Locus 5052

Sequence ID 3R_DroMel_CAF1
Location 13,304,199 – 13,304,289
Length 90
Max. P 0.800219
window8241 window8242

overview

Window 1

Location 13,304,199 – 13,304,289
Length 90
Sequences 3
Columns 90
Reading direction forward
Mean pairwise identity 91.85
Mean single sequence MFE -25.80
Consensus MFE -20.15
Energy contribution -20.60
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -2.28
Structure conservation index 0.78
SVM decision value 0.09
SVM RNA-class probability 0.580923
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13304199 90 + 27905053
GUAUCAUUUUCCAAGAACAUGGGGCACCCAAUUCAGAUGGGGAACGUGGCCAUCUGAAAUGUCCACCCAUGCAUUCAUUGCUAAUUUGGA
.........((((((...(((((.....((.(((((((((.........))))))))).))....)))))(((.....)))...)))))) ( -27.50)
>DroSec_CAF1 56668 83 + 1
GUAUCAUUUUUCAAGGACAUGGGGCACACAAUUCAGAUGGGGAACGUGGCCAUCUGAAAUG------CAUGC-UUCAUUACUAAUUUGGA
.........((((((...((((((((..((.(((((((((.........))))))))).))------..)))-)))))......)))))) ( -24.90)
>DroSim_CAF1 60294 90 + 1
GUAUCAUUUUUCAAGGACAUGGGGCACACAAUUCAGAUGGGGAACGUGGCCAUCUGAAAUGUCCACCCAUGCAUUCAUUACUAAUUUGGA
..............(((((((((....(((.(((((((((.........))))))))).)))...))))))..))).............. ( -25.00)
>consensus
GUAUCAUUUUUCAAGGACAUGGGGCACACAAUUCAGAUGGGGAACGUGGCCAUCUGAAAUGUCCACCCAUGCAUUCAUUACUAAUUUGGA
..............(((((((((.....((.(((((((((.........))))))))).))....))))))..))).............. (-20.15 = -20.60 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 13,304,199 – 13,304,289
Length 90
Sequences 3
Columns 90
Reading direction reverse
Mean pairwise identity 91.85
Mean single sequence MFE -27.50
Consensus MFE -20.68
Energy contribution -21.34
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.23
Structure conservation index 0.75
SVM decision value 0.61
SVM RNA-class probability 0.800219
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13304199 90 - 27905053
UCCAAAUUAGCAAUGAAUGCAUGGGUGGACAUUUCAGAUGGCCACGUUCCCCAUCUGAAUUGGGUGCCCCAUGUUCUUGGAAAAUGAUAC
(((((.(((....)))..(((((((.(.((..(((((((((.........)))))))))....)).))))))))..)))))......... ( -30.40)
>DroSec_CAF1 56668 83 - 1
UCCAAAUUAGUAAUGAA-GCAUG------CAUUUCAGAUGGCCACGUUCCCCAUCUGAAUUGUGUGCCCCAUGUCCUUGAAAAAUGAUAC
............(((..-(((((------((.(((((((((.........))))))))).)))))))..)))(((.((....)).))).. ( -24.70)
>DroSim_CAF1 60294 90 - 1
UCCAAAUUAGUAAUGAAUGCAUGGGUGGACAUUUCAGAUGGCCACGUUCCCCAUCUGAAUUGUGUGCCCCAUGUCCUUGAAAAAUGAUAC
.....((((.........(((((((.(.(((((((((((((.........)))))))))..)))).))))))))..........)))).. ( -27.41)
>consensus
UCCAAAUUAGUAAUGAAUGCAUGGGUGGACAUUUCAGAUGGCCACGUUCCCCAUCUGAAUUGUGUGCCCCAUGUCCUUGAAAAAUGAUAC
.....((((.........(((((((....((.(((((((((.........))))))))).)).....)))))))..........)))).. (-20.68 = -21.34 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:03 2006