Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
22	0.001016	0.1516	b0734	cydB	-13.57	0.015928	285 -- 300	49 -- 64	cytochrome d terminal oxidase subunit II		_____________284_____________300\n_____________\|_______________\|\n5'-CGA...GUUUC__C_____________-3'\n______________GA_AUGGGGGUGGGCA\n______________\|\|_\|\|:\|\|\|\|\|:::\|\|\n______________CU_UAUCCCCAUUUGU\n3'-UUU...GCCAA__U_____________CUGUA...UCG-5'\n_____________\|________________\|\n_____________65_______________48\n	294 -- 300	49 -- 55	-19.142 kcal/mol	4.83222 kcal/mol	0.738518 kcal/mol	284 300@LB@ \| \|@LB@5'-CGA...GUUUC C -3'@LB@ GA AUGGGGGUGGGCA@LB@ \|\| \|\|:\|\|\|\|\|:::\|\|@LB@ CU UAUCCCCAUUUGU@LB@3'-UUU...GCCAA U CUGUA...UCG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -19.142 kcal/mol@LB@Unfolding Energy - mRNA 4.83222 kcal/mol@LB@Unfolding Energy - sRNA 0.738518 kcal/mol@LB@@LB@Position - mRNA 285 -- 300@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 49 -- 55@LB@
43	0.004693	0.3568	b1395	paaH	-8.91	0.157263	246 -- 258	49 -- 61	3-hydroxyadipyl-CoA dehydrogenase NAD+-dependent		_____________245___________259\n_____________\|_____________\|\n5'-GGC...GCACC_______C_____UUGCU...UGU-3'\n______________AUGGGGG_AGGCA\n______________\|\|:\|\|\|\|_\|::\|\|\n______________UAUCCCC_UUUGU\n3'-UUU...AACUU_______A_____CUGUA...UCG-5'\n_____________\|_____________\|\n_____________62____________48\n	246 -- 252	55 -- 61	-14.1165 kcal/mol	4.46726 kcal/mol	0.738192 kcal/mol	245 259@LB@ \| \|@LB@5'-GGC...GCACC C UUGCU...UGU-3'@LB@ AUGGGGG AGGCA@LB@ \|\|:\|\|\|\| \|::\|\|@LB@ UAUCCCC UUUGU@LB@3'-UUU...AACUU A CUGUA...UCG-5'@LB@ \| \|@LB@ 62 48@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -14.1165 kcal/mol@LB@Unfolding Energy - mRNA 4.46726 kcal/mol@LB@Unfolding Energy - sRNA 0.738192 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 49 -- 61@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 55 -- 61@LB@
78	0.01113	0.4523	b2678	proW	-13.08	0.020853	190 -- 200	49 -- 59	glycine betaine/proline ABC transporter permease		_____________189_________201\n_____________\|___________\|\n5'-GUU...CGUGA___________AUGGC...ACG-3'\n______________GGGGGUAAAUA\n______________:\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUGU\n3'-UUU...CUUUA___________CUGUA...UCG-5'\n_____________\|___________\|\n_____________60__________48\n	194 -- 200	49 -- 55	-15.0309 kcal/mol	1.22377 kcal/mol	0.730523 kcal/mol	189 201@LB@ \| \|@LB@5'-GUU...CGUGA AUGGC...ACG-3'@LB@ GGGGGUAAAUA@LB@ :\|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUGU@LB@3'-UUU...CUUUA CUGUA...UCG-5'@LB@ \| \|@LB@ 60 48@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -15.0309 kcal/mol@LB@Unfolding Energy - mRNA 1.22377 kcal/mol@LB@Unfolding Energy - sRNA 0.730523 kcal/mol@LB@@LB@Position - mRNA 190 -- 200@LB@Position - sRNA 49 -- 59@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 49 -- 55@LB@
