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
195	0.01134	0.1946	b0633	rlpA	-8.12	0.339483	43 -- 55	25 -- 37	septal ring protein suppressor of prc minor lipoprotein		_____________42____________56\n_____________\|_____________\|\n5'-CGG...AAUAU_________A___GGUAU...CUG-3'\n______________UGGUAUGGU_AGC\n______________\|\|\|\|\|::\|:_\|\|\|\n______________ACCAUGUCG_UCG\n3'-UUU...CAAGG_________A___UAAAA...UCG-5'\n_____________\|_____________\|\n_____________38____________24\n	45 -- 51	29 -- 35	-15.087 kcal/mol	4.33932 kcal/mol	2.62824 kcal/mol	42 56@LB@ \| \|@LB@5'-CGG...AAUAU A GGUAU...CUG-3'@LB@ UGGUAUGGU AGC@LB@ \|\|\|\|\|::\|: \|\|\|@LB@ ACCAUGUCG UCG@LB@3'-UUU...CAAGG A UAAAA...UCG-5'@LB@ \| \|@LB@ 38 24@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -15.087 kcal/mol@LB@Unfolding Energy - mRNA 4.33932 kcal/mol@LB@Unfolding Energy - sRNA 2.62824 kcal/mol@LB@@LB@Position - mRNA 43 -- 55@LB@Position - sRNA 25 -- 37@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 29 -- 35@LB@
22	0.0002072	0.03165	b2341	fadJ	-8.08	0.343546	182 -- 217	1 -- 44	enoyl-CoA hydratase/epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase		_____________181__________________________________________218\n_____________\|____________________________________________\|\n5'-CAU...GGCAA__________A________AAUA______AA____ACA______GUUUA...CGG-3'\n______________UGGUUCU_GG___GGC_GG______AUGG___AUG____UCAGC\n______________\|\|\|\|\|\|:_\|\|___:\|\|_:\|______\|\|\|\|___\|\|\|____\|\|\|\|\|\n______________ACCAAGG_CC___UCG_UC______UACC___UAC____AGUCG\n3'-UUU...CCUCC_______A__AUG___A__GUAAAA____CAA___AAAA_____-5'\n_____________\|___________________________________________\|\n_____________45__________________________________________1\n	182 -- 188	38 -- 44	-22.4043 kcal/mol	9.71146 kcal/mol	4.60934 kcal/mol	181 218@LB@ \| \|@LB@5'-CAU...GGCAA A AAUA AA ACA GUUUA...CGG-3'@LB@ UGGUUCU GG GGC GG AUGG AUG UCAGC@LB@ \|\|\|\|\|\|: \|\| :\|\| :\| \|\|\|\| \|\|\| \|\|\|\|\|@LB@ ACCAAGG CC UCG UC UACC UAC AGUCG@LB@3'-UUU...CCUCC A AUG A GUAAAA CAA AAAA -5'@LB@ \| \|@LB@ 45 1@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -22.4043 kcal/mol@LB@Unfolding Energy - mRNA 9.71146 kcal/mol@LB@Unfolding Energy - sRNA 4.60934 kcal/mol@LB@@LB@Position - mRNA 182 -- 217@LB@Position - sRNA 1 -- 44@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 38 -- 44@LB@
165	0.008583	0.1748	b4075	nrfF	-7.99	0.354712	71 -- 77	63 -- 69	heme lyase (NrfEFG) for insertion of heme into c552 subunit NrfF		_____________70______78\n_____________\|_______\|\n5'-AGC...UCAUG_______AAACU...AAC-3'\n______________GGGGAGA\n______________:\|\|\|\|\|\|\n______________UCCCUCU\n3'-UUU...CACAU_______AAUGU...UCG-5'\n_____________\|_______\|\n_____________70______62\n	71 -- 77	63 -- 69	-11.2965 kcal/mol	2.37125 kcal/mol	0.939295 kcal/mol	70 78@LB@ \| \|@LB@5'-AGC...UCAUG AAACU...AAC-3'@LB@ GGGGAGA@LB@ :\|\|\|\|\|\|@LB@ UCCCUCU@LB@3'-UUU...CACAU AAUGU...UCG-5'@LB@ \| \|@LB@ 70 62@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -11.2965 kcal/mol@LB@Unfolding Energy - mRNA 2.37125 kcal/mol@LB@Unfolding Energy - sRNA 0.939295 kcal/mol@LB@@LB@Position - mRNA 71 -- 77@LB@Position - sRNA 63 -- 69@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 63 -- 69@LB@
