Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
47	0.003222	0.2306	b1667	ydhR	-16.61	0.002759	245 -- 266	34 -- 55	putative monooxygenase		_____________244____________________267\n_____________\|______________________\|\n5'-UUG...CCAUU______C_________G_____CUUAA...AAC-3'\n______________UGGCGA_GCAAUGGCU_AGCAG\n______________\|\|\|\|:\|_\|\|\|\|\|\|\|\|:_\|:\|\|\|\n______________ACCGUU_CGUUACCGG_UUGUC\n3'-UUU...UAGUC______A_________G_____UUUUA...UUG-5'\n_____________\|______________________\|\n_____________56_____________________33\n	254 -- 260	40 -- 46	-33.2096 kcal/mol	7.64311 kcal/mol	8.95438 kcal/mol	244 267@LB@ \| \|@LB@5'-UUG...CCAUU C G CUUAA...AAC-3'@LB@ UGGCGA GCAAUGGCU AGCAG@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|\|: \|:\|\|\|@LB@ ACCGUU CGUUACCGG UUGUC@LB@3'-UUU...UAGUC A G UUUUA...UUG-5'@LB@ \| \|@LB@ 56 33@LB@@LB@@LB@Energy -16.61 kcal/mol@LB@Hybridization Energy -33.2096 kcal/mol@LB@Unfolding Energy - mRNA 7.64311 kcal/mol@LB@Unfolding Energy - sRNA 8.95438 kcal/mol@LB@@LB@Position - mRNA 245 -- 266@LB@Position - sRNA 34 -- 55@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 40 -- 46@LB@
145	0.01667	0.3828	b1835	rsmF	-17.85	0.001164	186 -- 211	35 -- 58	16S rRNA m(5)C1407 methyltransferase SAM-dependent		_____________185________________________212\n_____________\|__________________________\|\n5'-CGC...UUUGC________C____UC___________CACCG...GUC-3'\n______________CAGUGGUA_AUGC__GUGGCCCAACA\n______________\|\|\|\|\|\|:\|_\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|\n______________GUCACCGU_UACG__UACCGGGUUGU\n3'-UUU...UUUUA_____________U____________CUUUU...UUG-5'\n_____________\|__________________________\|\n_____________59_________________________34\n	205 -- 211	35 -- 41	-37.9392 kcal/mol	9.33395 kcal/mol	10.7541 kcal/mol	185 212@LB@ \| \|@LB@5'-CGC...UUUGC C UC CACCG...GUC-3'@LB@ CAGUGGUA AUGC GUGGCCCAACA@LB@ \|\|\|\|\|\|:\| \|\|\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ GUCACCGU UACG UACCGGGUUGU@LB@3'-UUU...UUUUA U CUUUU...UUG-5'@LB@ \| \|@LB@ 59 34@LB@@LB@@LB@Energy -17.85 kcal/mol@LB@Hybridization Energy -37.9392 kcal/mol@LB@Unfolding Energy - mRNA 9.33395 kcal/mol@LB@Unfolding Energy - sRNA 10.7541 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 35 -- 58@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 35 -- 41@LB@
24	0.001299	0.182	b1267	yciO	-12.11	0.041783	4 -- 24	36 -- 58	putative RNA binding protein		_____________3_______________________25\n_____________\|_______________________\|\n________5'-GCG_____C_________C_______GAACG...CAA-3'\n______________CAGUG_CA__GCAAU_GCCCAAU\n______________\|\|\|\|\|_\|\|__\|\|\|\|\|_\|\|\|\|\|\|:\n______________GUCAC_GU__CGUUA_CGGGUUG\n3'-UUU...UUUUA_____C__UA_____C_______UCUUU...UUG-5'\n_____________\|_______________________\|\n_____________59______________________35\n	18 -- 24	36 -- 42	-24.2706 kcal/mol	1.86377 