Locus 4465

Sequence ID	2R_DroMel_CAF1
Location	14,679,711 – 14,679,837
Length	126
Max. P	0.999942

overview

Window 1

Location	14,679,711 – 14,679,811
Length	100
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	95.10
Mean single sequence MFE	-29.68
Consensus MFE	-26.91
Energy contribution	-26.19
Covariance contribution	-0.72
Combinations/Pair	1.13
Mean z-score	-3.48
Structure conservation index	0.91
SVM decision value	4.72
SVM RNA-class probability	0.999942
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14679711 100 + 20766785
GCGGAAGCAACCGA---CGACAUUGAACUUAAGUUUGAAUA--CAACACAGGCGAACUUGAAUAACUCGAUUGUAUUUUAUUUAAACUUGAGUGGCUUCCACUAU
..((((((...(((---.....))).(((((((((((((((--.((.((((.(((...........))).)))).)).))))))))))))))).))))))..... ( -29.50)
>DroSec_CAF1 10820 103 + 1
GCGGAAGCAACCCACUUCGACAUUGAACUUAAGUUUGAAUA--CAGCACAGGCGAACUUGAAUAACUCGAUUGUAUUUUAUUUAAACUUGAGUGGCUUCCACUAU
..((((((........(((....)))(((((((((((((((--.((.((((.(((...........))).)))).)).))))))))))))))).))))))..... ( -29.60)
>DroSim_CAF1 5898 100 + 1
GCGGAAGCAACCCA---CGACAUUGAACUUAAGUUUGAAUA--CAGCACAGGCGAACUUGAAUAACUCGAUUGUAUUUUAUUUAAACUUGAGUGGCUUCCACUAU
..((((((....((---......)).(((((((((((((((--.((.((((.(((...........))).)))).)).))))))))))))))).))))))..... ( -28.90)
>DroEre_CAF1 9345 100 + 1
GCGGAAGCAACCCA---CGACAUUGAACUUAAGUUUGAAUA--CAGCACAGGCGAACUUGAAUAACUCGAUUGUACUUUAUUUAAACUUGAGUGGCUUCUACUAU
(..(((((....((---......)).(((((((((((((((--.((.((((.(((...........))).)))).)).))))))))))))))).)))))..)... ( -28.50)
>DroYak_CAF1 9596 102 + 1
GCGGAAGCAACCCA---CGACAUUGAACUUAAGUUUGAAUACACAGCACAGGCGAACUUGAAUAACUCGAUUGUGUUUUAUUCAAACUUGAGUGGCUUCUUCUAU
(.((((((....((---......)).(((((((((((((((...(((((((.(((...........))).))))))).))))))))))))))).)))))).)... ( -31.90)
>consensus
GCGGAAGCAACCCA___CGACAUUGAACUUAAGUUUGAAUA__CAGCACAGGCGAACUUGAAUAACUCGAUUGUAUUUUAUUUAAACUUGAGUGGCUUCCACUAU
..((((((..................(((((((((((((((...((.((((.(((...........))).)))).)).))))))))))))))).))))))..... (-26.91 = -26.19 +  -0.72)

