Locus 3949

Sequence ID	3R_DroMel_CAF1
Location	10,678,257 – 10,678,377
Length	120
Max. P	0.999691

overview

Window 9

Location	10,678,257 – 10,678,349
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	97.83
Mean single sequence MFE	-24.98
Consensus MFE	-24.36
Energy contribution	-24.92
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.77
Structure conservation index	0.98
SVM decision value	2.34
SVM RNA-class probability	0.992594
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10678257 92 + 27905053
UUUGUCAUUGUUGCUGCGGUGAAUUAGUCAUGCCAGGCCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCA
........((.((.(((((.(((((((((......))).((((((((.(((((......)))))..)).))))))))))))))))).)).)) ( -27.10)
>DroSec_CAF1 19586 92 + 1
UUUGUCAUUGUUGCUGCGGUGAAUCAGUCAUGCCAGGCCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCA
........((.((.(((((.((((..(((......))).((((((((.(((((......)))))..)).))))))..))))))))).)).)) ( -24.30)
>DroSim_CAF1 21620 92 + 1
UUUGUCAUUGUUGCUGCGGUGAAUUAGUCAUGCCAGGCCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCA
........((.((.(((((.(((((((((......))).((((((((.(((((......)))))..)).))))))))))))))))).)).)) ( -27.10)
>DroEre_CAF1 16752 92 + 1
UUUGUCAUUGUUGCAGCGGUGAAUUAGUCAUGCCAAACCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCA
...............((((.((((((((........)).((((((((.(((((......)))))..)).))))))))))))))))....... ( -22.60)
>DroYak_CAF1 11666 92 + 1
UUUGUCAUUGUUGCUGCGGUGAAUUAGUCAUGCCAAACCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCA
........((.((.(((((.((((((((........)).((((((((.(((((......)))))..)).))))))))))))))))).)).)) ( -23.80)
>consensus
UUUGUCAUUGUUGCUGCGGUGAAUUAGUCAUGCCAGGCCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCA
........((.((.(((((.(((((((((......))).((((((((.(((((......)))))..)).))))))))))))))))).)).)) (-24.36 = -24.92 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	10,678,257 – 10,678,349
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-29.16
Consensus MFE	-28.18
Energy contribution	-27.78
Covariance contribution	-0.40
Combinations/Pair	1.07
Mean z-score	-2.46
Structure conservation index	0.97
SVM decision value	3.90
SVM RNA-class probability	0.999691
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10678257 92 - 27905053
UGGCGAUGCGGGAAUUACGAGUUUGAGGAGCAAUAACAUUUGCUUUCAACUCGGGCCUGGCAUGACUAAUUCACCGCAGCAACAAUGACAAA
..((..(((((((((((((((((.(((.(((((......)))))))))))))).((...)).....)))))).)))))))............ ( -28.80)
>DroSec_CAF1 19586 92 - 1
UGGCGAUGCGGGAAUUACGAGUUUGAGGAGCAAUAACAUUUGCUUUCAACUCGGGCCUGGCAUGACUGAUUCACCGCAGCAACAAUGACAAA
..((..(((((((((((((((((.(((.(((((......)))))))))))))).((...)).....)))))).)))))))............ ( -28.90)
>DroSim_CAF1 21620 92 - 1
UGGCGAUGCGGGAAUUACGAGUUUGAGGAGCAAUAACAUUUGCUUUCAACUCGGGCCUGGCAUGACUAAUUCACCGCAGCAACAAUGACAAA
..((..(((((((((((((((((.(((.(((((......)))))))))))))).((...)).....)))))).)))))))............ ( -28.80)
>DroEre_CAF1 16752 92 - 1
UGGCGAUGCGGGAAUUACGAGUUUGAGGAGCAAUAACAUUUGCUUUCAACUCGGGUUUGGCAUGACUAAUUCACCGCUGCAACAAUGACAAA
..(((..(((((((((.((((((.(((.(((((......))))))))))))))((((......))))))))).)))))))............ ( -29.30)
>DroYak_CAF1 11666 92 - 1
UGGCGAUGCGGGAAUUACGAGUUUGAGGAGCAAUAACAUUUGCUUUCAACUCGGGUUUGGCAUGACUAAUUCACCGCAGCAACAAUGACAAA
..((..((((((((((.((((((.(((.(((((......))))))))))))))((((......))))))))).)))))))............ ( -30.00)
>consensus
UGGCGAUGCGGGAAUUACGAGUUUGAGGAGCAAUAACAUUUGCUUUCAACUCGGGCCUGGCAUGACUAAUUCACCGCAGCAACAAUGACAAA
..((...((((((((((((((((.(((.(((((......)))))))))))))).((...)).....)))))).)))).))............ (-28.18 = -27.78 +  -0.40)

alignment

secondary structure

dotplot

Window 1

Location	10,678,269 – 10,678,377
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.97
Mean single sequence MFE	-33.62
Consensus MFE	-31.78
Energy contribution	-32.34
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.08
Structure conservation index	0.95
SVM decision value	0.16
SVM RNA-class probability	0.610659
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10678269 108 + 27905053
GCUGCGGUGAAUUAGUCAUGCCAGGCCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCAUGGUCGCGUUGCGAAUCGAGCU------------CCAGUU
(((((((.(((((((((......))).((((((((.(((((......)))))..)).)))))))))))))))).((((.(((....))).))))....))).------------...... ( -34.70)
>DroSec_CAF1 19598 108 + 1
GCUGCGGUGAAUCAGUCAUGCCAGGCCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCAUGGUCGCGUUGCGAAUCGAGCU------------CCAGUU
(((((((.((((..(((......))).((((((((.(((((......)))))..)).))))))..)))))))).((((.(((....))).))))....))).------------...... ( -31.90)
>DroSim_CAF1 21632 108 + 1
GCUGCGGUGAAUUAGUCAUGCCAGGCCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCAUGGUCGCGUUGCGAAUCGAGCU------------CCAGUU
(((((((.(((((((((......))).((((((((.(((((......)))))..)).)))))))))))))))).((((.(((....))).))))....))).------------...... ( -34.70)
>DroEre_CAF1 16764 108 + 1
GCAGCGGUGAAUUAGUCAUGCCAAACCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCAUGGUCGCGUUGCGAAUCGAGCU------------CCAGUU
((.((((.((((((((........)).((((((((.(((((......)))))..)).)))))))))))))))).((((.(((....))).)))).....)).------------...... ( -30.80)
>DroYak_CAF1 11678 120 + 1
GCUGCGGUGAAUUAGUCAUGCCAAACCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCAUGGUCGCGUUGCGAAUCGAGCUCCAGCUCCAGCUCCAGUU
(((((((.((((((((........)).((((((((.(((((......)))))..)).)))))))))))))))).((((.(((....))).))))...((((....)))).)))....... ( -36.00)
>consensus
GCUGCGGUGAAUUAGUCAUGCCAGGCCCGAGUUGAAAGCAAAUGUUAUUGCUCCUCAAACUCGUAAUUCCCGCAUCGCCAUGGUCGCGUUGCGAAUCGAGCU____________CCAGUU
(((((((.(((((((((......))).((((((((.(((((......)))))..)).)))))))))))))))).((((.(((....))).))))....)))................... (-31.78 = -32.34 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:15 2006