kcal/mol	10.2972 kcal/mol	3 25@LB@ \| \|@LB@ 5'-GCG C C GAACG...CAA-3'@LB@ CAGUG CA GCAAU GCCCAAU@LB@ \|\|\|\|\| \|\| \|\|\|\|\| \|\|\|\|\|\|:@LB@ GUCAC GU CGUUA CGGGUUG@LB@3'-UUU...UUUUA C UA C UCUUU...UUG-5'@LB@ \| \|@LB@ 59 35@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -24.2706 kcal/mol@LB@Unfolding Energy - mRNA 1.86377 kcal/mol@LB@Unfolding Energy - sRNA 10.2972 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 36 -- 58@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 36 -- 42@LB@
41	0.002667	0.2088	b2475	ypfJ	-12.17	0.040379	232 -- 266	38 -- 70	putative neutral zinc metallopeptidase		_____________231___________________________________267\n_____________\|_____________________________________\|\n5'-GUC...UGACA_______________GC____CA__UCU_________UCUAU...GCG-3'\n______________AUGUU_GAAGA_CAG__GCAA__GC___GGUGGUCCA\n______________\|\|\|\|\|_\|\|\|:\|_\|\|\|__\|\|\|\|__\|\|___::\|\|\|:\|\|\|\n______________UACAA_CUUUU_GUC__CGUU__CG___UUACCGGGU\n3'-UUU...AAAUA_____C_____A___AC____A_______________UGUCU...UUG-5'\n_____________\|_____________________________________\|\n_____________71____________________________________37\n	260 -- 266	38 -- 44	-27.4905 kcal/mol	8.02084 kcal/mol	7.29667 kcal/mol	231 267@LB@ \| \|@LB@5'-GUC...UGACA GC CA UCU UCUAU...GCG-3'@LB@ AUGUU GAAGA CAG GCAA GC GGUGGUCCA@LB@ \|\|\|\|\| \|\|\|:\| \|\|\| \|\|\|\| \|\| ::\|\|\|:\|\|\|@LB@ UACAA CUUUU GUC CGUU CG UUACCGGGU@LB@3'-UUU...AAAUA C A AC A UGUCU...UUG-5'@LB@ \| \|@LB@ 71 37@LB@@LB@@LB@Energy -12.17 kcal/mol@LB@Hybridization Energy -27.4905 kcal/mol@LB@Unfolding Energy - mRNA 8.02084 kcal/mol@LB@Unfolding Energy - sRNA 7.29667 kcal/mol@LB@@LB@Position - mRNA 232 -- 266@LB@Position - sRNA 38 -- 70@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 38 -- 44@LB@
43	0.002722	0.2088	b0192	nlpE	-8.83	0.206883	4 -- 33	38 -- 65	lipoprotein involved with copper homeostasis and adhesion		_____________3_______________________________34\n_____________\|_______________________________\|\n________5'-UCA____CUGAACC_____A____CUC_______GCUGG...CGC-3'\n______________GGAA________GCGA_GCAG___UGGCCCG\n______________\|\|\|\|________\|\|:\|_\|\|\|:___\|\|\|\|\|\|:\n______________CCUU________CGUU_CGUU___ACCGGGU\n3'-UUU...UACAA____UUAGUCAC____A______________UGUCU...UUG-5'\n_____________\|_______________________________\|\n_____________66______________________________37\n	27 -- 33	38 -- 44	-23.0011 kcal/mol	7.49976 kcal/mol	6.67322 kcal/mol	3 34@LB@ \| \|@LB@ 5'-UCA CUGAACC A CUC GCUGG...CGC-3'@LB@ GGAA GCGA GCAG UGGCCCG@LB@ \|\|\|\| \|\|:\| \|\|\|: \|\|\|\|\|\|:@LB@ CCUU CGUU CGUU ACCGGGU@LB@3'-UUU...UACAA UUAGUCAC A UGUCU...UUG-5'@LB@ \| \|@LB@ 66 37@LB@@LB@@LB@Energy -8.83 kcal/mol@LB@Hybridization Energy -23.0011 kcal/mol@LB@Unfolding Energy - mRNA 7.49976 kcal/mol@LB@Unfolding Energy - sRNA 6.67322 kcal/mol@LB@@LB@Position - mRNA 4 -- 33@LB@Position - sRNA 38 -- 65@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 38 -- 44@LB@
