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
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@
106	0.0109	0.3104	b2510	yfgJ	-10.53	0.098521	243 -- 261	5 -- 21	DUF1407 family protein	_____________242_________________262\n_____________\|___________________\|\n5'-UAA...AUCAG________CC_________GCCGA...UUU-3'\n______________GAUAACGG__AUGCGCGUU\n______________\|\|\|\|\|\|::__\|\|\|\|\|\|\|\|:\n______________CUAUUGUU__UACGCGCAG\n3'-UUU...UACUA___________________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	255 -- 261	5 -- 11	-20.9599 kcal/mol	9.18032 kcal/mol	1.24955 kcal/mol	242 262@LB@ \| \|@LB@5'-UAA...AUCAG CC GCCGA...UUU-3'@LB@ GAUAACGG AUGCGCGUU@LB@ \|\|\|\|\|\|:: \|\|\|\|\|\|\|\|:@LB@ CUAUUGUU UACGCGCAG@LB@3'-UUU...UACUA AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -20.9599 kcal/mol@LB@Unfolding Energy - mRNA 9.18032 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 243 -- 261@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 5 -- 11@LB@
132	0.01286	0.3104	b3176	glmM	-8.35	0.224806	246 -- 258	8 -- 20	phosphoglucosamine mutase	_____________245___________259\n_____________\|_____________\|\n5'-GUU...GUCGU____G________CGAUC...CGG-3'\n______________GUAG_GGAUGCGC\n______________:\|\|:_::\|\|\|\|\|\|\n______________UAUU_UUUACGCG\n3'-UUU...ACUAC____G________CAGAAAG-5'\n_____________\|_____________\|\n_____________21____________7\n	252 -- 258	8 -- 14	-14.3134 kcal/mol	4.73041 kcal/mol	1.23367 kcal/mol	245 259@LB@ \| \|@LB@5'-GUU...GUCGU G CGAUC...CGG-3'@LB@ GUAG GGAUGCGC@LB@ :\|\|: ::\|\|\|\|\|\|@LB@ UAUU UUUACGCG@LB@3'-UUU...ACUAC G CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -8.35 kcal/mol@LB@Hybridization Energy -14.3134 kcal/mol@LB@Unfolding Energy - mRNA 4.73041 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 8 -- 14@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@
101	0.01005	0.3104	b3288	fmt	-10.27	0.109217	249 -- 255	5 -- 11	10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase	_____________248_____256\n_____________\|_______\|\n5'-AUU...UUGCA_______AUCUC...UGU-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	249 -- 255	5 -- 11	-14.5658 kcal/mol	3.18739 kcal/mol	1.11145 kcal/mol	248 256@LB@ \| \|@LB@5'-AUU...UUGCA AUCUC...UGU-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -14.5658 kcal/mol@LB@Unfolding Energy - mRNA 3.18739 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 249 -- 255@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 5 -- 11@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@
71	0.006638	0.3087	b3857	mobA	-12.61	0.042607	253 -- 264	7 -- 18	molybdopterin-guanine dinucleotide synthase	_____________252__________265\n_____________\|____________\|\n5'-UCC...AGCCA________G___GCGUA...AAC-3'\n______________GACGAAUG_GCG\n______________:\|\|:\|\|\|\|_\|\|\|\n______________UUGUUUAC_CGC\n3'-UUU...UACUA________G___AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	254 -- 260	11 -- 17	-15.9619 kcal/mol	2.14186 kcal/mol	1.20891 kcal/mol	252 265@LB@ \| \|@LB@5'-UCC...AGCCA G GCGUA...AAC-3'@LB@ GACGAAUG GCG@LB@ :\|\|:\|\|\|\| \|\|\|@LB@ UUGUUUAC CGC@LB@3'-UUU...UACUA G AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -12.61 kcal/mol@LB@Hybridization Energy -15.9619 kcal/mol@LB@Unfolding Energy - mRNA 2.14186 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 253 -- 264@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 11 -- 17@LB@
189	0.01853	0.3104	b3743	asnC	-7.74	0.278830	255 -- 266	5 -- 18	transcriptional activator of asnA; autorepressor	_____________254____________267\n_____________\|______________\|\n5'-AUU...UAAUG______________ACCGC...GCG-3'\n______________GGC_AAUGCGCG_C\n______________::\|_\|\|\|\|\|\|\|\|_\|\n______________UUG_UUACGCGC_G\n3'-UUU...UACUA___U________A_AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	259 -- 265	7 -- 13	-14.4034 kcal/mol	5.44099 kcal/mol	1.2243 kcal/mol	254 267@LB@ \| \|@LB@5'-AUU...UAAUG ACCGC...GCG-3'@LB@ GGC AAUGCGCG C@LB@ ::\| \|\|\|\|\|\|\|\| \|@LB@ UUG UUACGCGC G@LB@3'-UUU...UACUA U A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -14.4034 kcal/mol@LB@Unfolding Energy - mRNA 5.44099 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 255 -- 266@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 7 -- 13@LB@
95	0.009629	0.3104	b0781	moaA	-11.57	0.065137	257 -- 279	1 -- 21	molybdopterin biosynthesis protein A	_____________256_____________________280\n_____________\|_______________________\|\n5'-ACG...CUGUC___U__C_________AA_____GUUGC...CGG-3'\n______________GAU_AC_GAUGUGUGU__CUUUC\n______________\|\|\|_\|\|_:\|\|\|:\|:\|\|__\|\|\|\|\|\n______________CUA_UG_UUACGCGCA__GAAAG\n3'-UUU...UACUA___U__U________________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	266 -- 272	6 -- 12	-18.6522 kcal/mol	5.82624 kcal/mol	1.25763 kcal/mol	256 280@LB@ \| \|@LB@5'-ACG...CUGUC U C AA GUUGC...CGG-3'@LB@ GAU AC GAUGUGUGU CUUUC@LB@ \|\|\| \|\| :\|\|\|:\|:\|\| \|\|\|\|\|@LB@ CUA UG UUACGCGCA GAAAG@LB@3'-UUU...UACUA U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.57 kcal/mol@LB@Hybridization Energy -18.6522 kcal/mol@LB@Unfolding Energy - mRNA 5.82624 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 257 -- 279@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 6 -- 12@LB@
149	0.01422	0.3104	b0415	ribE	-7.20	0.333957	258 -- 265	4 -- 11	riboflavin synthase beta chain	_____________257______266\n_____________\|________\|\n5'-CGG...CCAUC________CAACA...GUG-3'\n______________GCGCGUUU\n______________\|\|\|\|\|\|:\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	259 -- 265	4 -- 10	-13.1965 kcal/mol	4.83677 kcal/mol	1.15639 kcal/mol	257 266@LB@ \| \|@LB@5'-CGG...CCAUC CAACA...GUG-3'@LB@ GCGCGUUU@LB@ \|\|\|\|\|\|:\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.20 kcal/mol@LB@Hybridization Energy -13.1965 kcal/mol@LB@Unfolding Energy - mRNA 4.83677 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 258 -- 265@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 4 -- 10@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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