Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
165	0.0337	0.6177	b3983	rplK	-8.80	0.071896	189 -- 197	41 -- 49	50S ribosomal subunit protein L11	_____________188_______198\n_____________\|_________\|\n5'-ACC...AACUU_________AUAAU...UAA-3'\n______________GAGGAAUUU\n______________\|\|\|\|\|\|\|\|\|\n______________CUCCUUAAA\n3'-UUU...AGUUU_________GUAAA...ACA-5'\n_____________\|_________\|\n_____________50________40\n	191 -- 197	41 -- 47	-11.4231 kcal/mol	1.76644 kcal/mol	0.852225 kcal/mol	188 198@LB@ \| \|@LB@5'-ACC...AACUU AUAAU...UAA-3'@LB@ GAGGAAUUU@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUCCUUAAA@LB@3'-UUU...AGUUU GUAAA...ACA-5'@LB@ \| \|@LB@ 50 40@LB@@LB@@LB@Energy -8.80 kcal/mol@LB@Hybridization Energy -11.4231 kcal/mol@LB@Unfolding Energy - mRNA 1.76644 kcal/mol@LB@Unfolding Energy - sRNA 0.852225 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 41 -- 49@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 41 -- 47@LB@
16	0.003381	0.593	b0956	matP	-12.11	0.015217	269 -- 280	42 -- 53	Ter macrodomain organizer matS-binding protein	_____________268__________281\n_____________\|____________\|\n5'-UUU...CAUCG____________AAUCA...AAG-3'\n______________CGAAGGGGAGUU\n______________\|:\|\|\|:\|\|\|:\|\|\n______________GUUUCUCCUUAA\n3'-UUU...GGGCA____________AGUAA...ACA-5'\n_____________\|____________\|\n_____________54___________41\n	274 -- 280	42 -- 48	-15.3716 kcal/mol	2.33274 kcal/mol	0.933904 kcal/mol	268 281@LB@ \| \|@LB@5'-UUU...CAUCG AAUCA...AAG-3'@LB@ CGAAGGGGAGUU@LB@ \|:\|\|\|:\|\|\|:\|\|@LB@ GUUUCUCCUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -15.3716 kcal/mol@LB@Unfolding Energy - mRNA 2.33274 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 269 -- 280@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 42 -- 48@LB@
27	0.005027	0.5992	b3745	viaA	-10.46	0.033099	243 -- 253	42 -- 52	stimulator of RavA ATPase activity; von Willebrand factor domain protein	_____________242_________254\n_____________\|___________\|\n5'-ACG...UCAGC___________GAUCG...CGG-3'\n______________GAAGAGGGAUU\n______________:\|\|\|\|\|\|:\|\|\|\n______________UUUCUCCUUAA\n3'-UUU...GGCAG___________AGUAA...ACA-5'\n_____________\|___________\|\n_____________53__________41\n	247 -- 253	42 -- 48	-12.7293 kcal/mol	1.40033 kcal/mol	0.866923 kcal/mol	242 254@LB@ \| \|@LB@5'-ACG...UCAGC GAUCG...CGG-3'@LB@ GAAGAGGGAUU@LB@ :\|\|\|\|\|\|:\|\|\|@LB@ UUUCUCCUUAA@LB@3'-UUU...GGCAG AGUAA...ACA-5'@LB@ \| \|@LB@ 53 41@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -12.7293 kcal/mol@LB@Unfolding Energy - mRNA 1.40033 kcal/mol@LB@Unfolding Energy - sRNA 0.866923 kcal/mol@LB@@LB@Position - mRNA 243 -- 253@LB@Position - sRNA 42 -- 52@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 42 -- 48@LB@
