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	Additional homologs
197	0.01153	0.1967	b0610	rnk	-10.49	0.135367	130 -- 162	7 -- 39	regulator of nucleoside diphosphate kinase		_____________129__________________________________163\n_____________\|____________________________________\|\n5'-UCU...CGCCG___________G__G_____CUUU____________AUCUG...CGU-3'\n______________CCUG__ACGGU_AG_GUUUU____UGGG_UAUGUUU\n______________\|\|\|\|__\|\|:\|:_\|\|_:\|\|\|\|____\|\|\|\|_\|\|\|\|\|\|\|\n______________GGAC__UGUCG_UC_UAAAA____ACCC_AUACAAA\n3'-UUU...ACCAA____CA_____A__G_____U_______A_______AAGUCG-5'\n_____________\|____________________________________\|\n_____________40___________________________________6\n	156 -- 162	7 -- 13	-25.6411 kcal/mol	10.5512 kcal/mol	4.60345 kcal/mol	129 163@LB@ \| \|@LB@5'-UCU...CGCCG G G CUUU AUCUG...CGU-3'@LB@ CCUG ACGGU AG GUUUU UGGG UAUGUUU@LB@ \|\|\|\| \|\|:\|: \|\| :\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ GGAC UGUCG UC UAAAA ACCC AUACAAA@LB@3'-UUU...ACCAA CA A G U A AAGUCG-5'@LB@ \| \|@LB@ 40 6@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -25.6411 kcal/mol@LB@Unfolding Energy - mRNA 10.5512 kcal/mol@LB@Unfolding Energy - sRNA 4.60345 kcal/mol@LB@@LB@Position - mRNA 130 -- 162@LB@Position - sRNA 7 -- 39@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 7 -- 13@LB@
11	3.883e-05	0.01168	b4074	nrfE	-17.71	0.001322	131 -- 144	35 -- 48	heme lyase (NrfEFG) for insertion of heme into c552 subunit NrfE		_____________130____________145\n_____________\|______________\|\n5'-ACC...GAAAA______________ACGUA...UGC-3'\n______________GAGGUGGUUUCUGG\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\|\n______________CUCCACCAAGGACC\n3'-UUU...GAUUC______________AUGUC...UCG-5'\n_____________\|______________\|\n_____________49_____________34\n	138 -- 144	35 -- 41	-26.5218 kcal/mol	5.67902 kcal/mol	3.13693 kcal/mol	130 145@LB@ \| \|@LB@5'-ACC...GAAAA ACGUA...UGC-3'@LB@ GAGGUGGUUUCUGG@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|\|@LB@ CUCCACCAAGGACC@LB@3'-UUU...GAUUC AUGUC...UCG-5'@LB@ \| \|@LB@ 49 34@LB@@LB@@LB@Energy -17.71 kcal/mol@LB@Hybridization Energy -26.5218 kcal/mol@LB@Unfolding Energy - mRNA 5.67902 kcal/mol@LB@Unfolding Energy - sRNA 3.13693 kcal/mol@LB@@LB@Position - mRNA 131 -- 144@LB@Position - sRNA 35 -- 48@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 35 -- 41@LB@
112	0.004445	0.1334	b0132	yadD	-7.85	0.370183	131 -- 161	16 -- 48	transposase_31 family protein	b3411 b2244 b2305	_____________130________________________________162\n_____________\|__________________________________\|\n5'-CCC...AUAAA_____________ACG_____GC__C__GAC___AUACU...UGG-3'\n______________GAGGUGG___CUG___AUAGC__GC_UU___UGG\n______________\|\|\|\|\|\|\|___\|\|\|___\|:\|\|\|__\|\|_\|\|___\|\|\|\n______________CUCCACC___GAC___UGUCG__CG_AA___ACC\n3'-UUU...GAUUC_______AAG___CA______AU__U__AAU___CAAUA...UCG-5'\n_____________\|__________________________________\|\n_____________49_________________________________15\n	