Locus 3003

Sequence ID 3L_DroMel_CAF1
Location 8,648,268 – 8,648,388
Length 120
Max. P 0.955829
window4686 window4687

overview

Window 6

Location 8,648,268 – 8,648,388
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.00
Mean single sequence MFE -27.77
Consensus MFE -8.14
Energy contribution -8.70
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.39
Structure conservation index 0.29
SVM decision value 1.08
SVM RNA-class probability 0.912271
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8648268 120 + 23771897
UUAGCCAACUUGAAUGUUUAAAGCCUGACUGACUCAUUCCAAUGUAACUUUGUUGACGAUUCGUGGUUUUGGUAUAACUUCACUAAUCAGUGGUCAGAGUCCAAGUCAGGCUUUAAAAAU
................(((((((((((((((((((....(((.......))).((((.(((..((((...((.....))..))))...))).)))))))))..))))))))))))))... ( -35.60)
>DroSec_CAF1 36297 101 + 1
UUAGCCAACUUGAAUGUUUUAAGCCUGACUGACUCAUUCCAAUGUAACUUUGUUGACGAGUCGUGGUUUUGUUAUAACUUCACUAAUC-------------------AGGCUUUAAAAAU
................((((((((((((..(((((....(((((......)))))..)))))((((.............))))...))-------------------)))).)))))).. ( -21.92)
>DroSim_CAF1 33704 101 + 1
UUAGCCAACUUGAAUGUUUUAAGCCUGACUGACUCAUUCCAAUGUAACUUUGUUGACGAGUCGUGGUUUUGUUAUAACUUCACUAAUC-------------------AGGCUUUAAAAAU
................((((((((((((..(((((....(((((......)))))..)))))((((.............))))...))-------------------)))).)))))).. ( -21.92)
>DroEre_CAF1 37630 120 + 1
UUAGGCAACUUGAAUGUUUUUAGCCUAACUGACUCAUUCCAAUGUAACUUUGUUGACAAUUCGUGGUUUUGGUAUAACAUCACUAAUAAGUGGUCACGGCCCAAGUCAGGUUUUAAAAAC
(((((((((......)))....))))))((((((.....(((((......))))).....((((((((.......)))((((((....)))))))))))....))))))........... ( -24.80)
>DroYak_CAF1 37385 108 + 1
UAA------------GUUUUUUGCCUGACUGACUCAUUCCCAUGUAACUUUGUUGACCAUUUGUGGUUUCGGUAUAACUUCACUAAUAAGUGGUCAGAGUCCAAGUCAGGUUUUAAAAUU
..(------------(((((..(((((((((((((.....((........)).((((((((((((((...((.....))..))).))))))))))))))))..))))))))...)))))) ( -34.60)
>consensus
UUAGCCAACUUGAAUGUUUUAAGCCUGACUGACUCAUUCCAAUGUAACUUUGUUGACGAUUCGUGGUUUUGGUAUAACUUCACUAAUCAGUGGUCA__G_CCAAGUCAGGCUUUAAAAAU
................(((.((((((.............(((((......))))).......((((.............))))........................)))))).)))... ( -8.14 =  -8.70 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 8,648,268 – 8,648,388
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.00
Mean single sequence MFE -26.56
Consensus MFE -8.36
Energy contribution -10.84
Covariance contribution 2.48
Combinations/Pair 1.08
Mean z-score -2.57
Structure conservation index 0.31
SVM decision value 1.46
SVM RNA-class probability 0.955829
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8648268 120 - 23771897
AUUUUUAAAGCCUGACUUGGACUCUGACCACUGAUUAGUGAAGUUAUACCAAAACCACGAAUCGUCAACAAAGUUACAUUGGAAUGAGUCAGUCAGGCUUUAAACAUUCAAGUUGGCUAA
...((((((((((((((..(((((...(((..((((.(((..(((.......)))))).))))((.(((...)))))..)))...)))))))))))))))))))................ ( -33.60)
>DroSec_CAF1 36297 101 - 1
AUUUUUAAAGCCU-------------------GAUUAGUGAAGUUAUAACAAAACCACGACUCGUCAACAAAGUUACAUUGGAAUGAGUCAGUCAGGCUUAAAACAUUCAAGUUGGCUAA
.......((((((-------------------((((.(((..(((.......))))))(((((((...(((.......)))..))))))))))))))))).................... ( -25.20)
>DroSim_CAF1 33704 101 - 1
AUUUUUAAAGCCU-------------------GAUUAGUGAAGUUAUAACAAAACCACGACUCGUCAACAAAGUUACAUUGGAAUGAGUCAGUCAGGCUUAAAACAUUCAAGUUGGCUAA
.......((((((-------------------((((.(((..(((.......))))))(((((((...(((.......)))..))))))))))))))))).................... ( -25.20)
>DroEre_CAF1 37630 120 - 1
GUUUUUAAAACCUGACUUGGGCCGUGACCACUUAUUAGUGAUGUUAUACCAAAACCACGAAUUGUCAACAAAGUUACAUUGGAAUGAGUCAGUUAGGCUAAAAACAUUCAAGUUGCCUAA
...........((((((((..(((((((((((....)))).....................(((....))).)))))...))..))))))))((((((....(((......))))))))) ( -25.20)
>DroYak_CAF1 37385 108 - 1
AAUUUUAAAACCUGACUUGGACUCUGACCACUUAUUAGUGAAGUUAUACCGAAACCACAAAUGGUCAACAAAGUUACAUGGGAAUGAGUCAGUCAGGCAAAAAAC------------UUA
..........(((((((..(((((((((((((....))))..))))..((...((((....))))...((........))))...))))))))))))........------------... ( -23.60)
>consensus
AUUUUUAAAGCCUGACUUGG_C__UGACCACUGAUUAGUGAAGUUAUACCAAAACCACGAAUCGUCAACAAAGUUACAUUGGAAUGAGUCAGUCAGGCUUAAAACAUUCAAGUUGGCUAA
...(((.(((((((((................((((.(((..(((.......)))))).)))).............(((....))).....))))))))).)))................ ( -8.36 = -10.84 +   2.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:10 2006