Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
12	0.0004488	0.1198	b3133	agaV	-20.63	0.001136	94 -- 118	64 -- 86	N-acetylgalactosamine-specific enzyme IIB component of PTS	_____________93________________________119\n_____________\|_________________________\|\n5'-UCA...GGCGA_____A__________C_____C__AUUAU...UAG-3'\n______________GCUGC_GCCAACGCCA_GGGAA_UC\n______________:\|\|\|\|_\|\|\|\|\|\|:\|\|\|_\|\|\|\|\|_\|\|\n______________UGACG_CGGUUGUGGU_CCCUU_AG\n3'-UUU...GCUUA______________________U__AACCG...GUG-5'\n_____________\|_________________________\|\n_____________87________________________63\n	103 -- 109	72 -- 78	-36.2121 kcal/mol	8.19626 kcal/mol	7.38435 kcal/mol	93 119@LB@ \| \|@LB@5'-UCA...GGCGA A C C AUUAU...UAG-3'@LB@ GCUGC GCCAACGCCA GGGAA UC@LB@ :\|\|\|\| \|\|\|\|\|\|:\|\|\| \|\|\|\|\| \|\|@LB@ UGACG CGGUUGUGGU CCCUU AG@LB@3'-UUU...GCUUA U AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -20.63 kcal/mol@LB@Hybridization Energy -36.2121 kcal/mol@LB@Unfolding Energy - mRNA 8.19626 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 94 -- 118@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 72 -- 78@LB@
129	0.007194	0.1964	b3401	hslO	-8.25	0.287762	98 -- 107	1 -- 10	heat shock protein Hsp33	_____________97_________108\n_____________\|__________\|\n5'-GCC...UUAAC__U_______CCGGA...AGA-3'\n______________CA_GCCGCAC\n______________\|\|_\|\|\|\|\|\|\|\n______________GU_CGGCGUG\n3'-UUU...AAAAA__C_______-5'\n_____________\|_________\|\n_____________11________1\n	101 -- 107	1 -- 7	-14.7655 kcal/mol	1.13179 kcal/mol	5.44172 kcal/mol	97 108@LB@ \| \|@LB@5'-GCC...UUAAC U CCGGA...AGA-3'@LB@ CA GCCGCAC@LB@ \|\| \|\|\|\|\|\|\|@LB@ GU CGGCGUG@LB@3'-UUU...AAAAA C -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -14.7655 kcal/mol@LB@Unfolding Energy - mRNA 1.13179 kcal/mol@LB@Unfolding Energy - sRNA 5.44172 kcal/mol@LB@@LB@Position - mRNA 98 -- 107@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 1 -- 7@LB@
39	0.002105	0.1727	b3249	mreD	-13.67	0.026871	102 -- 115	74 -- 87	cell wall structural complex MreBCD transmembrane component MreD	_____________101____________116\n_____________\|______________\|\n5'-CCU...GCGCC______________AGCCU...UUU-3'\n______________UGCUGCGCCGACAC\n______________\|:\|\|\|\|\|\|\|:\|\|\|\|\n______________AUGACGCGGUUGUG\n3'-UUU...CGCUU______________GUCCC...GUG-5'\n_____________\|______________\|\n_____________88_____________73\n	109 -- 115	74 -- 80	-25.8251 kcal/mol	5.39353 kcal/mol	6.75739 kcal/mol	101 116@LB@ \| \|@LB@5'-CCU...GCGCC AGCCU...UUU-3'@LB@ UGCUGCGCCGACAC@LB@ \|:\|\|\|\|\|\|\|:\|\|\|\|@LB@ AUGACGCGGUUGUG@LB@3'-UUU...CGCUU GUCCC...GUG-5'@LB@ \| \|@LB@ 88 73@LB@@LB@@LB@Energy -13.67 kcal/mol@LB@Hybridization Energy -25.8251 kcal/mol@LB@Unfolding Energy - mRNA 5.39353 kcal/mol@LB@Unfolding Energy - sRNA 6.75739 kcal/mol@LB@@LB@Position - mRNA 102 -- 115@LB@Position - sRNA 74 -- 87@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 74 -- 80@LB@
103	0.005609	0.1855	b2912	fau	-11.92	0.059425	103 -- 124	64 -- 85	5-formyltetrahydrofolate cyclo-ligase family protein	_____________102____________________125\n_____________\|______________________\|\n5'-GAA...ACAGC_____G_______UC_______CCCUU...UGG-3'\n______________CUGCG_CGGCAUC__GGAGAUU\n______________\|\|\|\|\|_\|::\|\|:\|__\|\|\|:\|\|:\n______________GACGC_GUUGUGG__CCUUUAG\n3'-UUU...CUUAU_____G_______UC_______AACCG...GUG-5'\n_____________\|______________________\|\n_____________86_____________________63\n	118 -- 124	64 -- 70	-27.7471 kcal/mol	8.44142 kcal/mol	7.38387 kcal/mol	102 125@LB@ \| \|@LB@5'-GAA...ACAGC G UC CCCUU...UGG-3'@LB@ CUGCG CGGCAUC GGAGAUU@LB@ \|\|\|\|\| \|::\|\|:\| \|\|\|:\|\|:@LB@ GACGC GUUGUGG CCUUUAG@LB@3'-UUU...CUUAU G UC AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -27.7471 kcal/mol@LB@Unfolding Energy - mRNA 8.44142 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 103 -- 124@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 64 -- 70@LB@
