\|\|\|\|\|\|@LB@ AGUCU UCGAU AG ACCGCAA@LB@3'-UUU...AUCUC A GU UCUUA...GAA-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -6.89 kcal/mol@LB@Hybridization Energy -19.9844 kcal/mol@LB@Unfolding Energy - mRNA 4.64246 kcal/mol@LB@Unfolding Energy - sRNA 8.44936 kcal/mol@LB@@LB@Position - mRNA 262 -- 284@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 14 -- 20@LB@
136	0.05474	0.3262	ct_592	sdhA	-7.43	0.115894	38 -- 56	18 -- 34	succinate dehydrogenase flavoprotein subunit	_____________37__________________57\n_____________\|___________________\|\n5'-UCU...UGUUA___CU_____UU_______GUUUA...UGU-3'\n______________UAG__GCUGU__UCCAUGG\n______________:\|\|__\|\|\|:\|__\|\|\|\|\|\|\|\n______________GUC__CGAUA__AGGUACC\n3'-UUU...UCUCA___UU______________GCAAU...GAA-5'\n_____________\|___________________\|\n_____________35__________________17\n	50 -- 56	18 -- 24	-18.2308 kcal/mol	5.82664 kcal/mol	4.97803 kcal/mol	37 57@LB@ \| \|@LB@5'-UCU...UGUUA CU UU GUUUA...UGU-3'@LB@ UAG GCUGU UCCAUGG@LB@ :\|\| \|\|\|:\| \|\|\|\|\|\|\|@LB@ GUC CGAUA AGGUACC@LB@3'-UUU...UCUCA UU GCAAU...GAA-5'@LB@ \| \|@LB@ 35 17@LB@@LB@@LB@Energy -7.43 kcal/mol@LB@Hybridization Energy -18.2308 kcal/mol@LB@Unfolding Energy - mRNA 5.82664 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 38 -- 56@LB@Position - sRNA 18 -- 34@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 18 -- 24@LB@
137	0.05536	0.3262	ct_389	N/A	-5.69	0.269629	175 -- 181	80 -- 86		_____________174_____182\n_____________\|_______\|\n5'-GUU...AUAAC_______UCUCA...GCC-3'\n______________GCGGCUG\n______________:\|\|\|\|\|:\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	175 -- 181	80 -- 86	-10.4159 kcal/mol	3.66497 kcal/mol	1.06449 kcal/mol	174 182@LB@ \| \|@LB@5'-GUU...AUAAC UCUCA...GCC-3'@LB@ GCGGCUG@LB@ :\|\|\|\|\|:@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.69 kcal/mol@LB@Hybridization Energy -10.4159 kcal/mol@LB@Unfolding Energy - mRNA 3.66497 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 175 -- 181@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 80 -- 86@LB@
138	0.05554	0.3262	ct_806	ptr	-4.69	0.410459	54 -- 70	19 -- 33	insulinase/protease	_____________53________________71\n_____________\|_________________\|\n5'-GUU...UCCGA________AUAUA____AUAAA...UAA-3'\n______________AGAAGCUG_____CAUG\n______________\|\|\|\|\|\|\|:_____\|\|\|\|\n______________UCUUCGAU_____GUAC\n3'-UUU...CUCAG________AAG______CGCAA...GAA-5'\n_____________\|_________________\|\n_____________34________________18\n	55 -- 61	26 -- 32	-13.627 kcal/mol	3.96302 kcal/mol	4.97702 kcal/mol	53 71@LB@ \| \|@LB@5'-GUU...UCCGA AUAUA AUAAA...UAA-3'@LB@ AGAAGCUG CAUG@LB@ \|\|\|\|\|\|\|: \|\|\|\|@LB@ UCUUCGAU GUAC@LB@3'-UUU...CUCAG AAG CGCAA...GAA-5'@LB@ \| \|@LB@ 34 18@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -13.627 kcal/mol@LB@Unfolding Energy - mRNA 3.96302 kcal/mol@LB@Unfolding Energy - sRNA 4.97702 kcal/mol@LB@@LB@Position - mRNA 54 -- 70@LB@Position - sRNA 19 -- 33@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 26 -- 32@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@
140	0.05617	0.3262	ct_759	nlpD	-2.72	0.757894	26 -- 32	51 -- 57	muramidase	_____________25______33\n_____________\|_______\|\n5'-GAG...AGAGU_______AACCG...AGU-3'\n______________UCCCUGU\n______________:\|\|\|\|\|\|\n______________GGGGACA\n3'-UUU...GAAGG_______CAUGU...GAA-5'\n_____________\|_______\|\n_____________58______50\n	26 -- 32	51 -- 57	-10.8083 kcal/mol	0.989353 kcal/mol	7.09845 kcal/mol	25 33@LB@ \| \|@LB@5'-GAG...AGAGU AACCG...AGU-3'@LB@ UCCCUGU@LB@ :\|\|\|\|\|\|@LB@ GGGGACA@LB@3'-UUU...GAAGG CAUGU...GAA-5'@LB@ \| \|@LB@ 58 50@LB@@LB@@LB@Energy -2.72 kcal/mol@LB@Hybridization Energy -10.8083 kcal/mol@LB@Unfolding Energy - mRNA 0.989353 kcal/mol@LB@Unfolding Energy - sRNA 7.09845 kcal/mol@LB@@LB@Position - mRNA 26 -- 32@LB@Position - sRNA 51 -- 57@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 51 -- 57@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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