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
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@
72	0.001216	0.05856	b3699	gyrB	-10.53	0.031588	1 -- 17	9 -- 25	DNA gyrase subunit B		______________1________________18\n______________\|________________\|\n___________5'-___UG____________AGCUU...GCA-3'\n______________AGA__AUUUUGCCUCUG\n______________\|\|\|__\|\|:\|\|:\|\|\|\|\|\|\n______________UCU__UAGAAUGGAGAC\n3'-AUU...UUCUA___UG____________AUGGGAUG-5'\n_____________\|_________________\|\n_____________26________________8\n	11 -- 17	9 -- 15	-19.3204 kcal/mol	1.07855 kcal/mol	7.71376 kcal/mol	1 18@LB@ \| \|@LB@ 5'- UG AGCUU...GCA-3'@LB@ AGA AUUUUGCCUCUG@LB@ \|\|\| \|\|:\|\|:\|\|\|\|\|\|@LB@ UCU UAGAAUGGAGAC@LB@3'-AUU...UUCUA UG AUGGGAUG-5'@LB@ \| \|@LB@ 26 8@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -19.3204 kcal/mol@LB@Unfolding Energy - mRNA 1.07855 kcal/mol@LB@Unfolding Energy - sRNA 7.71376 kcal/mol@LB@@LB@Position - mRNA 1 -- 17@LB@Position - sRNA 9 -- 25@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 9 -- 15@LB@
73	0.001217	0.05856	b1702	ppsA	-8.47	0.118779	124 -- 132	50 -- 58	phosphoenolpyruvate synthase		_____________123_______133\n_____________\|_________\|\n5'-UAU...UUUUC_________AAUAU...AAA-3'\n______________AUCCGGUUA\n______________\|\|\|\|\|:\|\|\|\n______________UAGGCUAAU\n3'-AUU...CGGUU_________GCACU...AUG-5'\n_____________\|_________\|\n_____________59________49\n	126 -- 132	50 -- 56	-10.3571 kcal/mol	1.58803 kcal/mol	0.317553 kcal/mol	123 133@LB@ \| \|@LB@5'-UAU...UUUUC AAUAU...AAA-3'@LB@ AUCCGGUUA@LB@ \|\|\|\|\|:\|\|\|@LB@ UAGGCUAAU@LB@3'-AUU...CGGUU GCACU...AUG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -10.3571 kcal/mol@LB@Unfolding Energy - mRNA 1.58803 kcal/mol@LB@Unfolding Energy - sRNA 0.317553 kcal/mol@LB@@LB@Position - mRNA 124 -- 132@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 50 -- 56@LB@
74	0.001232	0.05856	b3139	agaC	-9.25	0.073815	213 -- 219	1 -- 7	N-acetylgalactosamine-specific enzyme IIC component of PTS		_____________212_____220\n_____________\|_______\|\n5'-AAC...AAAUA_______UUCAG...CGA-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	213 -- 219	1 -- 7	-11.8132 kcal/mol	0.545455 kcal/mol	2.03949 kcal/mol	212 220@LB@ \| \|@LB@5'-AAC...AAAUA UUCAG...CGA-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -11.8132 kcal/mol@LB@Unfolding Energy - mRNA 0.545455 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 213 -- 219@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 1 -- 7@LB@
75	0.001328	0.06227	b1748	astC	-8.39	0.124654	121 -- 127	1 -- 7	succinylornithine transaminase PLP-dependent		_____________120_____128\n_____________\|_______\|\n5'-UCA...CACGA_______AAUCU...UGU-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	121 -- 127	1 -- 7	-11.9071 kcal/mol	1.50434 kcal/mol	2.03949 kcal/mol	120 128@LB@ \| \|@LB@5'-UCA...CACGA AAUCU...UGU-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.39 kcal/mol@LB@Hybridization Energy -11.9071 kcal/mol@LB@Unfolding Energy - mRNA 1.50434 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 121 -- 127@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 1 -- 7@LB@
76	0.001511	0.06993	b3465	rsmD	-10.43	0.033857	227 -- 244	49 -- 65	16S rRNA m(2)G966 methyltransferase SAM-dependent		_____________226________________245\n_____________\|__________________\|\n5'-UUG...GGCAG____________C_____UGGCG...GCC-3'\n______________CGGCCAAAUCCG_AUUAU\n______________\|:\|\|\|\|\|\|\|\|\|\|_\|\|\|\|:\n______________GUCGGUUUAGGC_UAAUG\n3'-AUU...UAUAA__________________CACUU...AUG-5'\n_____________\|__________________\|\n_____________66_________________48\n	232 -- 238	54 -- 60	-22.129 kcal/mol	5.5281 kcal/mol	6.19707 kcal/mol	226 245@LB@ \| \|@LB@5'-UUG...GGCAG C UGGCG...GCC-3'@LB@ CGGCCAAAUCCG AUUAU@LB@ \|:\|\|\|\|\|\|\|\|\|\| \|\|\|\|:@LB@ GUCGGUUUAGGC UAAUG@LB@3'-AUU...UAUAA CACUU...AUG-5'@LB@ \| \|@LB@ 66 48@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -22.129 kcal/mol@LB@Unfolding Energy - mRNA 5.5281 kcal/mol@LB@Unfolding Energy - sRNA 6.19707 kcal/mol@LB@@LB@Position - mRNA 227 -- 244@LB@Position - sRNA 49 -- 65@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 54 -- 60@LB@