157	0.009216	0.2062	b3361	fic	-9.77	0.153316	103 -- 112	5 -- 14	stationary phase-induced protein putative toxin	_____________102________113\n_____________\|__________\|\n5'-CGC...CGUAA__________AGUCG...AAC-3'\n______________UUUUCAGGCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________AAAAGUCCGG\n3'-UUU...UGACA__________CGUG-5'\n_____________\|__________\|\n_____________15_________4\n	106 -- 112	5 -- 11	-15.6889 kcal/mol	1.64573 kcal/mol	4.24834 kcal/mol	102 113@LB@ \| \|@LB@5'-CGC...CGUAA AGUCG...AAC-3'@LB@ UUUUCAGGCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ AAAAGUCCGG@LB@3'-UUU...UGACA CGUG-5'@LB@ \| \|@LB@ 15 4@LB@@LB@@LB@Energy -9.77 kcal/mol@LB@Hybridization Energy -15.6889 kcal/mol@LB@Unfolding Energy - mRNA 1.64573 kcal/mol@LB@Unfolding Energy - sRNA 4.24834 kcal/mol@LB@@LB@Position - mRNA 103 -- 112@LB@Position - sRNA 5 -- 14@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 5 -- 11@LB@
114	0.006011	0.1855	b0422	xseB	-10.73	0.101337	104 -- 119	73 -- 87	exonuclease VII small subunit	_____________103______________120\n_____________\|________________\|\n5'-CAA...CGCUU________A__U____UUACC...AAG-3'\n______________UGCUGUGC_CA_CACC\n______________\|:\|\|\|:\|\|_\|\|_\|\|\|\|\n______________AUGACGCG_GU_GUGG\n3'-UUU...CGCUU___________U____UCCCU...GUG-5'\n_____________\|________________\|\n_____________88_______________72\n	105 -- 111	80 -- 86	-20.3088 kcal/mol	2.628 kcal/mol	6.95602 kcal/mol	103 120@LB@ \| \|@LB@5'-CAA...CGCUU A U UUACC...AAG-3'@LB@ UGCUGUGC CA CACC@LB@ \|:\|\|\|:\|\| \|\| \|\|\|\|@LB@ AUGACGCG GU GUGG@LB@3'-UUU...CGCUU U UCCCU...GUG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -10.73 kcal/mol@LB@Hybridization Energy -20.3088 kcal/mol@LB@Unfolding Energy - mRNA 2.628 kcal/mol@LB@Unfolding Energy - sRNA 6.95602 kcal/mol@LB@@LB@Position - mRNA 104 -- 119@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 80 -- 86@LB@
110	0.005921	0.1855	b0156	erpA	-16.74	0.006653	106 -- 166	29 -- 94	iron-sulfur cluster insertion protein	_____________105______________________________________________________________________167\n_____________\|________________________________________________________________________\|\n5'-UAG...AGCCA___A______U__AA_GA__________UAUU____AA_______________________________G__UUUGC...UAC-3'\n______________GCG_GAAUAC_UG__C__AAUACCAGGG____AGAU__UGGC_________GAUUAUUAU__UGGGUUA_AA\n______________\|\|\|_\|\|\|\|\|\|_\|\|__\|__\|\|:\|\|\|\|\|\|\|____\|:\|\|__\|\|\|\|_________:\|\|\|\|\|\|\|\|__\|\|:\|\|\|\|_\|\|\n______________CGC_CUUAUG_AC__G__UUGUGGUCCC____UUUA__ACCG_________UUAAUAAUA__ACUCAAU_UU\n3'-UUU...CCCCA___G_________GC_G___________________GA____ACGCGGCAU_________CU_______G__CCCGU...GUG-5'\n_____________\|________________________________________________________________________\|\n_____________95_______________________________________________________________________28\n	157 -- 163	32 -- 38	-45.8064 kcal/mol	11.5894 kcal/mol	17.4809 kcal/mol	105 167@LB@ \| \|@LB@5'-UAG...AGCCA A U AA GA UAUU AA G UUUGC...UAC-3'@LB@ GCG GAAUAC