Locus 1566

Sequence ID 3R_DroMel_CAF1
Location 4,495,736 – 4,495,881
Length 145
Max. P 0.874830
window2583 window2584

overview

Window 3

Location 4,495,736 – 4,495,841
Length 105
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 85.32
Mean single sequence MFE -23.32
Consensus MFE -19.62
Energy contribution -19.22
Covariance contribution -0.40
Combinations/Pair 1.18
Mean z-score -1.70
Structure conservation index 0.84
SVM decision value 0.56
SVM RNA-class probability 0.781255
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4495736 105 - 27905053
CACAUACAUAUGUAUGUAUGUAUUUAGCAGCCCCCUCAAAAACUUUUUCGCACCCACCCUGGAAAUGGAGGGGGUCACCUUUGAAGCAACAAGUGCAAGGUGCAC
.((((((((....)))))))).....((.((((((((.......((((((.........))))))..)))))))).(((((....(((.....)))))))))).. ( -31.10)
>DroSec_CAF1 5525 88 - 1
CAC--------------AUGUAUUUA---ACCCCCUCAAAAACUUUUUCGCACCCACCCUUGAAAUGGAGGGGGUCACCUUUGAAGCAACAAGUGCAAGGUGCAC
...--------------.........---((((((((........(((((..........)))))..))))))))((((((....(((.....)))))))))... ( -21.90)
>DroSim_CAF1 5551 90 - 1
CACAU------------AUGUAUUUA---GCCCCCUCAAAAACUUUUUCGCACCCACCCUUGAAAUGGAGGGGGUCACCUUUGAAGCAACAAGUGCAAGGUGCAC
.....------------.........---((((((((........(((((..........)))))..))))))))((((((....(((.....)))))))))... ( -22.20)
>DroEre_CAF1 5714 86 - 1
CAAA----------------UACUUA---GUCCCCUCAAAAACUUUUUCGCACCCACCCUUGAAAUGGAGGGGGUCACCUCUGAAGCAACAAGUGCAAGGUGCAC
....----------------......---....................((((((((..(((...((((((......))))))...)))...)))...))))).. ( -19.10)
>DroYak_CAF1 5601 86 - 1
CAAA----------------UUCUUA---GCCCCUUUCAAAACUUUUUCGCAGCCACCCUUGAAAUGGAAGGGGUCACCUUUGAAGCAACAAGUGCAAGGUGCAC
....----------------......---((((((((((......(((((.((.....)))))))))))))))))((((((....(((.....)))))))))... ( -22.30)
>consensus
CACA_____________AUGUAUUUA___GCCCCCUCAAAAACUUUUUCGCACCCACCCUUGAAAUGGAGGGGGUCACCUUUGAAGCAACAAGUGCAAGGUGCAC
.............................((((((((........(((((..........)))))..))))))))((((((....(((.....)))))))))... (-19.62 = -19.22 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,495,761 – 4,495,881
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.68
Mean single sequence MFE -20.12
Consensus MFE -12.80
Energy contribution -12.20
Covariance contribution -0.60
Combinations/Pair 1.31
Mean z-score -1.74
Structure conservation index 0.64
SVM decision value 0.89
SVM RNA-class probability 0.874830
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4495761 120 - 27905053
UAACUAUUUUUGUUUUAUUUUCUUUUGUAAUGUUUCAAAACACAUACAUAUGUAUGUAUGUAUUUAGCAGCCCCCUCAAAAACUUUUUCGCACCCACCCUGGAAAUGGAGGGGGUCACCU
..........((((..((....(((((........))))).((((((((....))))))))))..))))((((((((.......((((((.........))))))..))))))))..... ( -25.30)
>DroSec_CAF1 5550 103 - 1
UAACUGUUUUUGUUUUAUUUUCAUUUGUAAUGUUGCAAAACAC--------------AUGUAUUUA---ACCCCCUCAAAAACUUUUUCGCACCCACCCUUGAAAUGGAGGGGGUCACCU
..(((((((((((..((((.........))))..)))))).))--------------).)).....---((((((((........(((((..........)))))..))))))))..... ( -21.00)
>DroSim_CAF1 5576 105 - 1
UAACUGUUUUUGUUUUAUUUUCAUUUGUAAUGUUGCAAAGCACAU------------AUGUAUUUA---GCCCCCUCAAAAACUUUUUCGCACCCACCCUUGAAAUGGAGGGGGUCACCU
....(((((((((..((((.........))))..)))))).))).------------.........---((((((((........(((((..........)))))..))))))))..... ( -20.60)
>DroEre_CAF1 5739 95 - 1
UAACAGUUUUUAUUUUGGU------UAUUAAGUUGCAAAACAAA----------------UACUUA---GUCCCCUCAAAAACUUUUUCGCACCCACCCUUGAAAUGGAGGGGGUCACCU
....(((((((.....((.------.(((((((...........----------------.)))))---))..))..))))))).....(.((((.((((......)).))))))).... ( -18.60)
>DroYak_CAF1 5626 90 - 1
UAAUAGUUUUAACAAUAAA------UAAUAA-----UAAACAAA----------------UUCUUA---GCCCCUUUCAAAACUUUUUCGCAGCCACCCUUGAAAUGGAAGGGGUCACCU
...................------......-----........----------------......---((((((((((......(((((.((.....)))))))))))))))))..... ( -15.10)
>consensus
UAACUGUUUUUGUUUUAUUUUC_UUUGUAAUGUUGCAAAACACA_____________AUGUAUUUA___GCCCCCUCAAAAACUUUUUCGCACCCACCCUUGAAAUGGAGGGGGUCACCU
.....................................................................((((((((........(((((..........)))))..))))))))..... (-12.80 = -12.20 +  -0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:40 2006