Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
41	0.000458	0.03766	b3679	yidK	-16.91	0.000078	119 -- 159	1 -- 60	putative transporter	_____________118__________________________________________________________160\n_____________\|____________________________________________________________\|\n5'-UUU...UUUAA________C_____________________CCCGAC________________________AUUCA...AAG-3'\n______________GAAUCUGA_UGC______________CUGA________GCAUUUUACCUCU___CCCUAU\n______________:\|\|\|\|:\|\|_\|:\|______________\|\|\|\|________:\|\|\|:\|\|\|\|\|\|\|\|___\|\|\|\|\|:\n______________UUUAGGCU_AUG______________GACU________UGUAGAAUGGAGA___GGGAUG\n3'-AUU...GUCGG________A___CACUUCAUUUUCCA____UUCUAUCU_____________CAU______-5'\n_____________\|___________________________________________________________\|\n_____________61__________________________________________________________1\n	147 -- 153	10 -- 16	-34.139 kcal/mol	4.55251 kcal/mol	12.7042 kcal/mol	118 160@LB@ \| \|@LB@5'-UUU...UUUAA C CCCGAC AUUCA...AAG-3'@LB@ GAAUCUGA UGC CUGA GCAUUUUACCUCU CCCUAU@LB@ :\|\|\|\|:\|\| \|:\| \|\|\|\| :\|\|\|:\|\|\|\|\|\|\|\| \|\|\|\|\|:@LB@ UUUAGGCU AUG GACU UGUAGAAUGGAGA GGGAUG@LB@3'-AUU...GUCGG A CACUUCAUUUUCCA UUCUAUCU CAU -5'@LB@ \| \|@LB@ 61 1@LB@@LB@@LB@Energy -16.91 kcal/mol@LB@Hybridization Energy -34.139 kcal/mol@LB@Unfolding Energy - mRNA 4.55251 kcal/mol@LB@Unfolding Energy - sRNA 12.7042 kcal/mol@LB@@LB@Position - mRNA 119 -- 159@LB@Position - sRNA 1 -- 60@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 10 -- 16@LB@
32	0.0003261	0.03519	b2789	gudP	-8.38	0.124980	121 -- 127	1 -- 7	putative D-glucarate transporter	_____________120_____128\n_____________\|_______\|\n5'-UGA...AAAAC_______GUCAC...ACG-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	121 -- 127	1 -- 7	-11.2076 kcal/mol	0.809325 kcal/mol	2.03949 kcal/mol	120 128@LB@ \| \|@LB@5'-UGA...AAAAC GUCAC...ACG-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -11.2076 kcal/mol@LB@Unfolding Energy - mRNA 0.809325 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 121 -- 127@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 1 -- 7@LB@
75	0.001328	0.06227	b1748	astC	-8.39	0.124654	121 -- 127	1 -- 7	succinylornithine transaminase PLP-dependent	_____________120_____128\n_____________\|_______\|\n5'-UCA...CACGA_______AAUCU...UGU-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	121 -- 127	1 -- 7	-11.9071 kcal/mol	1.50434 kcal/mol	2.03949 kcal/mol	120 128@LB@ \| \|@LB@5'-UCA...CACGA AAUCU...UGU-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.39 kcal/mol@LB@Hybridization Energy -11.9071 kcal/mol@LB@Unfolding Energy - mRNA 1.50434 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 121 -- 127@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 1 -- 7@LB@
85	0.002234	0.09158	b0118	acnB	-9.43	0.065848	121 -- 128	1 -- 8	aconitate hydratase 2; aconitase B; 2-methyl-cis-aconitate hydratase	_____________120______129\n_____________\|________\|\n5'-GAG...GCAUU________AAACU...UGC-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	122 -- 128	1 -- 7	-13.4001 kcal/mol	1.87598 kcal/mol	2.11603 kcal/mol	120 129@LB@ \| \|@LB@5'-GAG...GCAUU AAACU...UGC-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.4001 kcal/mol@LB@Unfolding Energy - mRNA 1.87598 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 121 -- 128@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 1 -- 7@LB@