90	0.007755	0.2889	b1852	zwf	-12.23	0.039232	191 -- 223	38 -- 65	glucose-6-phosphate 1-dehydrogenase		_____________190_______________________________224\n_____________\|_________________________________\|\n5'-UCA...CUUAA_______G_CA_______AAC____ACA_____GGCCU...UGG-3'\n______________GGAGAAU_A__UGGCGGU___GCAA___GCCCA\n______________\|\|\|:\|\|\|_\|__\|\|\|\|::\|___\|\|\|\|___\|\|\|\|\|\n______________CCUUUUA_U__ACCGUUA___CGUU___CGGGU\n3'-UUU...UACAA_______G_C_______________AC______UGUCU...UUG-5'\n_____________\|_________________________________\|\n_____________66________________________________37\n	202 -- 208	49 -- 55	-27.1425 kcal/mol	8.24293 kcal/mol	6.67322 kcal/mol	190 224@LB@ \| \|@LB@5'-UCA...CUUAA G CA AAC ACA GGCCU...UGG-3'@LB@ GGAGAAU A UGGCGGU GCAA GCCCA@LB@ \|\|\|:\|\|\| \| \|\|\|\|::\| \|\|\|\| \|\|\|\|\|@LB@ CCUUUUA U ACCGUUA CGUU CGGGU@LB@3'-UUU...UACAA G C AC UGUCU...UUG-5'@LB@ \| \|@LB@ 66 37@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -27.1425 kcal/mol@LB@Unfolding Energy - mRNA 8.24293 kcal/mol@LB@Unfolding Energy - sRNA 6.67322 kcal/mol@LB@@LB@Position - mRNA 191 -- 223@LB@Position - sRNA 38 -- 65@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 49 -- 55@LB@
113	0.01136	0.3326	b3417	malP	-12.46	0.034450	250 -- 272	38 -- 60	maltodextrin phosphorylase		_____________249_____________________273\n_____________\|_______________________\|\n5'-ACA...UUCAC___________C__U________AAUUC...GCC-3'\n______________GUCAGUGGCAG_GU_AUGGCUUA\n______________:\|\|\|\|\|\|\|\|\|:_\|:_\|\|\|\|\|::\|\n______________UAGUCACCGUU_CG_UACCGGGU\n3'-UUU...CCUUU___________A__U________UGUCU...UUG-5'\n_____________\|_______________________\|\n_____________61______________________37\n	266 -- 272	38 -- 44	-30.8718 kcal/mol	11.793 kcal/mol	6.61394 kcal/mol	249 273@LB@ \| \|@LB@5'-ACA...UUCAC C U AAUUC...GCC-3'@LB@ GUCAGUGGCAG GU AUGGCUUA@LB@ :\|\|\|\|\|\|\|\|\|: \|: \|\|\|\|\|::\|@LB@ UAGUCACCGUU CG UACCGGGU@LB@3'-UUU...CCUUU A U UGUCU...UUG-5'@LB@ \| \|@LB@ 61 37@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -30.8718 kcal/mol@LB@Unfolding Energy - mRNA 11.793 kcal/mol@LB@Unfolding Energy - sRNA 6.61394 kcal/mol@LB@@LB@Position - mRNA 250 -- 272@LB@Position - sRNA 38 -- 60@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 38 -- 44@LB@
133	0.01445	0.3654	b1260	trpA	-8.36	0.252100	71 -- 77	38 -- 44	tryptophan synthase alpha subunit		_____________70______78\n_____________\|_______\|\n5'-GCC...CGCCC_______UGCGU...CAU-3'\n______________UGGCCCA\n______________\|\|\|\|\|\|\|\n______________ACCGGGU\n3'-UUU...ACGUU_______UGUCU...UUG-5'\n_____________\|_______\|\n_____________45______37\n	71 -- 77	38 -- 44	-13.3519 kcal/mol	1.05946 kcal/mol	3.93445 kcal/mol	70 78@LB@ \| \|@LB@5'-GCC...CGCCC UGCGU...CAU-3'@LB@ UGGCCCA@LB@ \|\|\|\|\|\|\|@LB@ ACCGGGU@LB@3'-UUU...ACGUU UGUCU...UUG-5'@LB@ \| \|@LB@ 45 37@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -13.3519 kcal/mol@LB@Unfolding Energy - mRNA 1.05946 kcal/mol@LB@Unfolding Energy - sRNA 3.93445 kcal/mol@LB@@LB@Position - mRNA 71 -- 77@LB@Position - sRNA 38 -- 44@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 38 -- 44@LB@
