Locus 2545

Sequence ID 3L_DroMel_CAF1
Location 7,130,353 – 7,130,450
Length 97
Max. P 0.762890
window3952 window3953

overview

Window 2

Location 7,130,353 – 7,130,450
Length 97
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 85.28
Mean single sequence MFE -28.98
Consensus MFE -19.56
Energy contribution -20.12
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.97
Structure conservation index 0.67
SVM decision value 0.51
SVM RNA-class probability 0.762890
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7130353 97 + 23771897
GCAGCUGGAGAAGAAGAAGAGCAUGAAUGAUCGCUCAAGGACUCGGUAUCGUCCUGCCGUUUCCUCUCUCU------CUUUCUCUCUCUGGUUCACUUCCUUU
(.(((..((((.((..(((((...((.(((....))).(((..(((((......)))))..)))))...))------)))..))))))..))))......... ( -30.00)
>DroSec_CAF1 45195 91 + 1
GCAGCUGGAGAAGAAGAAGAGCAUAAAUGAUCGCUCAAGGACUCGAAAUCGUCCUGCCCUUUCCUCUCUC------------UCUCUCUGGUUCACUUCCUUU
(.(((..((((((((((.((((..........)))).(((((........))))).........))).))------------).))))..))))......... ( -24.60)
>DroEre_CAF1 45475 95 + 1
GCAGCUGGAGAAGAAGAAGAGCACGAAUGAUCGCUCAAGGACUCGGUAUCGUCCUGCUGUUUCCUCUCUC--------UCUCCCUGUCUUGCUCACUUGCUUU
((((..((((((((.(((((((.(((....)))....(((((........)))))))).)))).))).))--------)))..))))...((......))... ( -26.10)
>DroYak_CAF1 47290 103 + 1
GCAGCUGGAGAAGAAGAAGAGCGCGAAUGAUCGCUCAAGGACUCGAAAUCGUCCUGCUGUUUCCUCUCUCGCUCUCGCUCUCUCUCUCUUGUUCAGUGCCUUU
(((.(((((.((((((((((((((((..((..((...(((((........)))))...))....))..))))....))))).))).)))).)))))))).... ( -35.20)
>consensus
GCAGCUGGAGAAGAAGAAGAGCACGAAUGAUCGCUCAAGGACUCGAAAUCGUCCUGCCGUUUCCUCUCUC________UCUCUCUCUCUGGUUCACUUCCUUU
(.((((((((((((.(((((((..........)))).(((((........))))).....))).))).................))))))))))......... (-19.56 = -20.12 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 7,130,353 – 7,130,450
Length 97
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 85.28
Mean single sequence MFE -30.30
Consensus MFE -22.46
Energy contribution -22.28
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -1.71
Structure conservation index 0.74
SVM decision value 0.38
SVM RNA-class probability 0.713022
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7130353 97 - 23771897
AAAGGAAGUGAACCAGAGAGAGAAAG------AGAGAGAGGAAACGGCAGGACGAUACCGAGUCCUUGAGCGAUCAUUCAUGCUCUUCUUCUUCUCCAGCUGC
.............(((...(((((..------((((.(((((..(((..........)))..)))))(((((........)))))))))..)))))...))). ( -26.60)
>DroSec_CAF1 45195 91 - 1
AAAGGAAGUGAACCAGAGAGA------------GAGAGAGGAAAGGGCAGGACGAUUUCGAGUCCUUGAGCGAUCAUUUAUGCUCUUCUUCUUCUCCAGCUGC
.............(((...((------------((.(((((((.(((((((((........)))).(((....)))....))))))))))))))))...))). ( -28.10)
>DroEre_CAF1 45475 95 - 1
AAAGCAAGUGAGCAAGACAGGGAGA--------GAGAGAGGAAACAGCAGGACGAUACCGAGUCCUUGAGCGAUCAUUCGUGCUCUUCUUCUUCUCCAGCUGC
..(((..((.......))..(((((--------(..((((((....(((((((........)))))...((((....))))))))))))..)))))).))).. ( -30.70)
>DroYak_CAF1 47290 103 - 1
AAAGGCACUGAACAAGAGAGAGAGAGCGAGAGCGAGAGAGGAAACAGCAGGACGAUUUCGAGUCCUUGAGCGAUCAUUCGCGCUCUUCUUCUUCUCCAGCUGC
....((((((.....(((((..((((.(((.(((((.(((....).(((((((........)))))...))..)).))))).)))))))..)))))))).))) ( -35.80)
>consensus
AAAGGAAGUGAACAAGAGAGAGAGA________GAGAGAGGAAACAGCAGGACGAUACCGAGUCCUUGAGCGAUCAUUCAUGCUCUUCUUCUUCUCCAGCUGC
.................................((((((((((.....(((((........))))).(((((........))))))))))).))))....... (-22.46 = -22.28 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:21 2006