124	0.01977	0.5155	b1920	fliY	-11.21	0.054671	192 -- 201	49 -- 58	cystine transporter subunit		_____________191________202\n_____________\|__________\|\n5'-CCA...CAUUC__________UGAAA...UGC-3'\n______________GGGGUGAAUA\n______________\|\|\|\|\|:\|\|:\|\n______________CCCCAUUUGU\n3'-UUU...UUUAU__________CUGUA...UCG-5'\n_____________\|__________\|\n_____________59_________48\n	195 -- 201	49 -- 55	-14.4557 kcal/mol	2.52037 kcal/mol	0.729386 kcal/mol	191 202@LB@ \| \|@LB@5'-CCA...CAUUC UGAAA...UGC-3'@LB@ GGGGUGAAUA@LB@ \|\|\|\|\|:\|\|:\|@LB@ CCCCAUUUGU@LB@3'-UUU...UUUAU CUGUA...UCG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -14.4557 kcal/mol@LB@Unfolding Energy - mRNA 2.52037 kcal/mol@LB@Unfolding Energy - sRNA 0.729386 kcal/mol@LB@@LB@Position - mRNA 192 -- 201@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 49 -- 55@LB@
161	0.02632	0.526	b3670	ilvN	-9.27	0.134814	179 -- 196	49 -- 65	acetolactate synthase 1 small subunit		_____________178________________197\n_____________\|__________________\|\n5'-UCA...AAUAC________U___GG____AGCCA...CUU-3'\n______________UGAAAUGG_GGG__AAUA\n______________\|\|\|\|\|\|:\|_\|\|\|__\|\|:\|\n______________ACUUUAUC_CCC__UUGU\n3'-UUU...GGCCA____________AU____CUGUA...UCG-5'\n_____________\|__________________\|\n_____________66_________________48\n	180 -- 186	58 -- 64	-15.3061 kcal/mol	4.40463 kcal/mol	1.63404 kcal/mol	178 197@LB@ \| \|@LB@5'-UCA...AAUAC U GG AGCCA...CUU-3'@LB@ UGAAAUGG GGG AAUA@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|:\|@LB@ ACUUUAUC CCC UUGU@LB@3'-UUU...GGCCA AU CUGUA...UCG-5'@LB@ \| \|@LB@ 66 48@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.3061 kcal/mol@LB@Unfolding Energy - mRNA 4.40463 kcal/mol@LB@Unfolding Energy - sRNA 1.63404 kcal/mol@LB@@LB@Position - mRNA 179 -- 196@LB@Position - sRNA 49 -- 65@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 58 -- 64@LB@
51	0.006039	0.3887	b3822	recQ	-9.34	0.130811	192 -- 200	50 -- 58	ATP-dependent DNA helicase		_____________191_______201\n_____________\|_________\|\n5'-CGC...CAAUC_________GUGGC...UUA-3'\n______________GGGGUGAAU\n______________\|\|\|\|\|:\|\|:\n______________CCCCAUUUG\n3'-UUU...UUUAU_________UCUGU...UCG-5'\n_____________\|_________\|\n_____________59________49\n	194 -- 200	50 -- 56	-13.8974 kcal/mol	3.8337 kcal/mol	0.72763 kcal/mol	191 201@LB@ \| \|@LB@5'-CGC...CAAUC GUGGC...UUA-3'@LB@ GGGGUGAAU@LB@ \|\|\|\|\|:\|\|:@LB@ CCCCAUUUG@LB@3'-UUU...UUUAU UCUGU...UCG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -13.8974 kcal/mol@LB@Unfolding Energy - mRNA 3.8337 kcal/mol@LB@Unfolding Energy - sRNA 0.72763 kcal/mol@LB@@LB@Position - mRNA 192 -- 200@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 50 -- 56@LB@