136	0.01532	0.3774	b3054	ygiF	-8.05	0.285135	192 -- 208	38 -- 53	inorganic triphosphatase		_____________191_______________209\n_____________\|_________________\|\n5'-GGC...GAUAA____AG__C________GGAAA...CCG-3'\n______________GUAA__GC_AUGGCUCA\n______________\|:\|\|__\|\|_\|\|\|\|\|:\|\|\n______________CGUU__CG_UACCGGGU\n3'-UUU...GUCAC____A___U________UGUCU...UUG-5'\n_____________\|_________________\|\n_____________54________________37\n	202 -- 208	38 -- 44	-16.8567 kcal/mol	4.04422 kcal/mol	4.7597 kcal/mol	191 209@LB@ \| \|@LB@5'-GGC...GAUAA AG C GGAAA...CCG-3'@LB@ GUAA GC AUGGCUCA@LB@ \|:\|\| \|\| \|\|\|\|\|:\|\|@LB@ CGUU CG UACCGGGU@LB@3'-UUU...GUCAC A U UGUCU...UUG-5'@LB@ \| \|@LB@ 54 37@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -16.8567 kcal/mol@LB@Unfolding Energy - mRNA 4.04422 kcal/mol@LB@Unfolding Energy - sRNA 4.7597 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 38 -- 53@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 38 -- 44@LB@
141	0.01633	0.3828	b2842	kduD	-11.01	0.074109	260 -- 295	38 -- 66	2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase; KDG oxidoreductase; 20-ketosteroid reductase	b4266 b2774	_____________259__________________________________296\n_____________\|____________________________________\|\n5'-CCG...GAUAC____CU_______GGGA_____U__G__C____G__AGCGG-3'\n______________UGGA__GGGUCAG____UGGCG_UG_GG_UGGC_CA\n______________\|\|\|\|__:::\|\|\|\|____\|\|\|\|:_\|\|_::_\|\|\|\|_\|\|\n______________ACCU__UUUAGUC____ACCGU_AC_UU_ACCG_GU\n3'-UUU...AUACA______________________U__G_______G__UGUCU...UUG-5'\n_____________\|____________________________________\|\n_____________67___________________________________37\n	266 -- 272	56 -- 62	-28.5955 kcal/mol	10.9072 kcal/mol	6.67608 kcal/mol	259 296@LB@ \| \|@LB@5'-CCG...GAUAC CU GGGA U G C G AGCGG-3'@LB@ UGGA GGGUCAG UGGCG UG GG UGGC CA@LB@ \|\|\|\| :::\|\|\|\| \|\|\|\|: \|\| :: \|\|\|\| \|\|@LB@ ACCU UUUAGUC ACCGU AC UU ACCG GU@LB@3'-UUU...AUACA U G G UGUCU...UUG-5'@LB@ \| \|@LB@ 67 37@LB@@LB@@LB@Energy -11.01 kcal/mol@LB@Hybridization Energy -28.5955 kcal/mol@LB@Unfolding Energy - mRNA 10.9072 kcal/mol@LB@Unfolding Energy - sRNA 6.67608 kcal/mol@LB@@LB@Position - mRNA 260 -- 295@LB@Position - sRNA 38 -- 66@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 56 -- 62@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)

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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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