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
49	0.004401	0.299	b0093	ftsQ	-10.19	0.112476	259 -- 274	4 -- 20	divisome assembly protein membrane anchored protein involved in growth of wall at septum	_____________258_______________275\n_____________\|_________________\|\n5'-GCU...CCGCA________A________GGCGG...CCG-3'\n______________AUAAUGGA__CGCGUCU\n______________\|\|\|\|:::\|__\|\|\|\|\|\|\|\n______________UAUUGUUU__GCGCAGA\n3'-UUU...ACUAC________AC_______AAG-5'\n_____________\|_________________\|\n_____________21________________3\n	268 -- 274	4 -- 10	-13.8485 kcal/mol	2.40331 kcal/mol	1.25368 kcal/mol	258 275@LB@ \| \|@LB@5'-GCU...CCGCA A GGCGG...CCG-3'@LB@ AUAAUGGA CGCGUCU@LB@ \|\|\|\|:::\| \|\|\|\|\|\|\|@LB@ UAUUGUUU GCGCAGA@LB@3'-UUU...ACUAC AC AAG-5'@LB@ \| \|@LB@ 21 3@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -13.8485 kcal/mol@LB@Unfolding Energy - mRNA 2.40331 kcal/mol@LB@Unfolding Energy - sRNA 1.25368 kcal/mol@LB@@LB@Position - mRNA 259 -- 274@LB@Position - sRNA 4 -- 20@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 4 -- 10@LB@
138	0.01331	0.3104	b2897	sdhE	-11.73	0.060976	261 -- 284	1 -- 21	flavinator of succinate dehydrogenase; antitoxin of CptAB toxin-antitoxin pair	_____________260_______________________285\n_____________\|_________________________\|\n5'-GUA...AACUC____UUU___UC_____________GAACA...ACA-3'\n______________GAUA___CAA__AUGC_CGUUUUUC\n______________\|\|\|\|___\|\|\|__\|\|\|\|_\|\|\|:\|\|\|\|\n______________CUAU___GUU__UACG_GCAGAAAG\n3'-UUU...UACUA____U___________C________-5'\n_____________\|________________________\|\n_____________22_______________________1\n	278 -- 284	1 -- 7	-16.4732 kcal/mol	3.48371 kcal/mol	1.25763 kcal/mol	260 285@LB@ \| \|@LB@5'-GUA...AACUC UUU UC GAACA...ACA-3'@LB@ GAUA CAA AUGC CGUUUUUC@LB@ \|\|\|\| \|\|\| \|\|\|\| \|\|\|:\|\|\|\|@LB@ CUAU GUU UACG GCAGAAAG@LB@3'-UUU...UACUA U C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -16.4732 kcal/mol@LB@Unfolding Energy - mRNA 3.48371 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 261 -- 284@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 1 -- 7@LB@
92	0.009361	0.3104	b3652	recG	-7.88	0.265686	265 -- 278	7 -- 20	ATP-dependent DNA helicase	_____________264_____________279\n_____________\|_______________\|\n5'-CAA...ACUUA________C______AAAAU...UGC-3'\n______________GUAACAAA_UG_GCG\n______________:\|\|\|\|\|\|\|_\|\|_\|\|\|\n______________UAUUGUUU_AC_CGC\n3'-UUU...ACUAC___________G___AGAAAG-5'\n_____________\|_______________\|\n_____________21______________6\n	266 -- 272	13 -- 19	-11.4583 kcal/mol	2.34189 kcal/mol	1.23906 kcal/mol	264 279@LB@ \| \|@LB@5'-CAA...ACUUA C AAAAU...UGC-3'@LB@ GUAACAAA UG GCG@LB@ :\|\|\|\|\|\|\| \|\| \|\|\|@LB@ UAUUGUUU AC CGC@LB@3'-UUU...ACUAC G AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -11.4583 kcal/mol@LB@Unfolding Energy - mRNA 2.34189 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 265 -- 278@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 13 -- 19@LB@
174	0.01734	0.3104	b3470	tusA	-9.03	0.174990	268 -- 281	8 -- 22	mnm(5)-s(2)U34-tRNA 2-thiolation sulfurtransferase	_____________267_____________282\n_____________\|_______________\|\n5'-CAU...ACCGG_______________AAAAC...UGC-3'\n______________UGAUGAU_GGUGCGC\n______________\|\|\|\|:\|:_::\|\|\|\|\|\n______________ACUAUUG_UUACGCG\n3'-UUU...CUACU_______U_______CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	275 -- 281	8 -- 14	-15.1295 kcal/mol	4.85785 kcal/mol	1.23838 kcal/mol	267 282@LB@ \| \|@LB@5'-CAU...ACCGG AAAAC...UGC-3'@LB@ UGAUGAU GGUGCGC@LB@ \|\|\|\|:\|: ::\|\|\|\|\|@LB@ ACUAUUG UUACGCG@LB@3'-UUU...CUACU U CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -15.1295 kcal/mol@LB@Unfolding Energy - mRNA 4.85785 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 268 -- 281@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 8 -- 14@LB@
32	0.001981	0.2094	b3110	yhaO	-10.61	0.095420	268 -- 283	7 -- 23	putative transporter	_____________267_______________284\n_____________\|_________________\|\n5'-AAU...AAUGA____G____________AGAAG...UCG-3'\n______________GUGA_AGCGAGUG_GCG\n______________:\|\|\|_\|:\|:\|:\|\|_\|\|\|\n______________UACU_UUGUUUAC_CGC\n3'-UUU...CCUAC____A________G___AGAAAG-5'\n_____________\|_________________\|\n_____________24________________6\n	274 -- 280	11 -- 17	-15.5882 kcal/mol	2.45682 kcal/mol	2.52012 kcal/mol	267 284@LB@ \| \|@LB@5'-AAU...AAUGA G AGAAG...UCG-3'@LB@ GUGA AGCGAGUG GCG@LB@ :\|\|\| \|:\|:\|:\|\| \|\|\|@LB@ UACU UUGUUUAC CGC@LB@3'-UUU...CCUAC A G AGAAAG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -15.5882 kcal/mol@LB@Unfolding Energy - mRNA 2.45682 kcal/mol@LB@Unfolding Energy - sRNA 2.52012 kcal/mol@LB@@LB@Position - mRNA 268 -- 283@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 11 -- 17@LB@
