Locus 4230

Sequence ID 3R_DroMel_CAF1
Location 11,371,567 – 11,371,685
Length 118
Max. P 0.903450
window6852 window6853

overview

Window 2

Location 11,371,567 – 11,371,685
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.86
Mean single sequence MFE -22.24
Consensus MFE -17.58
Energy contribution -17.38
Covariance contribution -0.20
Combinations/Pair 1.22
Mean z-score -1.99
Structure conservation index 0.79
SVM decision value 1.03
SVM RNA-class probability 0.903450
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11371567 118 + 27905053
UUGAUCGAAAUAUUGCCAGCCAAAGUUCCAGACUGUAACGAUACGAAAAUAAAUGUAUAACUCAAACU--AAUCAAAACAAAUCUACUUACGUUUCGCACUGGAACAUUGGCAAUCAAAU
..................(((((.(((((((..((((....)))).....(((((((...........--..................)))))))....))))))).)))))........ ( -21.85)
>DroSec_CAF1 119207 118 + 1
UUGAUCGAAACAUUGCCAGCCAAGGUUCCAGACUGUAACAAUACGAAAAUAAAUGUAUAACUCAAACU--AAUCAAAACAAAUCUACUUACGUUUCGCACUGGUACAUUGGCAAUCAAAU
..................(((((.((.((((..((((....)))).....(((((((...........--..................)))))))....)))).)).)))))........ ( -17.45)
>DroSim_CAF1 110242 118 + 1
UUGAUCGAAAUAUUGCCAGCCAAAGUUCCAGACUGUAACAAUACGAAAAUAAAUGUAUUACUCAAACU--AAUCUAAAAAAAUGUACUUACGUUUCGCACUGGAACAUUGGCAAUCAAAU
..................(((((.(((((((..(((...((((((........)))))).........--.........((((((....)))))).)))))))))).)))))........ ( -23.90)
>DroEre_CAF1 106991 120 + 1
UUAAUCGAAAUAUUGCCAGCCAAAGUUCCAGACUGUAAGGAGGGGAGAGGAAAGUUUCAAAUCAAGUUAUAAUCAAAUCAAAUCUACUUACGUUUCGCACUGGAACAUUGGCAAUCAAGU
..................(((((.(((((((...(((((.(((.((...((..((..(.......)..))..))...))...))).)))))(.....).))))))).)))))........ ( -26.80)
>DroYak_CAF1 109309 120 + 1
UUAAUCGAAAUGUUGCCAGCCAAAGUUCCAGACUGUUAAAAUAAGAAAAUAAAGUUAUAAAUUAAGUUACAAUCAAAACAAAUCUACUUACGUUUCGCACUGGAACAUUGGCAAUCAAAU
..................(((((.(((((((..(((.(((.((((.........(((.....)))(((........))).......))))..))).)))))))))).)))))........ ( -21.20)
>consensus
UUGAUCGAAAUAUUGCCAGCCAAAGUUCCAGACUGUAACAAUACGAAAAUAAAUGUAUAACUCAAACU__AAUCAAAACAAAUCUACUUACGUUUCGCACUGGAACAUUGGCAAUCAAAU
..................(((((.(((((((.........(((((........))))).................................(.....).))))))).)))))........ (-17.58 = -17.38 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,371,567 – 11,371,685
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.86
Mean single sequence MFE -28.62
Consensus MFE -21.22
Energy contribution -21.62
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.74
SVM decision value 0.76
SVM RNA-class probability 0.843658
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11371567 118 - 27905053
AUUUGAUUGCCAAUGUUCCAGUGCGAAACGUAAGUAGAUUUGUUUUGAUU--AGUUUGAGUUAUACAUUUAUUUUCGUAUCGUUACAGUCUGGAACUUUGGCUGGCAAUAUUUCGAUCAA
..(((...(((((.(((((((.((((.(((.(((((((..(((..(((((--......))))).)))))))))).))).))))......))))))).)))))...)))............ ( -33.20)
>DroSec_CAF1 119207 118 - 1
AUUUGAUUGCCAAUGUACCAGUGCGAAACGUAAGUAGAUUUGUUUUGAUU--AGUUUGAGUUAUACAUUUAUUUUCGUAUUGUUACAGUCUGGAACCUUGGCUGGCAAUGUUUCGAUCAA
.....(((((((.((((.((((((((((.((((((..((....((..(..--...)..))..))..)))))))))))))))).))))(((.(....)..))))))))))........... ( -27.90)
>DroSim_CAF1 110242 118 - 1
AUUUGAUUGCCAAUGUUCCAGUGCGAAACGUAAGUACAUUUUUUUAGAUU--AGUUUGAGUAAUACAUUUAUUUUCGUAUUGUUACAGUCUGGAACUUUGGCUGGCAAUAUUUCGAUCAA
..(((...(((((.((((((((((((((.((((((..(((..((((((..--..)))))).)))..)))))))))))))..........))))))).)))))...)))............ ( -28.10)
>DroEre_CAF1 106991 120 - 1
ACUUGAUUGCCAAUGUUCCAGUGCGAAACGUAAGUAGAUUUGAUUUGAUUAUAACUUGAUUUGAAACUUUCCUCUCCCCUCCUUACAGUCUGGAACUUUGGCUGGCAAUAUUUCGAUUAA
..(((...(((((.(((((((.((.....(((((.((.........(((((.....))))).((........))....)).))))).))))))))).)))))...)))............ ( -24.70)
>DroYak_CAF1 109309 120 - 1
AUUUGAUUGCCAAUGUUCCAGUGCGAAACGUAAGUAGAUUUGUUUUGAUUGUAACUUAAUUUAUAACUUUAUUUUCUUAUUUUAACAGUCUGGAACUUUGGCUGGCAACAUUUCGAUUAA
..(((((((((((.(((((((.((.(((.(((((.((((..(((..(((((.....)))))...)))...)))).))))))))....))))))))).)))))((....))....)))))) ( -29.20)
>consensus
AUUUGAUUGCCAAUGUUCCAGUGCGAAACGUAAGUAGAUUUGUUUUGAUU__AGUUUGAGUUAUACAUUUAUUUUCGUAUUGUUACAGUCUGGAACUUUGGCUGGCAAUAUUUCGAUCAA
..(((...(((((.(((((((.((...((....)).((((......)))).....................................))))))))).)))))...)))............ (-21.22 = -21.62 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:46 2006