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@
24	0.001457	0.1727	b0424	yajL	-16.26	0.008266	79 -- 97	64 -- 86	oxidative-stress-resistance chaperone	_____________78______________________98\n_____________\|_______________________\|\n5'-AGA...CGCGC_______________________GACUA...CCA-3'\n______________GCUGCGCCA_CACU___GAAAUC\n______________:\|\|\|\|\|\|\|\|_\|\|\|:___\|\|\|\|\|\|\n______________UGACGCGGU_GUGG___CUUUAG\n3'-UUU...GCUUA_________U____UCC______AACCG...GUG-5'\n_____________\|_______________________\|\n_____________87______________________63\n	81 -- 87	78 -- 84	-26.9283 kcal/mol	3.28429 kcal/mol	7.38435 kcal/mol	78 98@LB@ \| \|@LB@5'-AGA...CGCGC GACUA...CCA-3'@LB@ GCUGCGCCA CACU GAAAUC@LB@ :\|\|\|\|\|\|\|\| \|\|\|: \|\|\|\|\|\|@LB@ UGACGCGGU GUGG CUUUAG@LB@3'-UUU...GCUUA U UCC AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -16.26 kcal/mol@LB@Hybridization Energy -26.9283 kcal/mol@LB@Unfolding Energy - mRNA 3.28429 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 79 -- 97@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 78 -- 84@LB@
34	0.001871	0.1727	b4485	ytfR	-15.36	0.012458	204 -- 227	64 -- 86	putative sugar ABC transporter ATPase	_____________203_______________________228\n_____________\|_________________________\|\n5'-CCU...CCAUG__GAC__A_________________CUCCG...GCC-3'\n______________AC___CG_CCAACACCA_GGAGAUC\n______________\|\|___\|\|_\|\|\|\|\|\|\|\|\|_\|\|\|:\|\|\|\n______________UG___GC_GGUUGUGGU_CCUUUAG\n3'-UUU...GCUUA__AC_____________C_______AACCG...GUG-5'\n_____________\|_________________________\|\n_____________87________________________63\n	221 -- 227	64 -- 70	-26.9267 kcal/mol	4.18191 kcal/mol	7.38435 kcal/mol	203 228@LB@ \| \|@LB@5'-CCU...CCAUG GAC A CUCCG...GCC-3'@LB@ AC CG CCAACACCA GGAGAUC@LB@ \|\| \|\| \|\|\|\|\|\|\|\|\| \|\|\|:\|\|\|@LB@ UG GC GGUUGUGGU CCUUUAG@LB@3'-UUU...GCUUA AC C AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -26.9267 kcal/mol@LB@Unfolding Energy - mRNA 4.18191 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 204 -- 227@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 64 -- 70@LB@
36	0.001988	0.1727	b2573	rpoE	-9.66	0.161217	247 -- 255	64 -- 72	RNA polymerase sigma E factor	_____________246_______256\n_____________\|_________\|\n5'-ACA...CCAGA_________AGAAA...UGG-3'\n______________AGGGAGAUC\n______________\|\|\|\|\|:\|\|\|\n______________UCCCUUUAG\n3'-UUU...UGUGG_________AACCG...GUG-5'\n_____________\|_________\|\n_____________73________63\n	249 -- 255	64 -- 70	-13.5601 kcal/mol	1.40253 kcal/mol	2.50058 kcal/mol	246 256@LB@ \| \|@LB@5'-ACA...CCAGA AGAAA...UGG-3'@LB@ AGGGAGAUC@LB@ \|\|\|\|\|:\|\|\|@LB@ UCCCUUUAG@LB@3'-UUU...UGUGG AACCG...GUG-5'@LB@ \| \|@LB@ 73 63@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -13.5601 kcal/mol@LB@Unfolding Energy - mRNA 1.40253 kcal/mol@LB@Unfolding Energy - sRNA 2.50058 kcal/mol@LB@@LB@Position - mRNA 247 -- 255@LB@Position - sRNA 64 -- 72@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 64 -- 70@LB@
