Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
131	0.005571	0.1429	b3102	yqjG	-9.67	0.191738	57 -- 77	24 -- 46	putative S-transferase	_____________56_______________________78\n_____________\|________________________\|\n5'-GCA...UUUCU__C__A______CU__________AUUAC...GGC-3'\n______________GG_GG_UUCCUG_____GCUGGCA\n______________\|\|_\|\|_\|\|\|\|\|\|_____\|\|\|:\|\|\|\n______________CC_CC_AAGGAC_____CGAUCGU\n3'-UUU...UUCCU__A_________CAUGU_______AAAAU...UCG-5'\n_____________\|________________________\|\n_____________47_______________________23\n	71 -- 77	24 -- 30	-24.338 kcal/mol	10.1138 kcal/mol	4.55813 kcal/mol	56 78@LB@ \| \|@LB@5'-GCA...UUUCU C A CU AUUAC...GGC-3'@LB@ GG GG UUCCUG GCUGGCA@LB@ \|\| \|\| \|\|\|\|\|\| \|\|\|:\|\|\|@LB@ CC CC AAGGAC CGAUCGU@LB@3'-UUU...UUCCU A CAUGU AAAAU...UCG-5'@LB@ \| \|@LB@ 47 23@LB@@LB@@LB@Energy -9.67 kcal/mol@LB@Hybridization Energy -24.338 kcal/mol@LB@Unfolding Energy - mRNA 10.1138 kcal/mol@LB@Unfolding Energy - sRNA 4.55813 kcal/mol@LB@@LB@Position - mRNA 57 -- 77@LB@Position - sRNA 24 -- 46@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 24 -- 30@LB@
132	0.005751	0.146	b2294	yfbU	-8.39	0.309344	3 -- 25	24 -- 50	UPF0304 family protein	_____________2______________________________26\n_____________\|______________________________\|\n_________5'-GC____________________GGU_______CCCGU...AAA-3'\n______________AGGAG______UCUGG_ACA___GUUGGCA\n______________\|\|\|\|\|______:\|\|\|\|_\|\|\|___\|:\|:\|\|\|\n______________UCCUC______GGACC_UGU___CGAUCGU\n3'-UUU...CCGAU_____CACCAA_____A_____________AAAAU...UCG-5'\n_____________\|______________________________\|\n_____________51_____________________________23\n	19 -- 25	24 -- 30	-20.5947 kcal/mol	7.58762 kcal/mol	4.6134 kcal/mol	2 26@LB@ \| \|@LB@ 5'-GC GGU CCCGU...AAA-3'@LB@ AGGAG UCUGG ACA GUUGGCA@LB@ \|\|\|\|\| :\|\|\|\| \|\|\| \|:\|:\|\|\|@LB@ UCCUC GGACC UGU CGAUCGU@LB@3'-UUU...CCGAU CACCAA A AAAAU...UCG-5'@LB@ \| \|@LB@ 51 23@LB@@LB@@LB@Energy -8.39 kcal/mol@LB@Hybridization Energy -20.5947 kcal/mol@LB@Unfolding Energy - mRNA 7.58762 kcal/mol@LB@Unfolding Energy - sRNA 4.6134 kcal/mol@LB@@LB@Position - mRNA 3 -- 25@LB@Position - sRNA 24 -- 50@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 24 -- 30@LB@
133	0.005817	0.146	b3461	rpoH	-7.67	0.391921	235 -- 243	24 -- 32	RNA polymerase sigma 32 (sigma H) factor	_____________234_______244\n_____________\|_________\|\n5'-GGA...AGCCC_________ACCUG...AGG-3'\n______________CAGUUGGCA\n______________\|\|\|:\|:\|\|\|\n______________GUCGAUCGU\n3'-UUU...ACCAU_________AAAAU...UCG-5'\n_____________\|_________\|\n_____________33________23\n	237 -- 243	24 -- 30	-13.04 kcal/mol	3.94405 kcal/mol	1.424 kcal/mol	234 244@LB@ \| \|@LB@5'-GGA...AGCCC ACCUG...AGG-3'@LB@ CAGUUGGCA@LB@ \|\|\|:\|:\|\|\|@LB@ GUCGAUCGU@LB@3'-UUU...ACCAU AAAAU...UCG-5'@LB@ \| \|@LB@ 33 23@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -13.04 kcal/mol@LB@Unfolding Energy - mRNA 3.94405 kcal/mol@LB@Unfolding Energy - sRNA 1.424 kcal/mol@LB@@LB@Position - mRNA 235 -- 243@LB@Position - sRNA 24 -- 32@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 24 -- 30@LB@
