Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
116	0.007938	0.2401	b0008	talB	-12.38	0.104625	254 -- 276	7 -- 26	transaldolase B		_____________253_____________________277\n_____________\|_______________________\|\n5'-AGG...GACAC___________C__CAAU_____UGUAU...CAA-3'\n______________UGGGGACAUCG_GG____GAAGC\n______________\|\|\|\|\|\|\|\|\|\|:_:\|____:\|\|\|\|\n______________ACCCCUGUAGU_UC____UUUCG\n3'-UUU...GUUUU___________U__U________UCACCG-5'\n_____________\|_______________________\|\n_____________27______________________6\n	258 -- 264	16 -- 22	-23.5048 kcal/mol	10.4229 kcal/mol	0.706388 kcal/mol	253 277@LB@ \| \|@LB@5'-AGG...GACAC C CAAU UGUAU...CAA-3'@LB@ UGGGGACAUCG GG GAAGC@LB@ \|\|\|\|\|\|\|\|\|\|: :\| :\|\|\|\|@LB@ ACCCCUGUAGU UC UUUCG@LB@3'-UUU...GUUUU U U UCACCG-5'@LB@ \| \|@LB@ 27 6@LB@@LB@@LB@Energy -12.38 kcal/mol@LB@Hybridization Energy -23.5048 kcal/mol@LB@Unfolding Energy - mRNA 10.4229 kcal/mol@LB@Unfolding Energy - sRNA 0.706388 kcal/mol@LB@@LB@Position - mRNA 254 -- 276@LB@Position - sRNA 7 -- 26@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 16 -- 22@LB@
155	0.01136	0.2504	b2168	fruK	-7.75	0.545043	91 -- 105	7 -- 22	fructose-1-phosphate kinase		_____________90_______________106\n_____________\|________________\|\n5'-AAA...CACUU________________CAUCG...CCA-3'\n______________GGCGUU_AAGAAAGGU\n______________\|:\|:\|:_\|\|\|\|\|\|:\|:\n______________CUGUAG_UUCUUUUCG\n3'-UUU...UACCC______U_________UCACCG-5'\n_____________\|________________\|\n_____________23_______________6\n	99 -- 105	7 -- 13	-14.0922 kcal/mol	5.75103 kcal/mol	0.590875 kcal/mol	90 106@LB@ \| \|@LB@5'-AAA...CACUU CAUCG...CCA-3'@LB@ GGCGUU AAGAAAGGU@LB@ \|:\|:\|: \|\|\|\|\|\|:\|:@LB@ CUGUAG UUCUUUUCG@LB@3'-UUU...UACCC U UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -7.75 kcal/mol@LB@Hybridization Energy -14.0922 kcal/mol@LB@Unfolding Energy - mRNA 5.75103 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 91 -- 105@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 7 -- 13@LB@
165	0.01211	0.2504	b3642	pyrE	-11.74	0.138291	22 -- 41	7 -- 25	orotate phosphoribosyltransferase		_____________21___________________42\n_____________\|____________________\|\n5'-CGG...GUGCA_______GCA_____C____CGUUC...AUU-3'\n______________GGGGACG___GAAGG_GAGC\n______________\|\|\|\|\|\|:___:\|\|\|:_:\|\|\|\n______________CCCCUGU___UUUCU_UUCG\n3'-UUU...UUUUA_______AG______U____UCACCG-5'\n_____________\|____________________\|\n_____________26___________________6\n	22 -- 28	19 -- 25	-22.5653 kcal/mol	10.1153 kcal/mol	0.70626 kcal/mol	21 42@LB@ \| \|@LB@5'-CGG...GUGCA GCA C CGUUC...AUU-3'@LB@ GGGGACG GAAGG GAGC@LB@ \|\|\|\|\|\|: :\|\|\|: :\|\|\|@LB@ CCCCUGU UUUCU UUCG@LB@3'-UUU...UUUUA AG U UCACCG-5'@LB@ \| \|@LB@ 26 6@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -22.5653 kcal/mol@LB@Unfolding Energy - mRNA 10.1153 kcal/mol@LB@Unfolding Energy - sRNA 0.70626 kcal/mol@LB@@LB@Position - mRNA 22 -- 41@LB@Position - sRNA 7 -- 25@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 19 -- 25@LB@
