Locus 4392

Sequence ID 3L_DroMel_CAF1
Location 12,865,228 – 12,865,486
Length 258
Max. P 0.901531
window6807 window6808 window6809 window6810

overview

Window 7

Location 12,865,228 – 12,865,348
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.31
Mean single sequence MFE -31.56
Consensus MFE -21.88
Energy contribution -22.12
Covariance contribution 0.25
Combinations/Pair 1.11
Mean z-score -2.09
Structure conservation index 0.69
SVM decision value 0.30
SVM RNA-class probability 0.672599
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12865228 120 + 23771897
CCACCUCAGCCCAACCCACAGUACGCAAUUCAAUACCAGGCCAACCGGCAAUAUGCCAUGCAAGGACAACCCAAUUCGGCCAAUCCUUGGCUCCACUUCUCAGUAGGGAUGUCCUAUCCA
........................(((...........((....))(((.....))).))).((((((.(((.....(((((.....)))))..(((....))).))).))))))..... ( -29.30)
>DroSec_CAF1 103669 120 + 1
CCACCUCAGCCCAAUCCACAGUACGCAAUUCAAUACCAGGCCAACCGGCAAUAUGCCAUGCAAGGAAAACCCAACUCGGCCAAUCCUGGGCUCUACUUCUCAGUGGGGAUGUCCUAUCCA
.......((((((.......(....)............((((....(((.....)))......((.....)).....)))).....))))))(((((....)))))(((((...))))). ( -30.30)
>DroEre_CAF1 109017 120 + 1
CCACCUCAGCCCAACCCGCAAUACGCGAUUCAAUACCAGGCCAACAGGCAGUUCGCCCUGCAAGGACAGCCCAACUGGGGCCAUCCUGGGCUCUACUUCUCCGUAGGGAUGUCCUAUCCA
.......(((((.....(((....((((...........(((....)))...))))..))).((((..((((.....))))..)))))))))((((......))))(((((...))))). ( -37.64)
>DroYak_CAF1 115036 120 + 1
CCACCUCAGCUCAACCCACAGUACGCAAUUCAAUACCAGGCCCACAGGCAAUACGCCAUGCAAGGAGAUCCCAACUGGGCCAAUCCUGGGCUCUACUUCUCAAUGGGGAUGUCCUAUCCC
...(((((((...((.....))..))...........((((((...(((.....))).....((((...(((....)))....)))))))).)).........)))))............ ( -29.00)
>consensus
CCACCUCAGCCCAACCCACAGUACGCAAUUCAAUACCAGGCCAACAGGCAAUACGCCAUGCAAGGACAACCCAACUCGGCCAAUCCUGGGCUCUACUUCUCAGUAGGGAUGUCCUAUCCA
.......(((((............(((...........(.....).(((.....))).))).((((...((......))....)))))))))((((......))))(((((...))))). (-21.88 = -22.12 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,865,268 – 12,865,388
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.39
Mean single sequence MFE -38.26
Consensus MFE -25.81
Energy contribution -27.18
Covariance contribution 1.38
Combinations/Pair 1.04
Mean z-score -2.04
Structure conservation index 0.67
SVM decision value 0.49
SVM RNA-class probability 0.757707
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12865268 120 + 23771897
CCAACCGGCAAUAUGCCAUGCAAGGACAACCCAAUUCGGCCAAUCCUUGGCUCCACUUCUCAGUAGGGAUGUCCUAUCCAACGUAUAUGAACUAUAAUGGACGUUCCGCUGGGAACUCAC
......(((.....)))...((((((....((.....))....)))))).......((((((((.(((((((((........................)))))))))))))))))..... ( -36.06)
>DroSec_CAF1 103709 120 + 1
CCAACCGGCAAUAUGCCAUGCAAGGAAAACCCAACUCGGCCAAUCCUGGGCUCUACUUCUCAGUGGGGAUGUCCUAUCCAACGUAUAUGAGCUAUAAUGGACGUUCCGCUGGGAACUCCC
......(((.....)))..((.((((....((.....))....))))..)).....(((((((((((.((((((........................)))))))))))))))))..... ( -34.96)
>DroEre_CAF1 109057 120 + 1
CCAACAGGCAGUUCGCCCUGCAAGGACAGCCCAACUGGGGCCAUCCUGGGCUCUACUUCUCCGUAGGGAUGUCCUAUCCAACGUACAUGAAAUGUUAUGGCCGUUCAGCUGGGAACUACC
......((.(((((.((..((.((((((.(((.(((((((((......))))))).......)).))).))))))....((((..(((((....)))))..))))..)).))))))).)) ( -42.11)
>DroYak_CAF1 115076 120 + 1
CCCACAGGCAAUACGCCAUGCAAGGAGAUCCCAACUGGGCCAAUCCUGGGCUCUACUUCUCAAUGGGGAUGUCCUAUCCCACGUAUAUGAACUACAAUGGCCGUUCUGCCGGGAACUCCC
......((((..(((((((...((((.(((((....(((((.......)))))..(........)))))).)))).......(((.......))).)))).)))..))))(((....))) ( -39.90)
>consensus
CCAACAGGCAAUACGCCAUGCAAGGACAACCCAACUCGGCCAAUCCUGGGCUCUACUUCUCAGUAGGGAUGUCCUAUCCAACGUAUAUGAACUAUAAUGGACGUUCCGCUGGGAACUCCC
