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
24	0.001508	0.1943	b0150	fhuA	-11.07	0.079438	192 -- 210	5 -- 21	ferrichrome outer membrane transporter	_____________191_________________211\n_____________\|___________________\|\n5'-GGA...UCAGA____UAC___UG_______CCAAA...CAG-3'\n______________GAUA___CAA__GCGCGUU\n______________\|\|\|\|___\|\|\|__\|\|\|\|\|\|:\n______________CUAU___GUU__CGCGCAG\n3'-UUU...UACUA____U_____UA_______AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	204 -- 210	5 -- 11	-17.2518 kcal/mol	4.92886 kcal/mol	1.24955 kcal/mol	191 211@LB@ \| \|@LB@5'-GGA...UCAGA UAC UG CCAAA...CAG-3'@LB@ GAUA CAA GCGCGUU@LB@ \|\|\|\| \|\|\| \|\|\|\|\|\|:@LB@ CUAU GUU CGCGCAG@LB@3'-UUU...UACUA U UA AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -11.07 kcal/mol@LB@Hybridization Energy -17.2518 kcal/mol@LB@Unfolding Energy - mRNA 4.92886 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 192 -- 210@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 5 -- 11@LB@
27	0.001549	0.1943	b0440	hupB	-11.81	0.059023	134 -- 149	5 -- 20	HU DNA-binding transcriptional regulator beta subunit	_____________133______________150\n_____________\|________________\|\n5'-CGC...CUGAU_____UGC________CGUAC...CUG-3'\n______________AUAAC___UGCGCGUU\n______________\|\|\|\|\|___\|\|\|\|\|\|\|:\n______________UAUUG___ACGCGCAG\n3'-UUU...ACUAC_____UUU________AAAG-5'\n_____________\|________________\|\n_____________21_______________4\n	143 -- 149	5 -- 11	-15.9939 kcal/mol	2.93365 kcal/mol	1.24804 kcal/mol	133 150@LB@ \| \|@LB@5'-CGC...CUGAU UGC CGUAC...CUG-3'@LB@ AUAAC UGCGCGUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ UAUUG ACGCGCAG@LB@3'-UUU...ACUAC UUU AAAG-5'@LB@ \| \|@LB@ 21 4@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -15.9939 kcal/mol@LB@Unfolding Energy - mRNA 2.93365 kcal/mol@LB@Unfolding Energy - sRNA 1.24804 kcal/mol@LB@@LB@Position - mRNA 134 -- 149@LB@Position - sRNA 5 -- 20@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 5 -- 11@LB@
33	0.002096	0.2094	b0937	ssuE	-11.36	0.070700	201 -- 209	5 -- 13	NAD(P)H-dependent FMN reductase	_____________200_______210\n_____________\|_________\|\n5'-CUG...AGAGU_________AUCAC...AGG-3'\n______________AUGCGUGUC\n______________\|\|\|\|\|:\|\|\|\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	203 -- 209	5 -- 11	-14.6108 kcal/mol	2.09491 kcal/mol	1.15134 kcal/mol	200 210@LB@ \| \|@LB@5'-CUG...AGAGU AUCAC...AGG-3'@LB@ AUGCGUGUC@LB@ \|\|\|\|\|:\|\|\|@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -14.6108 kcal/mol@LB@Unfolding Energy - mRNA 2.09491 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 201 -- 209@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 5 -- 11@LB@
39	0.002561	0.2224	b3845	fadA	-14.30	0.021162	112 -- 126	5 -- 20	3-ketoacyl-CoA thiolase (thiolase I)	_____________111______________127\n_____________\|________________\|\n5'-UCC...UCUGC________________AUAAC...AUU-3'\n______________GUAAUAAA_GCGCGUC\n______________:\|\|\|:\|\|\|_\|\|\|\|\|\|\|\n______________UAUUGUUU_CGCGCAG\n3'-UUU...ACUAC________A_______AAAG-5'\n_____________\|________________\|\n_____________21_______________4\n	120 -- 126	5 -- 11	-19.3309 kcal/mol	3.78617 kcal/mol	1.24804 kcal/mol	111 127@LB@ \| \|@LB@5'-UCC...UCUGC AUAAC...AUU-3'@LB@ GUAAUAAA GCGCGUC@LB@ :\|\|\|:\|\|\| \|\|\|\|\|\|\|@LB@ UAUUGUUU CGCGCAG@LB@3'-UUU...ACUAC A AAAG-5'@LB@ \| \|@LB@ 21 4@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -19.3309 kcal/mol@LB@Unfolding Energy - mRNA 3.78617 kcal/mol@LB@Unfolding Energy - sRNA 1.24804 kcal/mol@LB@@LB@Position - mRNA 112 -- 126@LB@Position - sRNA 5 -- 20@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 5 -- 11@LB@
42	0.002847	0.2296	b1638	pdxH	-9.07	0.172497	29 -- 35	5 -- 11	pyridoxine 5'-phosphate oxidase	_____________28______36\n_____________\|_______\|\n5'-UCU...CUGGC_______ACACU...CCC-3'\n______________GCGCGUU\n______________\|\|\|\|\|\|:\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	29 -- 35	5 -- 11	-12.2635 kcal/mol	2.08033 kcal/mol	1.11145 kcal/mol	28 36@LB@ \| \|@LB@5'-UCU...CUGGC ACACU...CCC-3'@LB@ GCGCGUU@LB@ \|\|\|\|\|\|:@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -9.07 kcal/mol@LB@Hybridization Energy -12.2635 kcal/mol@LB@Unfolding Energy - mRNA 2.08033 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 29 -- 35@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 5 -- 11@LB@
