Locus 488

Sequence ID	2L_DroMel_CAF1
Location	1,445,504 – 1,445,643
Length	139
Max. P	0.856016

overview

Window 1

Location	1,445,504 – 1,445,608
Length	104
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	73.03
Mean single sequence MFE	-28.25
Consensus MFE	-11.23
Energy contribution	-12.73
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-2.12
Structure conservation index	0.40
SVM decision value	0.78
SVM RNA-class probability	0.849563
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1445504 104 - 22407834
GGCGCGACAUCCCCGCCCAUGCCCAUGCCCCUCCACCGACCACUAUCCA-CUCGAUUUGGGAACCCAUGUCGCACU---CACAUCCGUGCGUAUGAGCAUCAUCAGUU
((.(((.......)))))((((.(((((.....................-...(((.(((....))).)))((((.---.......))))))))).))))........ ( -27.60)
>DroSec_CAF1 63519 103 - 1
GGCGCGACA-CCCCGCCCAUGCCCAUGCCCCUCCACCGACCACUAUCCA-CUCGAUUUGGGACCCCAAGUCGCACU---CACAUCCGUGCGUAUGAGCAUCAUCAGUU
((.(((...-...)))))((((.(((((.....................-...(((((((....)))))))((((.---.......))))))))).))))........ ( -31.30)
>DroSim_CAF1 66037 104 - 1
GGCGCGACAUCCCCGCCCAUGCCCAUGCCCCUCCGCCGACCACUAUCCA-CUCGAUUUGGGACCCCAAGUCGCACU---CACAUCCGUGCGUAUGAGCAUCAUCAGUU
((.(((.......)))))((((.(((((.....................-...(((((((....)))))))((((.---.......))))))))).))))........ ( -30.80)
>DroEre_CAF1 66019 80 - 1
GGCGCGACCCCCC-----------------------CGCCCACUAUCCA-CUCGAUUUGGA-CCCCAAGUCGCACU---CACAUCCGUGCGUGUGAGCAUCAUCAGUU
((.(((.......-----------------------)))))........-((((((((((.-..)))))))((((.---(((....))).)))))))........... ( -22.90)
>DroYak_CAF1 64903 84 - 1
GGCGCAACUGCCC-----------------------CAACCACUGUUCA-CUCGAUUUGGAACCCCAAGUCGCAGUCCGCACAUCCGUGCGUAUGAGCAUCAUCAGUU
((.((....)).)-----------------------)......((((((-((((((((((....)))))))).))).(((((....)))))...)))))......... ( -27.70)
>DroAna_CAF1 63800 96 - 1
GGCGCGACAUCCCAUCC-AG--UCAGGCCAGUCCAGGCCUGACUCUGCUCCCCGAU------ACCCGUCCAAGAGU---CACAUCCGUGCGUAUGAGCAUCAUCAGUU
.(((((...........-((--(((((((......)))))))))..((((...(((------....)))...))))---......)))))...(((......)))... ( -29.20)
>consensus
GGCGCGACAUCCCCGCC_AU__CCAUGCCCCUCCACCGACCACUAUCCA_CUCGAUUUGGGACCCCAAGUCGCACU___CACAUCCGUGCGUAUGAGCAUCAUCAGUU
.((((...............................................((((((((....))))))))........((....)))))).(((......)))... (-11.23 = -12.73 +   1.50)

alignment

secondary structure

dotplot

Window 2

Location	1,445,533 – 1,445,643
Length	110
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	75.02
Mean single sequence MFE	-27.92
Consensus MFE	-16.18
Energy contribution	-17.68
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.58
SVM decision value	0.81
SVM RNA-class probability	0.856016
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1445533 110 - 22407834
CAGGUCUAAUCGCCUUGGCGACACCUAUUUUCGUAGGCGCGACAUCCCCGCCCAUGCCCAUGCCCCUCCACCGACCACUAUCCA-CUCGAUUUGGGAACCCAUGUCGCACU
..((((...((((....))))...........(((((.(((.......))))).)))...............))))........-..((((.(((....))).)))).... ( -27.30)
>DroSec_CAF1 63548 109 - 1
CAGGCCUAAUCGCCUUGGCGACACCUAUUUUCGUAGGCGCGACA-CCCCGCCCAUGCCCAUGCCCCUCCACCGACCACUAUCCA-CUCGAUUUGGGACCCCAAGUCGCACU
..(((....((((....))))...........(((((.(((...-...))))).)))....)))....................-..((((((((....)))))))).... ( -28.20)
>DroSim_CAF1 66066 110 - 1
CAGGUCUAAUCGCCUUGGCGACACCUAUUUUCGUAGGCGCGACAUCCCCGCCCAUGCCCAUGCCCCUCCGCCGACCACUAUCCA-CUCGAUUUGGGACCCCAAGUCGCACU
..((((...((((....))))..............((((((.......))).(((....))).......)))))))........-..((((((((....)))))))).... ( -31.40)
>DroEre_CAF1 66048 86 - 1
CAGGUCUAAUCGCCUUGGCGACACCUAUUUUCGUAGGCGCGACCCCCC-----------------------CGCCCACUAUCCA-CUCGAUUUGGA-CCCCAAGUCGCACU
.((((....((((....)))).))))......((.((((.(......)-----------------------)))).))......-..((((((((.-..)))))))).... ( -24.10)
>DroYak_CAF1 64935 87 - 1
CAGGUCUAAUCGCCUUGGCGACACCUAUUUUCGUAGGCGCAACUGCCC-----------------------CAACCACUGUUCA-CUCGAUUUGGAACCCCAAGUCGCAGU
.((((....((((....)))).))))......((.((.((....)).)-----------------------).))........(-((((((((((....)))))))).))) ( -25.20)
>DroAna_CAF1 63829 102 - 1
CAGGCCUAAUCGCCUUGGCGACACCUAUUUUCGUAGGCGCGACAUCCCAUCC-AG--UCAGGCCAGUCCAGGCCUGACUCUGCUCCCCGAU------ACCCGUCCAAGAGU
((((((((.((((....))))............)))))..............-((--(((((((......))))))))))))(((...(((------....)))...))). ( -31.32)
>consensus
CAGGUCUAAUCGCCUUGGCGACACCUAUUUUCGUAGGCGCGACAUCCCCGCC_AU__CCAUGCCCCUCCACCGACCACUAUCCA_CUCGAUUUGGGACCCCAAGUCGCACU
..((......(((((..((((.........)))))))))......))........................................((((((((....)))))))).... (-16.18 = -17.68 +   1.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:22 2006