50	0.002535	0.1727	b1879	flhA	-12.13	0.054078	218 -- 247	64 -- 89	putative flagellar export pore protein	_____________217______________________________248\n_____________\|________________________________\|\n5'-GCC...GCCGC___________U__CCGCAA___U________GACAC...CGA-3'\n______________GAUGCUGCGCC_GC______ACC___GAAAUC\n______________:\|\|:\|\|\|\|\|\|\|_:\|______\|\|\|___\|\|\|\|\|\|\n______________UUAUGACGCGG_UG______UGG___CUUUAG\n3'-UUU...CGCGC___________U___________UCC______AACCG...GUG-5'\n_____________\|________________________________\|\n_____________90_______________________________63\n	222 -- 228	79 -- 85	-26.8051 kcal/mol	6.79061 kcal/mol	7.88317 kcal/mol	217 248@LB@ \| \|@LB@5'-GCC...GCCGC U CCGCAA U GACAC...CGA-3'@LB@ GAUGCUGCGCC GC ACC GAAAUC@LB@ :\|\|:\|\|\|\|\|\|\| :\| \|\|\| \|\|\|\|\|\|@LB@ UUAUGACGCGG UG UGG CUUUAG@LB@3'-UUU...CGCGC U UCC AACCG...GUG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -26.8051 kcal/mol@LB@Unfolding Energy - mRNA 6.79061 kcal/mol@LB@Unfolding Energy - sRNA 7.88317 kcal/mol@LB@@LB@Position - mRNA 218 -- 247@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 79 -- 85@LB@
54	0.002681	0.1727	b3201	lptB	-14.37	0.019597	275 -- 293	64 -- 82	lipopolysaccharide export ABC transporter ATPase	_____________274_________________294\n_____________\|___________________\|\n5'-UUC...CUGAC_______U___________GUCGGUC-3'\n______________CGUCAAC_CCGGGGAAAUU\n______________\|\|:\|\|\|\|_\|\|:\|\|\|\|\|\|\|:\n______________GCGGUUG_GGUCCCUUUAG\n3'-UUU...AUGAC_______U___________AACCG...GUG-5'\n_____________\|___________________\|\n_____________83__________________63\n	287 -- 293	64 -- 70	-27.6824 kcal/mol	6.24463 kcal/mol	7.07066 kcal/mol	274 294@LB@ \| \|@LB@5'-UUC...CUGAC U GUCGGUC-3'@LB@ CGUCAAC CCGGGGAAAUU@LB@ \|\|:\|\|\|\| \|\|:\|\|\|\|\|\|\|:@LB@ GCGGUUG GGUCCCUUUAG@LB@3'-UUU...AUGAC U AACCG...GUG-5'@LB@ \| \|@LB@ 83 63@LB@@LB@@LB@Energy -14.37 kcal/mol@LB@Hybridization Energy -27.6824 kcal/mol@LB@Unfolding Energy - mRNA 6.24463 kcal/mol@LB@Unfolding Energy - sRNA 7.07066 kcal/mol@LB@@LB@Position - mRNA 275 -- 293@LB@Position - sRNA 64 -- 82@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 64 -- 70@LB@
75	0.003854	0.1809	b0606	ahpF	-8.17	0.297536	59 -- 82	64 -- 85	alkyl hydroperoxide reductase F52a subunit FAD/NAD(P)-binding	_____________58_______________________83\n_____________\|________________________\|\n5'-UCA...UUGCU___A___GA______UC_______CACCU...CGG-3'\n______________CUG_CGC__AAUACU__GGAAAUU\n______________\|\|\|_\|\|\|__\|\|:\|\|:__\|\|\|\|\|\|:\n______________GAC_GCG__UUGUGG__CCUUUAG\n3'-UUU...CUUAU_______G_______UC_______AACCG...GUG-5'\n_____________\|________________________\|\n_____________86_______________________63\n	76 -- 82	64 -- 70	-19.6667 kcal/mol	4.11652 kcal/mol	7.38387 kcal/mol	58 83@LB@ \| \|@LB@5'-UCA...UUGCU A GA UC CACCU...CGG-3'@LB@ CUG CGC AAUACU GGAAAUU@LB@ \|\|\| \|\|\| \|\|:\|\|: \|\|\|\|\|\|:@LB@ GAC GCG UUGUGG CCUUUAG@LB@3'-UUU...CUUAU G UC AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -19.6667 kcal/mol@LB@Unfolding Energy - mRNA 4.11652 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 59 -- 82@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 64 -- 70@LB@
