Locus 8080

Sequence ID X_DroMel_CAF1
Location 20,115,980 – 20,116,214
Length 234
Max. P 0.897024
window13263 window13264

overview

Window 3

Location 20,115,980 – 20,116,100
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.78
Mean single sequence MFE -14.35
Consensus MFE -13.45
Energy contribution -13.45
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.05
Structure conservation index 0.94
SVM decision value -0.05
SVM RNA-class probability 0.508223
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20115980 120 - 22224390
UUACAUUUACAUUCACAUUCACAUCCACAUCAACAACAUCUUCAUGCACUUGAGUCGGCAAUAUAAAUCAAAUCAAAAGCACAAACAAGCCGCGAGUGUGUACACAAUUCAAGUAAACUC
.............(((((((.........((((...(((....)))...))))(.((((.............................)))))))))))).................... ( -14.35)
>DroSec_CAF1 16534 114 - 1
UUACAUUUACAUC------CGCAUCCACAUCAACAACAUCUUCAUGCACUUGAGUCGGCAAUAUAAAUCAAAUCAAAAGCACAAACAAGCCGCGAGUGUGUACACAAUUCAAGUAAACUC
.............------.((((...................))))((((((((((((.............................))))...(((....))).))))))))...... ( -14.96)
>DroEre_CAF1 12982 109 - 1
-----------UCCAUAUACACAAUCACAUCAACAACAUCUUCAUGCACUUGAGUCGGCAAUAUAAAUCAAAUCAAAAGCACAAACAAGCCGCGAGUGUGUACACAAUUCAAGUAAACUC
-----------......((((((.((...((((...(((....)))...))))(.((((.............................))))))).)))))).................. ( -13.75)
>consensus
UUACAUUUACAUCCA_AU_CACAUCCACAUCAACAACAUCUUCAUGCACUUGAGUCGGCAAUAUAAAUCAAAUCAAAAGCACAAACAAGCCGCGAGUGUGUACACAAUUCAAGUAAACUC
...............................................((((((((((((.............................))))...(((....))).))))))))...... (-13.45 = -13.45 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 20,116,100 – 20,116,214
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.35
Mean single sequence MFE -18.70
Consensus MFE -14.09
Energy contribution -13.77
Covariance contribution -0.33
Combinations/Pair 1.19
Mean z-score -1.40
Structure conservation index 0.75
SVM decision value 1.00
SVM RNA-class probability 0.897024
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20116100 114 - 22224390
CCAACAGCAGACAGAGAUCAUCAUCAUCA------UGGUGGCCCGAAAAUCGGAGCACAAGUUCUGGCCCACUCACAUCCACAUCCACAUCCAUAUCCACACUCGCACUCACACUCACAU
...........(((((..((((((....)------)))))(((((.....))).)).....)))))...................................................... ( -15.80)
>DroSec_CAF1 16648 101 - 1
CCAACAGCAGACAGAGAUCAUCAUCAUCAUCAUCCUGGUGGCCCCA-AAUCGGAGCACAAGUUCUGGCCCACACACAUCCACAUCCA------UAUGCA------------CACUCACAU
......(((..(((.(((.((.......)).))))))((((.((..-....(((((....))))))).))))...............------..))).------------......... ( -16.80)
>DroEre_CAF1 13091 100 - 1
CCGACACCAGACAGAGAUCAUCAUCAUCGUCGUCAUGGUGGACCCG-AACCGGAGCACAAGCUCUGGCCCACUCACAUCCACAUCCACAUGCACAUCC------------------ACA-
.........(((.(((((....))).)))))(((((((((((...(-(.(((((((....))))))).....))...))))).....)))).))....------------------...- ( -23.50)
>consensus
CCAACAGCAGACAGAGAUCAUCAUCAUCAUC_UC_UGGUGGCCCCA_AAUCGGAGCACAAGUUCUGGCCCACUCACAUCCACAUCCACAU_CAUAUCCA____________CACUCACAU
.............(((.......((((((......))))))........(((((((....)))))))....))).............................................. (-14.09 = -13.77 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:58 2006