Locus 1609

Sequence ID X_DroMel_CAF1
Location 4,609,691 – 4,609,784
Length 93
Max. P 0.997792
window2633 window2634

overview

Window 3

Location 4,609,691 – 4,609,784
Length 93
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 78.02
Mean single sequence MFE -23.65
Consensus MFE -17.55
Energy contribution -18.33
Covariance contribution 0.78
Combinations/Pair 1.12
Mean z-score -1.98
Structure conservation index 0.74
SVM decision value 1.58
SVM RNA-class probability 0.965683
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4609691 93 + 22224390
AUAGGUU-GAGCGGUUAUGUCAGAGGUGAGCAUACAUACAUACAUACCUCUCACUUUCGCACACCUCUGCCCUCCCUCUCCCACGCUUCCGCGC
...((..-(((.((....(.((((((((.((...........................)).)))))))))...)))))..)).(((....))). ( -25.73)
>DroSec_CAF1 33835 85 + 1
AUAGGAU-GAAAGGUUAUGUCAGAGGUGAGCAUAC--------AUACCUCUCGCUUUCGCACACCUCUGCCCUCCCUCUCCCUCACUCGCGCGC
..(((..-((.(((....(.((((((((.((....--------...............)).)))))))))....))).)))))........... ( -19.41)
>DroEre_CAF1 36973 82 + 1
AUAGGGAAGAGGGGUUAAGUCAGAGGUGAACACAC--------AUACCUCUCGCUCUCGCACACCUCUGCCCUCCCUUUCUA----UCCUGCGC
..((((.(((((.((..(((.(((((((.......--------.))))))).)))...))...))))).)))).........----........ ( -25.80)
>consensus
AUAGGAU_GAGAGGUUAUGUCAGAGGUGAGCAUAC________AUACCUCUCGCUUUCGCACACCUCUGCCCUCCCUCUCCC_C_CUCCCGCGC
........((((((....(.((((((((.((...........................)).)))))))))....)))))).............. (-17.55 = -18.33 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 4,609,691 – 4,609,784
Length 93
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 78.02
Mean single sequence MFE -33.17
Consensus MFE -22.05
Energy contribution -22.50
Covariance contribution 0.45
Combinations/Pair 1.20
Mean z-score -2.82
Structure conservation index 0.66
SVM decision value 2.93
SVM RNA-class probability 0.997792
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4609691 93 - 22224390
GCGCGGAAGCGUGGGAGAGGGAGGGCAGAGGUGUGCGAAAGUGAGAGGUAUGUAUGUAUGUAUGCUCACCUCUGACAUAACCGCUC-AACCUAU
((((....)))).....(((..((((.(..((((((....)).((((((..(((((....)))))..)))))).))))..).))))-..))).. ( -36.00)
>DroSec_CAF1 33835 85 - 1
GCGCGCGAGUGAGGGAGAGGGAGGGCAGAGGUGUGCGAAAGCGAGAGGUAU--------GUAUGCUCACCUCUGACAUAACCUUUC-AUCCUAU
.(((....))).((((..(..(((.(((((((((((....)))...((((.--------...))))))))))))......)))..)-.)))).. ( -34.70)
>DroEre_CAF1 36973 82 - 1
GCGCAGGA----UAGAAAGGGAGGGCAGAGGUGUGCGAGAGCGAGAGGUAU--------GUGUGUUCACCUCUGACUUAACCCCUCUUCCCUAU
....(((.----.(((..((..(((((((((((.(((..(.(....).)..--------...))).)))))))).)))..))..)))..))).. ( -28.80)
>consensus
GCGCGGGAG_G_GGGAGAGGGAGGGCAGAGGUGUGCGAAAGCGAGAGGUAU________GUAUGCUCACCUCUGACAUAACCCCUC_AACCUAU
.(((....)))...(((.((....((((((((..((....))(((..((((........)))).)))))))))).)....)).)))........ (-22.05 = -22.50 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:35 2006