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
18	0.004135	0.1836	ct_799	N/A	-8.26	0.074627	30 -- 52	17 -- 35	50S ribosomal protein L25/general stress protein Ctc	_____________29______________________53\n_____________\|_______________________\|\n5'-AUC...AAUAA_________GCAA__A_______AGACG...GAA-3'\n______________UCAGAGGCU____GU_CCAUGGU\n______________\|\|\|\|\|:\|\|\|____:\|_\|\|\|\|\|\|:\n______________AGUCUUCGA____UA_GGUACCG\n3'-UUU...AUCUC_______________A_______CAAUC...GAA-5'\n_____________\|_______________________\|\n_____________36______________________16\n	46 -- 52	17 -- 23	-22.1109 kcal/mol	8.8748 kcal/mol	4.9781 kcal/mol	29 53@LB@ \| \|@LB@5'-AUC...AAUAA GCAA A AGACG...GAA-3'@LB@ UCAGAGGCU GU CCAUGGU@LB@ \|\|\|\|\|:\|\|\| :\| \|\|\|\|\|\|:@LB@ AGUCUUCGA UA GGUACCG@LB@3'-UUU...AUCUC A CAAUC...GAA-5'@LB@ \| \|@LB@ 36 16@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -22.1109 kcal/mol@LB@Unfolding Energy - mRNA 8.8748 kcal/mol@LB@Unfolding Energy - sRNA 4.9781 kcal/mol@LB@@LB@Position - mRNA 30 -- 52@LB@Position - sRNA 17 -- 35@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 17 -- 23@LB@
33	0.01042	0.2518	ct_780	N/A	-7.85	0.092931	30 -- 50	15 -- 34		_____________29____________________51\n_____________\|_____________________\|\n5'-UGU...AAAAA___C____GAA_G________GUCAA...UCA-3'\n______________CAG_AAGU___U_CAUGGCGU\n______________\|\|\|_\|\|\|:___\|_\|\|\|\|\|\|\|\|\n______________GUC_UUCG___A_GUACCGCA\n3'-UUU...UCUCA________AUA_G________AUCUU...GAA-5'\n_____________\|_____________________\|\n_____________35____________________14\n	44 -- 50	15 -- 21	-20.7959 kcal/mol	4.71518 kcal/mol	8.23265 kcal/mol	29 51@LB@ \| \|@LB@5'-UGU...AAAAA C GAA G GUCAA...UCA-3'@LB@ CAG AAGU U CAUGGCGU@LB@ \|\|\| \|\|\|: \| \|\|\|\|\|\|\|\|@LB@ GUC UUCG A GUACCGCA@LB@3'-UUU...UCUCA AUA G AUCUU...GAA-5'@LB@ \| \|@LB@ 35 14@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -20.7959 kcal/mol@LB@Unfolding Energy - mRNA 4.71518 kcal/mol@LB@Unfolding Energy - sRNA 8.23265 kcal/mol@LB@@LB@Position - mRNA 30 -- 50@LB@Position - sRNA 15 -- 34@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 15 -- 21@LB@
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@
50	0.01829	0.29	ct_588	rbsU	-10.49	0.021035	31 -- 46	21 -- 34	serine phosphatase RsbU	_____________30_______________47\n_____________\|________________\|\n5'-GUC...GGGUC________CU______AGAUU...UCC-3'\n______________CAGAAGCU__AUUCCA\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\n______________GUCUUCGA__UAAGGU\n3'-UUU...UCUCA________________ACCGC...GAA-5'\n_____________\|________________\|\n_____________35_______________20\n	32 -- 38	27 -- 33	-17.905 kcal/mol	2.68182 kcal/mol	4.73132 kcal/mol	30 47@LB@ \| \|@LB@5'-GUC...GGGUC CU AGAUU...UCC-3'@LB@ CAGAAGCU AUUCCA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCUUCGA UAAGGU@LB@3'-UUU...UCUCA ACCGC...GAA-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -17.905 kcal/mol@LB@Unfolding Energy - mRNA 2.68182 kcal/mol@LB@Unfolding Energy - sRNA 4.73132 kcal/mol@LB@@LB@Position - mRNA 31 -- 46@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 27 -- 33@LB@
91	0.03287	0.2942	ct_674	yscC	-7.61	0.105180	32 -- 46	36 -- 57	type II secretion system protein	_____________31_____________________47\n_____________\|______________________\|\n5'-UGG...ACACA______________G_______AUUUG...CGG-3'\n______________CCCC_______AAA_GCUAGAG\n______________\|\|\|\|_______\|\|\|_:\|\|\|\|\|\|\n______________GGGG_______UUU_UGAUCUC\n3'-UUU...GAAGG____ACACAUG___G_______AGUCU...GAA-5'\n_____________\|______________________\|\n_____________58_____________________35\n	40 -- 46	36 -- 42	-18.3 kcal/mol	2.71277 kcal/mol	7.97448 kcal/mol	31 47@LB@ \| \|@LB@5'-UGG...ACACA G AUUUG...CGG-3'@LB@ CCCC AAA GCUAGAG@LB@ \|\|\|\| \|\|\| :\|\|\|\|\|\|@LB@ GGGG UUU UGAUCUC@LB@3'-UUU...GAAGG ACACAUG G AGUCU...GAA-5'@LB@ \| \|@LB@ 58 35@LB@@LB@@LB@Energy -7.61 kcal/mol@LB@Hybridization Energy -18.3 kcal/mol@LB@Unfolding Energy - mRNA 2.71277 kcal/mol@LB@Unfolding Energy - sRNA 7.97448 kcal/mol@LB@@LB@Position - mRNA 32 -- 46@LB@Position - sRNA 36 -- 57@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 36 -- 42@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@