48	0.00405	0.2857	b0409	secF	-13.37	0.031213	166 -- 172	5 -- 11	SecYEG protein translocase auxillary subunit	_____________165_____173\n_____________\|_______\|\n5'-CUU...GGCAA_______AAGAA...UGU-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	166 -- 172	5 -- 11	-14.9857 kcal/mol	0.509172 kcal/mol	1.11145 kcal/mol	165 173@LB@ \| \|@LB@5'-CUU...GGCAA AAGAA...UGU-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -13.37 kcal/mol@LB@Hybridization Energy -14.9857 kcal/mol@LB@Unfolding Energy - mRNA 0.509172 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 166 -- 172@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 5 -- 11@LB@
50	0.004415	0.299	b0752	zitB	-14.03	0.023662	243 -- 258	5 -- 21	zinc efflux system	_____________242_______________259\n_____________\|_________________\|\n5'-CGC...CAGAA____________U____GCUUG...UGG-3'\n______________GAUAAUAA_UGC_CGUC\n______________\|\|\|\|\|:\|\|_\|\|\|_\|\|\|\|\n______________CUAUUGUU_ACG_GCAG\n3'-UUU...UACUA________U___C____AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	244 -- 250	14 -- 20	-17.36 kcal/mol	2.08049 kcal/mol	1.24955 kcal/mol	242 259@LB@ \| \|@LB@5'-CGC...CAGAA U GCUUG...UGG-3'@LB@ GAUAAUAA UGC CGUC@LB@ \|\|\|\|\|:\|\| \|\|\| \|\|\|\|@LB@ CUAUUGUU ACG GCAG@LB@3'-UUU...UACUA U C AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -17.36 kcal/mol@LB@Unfolding Energy - mRNA 2.08049 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 243 -- 258@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 14 -- 20@LB@
74	0.006875	0.3087	b2474	tmcA	-10.30	0.108021	196 -- 222	5 -- 31	elongator methionine tRNA (ac4C34) acetyltransferase	_____________195____________________________223\n_____________\|______________________________\|\n5'-GAU...CGGGG_________C___AC____________U__ACACA...UUG-3'\n______________CAGGGAUGG_UGA__UGAC___UGCGC_UC\n______________\|\|\|\|\|\|\|\|:_\|\|\|__\|:\|\|___\|\|\|\|\|_\|\|\n______________GUCCCUACU_ACU__AUUG___ACGCG_AG\n3'-UUU...CUUAA___________________UUU_____C__AAAG-5'\n_____________\|______________________________\|\n_____________32_____________________________4\n	198 -- 204	23 -- 29	-27.934 kcal/mol	9.88036 kcal/mol	7.7585 kcal/mol	195 223@LB@ \| \|@LB@5'-GAU...CGGGG C AC U ACACA...UUG-3'@LB@ CAGGGAUGG UGA UGAC UGCGC UC@LB@ \|\|\|\|\|\|\|\|: \|\|\| \|:\|\| \|\|\|\|\| \|\|@LB@ GUCCCUACU ACU AUUG ACGCG AG@LB@3'-UUU...CUUAA UUU C AAAG-5'@LB@ \| \|@LB@ 32 4@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -27.934 kcal/mol@LB@Unfolding Energy - mRNA 9.88036 kcal/mol@LB@Unfolding Energy - sRNA 7.7585 kcal/mol@LB@@LB@Position - mRNA 196 -- 222@LB@Position - sRNA 5 -- 31@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 23 -- 29@LB@
80	0.007305	0.3087	b2392	mntH	-9.52	0.145914	200 -- 218	5 -- 21	manganese/divalent cation transporter	_____________199_________________219\n_____________\|___________________\|\n5'-GCU...CACAA_________CUAU______GAGAG...UCG-3'\n______________GAUGACGAA____CGCGUU\n______________\|\|\|:\|\|:\|\|____\|\|\|\|\|:\n______________CUAUUGUUU____GCGCAG\n3'-UUU...UACUA_________AC________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	202 -- 208	13 -- 19	-16.4824 kcal/mol	5.71706 kcal/mol	1.24955 kcal/mol	199 219@LB@ \| \|@LB@5'-GCU...CACAA CUAU GAGAG...UCG-3'@LB@ GAUGACGAA CGCGUU@LB@ \|\|\|:\|\|:\|\| \|\|\|\|\|:@LB@ CUAUUGUUU GCGCAG@LB@3'-UUU...UACUA AC AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -16.4824 kcal/mol@LB@Unfolding Energy - mRNA 5.71706 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 200 -- 218@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 13 -- 19@LB@
84	0.008129	0.3104	b2579	grcA	-9.71	0.135356	279 -- 291	5 -- 18	autonomous glycyl radical cofactor	_____________278____________292\n_____________\|______________\|\n5'-UUG...AAAAA______________GCAUC...UUG-3'\n______________GGCGAA_GCGCGUU\n______________::\|:\|\|_\|\|\|\|\|\|:\n______________UUGUUU_CGCGCAG\n3'-UUU...UACUA______A_______AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	285 -- 291	5 -- 11	-16.0784 kcal/mol	5.14159 kcal/mol	1.2243 kcal/mol	278 292@LB@ \| \|@LB@5'-UUG...AAAAA GCAUC...UUG-3'@LB@ GGCGAA GCGCGUU@LB@ ::\|:\|\| \|\|\|\|\|\|:@LB@ UUGUUU CGCGCAG@LB@3'-UUU...UACUA A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -16.0784 kcal/mol@LB@Unfolding Energy - mRNA 5.14159 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 279 -- 291@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 5 -- 11@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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service.

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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