Locus 4277

Sequence ID 3L_DroMel_CAF1
Location 12,526,506 – 12,526,619
Length 113
Max. P 0.767775
window6608 window6609

overview

Window 8

Location 12,526,506 – 12,526,604
Length 98
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 82.70
Mean single sequence MFE -13.82
Consensus MFE -10.50
Energy contribution -10.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.76
SVM decision value 0.52
SVM RNA-class probability 0.767775
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12526506 98 + 23771897
GCCGCAAAAAACA---------------GCAAACUAAAACAGCAAAAAAA--AUAAAGGUAUAAAAACAUUAAACAUUAAACAGCGCUGAAUGUUUGUGGCUAUGUACAAUCGCA
((((((((...((---------------((...((.....))........--......((.(((.....))).))..........))))....)))))))).............. ( -15.20)
>DroSec_CAF1 14782 95 + 1
GCCGCAAAACGCC----------------AAAACUAAAACAGCAAAAAAA----AAAUGUAUAAAAACAUUAAACAUUAAACAGCGCUGAAUGUUUGUGGCUAUGUACAAUCGCA
((((((((..(..----------------....).....((((.......----.(((((.(((.....))).))))).......))))....)))))))).............. ( -15.36)
>DroSim_CAF1 14574 99 + 1
GCCGCAAAAAGCC----------------AAAACUAAAACAGCAAAAAAAGUAUAAAAGUAUAAAAACAUUAAACAUUAAACAGCGCUGAAUGUUUGUGGCUAUGUACAAUCGCA
((((((((.((..----------------....))....((((.......((((....)))).......(((.....))).....))))....)))))))).............. ( -13.50)
>DroEre_CAF1 14697 105 + 1
GCCGCAAAAAAACACAACAAAAAUAUAACCAAACUAAAACAGCAAAAA---------AGUAUAA-AACAUUAAACAUUAAACAGCGCUGAAUGUUUGUGGCUAUGUACAUUCGUA
((((((((.................((.......))...((((.....---------.((....-.)).(((.....))).....))))....)))))))).............. ( -11.20)
>consensus
GCCGCAAAAAACC________________AAAACUAAAACAGCAAAAAAA____AAAAGUAUAAAAACAUUAAACAUUAAACAGCGCUGAAUGUUUGUGGCUAUGUACAAUCGCA
(((((.....................................................((......))...(((((((...........)))))))))))).............. (-10.50 = -10.50 +   0.00)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 9

Location 12,526,526 – 12,526,619
Length 93
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 90.56
Mean single sequence MFE -14.19
Consensus MFE -10.81
Energy contribution -10.62
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -1.61
Structure conservation index 0.76
SVM decision value 0.09
SVM RNA-class probability 0.580354
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12526526 93 + 23771897
AAAACAGCAAAAAAA--AUAAAGGUAUAAAAACAUUAAACAUUAAACAGCGCUGAAUGUUUGUGGCUAUGUACAAUCGCACAGGCAGAAAUGUAC--
....((((.......--......((......)).(((.....))).....)))).((((((.((.((.(((......))).)).)).))))))..-- ( -12.40)
>DroSec_CAF1 14801 93 + 1
AAAACAGCAAAAAAA----AAAUGUAUAAAAACAUUAAACAUUAAACAGCGCUGAAUGUUUGUGGCUAUGUACAAUCGCACAGGCAGAAAUGUACAC
....((((.......----.(((((.(((.....))).))))).......)))).((((((.((.((.(((......))).)).)).)))))).... ( -15.86)
>DroSim_CAF1 14593 97 + 1
AAAACAGCAAAAAAAGUAUAAAAGUAUAAAAACAUUAAACAUUAAACAGCGCUGAAUGUUUGUGGCUAUGUACAAUCGCACAAGCAGAAAUGUACAC
...............(((((...(((((.(..(((.(((((((...........))))))))))..).)))))....((....)).....))))).. ( -14.00)
>DroEre_CAF1 14732 85 + 1
AAAACAGCAAAAA---------AGUAUAA-AACAUUAAACAUUAAACAGCGCUGAAUGUUUGUGGCUAUGUACAUUCGUACAGGCAGAAAUGUAC--
.............---------.......-.(((((...(((.(((((........))))))))(((.(((((....))))))))...)))))..-- ( -14.50)
>consensus
AAAACAGCAAAAAAA____AAAAGUAUAAAAACAUUAAACAUUAAACAGCGCUGAAUGUUUGUGGCUAUGUACAAUCGCACAGGCAGAAAUGUAC__
.......................(((((....(((.(((((((...........))))))))))(((.(((.(....).)))))).....))))).. (-10.81 = -10.62 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:18 2006