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
121	0.01226	0.3104	b3209	elbB	-12.57	0.043302	225 -- 240	4 -- 18	isoprenoid biosynthesis protein with amidotransferase-like domain		_____________224______________241\n_____________\|________________\|\n5'-GCG...UUCUG__________G_____AUGAC...GUG-3'\n______________AGCGGAUGCG_CGUCU\n______________\|:\|::\|\|\|\|\|_\|\|\|\|\|\n______________UUGUUUACGC_GCAGA\n3'-UUU...UACUA________________AAG-5'\n_____________\|________________\|\n_____________19_______________3\n	228 -- 234	9 -- 15	-20.315 kcal/mol	6.5132 kcal/mol	1.22995 kcal/mol	224 241@LB@ \| \|@LB@5'-GCG...UUCUG G AUGAC...GUG-3'@LB@ AGCGGAUGCG CGUCU@LB@ \|:\|::\|\|\|\|\| \|\|\|\|\|@LB@ UUGUUUACGC GCAGA@LB@3'-UUU...UACUA AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -20.315 kcal/mol@LB@Unfolding Energy - mRNA 6.5132 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 225 -- 240@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 9 -- 15@LB@
122	0.01233	0.3104	b3599	mtlA	-8.56	0.208645	247 -- 281	4 -- 32	mannitol-specific PTS enzyme: IIA IIB and IIC components		_____________246_________________________________282\n_____________\|___________________________________\|\n5'-GAU...UUUCC____CAAC_________C_____AUCG________AUCGC...UCA-3'\n______________UCAG____AUGGUGAUG_CAAAU____GCGCGUUU\n______________\|\|\|\|____\|\|\|:\|\|\|\|:_\|\|\|\|\|____\|\|\|\|\|\|:\|\n______________AGUC____UACUACUAU_GUUUA____CGCGCAGA\n3'-UUU...ACUUA____CC___________U_________________AAG-5'\n_____________\|___________________________________\|\n_____________33__________________________________3\n	275 -- 281	4 -- 10	-27.4972 kcal/mol	11.1013 kcal/mol	7.84022 kcal/mol	246 282@LB@ \| \|@LB@5'-GAU...UUUCC CAAC C AUCG AUCGC...UCA-3'@LB@ UCAG AUGGUGAUG CAAAU GCGCGUUU@LB@ \|\|\|\| \|\|\|:\|\|\|\|: \|\|\|\|\| \|\|\|\|\|\|:\|@LB@ AGUC UACUACUAU GUUUA CGCGCAGA@LB@3'-UUU...ACUUA CC U AAG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -27.4972 kcal/mol@LB@Unfolding Energy - mRNA 11.1013 kcal/mol@LB@Unfolding Energy - sRNA 7.84022 kcal/mol@LB@@LB@Position - mRNA 247 -- 281@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 4 -- 10@LB@
123	0.01235	0.3104	b0097	secM	-7.65	0.286972	189 -- 203	7 -- 21	regulator of secA translation		_____________188_____________204\n_____________\|_______________\|\n5'-UGG...AUCGG________UAA____AGUGG...CGC-3'\n______________GAUGGCAA___CGUG\n______________\|\|\|::\|\|\|___\|\|:\|\n______________CUAUUGUU___GCGC\n3'-UUU...UACUA________UAC____AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	190 -- 196	14 -- 20	-12.5088 kcal/mol	3.61266 kcal/mol	1.24179 kcal/mol	188 204@LB@ \| \|@LB@5'-UGG...AUCGG UAA AGUGG...CGC-3'@LB@ GAUGGCAA CGUG@LB@ \|\|\|::\|\|\| \|\|:\|@LB@ CUAUUGUU GCGC@LB@3'-UUU...UACUA UAC AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -12.5088 kcal/mol@LB@Unfolding Energy - mRNA 3.61266 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 189 -- 203@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 14 -- 20@LB@
124	0.0124	0.3104	b1860	ruvB	-8.20	0.236824	252 -- 265	8 -- 20	ATP-dependent DNA helicase component of RuvABC resolvasome		_____________251____________266\n_____________\|______________\|\n5'-ACG...AAGAU_________C____CAUUC...GUC-3'\n______________GUAGCAGAU_GCGC\n______________:\|\|:\|\|:\|\|_\|\|\|\|\n______________UAUUGUUUA_CGCG\n3'-UUU...ACUAC______________CAGAAAG-5'\n_____________\|______________\|\n_____________21_____________7\n	252 -- 258	14 -- 20	-14.7986 kcal/mol	5.36112 kcal/mol	1.23367 kcal/mol	251 266@LB@ \| \|@LB@5'-ACG...AAGAU C CAUUC...GUC-3'@LB@ GUAGCAGAU GCGC@LB@ :\|\|:\|\|:\|\| \|\|\|\|@LB@ UAUUGUUUA CGCG@LB@3'-UUU...ACUAC CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -8.20 kcal/mol@LB@Hybridization Energy -14.7986 kcal/mol@LB@Unfolding Energy - mRNA 5.36112 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 252 -- 265@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 14 -- 20@LB@