131 -- 137	42 -- 48	-24.9925 kcal/mol	12.5665 kcal/mol	4.57255 kcal/mol	130 162@LB@ \| \|@LB@5'-CCC...AUAAA ACG GC C GAC AUACU...UGG-3'@LB@ GAGGUGG CUG AUAGC GC UU UGG@LB@ \|\|\|\|\|\|\| \|\|\| \|:\|\|\| \|\| \|\| \|\|\|@LB@ CUCCACC GAC UGUCG CG AA ACC@LB@3'-UUU...GAUUC AAG CA AU U AAU CAAUA...UCG-5'@LB@ \| \|@LB@ 49 15@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -24.9925 kcal/mol@LB@Unfolding Energy - mRNA 12.5665 kcal/mol@LB@Unfolding Energy - sRNA 4.57255 kcal/mol@LB@@LB@Position - mRNA 131 -- 161@LB@Position - sRNA 16 -- 48@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 42 -- 48@LB@
181	0.0104	0.1919	b2106	rcnA	-12.10	0.062308	133 -- 155	15 -- 50	membrane protein conferring nickel and cobalt resistance		_____________132__________________________________156\n_____________\|____________________________________\|\n5'-UUC...CUACU_______A__A__A______________________GGGGA...ACU-3'\n______________GGGGGGU_GU_UC_GGUAC_____________UGGG\n______________:\|\|:\|\|\|_\|\|_:\|_\|\|\|\|\|_____________\|\|\|\|\n______________UCCUCCA_CA_GG_CCAUG_____________ACCC\n3'-UUU...CCGAU_______C__A__A_____UCGAUCGUAAAAU____AAUAC...UCG-5'\n_____________\|____________________________________\|\n_____________51___________________________________14\n	133 -- 139	44 -- 50	-22.0891 kcal/mol	5.35824 kcal/mol	4.62773 kcal/mol	132 156@LB@ \| \|@LB@5'-UUC...CUACU A A A GGGGA...ACU-3'@LB@ GGGGGGU GU UC GGUAC UGGG@LB@ :\|\|:\|\|\| \|\| :\| \|\|\|\|\| \|\|\|\|@LB@ UCCUCCA CA GG CCAUG ACCC@LB@3'-UUU...CCGAU C A A UCGAUCGUAAAAU AAUAC...UCG-5'@LB@ \| \|@LB@ 51 14@LB@@LB@@LB@Energy -12.10 kcal/mol@LB@Hybridization Energy -22.0891 kcal/mol@LB@Unfolding Energy - mRNA 5.35824 kcal/mol@LB@Unfolding Energy - sRNA 4.62773 kcal/mol@LB@@LB@Position - mRNA 133 -- 155@LB@Position - sRNA 15 -- 50@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 44 -- 50@LB@
58	0.001429	0.08147	b0698	kdpA	-14.04	0.020858	136 -- 172	7 -- 35	potassium translocating ATPase subunit A		_____________135___________________________________173\n_____________\|_____________________________________\|\n5'-GCU...CCGGC____U___________UAUUAC________CUG____AUGCC...ACA-3'\n______________GUAU_GCUGGUGUUUU______UGGGUUAU___GUUU\n______________\|\|\|:_\|\|\|:\|::\|\|\|\|______\|\|\|\|\|\|\|\|___\|\|\|\|\n______________CAUG_CGAUCGUAAAA______ACCCAAUA___CAAA\n3'-UUU...AGGAC____U___________U____________________AAGUCG-5'\n_____________\|_____________________________________\|\n_____________36____________________________________6\n	159 -- 165	11 -- 17	-23.8836 kcal/mol	8.35779 kcal/mol	1.49058 kcal/mol	135 173@LB@ \| \|@LB@5'-GCU...CCGGC U UAUUAC CUG AUGCC...ACA-3'@LB@ GUAU GCUGGUGUUUU UGGGUUAU GUUU@LB@ \|\|\|: \|\|\|:\|::\|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|@LB@ CAUG CGAUCGUAAAA ACCCAAUA CAAA@LB@3'-UUU...AGGAC U U AAGUCG-5'@LB@ \| \|@LB@ 36 6@LB@@LB@@LB@Energy -14.04 kcal/mol@LB@Hybridization Energy -23.8836 kcal/mol@LB@Unfolding Energy - mRNA 8.35779 kcal/mol@LB@Unfolding Energy - sRNA 1.49058 kcal/mol@LB@@LB@Position - mRNA 136 -- 172@LB@Position - sRNA 7 -- 35@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 11 -- 17@LB@