29	0.005664	0.6127	b3831	udp	-8.88	0.069383	184 -- 196	42 -- 54	uridine phosphorylase	_____________183___________197\n_____________\|_____________\|\n5'-AUC...CCGAU___C_________GUAUA...AGA-3'\n______________UCA_AGAGGAGUU\n______________\|\|\|_\|\|\|\|\|\|:\|\|\n______________AGU_UCUCCUUAA\n3'-UUU...CGGGC___U_________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________55____________41\n	190 -- 196	42 -- 48	-14.4874 kcal/mol	4.66075 kcal/mol	0.945538 kcal/mol	183 197@LB@ \| \|@LB@5'-AUC...CCGAU C GUAUA...AGA-3'@LB@ UCA AGAGGAGUU@LB@ \|\|\| \|\|\|\|\|\|:\|\|@LB@ AGU UCUCCUUAA@LB@3'-UUU...CGGGC U AGUAA...ACA-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -14.4874 kcal/mol@LB@Unfolding Energy - mRNA 4.66075 kcal/mol@LB@Unfolding Energy - sRNA 0.945538 kcal/mol@LB@@LB@Position - mRNA 184 -- 196@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 42 -- 48@LB@
56	0.01199	0.6177	b0836	bssR	-10.68	0.029916	18 -- 32	42 -- 55	repressor of biofilm formation by indole transport regulation	_____________17______________33\n_____________\|_______________\|\n5'-AUU...GAAAG_______C_______CUACA...ACA-3'\n______________GUCAGGG_AGGGAUU\n______________\|\|\|\|::\|_\|\|\|:\|\|\|\n______________CAGUUUC_UCCUUAA\n3'-UUU...CCGGG_______________AGUAA...ACA-5'\n_____________\|_______________\|\n_____________56______________41\n	26 -- 32	42 -- 48	-16.3055 kcal/mol	4.68166 kcal/mol	0.947316 kcal/mol	17 33@LB@ \| \|@LB@5'-AUU...GAAAG C CUACA...ACA-3'@LB@ GUCAGGG AGGGAUU@LB@ \|\|\|\|::\| \|\|\|:\|\|\|@LB@ CAGUUUC UCCUUAA@LB@3'-UUU...CCGGG AGUAA...ACA-5'@LB@ \| \|@LB@ 56 41@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -16.3055 kcal/mol@LB@Unfolding Energy - mRNA 4.68166 kcal/mol@LB@Unfolding Energy - sRNA 0.947316 kcal/mol@LB@@LB@Position - mRNA 18 -- 32@LB@Position - sRNA 42 -- 55@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 42 -- 48@LB@
75	0.01577	0.6177	b1345	intR	-9.71	0.047033	139 -- 151	42 -- 53	Rac prophage; integrase	_____________138___________152\n_____________\|_____________\|\n5'-UAA...GACAG____C________AUCUG...GGG-3'\n______________CAAA_GAGGGAUU\n______________\|\|\|\|_\|\|\|\|:\|\|\|\n______________GUUU_CUCCUUAA\n3'-UUU...GGGCA_____________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________54____________41\n	145 -- 151	42 -- 48	-12.4741 kcal/mol	1.8255 kcal/mol	0.933904 kcal/mol	138 152@LB@ \| \|@LB@5'-UAA...GACAG C AUCUG...GGG-3'@LB@ CAAA GAGGGAUU@LB@ \|\|\|\| \|\|\|\|:\|\|\|@LB@ GUUU CUCCUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -12.4741 kcal/mol@LB@Unfolding Energy - mRNA 1.8255 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 139 -- 151@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 42 -- 48@LB@
82	0.01753	0.6177	b2204	napH	-9.88	0.043521	152 -- 162	42 -- 52	ferredoxin-type protein	_____________151_________163\n_____________\|___________\|\n5'-CAC...UGGCG___________AGGUC...UCU-3'\n______________AAAGGGGAGUU\n______________\|\|\|\|:\|\|\|:\|\|\n______________UUUCUCCUUAA\n3'-UUU...GGCAG___________AGUAA...ACA-5'\n_____________\|___________\|\n_____________53__________41\n	156 -- 162	42 -- 48	-12.4472 kcal/mol	1.70007 kcal/mol	0.866923 kcal/mol	151 163@LB@ \| \|@LB@5'-CAC...UGGCG AGGUC...UCU-3'@LB@ AAAGGGGAGUU@LB@ \|\|\|\|:\|\|\|:\|\|@LB@ UUUCUCCUUAA@LB@3'-UUU...GGCAG AGUAA...ACA-5'@LB@ \| \|@LB@ 53 41@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -12.4472 kcal/mol@LB@Unfolding Energy - mRNA 1.70007 kcal/mol@LB@Unfolding Energy - sRNA 0.866923 kcal/mol@LB@@LB@Position - mRNA 152 -- 162@LB@Position - sRNA 42 -- 52@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 42 -- 48@LB@