125	0.01241	0.3104	b0002	thrA	-8.21	0.235915	191 -- 205	9 -- 21	Bifunctional aspartokinase/homoserine dehydrogenase 1		_____________190_____________206\n_____________\|_______________\|\n5'-CCA...AACGA________CC_____AGUGU...UGG-3'\n______________GGUAACAA__AUGCG\n______________\|:\|\|\|\|\|\|__\|\|\|\|\|\n______________CUAUUGUU__UACGC\n3'-UUU...UACUA_______________GCAGAAAG-5'\n_____________\|_______________\|\n_____________22______________8\n	192 -- 198	14 -- 20	-12.9357 kcal/mol	3.48482 kcal/mol	1.23627 kcal/mol	190 206@LB@ \| \|@LB@5'-CCA...AACGA CC AGUGU...UGG-3'@LB@ GGUAACAA AUGCG@LB@ \|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUU UACGC@LB@3'-UUU...UACUA GCAGAAAG-5'@LB@ \| \|@LB@ 22 8@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -12.9357 kcal/mol@LB@Unfolding Energy - mRNA 3.48482 kcal/mol@LB@Unfolding Energy - sRNA 1.23627 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 9 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 14 -- 20@LB@
126	0.01241	0.3104	b4379	yjjW	-11.82	0.058804	207 -- 217	8 -- 18	putative pyruvate formate lyase activating enzyme		_____________206_________218\n_____________\|___________\|\n5'-CGG...UGAAC___________UUUAG...UGC-3'\n______________AGCAGAUGCGC\n______________\|:\|\|:\|\|\|\|\|\|\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	211 -- 217	8 -- 14	-16.9543 kcal/mol	3.92931 kcal/mol	1.20363 kcal/mol	206 218@LB@ \| \|@LB@5'-CGG...UGAAC UUUAG...UGC-3'@LB@ AGCAGAUGCGC@LB@ \|:\|\|:\|\|\|\|\|\|@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -16.9543 kcal/mol@LB@Unfolding Energy - mRNA 3.92931 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 207 -- 217@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 8 -- 14@LB@
127	0.01249	0.3104	b2964	nupG	-12.57	0.043346	150 -- 164	1 -- 16	nucleoside transporter	b2406	_____________149______________165\n_____________\|________________\|\n5'-UCC...ACGGU________________AAACA...UGA-3'\n______________CAAAUGUGC_UUUUUC\n______________\|\|\|\|\|\|:\|\|_\|:\|\|\|\|\n______________GUUUACGCG_AGAAAG\n3'-UUU...CUAUU_________C______-5'\n_____________\|_______________\|\n_____________17______________1\n	152 -- 158	8 -- 14	-16.6758 kcal/mol	2.8679 kcal/mol	1.23857 kcal/mol	149 165@LB@ \| \|@LB@5'-UCC...ACGGU AAACA...UGA-3'@LB@ CAAAUGUGC UUUUUC@LB@ \|\|\|\|\|\|:\|\| \|:\|\|\|\|@LB@ GUUUACGCG AGAAAG@LB@3'-UUU...CUAUU C -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -16.6758 kcal/mol@LB@Unfolding Energy - mRNA 2.8679 kcal/mol@LB@Unfolding Energy - sRNA 1.23857 kcal/mol@LB@@LB@Position - mRNA 150 -- 164@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 8 -- 14@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@
129	0.01261	0.3104	b3025	qseB	-10.92	0.084347	141 -- 152	5 -- 17	quorum sensing DNA-binding response regulator in two-component regulatory system with QseC		_____________140___________153\n_____________\|_____________\|\n5'-GUG...GCUGU_____________ACAAC...GUC-3'\n______________ACAGA_GCGCGUU\n______________\|\|\|:\|_\|\|\|\|\|\|:\n______________UGUUU_CGCGCAG\n3'-UUU...ACUAU_____A_______AAAG-5'\n_____________\|_____________\|\n_____________18____________4\n	146 -- 152	5 -- 11	-15.7823 kcal/mol	3.63703 kcal/mol	1.22241 kcal/mol	140 153@LB@ \| \|@LB@5'-GUG...GCUGU ACAAC...GUC-3'@LB@ ACAGA GCGCGUU@LB@ \|\|\|:\| \|\|\|\|\|\|:@LB@ UGUUU CGCGCAG@LB@3'-UUU...ACUAU A AAAG-5'@LB@ \| \|@LB@ 18 4@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -15.7823 kcal/mol@LB@Unfolding Energy - mRNA 3.63703 kcal/mol@LB@Unfolding Energy - sRNA 1.22241 kcal/mol@LB@@LB@Position - mRNA 141 -- 152@LB@Position - sRNA 5 -- 17@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 5 -- 11@LB@
130	0.01263	0.3104	b1952	dsrB	-7.17	0.338083	230 -- 240	7 -- 18	uncharacterized protein		_____________229__________241\n_____________\|____________\|\n5'-CGU...GUCAA____________GUCCG...ACC-3'\n______________AACGGAUG_GCG\n______________\|\|\|::\|\|\|_\|\|\|\n______________UUGUUUAC_CGC\n3'-UUU...UACUA________G___AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	231 -- 237	11 -- 17	-11.9456 kcal/mol	3.57064 kcal/mol	1.20891 kcal/mol	229 241@LB@ \| \|@LB@5'-CGU...GUCAA GUCCG...ACC-3'@LB@ AACGGAUG GCG@LB@ \|\|\|::\|\|\| \|\|\|@LB@ UUGUUUAC CGC@LB@3'-UUU...UACUA G AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -11.9456 kcal/mol@LB@Unfolding Energy - mRNA 3.57064 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 230 -- 240@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 231 -- 237@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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