176	0.01279	0.2504	b3980	tufB	-13.59	0.058494	200 -- 216	7 -- 22	translation elongation factor EF-Tu 2	b3339	_____________199_______________217\n_____________\|_________________\|\n5'-UCC...CAAUC______U__________UUGAA...CUA-3'\n______________GAUGUC_AAAGAAAAGU\n______________\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________CUGUAG_UUUCUUUUCG\n3'-UUU...UACCC_________________UCACCG-5'\n_____________\|_________________\|\n_____________23________________6\n	210 -- 216	7 -- 13	-16.0105 kcal/mol	1.82662 kcal/mol	0.590875 kcal/mol	199 217@LB@ \| \|@LB@5'-UCC...CAAUC U UUGAA...CUA-3'@LB@ GAUGUC AAAGAAAAGU@LB@ \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ CUGUAG UUUCUUUUCG@LB@3'-UUU...UACCC UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -13.59 kcal/mol@LB@Hybridization Energy -16.0105 kcal/mol@LB@Unfolding Energy - mRNA 1.82662 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 200 -- 216@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 7 -- 13@LB@
179	0.01303	0.2504	b1276	acnA	-14.81	0.030801	184 -- 199	7 -- 22	aconitate hydratase 1; aconitase A		_____________183______________200\n_____________\|________________\|\n5'-CUU...ACCCU_U______________UAUGU...GCG-3'\n______________G_CAUUAAGGAGGAGC\n______________\|_\|\|\|:\|\|:\|\|::\|\|\|\n______________C_GUAGUUUCUUUUCG\n3'-UUU...UACCC_U______________UCACCG-5'\n_____________\|________________\|\n_____________23_______________6\n	193 -- 199	7 -- 13	-17.7225 kcal/mol	2.31939 kcal/mol	0.590875 kcal/mol	183 200@LB@ \| \|@LB@5'-CUU...ACCCU U UAUGU...GCG-3'@LB@ G CAUUAAGGAGGAGC@LB@ \| \|\|\|:\|\|:\|\|::\|\|\|@LB@ C GUAGUUUCUUUUCG@LB@3'-UUU...UACCC U UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -14.81 kcal/mol@LB@Hybridization Energy -17.7225 kcal/mol@LB@Unfolding Energy - mRNA 2.31939 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 184 -- 199@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 7 -- 13@LB@
184	0.0132	0.2504	b2897	sdhE	-10.91	0.194803	203 -- 220	7 -- 23	flavinator of succinate dehydrogenase; antitoxin of CptAB toxin-antitoxin pair		_____________202________________221\n_____________\|__________________\|\n5'-GUA...AAGAU_________CAAC_____CCGCA...ACA-3'\n______________GGACAUUAA____AAAGC\n______________\|\|\|\|\|\|:\|\|____\|\|\|\|\|\n______________CCUGUAGUU____UUUCG\n3'-UUU...UUACC_________UCU______UCACCG-5'\n_____________\|__________________\|\n_____________24_________________6\n	205 -- 211	15 -- 21	-14.6885 kcal/mol	3.17611 kcal/mol	0.599063 kcal/mol	202 221@LB@ \| \|@LB@5'-GUA...AAGAU CAAC CCGCA...ACA-3'@LB@ GGACAUUAA AAAGC@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\|@LB@ CCUGUAGUU UUUCG@LB@3'-UUU...UUACC UCU UCACCG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -14.6885 kcal/mol@LB@Unfolding Energy - mRNA 3.17611 kcal/mol@LB@Unfolding Energy - sRNA 0.599063 kcal/mol@LB@@LB@Position - mRNA 203 -- 220@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 15 -- 21@LB@
196	0.01416	0.2529	b0870	ltaE	-12.27	0.109556	23 -- 39	7 -- 23	L-allo-threonine aldolase PLP-dependent		_____________22________________40\n_____________\|_________________\|\n5'-GUC...GUGGU__U__C___________UAGCC...ACC-3'\n______________GG_CG_CAAAGAAGAGU\n______________\|\|_\|:_\|\|\|\|\|\|\|:\|\|:\n______________CC_GU_GUUUCUUUUCG\n3'-UUU...UUACC__U__A___________UCACCG-5'\n_____________\|_________________\|\n_____________24________________6\n	33 -- 39	7 -- 13	-15.8177 kcal/mol	2.94498 kcal/mol	0.599063 kcal/mol	22 40@LB@ \| \|@LB@5'-GUC...GUGGU U C UAGCC...ACC-3'@LB@ GG CG CAAAGAAGAGU@LB@ \|\| \|: \|\|\|\|\|\|\|:\|\|:@LB@ CC GU GUUUCUUUUCG@LB@3'-UUU...UUACC U A UCACCG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -12.27 kcal/mol@LB@Hybridization Energy -15.8177 kcal/mol@LB@Unfolding Energy - mRNA 2.94498 kcal/mol@LB@Unfolding Energy - sRNA 0.599063 kcal/mol@LB@@LB@Position - mRNA 23 -- 39@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 7 -- 13@LB@
