Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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_000913 Escherichia coli str. K-12 substr. MG1655

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
174	0.01972	0.3812	b0478	ybaL	-7.90	0.612018	5 -- 14	166 -- 176	inner membrane putative NAD(P)-binding transporter	_____________4___________15\n_____________\|___________\|\n_______5'-UUUA___________AAGCC...UGG-3'\n______________CAGUCGC_CAU\n______________\|\|\|\|\|:\|_\|\|\|\n______________GUCAGUG_GUA\n3'-UUU...UAUGA_______U___CUACG...UAG-5'\n_____________\|___________\|\n_____________177_________165\n	5 -- 11	170 -- 176	-11.743 kcal/mol	0.493889 kcal/mol	0.598087 kcal/mol	4 15@LB@ \| \|@LB@ 5'-UUUA AAGCC...UGG-3'@LB@ CAGUCGC CAU@LB@ \|\|\|\|\|:\| \|\|\|@LB@ GUCAGUG GUA@LB@3'-UUU...UAUGA U CUACG...UAG-5'@LB@ \| \|@LB@ 177 165@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -11.743 kcal/mol@LB@Unfolding Energy - mRNA 0.493889 kcal/mol@LB@Unfolding Energy - sRNA 0.598087 kcal/mol@LB@@LB@Position - mRNA 5 -- 14@LB@Position - sRNA 166 -- 176@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 170 -- 176@LB@
30	0.002398	0.2633	b0494	tesA	-12.69	0.080698	14 -- 26	126 -- 138	acyl-CoA thioesterase 1 and protease I and lysophospholipase L1	_____________13____________27\n_____________\|_____________\|\n5'-UCC...AUGUA_____________CAGAC...UGG-3'\n______________GCGGUUGUCCCAC\n______________\|\|\|\|\|::\|\|\|\|\|\|\n______________CGCCAGUAGGGUG\n3'-UUU...CUUAA_____________ACGUA...UAG-5'\n_____________\|_____________\|\n_____________139___________125\n	20 -- 26	126 -- 132	-24.3083 kcal/mol	5.59054 kcal/mol	8.249 kcal/mol	13 27@LB@ \| \|@LB@5'-UCC...AUGUA CAGAC...UGG-3'@LB@ GCGGUUGUCCCAC@LB@ \|\|\|\|\|::\|\|\|\|\|\|@LB@ CGCCAGUAGGGUG@LB@3'-UUU...CUUAA ACGUA...UAG-5'@LB@ \| \|@LB@ 139 125@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -24.3083 kcal/mol@LB@Unfolding Energy - mRNA 5.59054 kcal/mol@LB@Unfolding Energy - sRNA 8.249 kcal/mol@LB@@LB@Position - mRNA 14 -- 26@LB@Position - sRNA 126 -- 138@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 126 -- 132@LB@
142	0.01524	0.3575	b0611	rna	-12.80	0.076457	138 -- 176	173 -- 202	ribonuclease I	_____________137_____________________________________177\n_____________\|_______________________________________\|\n5'-UAC...CCCAC________CUUUUUUA______A___GA___________GUAUG...AUU-3'\n______________CUGGCGGG________UGAUUU_AUA__UAGUAUUCAGU\n______________\|\|\|\|\|\|\|\|________\|\|\|\|\|\|_\|:\|__:\|:\|\|:\|\|\|\|\|\n______________GACCGCCC________ACUAAA_UGU__GUUAUGAGUCA\n3'-UUU...UAGAC______________________A___G____________GUGUG...UAG-5'\n_____________\|_______________________________________\|\n_____________203_____________________________________172\n	170 -- 176	173 -- 179	-31.7889 kcal/mol	9.30484 kcal/mol	14.6886 kcal/mol	137 177@LB@ \| \|@LB@5'-UAC...CCCAC CUUUUUUA A GA GUAUG...AUU-3'@LB@ CUGGCGGG UGAUUU AUA UAGUAUUCAGU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\| \|:\| :\|:\|\|:\|\|\|\|\|@LB@ GACCGCCC ACUAAA UGU GUUAUGAGUCA@LB@3'-UUU...UAGAC A G GUGUG...UAG-5'@LB@ \| \|@LB@ 203 172@LB@@LB@@LB@Energy -12.80 kcal/mol@LB@Hybridization Energy -31.7889 kcal/mol@LB@Unfolding Energy - mRNA 9.30484 kcal/mol@LB@Unfolding Energy - sRNA 14.6886 kcal/mol@LB@@LB@Position - mRNA 138 -- 176@LB@Position - sRNA 173 -- 202@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 173 -- 179@LB@
