Locus 4308

Sequence ID 3L_DroMel_CAF1
Location 12,648,315 – 12,648,408
Length 93
Max. P 0.685766
window6664 window6665

overview

Window 4

Location 12,648,315 – 12,648,408
Length 93
Sequences 3
Columns 99
Reading direction forward
Mean pairwise identity 93.94
Mean single sequence MFE -25.37
Consensus MFE -22.32
Energy contribution -22.10
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.88
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12648315 93 + 23771897
UUCGUAUUCUCAAUCU------GAAUCUGAAUCCGAAUCUGAAUCUGAAUCGGUAUCUGAAUUGGUAUCGGAAUCCGUUCGAUUGCAGACUACAGAUGC
...(((.((((((((.------((((..((.(((((.((.......)).))((((((......))))))))).)).))))))))).))).)))...... ( -24.40)
>DroSec_CAF1 12552 99 + 1
UUCGUAUUCUCAAUCUCAAUCUGAAUCGGAGUCCGAAUCUGAAUCUGAAUCGGUAUCUGAAUUGGUAUCGGAAUCCGUUCGAUUGCAGACUACAGAUGC
...(((((.....((((((((.(((.((((.(((((.((.......)).))((((((......))))))))).)))))))))))).))).....))))) ( -28.60)
>DroSim_CAF1 12450 99 + 1
UUCGAAUUCUCAAUCUCAAUCUGAAUCUGAGUCCGAAUCUGAAUCUGAAUCGGUAUCUGAAUUGGUAUCGGAAUCCGUUCGAUUGCAGACUACAGAUGC
........................(((((((((.(((((.((((.....((((((((......)))))))).....)))))))).).)))).))))).. ( -23.10)
>consensus
UUCGUAUUCUCAAUCUCAAUCUGAAUCUGAGUCCGAAUCUGAAUCUGAAUCGGUAUCUGAAUUGGUAUCGGAAUCCGUUCGAUUGCAGACUACAGAUGC
.(((.((((....((.......))....)))).)))(((((..((((((((((((((......)))))).(((....))))))).))))...))))).. (-22.32 = -22.10 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 12,648,315 – 12,648,408
Length 93
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 93.94
Mean single sequence MFE -25.68
Consensus MFE -22.75
Energy contribution -23.20
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.97
Structure conservation index 0.89
SVM decision value 0.32
SVM RNA-class probability 0.685766
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12648315 93 - 23771897
GCAUCUGUAGUCUGCAAUCGAACGGAUUCCGAUACCAAUUCAGAUACCGAUUCAGAUUCAGAUUCGGAUUCAGAUUC------AGAUUGAGAAUACGAA
..(((((.((((((.((((((((((..((.((.......)).))..))).))).)))))))))))))))((..((((------.......))))..)). ( -22.30)
>DroSec_CAF1 12552 99 - 1
GCAUCUGUAGUCUGCAAUCGAACGGAUUCCGAUACCAAUUCAGAUACCGAUUCAGAUUCAGAUUCGGACUCCGAUUCAGAUUGAGAUUGAGAAUACGAA
...(((.((((((.((((((((((((.(((((.......((.((.......)).)).......))))).)))).))).))))))))))))))....... ( -28.44)
>DroSim_CAF1 12450 99 - 1
GCAUCUGUAGUCUGCAAUCGAACGGAUUCCGAUACCAAUUCAGAUACCGAUUCAGAUUCAGAUUCGGACUCAGAUUCAGAUUGAGAUUGAGAAUUCGAA
...((((.((((((.((((((((((..((.((.......)).))..))).))).))))))))))))))(((((.(((.....))).)))))........ ( -26.30)
>consensus
GCAUCUGUAGUCUGCAAUCGAACGGAUUCCGAUACCAAUUCAGAUACCGAUUCAGAUUCAGAUUCGGACUCAGAUUCAGAUUGAGAUUGAGAAUACGAA
...((((.((((((.((((((((((..((.((.......)).))..))).))).))))))))))))))(((((.(((.....))).)))))........ (-22.75 = -23.20 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:10 2006