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
107	0.02168	0.6177	b1738	chbB	-9.32	0.056668	26 -- 34	47 -- 55	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________25________35\n_____________\|_________\|\n5'-AAU...CACAG_________AAACA...CGG-3'\n______________GUCAAGGAG\n______________\|\|\|\|\|:\|\|\|\n______________CAGUUUCUC\n3'-UUU...CCGGG_________CUUAA...ACA-5'\n_____________\|_________\|\n_____________56________46\n	28 -- 34	47 -- 53	-13.6925 kcal/mol	3.47679 kcal/mol	0.899516 kcal/mol	25 35@LB@ \| \|@LB@5'-AAU...CACAG AAACA...CGG-3'@LB@ GUCAAGGAG@LB@ \|\|\|\|\|:\|\|\|@LB@ CAGUUUCUC@LB@3'-UUU...CCGGG CUUAA...ACA-5'@LB@ \| \|@LB@ 56 46@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -13.6925 kcal/mol@LB@Unfolding Energy - mRNA 3.47679 kcal/mol@LB@Unfolding Energy - sRNA 0.899516 kcal/mol@LB@@LB@Position - mRNA 26 -- 34@LB@Position - sRNA 47 -- 55@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 47 -- 53@LB@
2	6.241e-06	0.01004	b1737	chbC	-18.35	0.000789	134 -- 152	38 -- 56	N N'-diacetylchitobiose-specific enzyme IIC component of PTS	_____________133_________________153\n_____________\|___________________\|\n5'-GUU...UUUCC__________UU_______AAAUC...UUC-3'\n______________CGUCAAAGAG__AUUUCAU\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________GCAGUUUCUC__UAAAGUA\n3'-UUU...ACCGG__________CU_______AAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________37\n	146 -- 152	38 -- 44	-21.3647 kcal/mol	1.83077 kcal/mol	1.17918 kcal/mol	133 153@LB@ \| \|@LB@5'-GUU...UUUCC UU AAAUC...UUC-3'@LB@ CGUCAAAGAG AUUUCAU@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ GCAGUUUCUC UAAAGUA@LB@3'-UUU...ACCGG CU AAAAA...ACA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -18.35 kcal/mol@LB@Hybridization Energy -21.3647 kcal/mol@LB@Unfolding Energy - mRNA 1.83077 kcal/mol@LB@Unfolding Energy - sRNA 1.17918 kcal/mol@LB@@LB@Position - mRNA 134 -- 152@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 38 -- 44@LB@
15	0.003313	0.593	b3133	agaV	-12.53	0.012445	185 -- 194	44 -- 53	N-acetylgalactosamine-specific enzyme IIB component of PTS	_____________184________195\n_____________\|__________\|\n5'-UCA...CAAAA__________CACGC...UAG-3'\n______________CAAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	188 -- 194	44 -- 50	-14.1596 kcal/mol	0.702602 kcal/mol	0.927997 kcal/mol	184 195@LB@ \| \|@LB@5'-UCA...CAAAA CACGC...UAG-3'@LB@ CAAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -14.1596 kcal/mol@LB@Unfolding Energy - mRNA 0.702602 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
63	0.01324	0.6177	b3140	agaD	-9.33	0.056359	182 -- 192	45 -- 55	N-acetylgalactosamine-specific enzyme IID component of PTS	_____________181_________193\n_____________\|___________\|\n5'-GCG...AAAAU_AA________CUACA...GUU-3'\n______________G__GAAGAGGA\n______________\|__:\|\|\|\|\|\|\|\n______________C__UUUCUCCU\n3'-UUU...CCGGG_AG________UAAAG...ACA-5'\n_____________\|___________\|\n_____________56__________44\n	186 -- 192	45 -- 51	-11.186 kcal/mol	0.927202 kcal/mol	0.930875 kcal/mol	181 193@LB@ \| \|@LB@5'-GCG...AAAAU AA CUACA...GUU-3'@LB@ G GAAGAGGA@LB@ \| :\|\|\|\|\|\|\|@LB@ C UUUCUCCU@LB@3'-UUU...CCGGG AG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -11.186 kcal/mol@LB@Unfolding Energy - mRNA 0.927202 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 182 -- 192@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 45 -- 51@LB@
41	0.008018	0.6129	b1740	nadE	-11.27	0.022577	258 -- 272	38 -- 52	NAD synthetase NH3/glutamine-dependent	_____________257_____________273\n_____________\|_______________\|\n5'-UUC...AUGCU_________A_____CGUAG...ACC-3'\n______________GAAGAGGAA_UUCGU\n______________:\|\|\|\|\|\|\|\|_\|\|\|:\|\n______________UUUCUCCUU_AAGUA\n3'-UUU...GGCAG_________A_____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	260 -- 266	44 -- 50	-15.8385 kcal/mol	3.49717 kcal/mol	1.0693 kcal/mol	257 273@LB@ \| \|@LB@5'-UUC...AUGCU A CGUAG...ACC-3'@LB@ GAAGAGGAA UUCGU@LB@ :\|\|\|\|\|\|\|\| \|\|\|:\|@LB@ UUUCUCCUU AAGUA@LB@3'-UUU...GGCAG A AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -15.8385 kcal/mol@LB@Unfolding Energy - mRNA 3.49717 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 44 -- 50@LB@