99	0.003591	0.1219	b0533	sfmH	-7.90	0.364135	113 -- 140	1 -- 34	FimA homolog function unknown	b3145 b0941	_____________112________________________________141\n_____________\|__________________________________\|\n5'-GAC...AAGCU______A___CGUCACU_________________AGUUU...AUA-3'\n______________UACAGC_AGC_________GUUA____UUUCGGC\n______________\|\|\|\|\|\|_\|\|\|_________\|\|\|\|____\|\|\|\|:\|\|\n______________AUGUCG_UCG_________CAAU____AAAGUCG\n3'-UUU...GGACC______A___UAAAAUACC____ACAA_______-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	134 -- 140	1 -- 7	-18.6412 kcal/mol	9.24123 kcal/mol	1.49507 kcal/mol	112 141@LB@ \| \|@LB@5'-GAC...AAGCU A CGUCACU AGUUU...AUA-3'@LB@ UACAGC AGC GUUA UUUCGGC@LB@ \|\|\|\|\|\| \|\|\| \|\|\|\| \|\|\|\|:\|\|@LB@ AUGUCG UCG CAAU AAAGUCG@LB@3'-UUU...GGACC A UAAAAUACC ACAA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -18.6412 kcal/mol@LB@Unfolding Energy - mRNA 9.24123 kcal/mol@LB@Unfolding Energy - sRNA 1.49507 kcal/mol@LB@@LB@Position - mRNA 113 -- 140@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 1 -- 7@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@
106	0.003955	0.1254	b1767	ansA	-7.74	0.383564	250 -- 272	11 -- 34	cytoplasmic L-asparaginase 1		_____________249______________________273\n_____________\|________________________\|\n5'-UGC...CGGGA______GUUCCGAGCA________AUACC...GCC-3'\n______________UGCAGC___________GGGUUAU\n______________\|:\|\|\|\|___________\|\|\|\|\|\|\|\n______________AUGUCG___________CCCAAUA\n3'-UUU...GGACC______AUCGUAAAAUA_______CAAAA...UCG-5'\n_____________\|________________________\|\n_____________35_______________________10\n	266 -- 272	11 -- 17	-16.5796 kcal/mol	7.36686 kcal/mol	1.47152 kcal/mol	249 273@LB@ \| \|@LB@5'-UGC...CGGGA GUUCCGAGCA AUACC...GCC-3'@LB@ UGCAGC GGGUUAU@LB@ \|:\|\|\|\| \|\|\|\|\|\|\|@LB@ AUGUCG CCCAAUA@LB@3'-UUU...GGACC AUCGUAAAAUA CAAAA...UCG-5'@LB@ \| \|@LB@ 35 10@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -16.5796 kcal/mol@LB@Unfolding Energy - mRNA 7.36686 kcal/mol@LB@Unfolding Energy - sRNA 1.47152 kcal/mol@LB@@LB@Position - mRNA 250 -- 272@LB@Position - sRNA 11 -- 34@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 11 -- 17@LB@
187	0.01074	0.1919	b2536	hcaT	-7.74	0.383266	275 -- 291	25 -- 41	putative 3-phenylpropionic transporter		_____________274_______________292\n_____________\|_________________\|\n5'-UCG...CUACC_______A___U_____UUAAA...GGA-3'\n______________UUUCUGG_GCG_CUGGC\n______________\|\|:\|\|\|\|_:\|:_\|\|:\|\|\n______________AAGGACC_UGU_GAUCG\n3'-UUU...CCACC_______A___C_____UAAAA...UCG-5'\n_____________\|_________________\|\n_____________42________________24\n	275 -- 281	35 -- 41	-17.8602 kcal/mol	5.56231 kcal/mol	4.55428 kcal/mol	274 292@LB@ \| \|@LB@5'-UCG...CUACC A U UUAAA...GGA-3'@LB@ UUUCUGG GCG CUGGC@LB@ \|\|:\|\|\|\| :\|: \|\|:\|\|@LB@ AAGGACC UGU GAUCG@LB@3'-UUU...CCACC A C UAAAA...UCG-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -17.8602 kcal/mol@LB@Unfolding Energy - mRNA 5.56231 kcal/mol@LB@Unfolding Energy - sRNA 4.55428 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 35 -- 41@LB@
30	0.0004774	0.05348	b2148	mglC	-7.69	0.389595	275 -- 281	24 -- 30	methyl-galactoside transporter subunit		_____________274_____282\n_____________\|_______\|\n5'-AUC...GUUUU_______AUUAU...ACC-3'\n______________GCUGGCG\n______________\|\|\|:\|\|:\n______________CGAUCGU\n3'-UUU...CAUGU_______AAAAU...UCG-5'\n_____________\|_______\|\n_____________31______23\n	275 -- 281	24 -- 30	-10.2126 kcal/mol	1.14582 kcal/mol	1.37559 kcal/mol	274 282@LB@ \| \|@LB@5'-AUC...GUUUU AUUAU...ACC-3'@LB@ GCUGGCG@LB@ \|\|\|:\|\|:@LB@ CGAUCGU@LB@3'-UUU...CAUGU AAAAU...UCG-5'@LB@ \| \|@LB@ 31 23@LB@@LB@@LB@Energy -7.69 kcal/mol@LB@Hybridization Energy -10.2126 kcal/mol@LB@Unfolding Energy - mRNA 1.14582 kcal/mol@LB@Unfolding Energy - sRNA 1.37559 kcal/mol@LB@@LB@Position - mRNA 275 -- 281@LB@Position - sRNA 24 -- 30@LB@Position Seed - mRNA 275 -- 281@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@
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@

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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