Locus 3301

Sequence ID 3L_DroMel_CAF1
Location 9,680,174 – 9,680,281
Length 107
Max. P 0.988032
window5135 window5136

overview

Window 5

Location 9,680,174 – 9,680,281
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 96.26
Mean single sequence MFE -41.43
Consensus MFE -39.39
Energy contribution -39.83
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.64
Structure conservation index 0.95
SVM decision value 1.64
SVM RNA-class probability 0.969060
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9680174 107 + 23771897
GAAGGAUCUGCUGGACGAUGCCGAUGAUCUGCUACAGAAUUGUAGCAGUGAAAACGGCAGCAGUGGAGCGGAUUUGCUCGACUCGCUGGUCAAGCGAAGUUGCGAGG
...(((((((((..((..(((((.....(((((((......)))))))......)))))...))..))))))))).(((((((((((.....)))).)))..)))). ( -44.80)
>DroSim_CAF1 79511 107 + 1
UAAGGAUCUGCUGGACGAUGCCGAUGAUCUGCUACAGAAUUGCAGCAGUGAAAACGGCAGCAGUGGAGCGGAUCUGCUCGACUCGCUGGUCAAGCGAAGUUGCGAGG
...(((((((((..((..(((((.....(((((.(......).)))))......)))))...))..))))))))).(((((((((((.....)))).)))..)))). ( -42.90)
>DroYak_CAF1 76331 107 + 1
GAAGGAUCUGCUGGACGACGCCGAUGAUCUGCUACAGAAUUGCAGCAGUGAAAACGGCAGCAGUGGAGCUGAUCUUCUCGACUCGCUGGUCAAGCGAAGUUGCGAGG
...(((((.(((..((..(((((.....(((((.(......).)))))......)))).)..))..))).)))))((.(((((((((.....)))).))))).)).. ( -36.60)
>consensus
GAAGGAUCUGCUGGACGAUGCCGAUGAUCUGCUACAGAAUUGCAGCAGUGAAAACGGCAGCAGUGGAGCGGAUCUGCUCGACUCGCUGGUCAAGCGAAGUUGCGAGG
...(((((((((..((..(((((.....(((((.(......).)))))......)))))...))..))))))))).(((((((((((.....)))).)))..)))). (-39.39 = -39.83 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 9,680,174 – 9,680,281
Length 107
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 96.26
Mean single sequence MFE -37.93
Consensus MFE -36.07
Energy contribution -35.97
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -3.77
Structure conservation index 0.95
SVM decision value 2.10
SVM RNA-class probability 0.988032
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9680174 107 - 23771897
CCUCGCAACUUCGCUUGACCAGCGAGUCGAGCAAAUCCGCUCCACUGCUGCCGUUUUCACUGCUACAAUUCUGUAGCAGAUCAUCGGCAUCGUCCAGCAGAUCCUUC
............(((.(((.(((.(((.((((......)))).))))))((((......((((((((....)))))))).....))))...))).)))......... ( -37.60)
>DroSim_CAF1 79511 107 - 1
CCUCGCAACUUCGCUUGACCAGCGAGUCGAGCAGAUCCGCUCCACUGCUGCCGUUUUCACUGCUGCAAUUCUGUAGCAGAUCAUCGGCAUCGUCCAGCAGAUCCUUA
............(((((((......))))))).((((.(((..((.(.(((((......((((((((....)))))))).....))))).)))..))).)))).... ( -38.30)
>DroYak_CAF1 76331 107 - 1
CCUCGCAACUUCGCUUGACCAGCGAGUCGAGAAGAUCAGCUCCACUGCUGCCGUUUUCACUGCUGCAAUUCUGUAGCAGAUCAUCGGCGUCGUCCAGCAGAUCCUUC
.((((..(((.((((.....)))))))))))..((((.(((..((.((.((((......((((((((....)))))))).....)))))).))..))).)))).... ( -37.90)
>consensus
CCUCGCAACUUCGCUUGACCAGCGAGUCGAGCAGAUCCGCUCCACUGCUGCCGUUUUCACUGCUGCAAUUCUGUAGCAGAUCAUCGGCAUCGUCCAGCAGAUCCUUC
.((((..(((.((((.....)))))))))))..((((.(((..((.(.(((((......((((((((....)))))))).....))))).)))..))).)))).... (-36.07 = -35.97 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:20 2006