39	0.01357	0.2859	ct_401	gltT	-7.80	0.095127	36 -- 47	44 -- 55	sodium:dicarboxylate symport protein	_____________35___________48\n_____________\|____________\|\n5'-UGU...GGUAU____________AAAGG...AUA-3'\n______________CCUGUGUACAGA\n______________\|\|\|\|\|\|\|\|\|\|:\|\n______________GGACACAUGUUU\n3'-UUU...AGGGG____________GUGAU...GAA-5'\n_____________\|____________\|\n_____________56___________43\n	41 -- 47	44 -- 50	-17.8988 kcal/mol	2.58215 kcal/mol	7.51272 kcal/mol	35 48@LB@ \| \|@LB@5'-UGU...GGUAU AAAGG...AUA-3'@LB@ CCUGUGUACAGA@LB@ \|\|\|\|\|\|\|\|\|\|:\|@LB@ GGACACAUGUUU@LB@3'-UUU...AGGGG GUGAU...GAA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -17.8988 kcal/mol@LB@Unfolding Energy - mRNA 2.58215 kcal/mol@LB@Unfolding Energy - sRNA 7.51272 kcal/mol@LB@@LB@Position - mRNA 36 -- 47@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 44 -- 50@LB@
81	0.02893	0.29	ct_185	zwf	-6.95	0.147965	38 -- 47	51 -- 60	glucose-6-phosphate 1-dehydrogenase	_____________37_________48\n_____________\|__________\|\n5'-AAG...GCCUG__________AUCGU...UUU-3'\n______________UCCUCCCUGU\n______________\|\|\|:\|\|\|\|\|\|\n______________AGGGGGGACA\n3'-UUU...ACUGA__________CAUGU...GAA-5'\n_____________\|__________\|\n_____________61_________50\n	41 -- 47	51 -- 57	-17.9011 kcal/mol	1.87917 kcal/mol	9.07545 kcal/mol	37 48@LB@ \| \|@LB@5'-AAG...GCCUG AUCGU...UUU-3'@LB@ UCCUCCCUGU@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGGGGGGACA@LB@3'-UUU...ACUGA CAUGU...GAA-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -17.9011 kcal/mol@LB@Unfolding Energy - mRNA 1.87917 kcal/mol@LB@Unfolding Energy - sRNA 9.07545 kcal/mol@LB@@LB@Position - mRNA 38 -- 47@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 51 -- 57@LB@
86	0.03096	0.29	ct_221	yqfU	-7.15	0.133289	38 -- 44	80 -- 86		_____________37______45\n_____________\|_______\|\n5'-AUA...GCUCA_______GAGCA...GUG-3'\n______________GCGGUUA\n______________:\|\|\|:\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	38 -- 44	80 -- 86	-8.46136 kcal/mol	0.243281 kcal/mol	1.06449 kcal/mol	37 45@LB@ \| \|@LB@5'-AUA...GCUCA GAGCA...GUG-3'@LB@ GCGGUUA@LB@ :\|\|\|:\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -8.46136 kcal/mol@LB@Unfolding Energy - mRNA 0.243281 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 38 -- 44@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 80 -- 86@LB@
98	0.03528	0.2959	ct_676	N/A	-6.99	0.144558	38 -- 44	80 -- 86	protein-arginine kinase activator protein	_____________37______45\n_____________\|_______\|\n5'-GGG...GCUCA_______GAGCA...GUU-3'\n______________GCGGUUA\n______________:\|\|\|:\|\|\n______________UGCCGAU\n3'-UUU...CUCUA_______UGAGG...GAA-5'\n_____________\|_______\|\n_____________87______79\n	38 -- 44	80 -- 86	-8.44953 kcal/mol	0.39201 kcal/mol	1.06449 kcal/mol	37 45@LB@ \| \|@LB@5'-GGG...GCUCA GAGCA...GUU-3'@LB@ GCGGUUA@LB@ :\|\|\|:\|\|@LB@ UGCCGAU@LB@3'-UUU...CUCUA UGAGG...GAA-5'@LB@ \| \|@LB@ 87 79@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -8.44953 kcal/mol@LB@Unfolding Energy - mRNA 0.39201 kcal/mol@LB@Unfolding Energy - sRNA 1.06449 kcal/mol@LB@@LB@Position - mRNA 38 -- 44@LB@Position - sRNA 80 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 80 -- 86@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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