Locus 4

Sequence ID 3L_DroMel_CAF1
Location 24,624 – 24,735
Length 111
Max. P 0.979444
window5 window6

overview

Window 5

Location 24,624 – 24,735
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.84
Mean single sequence MFE -20.97
Consensus MFE -13.84
Energy contribution -13.40
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -2.27
Structure conservation index 0.66
SVM decision value 1.84
SVM RNA-class probability 0.979444
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 24624 111 + 23771897
UACAUAAAUUUAUUCGCAUGUCACAAAAAUGCGA---------CAUCCUCUCUGGAAAAGUUCAAGAAUUUCUAUAAUUACGAAAUUUUCCAGAAUAUGUACAUAUGUAUAUAAAUUCGC
.............((((((.........))))))---------.......(((((((((.(((...((((.....))))..))).))))))))).(((((((....)))))))....... ( -24.90)
>DroSec_CAF1 14200 103 + 1
UAU----UUUUAUUCGCAUGCCAAAAAAAUGCGAUACCGGACGCAUCCUCACUGGAAAAGUUCAUGAGUUUUCAUAACUACGAAAUU-UCCACAAUAUGU------------AAAUUCGC
...----......((((((.........))))))....((((...(((.....)))...))))..((((((.((((.....((....-)).....)))).------------)))))).. ( -19.40)
>DroSim_CAF1 15750 103 + 1
UAU----UUUUAUUCGCAUGCCAAAAAAAUGCGAUACCGGACGCAUCCUCACUGGAAAAGUUCAUGAGUUUUUAUAACUACGAAAUU-UCCACAAUAUGU------------AAAUUCGU
...----......((((((.........))))))....((((...(((.....)))...))))((((((((.((((.....((....-)).....)))).------------)))))))) ( -18.60)
>consensus
UAU____UUUUAUUCGCAUGCCAAAAAAAUGCGAUACCGGACGCAUCCUCACUGGAAAAGUUCAUGAGUUUUUAUAACUACGAAAUU_UCCACAAUAUGU____________AAAUUCGC
.............((((((.........))))))..................((((....(((...((((.....))))..)))....))))............................ (-13.84 = -13.40 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 24,624 – 24,735
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.84
Mean single sequence MFE -25.00
Consensus MFE -14.34
Energy contribution -14.10
Covariance contribution -0.24
Combinations/Pair 1.20
Mean z-score -1.93
Structure conservation index 0.57
SVM decision value 0.11
SVM RNA-class probability 0.588448
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 24624 111 - 23771897
GCGAAUUUAUAUACAUAUGUACAUAUUCUGGAAAAUUUCGUAAUUAUAGAAAUUCUUGAACUUUUCCAGAGAGGAUG---------UCGCAUUUUUGUGACAUGCGAAUAAAUUUAUGUA
..((((((((...............((((((((((.((((.((((.....))))..)))).)))))))))).(.(((---------(((((....)))))))).)..))))))))..... ( -30.30)
>DroSec_CAF1 14200 103 - 1
GCGAAUUU------------ACAUAUUGUGGA-AAUUUCGUAGUUAUGAAAACUCAUGAACUUUUCCAGUGAGGAUGCGUCCGGUAUCGCAUUUUUUUGGCAUGCGAAUAAAA----AUA
.....(((------------((.....)))))-...((((((.((((((....))))))......((((.(((((((((........)))))))))))))..)))))).....----... ( -22.40)
>DroSim_CAF1 15750 103 - 1
ACGAAUUU------------ACAUAUUGUGGA-AAUUUCGUAGUUAUAAAAACUCAUGAACUUUUCCAGUGAGGAUGCGUCCGGUAUCGCAUUUUUUUGGCAUGCGAAUAAAA----AUA
....(((.------------.(((....((((-((.(((((((((.....)))).)))))..))))))(((((((((((........)))))))))...)))))..)))....----... ( -22.30)
>consensus
GCGAAUUU____________ACAUAUUGUGGA_AAUUUCGUAGUUAUAAAAACUCAUGAACUUUUCCAGUGAGGAUGCGUCCGGUAUCGCAUUUUUUUGGCAUGCGAAUAAAA____AUA
....................................((((((((((.((((((((((...........)))))(((((.....)))))...))))).)))).))))))............ (-14.34 = -14.10 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:29:42 2006