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
111	0.04436	0.3262	ct_405	ribC	-3.97	0.532190	3 -- 10	49 -- 56	riboflavin synthase	_____________2________11\n_____________\|________\|\n_________5'-AA________CUUGU...AUG-3'\n______________UCCUGUGU\n______________:\|\|\|\|\|\|\|\n______________GGGACACA\n3'-UUU...AAGGG________UGUUU...GAA-5'\n_____________\|________\|\n_____________57_______48\n	4 -- 10	49 -- 55	-11.4476 kcal/mol	0.227857 kcal/mol	7.24525 kcal/mol	2 11@LB@ \| \|@LB@ 5'-AA CUUGU...AUG-3'@LB@ UCCUGUGU@LB@ :\|\|\|\|\|\|\|@LB@ GGGACACA@LB@3'-UUU...AAGGG UGUUU...GAA-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -3.97 kcal/mol@LB@Hybridization Energy -11.4476 kcal/mol@LB@Unfolding Energy - mRNA 0.227857 kcal/mol@LB@Unfolding Energy - sRNA 7.24525 kcal/mol@LB@@LB@Position - mRNA 3 -- 10@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 49 -- 55@LB@
154	0.06467	0.3424	ct_517	rl24	-3.21	0.671117	143 -- 150	27 -- 34	50S ribosomal protein L24	_____________142______151\n_____________\|________\|\n5'-UAA...CGAGA________UUGUU...AGG-3'\n______________CAGAGGCU\n______________\|\|\|\|:\|\|\|\n______________GUCUUCGA\n3'-UUU...UCUCA________UAAGG...GAA-5'\n_____________\|________\|\n_____________35_______26\n	144 -- 150	27 -- 33	-11.3134 kcal/mol	3.50051 kcal/mol	4.59929 kcal/mol	142 151@LB@ \| \|@LB@5'-UAA...CGAGA UUGUU...AGG-3'@LB@ CAGAGGCU@LB@ \|\|\|\|:\|\|\|@LB@ GUCUUCGA@LB@3'-UUU...UCUCA UAAGG...GAA-5'@LB@ \| \|@LB@ 35 26@LB@@LB@@LB@Energy -3.21 kcal/mol@LB@Hybridization Energy -11.3134 kcal/mol@LB@Unfolding Energy - mRNA 3.50051 kcal/mol@LB@Unfolding Energy - sRNA 4.59929 kcal/mol@LB@@LB@Position - mRNA 143 -- 150@LB@Position - sRNA 27 -- 34@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 27 -- 33@LB@
99	0.03647	0.3007	ct_810	rl32	-4.11	0.507281	35 -- 46	46 -- 58	50S ribosomal protein L32	_____________34____________47\n_____________\|_____________\|\n5'-UUC...CAAGU_____________CGUUU...GCA-3'\n______________CUUCCUG_GUAUA\n______________\|::\|\|\|\|_\|\|\|:\|\n______________GGGGGAC_CAUGU\n3'-UUU...UGAAG_______A_____UUGUG...GAA-5'\n_____________\|_____________\|\n_____________59____________45\n	35 -- 41	52 -- 58	-13.0221 kcal/mol	1.6119 kcal/mol	7.29598 kcal/mol	34 47@LB@ \| \|@LB@5'-UUC...CAAGU CGUUU...GCA-3'@LB@ CUUCCUG GUAUA@LB@ \|::\|\|\|\| \|\|\|:\|@LB@ GGGGGAC CAUGU@LB@3'-UUU...UGAAG A UUGUG...GAA-5'@LB@ \| \|@LB@ 59 45@LB@@LB@@LB@Energy -4.11 kcal/mol@LB@Hybridization Energy -13.0221 kcal/mol@LB@Unfolding Energy - mRNA 1.6119 kcal/mol@LB@Unfolding Energy - sRNA 7.29598 kcal/mol@LB@@LB@Position - mRNA 35 -- 46@LB@Position - sRNA 46 -- 58@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 52 -- 58@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@
55	0.02093	0.29	ct_785	rl34	-4.69	0.410747	264 -- 270	80 -- 86	50S ribosomal protein L34	_____________263_____271\n_____________\|_______\|\n5'-ACA...CUCGC_______CAAAA...GCC-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	264 -- 270	80 -- 86	-8.67787 kcal/mol	2.92801 kcal/mol	1.06449 kcal/mol	263 271@LB@ \| \|@LB@5'-ACA...CUCGC CAAAA...GCC-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -4.69 kcal/mol@LB@Hybridization Energy -8.67787 kcal/mol@LB@Unfolding Energy - mRNA 2.92801 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 264 -- 270@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 80 -- 86@LB@
52	0.01886	0.29	ct_784	rnpA	-5.05	0.354130	114 -- 120	80 -- 86	ribonuclease P protein component	_____________113_____121\n_____________\|_______\|\n5'-UCU...CUCGC_______CAAAA...UGA-3'\n______________AUGGCUA\n______________\|:\|\|\|\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	114 -- 120	80 -- 86	-8.53572 kcal/mol	2.4168 kcal/mol	1.06449 kcal/mol	113 121@LB@ \| \|@LB@5'-UCU...CUCGC CAAAA...UGA-3'@LB@ AUGGCUA@LB@ \|:\|\|\|\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -5.05 kcal/mol@LB@Hybridization Energy -8.53572 kcal/mol@LB@Unfolding Energy - mRNA 2.4168 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 114 -- 120@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 80 -- 86@LB@
