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
29	0.008327	0.236	ct_722	pgm	-9.49	0.037543	218 -- 230	17 -- 29	2 3-bisphosphoglycerate-dependent phosphoglycerate mutase	_____________217___________231\n_____________\|_____________\|\n5'-CUU...AUCUU____CG_______CAAUC...UUC-3'\n______________GCUA__CCAUGGC\n______________\|\|\|\|__\|\|\|\|\|\|\|\n______________CGAU__GGUACCG\n3'-UUU...GUCUU____AA_______CAAUC...GAA-5'\n_____________\|_____________\|\n_____________30____________16\n	224 -- 230	17 -- 23	-17.8075 kcal/mol	3.64492 kcal/mol	4.66832 kcal/mol	217 231@LB@ \| \|@LB@5'-CUU...AUCUU CG CAAUC...UUC-3'@LB@ GCUA CCAUGGC@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ CGAU GGUACCG@LB@3'-UUU...GUCUU AA CAAUC...GAA-5'@LB@ \| \|@LB@ 30 16@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -17.8075 kcal/mol@LB@Unfolding Energy - mRNA 3.64492 kcal/mol@LB@Unfolding Energy - sRNA 4.66832 kcal/mol@LB@@LB@Position - mRNA 218 -- 230@LB@Position - sRNA 17 -- 29@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 17 -- 23@LB@
148	0.06134	0.3407	ct_434	ygbB	-10.66	0.019089	186 -- 200	41 -- 57	2-C-methyl-D-erythritol 2 4-cyclodiphosphate synthase	_____________185_______________201\n_____________\|_________________\|\n5'-GGU...CCUGU_____U___________AUGAC...AUC-3'\n______________CCCCU___UGCAAGCAC\n______________\|\|\|\|\|___\|:\|\|\|:\|\|\|\n______________GGGGA___AUGUUUGUG\n3'-UUU...GAAGG_____CAC_________AUCUC...GAA-5'\n_____________\|_________________\|\n_____________58________________40\n	194 -- 200	41 -- 47	-19.7128 kcal/mol	1.2348 kcal/mol	7.82241 kcal/mol	185 201@LB@ \| \|@LB@5'-GGU...CCUGU U AUGAC...AUC-3'@LB@ CCCCU UGCAAGCAC@LB@ \|\|\|\|\| \|:\|\|\|:\|\|\|@LB@ GGGGA AUGUUUGUG@LB@3'-UUU...GAAGG CAC AUCUC...GAA-5'@LB@ \| \|@LB@ 58 40@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -19.7128 kcal/mol@LB@Unfolding Energy - mRNA 1.2348 kcal/mol@LB@Unfolding Energy - sRNA 7.82241 kcal/mol@LB@@LB@Position - mRNA 186 -- 200@LB@Position - sRNA 41 -- 57@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 41 -- 47@LB@
146	0.05858	0.3298	ct_655	kdsA	-5.70	0.267824	236 -- 245	48 -- 57	2-dehydro-3-deoxyphosphooctonate aldolase	_____________235________246\n_____________\|__________\|\n5'-GCU...GCAGG__________AUUGA...CUC-3'\n______________CCCUUGUGUA\n______________\|\|\|:\|\|\|\|\|\|\n______________GGGGACACAU\n3'-UUU...GAAGG__________GUUUG...GAA-5'\n_____________\|__________\|\n_____________58_________47\n	237 -- 243	50 -- 56	-16.3498 kcal/mol	3.37377 kcal/mol	7.27486 kcal/mol	235 246@LB@ \| \|@LB@5'-GCU...GCAGG AUUGA...CUC-3'@LB@ CCCUUGUGUA@LB@ \|\|\|:\|\|\|\|\|\|@LB@ GGGGACACAU@LB@3'-UUU...GAAGG GUUUG...GAA-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -5.70 kcal/mol@LB@Hybridization Energy -16.3498 kcal/mol@LB@Unfolding Energy - mRNA 3.37377 kcal/mol@LB@Unfolding Energy - sRNA 7.27486 kcal/mol@LB@@LB@Position - mRNA 236 -- 245@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 50 -- 56@LB@
