Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
135	0.01297	0.3104	b3409	feoB	-9.25	0.161231	74 -- 82	5 -- 13	ferrous iron transporter protein B and GTP-binding protein; membrane protein		_____________73________83\n_____________\|_________\|\n5'-CCG...AUGUG_________GCUCC...GGG-3'\n______________GUGCGCGUC\n______________:\|\|\|\|\|\|\|\|\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	76 -- 82	5 -- 11	-15.2985 kcal/mol	4.89519 kcal/mol	1.15134 kcal/mol	73 83@LB@ \| \|@LB@5'-CCG...AUGUG GCUCC...GGG-3'@LB@ GUGCGCGUC@LB@ :\|\|\|\|\|\|\|\|@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -15.2985 kcal/mol@LB@Unfolding Energy - mRNA 4.89519 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 74 -- 82@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 5 -- 11@LB@
137	0.01327	0.3104	b3858	yihD	-10.36	0.105347	5 -- 11	5 -- 11	DUF1040 protein YihD		_____________4_______12\n_____________\|_______\|\n_______5'-AUAA_______AGCGA...CGA-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	5 -- 11	5 -- 11	-14.974 kcal/mol	3.50324 kcal/mol	1.11145 kcal/mol	4 12@LB@ \| \|@LB@ 5'-AUAA AGCGA...CGA-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -14.974 kcal/mol@LB@Unfolding Energy - mRNA 3.50324 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 5 -- 11@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 5 -- 11@LB@
143	0.01362	0.3104	b3284	smg	-7.50	0.302399	64 -- 82	5 -- 21	DUF494 family putative periplasmic protein		_____________63__________________83\n_____________\|___________________\|\n5'-UUC...GAUGA_______CC__U__A____GUCGC...CAG-3'\n______________GGUAACA__UG_UG_CGUC\n______________\|:\|\|\|\|\|__\|\|_:\|_\|\|\|\|\n______________CUAUUGU__AC_GC_GCAG\n3'-UUU...UACUA_______UU__________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	64 -- 70	15 -- 21	-13.2614 kcal/mol	4.51132 kcal/mol	1.24955 kcal/mol	63 83@LB@ \| \|@LB@5'-UUC...GAUGA CC U A GUCGC...CAG-3'@LB@ GGUAACA UG UG CGUC@LB@ \|:\|\|\|\|\| \|\| :\| \|\|\|\|@LB@ CUAUUGU AC GC GCAG@LB@3'-UUU...UACUA UU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -13.2614 kcal/mol@LB@Unfolding Energy - mRNA 4.51132 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 64 -- 82@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 15 -- 21@LB@
144	0.01383	0.3104	b1135	rluE	-11.03	0.080673	174 -- 189	5 -- 20	23S rRNA pseudouridine(2457) synthase		_____________173______________190\n_____________\|________________\|\n5'-UGU...CCGUC____A___________AUUAG...AAC-3'\n______________AUGA_AGAUGCGCGUU\n______________\|\|:\|_\|:\|\|\|\|\|\|\|\|:\n______________UAUU_UUUACGCGCAG\n3'-UUU...ACUAC____G___________AAAG-5'\n_____________\|________________\|\n_____________21_______________4\n	183 -- 189	5 -- 11	-17.9797 kcal/mol	5.69694 kcal/mol	1.24804 kcal/mol	173 190@LB@ \| \|@LB@5'-UGU...CCGUC A AUUAG...AAC-3'@LB@ AUGA AGAUGCGCGUU@LB@ \|\|:\| \|:\|\|\|\|\|\|\|\|:@LB@ UAUU UUUACGCGCAG@LB@3'-UUU...ACUAC G AAAG-5'@LB@ \| \|@LB@ 21 4@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -17.9797 kcal/mol@LB@Unfolding Energy - mRNA 5.69694 kcal/mol@LB@Unfolding Energy - sRNA 1.24804 kcal/mol@LB@@LB@Position - mRNA 174 -- 189@LB@Position - sRNA 5 -- 20@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 5 -- 11@LB@
148	0.01421	0.3104	b2379	alaC	-8.54	0.209762	290 -- 297	5 -- 12	glutamate-pyruvate aminotransferase; glutamic-pyruvic transaminase (GPT); alanine transaminase		_____________289______298\n_____________\|________\|\n5'-UGU...AUGGC________GGC-3'\n______________UGCGCGUC\n______________\|\|\|\|\|\|\|\|\n______________ACGCGCAG\n3'-UUU...UGUUU________AAAG-5'\n_____________\|________\|\n_____________13_______4\n	291 -- 297	5 -- 11	-14.909 kcal/mol	5.25295 kcal/mol	1.11508 kcal/mol	289 298@LB@ \| \|@LB@5'-UGU...AUGGC GGC-3'@LB@ UGCGCGUC@LB@ \|\|\|\|\|\|\|\|@LB@ ACGCGCAG@LB@3'-UUU...UGUUU AAAG-5'@LB@ \| \|@LB@ 13 4@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -14.909 kcal/mol@LB@Unfolding Energy - mRNA 5.25295 kcal/mol@LB@Unfolding Energy - sRNA 1.11508 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 5 -- 12@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 5 -- 11@LB@
