Locus 9635

Sequence ID 3R_DroMel_CAF1
Location 25,462,819 – 25,462,917
Length 98
Max. P 0.952075
window15405 window15406

overview

Window 5

Location 25,462,819 – 25,462,917
Length 98
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 86.65
Mean single sequence MFE -32.38
Consensus MFE -21.45
Energy contribution -23.45
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -4.26
Structure conservation index 0.66
SVM decision value 1.42
SVM RNA-class probability 0.952075
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25462819 98 + 27905053
AUGAUGACAGACACAUCGCAA-AGAAAACCCCCAAAAUCGAAAGGAGCGGAUGCGGAAAGGCAUUCGCA------------UCCGCAUCCGCAUCCGCAUCCUUAUCCCUA
..((((.......))))....-.................((((((((((((((((((...((.......------------...)).))))))))))).))))).)).... ( -32.40)
>DroSec_CAF1 145886 91 + 1
AUGAUGACAGACACAUCGCAA-AGAAAAACCCCA-AAUCCAAAGGAGCGGAUGCGGAAAGGCAUUCGCA------------UCCGC------AUCCGCAUCCUUAUCCCUA
..((((.......))))....-............-......((((((((((((((((...((....)).------------)))))------)))))).)))))....... ( -33.20)
>DroEre_CAF1 153191 110 + 1
AUGAUGACAGACACAUCGCAGAAGAAAACCCCC-AAAUCGAAAGAAGCGGAUGCGGAAAGGCAUUCGCAUUCGCAUCCGCAUCCGCAUCCGCAUCCGCAUCCUUAUCCCUA
..((((.......))))((.((...........-...((....)).(((((((((((...((....))....((....)).))))))))))).)).))............. ( -34.90)
>DroYak_CAF1 156387 99 + 1
AUGAUGACAGACACAUCGCAAAAGAAAACCCCCGAAAUCCAAAGGAGCGGAUGCGGAAAGGCAUUCGCA------------UCCGCAUCAGCAUCAGCAUCCUUAUCCCUA
..((((.......))))........................((((((((((((((((......))))))------------)))))....((....)).)))))....... ( -29.00)
>consensus
AUGAUGACAGACACAUCGCAA_AGAAAACCCCCAAAAUCCAAAGGAGCGGAUGCGGAAAGGCAUUCGCA____________UCCGCAUCCGCAUCCGCAUCCUUAUCCCUA
..((((.......))))........................((((((((((((((((...((......................)).))))))))))).)))))....... (-21.45 = -23.45 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 25,462,819 – 25,462,917
Length 98
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 86.65
Mean single sequence MFE -36.32
Consensus MFE -24.50
Energy contribution -25.82
Covariance contribution 1.31
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 0.67
SVM decision value 0.87
SVM RNA-class probability 0.870563
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25462819 98 - 27905053
UAGGGAUAAGGAUGCGGAUGCGGAUGCGGA------------UGCGAAUGCCUUUCCGCAUCCGCUCCUUUCGAUUUUGGGGGUUUUCU-UUGCGAUGUGUCUGUCAUCAU
..........((((((((((((((((((((------------.((....))...)))))))))((((((.........)))))).....-.......))))))).)))).. ( -37.90)
>DroSec_CAF1 145886 91 - 1
UAGGGAUAAGGAUGCGGAU------GCGGA------------UGCGAAUGCCUUUCCGCAUCCGCUCCUUUGGAUU-UGGGGUUUUUCU-UUGCGAUGUGUCUGUCAUCAU
((((((.(((((.((((((------(((((------------.((....))...))))))))))))))))......-.........)))-))).((((.......)))).. ( -33.19)
>DroEre_CAF1 153191 110 - 1
UAGGGAUAAGGAUGCGGAUGCGGAUGCGGAUGCGGAUGCGAAUGCGAAUGCCUUUCCGCAUCCGCUUCUUUCGAUUU-GGGGGUUUUCUUCUGCGAUGUGUCUGUCAUCAU
..........((((((((((((((.(((((((((((.(((........)))...))))))))))).))).(((....-(((((....))))).))).))))))).)))).. ( -43.60)
>DroYak_CAF1 156387 99 - 1
UAGGGAUAAGGAUGCUGAUGCUGAUGCGGA------------UGCGAAUGCCUUUCCGCAUCCGCUCCUUUGGAUUUCGGGGGUUUUCUUUUGCGAUGUGUCUGUCAUCAU
....(((..((((((...(((....(((((------------((((..........))))))))).((((((.....)))))).........)))..))))))...))).. ( -30.60)
>consensus
UAGGGAUAAGGAUGCGGAUGCGGAUGCGGA____________UGCGAAUGCCUUUCCGCAUCCGCUCCUUUCGAUUUUGGGGGUUUUCU_UUGCGAUGUGUCUGUCAUCAU
.((..(...(((((((((........((.(((((....))))).))........)))))))))((((((.........)))))))..)).....((((.......)))).. (-24.50 = -25.82 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:50 2006