134	0.005847	0.146	b0065	yabI	-9.48	0.206647	266 -- 290	24 -- 46	DedA family inner membrane protein	_____________265_______________________291\n_____________\|_________________________\|\n5'-UGA...GUGUU_____CC_______AGUC_______CUGGU...GUU-3'\n______________GGUGG__UUUCUGG____GCUGGCG\n______________\|\|\|\|\|__\|\|:\|\|\|\|____\|\|\|:\|\|:\n______________CCACC__AAGGACC____CGAUCGU\n3'-UUU...UUCCU______________AUGU_______AAAAU...UCG-5'\n_____________\|_________________________\|\n_____________47________________________23\n	284 -- 290	24 -- 30	-26.6068 kcal/mol	12.5692 kcal/mol	4.55813 kcal/mol	265 291@LB@ \| \|@LB@5'-UGA...GUGUU CC AGUC CUGGU...GUU-3'@LB@ GGUGG UUUCUGG GCUGGCG@LB@ \|\|\|\|\| \|\|:\|\|\|\| \|\|\|:\|\|:@LB@ CCACC AAGGACC CGAUCGU@LB@3'-UUU...UUCCU AUGU AAAAU...UCG-5'@LB@ \| \|@LB@ 47 23@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -26.6068 kcal/mol@LB@Unfolding Energy - mRNA 12.5692 kcal/mol@LB@Unfolding Energy - sRNA 4.55813 kcal/mol@LB@@LB@Position - mRNA 266 -- 290@LB@Position - sRNA 24 -- 46@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 24 -- 30@LB@
135	0.005891	0.146	b3009	yghB	-12.71	0.045213	257 -- 299	7 -- 46	general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter	_____________256_________________________________________300\n_____________\|___________________________________________\|\n5'-UCU...GCGCU__C__A____CA___U_________GUUUACUUU__C______G-3'\n______________GG_GG_UCCU__UAU_GUUAGCGUU_________GU_AUGUUU\n______________\|\|_\|\|_\|\|\|\|__\|\|:_\|:\|\|\|\|:\|\|_________\|\|_\|\|\|\|\|\|\n______________CC_CC_AGGA__AUG_CGAUCGUAA_________CA_UACAAA\n3'-UUU...UUCCU__A__A____CC___U_________AAUACC_____A______AAGUCG-5'\n_____________\|___________________________________________\|\n_____________47__________________________________________6\n	275 -- 281	22 -- 28	-27.0814 kcal/mol	9.76724 kcal/mol	4.60844 kcal/mol	256 300@LB@ \| \|@LB@5'-UCU...GCGCU C A CA U GUUUACUUU C G-3'@LB@ GG GG UCCU UAU GUUAGCGUU GU AUGUUU@LB@ \|\| \|\| \|\|\|\| \|\|: \|:\|\|\|\|:\|\| \|\| \|\|\|\|\|\|@LB@ CC CC AGGA AUG CGAUCGUAA CA UACAAA@LB@3'-UUU...UUCCU A A CC U AAUACC A AAGUCG-5'@LB@ \| \|@LB@ 47 6@LB@@LB@@LB@Energy -12.71 kcal/mol@LB@Hybridization Energy -27.0814 kcal/mol@LB@Unfolding Energy - mRNA 9.76724 kcal/mol@LB@Unfolding Energy - sRNA 4.60844 kcal/mol@LB@@LB@Position - mRNA 257 -- 299@LB@Position - sRNA 7 -- 46@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 22 -- 28@LB@