......(((.....)))..((.((((...((......))....))))..)).....((((((((.(((((((((........................)))))))))))))))))..... (-25.81 = -27.18 +   1.38)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,865,308 – 12,865,428
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.92
Mean single sequence MFE -28.13
Consensus MFE -20.35
Energy contribution -21.79
Covariance contribution 1.44
Combinations/Pair 1.08
Mean z-score -1.54
Structure conservation index 0.72
SVM decision value 0.09
SVM RNA-class probability 0.578651
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12865308 120 + 23771897
CAAUCCUUGGCUCCACUUCUCAGUAGGGAUGUCCUAUCCAACGUAUAUGAACUAUAAUGGACGUUCCGCUGGGAACUCACUUCCAUCAUUUUACAAUCCGUACCCACCCAGUUAUAGUAC
......((((......((((((((.(((((((((........................)))))))))))))))))................(((.....))).....))))......... ( -24.56)
>DroSec_CAF1 103749 120 + 1
CAAUCCUGGGCUCUACUUCUCAGUGGGGAUGUCCUAUCCAACGUAUAUGAGCUAUAAUGGACGUUCCGCUGGGAACUCCCCUCCAUCAUUUUACAAUCCGUACCCACCCAGUUAUAGUAC
.....(((((......(((((((((((.((((((........................)))))))))))))))))................(((.....)))....)))))......... ( -30.26)
>DroEre_CAF1 109097 120 + 1
CCAUCCUGGGCUCUACUUCUCCGUAGGGAUGUCCUAUCCAACGUACAUGAAAUGUUAUGGCCGUUCAGCUGGGAACUACCCUUCAUCAUUUUACAAUCCGUAUCUACCCGGUUAUUGCAG
.....(((((((((((......))))))...(((((.(.((((..(((((....)))))..))))..).)))))................................)))))......... ( -25.50)
>DroYak_CAF1 115116 120 + 1
CAAUCCUGGGCUCUACUUCUCAAUGGGGAUGUCCUAUCCCACGUAUAUGAACUACAAUGGCCGUUCUGCCGGGAACUCCCCUCCAUCAUUUUACAAUCCGUAUCUGCCCAGUUAUAGUAC
.....((((((..(((.........((((((...))))))..(((.((((........(((......)))(((....))).....))))..))).....)))...))))))......... ( -32.20)
>consensus
CAAUCCUGGGCUCUACUUCUCAGUAGGGAUGUCCUAUCCAACGUAUAUGAACUAUAAUGGACGUUCCGCUGGGAACUCCCCUCCAUCAUUUUACAAUCCGUACCCACCCAGUUAUAGUAC
.....(((((......((((((((.(((((((((........................)))))))))))))))))................(((.....)))....)))))......... (-20.35 = -21.79 +   1.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,865,388 – 12,865,486
Length 98
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.96
Mean single sequence MFE -15.80
Consensus MFE -8.24
Energy contribution -8.47
Covariance contribution 0.23
Combinations/Pair 1.23
Mean z-score -2.33
Structure conservation index 0.52
SVM decision value 1.02
SVM RNA-class probability 0.901531
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12865388 98 + 23771897
UUCCAUCAUUUUACAAUCCGUACCCACCCAGUUAUAGUACCUAUAAUUACAAUAUUAACUUACCCUUUUCGGGUGGAU----------------------CUUCCUAAGAUCUUCGAUAC
....(((.................(((((((((((((...))))))))....((......))........)))))(((----------------------((.....)))))...))).. ( -16.00)
>DroEre_CAF1 109177 120 + 1
CUUCAUCAUUUUACAAUCCGUAUCUACCCGGUUAUUGCAGCAAUAAUUACAAUAUUAACUUACCCUUUUAGUACUGCUAUAGUUAUGCAGUUUUAUUCUGCUUCCUAAGAUCUUUAAUAC
....(((..........(((........))).....((((.(((((...........(((.........)))(((((.........))))).))))))))).......)))......... ( -14.20)
>DroYak_CAF1 115196 98 + 1
CUCCAUCAUUUUACAAUCCGUAUCUGCCCAGUUAUAGUACCUAUAACUACAAUAUUAACUUACCCUUUUCGGGUGGAU----------------------CUCCAUAGGAUCUUUAAUAC
.(((.......(((.....)))((..(((((((((((...))))))))....((......))........)))..)).----------------------.......))).......... ( -17.20)
>consensus
CUCCAUCAUUUUACAAUCCGUAUCUACCCAGUUAUAGUACCUAUAAUUACAAUAUUAACUUACCCUUUUCGGGUGGAU______________________CUUCCUAAGAUCUUUAAUAC
....(((....(((.....))).((((((((((((((...))))))))....((......))........))))))................................)))......... ( -8.24 =  -8.47 +   0.23)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:31 2006