Locus 4760

Sequence ID X_DroMel_CAF1
Location 12,383,334 – 12,383,438
Length 104
Max. P 0.970814
window7798 window7799

overview

Window 8

Location 12,383,334 – 12,383,438
Length 104
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 85.67
Mean single sequence MFE -34.63
Consensus MFE -30.89
Energy contribution -30.67
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.55
Structure conservation index 0.89
SVM decision value 1.66
SVM RNA-class probability 0.970814
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12383334 104 + 22224390
CCAAACGCCAAAGUUGGCUUAAUGAGAAGUUUAGCUCAUGUUCCCACAGCCAUUCAUGGAUGGGGAAGUUAUCUUUGGUGGGGUGGGGGGUUGGCU------------AUAUGAAA
(((..((((((((.((((...(((((........))))).(((((.((.(((....))).))))))))))).))))))))...)))..........------------........ ( -33.80)
>DroSim_CAF1 15204 103 + 1
C-AAACGCCAAAGUUGGCUUAAUGAGUAGUUUAGCUCAUGUUCCCACAGCCAUUCAUGGACGGGGAAGUCAUCUUUGGUGGG----GGGGUUAGCUAC--------AUAUAUGAAA
.-...((((((((.((((...((((((......)))))).(((((....(((....)))...))))))))).))))))))..----............--------.......... ( -32.70)
>DroYak_CAF1 2465 110 + 1
G-AAACGCCAAAGUUGGCUUAAUGAGUAGUUUAGCUCAUGUUCCCACAGCCAUUCAUGGACGGGGAAGUCAACUUUGGUGG-----GGGGUUAGCUACAUACAUACAUAUAUGAAA
.-...(((((((((((((...((((((......)))))).(((((....(((....)))...)))))))))))))))))).-----...............((((....))))... ( -37.40)
>consensus
C_AAACGCCAAAGUUGGCUUAAUGAGUAGUUUAGCUCAUGUUCCCACAGCCAUUCAUGGACGGGGAAGUCAUCUUUGGUGGG____GGGGUUAGCUAC________AUAUAUGAAA
.....((((((((.((((...(((((........))))).(((((....(((....)))...))))))))).)))))))).................................... (-30.89 = -30.67 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,383,334 – 12,383,438
Length 104
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 85.67
Mean single sequence MFE -23.93
Consensus MFE -20.69
Energy contribution -20.47
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.45
Structure conservation index 0.86
SVM decision value 0.05
SVM RNA-class probability 0.560720
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12383334 104 - 22224390
UUUCAUAU------------AGCCAACCCCCCACCCCACCAAAGAUAACUUCCCCAUCCAUGAAUGGCUGUGGGAACAUGAGCUAAACUUCUCAUUAAGCCAACUUUGGCGUUUGG
........------------..........(((...(.((((((.....(((((((.(((....))).)).))))).(((((........)))))........)))))).)..))) ( -22.50)
>DroSim_CAF1 15204 103 - 1
UUUCAUAUAU--------GUAGCUAACCCC----CCCACCAAAGAUGACUUCCCCGUCCAUGAAUGGCUGUGGGAACAUGAGCUAAACUACUCAUUAAGCCAACUUUGGCGUUU-G
..........--------............----..(.((((((.((..(((((((.(((....))).)).))))).(((((........))))).....)).)))))).)...-. ( -21.40)
>DroYak_CAF1 2465 110 - 1
UUUCAUAUAUGUAUGUAUGUAGCUAACCCC-----CCACCAAAGUUGACUUCCCCGUCCAUGAAUGGCUGUGGGAACAUGAGCUAAACUACUCAUUAAGCCAACUUUGGCGUUU-C
...((((((....))))))...........-----.(.(((((((((..(((((((.(((....))).)).))))).(((((........))))).....))))))))).)...-. ( -27.90)
>consensus
UUUCAUAUAU________GUAGCUAACCCC____CCCACCAAAGAUGACUUCCCCGUCCAUGAAUGGCUGUGGGAACAUGAGCUAAACUACUCAUUAAGCCAACUUUGGCGUUU_G
....................................(.((((((.....(((((((.(((....))).)).))))).(((((........)))))........)))))).)..... (-20.69 = -20.47 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:36 2006