128	0.01258	0.3104	b0677	nagA	-7.18	0.336330	272 -- 297	1 -- 22	N-acetylglucosamine-6-phosphate deacetylase	_____________271________________________298\n_____________\|__________________________\|\n5'-AAC...AUCGC_______CU___UAAAA______G__CGG-3'\n______________UGAUGGC__GAU_____GCGUCU_UC\n______________\|\|\|\|::\|__:\|\|_____\|\|\|\|\|\|_\|\|\n______________ACUAUUG__UUA_____CGCAGA_AG\n3'-UUU...CUACU_______U____CG_________A__-5'\n_____________\|_________________________\|\n_____________23________________________1\n	272 -- 278	16 -- 22	-15.3811 kcal/mol	6.93964 kcal/mol	1.25963 kcal/mol	271 298@LB@ \| \|@LB@5'-AAC...AUCGC CU UAAAA G CGG-3'@LB@ UGAUGGC GAU GCGUCU UC@LB@ \|\|\|\|::\| :\|\| \|\|\|\|\|\| \|\|@LB@ ACUAUUG UUA CGCAGA AG@LB@3'-UUU...CUACU U CG A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -15.3811 kcal/mol@LB@Unfolding Energy - mRNA 6.93964 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 272 -- 297@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 16 -- 22@LB@
104	0.01032	0.3104	b1714	pheS	-13.82	0.025875	273 -- 287	5 -- 21	phenylalanine tRNA synthetase alpha subunit	_____________272_______________288\n_____________\|_________________\|\n5'-UUG...CGUUA_________________GAAUA...GUA-3'\n______________GAUAAU__GUGCGCGUC\n______________\|\|\|\|\|:__:\|\|\|\|\|\|\|\|\n______________CUAUUG__UACGCGCAG\n3'-UUU...UACUA______UU_________AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	281 -- 287	5 -- 11	-20.2911 kcal/mol	5.22554 kcal/mol	1.24955 kcal/mol	272 288@LB@ \| \|@LB@5'-UUG...CGUUA GAAUA...GUA-3'@LB@ GAUAAU GUGCGCGUC@LB@ \|\|\|\|\|: :\|\|\|\|\|\|\|\|@LB@ CUAUUG UACGCGCAG@LB@3'-UUU...UACUA UU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -20.2911 kcal/mol@LB@Unfolding Energy - mRNA 5.22554 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 273 -- 287@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 5 -- 11@LB@
136	0.01311	0.3104	b0694	kdpE	-14.36	0.020608	275 -- 287	2 -- 14	response regulator in two-component regulatory system with KdpD	_____________274___________288\n_____________\|_____________\|\n5'-ACG...GACGG_____________GAGGC...CGC-3'\n______________GAUGCGCGUCUUU\n______________:\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUACGCGCAGAAA\n3'-UUU...AUUGU_____________G-5'\n_____________\|_____________\|\n_____________15____________1\n	281 -- 287	2 -- 8	-20.3279 kcal/mol	4.79291 kcal/mol	1.17514 kcal/mol	274 288@LB@ \| \|@LB@5'-ACG...GACGG GAGGC...CGC-3'@LB@ GAUGCGCGUCUUU@LB@ :\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUACGCGCAGAAA@LB@3'-UUU...AUUGU G-5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -20.3279 kcal/mol@LB@Unfolding Energy - mRNA 4.79291 kcal/mol@LB@Unfolding Energy - sRNA 1.17514 kcal/mol@LB@@LB@Position - mRNA 275 -- 287@LB@Position - sRNA 2 -- 14@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 2 -- 8@LB@
73	0.006809	0.3087	b4146	epmB	-12.79	0.039583	278 -- 298	1 -- 22	EF-P-Lys34 lysylation protein; weak lysine 2 3-aminomutase	_____________277____________________299\n_____________\|______________________\|\n5'-UUC...GAUCC______ACUUC___________GA-3'\n______________UGAUGA______UGCGUCUUUU\n______________\|\|\|\|:\|______:\|\|\|\|\|\|\|\|:\n______________ACUAUU______GCGCAGAAAG\n3'-UUU...CUACU______GUUUAC__________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	292 -- 298	1 -- 7	-16.8007 kcal/mol	2.75078 kcal/mol	1.25963 kcal/mol	277 299@LB@ \| \|@LB@5'-UUC...GAUCC ACUUC GA-3'@LB@ UGAUGA UGCGUCUUUU@LB@ \|\|\|\|:\| :\|\|\|\|\|\|\|\|:@LB@ ACUAUU GCGCAGAAAG@LB@3'-UUU...CUACU GUUUAC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.79 kcal/mol@LB@Hybridization Energy -16.8007 kcal/mol@LB@Unfolding Energy - mRNA 2.75078 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 278 -- 298@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@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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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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