Locus 5912

Sequence ID 3L_DroMel_CAF1
Location 15,880,857 – 15,880,966
Length 109
Max. P 0.884423
window9422 window9423

overview

Window 2

Location 15,880,857 – 15,880,966
Length 109
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 94.19
Mean single sequence MFE -30.42
Consensus MFE -26.48
Energy contribution -27.10
Covariance contribution 0.62
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.87
SVM decision value 0.48
SVM RNA-class probability 0.751800
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15880857 109 + 23771897
AUGG-GCUCCCCCUUCUGACAAGAGUUUUGUGAGAAGGCGAAUUGAGGAAAUUCUGAAACAGCAGCAGAAACCAAAUGAGGAACAGCAAAAGGGCGUUGCUGCCAAGAGC
....-((((..((((((.(((((...))))).)))))).(((((.....))))).....(((((((.....((......))....((......)))))))))....)))) ( -31.40)
>DroSec_CAF1 25944 110 + 1
AUGGGGCACCCCCUUCUGACAAGAGUUUUGUGAGAAGGGGAAUUGAGGAAAUUCUGAAACAGCAGCAGAAACCAAAUGAGGAACAGCAAAAGGGCGUUGCUGCCAAGAGC
....(((..((((((((.(((((...))))).))))))))....................((((((.....((......))....((......)))))))))))...... ( -35.20)
>DroEre_CAF1 18963 106 + 1
AUGG----CCCCCUCCUGACAAGAGUUCUGUGAGAAGGCGAAUUGAGGAAAUUCUGAAACAGCAGCAGAAACCAAAUGAGGAACAGCAAAAGGGCGUUGCUGCCAAGGGA
....----..((((.((.(((.(....)))).))..((((((((.....)))))......((((((.....((......))....((......))))))))))).)))). ( -27.60)
>DroYak_CAF1 28942 106 + 1
AUGG----CCCCCUUCUGACAAGAGUUUCGUGAGGAGGCGAAUUGAGGAAAUUCUGAAACAGCAGCAGAAACCAAAUGAGGAACAGCAAAAGGGCGUUGCUGCCAAGAGA
...(----((.((((.(((........))).)))).)))(((((.....))))).....(((((((.....((......))....((......)))))))))........ ( -27.50)
>consensus
AUGG____CCCCCUUCUGACAAGAGUUUUGUGAGAAGGCGAAUUGAGGAAAUUCUGAAACAGCAGCAGAAACCAAAUGAGGAACAGCAAAAGGGCGUUGCUGCCAAGAGA
.(((.......((((((.((((.....)))).)))))).(((((.....))))).....(((((((.....((......))....((......))))))))))))..... (-26.48 = -27.10 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 15,880,857 – 15,880,966
Length 109
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 94.19
Mean single sequence MFE -28.85
Consensus MFE -24.96
Energy contribution -24.52
Covariance contribution -0.44
Combinations/Pair 1.14
Mean z-score -2.06
Structure conservation index 0.87
SVM decision value 0.93
SVM RNA-class probability 0.884423
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15880857 109 - 23771897
GCUCUUGGCAGCAACGCCCUUUUGCUGUUCCUCAUUUGGUUUCUGCUGCUGUUUCAGAAUUUCCUCAAUUCGCCUUCUCACAAAACUCUUGUCAGAAGGGGGAGC-CCAU
(((((((((((((..((......))....((......))....)))))))......(((((.....))))).((((((.((((.....)))).))))))))))))-.... ( -31.60)
>DroSec_CAF1 25944 110 - 1
GCUCUUGGCAGCAACGCCCUUUUGCUGUUCCUCAUUUGGUUUCUGCUGCUGUUUCAGAAUUUCCUCAAUUCCCCUUCUCACAAAACUCUUGUCAGAAGGGGGUGCCCCAU
((....(((((((..((......))....((......))....)))))))...................(((((((((.((((.....)))).))))))))).))..... ( -30.70)
>DroEre_CAF1 18963 106 - 1
UCCCUUGGCAGCAACGCCCUUUUGCUGUUCCUCAUUUGGUUUCUGCUGCUGUUUCAGAAUUUCCUCAAUUCGCCUUCUCACAGAACUCUUGUCAGGAGGGGG----CCAU
.(((..(((((((..((......))....((......))....)))))))......(((((.....))))).((((((.((((.....)))).)))))))))----.... ( -27.20)
>DroYak_CAF1 28942 106 - 1
UCUCUUGGCAGCAACGCCCUUUUGCUGUUCCUCAUUUGGUUUCUGCUGCUGUUUCAGAAUUUCCUCAAUUCGCCUCCUCACGAAACUCUUGUCAGAAGGGGG----CCAU
......(((((((..((......))....((......))....)))))))......(((((.....)))))((((((((((((.....))))..).))))))----)... ( -25.90)
>consensus
GCUCUUGGCAGCAACGCCCUUUUGCUGUUCCUCAUUUGGUUUCUGCUGCUGUUUCAGAAUUUCCUCAAUUCGCCUUCUCACAAAACUCUUGUCAGAAGGGGG____CCAU
.(((..(((((((..((......))....((......))....)))))))......(((((.....))))).((((((.((((.....)))).)))))))))........ (-24.96 = -24.52 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:36 2006