Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
165	0.0337	0.6177	b3983	rplK	-8.80	0.071896	189 -- 197	41 -- 49	50S ribosomal subunit protein L11	_____________188_______198\n_____________\|_________\|\n5'-ACC...AACUU_________AUAAU...UAA-3'\n______________GAGGAAUUU\n______________\|\|\|\|\|\|\|\|\|\n______________CUCCUUAAA\n3'-UUU...AGUUU_________GUAAA...ACA-5'\n_____________\|_________\|\n_____________50________40\n	191 -- 197	41 -- 47	-11.4231 kcal/mol	1.76644 kcal/mol	0.852225 kcal/mol	188 198@LB@ \| \|@LB@5'-ACC...AACUU AUAAU...UAA-3'@LB@ GAGGAAUUU@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUCCUUAAA@LB@3'-UUU...AGUUU GUAAA...ACA-5'@LB@ \| \|@LB@ 50 40@LB@@LB@@LB@Energy -8.80 kcal/mol@LB@Hybridization Energy -11.4231 kcal/mol@LB@Unfolding Energy - mRNA 1.76644 kcal/mol@LB@Unfolding Energy - sRNA 0.852225 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 41 -- 49@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 41 -- 47@LB@
171	0.0346	0.6177	b1865	nudB	-7.50	0.130652	189 -- 196	46 -- 53	dihydroneopterin triphosphate pyrophosphatase	_____________188______197\n_____________\|________\|\n5'-UGA...GUCAA________CAGCG...CCG-3'\n______________CGAAGAGG\n______________\|:\|\|\|\|\|\|\n______________GUUUCUCC\n3'-UUU...GGGCA________UUAAA...ACA-5'\n_____________\|________\|\n_____________54_______45\n	190 -- 196	46 -- 52	-10.7995 kcal/mol	2.39118 kcal/mol	0.910679 kcal/mol	188 197@LB@ \| \|@LB@5'-UGA...GUCAA CAGCG...CCG-3'@LB@ CGAAGAGG@LB@ \|:\|\|\|\|\|\|@LB@ GUUUCUCC@LB@3'-UUU...GGGCA UUAAA...ACA-5'@LB@ \| \|@LB@ 54 45@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -10.7995 kcal/mol@LB@Unfolding Energy - mRNA 2.39118 kcal/mol@LB@Unfolding Energy - sRNA 0.910679 kcal/mol@LB@@LB@Position - mRNA 189 -- 196@LB@Position - sRNA 46 -- 53@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 46 -- 52@LB@
180	0.03697	0.6177	b1325	ycjG	-6.24	0.226397	189 -- 195	47 -- 53	L-Ala-D/L-Glu epimerase	_____________188_____196\n_____________\|_______\|\n5'-AAG...GACAA_______UAAAG...AAC-3'\n______________CAAGGAG\n______________\|\|\|:\|\|\|\n______________GUUUCUC\n3'-UUU...GGGCA_______CUUAA...ACA-5'\n_____________\|_______\|\n_____________54______46\n	189 -- 195	47 -- 53	-8.11062 kcal/mol	0.981925 kcal/mol	0.886139 kcal/mol	188 196@LB@ \| \|@LB@5'-AAG...GACAA UAAAG...AAC-3'@LB@ CAAGGAG@LB@ \|\|\|:\|\|\|@LB@ GUUUCUC@LB@3'-UUU...GGGCA CUUAA...ACA-5'@LB@ \| \|@LB@ 54 46@LB@@LB@@LB@Energy -6.24 kcal/mol@LB@Hybridization Energy -8.11062 kcal/mol@LB@Unfolding Energy - mRNA 0.981925 kcal/mol@LB@Unfolding Energy - sRNA 0.886139 kcal/mol@LB@@LB@Position - mRNA 189 -- 195@LB@Position - sRNA 47 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 47 -- 53@LB@
187	0.03882	0.6177	b0403	malZ	-7.79	0.114240	189 -- 197	42 -- 50	maltodextrin glucosidase	_____________188_______198\n_____________\|_________\|\n5'-UUU...AUCAC_________AUGAU...AGC-3'\n______________AGGGGAAUU\n______________\|\|:\|\|\|\|\|\|\n______________UCUCCUUAA\n3'-UUU...CAGUU_________AGUAA...ACA-5'\n_____________\|_________\|\n_____________51________41\n	191 -- 197	42 -- 48	-10.7884 kcal/mol	2.13721 kcal/mol	0.856185 kcal/mol	188 198@LB@ \| \|@LB@5'-UUU...AUCAC AUGAU...AGC-3'@LB@ AGGGGAAUU@LB@ \|\|:\|\|\|\|\|\|@LB@ UCUCCUUAA@LB@3'-UUU...CAGUU AGUAA...ACA-5'@LB@ \| \|@LB@ 51 41@LB@@LB@@LB@Energy -7.79 kcal/mol@LB@Hybridization Energy -10.7884 kcal/mol@LB@Unfolding Energy - mRNA 2.13721 kcal/mol@LB@Unfolding Energy - sRNA 0.856185 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 42 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 42 -- 48@LB@
195	0.04073	0.6177	b3166	truB	-9.24	0.058593	189 -- 197	45 -- 53	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase	_____________188_______198\n_____________\|_________\|\n5'-GGC...GACAG_________CUAAU...AAC-3'\n______________CAAGGAGGA\n______________\|\|\|:\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	191 -- 197	45 -- 51	-13.1895 kcal/mol	3.02734 kcal/mol	0.917553 kcal/mol	188 198@LB@ \| \|@LB@5'-GGC...GACAG CUAAU...AAC-3'@LB@ CAAGGAGGA@LB@ \|\|\|:\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.24 kcal/mol@LB@Hybridization Energy -13.1895 kcal/mol@LB@Unfolding Energy - mRNA 3.02734 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 45 -- 51@LB@