29	0.002294	0.2633	b0624	flc	-16.49	0.013425	233 -- 293	118 -- 176	fluoride efflux channel dual topology membrane protein	_____________232_____________________294\n_____________\|_______________________\|\n5'-AAA...CGGCG_______UA______C_______AAUCA...UUC-3'\n______________UUACACU_____UCA_UCAUACA\n______________\|\|\|\|\|\|:_____\|\|\|_\|\|\|:\|\|\|\n______________AAUGUGG_____AGU_AGUGUGU\n3'-UUU...ACUAA_______UUAUG___C_______ACUAC...UAG-5'\n_____________\|_______________________\|\n_____________177_____________________117\n	172 -- 178	167 -- 173	-16.8792 kcal/mol	2.93634 kcal/mol	5.08824 kcal/mol	232 294@LB@ \| \|@LB@5'-AAA...CGGCG UA C AAUCA...UUC-3'@LB@ UUACACU UCA UCAUACA@LB@ \|\|\|\|\|\|: \|\|\| \|\|\|:\|\|\|@LB@ AAUGUGG AGU AGUGUGU@LB@3'-UUU...ACUAA UUAUG C ACUAC...UAG-5'@LB@ \| \|@LB@ 177 117@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -16.8792 kcal/mol@LB@Unfolding Energy - mRNA 2.93634 kcal/mol@LB@Unfolding Energy - sRNA 5.08824 kcal/mol@LB@@LB@Position - mRNA 233 -- 293@LB@Position - sRNA 118 -- 176@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 167 -- 173@LB@
102	0.01106	0.3575	b0647	ybeT	-15.01	0.026876	192 -- 264	115 -- 176	Sel1 family TPR-like repeat protein	_____________191___________265\n_____________\|_____________\|\n5'-AUA...CGAAG__U__________AUAAA...UGG-3'\n______________CA_UCACACAUGA\n______________\|\|_\|\|\|\|\|\|\|\|\|\|\n______________GU_AGUGUGUACU\n3'-UUU...UAUGA__C__________ACGUC...UAG-5'\n_____________\|_____________\|\n_____________177___________114\n	198 -- 204	164 -- 170	-15.9732 kcal/mol	2.87622 kcal/mol	4.17773 kcal/mol	191 265@LB@ \| \|@LB@5'-AUA...CGAAG U AUAAA...UGG-3'@LB@ CA UCACACAUGA@LB@ \|\| \|\|\|\|\|\|\|\|\|\|@LB@ GU AGUGUGUACU@LB@3'-UUU...UAUGA C ACGUC...UAG-5'@LB@ \| \|@LB@ 177 114@LB@@LB@@LB@Energy -15.01 kcal/mol@LB@Hybridization Energy -15.9732 kcal/mol@LB@Unfolding Energy - mRNA 2.87622 kcal/mol@LB@Unfolding Energy - sRNA 4.17773 kcal/mol@LB@@LB@Position - mRNA 192 -- 264@LB@Position - sRNA 115 -- 176@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 164 -- 170@LB@
45	0.003942	0.2948	b0686	ybfF	-11.97	0.113030	234 -- 245	63 -- 74	acyl-CoA esterase	_____________233__________246\n_____________\|____________\|\n5'-CUU...CACAA____________AAUUC...GCG-3'\n______________AACCAGCACAAU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UUGGUCGUGUUG\n3'-UUU...UUGCG____________AAGCG...UAG-5'\n_____________\|____________\|\n_____________75___________62\n	239 -- 245	63 -- 69	-18.9732 kcal/mol	1.15073 kcal/mol	9.24135 kcal/mol	233 246@LB@ \| \|@LB@5'-CUU...CACAA AAUUC...GCG-3'@LB@ AACCAGCACAAU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UUGGUCGUGUUG@LB@3'-UUU...UUGCG AAGCG...UAG-5'@LB@ \| \|@LB@ 75 62@LB@@LB@@LB@Energy -11.97 kcal/mol@LB@Hybridization Energy -18.9732 kcal/mol@LB@Unfolding Energy - mRNA 1.15073 kcal/mol@LB@Unfolding Energy - sRNA 9.24135 kcal/mol@LB@@LB@Position - mRNA 234 -- 245@LB@Position - sRNA 63 -- 74@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 63 -- 69@LB@
66	0.006473	0.3261	b0712	ybgK	-17.58	0.008094	217 -- 255	130 -- 164	putative allophanate hydrolase subunit 2	_____________216________________________________________________________256\n_____________\|__________________________________________________________\|\n5'-CGC...GGAGU_____GA__A____U_____________U__AUACC___GUG______G_________ACGGU...AUA-3'\n______________AUGCU__AG_UUAU_C___GUGCGGGCA_GU_____ACU___CAGGAU_GCGGUCGUC\n______________\|\|:\|\|__\|\|_\|:\|:_\|___:\|\|\|:\|\|\|\|_\|\|_____\|\|\|___\|\|\|:\|\|_\|\|\|\|\|\|:\|\|\n______________UAUGA__UC_AGUG_G___UACGUCCGU_CA_____UGA___GUCUUA_CGCCAGUAG\n3'-UUU...GUGGU_____G________U_UAC_________U__GU______AA_______A_________GGUGA...UAG-5'\n_____________\|__________________________________________________________\|\n_____________165________________________________________________________129\n	249 -- 255	130 -- 136	-44.2735 kcal/mol	15.0195 kcal/mol	15.1988 kcal/mol	216 256@LB@ \| \|@LB@5'-CGC...GGAGU GA A U U AUACC GUG G