Locus 8565

Sequence ID 3L_DroMel_CAF1
Location 22,349,702 – 22,349,839
Length 137
Max. P 0.696608
window14038 window14039

overview

Window 8

Location 22,349,702 – 22,349,799
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 82.43
Mean single sequence MFE -22.85
Consensus MFE -11.64
Energy contribution -14.38
Covariance contribution 2.75
Combinations/Pair 1.05
Mean z-score -2.80
Structure conservation index 0.51
SVM decision value 0.34
SVM RNA-class probability 0.696608
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22349702 97 + 23771897
GCCACAAAAUGUGCAGAACUUAAGGAUUAUUCAUUCUGCACAGUCGUGGCCAGGCCGCACACAUUUGCUUAAAUAUGCAAGUGAGAUUUCAAUUACA
(((((....(((((((((......((....)).)))))))))...)))))...........(((((((........))))))).............. ( -28.90)
>DroSec_CAF1 657 87 + 1
GCCACAGAAUUUGCAGAACU-AAGCAUUAUUCAUUCGACACAGUCGUGGCC---------ACAUUGGCUUAAAUAUGCAAGUGAGAUUUCAAUUACA
(((((.((((.(((......-..)))..))))....(((...)))))))).---------.((((.((........)).)))).............. ( -19.50)
>DroSim_CAF1 14098 87 + 1
GCCACAGAAUUUGCAGAACU-AAGCAUUAUUCAUUCGACACAGUCGUGGCC---------ACACUGGCUUAAAUAUGCAAGUGAGAUUUCAAUUACA
(((((.((((.(((......-..)))..))))....(((...)))))))).---------.((((.((........)).)))).............. ( -21.80)
>DroEre_CAF1 17576 77 + 1
GCCACAGAAGUUGCAGAACC-CAGCAUUAUUCAUGCUGCAC-------------------ACACUUGCUUAAAUAUGCAAGUGAGAUUUCAAUUACA
......((((((........-((((((.....))))))...-------------------.(((((((........))))))).))))))....... ( -21.20)
>consensus
GCCACAGAAUUUGCAGAACU_AAGCAUUAUUCAUUCGACACAGUCGUGGCC_________ACACUGGCUUAAAUAUGCAAGUGAGAUUUCAAUUACA
(((((......(((((((...............))))))).....)))))...........(((((((........))))))).............. (-11.64 = -14.38 +   2.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 22,349,742 – 22,349,839
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 86.67
Mean single sequence MFE -20.48
Consensus MFE -14.20
Energy contribution -15.20
Covariance contribution 1.00
Combinations/Pair 1.05
Mean z-score -1.59
Structure conservation index 0.69
SVM decision value 0.11
SVM RNA-class probability 0.588817
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22349742 97 + 23771897
CAGUCGUGGCCAGGCCGCACACAUUUGCUUAAAUAUGCAAGUGAGAUUUCAAUUACACUCGUUUCGUUAAUUGAUUACAUCAGGCUGCCGAUCCCCU
((((((((((...)))))...(((((((........))))))).(((.(((((((.((.......)))))))))....))).))))).......... ( -25.80)
>DroSec_CAF1 696 88 + 1
CAGUCGUGGCC---------ACAUUGGCUUAAAUAUGCAAGUGAGAUUUCAAUUACACUCGUUUCGUUAAUUGAUUACAUCAGGCAGCCGAUCCCCU
..((((..(((---------.((((.((........)).)))).(((.(((((((.((.......)))))))))....))).)))...))))..... ( -18.20)
>DroSim_CAF1 14137 88 + 1
CAGUCGUGGCC---------ACACUGGCUUAAAUAUGCAAGUGAGAUUUCAAUUACACUCGUUUCGUUAAUUGAUUACAUCAGGCAGCCGAUCCCCU
..((((..(((---------.((((.((........)).)))).(((.(((((((.((.......)))))))))....))).)))...))))..... ( -20.50)
>DroEre_CAF1 17615 78 + 1
C-------------------ACACUUGCUUAAAUAUGCAAGUGAGAUUUCAAUUACACUCGUUUCGUUAAUUGAUUACAUCAGGCAAGCGAUCCCCU
.-------------------.(((((((........))))))).................(..(((((..(((((...)))))...)))))..)... ( -17.40)
>consensus
CAGUCGUGGCC_________ACACUGGCUUAAAUAUGCAAGUGAGAUUUCAAUUACACUCGUUUCGUUAAUUGAUUACAUCAGGCAGCCGAUCCCCU
.......(((...........(((((((........))))))).(((.(((((((.((.......)))))))))....))).....)))........ (-14.20 = -15.20 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:12 2006