157	0.06639	0.3424	ct_213	rpiA	-7.48	0.112460	245 -- 274	28 -- 57	ribose-5-phosphate isomerase A	_____________244____________________________275\n_____________\|______________________________\|\n5'-GAA...UUUUU____AUCAA_____A_____C_C_______AGUAG...UGU-3'\n______________CCCU_____GCAGA_ACUAG_G_UAGAGGC\n______________\|\|\|:_____:\|\|:\|_\|\|\|\|\|_\|_:\|\|\|:\|\|\n______________GGGG_____UGUUU_UGAUC_C_GUCUUCG\n3'-UUU...GAAGG____ACACA_____G_____U_A_______AUAAG...GAA-5'\n_____________\|______________________________\|\n_____________58_____________________________27\n	268 -- 274	28 -- 34	-25.4315 kcal/mol	5.87242 kcal/mol	12.0748 kcal/mol	244 275@LB@ \| \|@LB@5'-GAA...UUUUU AUCAA A C C AGUAG...UGU-3'@LB@ CCCU GCAGA ACUAG G UAGAGGC@LB@ \|\|\|: :\|\|:\| \|\|\|\|\| \| :\|\|\|:\|\|@LB@ GGGG UGUUU UGAUC C GUCUUCG@LB@3'-UUU...GAAGG ACACA G U A AUAAG...GAA-5'@LB@ \| \|@LB@ 58 27@LB@@LB@@LB@Energy -7.48 kcal/mol@LB@Hybridization Energy -25.4315 kcal/mol@LB@Unfolding Energy - mRNA 5.87242 kcal/mol@LB@Unfolding Energy - sRNA 12.0748 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 28 -- 57@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 28 -- 34@LB@
17	0.003987	0.1836	ct_843	rs15	-6.01	0.232273	282 -- 295	22 -- 34	30S ribosomal protein S15	_____________281____________296\n_____________\|______________\|\n5'-AGG...AUGUG____UU________GACUG-3'\n______________CAGA__GCUAUUCU\n______________\|\|\|\|__\|\|\|\|\|\|\|:\n______________GUCU__CGAUAAGG\n3'-UUU...UCUCA____U_________UACCG...GAA-5'\n_____________\|______________\|\n_____________35_____________21\n	288 -- 294	23 -- 29	-14.3687 kcal/mol	3.62939 kcal/mol	4.72608 kcal/mol	281 296@LB@ \| \|@LB@5'-AGG...AUGUG UU GACUG-3'@LB@ CAGA GCUAUUCU@LB@ \|\|\|\| \|\|\|\|\|\|\|:@LB@ GUCU CGAUAAGG@LB@3'-UUU...UCUCA U UACCG...GAA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -6.01 kcal/mol@LB@Hybridization Energy -14.3687 kcal/mol@LB@Unfolding Energy - mRNA 3.62939 kcal/mol@LB@Unfolding Energy - sRNA 4.72608 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 23 -- 29@LB@
20	0.004812	0.1918	ct_026	rs16	-8.27	0.073959	26 -- 51	3 -- 33	30S ribosomal protein S16	_____________25______________________________52\n_____________\|_______________________________\|\n5'-CUG...ACGAA________________AA_________G___CGGAU...AUA-3'\n______________AGGAGUUA____GUGG__UU_GAGUAU_AGC\n______________\|\|:\|\|:\|\|____:\|\|\|__\|\|_\|\|:\|\|:_\|:\|\n______________UCUUCGAU____UACC__AA_CUUAUG_UUG\n3'-UUU...CUCAG________AAGG____GC__U______G___AA-5'\n_____________\|_______________________________\|\n_____________34______________________________2\n	27 -- 33	26 -- 32	-20.5759 kcal/mol	3.70935 kcal/mol	8.59196 kcal/mol	25 52@LB@ \| \|@LB@5'-CUG...ACGAA AA G CGGAU...AUA-3'@LB@ AGGAGUUA GUGG UU GAGUAU AGC@LB@ \|\|:\|\|:\|\| :\|\|\| \|\| \|\|:\|\|: \|:\|@LB@ UCUUCGAU UACC AA CUUAUG UUG@LB@3'-UUU...CUCAG AAGG GC U G AA-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -20.5759 kcal/mol@LB@Unfolding Energy - mRNA 3.70935 kcal/mol@LB@Unfolding Energy - sRNA 8.59196 kcal/mol@LB@@LB@Position - mRNA 26 -- 51@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 26 -- 32@LB@
2	8.171e-05	0.03358	ct_802	rs18	-7.95	0.088258	66 -- 79	21 -- 34	30S ribosomal protein S18	_____________65_____________80\n_____________\|______________\|\n5'-GUU...AGCCC__________CG__GAGUU...UUA-3'\n______________CAGAAGCUAU__CA\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\n______________GUCUUCGAUA__GU\n3'-UUU...UCUCA__________AG__ACCGC...GAA-5'\n_____________\|______________\|\n_____________35_____________20\n	68 -- 74	26 -- 32	-17.0234 kcal/mol	4.34679 kcal/mol	4.73132 kcal/mol	65 80@LB@ \| \|@LB@5'-GUU...AGCCC CG GAGUU...UUA-3'@LB@ CAGAAGCUAU CA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ GUCUUCGAUA GU@LB@3'-UUU...UCUCA AG ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -17.0234 kcal/mol@LB@Unfolding Energy - mRNA 4.34679 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 66 -- 79@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 68 -- 74@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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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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