Locus 340

Sequence ID 2R_DroMel_CAF1
Location 2,238,445 – 2,238,539
Length 94
Max. P 0.903031
window682 window683

overview

Window 2

Location 2,238,445 – 2,238,539
Length 94
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 89.00
Mean single sequence MFE -23.90
Consensus MFE -19.05
Energy contribution -19.17
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.05
Structure conservation index 0.80
SVM decision value 0.15
SVM RNA-class probability 0.607328
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2238445 94 + 20766785
UGGCAGCCUAUGAUUCAAAAUAUAUGGUUUUUGAGGGGGACAUAUGCCUCUGACGAACAUACA----UACAUAUGUACAUCGUCAAGGAUAUAUUCAA
.((((.(((....(((((((........))))))).))).....))))..((((((...((((----(....)))))..))))))............. ( -23.50)
>DroSec_CAF1 4999 95 + 1
UGGCAGCCUAUGACUCAAAAUAUAUGGUUUUUGAGGGGGACAGUUGCCACUGACAAACAUACAUUCAUAAAUAUGUACAUCGUCAAGGU---UUUCAA
(((((((......(((((((........)))))))(....).))))))).((((.....(((((........)))))....))))....---...... ( -23.90)
>DroSim_CAF1 5010 95 + 1
UGGCAGCCUAUGACUCAAAAUAUAUGGUUUUUGAGGGGGUCAGUUGCCACUGACAAACAUACAUUCAUACAUAUGUACAUCGUCAAGGU---UUUCAA
(((.(((((.((((.....(((((((.....((((.(.((((((....))))))...).....))))..))))))).....))))))))---).))). ( -24.30)
>consensus
UGGCAGCCUAUGACUCAAAAUAUAUGGUUUUUGAGGGGGACAGUUGCCACUGACAAACAUACAUUCAUACAUAUGUACAUCGUCAAGGU___UUUCAA
.((((.(((....(((((((........))))))).))).....))))..((((.....(((((........)))))....))))............. (-19.05 = -19.17 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 2,238,445 – 2,238,539
Length 94
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 89.00
Mean single sequence MFE -23.23
Consensus MFE -20.92
Energy contribution -21.70
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -2.19
Structure conservation index 0.90
SVM decision value 1.03
SVM RNA-class probability 0.903031
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2238445 94 - 20766785
UUGAAUAUAUCCUUGACGAUGUACAUAUGUA----UGUAUGUUCGUCAGAGGCAUAUGUCCCCCUCAAAAACCAUAUAUUUUGAAUCAUAGGCUGCCA
.(((((((((((((((((((((((((....)----)))))).)))))).))).)))))).....((((((........)))))).))).......... ( -21.80)
>DroSec_CAF1 4999 95 - 1
UUGAAA---ACCUUGACGAUGUACAUAUUUAUGAAUGUAUGUUUGUCAGUGGCAACUGUCCCCCUCAAAAACCAUAUAUUUUGAGUCAUAGGCUGCCA
......---...((((((((((((((........))))))).)))))))(((((.((((....(((((((........)))))))..))))..))))) ( -24.50)
>DroSim_CAF1 5010 95 - 1
UUGAAA---ACCUUGACGAUGUACAUAUGUAUGAAUGUAUGUUUGUCAGUGGCAACUGACCCCCUCAAAAACCAUAUAUUUUGAGUCAUAGGCUGCCA
......---...((((((((((((((........))))))).)))))))(((((.((......(((((((........))))))).....)).))))) ( -23.40)
>consensus
UUGAAA___ACCUUGACGAUGUACAUAUGUAUGAAUGUAUGUUUGUCAGUGGCAACUGUCCCCCUCAAAAACCAUAUAUUUUGAGUCAUAGGCUGCCA
............((((((((((((((........))))))).))))))).((((.((......(((((((........))))))).....)).)))). (-20.92 = -21.70 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:56 2006