alignment

secondary structure

dotplot

Window 2

Location	14,679,711 – 14,679,811
Length	100
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	95.10
Mean single sequence MFE	-26.36
Consensus MFE	-20.88
Energy contribution	-21.52
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-2.05
Structure conservation index	0.79
SVM decision value	0.85
SVM RNA-class probability	0.867410
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14679711 100 - 20766785
AUAGUGGAAGCCACUCAAGUUUAAAUAAAAUACAAUCGAGUUAUUCAAGUUCGCCUGUGUUG--UAUUCAAACUUAAGUUCAAUGUCG---UCGGUUGCUUCCGC
...((((((((.(((.((((((.((((.((((((..(((..(.....)..)))..)))))).--)))).))))))..(........).---..))).)))))))) ( -25.50)
>DroSec_CAF1 10820 103 - 1
AUAGUGGAAGCCACUCAAGUUUAAAUAAAAUACAAUCGAGUUAUUCAAGUUCGCCUGUGCUG--UAUUCAAACUUAAGUUCAAUGUCGAAGUGGGUUGCUUCCGC
...((((((((.((((((((((.((((...((((..(((..(.....)..)))..))))...--)))).)))))).(.(((......))).))))).)))))))) ( -28.40)
>DroSim_CAF1 5898 100 - 1
AUAGUGGAAGCCACUCAAGUUUAAAUAAAAUACAAUCGAGUUAUUCAAGUUCGCCUGUGCUG--UAUUCAAACUUAAGUUCAAUGUCG---UGGGUUGCUUCCGC
...((((((((.((((((((((.((((...((((..(((..(.....)..)))..))))...--)))).))))))..(........).---.)))).)))))))) ( -25.90)
>DroEre_CAF1 9345 100 - 1
AUAGUAGAAGCCACUCAAGUUUAAAUAAAGUACAAUCGAGUUAUUCAAGUUCGCCUGUGCUG--UAUUCAAACUUAAGUUCAAUGUCG---UGGGUUGCUUCCGC
...(..(((((.((((((((((.((((.((((((..(((..(.....)..)))..)))))).--)))).))))))..(........).---.)))).)))))..) ( -25.80)
>DroYak_CAF1 9596 102 - 1
AUAGAAGAAGCCACUCAAGUUUGAAUAAAACACAAUCGAGUUAUUCAAGUUCGCCUGUGCUGUGUAUUCAAACUUAAGUUCAAUGUCG---UGGGUUGCUUCCGC
......(((((.(((((((((((((((...((((..(((..(.....)..)))..)))).....)))))))))))..(........).---.)))).)))))... ( -26.20)
>consensus
AUAGUGGAAGCCACUCAAGUUUAAAUAAAAUACAAUCGAGUUAUUCAAGUUCGCCUGUGCUG__UAUUCAAACUUAAGUUCAAUGUCG___UGGGUUGCUUCCGC
...((((((((.((((((((((.((((...((((..(((..(.....)..)))..)))).....)))).))))))..(........).....)))).)))))))) (-20.88 = -21.52 +   0.64)

alignment

secondary structure

dotplot

Window 3

Location	14,679,733 – 14,679,837
Length	104
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	95.61
Mean single sequence MFE	-21.22
Consensus MFE	-18.96
Energy contribution	-18.48
Covariance contribution	-0.48
Combinations/Pair	1.12
Mean z-score	-1.30
Structure conservation index	0.89
SVM decision value	0.46
SVM RNA-class probability	0.743618
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14679733 104 + 20766785
AACUUAAGUUUGAAUA--CAACACAGGCGAACUUGAAUAACUCGAUUGUAUUUUAUUUAAACUUGAGUGGCUUCCACUAUUCUGUUUUUGAUUAUCUGUAACUUGA
.(((((((((((((((--.((.((((.(((...........))).)))).)).)))))))))))))))...................................... ( -19.70)
>DroSec_CAF1 10845 104 + 1
AACUUAAGUUUGAAUA--CAGCACAGGCGAACUUGAAUAACUCGAUUGUAUUUUAUUUAAACUUGAGUGGCUUCCACUAUUCUGUUUUUGAUUAUCUGUAACUUGA
.(((((((((((((((--.((.((((.(((...........))).)))).)).)))))))))))))))...................................... ( -19.40)
>DroSim_CAF1 5920 104 + 1
AACUUAAGUUUGAAUA--CAGCACAGGCGAACUUGAAUAACUCGAUUGUAUUUUAUUUAAACUUGAGUGGCUUCCACUAUUCUGUUUUUGAUUAUCUGUAACUUGA
.(((((((((((((((--.((.((((.(((...........))).)))).)).)))))))))))))))...................................... ( -19.40)
>DroEre_CAF1 9367 104 + 1
AACUUAAGUUUGAAUA--CAGCACAGGCGAACUUGAAUAACUCGAUUGUACUUUAUUUAAACUUGAGUGGCUUCUACUAUUCAGUUUUUGAUUAUCUGUAACUUGC
.(((((((((((((((--.((.((((.(((...........))).)))).)).)))))))))))))))..............((((...(.....)...))))... ( -21.80)
>DroYak_CAF1 9618 106 + 1
AACUUAAGUUUGAAUACACAGCACAGGCGAACUUGAAUAACUCGAUUGUGUUUUAUUCAAACUUGAGUGGCUUCUUCUAUUCAGUUUUUGAUUAUCUGUAACUUGC
.(((((((((((((((...(((((((.(((...........))).))))))).)))))))))))))))..............((((...(.....)...))))... ( -25.80)
>consensus
AACUUAAGUUUGAAUA__CAGCACAGGCGAACUUGAAUAACUCGAUUGUAUUUUAUUUAAACUUGAGUGGCUUCCACUAUUCUGUUUUUGAUUAUCUGUAACUUGA
.(((((((((((((((...((.((((.(((...........))).)))).)).)))))))))))))))...................................... (-18.96 = -18.48 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:26 2006