126	0.02445	0.6177	b4364	yjjP	-5.95	0.256190	188 -- 200	42 -- 53	DUF1212 family inner membrane protein	_____________187___________201\n_____________\|_____________\|\n5'-UCA...UAUGA_______C_____AUGCA...UUU-3'\n______________CAAAGGG_GAGUU\n______________\|\|\|\|\|:\|_\|\|:\|\|\n______________GUUUCUC_CUUAA\n3'-UUU...GGGCA_____________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________54____________41\n	188 -- 194	47 -- 53	-11.6429 kcal/mol	4.76073 kcal/mol	0.933904 kcal/mol	187 201@LB@ \| \|@LB@5'-UCA...UAUGA C AUGCA...UUU-3'@LB@ CAAAGGG GAGUU@LB@ \|\|\|\|\|:\| \|\|:\|\|@LB@ GUUUCUC CUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -5.95 kcal/mol@LB@Hybridization Energy -11.6429 kcal/mol@LB@Unfolding Energy - mRNA 4.76073 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 188 -- 200@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
187	0.03882	0.6177	b0403	malZ	-7.79	0.114240	189 -- 197	42 -- 50	maltodextrin glucosidase	_____________188_______198\n_____________\|_________\|\n5'-UUU...AUCAC_________AUGAU...AGC-3'\n______________AGGGGAAUU\n______________\|\|:\|\|\|\|\|\|\n______________UCUCCUUAA\n3'-UUU...CAGUU_________AGUAA...ACA-5'\n_____________\|_________\|\n_____________51________41\n	191 -- 197	42 -- 48	-10.7884 kcal/mol	2.13721 kcal/mol	0.856185 kcal/mol	188 198@LB@ \| \|@LB@5'-UUU...AUCAC AUGAU...AGC-3'@LB@ AGGGGAAUU@LB@ \|\|:\|\|\|\|\|\|@LB@ UCUCCUUAA@LB@3'-UUU...CAGUU AGUAA...ACA-5'@LB@ \| \|@LB@ 51 41@LB@@LB@@LB@Energy -7.79 kcal/mol@LB@Hybridization Energy -10.7884 kcal/mol@LB@Unfolding Energy - mRNA 2.13721 kcal/mol@LB@Unfolding Energy - sRNA 0.856185 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 42 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 42 -- 48@LB@
19	0.003501	0.593	b2019	hisG	-12.73	0.011332	183 -- 194	43 -- 54	ATP phosphoribosyltransferase	_____________182__________195\n_____________\|____________\|\n5'-UUU...CAGGU____________AACAA...AUC-3'\n______________UUAAAGAGGAAU\n______________\|:\|\|\|\|\|\|\|\|\|\|\n______________AGUUUCUCCUUA\n3'-UUU...CGGGC____________AAGUA...ACA-5'\n_____________\|____________\|\n_____________55___________42\n	188 -- 194	43 -- 49	-14.9017 kcal/mol	1.23041 kcal/mol	0.944705 kcal/mol	182 195@LB@ \| \|@LB@5'-UUU...CAGGU AACAA...AUC-3'@LB@ UUAAAGAGGAAU@LB@ \|:\|\|\|\|\|\|\|\|\|\|@LB@ AGUUUCUCCUUA@LB@3'-UUU...CGGGC AAGUA...ACA-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -12.73 kcal/mol@LB@Hybridization Energy -14.9017 kcal/mol@LB@Unfolding Energy - mRNA 1.23041 kcal/mol@LB@Unfolding Energy - sRNA 0.944705 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@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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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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