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
67	0.006163	0.3087	b0773	ybhB	-10.36	0.105479	214 -- 228	7 -- 20	kinase inhibitor homolog UPF0098 family	b0545	_____________213_____________229\n_____________\|_______________\|\n5'-UGU...CAUCA_______UC______AUGGC...AUC-3'\n______________GUAACGA__UGCGCG\n______________:\|\|\|\|:\|__\|\|\|\|\|\|\n______________UAUUGUU__ACGCGC\n3'-UUU...ACUAC_______U_______AGAAAG-5'\n_____________\|_______________\|\n_____________21______________6\n	214 -- 220	14 -- 20	-16.0436 kcal/mol	4.44842 kcal/mol	1.23906 kcal/mol	213 229@LB@ \| \|@LB@5'-UGU...CAUCA UC AUGGC...AUC-3'@LB@ GUAACGA UGCGCG@LB@ :\|\|\|\|:\| \|\|\|\|\|\|@LB@ UAUUGUU ACGCGC@LB@3'-UUU...ACUAC U AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -16.0436 kcal/mol@LB@Unfolding Energy - mRNA 4.44842 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 214 -- 228@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 14 -- 20@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@
21	0.0009524	0.1536	b0241	phoE	-11.39	0.070016	174 -- 180	5 -- 11	outer membrane phosphoporin protein E	b0929 b2215 b1377	_____________173_____181\n_____________\|_______\|\n5'-AGC...UAUUC_______AAUUA...AUG-3'\n______________GCGCGUU\n______________\|\|\|\|\|\|:\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	174 -- 180	5 -- 11	-12.879 kcal/mol	0.378776 kcal/mol	1.11145 kcal/mol	173 181@LB@ \| \|@LB@5'-AGC...UAUUC AAUUA...AUG-3'@LB@ GCGCGUU@LB@ \|\|\|\|\|\|:@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -12.879 kcal/mol@LB@Unfolding Energy - mRNA 0.378776 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 174 -- 180@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 5 -- 11@LB@
183	0.01807	0.3104	b1508	hipB	-7.23	0.331427	238 -- 247	10 -- 19	antitoxin of HipAB toxin-antitoxin system	b1299 b1434	_____________237________248\n_____________\|__________\|\n5'-AUG...GCAAU__________AAUGA...AAA-3'\n______________UGGCGAAUGC\n______________\|::\|:\|\|\|\|\|\n______________AUUGUUUACG\n3'-UUU...CUACU__________CGCAG...AAG-5'\n_____________\|__________\|\n_____________20_________9\n	241 -- 247	10 -- 16	-11.7956 kcal/mol	3.36082 kcal/mol	1.20833 kcal/mol	237 248@LB@ \| \|@LB@5'-AUG...GCAAU AAUGA...AAA-3'@LB@ UGGCGAAUGC@LB@ \|::\|:\|\|\|\|\|@LB@ AUUGUUUACG@LB@3'-UUU...CUACU CGCAG...AAG-5'@LB@ \| \|@LB@ 20 9@LB@@LB@@LB@Energy -7.23 kcal/mol@LB@Hybridization Energy -11.7956 kcal/mol@LB@Unfolding Energy - mRNA 3.36082 kcal/mol@LB@Unfolding Energy - sRNA 1.20833 kcal/mol@LB@@LB@Position - mRNA 238 -- 247@LB@Position - sRNA 10 -- 19@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 10 -- 16@LB@
179	0.01766	0.3104	b0377	sbmA	-9.49	0.147268	6 -- 15	3 -- 12	peptide antibiotic transporter	b1496	_____________5__________16\n_____________\|__________\|\n______5'-GAUCC_______G__AAUCC...ACU-3'\n______________UGCGCGU_UU\n______________\|\|\|\|\|\|\|_\|\|\n______________ACGCGCA_AA\n3'-UUU...UGUUU_______G__AG-5'\n_____________\|__________\|\n_____________13_________2\n	6 -- 12	6 -- 12	-14.1156 kcal/mol	3.45883 kcal/mol	1.16529 kcal/mol	5 16@LB@ \| \|@LB@ 5'-GAUCC G AAUCC...ACU-3'@LB@ UGCGCGU UU@LB@ \|\|\|\|\|\|\| \|\|@LB@ ACGCGCA AA@LB@3'-UUU...UGUUU G AG-5'@LB@ \| \|@LB@ 13 2@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -14.1156 kcal/mol@LB@Unfolding Energy - mRNA 3.45883 kcal/mol@LB@Unfolding Energy - sRNA 1.16529 kcal/mol@LB@@LB@Position - mRNA 6 -- 15@LB@Position - sRNA 3 -- 12@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 6 -- 12@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@
