Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
30	0.0002612	0.03063	b3789	rffH	-9.15	0.078548	244 -- 254	48 -- 58	glucose-1-phosphate thymidylyltransferase		_____________243_________255\n_____________\|___________\|\n5'-GGC...AUUGC___________CGCGG...UGA-3'\n______________AUCCGAUUACG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UAGGCUAAUGC\n3'-AUU...CGGUU___________ACUUC...AUG-5'\n_____________\|___________\|\n_____________59__________47\n	248 -- 254	48 -- 54	-15.7126 kcal/mol	4.98099 kcal/mol	1.55987 kcal/mol	243 255@LB@ \| \|@LB@5'-GGC...AUUGC CGCGG...UGA-3'@LB@ AUCCGAUUACG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UAGGCUAAUGC@LB@3'-AUU...CGGUU ACUUC...AUG-5'@LB@ \| \|@LB@ 59 47@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -15.7126 kcal/mol@LB@Unfolding Energy - mRNA 4.98099 kcal/mol@LB@Unfolding Energy - sRNA 1.55987 kcal/mol@LB@@LB@Position - mRNA 244 -- 254@LB@Position - sRNA 48 -- 58@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 48 -- 54@LB@
159	0.006413	0.1413	b4242	mgtA	-7.15	0.243258	247 -- 262	45 -- 58	magnesium transporter		_____________246______________263\n_____________\|________________\|\n5'-GGU...UUCCC________CAU_____UCCAU...UGG-3'\n______________GUCUGGUU___CGUGA\n______________:\|\|:\|:\|\|___\|\|\|\|\|\n______________UAGGCUAA___GCACU\n3'-AUU...CGGUU________U_______UCAUU...AUG-5'\n_____________\|________________\|\n_____________59_______________44\n	248 -- 254	51 -- 57	-12.639 kcal/mol	3.2244 kcal/mol	2.28003 kcal/mol	246 263@LB@ \| \|@LB@5'-GGU...UUCCC CAU UCCAU...UGG-3'@LB@ GUCUGGUU CGUGA@LB@ :\|\|:\|:\|\| \|\|\|\|\|@LB@ UAGGCUAA GCACU@LB@3'-AUU...CGGUU U UCAUU...AUG-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -12.639 kcal/mol@LB@Unfolding Energy - mRNA 3.2244 kcal/mol@LB@Unfolding Energy - sRNA 2.28003 kcal/mol@LB@@LB@Position - mRNA 247 -- 262@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 51 -- 57@LB@
196	0.008709	0.1558	b2498	upp	-7.14	0.244299	249 -- 259	45 -- 56	uracil phosphoribosyltransferase		_____________248__________260\n_____________\|____________\|\n5'-GGC...UGGGA____________GCAAG...CCG-3'\n______________CUGA_UGCGUGA\n______________\|:\|\|_\|:\|\|\|\|\|\n______________GGCU_AUGCACU\n3'-AUU...GUUUA____A_______UCAUU...AUG-5'\n_____________\|____________\|\n_____________57___________44\n	253 -- 259	45 -- 51	-12.6155 kcal/mol	3.20986 kcal/mol	2.27945 kcal/mol	248 260@LB@ \| \|@LB@5'-GGC...UGGGA GCAAG...CCG-3'@LB@ CUGA UGCGUGA@LB@ \|:\|\| \|:\|\|\|\|\|@LB@ GGCU AUGCACU@LB@3'-AUU...GUUUA A UCAUU...AUG-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -7.14 kcal/mol@LB@Hybridization Energy -12.6155 kcal/mol@LB@Unfolding Energy - mRNA 3.20986 kcal/mol@LB@Unfolding Energy - sRNA 2.27945 kcal/mol@LB@@LB@Position - mRNA 249 -- 259@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 45 -- 51@LB@
152	0.006159	0.1406	b2467	nudK	-9.74	0.053801	255 -- 261	1 -- 7	GDP-mannose pyrophosphatase		_____________254_____262\n_____________\|_______\|\n5'-CAA...AUUUC_______ACAAC...AAG-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	255 -- 261	1 -- 7	-11.9691 kcal/mol	0.21022 kcal/mol	2.03949 kcal/mol	254 262@LB@ \| \|@LB@5'-CAA...AUUUC ACAAC...AAG-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -11.9691 kcal/mol@LB@Unfolding Energy - mRNA 0.21022 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 255 -- 261@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 1 -- 7@LB@
110	0.003442	0.1101	b0528	ybcJ	-8.36	0.126664	258 -- 272	21 -- 34	ribosome-associated protein; putative RNA-binding protein		_____________257_____________273\n_____________\|_______________\|\n5'-AGG...UGAAA________C______GAAAG...CGA-3'\n______________CUGGAAGG_UGGAGC\n______________\|\|\|:\|\|\|:_\|:\|\|:\|\n______________GACUUUCU_AUCUUG\n3'-AUU...UUCCA_______________UAGAA...AUG-5'\n_____________\|_______________\|\n_____________35______________20\n	259 -- 265	27 -- 33	-15.4755 kcal/mol	3.05057 kcal/mol	4.02417 kcal/mol	257 273@LB@ \| \|@LB@5'-AGG...UGAAA C GAAAG...CGA-3'@LB@ CUGGAAGG UGGAGC@LB@ \|\|\|:\|\|\|: \|:\|\|:\|@LB@ GACUUUCU AUCUUG@LB@3'-AUU...UUCCA UAGAA...AUG-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -15.4755 kcal/mol@LB@Unfolding Energy - mRNA 3.05057 kcal/mol@LB@Unfolding Energy - sRNA 4.02417 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 27 -- 33@LB@
