Locus 248

Sequence ID X_DroMel_CAF1
Location 838,173 – 838,273
Length 100
Max. P 0.983539
window374 window375

overview

Window 4

Location 838,173 – 838,273
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.94
Mean single sequence MFE -26.05
Consensus MFE -23.41
Energy contribution -23.93
Covariance contribution 0.53
Combinations/Pair 1.04
Mean z-score -1.28
Structure conservation index 0.90
SVM decision value 0.21
SVM RNA-class probability 0.637441
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 838173 100 + 22224390
--------------------GCAGUGGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
--------------------((.((((((....((..((((((((.....))))))))....))......((((((..((((((........)))..))).))))))))))))..))... ( -26.50)
>DroSec_CAF1 39029 100 + 1
--------------------GCAGUGGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
--------------------((.((((((....((..((((((((.....))))))))....))......((((((..((((((........)))..))).))))))))))))..))... ( -26.50)
>DroSim_CAF1 35276 100 + 1
--------------------GCAGUGGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
--------------------((.((((((....((..((((((((.....))))))))....))......((((((..((((((........)))..))).))))))))))))..))... ( -26.50)
>DroEre_CAF1 38541 100 + 1
--------------------GCAGUGGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
--------------------((.((((((....((..((((((((.....))))))))....))......((((((..((((((........)))..))).))))))))))))..))... ( -26.50)
>DroYak_CAF1 35883 100 + 1
--------------------GCAGUGGCAAUUUGCUAAUUUGGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
--------------------((.((((((..(((.(((...(..(((...((..(((((((.(((.(((...)))))).)))))))..)).)))..)))).)))...))))))..))... ( -24.70)
>DroAna_CAF1 38000 120 + 1
CCACCUAAAACUACAAAAACCCAACAGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCACGCCGUGGGCGUG
.(((...((((..............(((.....))).((((((((.....))))))))))))(((((...((((((..((((((........)))..))).)))))).....)))))))) ( -25.60)
>consensus
____________________GCAGUGGCAAUUUGCUAAUUUCGAAUGCACUUCGAAAUGUUUGCCCAAUUUGGUUGGCCAACAUUUUAAAACAUGACUUGACAAUCAUGCCGCGGGCGAU
........................((((.....))))((((((((.....))))))))..((((((...((((....))))..........(((((........)))))....)))))). (-23.41 = -23.93 +   0.53) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 838,173 – 838,273
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.94
Mean single sequence MFE -27.25
Consensus MFE -26.13
Energy contribution -26.02
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -1.59
Structure conservation index 0.96
SVM decision value 1.95
SVM RNA-class probability 0.983539
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 838173 100 - 22224390
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCCACUGC--------------------
...((((..(((((((((....)))))))))........((((....))))...))))....((((((((.....))))))))..((.....))......-------------------- ( -26.80)
>DroSec_CAF1 39029 100 - 1
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCCACUGC--------------------
...((((..(((((((((....)))))))))........((((....))))...))))....((((((((.....))))))))..((.....))......-------------------- ( -26.80)
>DroSim_CAF1 35276 100 - 1
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCCACUGC--------------------
...((((..(((((((((....)))))))))........((((....))))...))))....((((((((.....))))))))..((.....))......-------------------- ( -26.80)
>DroEre_CAF1 38541 100 - 1
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCCACUGC--------------------
...((((..(((((((((....)))))))))........((((....))))...))))....((((((((.....))))))))..((.....))......-------------------- ( -26.80)
>DroYak_CAF1 35883 100 - 1
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCCAAAUUAGCAAAUUGCCACUGC--------------------
.......(((((((((((....))))))))((..((((((((.((((.....)))).).)))))))..)).)))...........((.....))......-------------------- ( -22.50)
>DroAna_CAF1 38000 120 - 1
CACGCCCACGGCGUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCUGUUGGGUUUUUGUAGUUUUAGGUGG
((((((((.(((((((((....)))))))))........((((....))))..)))))((((((((((((.....))))))))..(((((..(((....))).))))).))))...))). ( -33.80)
>consensus
AUCGCCCGCGGCAUGAUUGUCAAGUCAUGUUUUAAAAUGUUGGCCAACCAAAUUGGGCAAACAUUUCGAAGUGCAUUCGAAAUUAGCAAAUUGCCACUGC____________________
...(((((.(((((((((....)))))))))........((((....))))..)))))....((((((((.....))))))))..((.....)).......................... (-26.13 = -26.02 +  -0.11) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:55 2006