68	0.006348	0.3087	b1202	ycgV	-6.40	0.429936	233 -- 244	4 -- 18	putative adhesin	b2647	_____________232_____________245\n_____________\|_______________\|\n5'-ACU...ACCAA_______________CGCUG...UUG-3'\n______________AGCAGAU___CGUCU\n______________\|:\|\|:\|\|___\|\|\|\|\|\n______________UUGUUUA___GCAGA\n3'-UUU...UACUA_______CGC_____AAG-5'\n_____________\|_______________\|\n_____________19______________3\n	233 -- 239	12 -- 18	-9.8712 kcal/mol	2.23703 kcal/mol	1.22995 kcal/mol	232 245@LB@ \| \|@LB@5'-ACU...ACCAA CGCUG...UUG-3'@LB@ AGCAGAU CGUCU@LB@ \|:\|\|:\|\| \|\|\|\|\|@LB@ UUGUUUA GCAGA@LB@3'-UUU...UACUA CGC AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -9.8712 kcal/mol@LB@Unfolding Energy - mRNA 2.23703 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 233 -- 244@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 12 -- 18@LB@
40	0.002726	0.2279	b1799	dmlR	-13.48	0.029707	223 -- 239	2 -- 20	transcriptional activator of dmlA	b3060	_____________222_________________240\n_____________\|___________________\|\n5'-CGC...GCUGA_____U_____________AUGCU...CGG-3'\n______________AUGAU___UGCGCGUCUUU\n______________\|\|:\|:___\|\|\|\|\|\|\|\|\|\|\|\n______________UAUUG___ACGCGCAGAAA\n3'-UUU...ACUAC_____UUU___________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	233 -- 239	2 -- 8	-19.9945 kcal/mol	5.2543 kcal/mol	1.25604 kcal/mol	222 240@LB@ \| \|@LB@5'-CGC...GCUGA U AUGCU...CGG-3'@LB@ AUGAU UGCGCGUCUUU@LB@ \|\|:\|: \|\|\|\|\|\|\|\|\|\|\|@LB@ UAUUG ACGCGCAGAAA@LB@3'-UUU...ACUAC UUU G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -19.9945 kcal/mol@LB@Unfolding Energy - mRNA 5.2543 kcal/mol@LB@Unfolding Energy - sRNA 1.25604 kcal/mol@LB@@LB@Position - mRNA 223 -- 239@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 2 -- 8@LB@
96	0.009671	0.3104	b0941	elfG	-12.70	0.041082	222 -- 232	5 -- 15	putative fimbrial-like adhesin protein	b3145 b0533	_____________221_________233\n_____________\|___________\|\n5'-UUU...GAGAA___________AUUAC...GGC-3'\n______________AAAUGCGUGUC\n______________\|\|\|\|\|\|\|:\|\|\|\n______________UUUACGCGCAG\n3'-UUU...UAUUG___________AAAG-5'\n_____________\|___________\|\n_____________16__________4\n	226 -- 232	5 -- 11	-17.0283 kcal/mol	3.13128 kcal/mol	1.19708 kcal/mol	221 233@LB@ \| \|@LB@5'-UUU...GAGAA AUUAC...GGC-3'@LB@ AAAUGCGUGUC@LB@ \|\|\|\|\|\|\|:\|\|\|@LB@ UUUACGCGCAG@LB@3'-UUU...UAUUG AAAG-5'@LB@ \| \|@LB@ 16 4@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -17.0283 kcal/mol@LB@Unfolding Energy - mRNA 3.13128 kcal/mol@LB@Unfolding Energy - sRNA 1.19708 kcal/mol@LB@@LB@Position - mRNA 222 -- 232@LB@Position - sRNA 5 -- 15@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 5 -- 11@LB@
171	0.01687	0.3104	b1512	lsrR	-11.43	0.068975	231 -- 262	7 -- 31	lsr operon transcriptional repressor	b4295	_____________230______________________________263\n_____________\|________________________________\|\n5'-GCU...CAGAA______AUGUG___A__AG_______C_____GAUCG...AGA-3'\n______________CAGGGA_____UGA_GA__AACAGGU_GCGCG\n______________\|\|\|\|\|\|_____\|\|\|_\|\|__\|\|\|\|::\|_\|\|\|\|\|\n______________GUCCCU_____ACU_CU__UUGUUUA_CGCGC\n3'-UUU...CUUAA______________A__A______________AGAAAG-5'\n_____________\|________________________________\|\n_____________32_______________________________6\n	250 -- 256	12 -- 18	-27.0439 kcal/mol	7.86672 kcal/mol	7.75103 kcal/mol	230 263@LB@ \| \|@LB@5'-GCU...CAGAA AUGUG A AG C GAUCG...AGA-3'@LB@ CAGGGA UGA GA AACAGGU GCGCG@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|::\| \|\|\|\|\|@LB@ GUCCCU ACU CU UUGUUUA CGCGC@LB@3'-UUU...CUUAA A A AGAAAG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -27.0439 kcal/mol@LB@Unfolding Energy - mRNA 7.86672 kcal/mol@LB@Unfolding Energy - sRNA 7.75103 kcal/mol@LB@@LB@Position - mRNA 231 -- 262@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 12 -- 18@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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