127	0.009277	0.2491	b2781	mazG	-12.70	0.090074	53 -- 69	8 -- 24	nucleoside triphosphate pyrophosphohydrolase		_____________52________________70\n_____________\|_________________\|\n5'-UGA...CAAGA__A___A__________AACAG...CGC-3'\n______________GG_GCA_CGAAGAAAGG\n______________\|\|_:\|\|_\|:\|\|\|\|\|\|:\|\n______________CC_UGU_GUUUCUUUUC\n3'-UUU...UUUAC__C___A__________GUCACCG-5'\n_____________\|_________________\|\n_____________25________________7\n	63 -- 69	8 -- 14	-16.258 kcal/mol	2.86814 kcal/mol	0.688982 kcal/mol	52 70@LB@ \| \|@LB@5'-UGA...CAAGA A A AACAG...CGC-3'@LB@ GG GCA CGAAGAAAGG@LB@ \|\| :\|\| \|:\|\|\|\|\|\|:\|@LB@ CC UGU GUUUCUUUUC@LB@3'-UUU...UUUAC C A GUCACCG-5'@LB@ \| \|@LB@ 25 7@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -16.258 kcal/mol@LB@Unfolding Energy - mRNA 2.86814 kcal/mol@LB@Unfolding Energy - sRNA 0.688982 kcal/mol@LB@@LB@Position - mRNA 53 -- 69@LB@Position - sRNA 8 -- 24@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 8 -- 14@LB@
183	0.01318	0.2504	b4483	tatD	-12.95	0.080004	100 -- 117	8 -- 25	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase		_____________99__________________118\n_____________\|___________________\|\n5'-CUG...GUAAA___C__A____________GAAAA...UCA-3'\n______________GGG_GA_AUC_GGGAAGAG\n______________\|\|\|_\|\|_\|\|\|_::\|\|\|:\|\|\n______________CCC_CU_UAG_UUCUUUUC\n3'-UUU...UUUUA______G___U________GUCACCG-5'\n_____________\|___________________\|\n_____________26__________________7\n	111 -- 117	8 -- 14	-16.1661 kcal/mol	2.51597 kcal/mol	0.697717 kcal/mol	99 118@LB@ \| \|@LB@5'-CUG...GUAAA C A GAAAA...UCA-3'@LB@ GGG GA AUC GGGAAGAG@LB@ \|\|\| \|\| \|\|\| ::\|\|\|:\|\|@LB@ CCC CU UAG UUCUUUUC@LB@3'-UUU...UUUUA G U GUCACCG-5'@LB@ \| \|@LB@ 26 7@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -16.1661 kcal/mol@LB@Unfolding Energy - mRNA 2.51597 kcal/mol@LB@Unfolding Energy - sRNA 0.697717 kcal/mol@LB@@LB@Position - mRNA 100 -- 117@LB@Position - sRNA 8 -- 25@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 8 -- 14@LB@
5	2.356e-05	0.01653	b1123	potD	-19.53	0.001282	190 -- 207	9 -- 25	spermidine/putrescine ABC transporter periplasmic binding protein		_____________189________________208\n_____________\|__________________\|\n5'-GAC...ACACA____________U_____AAUGG...ACU-3'\n______________GGGGACGUUAAA_GAAAA\n______________\|\|\|\|\|\|:\|:\|\|\|_\|\|\|\|\|\n______________CCCCUGUAGUUU_CUUUU\n3'-UUU...UUUUA__________________CGUCACCG-5'\n_____________\|__________________\|\n_____________26_________________8\n	195 -- 201	14 -- 20	-22.5319 kcal/mol	2.32696 kcal/mol	0.671024 kcal/mol	189 208@LB@ \| \|@LB@5'-GAC...ACACA U AAUGG...ACU-3'@LB@ GGGGACGUUAAA GAAAA@LB@ \|\|\|\|\|\|:\|:\|\|\| \|\|\|\|\|@LB@ CCCCUGUAGUUU CUUUU@LB@3'-UUU...UUUUA CGUCACCG-5'@LB@ \| \|@LB@ 26 8@LB@@LB@@LB@Energy -19.53 kcal/mol@LB@Hybridization Energy -22.5319 kcal/mol@LB@Unfolding Energy - mRNA 2.32696 kcal/mol@LB@Unfolding Energy - sRNA 0.671024 kcal/mol@LB@@LB@Position - mRNA 190 -- 207@LB@Position - sRNA 9 -- 25@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 14 -- 20@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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