Locus 7489

Sequence ID X_DroMel_CAF1
Location 18,678,383 – 18,678,517
Length 134
Max. P 0.898443
window12284 window12285

overview

Window 4

Location 18,678,383 – 18,678,477
Length 94
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 71.56
Mean single sequence MFE -30.54
Consensus MFE -23.62
Energy contribution -23.73
Covariance contribution 0.12
Combinations/Pair 1.18
Mean z-score -1.16
Structure conservation index 0.77
SVM decision value 1.00
SVM RNA-class probability 0.898443
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18678383 94 + 22224390
------AGCUGCUCU--CGUUAACUU------------------AUUCAAAACUGAAAUUUCUUUAUCAUUUCAGCAAAUGGACGAUCCGCCUUCGCUGCCCGUGGGCACGGAGGUGAGU
------....(((((--((((.....------------------.((((....))))..........(((((....))))))))))...(((((((.((((....))))))))))))))) ( -27.70)
>DroSim_CAF1 3925 94 + 1
------AGGUGCUCU--CGUCAACUU------------------AUCUAAAUCUGGAAUUCCUUUGUCUUUCCAGCAAAUGGACGAUCCGCCUUCGCUGCCCGUGGGCACGGAGGUGAGU
------....(((((--((((.....------------------........((((((...........))))))(....))))))...(((((((.((((....))))))))))))))) ( -31.60)
>DroYak_CAF1 3748 117 + 1
AGCCCAAGCUGGUCCGCCUCU-GUUUGCCAAAGUGAAUAUGCUCAUCCAAAUCUGGAACU-CUUUGUCU-UUCAGCAAAUGGACGAUCCGCCAUCGCUGCCCGUGGGCACGGAGGUAAGU
(((....)))((..((..(((-((((((((((((((......)))((((....))))...-)))))...-....)))))))))))..))(((..((.((((....))))))..))).... ( -32.31)
>consensus
______AGCUGCUCU__CGUUAACUU__________________AUCCAAAUCUGGAAUU_CUUUGUCUUUUCAGCAAAUGGACGAUCCGCCUUCGCUGCCCGUGGGCACGGAGGUGAGU
.............................................((((...((((((...........))))))....)))).....((((((((.((((....))))))))))))... (-23.62 = -23.73 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 18,678,401 – 18,678,517
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.73
Mean single sequence MFE -42.07
Consensus MFE -39.12
Energy contribution -38.57
Covariance contribution -0.55
Combinations/Pair 1.11
Mean z-score -1.40
Structure conservation index 0.93
SVM decision value -0.00
SVM RNA-class probability 0.531535
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18678401 116 + 22224390
----AUUCAAAACUGAAAUUUCUUUAUCAUUUCAGCAAAUGGACGAUCCGCCUUCGCUGCCCGUGGGCACGGAGGUGAGUGCCAAGUACAAGGGCGCCUUCUGCGAGGCGAAGGUCAGCA
----.((((...(((((((.........)))))))....)))).((((((((((((.((((....))))))))))))..((((..(((.((((...)))).)))..))))..)))).... ( -39.80)
>DroSim_CAF1 3943 116 + 1
----AUCUAAAUCUGGAAUUCCUUUGUCUUUCCAGCAAAUGGACGAUCCGCCUUCGCUGCCCGUGGGCACGGAGGUGAGUGCCAAGUACAAGGGCGCCUUCUGCGAGGCGAAGGUCAGCA
----........((((....((((((((((....(((...((.((.((((((((((.((((....)))))))))))..((((...))))..)))))))...))))))))))))))))).. ( -44.00)
>DroYak_CAF1 3787 118 + 1
GCUCAUCCAAAUCUGGAACU-CUUUGUCU-UUCAGCAAAUGGACGAUCCGCCAUCGCUGCCCGUGGGCACGGAGGUAAGUGCCAAGUACAAGGGCGCCUUCUGCGAGGCGAAGGUCAGCA
(((..((((....))))..(-((((((((-(.(((.....((.((.((((((..((.((((....))))))..)))..((((...))))..)))))))..))).))))))))))..))). ( -42.40)
>consensus
____AUCCAAAUCUGGAAUU_CUUUGUCUUUUCAGCAAAUGGACGAUCCGCCUUCGCUGCCCGUGGGCACGGAGGUGAGUGCCAAGUACAAGGGCGCCUUCUGCGAGGCGAAGGUCAGCA
.....((((...((((((...........))))))....)))).((((((((.((((((((....)))).(((((...(((((.........))))))))))))))))))..)))).... (-39.12 = -38.57 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:12 2006