127	0.005388	0.142	b2721	hycE	-10.66	0.125013	137 -- 158	1 -- 36	hydrogenase 3 large subunit		_____________136___________________________________159\n_____________\|_____________________________________\|\n5'-UUC...GGCUG___UU____UU__________________________GUUCG...UGA-3'\n______________GGU__GGCU__GCAU_______________UUUUAGC\n______________\|\|\|__:\|\|\|__\|\|\|\|_______________\|\|\|:\|\|\|\n______________CCA__UCGA__CGUA_______________AAAGUCG\n3'-UUU...AAGGA___UG____U_____AAAUACCCAAUACAA_______-5'\n_____________\|____________________________________\|\n_____________37___________________________________1\n	152 -- 158	1 -- 7	-16.3373 kcal/mol	4.17778 kcal/mol	1.49509 kcal/mol	136 159@LB@ \| \|@LB@5'-UUC...GGCUG UU UU GUUCG...UGA-3'@LB@ GGU GGCU GCAU UUUUAGC@LB@ \|\|\| :\|\|\| \|\|\|\| \|\|\|:\|\|\|@LB@ CCA UCGA CGUA AAAGUCG@LB@3'-UUU...AAGGA UG U AAAUACCCAAUACAA -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -16.3373 kcal/mol@LB@Unfolding Energy - mRNA 4.17778 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 137 -- 158@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 1 -- 7@LB@
9	2.519e-05	0.009407	b0435	bolA	-15.32	0.008970	138 -- 163	15 -- 36	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC		_____________137________________________164\n_____________\|__________________________\|\n5'-UGA...GAAAC___AAAA_____________AAA___AUGGA...CCG-3'\n______________GGU____GCGGCUAGUAUUU___GGG\n______________\|\|\|____:\|:\|\|\|\|\|:\|\|\|\|___\|\|\|\n______________CCA____UGUCGAUCGUAAA___CCC\n3'-UUU...AAGGA____________________AUA___AAUAC...UCG-5'\n_____________\|__________________________\|\n_____________37_________________________14\n	151 -- 157	21 -- 27	-22.9811 kcal/mol	6.21269 kcal/mol	1.45166 kcal/mol	137 164@LB@ \| \|@LB@5'-UGA...GAAAC AAAA AAA AUGGA...CCG-3'@LB@ GGU GCGGCUAGUAUUU GGG@LB@ \|\|\| :\|:\|\|\|\|\|:\|\|\|\| \|\|\|@LB@ CCA UGUCGAUCGUAAA CCC@LB@3'-UUU...AAGGA AUA AAUAC...UCG-5'@LB@ \| \|@LB@ 37 14@LB@@LB@@LB@Energy -15.32 kcal/mol@LB@Hybridization Energy -22.9811 kcal/mol@LB@Unfolding Energy - mRNA 6.21269 kcal/mol@LB@Unfolding Energy - sRNA 1.45166 kcal/mol@LB@@LB@Position - mRNA 138 -- 163@LB@Position - sRNA 15 -- 36@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 21 -- 27@LB@
