Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
153	0.02565	0.5485	b2764	cysJ	-8.62	0.180864	16 -- 26	74 -- 84	sulfite reductase alpha subunit flavoprotein	_____________15__________27\n_____________\|___________\|\n5'-UUC...UUUCA___G_______AAUCU...UUG-3'\n______________UUA_GUUGGUU\n______________\|:\|_\|\|\|\|\|:\|\n______________AGU_CAACCGA\n3'-CGC...UUUCA___G_______AAUCA...AAG-5'\n_____________\|___________\|\n_____________85__________73\n	20 -- 26	74 -- 80	-11.948 kcal/mol	2.81948 kcal/mol	0.508159 kcal/mol	15 27@LB@ \| \|@LB@5'-UUC...UUUCA G AAUCU...UUG-3'@LB@ UUA GUUGGUU@LB@ \|:\| \|\|\|\|\|:\|@LB@ AGU CAACCGA@LB@3'-CGC...UUUCA G AAUCA...AAG-5'@LB@ \| \|@LB@ 85 73@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -11.948 kcal/mol@LB@Unfolding Energy - mRNA 2.81948 kcal/mol@LB@Unfolding Energy - sRNA 0.508159 kcal/mol@LB@@LB@Position - mRNA 16 -- 26@LB@Position - sRNA 74 -- 84@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 74 -- 80@LB@
75	0.01364	0.5385	b0107	hofB	-15.68	0.010425	272 -- 289	69 -- 87	T2SE secretion family protein; P-loop ATPase superfamily protein	_____________271_________________290\n_____________\|___________________\|\n5'-CCA...GAGGU_____________GG____CGAUG...CUU-3'\n______________GGUUCAUGUUG_C__UAGU\n______________:\|\|\|\|\|:\|\|\|\|_\|__\|\|\|\|\n______________UCAAGUGCAAC_G__AUCA\n3'-CGC...CGUUU___________C_AA____AUAAG...AAG-5'\n_____________\|___________________\|\n_____________88__________________68\n	276 -- 282	77 -- 83	-18.3354 kcal/mol	2.08484 kcal/mol	0.569189 kcal/mol	271 290@LB@ \| \|@LB@5'-CCA...GAGGU GG CGAUG...CUU-3'@LB@ GGUUCAUGUUG C UAGU@LB@ :\|\|\|\|\|:\|\|\|\| \| \|\|\|\|@LB@ UCAAGUGCAAC G AUCA@LB@3'-CGC...CGUUU C AA AUAAG...AAG-5'@LB@ \| \|@LB@ 88 68@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -18.3354 kcal/mol@LB@Unfolding Energy - mRNA 2.08484 kcal/mol@LB@Unfolding Energy - sRNA 0.569189 kcal/mol@LB@@LB@Position - mRNA 272 -- 289@LB@Position - sRNA 69 -- 87@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 77 -- 83@LB@
76	0.01392	0.5385	b0066	thiQ	-9.74	0.117374	220 -- 232	71 -- 84	thiamine/thiamine pyrophosphate ABC transporter ATPase	_____________219____________233\n_____________\|______________\|\n5'-GCU...UGAUA____C_________CCACC...CAA-3'\n______________UCAC__UGGCUUUA\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\n______________AGUG__ACCGAAAU\n3'-CGC...UUUCA____CA________CAAUA...AAG-5'\n_____________\|______________\|\n_____________85_____________70\n	226 -- 232	71 -- 77	-13.9563 kcal/mol	3.66363 kcal/mol	0.5567 kcal/mol	219 233@LB@ \| \|@LB@5'-GCU...UGAUA C CCACC...CAA-3'@LB@ UCAC UGGCUUUA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGUG ACCGAAAU@LB@3'-CGC...UUUCA CA CAAUA...AAG-5'@LB@ \| \|@LB@ 85 70@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -13.9563 kcal/mol@LB@Unfolding Energy - mRNA 3.66363 kcal/mol@LB@Unfolding Energy - sRNA 0.5567 kcal/mol@LB@@LB@Position - mRNA 220 -- 232@LB@Position - sRNA 71 -- 84@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 71 -- 77@LB@
