Locus 8477

Sequence ID 3L_DroMel_CAF1
Location 22,276,800 – 22,276,988
Length 188
Max. P 0.984212
window13863 window13864 window13865 window13866

overview

Window 3

Location 22,276,800 – 22,276,908
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.95
Mean single sequence MFE -25.72
Consensus MFE -19.34
Energy contribution -19.22
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -2.06
Structure conservation index 0.75
SVM decision value 1.16
SVM RNA-class probability 0.924476
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22276800 108 + 23771897
CUACUGUCGCCUGUUUGCCUGCCAGUUGGAGUCCGCAUCCACAUCCAC------AUCCGCAUGCACAUCCGC------ACUCCCAUCCUCGUCCGCAUUUAUAUCCACAUGCAGACAGGC
........((((((((((.((......(((((.((.((...(((.(..------....).)))...)).)).------))))).......(....)...........)).)))))))))) ( -24.30)
>DroSec_CAF1 35184 96 + 1
CUGCUGUCGCCUGUUUGCCUGCCAGUUGGCAUCCGCAUCCACAUCCAC------AUC------------CGC------AUCCACAUCCCCGUCCGCAUUUAUAUCCACAUGCAGAUAGGC
........((((((((((.((((....)))).................------...------------.((------....((......))..))..............)))))))))) ( -20.30)
>DroSim_CAF1 26776 108 + 1
CUGCUGUCGCCUGUUUGCCUGCCAGUUGGCAUCCGCAUCCACAUCCAC------AUCCGCAUGCACAUCCGC------AUCCACAUCCCCGUCCGCAUUUAUAUCCACAUGCAGACAGGC
........((((((((((.((((....))))...((............------....(.((((......))------)).)((......))..))..............)))))))))) ( -26.80)
>DroEre_CAF1 33978 120 + 1
CUGCUGUCGCCUGUUUGCCUGCCAGUUGGCAUCCGCAUCCACAUCCACAUCCACAUCCGCAUGCAGAUCCGCAUGCACAUCCGCAUCCCCAUCCGCAUUUAUAUCCUCAUGCAGACAGGC
........((((((((((.((((....))))...((......................((((((......))))))......(......)....))..............)))))))))) ( -32.50)
>DroYak_CAF1 33 96 + 1
CUGCUGUCGCCUGUUUGCCUGCCAGUUGGCAUCCGCAUCCACAUCC------------------------UUAUGCACAUCCGCAUCCCCAUCCGCAUUUCUAUCCACAUGCAGACAGGC
........((((((((((.((((....))))...............------------------------..((((......))))........................)))))))))) ( -24.70)
>consensus
CUGCUGUCGCCUGUUUGCCUGCCAGUUGGCAUCCGCAUCCACAUCCAC______AUCCGCAUGCA_AUCCGC______AUCCACAUCCCCGUCCGCAUUUAUAUCCACAUGCAGACAGGC
........((((((((((.((((....))))...((..........................................................))..............)))))))))) (-19.34 = -19.22 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,276,800 – 22,276,908
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.95
Mean single sequence MFE -37.68
Consensus MFE -25.82
Energy contribution -26.86
Covariance contribution 1.04
Combinations/Pair 1.04
Mean z-score -2.33
Structure conservation index 0.69
SVM decision value 1.45
SVM RNA-class probability 0.955081
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22276800 108 - 23771897
GCCUGUCUGCAUGUGGAUAUAAAUGCGGACGAGGAUGGGAGU------GCGGAUGUGCAUGCGGAU------GUGGAUGUGGAUGCGGACUCCAACUGGCAGGCAAACAGGCGACAGUAG
.(((((((((((..........)))))))).)))...(((((------.((.((.(((((.((...------.)).))))).)).)).))))).((((...(.(.....).)..)))).. ( -39.50)
>DroSec_CAF1 35184 96 - 1
GCCUAUCUGCAUGUGGAUAUAAAUGCGGACGGGGAUGUGGAU------GCG------------GAU------GUGGAUGUGGAUGCGGAUGCCAACUGGCAGGCAAACAGGCGACAGCAG
.((..(((((((..........)))))))..))........(------((.------------..(------((.(.(.((..(((...((((....)))).)))..)).)).)))))). ( -30.10)
>DroSim_CAF1 26776 108 - 1
GCCUGUCUGCAUGUGGAUAUAAAUGCGGACGGGGAUGUGGAU------GCGGAUGUGCAUGCGGAU------GUGGAUGUGGAUGCGGAUGCCAACUGGCAGGCAAACAGGCGACAGCAG
.(((((((((((..........)))))))))))..((((.((------(((....))))).)...(------((.(.(.((..(((...((((....)))).)))..)).)).)))))). ( -39.60)
>DroEre_CAF1 33978 120 - 1
GCCUGUCUGCAUGAGGAUAUAAAUGCGGAUGGGGAUGCGGAUGUGCAUGCGGAUCUGCAUGCGGAUGUGGAUGUGGAUGUGGAUGCGGAUGCCAACUGGCAGGCAAACAGGCGACAGCAG
.(((((((((((..........)))))))))))..((((.((.((((((((....)))))))).)).)...(((.(.(.((..(((...((((....)))).)))..)).)).)))))). ( -46.80)
>DroYak_CAF1 33 96 - 1
GCCUGUCUGCAUGUGGAUAGAAAUGCGGAUGGGGAUGCGGAUGUGCAUAA------------------------GGAUGUGGAUGCGGAUGCCAACUGGCAGGCAAACAGGCGACAGCAG
((((((.(((.(((...((....))(((...((.((.((.((.(((((..------------------------..))))).)).)).)).))..)))))).))).))))))........ ( -32.40)
>consensus
GCCUGUCUGCAUGUGGAUAUAAAUGCGGACGGGGAUGCGGAU______GCGGAU_UGCAUGCGGAU______GUGGAUGUGGAUGCGGAUGCCAACUGGCAGGCAAACAGGCGACAGCAG
.(((((((((((..........))))))))))).......................................((.(.(.((..(((...((((....)))).)))..)).)).))..... (-25.82 = -26.86 +   1.04)