199	0.0896	0.3683	ct_774	cysQ	-5.35	0.311933	207 -- 214	53 -- 60	3'(2') 5'-bisphosphate nucleotidase	_____________206______215\n_____________\|________\|\n5'-UCA...UGUUC________CAAUG...UUC-3'\n______________UCCCUCCU\n______________\|\|\|\|:\|\|\|\n______________AGGGGGGA\n3'-UUU...ACUGA________CACAU...GAA-5'\n_____________\|________\|\n_____________61_______52\n	208 -- 214	53 -- 59	-13.0073 kcal/mol	1.20108 kcal/mol	6.45136 kcal/mol	206 215@LB@ \| \|@LB@5'-UCA...UGUUC CAAUG...UUC-3'@LB@ UCCCUCCU@LB@ \|\|\|\|:\|\|\|@LB@ AGGGGGGA@LB@3'-UUU...ACUGA CACAU...GAA-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -5.35 kcal/mol@LB@Hybridization Energy -13.0073 kcal/mol@LB@Unfolding Energy - mRNA 1.20108 kcal/mol@LB@Unfolding Energy - sRNA 6.45136 kcal/mol@LB@@LB@Position - mRNA 207 -- 214@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 53 -- 59@LB@
68	0.02545	0.29	ct_369	aroB	-8.93	0.051509	264 -- 292	1 -- 31	3-dehydroquinate synthase	_____________263_____________________________293\n_____________\|_______________________________\|\n5'-GGC...ACCCU_________GCUU_______UC_________CCCUCUCA-3'\n______________AAGCUGUUU_____CGUU_G__UACCGACUU\n______________\|\|\|\|\|:\|\|:_____\|\|\|\|_\|__\|\|\|\|:\|\|\|\|\n______________UUCGAUAAG_____GCAA_C__AUGGUUGAA\n3'-UUU...CAGUC_________GUACC____U_UU_________-5'\n_____________\|______________________________\|\n_____________32_____________________________1\n	286 -- 292	1 -- 7	-23.4181 kcal/mol	6.00993 kcal/mol	8.47514 kcal/mol	263 293@LB@ \| \|@LB@5'-GGC...ACCCU GCUU UC CCCUCUCA-3'@LB@ AAGCUGUUU CGUU G UACCGACUU@LB@ \|\|\|\|\|:\|\|: \|\|\|\| \| \|\|\|\|:\|\|\|\|@LB@ UUCGAUAAG GCAA C AUGGUUGAA@LB@3'-UUU...CAGUC GUACC U UU -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -8.93 kcal/mol@LB@Hybridization Energy -23.4181 kcal/mol@LB@Unfolding Energy - mRNA 6.00993 kcal/mol@LB@Unfolding Energy - sRNA 8.47514 kcal/mol@LB@@LB@Position - mRNA 264 -- 292@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 1 -- 7@LB@
103	0.03832	0.3036	ct_382	aroG	-9.59	0.035559	138 -- 150	48 -- 60	3-deoxy-7-phosphoheptulonate synthase	_____________137___________151\n_____________\|_____________\|\n5'-UUU...UUUUC_____________UAUGA...CUA-3'\n______________UCUUCCCUGUGUG\n______________\|\|::\|\|\|\|\|\|\|\|:\n______________AGGGGGGACACAU\n3'-UUU...ACUGA_____________GUUUG...GAA-5'\n_____________\|_____________\|\n_____________61____________47\n	144 -- 150	48 -- 54	-20.2814 kcal/mol	1.44568 kcal/mol	9.24642 kcal/mol	137 151@LB@ \| \|@LB@5'-UUU...UUUUC UAUGA...CUA-3'@LB@ UCUUCCCUGUGUG@LB@ \|\|::\|\|\|\|\|\|\|\|:@LB@ AGGGGGGACACAU@LB@3'-UUU...ACUGA GUUUG...GAA-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -20.2814 kcal/mol@LB@Unfolding Energy - mRNA 1.44568 kcal/mol@LB@Unfolding Energy - sRNA 9.24642 kcal/mol@LB@@LB@Position - mRNA 138 -- 150@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 48 -- 54@LB@
