Locus 1155

Sequence ID 3R_DroMel_CAF1
Location 3,484,831 – 3,484,997
Length 166
Max. P 0.967151
window1896 window1897 window1898

overview

Window 6

Location 3,484,831 – 3,484,938
Length 107
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 89.35
Mean single sequence MFE -23.52
Consensus MFE -19.82
Energy contribution -19.00
Covariance contribution -0.81
Combinations/Pair 1.17
Mean z-score -1.48
Structure conservation index 0.84
SVM decision value 0.21
SVM RNA-class probability 0.633472
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3484831 107 + 27905053
GUGUAUUAGAUUUGAAUUCGGGUGCUCCCAUUUGCAAAUUAGCUUUUUCGGGCCUUAAACACAAGGCUCAUACAAGUUUACUCGAA-----AUAAAUGCAAACAAAAUCCUU
.((((((.((((((.....(((....))).....))))))(((((....(((((((......)))))))....)))))........-----...))))))............ ( -23.00)
>DroSec_CAF1 82419 107 + 1
GUGUAUUAGAUUUGAAUUCGGGUGCUCCCAUUUGCAAAUUAGCUUUUUCGGGCCUUAAACACGAGGCUCACAGCAGUUUACUCGAA-----AUAAAUGAAAACAAAAUCCUU
.(((.((..(((((..(((((((((........))(((((.(((.....(((((((......)))))))..)))))))))))))))-----.))))).)).)))........ ( -22.80)
>DroSim_CAF1 106217 107 + 1
GUGUAUUAGAUUUGAAUUCGGGUGCUCCCAUUUGCAAAUUAGCUUUUUCGGGCCUUAAACACGAGGCUCACACCAGUUUACUCGAA-----AUAAAUGAAAACAAAAUCCUU
((((....((((((.....(((....))).....)))))).........(((((((......)))))))))))..((((.(.....-----......).))))......... ( -21.90)
>DroYak_CAF1 147111 111 + 1
GUUUAUUAAAUUCGAAUUCGGGUGCUCCCAAUUGCAAAAAAGCUUUUU-GGGCUUUAAACACAAGGCUCAUACAAGUUUACCCGAACGGUGUUAAAUACAAACAAAAUCCCU
((((.((((..(((..(((((((((........))....((((((..(-(((((((......))))))))...))))))))))))))))..))))....))))......... ( -26.40)
>consensus
GUGUAUUAGAUUUGAAUUCGGGUGCUCCCAUUUGCAAAUUAGCUUUUUCGGGCCUUAAACACAAGGCUCACACAAGUUUACUCGAA_____AUAAAUGAAAACAAAAUCCUU
((.((((.........((((((((..(......((......))......(((((((......)))))))......)..))))))))........))))...))......... (-19.82 = -19.00 +  -0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 3,484,904 – 3,484,997
Length 93
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 92.32
Mean single sequence MFE -20.14
Consensus MFE -16.10
Energy contribution -16.85
Covariance contribution 0.75
Combinations/Pair 1.03
Mean z-score -3.24
Structure conservation index 0.80
SVM decision value 1.34
SVM RNA-class probability 0.943845
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3484904 93 + 27905053
AAGUUUACUCGAA-----AUAAAUGCAAACAAAAUCCUUUUGCAUUGCACAAAACAAUUGUGUAAACAAAUUUAACUAAAUUGCUUGUGUUUCGAGUA
.....((((((((-----(((...((((..........((((..((((((((.....)))))))).))))..........))))...))))))))))) ( -25.65)
>DroSec_CAF1 82492 93 + 1
CAGUUUACUCGAA-----AUAAAUGAAAACAAAAUCCUUUUUCAUUGCACAAAACAAUUGUGUAAACAAAUUUAACUAAAUUGCUUGUGUUUCGAGUA
.....((((((((-----(((..((((((.........))))))((((((((.....))))))))......................))))))))))) ( -21.00)
>DroSim_CAF1 106290 93 + 1
CAGUUUACUCGAA-----AUAAAUGAAAACAAAAUCCUUUUUCAUUGCACAAAACAAUUGUGUAAACAAAUUUAGCUAAAUUGCUUGUGUUUCGAGUA
.....((((((((-----(((..((((((.........))))))((((((((.....))))))))........(((......)))..))))))))))) ( -22.50)
>DroYak_CAF1 147183 98 + 1
AAGUUUACCCGAACGGUGUUAAAUACAAACAAAAUCCCUUUUCAUUGCACAAAACAAUAGUGUAAACAAAUUUAACUAAAUUGCUUGUGUUUCGAGUA
.((((((.((....)).(((((((......((((....))))..((((((.........))))))....)))))))))))))(((((.....))))). ( -11.40)
>consensus
AAGUUUACUCGAA_____AUAAAUGAAAACAAAAUCCUUUUUCAUUGCACAAAACAAUUGUGUAAACAAAUUUAACUAAAUUGCUUGUGUUUCGAGUA
.....((((((((........((((((((.........))))))))((((((..(((((...((((....))))....))))).)))))))))))))) (-16.10 = -16.85 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 3,484,904 – 3,484,997
Length 93
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 92.32
Mean single sequence MFE -20.77
Consensus MFE -18.30
Energy contribution -18.18
Covariance contribution -0.12
Combinations/Pair 1.10
Mean z-score -2.29
Structure conservation index 0.88
SVM decision value 1.61
SVM RNA-class probability 0.967151
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3484904 93 - 27905053
UACUCGAAACACAAGCAAUUUAGUUAAAUUUGUUUACACAAUUGUUUUGUGCAAUGCAAAAGGAUUUUGUUUGCAUUUAU-----UUCGAGUAAACUU
(((((((((....(((......))).....(((..(((.((((.((((((.....)))))).)))).)))..)))....)-----))))))))..... ( -22.80)
>DroSec_CAF1 82492 93 - 1
UACUCGAAACACAAGCAAUUUAGUUAAAUUUGUUUACACAAUUGUUUUGUGCAAUGAAAAAGGAUUUUGUUUUCAUUUAU-----UUCGAGUAAACUG
((((((((((((((((((((..((((((....)))).))))))).)))))).((((((((.........))))))))..)-----))))))))..... ( -20.20)
>DroSim_CAF1 106290 93 - 1
UACUCGAAACACAAGCAAUUUAGCUAAAUUUGUUUACACAAUUGUUUUGUGCAAUGAAAAAGGAUUUUGUUUUCAUUUAU-----UUCGAGUAAACUG
((((((((((((((((((((.(((.......))).....))))).)))))).((((((((.........))))))))..)-----))))))))..... ( -20.60)
>DroYak_CAF1 147183 98 - 1
UACUCGAAACACAAGCAAUUUAGUUAAAUUUGUUUACACUAUUGUUUUGUGCAAUGAAAAGGGAUUUUGUUUGUAUUUAACACCGUUCGGGUAAACUU
((((((((....((((((.((.....)).)))))).......((((..((((((..((((....))))..))))))..))))...))))))))..... ( -19.50)
>consensus
UACUCGAAACACAAGCAAUUUAGUUAAAUUUGUUUACACAAUUGUUUUGUGCAAUGAAAAAGGAUUUUGUUUGCAUUUAU_____UUCGAGUAAACUG
((((((((.(((((((((((....((((....))))...))))).)))))).((((((((.........))))))))........))))))))..... (-18.30 = -18.18 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:25 2006