Locus 948

Sequence ID 3R_DroMel_CAF1
Location 3,126,812 – 3,126,947
Length 135
Max. P 0.724941
window1514 window1515

overview

Window 4

Location 3,126,812 – 3,126,918
Length 106
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 90.25
Mean single sequence MFE -22.62
Consensus MFE -20.24
Energy contribution -20.30
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -1.34
Structure conservation index 0.89
SVM decision value 0.06
SVM RNA-class probability 0.566024
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3126812 106 - 27905053
CAAACCAUUUUUCAUUGCAGAAGCCGCACAACAACAACGGUUACUCGUGGUCCACCGGCAACAACAACGAGGUUGUCAGUCAUAGCAGCAACGGCCACACCAACAA
................(.((.(((((...........))))).)))((((((....(....)......(..(((((........)))))..)))))))........ ( -20.30)
>DroSec_CAF1 2488 106 - 1
CAAACCAUUUUUCAUUGCAGAAGCCGCACAACAACAACGGCUACUCGUGGUCCACCGGCAACAACAACGAGGUUGUCAGUCAUAGCAGCAACGGCCACAACAACAA
................(.((.(((((...........))))).)))((((((....(....)......(..(((((........)))))..)))))))........ ( -22.70)
>DroSim_CAF1 2860 106 - 1
CAAACCAUUUUUCAUUGCAGAAGCCGCACAACAACAACGGCUACUCGUGGUCCACCGGCAACAACAACGAGGUUGUCAGUCAUAGCAGCAACGGCCACAACAACAA
................(.((.(((((...........))))).)))((((((....(....)......(..(((((........)))))..)))))))........ ( -22.70)
>DroEre_CAF1 2565 91 - 1
CAAACCAUUUUUCAUUGCAGAAGCCGCACAACAACAGCGGCUACUCGUGGUCCGCCGGCAACAACAACGAGGUUGUCACUAAUAGCAGCA---------------A
..............((((...((((((.........)))))).(((((((....))(....)....)))))(((((.....))))).)))---------------) ( -24.80)
>consensus
CAAACCAUUUUUCAUUGCAGAAGCCGCACAACAACAACGGCUACUCGUGGUCCACCGGCAACAACAACGAGGUUGUCAGUCAUAGCAGCAACGGCCACAACAACAA
..............((((...(((((...........))))).(((((((....))(....)....)))))(((((.....))))).))))............... (-20.24 = -20.30 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 3,126,838 – 3,126,947
Length 109
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 96.79
Mean single sequence MFE -25.20
Consensus MFE -23.67
Energy contribution -23.80
Covariance contribution 0.13
Combinations/Pair 1.09
Mean z-score -1.71
Structure conservation index 0.94
SVM decision value 0.41
SVM RNA-class probability 0.724941
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3126838 109 - 27905053
UUUGACGAAACCCUUUUUCACACAGACAACAAACCAUUUUUCAUUGCAGAAGCCGCACAACAACAACGGUUACUCGUGGUCCACCGGCAACAACAACGAGGUUGUCAGU
......((((.....)))).....((((((....................(((((...........))))).(((((((....))(....)....)))))))))))... ( -22.80)
>DroSec_CAF1 2514 109 - 1
UUUGACGAAACCCUUUUUCACACAGACAACAAACCAUUUUUCAUUGCAGAAGCCGCACAACAACAACGGCUACUCGUGGUCCACCGGCAACAACAACGAGGUUGUCAGU
......((((.....)))).....((((((....................(((((...........))))).(((((((....))(....)....)))))))))))... ( -25.20)
>DroSim_CAF1 2886 109 - 1
UUUGACGAAACCCUUUUUCACACAGACAACAAACCAUUUUUCAUUGCAGAAGCCGCACAACAACAACGGCUACUCGUGGUCCACCGGCAACAACAACGAGGUUGUCAGU
......((((.....)))).....((((((....................(((((...........))))).(((((((....))(....)....)))))))))))... ( -25.20)
>DroEre_CAF1 2576 107 - 1
UUUGACGAAACCCUU-UUCACACAGGCA-CAAACCAUUUUUCAUUGCAGAAGCCGCACAACAACAGCGGCUACUCGUGGUCCGCCGGCAACAACAACGAGGUUGUCACU
..((((((...((((-........(((.-...(((((...((......))((((((.........))))))....)))))..)))(....)......)))))))))).. ( -27.60)
>consensus
UUUGACGAAACCCUUUUUCACACAGACAACAAACCAUUUUUCAUUGCAGAAGCCGCACAACAACAACGGCUACUCGUGGUCCACCGGCAACAACAACGAGGUUGUCAGU
......((((.....)))).....((((((....................(((((...........))))).(((((((....))(....)....)))))))))))... (-23.67 = -23.80 +   0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:19 2006