114	0.01931	0.5385	b1951	rcsA	-10.71	0.079523	269 -- 285	16 -- 29	transcriptional regulator of colanic acid capsular biosynthesis	_____________268_______________286\n_____________\|_________________\|\n5'-GUU...AGUAG__________AAA____AAAUC...UUG-3'\n______________AGGGGUUAAA___AGAG\n______________\|:\|\|\|\|\|\|\|\|___\|\|\|\|\n______________UUCCCAAUUU___UCUC\n3'-CGC...UGAAG_________________CACGG...AAG-5'\n_____________\|_________________\|\n_____________30________________15\n	272 -- 278	20 -- 26	-15.5636 kcal/mol	1.76121 kcal/mol	3.08831 kcal/mol	268 286@LB@ \| \|@LB@5'-GUU...AGUAG AAA AAAUC...UUG-3'@LB@ AGGGGUUAAA AGAG@LB@ \|:\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUCCCAAUUU UCUC@LB@3'-CGC...UGAAG CACGG...AAG-5'@LB@ \| \|@LB@ 30 15@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -15.5636 kcal/mol@LB@Unfolding Energy - mRNA 1.76121 kcal/mol@LB@Unfolding Energy - sRNA 3.08831 kcal/mol@LB@@LB@Position - mRNA 269 -- 285@LB@Position - sRNA 16 -- 29@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 20 -- 26@LB@
177	0.03112	0.5559	b0080	cra	-12.94	0.032158	57 -- 78	62 -- 84	transcriptional repressor-activator for carbon metabolism	_____________56_______________________79\n_____________\|________________________\|\n5'-GGC...ACAUG_________G____UU________AAUCA...AAA-3'\n______________UCACGUUGG_CUUU__UUG__CGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|__\|\|:__\|\|\|\n______________AGUGCAACC_GAAA__AAU__GCU\n3'-CGC...UUUCA______________UC___AA___CAACU...AAG-5'\n_____________\|________________________\|\n_____________85_______________________61\n	59 -- 65	76 -- 82	-19.2849 kcal/mol	4.65103 kcal/mol	1.6921 kcal/mol	56 79@LB@ \| \|@LB@5'-GGC...ACAUG G UU AAUCA...AAA-3'@LB@ UCACGUUGG CUUU UUG CGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\| \|\|: \|\|\|@LB@ AGUGCAACC GAAA AAU GCU@LB@3'-CGC...UUUCA UC AA CAACU...AAG-5'@LB@ \| \|@LB@ 85 61@LB@@LB@@LB@Energy -12.94 kcal/mol@LB@Hybridization Energy -19.2849 kcal/mol@LB@Unfolding Energy - mRNA 4.65103 kcal/mol@LB@Unfolding Energy - sRNA 1.6921 kcal/mol@LB@@LB@Position - mRNA 57 -- 78@LB@Position - sRNA 62 -- 84@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 76 -- 82@LB@
64	0.01278	0.5385	b1718	infC	-10.82	0.076139	1 -- 9	71 -- 79	translation initiation factor IF-3	______________1________10\n______________\|________\|\n___________5'-_________AAAUC...AGC-3'\n______________UUGGCUUUA\n______________\|\|\|\|\|\|\|\|\|\n______________AACCGAAAU\n3'-CGC...AGUGC_________CAAUA...AAG-5'\n_____________\|_________\|\n_____________80________70\n	3 -- 9	71 -- 77	-11.2516 kcal/mol	0.206511 kcal/mol	0.222833 kcal/mol	1 10@LB@ \| \|@LB@ 5'- AAAUC...AGC-3'@LB@ UUGGCUUUA@LB@ \|\|\|\|\|\|\|\|\|@LB@ AACCGAAAU@LB@3'-CGC...AGUGC CAAUA...AAG-5'@LB@ \| \|@LB@ 80 70@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -11.2516 kcal/mol@LB@Unfolding Energy - mRNA 0.206511 kcal/mol@LB@Unfolding Energy - sRNA 0.222833 kcal/mol@LB@@LB@Position - mRNA 1 -- 9@LB@Position - sRNA 71 -- 79@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 71 -- 77@LB@
84	0.01516	0.5385	b1871	cmoB	-9.91	0.109770	166 -- 183	71 -- 87	tRNA (cmo5U34)-carboxymethyltransferase carboxy-SAM-dependent	_____________165________________184\n_____________\|__________________\|\n5'-CAC...ACUUU_______U_G____A___AAAGC...AGC-3'\n______________GGUUCAC_G_UGGC_UUA\n______________:\|\|\|\|\|\|_\|_\|\|\|\|_\|\|\|\n______________UCAAGUG_C_ACCG_AAU\n3'-CGC...CGUUU_________A____A___CAAUA...AAG-5'\n_____________\|__________________\|\n_____________88_________________70\n	166 -- 172	81 -- 87	-14.4863 kcal/mol	4.01825 kcal/mol	0.562376 kcal/mol	165 184@LB@ \| \|@LB@5'-CAC...ACUUU U G A AAAGC...AGC-3'@LB@ GGUUCAC G UGGC UUA@LB@ :\|\|\|\|\|\| \| \|\|\|\| \|\|\|@LB@ UCAAGUG C ACCG AAU@LB@3'-CGC...CGUUU A A CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -14.4863 kcal/mol@LB@Unfolding Energy - mRNA 4.01825 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 166 -- 183@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 81 -- 87@LB@