150	0.01436	0.3104	b3951	pflD	-11.87	0.057659	67 -- 75	5 -- 13	putative glycine radical domain-containing pyruvate formate-lyase	b0823	_____________66________76\n_____________\|_________\|\n5'-GAU...CCAUC_________AACAU...AAA-3'\n______________GUGCGCGUC\n______________:\|\|\|\|\|\|\|\|\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	69 -- 75	5 -- 11	-16.8274 kcal/mol	3.80607 kcal/mol	1.15134 kcal/mol	66 76@LB@ \| \|@LB@5'-GAU...CCAUC AACAU...AAA-3'@LB@ GUGCGCGUC@LB@ :\|\|\|\|\|\|\|\|@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -16.8274 kcal/mol@LB@Unfolding Energy - mRNA 3.80607 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 67 -- 75@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 5 -- 11@LB@
153	0.0145	0.3104	b3866	yihI	-12.31	0.048207	234 -- 252	5 -- 21	activator of Der GTPase		_____________233_________________253\n_____________\|___________________\|\n5'-GAA...GCAAA___CAU_____A_______GAAAA...GUC-3'\n______________GGU___GCAAA_GCGCGUC\n______________\|:\|___:\|\|\|\|_\|\|\|\|\|\|\|\n______________CUA___UGUUU_CGCGCAG\n3'-UUU...UACUA___U_______A_______AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	246 -- 252	5 -- 11	-18.8767 kcal/mol	5.31745 kcal/mol	1.24955 kcal/mol	233 253@LB@ \| \|@LB@5'-GAA...GCAAA CAU A GAAAA...GUC-3'@LB@ GGU GCAAA GCGCGUC@LB@ \|:\| :\|\|\|\| \|\|\|\|\|\|\|@LB@ CUA UGUUU CGCGCAG@LB@3'-UUU...UACUA U A AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -12.31 kcal/mol@LB@Hybridization Energy -18.8767 kcal/mol@LB@Unfolding Energy - mRNA 5.31745 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 234 -- 252@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 5 -- 11@LB@
157	0.01467	0.3104	b0906	ycaP	-12.44	0.045773	54 -- 69	5 -- 18	UPF0702 family putative inner membrane protein		_____________53_______________70\n_____________\|________________\|\n5'-AGU...CCGGG_________UU_____AUGAA...UCU-3'\n______________GAUAAAUGU__GCGUC\n______________:\|:\|\|\|\|\|:__\|\|\|\|\|\n______________UUGUUUACG__CGCAG\n3'-UUU...UACUA________________AAAG-5'\n_____________\|________________\|\n_____________19_______________4\n	56 -- 62	10 -- 16	-16.0437 kcal/mol	2.38303 kcal/mol	1.2243 kcal/mol	53 70@LB@ \| \|@LB@5'-AGU...CCGGG UU AUGAA...UCU-3'@LB@ GAUAAAUGU GCGUC@LB@ :\|:\|\|\|\|\|: \|\|\|\|\|@LB@ UUGUUUACG CGCAG@LB@3'-UUU...UACUA AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -16.0437 kcal/mol@LB@Unfolding Energy - mRNA 2.38303 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 54 -- 69@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 10 -- 16@LB@
160	0.015	0.3104	b2022	hisB	-11.12	0.077869	165 -- 171	5 -- 11	histidinol-phosphatase and imidazoleglycerol-phosphate dehydratase		_____________164_____172\n_____________\|_______\|\n5'-CAG...AGCCA_______AUUGA...AAC-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	165 -- 171	5 -- 11	-14.7431 kcal/mol	2.50821 kcal/mol	1.11145 kcal/mol	164 172@LB@ \| \|@LB@5'-CAG...AGCCA AUUGA...AAC-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -14.7431 kcal/mol@LB@Unfolding Energy - mRNA 2.50821 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 165 -- 171@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 5 -- 11@LB@
165	0.01591	0.3104	b4393	trpR	-12.13	0.051953	230 -- 246	5 -- 21	transcriptional repressor tryptophan-binding		_____________229_______________247\n_____________\|_________________\|\n5'-GAG...GCAGC_________ACA_____ACCAG...AUC-3'\n______________GAUGGCAGA___GCGUC\n______________\|\|\|::\|\|:\|___\|\|\|\|\|\n______________CUAUUGUUU___CGCAG\n3'-UUU...UACUA_________ACG_____AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	232 -- 238	13 -- 19	-18.7652 kcal/mol	5.38929 kcal/mol	1.24955 kcal/mol	229 247@LB@ \| \|@LB@5'-GAG...GCAGC ACA ACCAG...AUC-3'@LB@ GAUGGCAGA GCGUC@LB@ \|\|\|::\|\|:\| \|\|\|\|\|@LB@ CUAUUGUUU CGCAG@LB@3'-UUU...UACUA ACG AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -18.7652 kcal/mol@LB@Unfolding Energy - mRNA 5.38929 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 230 -- 246@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 13 -- 19@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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