Locus 5530

Sequence ID	X_DroMel_CAF1
Location	14,310,787 – 14,310,883
Length	96
Max. P	0.875689

overview

Window 9

Location	14,310,787 – 14,310,883
Length	96
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	93.09
Mean single sequence MFE	-31.56
Consensus MFE	-26.06
Energy contribution	-26.30
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.41
Structure conservation index	0.83
SVM decision value	0.26
SVM RNA-class probability	0.658477
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14310787 96 + 22224390
AUUUU------UUGGCCAACGUCGGAGGCGCUAAUUAAUCCAUUAAGGCCAAGUUUGUUGCGUGGUGUAAUUGGCAUUGCGGUUGCGCAGAAAACGUUGGCG
.....------...((((((((.....((((....(((((((...(.((((.((.....)).)))).)...))).)))).....)))).....)))))))). ( -31.60)
>DroSec_CAF1 23535 96 + 1
AUUUU------UUGGCCAACGGCGGAGGCGCUAAUUAAUCCAUUAAGGCCAAGUUUGUUGCGCGGUGUAAUUGUCAUUGCGGUUGCCCAGAAAACGUUGGCG
.....------...(((((((......((((.((((...((.....))...))))....))))((.((((((((....))))))))))......))))))). ( -30.30)
>DroSim_CAF1 20840 96 + 1
AUUUU------UUGGCCAACGGCGGAGGCGCUAAUUAAUCCAUUAAGGCCAAGUUUGUUGCGCGGUGUAAUUGGCAUUGCGGUUGCCCAGAAAACGUUGGCG
.....------...(((((((......((((.((((...((.....))...))))....))))((.(((((((......)))))))))......))))))). ( -29.40)
>DroEre_CAF1 20444 96 + 1
GCUUU------UCGGCCAACGGAGGAGGCGCUAAUUAGUCCAUUAAGGCCAAGUUUGUUGCGCGGUGUAAUUGGCAUUGCGGUUGCCCAGAAAACGUUGGCG
.....------...(((((((......((((.((((.(.((.....)).).))))....))))((.(((((((......)))))))))......))))))). ( -30.60)
>DroYak_CAF1 24800 102 + 1
GUUUUUUGUUUUUGGGCAACGGAGGAGGCGCUAAUUAAUCCAUUAAGGCCAAGUUUGUUGCGCGGUGUAAUUGGCAUUGCGGUUGCCCAGAAAACGUUGGCG
(((.....((((((((((((......(((..((((......))))..)))..........((((((((.....)))))))))))))))))))).....))). ( -35.90)
>consensus
AUUUU______UUGGCCAACGGCGGAGGCGCUAAUUAAUCCAUUAAGGCCAAGUUUGUUGCGCGGUGUAAUUGGCAUUGCGGUUGCCCAGAAAACGUUGGCG
..............(((((((......((((.((((...((.....))...))))....))))((.(((((((......)))))))))......))))))). (-26.06 = -26.30 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	14,310,787 – 14,310,883
Length	96
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	93.09
Mean single sequence MFE	-25.25
Consensus MFE	-19.36
Energy contribution	-19.76
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.19
Structure conservation index	0.77
SVM decision value	0.89
SVM RNA-class probability	0.875689
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14310787 96 - 22224390
CGCCAACGUUUUCUGCGCAACCGCAAUGCCAAUUACACCACGCAACAAACUUGGCCUUAAUGGAUUAAUUAGCGCCUCCGACGUUGGCCAA------AAAAU
.(((((((((....((((.........(((((..................)))))..((((......))))))))....)))))))))...------..... ( -25.87)
>DroSec_CAF1 23535 96 - 1
CGCCAACGUUUUCUGGGCAACCGCAAUGACAAUUACACCGCGCAACAAACUUGGCCUUAAUGGAUUAAUUAGCGCCUCCGCCGUUGGCCAA------AAAAU
.(((((((((...(((....)))....))).........(((..........(((.(((((......))))).)))..))).))))))...------..... ( -23.90)
>DroSim_CAF1 20840 96 - 1
CGCCAACGUUUUCUGGGCAACCGCAAUGCCAAUUACACCGCGCAACAAACUUGGCCUUAAUGGAUUAAUUAGCGCCUCCGCCGUUGGCCAA------AAAAU
.(((((((......((....))((..((((.........).)))........(((.(((((......))))).)))...)))))))))...------..... ( -25.30)
>DroEre_CAF1 20444 96 - 1
CGCCAACGUUUUCUGGGCAACCGCAAUGCCAAUUACACCGCGCAACAAACUUGGCCUUAAUGGACUAAUUAGCGCCUCCUCCGUUGGCCGA------AAAGC
.(((((((.......((((.......)))).........((((.......((((((.....)).))))...))))......)))))))...------..... ( -25.00)
>DroYak_CAF1 24800 102 - 1
CGCCAACGUUUUCUGGGCAACCGCAAUGCCAAUUACACCGCGCAACAAACUUGGCCUUAAUGGAUUAAUUAGCGCCUCCUCCGUUGCCCAAAAACAAAAAAC
.......(((((.(((((((((((..((.......))..)))..........(((.(((((......))))).)))......)))))))))))))....... ( -26.20)
>consensus
CGCCAACGUUUUCUGGGCAACCGCAAUGCCAAUUACACCGCGCAACAAACUUGGCCUUAAUGGAUUAAUUAGCGCCUCCGCCGUUGGCCAA______AAAAU
.(((((((......((....))..............................(((.(((((......))))).))).....))))))).............. (-19.36 = -19.76 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:17 2006