64	0.001739	0.09016	b4463	ygcU	-11.99	0.066010	140 -- 150	36 -- 46	putative FAD-linked oxidoreductase		_____________139_________151\n_____________\|___________\|\n5'-AUC...AUAAC___________UUUUC...UUG-3'\n______________GGUGGUUUCUG\n______________\|\|\|\|\|\|\|:\|\|\|\n______________CCACCAAGGAC\n3'-UUU...UUCCU___________CAUGU...UCG-5'\n_____________\|___________\|\n_____________47__________35\n	144 -- 150	36 -- 42	-19.2157 kcal/mol	4.08908 kcal/mol	3.13564 kcal/mol	139 151@LB@ \| \|@LB@5'-AUC...AUAAC UUUUC...UUG-3'@LB@ GGUGGUUUCUG@LB@ \|\|\|\|\|\|\|:\|\|\|@LB@ CCACCAAGGAC@LB@3'-UUU...UUCCU CAUGU...UCG-5'@LB@ \| \|@LB@ 47 35@LB@@LB@@LB@Energy -11.99 kcal/mol@LB@Hybridization Energy -19.2157 kcal/mol@LB@Unfolding Energy - mRNA 4.08908 kcal/mol@LB@Unfolding Energy - sRNA 3.13564 kcal/mol@LB@@LB@Position - mRNA 140 -- 150@LB@Position - sRNA 36 -- 46@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 36 -- 42@LB@
63	0.00172	0.09016	b1209	lolB	-15.80	0.006355	144 -- 167	11 -- 36	lipoprotein localization factor		_____________143________________________168\n_____________\|__________________________\|\n5'-AAU...CGGAC____AC_________AA_________AACUG...GCC-3'\n______________GGUA__GCUAGCAUU____GGGUUAU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\|____\|\|\|\|\|\|\|\n______________CCAU__CGAUCGUAA____CCCAAUA\n3'-UUU...AAGGA____GU_________AAUA_______CAAAA...UCG-5'\n_____________\|__________________________\|\n_____________37_________________________10\n	161 -- 167	11 -- 17	-25.6291 kcal/mol	8.35909 kcal/mol	1.47376 kcal/mol	143 168@LB@ \| \|@LB@5'-AAU...CGGAC AC AA AACUG...GCC-3'@LB@ GGUA GCUAGCAUU GGGUUAU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CCAU CGAUCGUAA CCCAAUA@LB@3'-UUU...AAGGA GU AAUA CAAAA...UCG-5'@LB@ \| \|@LB@ 37 10@LB@@LB@@LB@Energy -15.80 kcal/mol@LB@Hybridization Energy -25.6291 kcal/mol@LB@Unfolding Energy - mRNA 8.35909 kcal/mol@LB@Unfolding Energy - sRNA 1.47376 kcal/mol@LB@@LB@Position - mRNA 144 -- 167@LB@Position - sRNA 11 -- 36@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 11 -- 17@LB@
178	0.009929	0.1875	b1278	pgpB	-11.49	0.084643	145 -- 171	10 -- 41	phosphatidylglycerophosphatase B		_____________144______________________________172\n_____________\|________________________________\|\n5'-GUU...AAUUU_______AA_____________CA________AUUGU...AAC-3'\n______________UUCCUGG_____CUGGCGUUUU____GUUAUG\n______________\|\|\|\|\|\|\|_____\|\|:\|\|:\|\|\|\|____\|\|\|\|\|\|\n______________AAGGACC_____GAUCGUAAAA____CAAUAC\n3'-UUU...CCACC_______AUGUC__________UACC______AAAAA...UCG-5'\n_____________\|________________________________\|\n_____________42_______________________________9\n	157 -- 163	20 -- 26	-25.137 kcal/mol	9.03979 kcal/mol	4.60294 kcal/mol	144 172@LB@ \| \|@LB@5'-GUU...AAUUU AA CA AUUGU...AAC-3'@LB@ UUCCUGG CUGGCGUUUU GUUAUG@LB@ \|\|\|\|\|\|\| \|\|:\|\|:\|\|\|\| \|\|\|\|\|\|@LB@ AAGGACC GAUCGUAAAA CAAUAC@LB@3'-UUU...CCACC AUGUC UACC AAAAA...UCG-5'@LB@ \| \|@LB@ 42 9@LB@@LB@@LB@Energy -11.49 kcal/mol@LB@Hybridization Energy -25.137 kcal/mol@LB@Unfolding Energy - mRNA 9.03979 kcal/mol@LB@Unfolding Energy - sRNA 4.60294 kcal/mol@LB@@LB@Position - mRNA 145 -- 171@LB@Position - sRNA 10 -- 41@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 20 -- 26@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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