84	0.004676	0.1855	b0526	cysS	-14.43	0.019007	256 -- 269	64 -- 77	cysteinyl-tRNA synthetase	_____________255____________270\n_____________\|______________\|\n5'-GCC...UAUUC______________GGCAU...ACG-3'\n______________ACGCCGGGGAAGUC\n______________\|\|:\|\|:\|\|\|\|\|:\|\|\n______________UGUGGUCCCUUUAG\n3'-UUU...GCGGU______________AACCG...GUG-5'\n_____________\|______________\|\n_____________78_____________63\n	263 -- 269	64 -- 70	-23.2043 kcal/mol	4.03864 kcal/mol	4.72709 kcal/mol	255 270@LB@ \| \|@LB@5'-GCC...UAUUC GGCAU...ACG-3'@LB@ ACGCCGGGGAAGUC@LB@ \|\|:\|\|:\|\|\|\|\|:\|\|@LB@ UGUGGUCCCUUUAG@LB@3'-UUU...GCGGU AACCG...GUG-5'@LB@ \| \|@LB@ 78 63@LB@@LB@@LB@Energy -14.43 kcal/mol@LB@Hybridization Energy -23.2043 kcal/mol@LB@Unfolding Energy - mRNA 4.03864 kcal/mol@LB@Unfolding Energy - sRNA 4.72709 kcal/mol@LB@@LB@Position - mRNA 256 -- 269@LB@Position - sRNA 64 -- 77@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 64 -- 70@LB@
85	0.004761	0.1855	b2077	iceT	-11.46	0.073016	53 -- 74	64 -- 86	putative citrate/iron-citrate/zinc-citrate efflux transporter	_____________52______________________75\n_____________\|_______________________\|\n5'-CGG...UCGGA______G_______CU_______ACCAU...UUC-3'\n______________GCUGCG_CAAC_CC__GGGGAUC\n______________:\|\|\|\|\|_\|\|\|\|_\|\|__\|\|::\|\|\|\n______________UGACGC_GUUG_GG__CCUUUAG\n3'-UUU...GCUUA______G____U__UC_______AACCG...GUG-5'\n_____________\|_______________________\|\n_____________87______________________63\n	68 -- 74	64 -- 70	-29.0378 kcal/mol	10.1908 kcal/mol	7.38435 kcal/mol	52 75@LB@ \| \|@LB@5'-CGG...UCGGA G CU ACCAU...UUC-3'@LB@ GCUGCG CAAC CC GGGGAUC@LB@ :\|\|\|\|\| \|\|\|\| \|\| \|\|::\|\|\|@LB@ UGACGC GUUG GG CCUUUAG@LB@3'-UUU...GCUUA G U UC AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -11.46 kcal/mol@LB@Hybridization Energy -29.0378 kcal/mol@LB@Unfolding Energy - mRNA 10.1908 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 53 -- 74@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 64 -- 70@LB@
102	0.005508	0.1855	b0659	ybeY	-7.73	0.351978	30 -- 54	64 -- 89	ssRNA-specific endoribonuclease; 16S rRNA 3' end maturation and quality control co-endoribonuclease working with RNase R; rRNA transcription antitermination factor	_____________29_________________________55\n_____________\|__________________________\|\n5'-ACU...AUCGA__________________AA______AGCUU...CGC-3'\n______________AGUGCUG_GCCGAUGUCG__GAGAUC\n______________\|:\|:\|\|\|_\|\|\|:\|:::\|:__\|\|:\|\|\|\n______________UUAUGAC_CGGUUGUGGU__CUUUAG\n3'-UUU...CGCGC_______G__________CC______AACCG...GUG-5'\n_____________\|__________________________\|\n_____________90_________________________63\n	30 -- 36	83 -- 89	-23.8058 kcal/mol	8.19456 kcal/mol	7.88317 kcal/mol	29 55@LB@ \| \|@LB@5'-ACU...AUCGA AA AGCUU...CGC-3'@LB@ AGUGCUG GCCGAUGUCG GAGAUC@LB@ \|:\|:\|\|\| \|\|\|:\|:::\|: \|\|:\|\|\|@LB@ UUAUGAC CGGUUGUGGU CUUUAG@LB@3'-UUU...CGCGC G CC AACCG...GUG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -7.73 kcal/mol@LB@Hybridization Energy -23.8058 kcal/mol@LB@Unfolding Energy - mRNA 8.19456 kcal/mol@LB@Unfolding Energy - sRNA 7.88317 kcal/mol@LB@@LB@Position - mRNA 30 -- 54@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 83 -- 89@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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