Locus 1832

Sequence ID 3L_DroMel_CAF1
Location 5,140,396 – 5,140,490
Length 94
Max. P 0.999627
window2861 window2862

overview

Window 1

Location 5,140,396 – 5,140,490
Length 94
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 72.61
Mean single sequence MFE -20.62
Consensus MFE -11.28
Energy contribution -12.52
Covariance contribution 1.24
Combinations/Pair 1.06
Mean z-score -1.83
Structure conservation index 0.55
SVM decision value 0.83
SVM RNA-class probability 0.861664
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5140396 94 + 23771897
UUUUGACGCCUUCUGAGUUUGUAAGUUUGAGAAUAUGAAUAUUCUCAGGAAGUGGAAACCCACUUAAU-UUUUAGGCUCCUGUAUCUAUGCAUAU
.......((((...(((((......((((((((((....))))))))))((((((....)))))))))-))..))))...((((....))))... ( -23.60)
>DroSec_CAF1 3945 72 + 1
UUUUGGCGCCUCCUUAGGUUGUAAGUUUGAGAAUAUGAAUAUUCUCAGAAAGUGGAAGCCCACUUAAU-UUGU----------------------
.....((((((....))).)))...((((((((((....))))))))))((((((....))))))...-....---------------------- ( -19.40)
>DroSim_CAF1 2826 72 + 1
UUUUGGCGCCUCCUUAGGUUGUAAGUUUGAGAAUAUGAAUAUUCUCAGGAAGUGGAAGCCCACUUAAU-UUGU----------------------
.....((((((....))).)))...((((((((((....))))))))))((((((....))))))...-....---------------------- ( -18.70)
>DroEre_CAF1 3894 92 + 1
UUUUGGCGCCUCCUUAGGAUAUAAUUUUGAGAAUAUGAC--UUCUCAGGAAGUCGGAACCCAAUUAAU-UUGUGGGCUGCUGUAUCUAUGCAUUC
....(((((((.((((((((...))))))))....((((--(((....))))))).............-....)))).))).............. ( -19.80)
>DroYak_CAF1 3914 90 + 1
UUUUGGCACCUCAU---AAUAUAAGUUUGAGAAUAUAAC--UUCUCAGGAAGUGGGAACCCAAUUAAUUUUGUAGGCUCCUGUUUCUAUGCAUAU
.....(((......---..........((((((......--))))))(((((..(((.(((((......)))..)).)))..))))).))).... ( -21.60)
>consensus
UUUUGGCGCCUCCUUAGGUUGUAAGUUUGAGAAUAUGAAUAUUCUCAGGAAGUGGAAACCCACUUAAU_UUGU_GGCU_CUGU_UCUAUGCAU__
.........................((((((((((....))))))))))((((((....)))))).............................. (-11.28 = -12.52 +   1.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 5,140,396 – 5,140,490
Length 94
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 72.61
Mean single sequence MFE -19.74
Consensus MFE -8.80
Energy contribution -10.20
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -2.96
Structure conservation index 0.45
SVM decision value 3.80
SVM RNA-class probability 0.999627
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5140396 94 - 23771897
AUAUGCAUAGAUACAGGAGCCUAAAA-AUUAAGUGGGUUUCCACUUCCUGAGAAUAUUCAUAUUCUCAAACUUACAAACUCAGAAGGCGUCAAAA
...............(..((((....-...((((((....))))))..((((((((....))))))))................))))..).... ( -21.30)
>DroSec_CAF1 3945 72 - 1
----------------------ACAA-AUUAAGUGGGCUUCCACUUUCUGAGAAUAUUCAUAUUCUCAAACUUACAACCUAAGGAGGCGCCAAAA
----------------------....-......(((((((((......((((((((....))))))))...(((.....))))))))).)))... ( -19.10)
>DroSim_CAF1 2826 72 - 1
----------------------ACAA-AUUAAGUGGGCUUCCACUUCCUGAGAAUAUUCAUAUUCUCAAACUUACAACCUAAGGAGGCGCCAAAA
----------------------....-......(((((((((......((((((((....))))))))...(((.....))))))))).)))... ( -19.10)
>DroEre_CAF1 3894 92 - 1
GAAUGCAUAGAUACAGCAGCCCACAA-AUUAAUUGGGUUCCGACUUCCUGAGAA--GUCAUAUUCUCAAAAUUAUAUCCUAAGGAGGCGCCAAAA
....((.........(.((((((...-......)))))).)(.(((((((((((--......))))))...(((.....)))))))))))..... ( -18.30)
>DroYak_CAF1 3914 90 - 1
AUAUGCAUAGAAACAGGAGCCUACAAAAUUAAUUGGGUUCCCACUUCCUGAGAA--GUUAUAUUCUCAAACUUAUAUU---AUGAGGUGCCAAAA
....((((.(((...((((((((..........))))))))...))).((((((--......))))))..(((((...---)))))))))..... ( -20.90)
>consensus
__AUGCAUAGA_ACAG_AGCC_ACAA_AUUAAGUGGGUUUCCACUUCCUGAGAAUAUUCAUAUUCUCAAACUUACAACCUAAGGAGGCGCCAAAA
..............................((((((....))))))..((((((((....))))))))........................... ( -8.80 = -10.20 +   1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:54 2006