116	0.003844	0.1165	b1004	wrbA	-12.42	0.007537	123 -- 145	10 -- 35	NAD(P)H:quinone oxidoreductase	_____________122________________________146\n_____________\|__________________________\|\n5'-UUA...UGCAC__________________________AAAUA...AAG-3'\n______________UCUGAAA___AGGACGUCUUAUCUUU\n______________\|\|\|\|\|\|\|___\|\|:\|\|:\|\|\|\|\|:\|\|:\|\n______________AGACUUU___UCUUGUAGAAUGGAGA\n3'-AUU...UUUCC_______CUA________________CAUGG...AUG-5'\n_____________\|__________________________\|\n_____________36_________________________9\n	133 -- 139	16 -- 22	-25.4666 kcal/mol	4.32254 kcal/mol	8.70229 kcal/mol	122 146@LB@ \| \|@LB@5'-UUA...UGCAC AAAUA...AAG-3'@LB@ UCUGAAA AGGACGUCUUAUCUUU@LB@ \|\|\|\|\|\|\| \|\|:\|\|:\|\|\|\|\|:\|\|:\|@LB@ AGACUUU UCUUGUAGAAUGGAGA@LB@3'-AUU...UUUCC CUA CAUGG...AUG-5'@LB@ \| \|@LB@ 36 9@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -25.4666 kcal/mol@LB@Unfolding Energy - mRNA 4.32254 kcal/mol@LB@Unfolding Energy - sRNA 8.70229 kcal/mol@LB@@LB@Position - mRNA 123 -- 145@LB@Position - sRNA 10 -- 35@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 16 -- 22@LB@
73	0.001217	0.05856	b1702	ppsA	-8.47	0.118779	124 -- 132	50 -- 58	phosphoenolpyruvate synthase	_____________123_______133\n_____________\|_________\|\n5'-UAU...UUUUC_________AAUAU...AAA-3'\n______________AUCCGGUUA\n______________\|\|\|\|\|:\|\|\|\n______________UAGGCUAAU\n3'-AUU...CGGUU_________GCACU...AUG-5'\n_____________\|_________\|\n_____________59________49\n	126 -- 132	50 -- 56	-10.3571 kcal/mol	1.58803 kcal/mol	0.317553 kcal/mol	123 133@LB@ \| \|@LB@5'-UAU...UUUUC AAUAU...AAA-3'@LB@ AUCCGGUUA@LB@ \|\|\|\|\|:\|\|\|@LB@ UAGGCUAAU@LB@3'-AUU...CGGUU GCACU...AUG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -10.3571 kcal/mol@LB@Unfolding Energy - mRNA 1.58803 kcal/mol@LB@Unfolding Energy - sRNA 0.317553 kcal/mol@LB@@LB@Position - mRNA 124 -- 132@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 50 -- 56@LB@
28	0.0002139	0.02687	b4174	hflK	-10.82	0.025576	125 -- 140	42 -- 58	modulator for HflB protease specific for phage lambda cII repressor	_____________124_______________141\n_____________\|_________________\|\n5'-AGA...GUAGC______A__________CAUAU...GUC-3'\n______________GUCUGA__GCGUGGAGU\n______________:\|\|:\|\|__:\|\|\|\|:\|\|\|\n______________UAGGCU__UGCACUUCA\n3'-AUU...CGGUU______AA_________UUUUC...AUG-5'\n_____________\|_________________\|\n_____________59________________41\n	134 -- 140	42 -- 48	-18.0833 kcal/mol	3.99428 kcal/mol	3.27972 kcal/mol	124 141@LB@ \| \|@LB@5'-AGA...GUAGC A CAUAU...GUC-3'@LB@ GUCUGA GCGUGGAGU@LB@ :\|\|:\|\| :\|\|\|\|:\|\|\|@LB@ UAGGCU UGCACUUCA@LB@3'-AUU...CGGUU AA UUUUC...AUG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -18.0833 kcal/mol@LB@Unfolding Energy - mRNA 3.99428 kcal/mol@LB@Unfolding Energy - sRNA 3.27972 kcal/mol@LB@@LB@Position - mRNA 125 -- 140@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 42 -- 48@LB@
