Locus 2136

Sequence ID X_DroMel_CAF1
Location 5,799,708 – 5,799,819
Length 111
Max. P 0.879996
window3467 window3468

overview

Window 7

Location 5,799,708 – 5,799,819
Length 111
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 74.54
Mean single sequence MFE -32.53
Consensus MFE -21.01
Energy contribution -22.82
Covariance contribution 1.81
Combinations/Pair 1.06
Mean z-score -1.79
Structure conservation index 0.65
SVM decision value 0.91
SVM RNA-class probability 0.879996
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5799708 111 + 22224390
UCUUUAUGCCACCAGACGGUCAGGGACUCAAGGAAUGGAGUCCGUGACUGCAUAUGGAUCGGUAUACUCCGUAAGUAAAUCCAGUUUGACUUAUCAAGCGAUGUGGCUCUU
.......(((((..(.((((((.((((((........)))))).)))))))...((((((((......))).......)))))((((((....))))))...))))).... ( -40.01)
>DroSim_CAF1 5400 110 + 1
UCUUUAUGCCACCAGACGGUCAGGGACUCGAGGAAUGGAGUCCGUGACUGCAUAUGGAUCGGUAUACU-CGUAAGUAAAUCCAGUUUGACUUAUCAAGCGAUGUGGCUCUU
.......(((((((..((((((.((((((.(....).)))))).))))))....)))(((((..((((-....))))...)).((((((....))))))))).)))).... ( -39.70)
>DroEre_CAF1 5120 84 + 1
UCUUUAUGCCACCAGACGGUCAGGGACUCGAGGAAUGGAGUGCGUGACUGCAGGUGGAUCUG--------G-------------------CGAUCAAGCGAUCUGGCUCUU
.......((((((.(.((((((.(.((((.(....).)))).).))))))).)))(((((..--------(-------------------(......)))))))))).... ( -30.70)
>DroYak_CAF1 5911 95 + 1
UCUUUAUGCCACCAGACGGUCAGGGACUUGAAGAAUGGCGUCCGUGACUGCAGGUAAAUCCC--------G--------UCCAGACCAACUAAUCAAGCAAUCUAAGUCUU
......(((.(((.(.((((((.((((............)))).))))))).))).......--------(--------(....))...........)))........... ( -19.70)
>consensus
UCUUUAUGCCACCAGACGGUCAGGGACUCGAGGAAUGGAGUCCGUGACUGCAGAUGGAUCGG________G________UCCAGUUUGACUUAUCAAGCGAUCUGGCUCUU
........(((((.(.((((((.((((((........)))))).))))))).)))))...................................................... (-21.01 = -22.82 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 5,799,708 – 5,799,819
Length 111
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 74.54
Mean single sequence MFE -28.95
Consensus MFE -17.96
Energy contribution -18.65
Covariance contribution 0.69
Combinations/Pair 1.19
Mean z-score -1.55
Structure conservation index 0.62
SVM decision value -0.04
SVM RNA-class probability 0.515672
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5799708 111 - 22224390
AAGAGCCACAUCGCUUGAUAAGUCAAACUGGAUUUACUUACGGAGUAUACCGAUCCAUAUGCAGUCACGGACUCCAUUCCUUGAGUCCCUGACCGUCUGGUGGCAUAAAGA
....(((((...((((((....))))..(((((((((((...)))))....))))))...)).((((.((((((........)))))).))))......)))))....... ( -33.50)
>DroSim_CAF1 5400 110 - 1
AAGAGCCACAUCGCUUGAUAAGUCAAACUGGAUUUACUUACG-AGUAUACCGAUCCAUAUGCAGUCACGGACUCCAUUCCUCGAGUCCCUGACCGUCUGGUGGCAUAAAGA
....(((((...((((((....))))..((((((((((....-))))....))))))...)).((((.((((((........)))))).))))......)))))....... ( -33.40)
>DroEre_CAF1 5120 84 - 1
AAGAGCCAGAUCGCUUGAUCG-------------------C--------CAGAUCCACCUGCAGUCACGCACUCCAUUCCUCGAGUCCCUGACCGUCUGGUGGCAUAAAGA
....(((.((((....))))(-------------------(--------(((((.........((((.(.((((........)))).).)))).))))))))))....... ( -23.60)
>DroYak_CAF1 5911 95 - 1
AAGACUUAGAUUGCUUGAUUAGUUGGUCUGGA--------C--------GGGAUUUACCUGCAGUCACGGACGCCAUUCUUCAAGUCCCUGACCGUCUGGUGGCAUAAAGA
....(((....((((..(((((.(((((.(((--------(--------((......)).((.(((...)))))..........))))..))))).)))))))))..))). ( -25.30)
>consensus
AAGAGCCACAUCGCUUGAUAAGUCAAACUGGA________C________CCGAUCCACAUGCAGUCACGGACUCCAUUCCUCGAGUCCCUGACCGUCUGGUGGCAUAAAGA
..((((......))))......................................(((((.((.((((.((((((........)))))).)))).).).)))))........ (-17.96 = -18.65 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:05 2006