Locus 3941

Sequence ID 2R_DroMel_CAF1
Location 13,012,193 – 13,012,345
Length 152
Max. P 0.855672
window6362 window6363

overview

Window 2

Location 13,012,193 – 13,012,283
Length 90
Sequences 3
Columns 90
Reading direction forward
Mean pairwise identity 85.23
Mean single sequence MFE -16.21
Consensus MFE -12.82
Energy contribution -13.48
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.31
Structure conservation index 0.79
SVM decision value 0.81
SVM RNA-class probability 0.855672
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13012193 90 + 20766785
GAGGGGUUCUUGAACCCGAGUGUAUACCAUACCAUUGCUAUUCCCAUAGCUACAUCCACACCCACACCAGCCACAUCCACAUUACAUCCA
...(((((....)))))(.((((.............(((((....))))).............)))))...................... ( -13.87)
>DroSec_CAF1 25974 76 + 1
GAGGGGUUCUUGAACCCGAGUGUGUACCAUAACAUAGCUAUUCCCAUAGCUACAUCCACACCCACACCAGCCACAU--------------
...(((((....)))))(.(((((..........(((((((....)))))))..........))))))........-------------- ( -18.95)
>DroSim_CAF1 22318 84 + 1
GAGGGGUUCUUGAACCCGAGAGUAUACCAUACCAUAGCUAUUCCCAUAGCUACAUGCACACCCACACCAGCCACAUCCACAUCA------
..(((.((((((....))))))............(((((((....)))))))........))).....................------ ( -15.80)
>consensus
GAGGGGUUCUUGAACCCGAGUGUAUACCAUACCAUAGCUAUUCCCAUAGCUACAUCCACACCCACACCAGCCACAUCCACAU_A______
...(((((....)))))(.((((...........(((((((....)))))))...........)))))...................... (-12.82 = -13.48 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,012,253 – 13,012,345
Length 92
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 81.29
Mean single sequence MFE -16.32
Consensus MFE -9.10
Energy contribution -9.13
Covariance contribution 0.03
Combinations/Pair 1.09
Mean z-score -2.30
Structure conservation index 0.56
SVM decision value 0.33
SVM RNA-class probability 0.692616
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13012253 92 + 20766785
----CCCACACCAGCCACAUCCACAUUACAUCCACAUCCACACCCGCAUAAAGGUUGGCAGUGGCAUUUCAAUUUCGCAAAUGAA---CCCCA----CUGCCC
----.....................................(((........))).((((((((...((((..........))))---..)))----))))). ( -16.30)
>DroSec_CAF1 26034 75 + 1
----CCCACACCAGCCACAU-----------------CCACACCCGCAUAAAGGUUGGCAGUGGCAUUUCAAUUUCGCAAAUGAA---CCCCA----CUGCCC
----........((((....-----------------...............))))((((((((...((((..........))))---..)))----))))). ( -16.71)
>DroSim_CAF1 22378 86 + 1
----CCCACACCAGCCACAUCCACAUCA------CAUCCACACCCGCAUAAAGGUUGGCAGUGGCAUUUCAAUUUCGCAAAUGAA---CCCCA----CUGCCC
----........................------.......(((........))).((((((((...((((..........))))---..)))----))))). ( -16.30)
>DroEre_CAF1 21962 81 + 1
----CCCACACUAGCCACAUCC-----------ACAUCCACACCCGCAUAAAGGUUGGCAGUGGCAUUUCAAUUUCGCAAAUGAA---CCCCG----CUGCCC
----........((((......-----------...................))))((((((((...((((..........))))---..)))----))))). ( -15.91)
>DroYak_CAF1 22666 89 + 1
ACACCCCACACCAGCCACAUUC-----------ACAUCCACACCCGCAUAAAGGUUGGCAGUGGCAUUUCAAUUUCGCAAAUGAA---CCCCACUCACUGCCC
.....((((.((((((......-----------...................))))))..))))............(((..(((.---......))).))).. ( -13.91)
>DroAna_CAF1 29145 83 + 1
-----------CUGCCACAUCCGCAC-----CCGCACCAGCACCCGCAUAAAGGUUGGCAGUGGCAUUUCAAUUUCGCAAAUGAAUAGCCCCC----CUUCCC
-----------((((((...((((..-----..))....((....)).....)).)))))).(((..((((..........))))..)))...----...... ( -18.80)
>consensus
____CCCACACCAGCCACAUCC___________ACAUCCACACCCGCAUAAAGGUUGGCAGUGGCAUUUCAAUUUCGCAAAUGAA___CCCCA____CUGCCC
.............(((((...................(((.(((........))))))..)))))...................................... ( -9.10 =  -9.13 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:52 2006