71	0.001214	0.05856	b1921	fliZ	-11.32	0.017729	260 -- 276	48 -- 65	RpoS antagonist; putative regulator of FliA activity		_____________259________________277\n_____________\|__________________\|\n5'-UGC...AAACA___________C______CGCAU...AUC-3'\n______________CAGCCAGA_CC_AUUGCG\n______________\|\|\|\|\|\|:\|_\|\|_\|\|\|:\|\|\n______________GUCGGUUU_GG_UAAUGC\n3'-AUU...UAUAA________A__C______ACUUC...AUG-5'\n_____________\|__________________\|\n_____________66_________________47\n	261 -- 267	58 -- 64	-20.8295 kcal/mol	2.05358 kcal/mol	7.47467 kcal/mol	259 277@LB@ \| \|@LB@5'-UGC...AAACA C CGCAU...AUC-3'@LB@ CAGCCAGA CC AUUGCG@LB@ \|\|\|\|\|\|:\| \|\| \|\|\|:\|\|@LB@ GUCGGUUU GG UAAUGC@LB@3'-AUU...UAUAA A C ACUUC...AUG-5'@LB@ \| \|@LB@ 66 47@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -20.8295 kcal/mol@LB@Unfolding Energy - mRNA 2.05358 kcal/mol@LB@Unfolding Energy - sRNA 7.47467 kcal/mol@LB@@LB@Position - mRNA 260 -- 276@LB@Position - sRNA 48 -- 65@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 58 -- 64@LB@
88	0.002339	0.09349	b3878	yihQ	-11.00	0.022508	260 -- 267	1 -- 8	putative sulpholipid alpha-glucosidase; alpha-glucosyl fluoride glucosidase	b3656	_____________259______268\n_____________\|________\|\n5'-AAC...AGUUU________AUUUU...GCA-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	261 -- 267	1 -- 7	-13.427 kcal/mol	0.33456 kcal/mol	2.11603 kcal/mol	259 268@LB@ \| \|@LB@5'-AAC...AGUUU AUUUU...GCA-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -13.427 kcal/mol@LB@Unfolding Energy - mRNA 0.33456 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 260 -- 267@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 1 -- 7@LB@
118	0.003907	0.1165	b3827	yigM	-8.32	0.129405	260 -- 268	1 -- 9	putative inner membrane EamA-like transporter		_____________259_______269\n_____________\|_________\|\n5'-GGA...GGCGA_________GGGGC...UGG-3'\n______________GUACCUUGC\n______________\|\|\|\|\|:\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	262 -- 268	1 -- 7	-12.9582 kcal/mol	2.53078 kcal/mol	2.12872 kcal/mol	259 269@LB@ \| \|@LB@5'-GGA...GGCGA GGGGC...UGG-3'@LB@ GUACCUUGC@LB@ \|\|\|\|\|:\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -12.9582 kcal/mol@LB@Unfolding Energy - mRNA 2.53078 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 260 -- 268@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 1 -- 7@LB@
24	0.0002009	0.02687	b1487	ddpA	-9.43	0.065911	261 -- 269	48 -- 56	D D-dipeptide ABC transporter periplasmic binding protein		_____________260_______270\n_____________\|_________\|\n5'-UCA...AUUUC_________CACGC...UGA-3'\n______________CCGGUUGCG\n______________\|\|\|:\|\|:\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	263 -- 269	48 -- 54	-13.2683 kcal/mol	2.26031 kcal/mol	1.55919 kcal/mol	260 270@LB@ \| \|@LB@5'-UCA...AUUUC CACGC...UGA-3'@LB@ CCGGUUGCG@LB@ \|\|\|:\|\|:\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.2683 kcal/mol@LB@Unfolding Energy - mRNA 2.26031 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 261 -- 269@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 48 -- 54@LB@
122	0.004081	0.1177	b3940	metL	-10.48	0.032541	261 -- 280	41 -- 59	Bifunctional aspartokinase/homoserine dehydrogenase 2		_____________260__________________281\n_____________\|____________________\|\n5'-ACG...GCAGU_______CUG__________UUAUU...GCA-3'\n______________AGUCUGG___AUGUGAAGUG\n______________\|:\|\|:\|:___\|:\|\|\|\|\|\|\|:\n______________UUAGGCU___UGCACUUCAU\n3'-AUU...UCGGU_______AA___________UUUCC...AUG-5'\n_____________\|____________________\|\n_____________60___________________40\n	274 -- 280	41 -- 47	-17.3741 kcal/mol	3.59224 kcal/mol	3.31634 kcal/mol	260 281@LB@ \| \|@LB@5'-ACG...GCAGU CUG UUAUU...GCA-3'@LB@ AGUCUGG AUGUGAAGUG@LB@ \|:\|\|:\|: \|:\|\|\|\|\|\|\|:@LB@ UUAGGCU UGCACUUCAU@LB@3'-AUU...UCGGU AA UUUCC...AUG-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -17.3741 kcal/mol@LB@Unfolding Energy - mRNA 3.59224 kcal/mol@LB@Unfolding Energy - sRNA 3.31634 kcal/mol@LB@@LB@Position - mRNA 261 -- 280@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 41 -- 47@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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