96	0.01897	0.6177	b2422	cysA	-7.76	0.115977	190 -- 202	38 -- 50	sulfate/thiosulfate transporter subunit	_____________189___________203\n_____________\|_____________\|\n5'-GGU...CAGCA_______CA____GAGCA...UGC-3'\n______________GGAGGAA__UCAU\n______________:\|\|\|\|\|\|__\|\|\|\|\n______________UCUCCUU__AGUA\n3'-UUU...CAGUU_______AA____AAAAA...ACA-5'\n_____________\|_____________\|\n_____________51____________37\n	190 -- 196	44 -- 50	-11.8687 kcal/mol	3.04673 kcal/mol	1.0603 kcal/mol	189 203@LB@ \| \|@LB@5'-GGU...CAGCA CA GAGCA...UGC-3'@LB@ GGAGGAA UCAU@LB@ :\|\|\|\|\|\| \|\|\|\|@LB@ UCUCCUU AGUA@LB@3'-UUU...CAGUU AA AAAAA...ACA-5'@LB@ \| \|@LB@ 51 37@LB@@LB@@LB@Energy -7.76 kcal/mol@LB@Hybridization Energy -11.8687 kcal/mol@LB@Unfolding Energy - mRNA 3.04673 kcal/mol@LB@Unfolding Energy - sRNA 1.0603 kcal/mol@LB@@LB@Position - mRNA 190 -- 202@LB@Position - sRNA 38 -- 50@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
49	0.009604	0.6129	b1175	minD	-8.49	0.083180	191 -- 199	40 -- 48	inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system	_____________190_______200\n_____________\|_________\|\n5'-CUG...UAACA_________UAUGG...AAA-3'\n______________AGGAAUUUC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCUUAAAG\n3'-UUU...GUUUC_________UAAAA...ACA-5'\n_____________\|_________\|\n_____________49________39\n	193 -- 199	40 -- 46	-11.0161 kcal/mol	1.62901 kcal/mol	0.898161 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAACA UAUGG...AAA-3'@LB@ AGGAAUUUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCUUAAAG@LB@3'-UUU...GUUUC UAAAA...ACA-5'@LB@ \| \|@LB@ 49 39@LB@@LB@@LB@Energy -8.49 kcal/mol@LB@Hybridization Energy -11.0161 kcal/mol@LB@Unfolding Energy - mRNA 1.62901 kcal/mol@LB@Unfolding Energy - sRNA 0.898161 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 40 -- 48@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 40 -- 46@LB@
181	0.03769	0.6177	b0912	ihfB	-7.34	0.140491	192 -- 199	43 -- 50	integration host factor (IHF) DNA-binding protein beta subunit	_____________191______200\n_____________\|________\|\n5'-ACG...GAACC________CAUGA...UGG-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	193 -- 199	43 -- 49	-10.3812 kcal/mol	2.20002 kcal/mol	0.845564 kcal/mol	191 200@LB@ \| \|@LB@5'-ACG...GAACC CAUGA...UGG-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -7.34 kcal/mol@LB@Hybridization Energy -10.3812 kcal/mol@LB@Unfolding Energy - mRNA 2.20002 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 192 -- 199@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 43 -- 49@LB@
45	0.009176	0.6129	b3389	aroB	-8.88	0.069424	203 -- 218	37 -- 52	3-dehydroquinate synthase	_____________202______________219\n_____________\|________________\|\n5'-ACA...GUUAU________UUG_____ACUCU...CGG-3'\n______________GGAGAGGA___UCGUU\n______________::\|\|\|\|\|\|___\|\|:\|\|\n______________UUUCUCCU___AGUAA\n3'-UUU...GGCAG________UAA_____AAAAA...ACA-5'\n_____________\|________________\|\n_____________53_______________36\n	204 -- 210	45 -- 51	-14.6346 kcal/mol	4.67835 kcal/mol	1.07641 kcal/mol	202 219@LB@ \| \|@LB@5'-ACA...GUUAU UUG ACUCU...CGG-3'@LB@ GGAGAGGA UCGUU@LB@ ::\|\|\|\|\|\| \|\|:\|\|@LB@ UUUCUCCU AGUAA@LB@3'-UUU...GGCAG UAA AAAAA...ACA-5'@LB@ \| \|@LB@ 53 36@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -14.6346 kcal/mol@LB@Unfolding Energy - mRNA 4.67835 kcal/mol@LB@Unfolding Energy - sRNA 1.07641 kcal/mol@LB@@LB@Position - mRNA 203 -- 218@LB@Position - sRNA 37 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 45 -- 51@LB@
179	0.03684	0.6177	b0335	prpE	-7.81	0.113441	203 -- 221	38 -- 55	propionate--CoA ligase	_____________202_________________222\n_____________\|___________________\|\n5'-GCC...AUUAU___UUUU__C_________CAGCG...AAA-3'\n______________GUC____AG_GAAUUUUAU\n______________\|\|\|____\|\|_\|\|\|\|\|\|:\|\|\n______________CAG____UC_CUUAAAGUA\n3'-UUU...CCGGG___UUUC____________AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	215 -- 221	38 -- 44	-10.8576 kcal/mol	1.87676 kcal/mol	1.17036 kcal/mol	202 222@LB@ \| \|@LB@5'-GCC...AUUAU UUUU C CAGCG...AAA-3'@LB@ GUC AG GAAUUUUAU@LB@ \|\|\| \|\| \|\|\|\|\|\|:\|\|@LB@ CAG UC CUUAAAGUA@LB@3'-UUU...CCGGG UUUC AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -10.8576 kcal/mol@LB@Unfolding Energy - mRNA 1.87676 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@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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