150	0.06394	0.3424	ct_208	gseA	-4.42	0.454874	290 -- 300	19 -- 29	3-deoxy-D-manno-octulosonic acid transferase	_____________289________300\n_____________\|__________\|\n5'-UUG...AAAGU___U_______-3'\n______________GUU_UUCCAUG\n______________\|:\|_\|\|\|\|\|\|\|\n______________CGA_AAGGUAC\n3'-UUU...GUCUU___U_______CGCAA...GAA-5'\n_____________\|___________\|\n_____________30__________18\n	294 -- 300	19 -- 25	-10.2082 kcal/mol	1.1238 kcal/mol	4.66719 kcal/mol	289 300@LB@ \| \|@LB@5'-UUG...AAAGU U -3'@LB@ GUU UUCCAUG@LB@ \|:\| \|\|\|\|\|\|\|@LB@ CGA AAGGUAC@LB@3'-UUU...GUCUU U CGCAA...GAA-5'@LB@ \| \|@LB@ 30 18@LB@@LB@@LB@Energy -4.42 kcal/mol@LB@Hybridization Energy -10.2082 kcal/mol@LB@Unfolding Energy - mRNA 1.1238 kcal/mol@LB@Unfolding Energy - sRNA 4.66719 kcal/mol@LB@@LB@Position - mRNA 290 -- 300@LB@Position - sRNA 19 -- 29@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 19 -- 25@LB@
117	0.04834	0.3262	ct_237	fabG	-8.76	0.056710	143 -- 164	34 -- 58	3-oxoacyl-[acyl-carrier-protein] reductase	_____________142________________________165\n_____________\|__________________________\|\n5'-CGU...GAGUU_________________U________UAUGG...AUG-3'\n______________CCCCUUGU____AAACA_UUAGGGUC\n______________\|\|\|\|:\|\|\|____\|\|\|\|\|_:\|\|\|:\|\|\|\n______________GGGGGACA____UUUGU_GAUCUCAG\n3'-UUU...UGAAG________CAUG______________UCUUC...GAA-5'\n_____________\|__________________________\|\n_____________59_________________________33\n	144 -- 150	51 -- 57	-24.3621 kcal/mol	7.62467 kcal/mol	7.97757 kcal/mol	142 165@LB@ \| \|@LB@5'-CGU...GAGUU U UAUGG...AUG-3'@LB@ CCCCUUGU AAACA UUAGGGUC@LB@ \|\|\|\|:\|\|\| \|\|\|\|\| :\|\|\|:\|\|\|@LB@ GGGGGACA UUUGU GAUCUCAG@LB@3'-UUU...UGAAG CAUG UCUUC...GAA-5'@LB@ \| \|@LB@ 59 33@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -24.3621 kcal/mol@LB@Unfolding Energy - mRNA 7.62467 kcal/mol@LB@Unfolding Energy - sRNA 7.97757 kcal/mol@LB@@LB@Position - mRNA 143 -- 164@LB@Position - sRNA 34 -- 58@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 51 -- 57@LB@
158	0.06677	0.3424	ct_770	fabF	-2.81	0.742017	6 -- 13	26 -- 33	3-oxoacyl-ACP synthase	_____________5________14\n_____________\|________\|\n______5'-UAUAG________AAAAA...GUG-3'\n______________AGGAGUUA\n______________\|\|:\|\|:\|\|\n______________UCUUCGAU\n3'-UUU...CUCAG________AAGGU...GAA-5'\n_____________\|________\|\n_____________34_______25\n	7 -- 13	26 -- 32	-8.27201 kcal/mol	0.759487 kcal/mol	4.69868 kcal/mol	5 14@LB@ \| \|@LB@ 5'-UAUAG AAAAA...GUG-3'@LB@ AGGAGUUA@LB@ \|\|:\|\|:\|\|@LB@ UCUUCGAU@LB@3'-UUU...CUCAG AAGGU...GAA-5'@LB@ \| \|@LB@ 34 25@LB@@LB@@LB@Energy -2.81 kcal/mol@LB@Hybridization Energy -8.27201 kcal/mol@LB@Unfolding Energy - mRNA 0.759487 kcal/mol@LB@Unfolding Energy - sRNA 4.69868 kcal/mol@LB@@LB@Position - mRNA 6 -- 13@LB@Position - sRNA 26 -- 33@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 26 -- 32@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@

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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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