59	0.008416	0.4523	b0566	envY	-9.46	0.123665	249 -- 263	50 -- 64	porin thermoregulatory transcriptional activator	b1499 b0564 b3515 b4116 b3516	_____________248_____________264\n_____________\|_______________\|\n5'-GGC...AAAAA_______A_______GUCAA...ACU-3'\n______________GAGGUAG_GGUAAGC\n______________\|\|::\|\|\|_\|\|\|\|\|:\|\n______________CUUUAUC_CCAUUUG\n3'-UUU...GCCAA_______C_______UCUGU...UCG-5'\n_____________\|_______________\|\n_____________65______________49\n	257 -- 263	50 -- 56	-15.2892 kcal/mol	5.08919 kcal/mol	0.736811 kcal/mol	248 264@LB@ \| \|@LB@5'-GGC...AAAAA A GUCAA...ACU-3'@LB@ GAGGUAG GGUAAGC@LB@ \|\|::\|\|\| \|\|\|\|\|:\|@LB@ CUUUAUC CCAUUUG@LB@3'-UUU...GCCAA C UCUGU...UCG-5'@LB@ \| \|@LB@ 65 49@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -15.2892 kcal/mol@LB@Unfolding Energy - mRNA 5.08919 kcal/mol@LB@Unfolding Energy - sRNA 0.736811 kcal/mol@LB@@LB@Position - mRNA 249 -- 263@LB@Position - sRNA 50 -- 64@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 50 -- 56@LB@
118	0.01863	0.5155	b0738	tolR	-11.80	0.040697	190 -- 199	50 -- 59	membrane spanning protein in TolA-TolQ-TolR complex		_____________189________200\n_____________\|__________\|\n5'-UGG...CAACA__________CAUGG...UGG-3'\n______________AGGGGUAAGC\n______________\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	193 -- 199	50 -- 56	-16.6396 kcal/mol	4.1136 kcal/mol	0.728772 kcal/mol	189 200@LB@ \| \|@LB@5'-UGG...CAACA CAUGG...UGG-3'@LB@ AGGGGUAAGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -16.6396 kcal/mol@LB@Unfolding Energy - mRNA 4.1136 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 190 -- 199@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 50 -- 56@LB@
133	0.02154	0.526	b1105	lpoB	-10.17	0.089721	187 -- 196	50 -- 59	OM lipoprotein stimulator of MrcB transpeptidase		_____________186________197\n_____________\|__________\|\n5'-UUA...UUGUA__________CUUGA...AAC-3'\n______________AGGGGUGAAU\n______________\|\|\|\|\|\|:\|\|:\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	190 -- 196	50 -- 56	-15.1396 kcal/mol	4.24097 kcal/mol	0.728772 kcal/mol	186 197@LB@ \| \|@LB@5'-UUA...UUGUA CUUGA...AAC-3'@LB@ AGGGGUGAAU@LB@ \|\|\|\|\|\|:\|\|:@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -15.1396 kcal/mol@LB@Unfolding Energy - mRNA 4.24097 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 187 -- 196@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 50 -- 56@LB@
17	0.000872	0.1482	b3940	metL	-12.03	0.036099	191 -- 199	51 -- 59	Bifunctional aspartokinase/homoserine dehydrogenase 2		_____________190_______200\n_____________\|_________\|\n5'-ACG...AAACA_________AAUGA...GCA-3'\n______________AGGGGUAAA\n______________\|\|\|\|\|\|\|\|\|\n______________UCCCCAUUU\n3'-UUU...CUUUA_________GUCUG...UCG-5'\n_____________\|_________\|\n_____________60________50\n	193 -- 199	51 -- 57	-13.5839 kcal/mol	1.01846 kcal/mol	0.532875 kcal/mol	190 200@LB@ \| \|@LB@5'-ACG...AAACA AAUGA...GCA-3'@LB@ AGGGGUAAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCCCAUUU@LB@3'-UUU...CUUUA GUCUG...UCG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -13.5839 kcal/mol@LB@Unfolding Energy - mRNA 1.01846 kcal/mol@LB@Unfolding Energy - sRNA 0.532875 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 51 -- 57@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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