136	0.005909	0.146	b1291	sapD	-11.34	0.091029	118 -- 151	12 -- 36	antimicrobial peptide ABC transporter ATPase	_____________117________________________________152\n_____________\|__________________________________\|\n5'-AUC...UGCCA________AAUUAUGAU______G____U_____ACCUC...GUG-3'\n______________GGUGCGGC_________UAGCGU_UUGU_GGUUA\n______________\|\|\|:\|:\|\|_________\|\|\|\|:\|_\|\|:\|_\|\|\|\|\|\n______________CCAUGUCG_________AUCGUA_AAUA_CCAAU\n3'-UUU...AAGGA_______________________A____C_____ACAAA...UCG-5'\n_____________\|__________________________________\|\n_____________37_________________________________11\n	119 -- 125	29 -- 35	-24.3443 kcal/mol	11.5428 kcal/mol	1.45699 kcal/mol	117 152@LB@ \| \|@LB@5'-AUC...UGCCA AAUUAUGAU G U ACCUC...GUG-3'@LB@ GGUGCGGC UAGCGU UUGU GGUUA@LB@ \|\|\|:\|:\|\| \|\|\|\|:\| \|\|:\| \|\|\|\|\|@LB@ CCAUGUCG AUCGUA AAUA CCAAU@LB@3'-UUU...AAGGA A C ACAAA...UCG-5'@LB@ \| \|@LB@ 37 11@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -24.3443 kcal/mol@LB@Unfolding Energy - mRNA 11.5428 kcal/mol@LB@Unfolding Energy - sRNA 1.45699 kcal/mol@LB@@LB@Position - mRNA 118 -- 151@LB@Position - sRNA 12 -- 36@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 29 -- 35@LB@
137	0.006165	0.1512	b1024	pgaA	-6.60	0.530802	267 -- 274	1 -- 8	biofilm adhesin polysaccharide PGA secretin; OM porin; poly-beta-1 6-N-acetyl-D-glucosamine export protein	_____________266______275\n_____________\|________\|\n5'-CUC...CCGCA________AGCGA...CUG-3'\n______________UUUUUAGC\n______________\|\|\|\|:\|\|\|\n______________AAAAGUCG\n3'-UUU...AUACA________-5'\n_____________\|_______\|\n_____________9_______1\n	268 -- 274	1 -- 7	-8.19691 kcal/mol	0.802454 kcal/mol	0.799201 kcal/mol	266 275@LB@ \| \|@LB@5'-CUC...CCGCA AGCGA...CUG-3'@LB@ UUUUUAGC@LB@ \|\|\|\|:\|\|\|@LB@ AAAAGUCG@LB@3'-UUU...AUACA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.60 kcal/mol@LB@Hybridization Energy -8.19691 kcal/mol@LB@Unfolding Energy - mRNA 0.802454 kcal/mol@LB@Unfolding Energy - sRNA 0.799201 kcal/mol@LB@@LB@Position - mRNA 267 -- 274@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 1 -- 7@LB@
138	0.006247	0.1521	b1063	yceB	-7.15	0.457702	84 -- 117	1 -- 32	lipoprotein DUF1439 family	_____________83__________________________________118\n_____________\|___________________________________\|\n5'-UGC...CGCGG____CU_____CGC_______CCGCCG________UUUUU...ACC-3'\n______________CAGC__GUAUU____GGGUUG______UUUUCAGU\n______________\|\|\|\|__\|:\|\|\|____\|\|\|\|\|:______\|\|\|\|\|\|\|:\n______________GUCG__CGUAA____CCCAAU______AAAAGUCG\n3'-UUU...ACCAU____AU_____AAUA______ACA___________-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	111 -- 117	1 -- 7	-22.6034 kcal/mol	13.9644 kcal/mol	1.49075 kcal/mol	83 118@LB@ \| \|@LB@5'-UGC...CGCGG CU CGC CCGCCG UUUUU...ACC-3'@LB@ CAGC GUAUU GGGUUG UUUUCAGU@LB@ \|\|\|\| \|:\|\|\| \|\|\|\|\|: \|\|\|\|\|\|\|:@LB@ GUCG CGUAA CCCAAU AAAAGUCG@LB@3'-UUU...ACCAU AU AAUA ACA -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -22.6034 kcal/mol@LB@Unfolding Energy - mRNA 13.9644 kcal/mol@LB@Unfolding Energy - sRNA 1.49075 kcal/mol@LB@@LB@Position - mRNA 84 -- 117@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 1 -- 7@LB@