ACGGU...AUA-3'@LB@ AUGCU AG UUAU C GUGCGGGCA GU ACU CAGGAU GCGGUCGUC@LB@ \|\|:\|\| \|\| \|:\|: \| :\|\|\|:\|\|\|\| \|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|\|:\|\|@LB@ UAUGA UC AGUG G UACGUCCGU CA UGA GUCUUA CGCCAGUAG@LB@3'-UUU...GUGGU G U UAC U GU AA A GGUGA...UAG-5'@LB@ \| \|@LB@ 165 129@LB@@LB@@LB@Energy -17.58 kcal/mol@LB@Hybridization Energy -44.2735 kcal/mol@LB@Unfolding Energy - mRNA 15.0195 kcal/mol@LB@Unfolding Energy - sRNA 15.1988 kcal/mol@LB@@LB@Position - mRNA 217 -- 255@LB@Position - sRNA 130 -- 164@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 130 -- 136@LB@
164	0.01856	0.3808	b0715	abrB	-11.36	0.150074	79 -- 113	125 -- 160	regulator of aidB expression; inner membrane protein	_____________78_____________114\n_____________\|______________\|\n5'-GGC...CGGCG______U_______GCCGA-3'\n______________GCGCUA_UACUUGG\n______________:\|:\|:\|_\|\|\|\|::\|\n______________UGUGGU_AUGAGUC\n3'-UUU...UAAAA______U_______AGUGU...UAG-5'\n_____________\|______________\|\n_____________161____________124\n	289 -- 295	174 -- 180	-13.5584 kcal/mol	1.79119 kcal/mol	3.6661 kcal/mol	78 114@LB@ \| \|@LB@5'-GGC...CGGCG U GCCGA-3'@LB@ GCGCUA UACUUGG@LB@ :\|:\|:\| \|\|\|\|::\|@LB@ UGUGGU AUGAGUC@LB@3'-UUU...UAAAA U AGUGU...UAG-5'@LB@ \| \|@LB@ 161 124@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -13.5584 kcal/mol@LB@Unfolding Energy - mRNA 1.79119 kcal/mol@LB@Unfolding Energy - sRNA 3.6661 kcal/mol@LB@@LB@Position - mRNA 79 -- 113@LB@Position - sRNA 125 -- 160@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 174 -- 180@LB@
108	0.01175	0.3575	b0723	sdhA	-10.39	0.232370	178 -- 209	28 -- 62	succinate dehydrogenase flavoprotein subunit	_____________177_______________________210\n_____________\|_________________________\|\n5'-GGU...GAAAU__________G_G_AUU________UUGUG...GUG-3'\n______________UGC_CAGUCA_A_A___UGAUGCAG\n______________\|:\|_\|\|\|\|\|\|_\|_\|___\|\|\|\|\|\|\|\|\n______________AUG_GUCAGU_U_U___ACUACGUC\n3'-UUU...UGGUU___A______G_G____________CGUUC...UAG-5'\n_____________\|_________________________\|\n_____________63________________________27\n	225 -- 231	159 -- 165	-22.5908 kcal/mol	8.24888 kcal/mol	4.81331 kcal/mol	177 210@LB@ \| \|@LB@5'-GGU...GAAAU G G AUU UUGUG...GUG-3'@LB@ UGC CAGUCA A A UGAUGCAG@LB@ \|:\| \|\|\|\|\|\| \| \| \|\|\|\|\|\|\|\|@LB@ AUG GUCAGU U U ACUACGUC@LB@3'-UUU...UGGUU A G G CGUUC...UAG-5'@LB@ \| \|@LB@ 63 27@LB@@LB@@LB@Energy -10.39 kcal/mol@LB@Hybridization Energy -22.5908 kcal/mol@LB@Unfolding Energy - mRNA 8.24888 kcal/mol@LB@Unfolding Energy - sRNA 4.81331 kcal/mol@LB@@LB@Position - mRNA 178 -- 209@LB@Position - sRNA 28 -- 62@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 159 -- 165@LB@
70	0.00686	0.3298	b0761	modE	-10.05	0.269682	248 -- 271	57 -- 77	transcriptional repressor for the molybdenum transport operon modABC	_____________247______272\n_____________\|________\|\n5'-ACC...GAAAA________CUUUU...CCA-3'\n______________GCACUCCC\n______________\|\|\|\|:\|\|\|\n______________CGUGGGGG\n3'-UUU...UACCC________AACGA...UAG-5'\n_____________\|________\|\n_____________78_______56\n	126 -- 132	11 -- 17	-14.7879 kcal/mol	0.633098 kcal/mol	5.13224 kcal/mol	247 272@LB@ \| \|@LB@5'-ACC...GAAAA CUUUU...CCA-3'@LB@ GCACUCCC@LB@ \|\|\|\|:\|\|\|@LB@ CGUGGGGG@LB@3'-UUU...UACCC AACGA...UAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -10.05 kcal/mol@LB@Hybridization Energy -14.7879 kcal/mol@LB@Unfolding Energy - mRNA 0.633098 kcal/mol@LB@Unfolding Energy - sRNA 5.13224 kcal/mol@LB@@LB@Position - mRNA 248 -- 271@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 11 -- 17@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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