UG C AAUACCAGGG AGAU UGGC GAUUAUUAU UGGGUUA AA@LB@ \|\|\| \|\|\|\|\|\| \|\| \| \|\|:\|\|\|\|\|\|\| \|:\|\| \|\|\|\| :\|\|\|\|\|\|\|\| \|\|:\|\|\|\| \|\|@LB@ CGC CUUAUG AC G UUGUGGUCCC UUUA ACCG UUAAUAAUA ACUCAAU UU@LB@3'-UUU...CCCCA G GC G GA ACGCGGCAU CU G CCCGU...GUG-5'@LB@ \| \|@LB@ 95 28@LB@@LB@@LB@Energy -16.74 kcal/mol@LB@Hybridization Energy -45.8064 kcal/mol@LB@Unfolding Energy - mRNA 11.5894 kcal/mol@LB@Unfolding Energy - sRNA 17.4809 kcal/mol@LB@@LB@Position - mRNA 106 -- 166@LB@Position - sRNA 29 -- 94@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 32 -- 38@LB@
136	0.007706	0.1993	b2188	yejM	-8.60	0.250530	107 -- 119	70 -- 83	essential inner membrane DUF3413 domain-containing protein; lipid A production and membrane permeability factor	_____________106____________120\n_____________\|______________\|\n5'-CGC...CCCCG______________CAAUU...UUG-3'\n______________GC_CCAACGCCAGG\n______________\|\|_\|\|\|\|\|:\|\|\|\|\|\n______________CG_GGUUGUGGUCC\n3'-UUU...UAUGA__C___________CUUUA...GUG-5'\n_____________\|______________\|\n_____________84_____________69\n	113 -- 119	70 -- 76	-22.9581 kcal/mol	7.21499 kcal/mol	7.14463 kcal/mol	106 120@LB@ \| \|@LB@5'-CGC...CCCCG CAAUU...UUG-3'@LB@ GC CCAACGCCAGG@LB@ \|\| \|\|\|\|\|:\|\|\|\|\|@LB@ CG GGUUGUGGUCC@LB@3'-UUU...UAUGA C CUUUA...GUG-5'@LB@ \| \|@LB@ 84 69@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -22.9581 kcal/mol@LB@Unfolding Energy - mRNA 7.21499 kcal/mol@LB@Unfolding Energy - sRNA 7.14463 kcal/mol@LB@@LB@Position - mRNA 107 -- 119@LB@Position - sRNA 70 -- 83@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 70 -- 76@LB@
53	0.002649	0.1727	b2289	lrhA	-9.83	0.149509	112 -- 119	68 -- 75	transcriptional repressor of flagellar motility and chemotaxis genes	_____________111______120\n_____________\|________\|\n5'-CUG...AAACU________GGCAC...CCG-3'\n______________GCCAGGGA\n______________:\|\|\|\|\|\|\|\n______________UGGUCCCU\n3'-UUU...GGUUG________UUAGA...GUG-5'\n_____________\|________\|\n_____________76_______67\n	113 -- 119	68 -- 74	-14.981 kcal/mol	1.464 kcal/mol	3.68273 kcal/mol	111 120@LB@ \| \|@LB@5'-CUG...AAACU GGCAC...CCG-3'@LB@ GCCAGGGA@LB@ :\|\|\|\|\|\|\|@LB@ UGGUCCCU@LB@3'-UUU...GGUUG UUAGA...GUG-5'@LB@ \| \|@LB@ 76 67@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -14.981 kcal/mol@LB@Unfolding Energy - mRNA 1.464 kcal/mol@LB@Unfolding Energy - sRNA 3.68273 kcal/mol@LB@@LB@Position - mRNA 112 -- 119@LB@Position - sRNA 68 -- 75@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 68 -- 74@LB@
60	0.003031	0.1727	b3432	glgB	-10.57	0.108575	114 -- 123	51 -- 60	1 4-alpha-glucan branching enzyme	_____________113________124\n_____________\|__________\|\n5'-CAU...AGAGU__________UCAGG...GAC-3'\n______________GCUGCGCCGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGACGCGGCA\n3'-UUU...AGAAC__________UUUAA...GUG-5'\n_____________\|__________\|\n_____________61_________50\n	117 -- 123	51 -- 57	-20.705 kcal/mol	5.26394 kcal/mol	4.87294 kcal/mol	113 124@LB@ \| \|@LB@5'-CAU...AGAGU UCAGG...GAC-3'@LB@ GCUGCGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGACGCGGCA@LB@3'-UUU...AGAAC UUUAA...GUG-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -20.705 kcal/mol@LB@Unfolding Energy - mRNA 5.26394 kcal/mol@LB@Unfolding Energy - sRNA 4.87294 kcal/mol@LB@@LB@Position - mRNA 114 -- 123@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 51 -- 57@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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