139	0.00635	0.1535	b0800	ybiB	-9.74	0.186276	120 -- 129	27 -- 36	putative family 3 glycosyltransferase	_____________119________130\n_____________\|__________\|\n5'-GCC...CUGAA__________AAAAG...UCA-3'\n______________GGUAUAGUUA\n______________\|\|\|\|:\|\|:\|\|\n______________CCAUGUCGAU\n3'-UUU...AAGGA__________CGUAA...UCG-5'\n_____________\|__________\|\n_____________37_________26\n	123 -- 129	27 -- 33	-12.0711 kcal/mol	1.15693 kcal/mol	1.17709 kcal/mol	119 130@LB@ \| \|@LB@5'-GCC...CUGAA AAAAG...UCA-3'@LB@ GGUAUAGUUA@LB@ \|\|\|\|:\|\|:\|\|@LB@ CCAUGUCGAU@LB@3'-UUU...AAGGA CGUAA...UCG-5'@LB@ \| \|@LB@ 37 26@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -12.0711 kcal/mol@LB@Unfolding Energy - mRNA 1.15693 kcal/mol@LB@Unfolding Energy - sRNA 1.17709 kcal/mol@LB@@LB@Position - mRNA 120 -- 129@LB@Position - sRNA 27 -- 36@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 27 -- 33@LB@
140	0.006493	0.1559	b1916	sdiA	-12.48	0.051059	182 -- 224	1 -- 50	quorum-sensing transcriptional activator	_____________181_________________________________________________225\n_____________\|___________________________________________________\|\n5'-UGU...CUCUC_____C_____G_____U______U___GGAUAA___AU____________UGGCG...AGG-3'\n______________AGGGG___GUU_C_GGU_UA_CUA_GCA_______GG_____UUUUUCAGC\n______________\|\|\|:\|___\|\|\|_\|_\|\|\|_:\|_\|\|\|_\|\|\|_______\|\|_____\|\|\|\|\|\|\|\|\|\n______________UCCUC___CAA_G_CCA_GU_GAU_CGU_______CC_____AAAAAGUCG\n3'-UUU...CCGAU_____CAC___G_A___U__C_______AAAAUAC__AAUAC_________-5'\n_____________\|__________________________________________________\|\n_____________51_________________________________________________1\n	218 -- 224	1 -- 7	-26.3158 kcal/mol	9.17132 kcal/mol	4.6634 kcal/mol	181 225@LB@ \| \|@LB@5'-UGU...CUCUC C G U U GGAUAA AU UGGCG...AGG-3'@LB@ AGGGG GUU C GGU UA CUA GCA GG UUUUUCAGC@LB@ \|\|\|:\| \|\|\| \| \|\|\| :\| \|\|\| \|\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ UCCUC CAA G CCA GU GAU CGU CC AAAAAGUCG@LB@3'-UUU...CCGAU CAC G A U C AAAAUAC AAUAC -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -26.3158 kcal/mol@LB@Unfolding Energy - mRNA 9.17132 kcal/mol@LB@Unfolding Energy - sRNA 4.6634 kcal/mol@LB@@LB@Position - mRNA 182 -- 224@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 1 -- 7@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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