Locus 1946

Sequence ID 3L_DroMel_CAF1
Location 5,400,024 – 5,400,144
Length 120
Max. P 0.851165
window3041 window3042

overview

Window 1

Location 5,400,024 – 5,400,144
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.39
Mean single sequence MFE -40.97
Consensus MFE -33.53
Energy contribution -33.20
Covariance contribution -0.33
Combinations/Pair 1.09
Mean z-score -2.08
Structure conservation index 0.82
SVM decision value 0.51
SVM RNA-class probability 0.765257
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5400024 120 + 23771897
AUCCACAUUCAGGCAUCUGCAAACAAUUCCAUGUGCGCUGGCUGUCAGAUCUGCAGGAAUUGCUCAGCUGCCUGGCCGACGAUUCUCCUGUCGCGGAAAGAGACAGCCUGAAUGGGCAGA
..((.(((((((((.(((((...(((((((.((((..(((.....)))...)))))))))))....))...((..(((.((((......)))))))..)))))..))))))))))).... ( -42.10)
>DroSec_CAF1 48890 104 + 1
AUCCACAUUCAGGCAUCUGCAAACAAUUCCAUUUGCGCUGGCUGUCAGAUCUGCAGGAAUUGCUCAGCUGCCUGGCCGACGAUUCUCC----------------AGCCUGAAUGGGCAGA
..((.(((((((((....(((((........)))))..((((((.((....)))))((((((.((.(((....))).)))))))).))----------------)))))))))))).... ( -35.50)
>DroYak_CAF1 48865 120 + 1
AUCCACAUUCAGGCGCCUGCUAACAAUUCCAUUUGCGCUGGCUGUCAGAUCUGCAGGAAUUGCUCAGCUGCCUGGUCGACAAUUCUCCUGUCGCAGAAAGAGACAGCCUGAGUGGGGAGA
.(((.((((((((((((.((...(((......))).)).)))((((...(((((((((((((.((.(((....))).))))))..))))...)))))....))))))))))))).))).. ( -45.30)
>consensus
AUCCACAUUCAGGCAUCUGCAAACAAUUCCAUUUGCGCUGGCUGUCAGAUCUGCAGGAAUUGCUCAGCUGCCUGGCCGACGAUUCUCCUGUCGC_GAAAGAGACAGCCUGAAUGGGCAGA
..((.(((((((((..((((...(((......)))..(((.....)))....))))((((((.((.(((....))).))))))))....................))))))))))).... (-33.53 = -33.20 +  -0.33)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 5,400,024 – 5,400,144
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.39
Mean single sequence MFE -43.40
Consensus MFE -35.10
Energy contribution -35.77
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.35
Structure conservation index 0.81
SVM decision value 0.79
SVM RNA-class probability 0.851165
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5400024 120 - 23771897
UCUGCCCAUUCAGGCUGUCUCUUUCCGCGACAGGAGAAUCGUCGGCCAGGCAGCUGAGCAAUUCCUGCAGAUCUGACAGCCAGCGCACAUGGAAUUGUUUGCAGAUGCCUGAAUGUGGAU
....(((((((.(((((.(..(((((......)))))...).)))))(((((.(((.(((((((((((....(((.....))).)))...))))))))...))).)))))))))).)).. ( -45.90)
>DroSec_CAF1 48890 104 - 1
UCUGCCCAUUCAGGCU----------------GGAGAAUCGUCGGCCAGGCAGCUGAGCAAUUCCUGCAGAUCUGACAGCCAGCGCAAAUGGAAUUGUUUGCAGAUGCCUGAAUGUGGAU
....(((((((.((((----------------((.......))))))(((((.(((.(((((((((((....(((.....))).)))...))))))))...))).)))))))))).)).. ( -39.70)
>DroYak_CAF1 48865 120 - 1
UCUCCCCACUCAGGCUGUCUCUUUCUGCGACAGGAGAAUUGUCGACCAGGCAGCUGAGCAAUUCCUGCAGAUCUGACAGCCAGCGCAAAUGGAAUUGUUAGCAGGCGCCUGAAUGUGGAU
..(((.((.((((((.((((...((((((((((.....))))))..))))..(((((.((((((((((....(((.....))).)))...)))))))))))))))))))))).)).))). ( -44.60)
>consensus
UCUGCCCAUUCAGGCUGUCUCUUUC_GCGACAGGAGAAUCGUCGGCCAGGCAGCUGAGCAAUUCCUGCAGAUCUGACAGCCAGCGCAAAUGGAAUUGUUUGCAGAUGCCUGAAUGUGGAU
....(((((((((((.........................(((.....))).((.(((((((((((((....(((.....))).)))...))))))))))))....))))))))).)).. (-35.10 = -35.77 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:44 2006