77	0.00159	0.07263	b2159	nfo	-11.23	0.018951	134 -- 154	4 -- 22	endonuclease IV with intrinsic 3'-5' exonuclease activity		_____________133___________________155\n_____________\|_____________________\|\n5'-GAC...CCACU__________C____UA____GCUAU...CCA-3'\n______________ACAUCUUGCU_CUGU__ACCC\n______________\|\|\|\|\|\|\|:\|:_\|\|\|\|__\|\|\|\|\n______________UGUAGAAUGG_GACA__UGGG\n3'-AUU...UAUCU__________A__________AUG-5'\n_____________\|_____________________\|\n_____________23____________________3\n	134 -- 140	16 -- 22	-23.2044 kcal/mol	4.007 kcal/mol	7.98841 kcal/mol	133 155@LB@ \| \|@LB@5'-GAC...CCACU C UA GCUAU...CCA-3'@LB@ ACAUCUUGCU CUGU ACCC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\| \|\|\|\|@LB@ UGUAGAAUGG GACA UGGG@LB@3'-AUU...UAUCU A AUG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -23.2044 kcal/mol@LB@Unfolding Energy - mRNA 4.007 kcal/mol@LB@Unfolding Energy - sRNA 7.98841 kcal/mol@LB@@LB@Position - mRNA 134 -- 154@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 16 -- 22@LB@
78	0.001629	0.07345	b2624	alpA	-3.42	0.861549	231 -- 237	49 -- 55	CP4-57 prophage; DNA-binding transcriptional activator		_____________230_____238\n_____________\|_______\|\n5'-CGC...UACUA_______CAGCG...AAU-3'\n______________CGGUUAC\n______________\|\|:\|\|\|\|\n______________GCUAAUG\n3'-AUU...UUUAG_______CACUU...AUG-5'\n_____________\|_______\|\n_____________56______48\n	231 -- 237	49 -- 55	-7.04991 kcal/mol	3.33366 kcal/mol	0.311712 kcal/mol	230 238@LB@ \| \|@LB@5'-CGC...UACUA CAGCG...AAU-3'@LB@ CGGUUAC@LB@ \|\|:\|\|\|\|@LB@ GCUAAUG@LB@3'-AUU...UUUAG CACUU...AUG-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -3.42 kcal/mol@LB@Hybridization Energy -7.04991 kcal/mol@LB@Unfolding Energy - mRNA 3.33366 kcal/mol@LB@Unfolding Energy - sRNA 0.311712 kcal/mol@LB@@LB@Position - mRNA 231 -- 237@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 49 -- 55@LB@
79	0.001698	0.07533	b2890	lysS	-8.16	0.142186	53 -- 64	54 -- 65	lysine tRNA synthetase constitutive	b4129	_____________52___________65\n_____________\|____________\|\n5'-AAA...UGGGG____________UUCUU...GGA-3'\n______________CAGCCAGAUUCG\n______________\|\|\|\|\|\|:\|\|:\|\|\n______________GUCGGUUUAGGC\n3'-AUU...UAUAA____________UAAUG...AUG-5'\n_____________\|____________\|\n_____________66___________53\n	58 -- 64	54 -- 60	-18.439 kcal/mol	4.14677 kcal/mol	6.15795 kcal/mol	52 65@LB@ \| \|@LB@5'-AAA...UGGGG UUCUU...GGA-3'@LB@ CAGCCAGAUUCG@LB@ \|\|\|\|\|\|:\|\|:\|\|@LB@ GUCGGUUUAGGC@LB@3'-AUU...UAUAA UAAUG...AUG-5'@LB@ \| \|@LB@ 66 53@LB@@LB@@LB@Energy -8.16 kcal/mol@LB@Hybridization Energy -18.439 kcal/mol@LB@Unfolding Energy - mRNA 4.14677 kcal/mol@LB@Unfolding Energy - sRNA 6.15795 kcal/mol@LB@@LB@Position - mRNA 53 -- 64@LB@Position - sRNA 54 -- 65@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 54 -- 60@LB@
80	0.001713	0.07533	b1343	dbpA	-13.62	0.002663	221 -- 243	1 -- 24	ATP-dependent RNA helicase specific for 23S rRNA		_____________220______________________244\n_____________\|________________________\|\n5'-ACG...ACCCU______________CC_____A__UCACG...CGC-3'\n______________GAAUGUUUUGCCUC___GCCC_AC\n______________\|\|\|::\|:\|\|:\|\|\|\|___:\|\|\|_\|\|\n______________CUUGUAGAAUGGAG___UGGG_UG\n3'-AUU...UCUAU______________ACA____A__-5'\n_____________\|_______________________\|\n_____________25______________________1\n	228 -- 234	11 -- 17	-24.5457 kcal/mol	2.92371 kcal/mol	8.02158 kcal/mol	220 244@LB@ \| \|@LB@5'-ACG...ACCCU CC A UCACG...CGC-3'@LB@ GAAUGUUUUGCCUC GCCC AC@LB@ \|\|\|::\|:\|\|:\|\|\|\| :\|\|\| \|\|@LB@ CUUGUAGAAUGGAG UGGG UG@LB@3'-AUU...UCUAU ACA A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -24.5457 kcal/mol@LB@Unfolding Energy - mRNA 2.92371 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 221 -- 243@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 11 -- 17@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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