118	0.01985	0.5385	b2318	truA	-10.16	0.099312	131 -- 143	70 -- 82	tRNA pseudouridine(38-40) synthase	_____________130___________144\n_____________\|_____________\|\n5'-GUG...CGAUA_____C_______CGGCG...GCA-3'\n______________ACGUU_GCUUUGG\n______________\|\|\|\|\|_\|\|\|\|\|:\|\n______________UGCAA_CGAAAUC\n3'-CGC...UCAAG_____C_______AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	137 -- 143	70 -- 76	-13.1761 kcal/mol	2.62838 kcal/mol	0.389672 kcal/mol	130 144@LB@ \| \|@LB@5'-GUG...CGAUA C CGGCG...GCA-3'@LB@ ACGUU GCUUUGG@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ UGCAA CGAAAUC@LB@3'-CGC...UCAAG C AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -13.1761 kcal/mol@LB@Unfolding Energy - mRNA 2.62838 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 131 -- 143@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 70 -- 76@LB@
50	0.0104	0.5385	b0661	miaB	-10.15	0.099644	35 -- 45	74 -- 85	tRNA-i(6)A37 methylthiotransferase	_____________34___________46\n_____________\|____________\|\n5'-CGC...GCAAU____________GAUUU...AAC-3'\n______________UUC_CGUUGGUU\n______________\|\|\|_\|\|\|\|\|\|:\|\n______________AAG_GCAACCGA\n3'-CGC...UUUUC___U________AAUCA...AAG-5'\n_____________\|____________\|\n_____________86___________73\n	39 -- 45	74 -- 80	-13.4892 kcal/mol	2.82751 kcal/mol	0.512001 kcal/mol	34 46@LB@ \| \|@LB@5'-CGC...GCAAU GAUUU...AAC-3'@LB@ UUC CGUUGGUU@LB@ \|\|\| \|\|\|\|\|\|:\|@LB@ AAG GCAACCGA@LB@3'-CGC...UUUUC U AAUCA...AAG-5'@LB@ \| \|@LB@ 86 73@LB@@LB@@LB@Energy -10.15 kcal/mol@LB@Hybridization Energy -13.4892 kcal/mol@LB@Unfolding Energy - mRNA 2.82751 kcal/mol@LB@Unfolding Energy - sRNA 0.512001 kcal/mol@LB@@LB@Position - mRNA 35 -- 45@LB@Position - sRNA 74 -- 85@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 74 -- 80@LB@
34	0.00612	0.5385	b1837	yebW	-12.39	0.040382	203 -- 226	63 -- 86	uncharacterized protein	_____________202______________________227\n_____________\|________________________\|\n5'-ACC...GAAAU_______C____ACUUU_______CUACC...UGA-3'\n______________GUUCGCG_UGGU_____UUGUUUG\n______________\|\|\|\|:\|\|_\|\|\|:_____\|\|:\|\|:\|\n______________CAAGUGC_ACCG_____AAUAAGC\n3'-CGC...GUUUU_______A____AAAUC_______UCAAC...AAG-5'\n_____________\|________________________\|\n_____________87_______________________62\n	220 -- 226	63 -- 69	-18.9836 kcal/mol	4.90011 kcal/mol	1.69827 kcal/mol	202 227@LB@ \| \|@LB@5'-ACC...GAAAU C ACUUU CUACC...UGA-3'@LB@ GUUCGCG UGGU UUGUUUG@LB@ \|\|\|\|:\|\| \|\|\|: \|\|:\|\|:\|@LB@ CAAGUGC ACCG AAUAAGC@LB@3'-CGC...GUUUU A AAAUC UCAAC...AAG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -18.9836 kcal/mol@LB@Unfolding Energy - mRNA 4.90011 kcal/mol@LB@Unfolding Energy - sRNA 1.69827 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 63 -- 69@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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