199	0.0417	0.6177	b4070	nrfA	-7.95	0.106497	2 -- 16	44 -- 55	nitrite reductase formate-dependent cytochrome	_____________1_______________17\n_____________\|_______________\|\n__________5'-U___GAA_________GAUAC...CAA-3'\n______________GUU___AAAGAGGAA\n______________\|\|:___\|\|\|\|\|\|\|\|\|\n______________CAG___UUUCUCCUU\n3'-UUU...CCGGG_______________AAAGU...ACA-5'\n_____________\|_______________\|\n_____________56______________43\n	10 -- 16	44 -- 50	-11.2989 kcal/mol	2.40804 kcal/mol	0.941432 kcal/mol	1 17@LB@ \| \|@LB@ 5'-U GAA GAUAC...CAA-3'@LB@ GUU AAAGAGGAA@LB@ \|\|: \|\|\|\|\|\|\|\|\|@LB@ CAG UUUCUCCUU@LB@3'-UUU...CCGGG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -11.2989 kcal/mol@LB@Unfolding Energy - mRNA 2.40804 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 2 -- 16@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 44 -- 50@LB@
8	0.001474	0.5928	b1048	opgG	-11.67	0.018726	159 -- 168	44 -- 53	OPG biosynthetic periplasmic beta-1 6 branching glycosyltransferase	_____________158________169\n_____________\|__________\|\n5'-ACA...GCACA__________AGUGC...AAU-3'\n______________CAAAGGGGGA\n______________\|\|\|\|\|:\|\|:\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	162 -- 168	44 -- 50	-12.9473 kcal/mol	0.352192 kcal/mol	0.927997 kcal/mol	158 169@LB@ \| \|@LB@5'-ACA...GCACA AGUGC...AAU-3'@LB@ CAAAGGGGGA@LB@ \|\|\|\|\|:\|\|:\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -12.9473 kcal/mol@LB@Unfolding Energy - mRNA 0.352192 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 159 -- 168@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 44 -- 50@LB@
128	0.02532	0.6177	b3642	pyrE	-8.06	0.101423	72 -- 92	43 -- 68	orotate phosphoribosyltransferase	_____________71_________________________93\n_____________\|__________________________\|\n5'-CGG...CUUGU_G___C____________________CGAAU...AUU-3'\n______________U_GCU__UGGCCCG____AGGGGAAU\n______________\|_\|\|\|__\|\|\|\|\|\|\|____\|\|:\|\|\|\|\|\n______________A_CGA__ACCGGGC____UCUCCUUA\n3'-UUU...GUUAU_G___UA_______AGUU________AAGUA...ACA-5'\n_____________\|__________________________\|\n_____________69_________________________42\n	86 -- 92	43 -- 49	-26.5136 kcal/mol	7.12642 kcal/mol	11.3306 kcal/mol	71 93@LB@ \| \|@LB@5'-CGG...CUUGU G C CGAAU...AUU-3'@LB@ U GCU UGGCCCG AGGGGAAU@LB@ \| \|\|\| \|\|\|\|\|\|\| \|\|:\|\|\|\|\|@LB@ A CGA ACCGGGC UCUCCUUA@LB@3'-UUU...GUUAU G UA AGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 69 42@LB@@LB@@LB@Energy -8.06 kcal/mol@LB@Hybridization Energy -26.5136 kcal/mol@LB@Unfolding Energy - mRNA 7.12642 kcal/mol@LB@Unfolding Energy - sRNA 11.3306 kcal/mol@LB@@LB@Position - mRNA 72 -- 92@LB@Position - sRNA 43 -- 68@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 43 -- 49@LB@
194	0.04051	0.6177	b0814	ompX	-6.96	0.165642	107 -- 118	50 -- 61	outer membrane protein X	_____________106__________119\n_____________\|____________\|\n5'-CUG...UGAAA____________CAUCA...CAC-3'\n______________UGGCCCGUUAGA\n______________\|\|\|\|\|\|\|\|:\|:\|\n______________ACCGGGCAGUUU\n3'-UUU...CGAUA____________CUCCU...ACA-5'\n_____________\|____________\|\n_____________62___________49\n	111 -- 117	51 -- 57	-20.1081 kcal/mol	2.98628 kcal/mol	10.1573 kcal/mol	106 119@LB@ \| \|@LB@5'-CUG...UGAAA CAUCA...CAC-3'@LB@ UGGCCCGUUAGA@LB@ \|\|\|\|\|\|\|\|:\|:\|@LB@ ACCGGGCAGUUU@LB@3'-UUU...CGAUA CUCCU...ACA-5'@LB@ \| \|@LB@ 62 49@LB@@LB@@LB@Energy -6.96 kcal/mol@LB@Hybridization Energy -20.1081 kcal/mol@LB@Unfolding Energy - mRNA 2.98628 kcal/mol@LB@Unfolding Energy - sRNA 10.1573 kcal/mol@LB@@LB@Position - mRNA 107 -- 118@LB@Position - sRNA 50 -- 61@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 51 -- 57@LB@
105	0.0216	0.6177	b2962	yggX	-9.20	0.059738	186 -- 194	45 -- 53	oxidative damage protective factor for iron-sulfur proteins	_____________185_______195\n_____________\|_________\|\n5'-UCA...GUCGA_________UGAUU...AGA-3'\n______________UAAAGAGGA\n______________:\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	188 -- 194	45 -- 51	-10.7665 kcal/mol	0.645872 kcal/mol	0.917553 kcal/mol	185 195@LB@ \| \|@LB@5'-UCA...GUCGA UGAUU...AGA-3'@LB@ UAAAGAGGA@LB@ :\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -10.7665 kcal/mol@LB@Unfolding Energy - mRNA 0.645872 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 45 -- 51@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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