154	0.006224	0.1406	b0882	clpA	-11.36	0.017252	127 -- 158	2 -- 32	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity	_____________126______________________________159\n_____________\|________________________________\|\n5'-UUU...CGCGA______AU_______CAUUG__G_____G___GAAAA...CGC-3'\n______________GGGAGA__GAGCAUC_____CU_UGUAC_CUA\n______________\|::\|\|\|__\|\|:\|\|\|\|_____\|\|_\|\|\|\|\|_\|\|\|\n______________CUUUCU__CUUGUAG_____GA_ACAUG_GAU\n3'-AUU...CCAGA______AU_______AAUG___G_____G___G-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	135 -- 141	18 -- 24	-27.9684 kcal/mol	7.80814 kcal/mol	8.82442 kcal/mol	126 159@LB@ \| \|@LB@5'-UUU...CGCGA AU CAUUG G G GAAAA...CGC-3'@LB@ GGGAGA GAGCAUC CU UGUAC CUA@LB@ \|::\|\|\| \|\|:\|\|\|\| \|\| \|\|\|\|\| \|\|\|@LB@ CUUUCU CUUGUAG GA ACAUG GAU@LB@3'-AUU...CCAGA AU AAUG G G G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -27.9684 kcal/mol@LB@Unfolding Energy - mRNA 7.80814 kcal/mol@LB@Unfolding Energy - sRNA 8.82442 kcal/mol@LB@@LB@Position - mRNA 127 -- 158@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 18 -- 24@LB@
68	0.001174	0.05856	b1253	yciA	-8.30	0.130708	128 -- 145	3 -- 21	acyl-CoA esterase	_____________127__________________146\n_____________\|____________________\|\n5'-UUU...CGCUG______________UC____CAGGA...GGU-3'\n______________UAUCU__CCUCUGU__UCCU\n______________:\|\|\|\|__\|\|\|\|\|\|\|__:\|\|\|\n______________GUAGA__GGAGACA__GGGA\n3'-AUU...AUCUU_____AU_______U_____UG-5'\n_____________\|____________________\|\n_____________22___________________2\n	133 -- 139	8 -- 14	-17.321 kcal/mol	1.04882 kcal/mol	7.99052 kcal/mol	127 146@LB@ \| \|@LB@5'-UUU...CGCUG UC CAGGA...GGU-3'@LB@ UAUCU CCUCUGU UCCU@LB@ :\|\|\|\| \|\|\|\|\|\|\| :\|\|\|@LB@ GUAGA GGAGACA GGGA@LB@3'-AUU...AUCUU AU U UG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -8.30 kcal/mol@LB@Hybridization Energy -17.321 kcal/mol@LB@Unfolding Energy - mRNA 1.04882 kcal/mol@LB@Unfolding Energy - sRNA 7.99052 kcal/mol@LB@@LB@Position - mRNA 128 -- 145@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 8 -- 14@LB@
63	0.001074	0.05856	b0448	mdlA	-11.87	0.011698	129 -- 162	4 -- 28	putative multidrug ABC transporter ATPase	_____________128________________________________163\n_____________\|__________________________________\|\n5'-UGG...UUCGC_________GA__AAAUACACC______U_____AUCGA...UGG-3'\n______________GAUGGAACA__UU_________ACUUCU_UACCC\n______________\|\|\|:\|\|\|\|\|__\|\|_________\|\|:\|\|\|_\|\|\|\|\|\n______________CUAUCUUGU__AA_________UGGAGA_AUGGG\n3'-AUU...ACUUU_________AG_________________C_____AUG-5'\n_____________\|__________________________________\|\n_____________29_________________________________3\n	131 -- 137	20 -- 26	-24.4185 kcal/mol	4.52675 kcal/mol	8.04825 kcal/mol	128 163@LB@ \| \|@LB@5'-UGG...UUCGC GA AAAUACACC U AUCGA...UGG-3'@LB@ GAUGGAACA UU ACUUCU UACCC@LB@ \|\|\|:\|\|\|\|\| \|\| \|\|:\|\|\| \|\|\|\|\|@LB@ CUAUCUUGU AA UGGAGA AUGGG@LB@3'-AUU...ACUUU AG C AUG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -24.4185 kcal/mol@LB@Unfolding Energy - mRNA 4.52675 kcal/mol@LB@Unfolding Energy - sRNA 8.04825 kcal/mol@LB@@LB@Position - mRNA 129 -- 162@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 20 -- 26@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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