alignment

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secondary structure

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Window 5

Location 22,276,840 – 22,276,948
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.66
Mean single sequence MFE -43.74
Consensus MFE -30.80
Energy contribution -30.76
Covariance contribution -0.04
Combinations/Pair 1.15
Mean z-score -2.66
Structure conservation index 0.70
SVM decision value 1.97
SVM RNA-class probability 0.984212
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22276840 108 - 23771897
GGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUACGCCUGUCUGCAUGUGGAUAUAAAUGCGGACGAGGAUGGGAGU------GCGGAUGUGCAUGCGGAU------GUGGAUGU
.(((((((((((.(((((((.(((..(((...........))).((((((((..........)))))))))))..)))))((------(((....))))))).)))------)))))))) ( -45.00)
>DroSec_CAF1 35224 96 - 1
GGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUACGCCUAUCUGCAUGUGGAUAUAAAUGCGGACGGGGAUGUGGAU------GCG------------GAU------GUGGAUGU
.(((((((((..((((.(((.....))).))))..(((((((((.(((((((..........)))))))..))).)))))))------)))------------)))------))...... ( -37.70)
>DroSim_CAF1 26816 108 - 1
GGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUCCGCCUGUCUGCAUGUGGAUAUAAAUGCGGACGGGGAUGUGGAU------GCGGAUGUGCAUGCGGAU------GUGGAUGU
.(((((((((((.((...((.....))(((..(((.((((((((((((((((..........)))))))))))....)))).------).)))..)))..)).)))------)))))))) ( -45.20)
>DroEre_CAF1 34018 120 - 1
GGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUACGCCUGUCUGCAUGAGGAUAUAAAUGCGGAUGGGGAUGCGGAUGUGCAUGCGGAUCUGCAUGCGGAUGUGGAUGUGGAUGU
.(((((((((((((((.(((.....))).))))........(((((((((((..........))))))))))))))))))))))((((.((.(((..(((....)))..))).)).)))) ( -52.40)
>DroYak_CAF1 73 96 - 1
GGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUACGCCUGUCUGCAUGUGGAUAGAAAUGCGGAUGGGGAUGCGGAUGUGCAUAA------------------------GGAUGU
.(((((((((((((((.(((.....))).))))........(((((((((((..........))))))))))))))))))))))((((..------------------------..)))) ( -38.40)
>consensus
GGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUACGCCUGUCUGCAUGUGGAUAUAAAUGCGGACGGGGAUGCGGAU______GCGGAU_UGCAUGCGGAU______GUGGAUGU
...(((((((((((((.(((.....))).))))........(((((((((((..........))))))))))))))))))))...................................... (-30.80 = -30.76 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 22,276,868 – 22,276,988
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.42
Mean single sequence MFE -43.28
Consensus MFE -41.36
Energy contribution -41.72
Covariance contribution 0.36
Combinations/Pair 1.11
Mean z-score -1.36
Structure conservation index 0.96
SVM decision value 1.28
SVM RNA-class probability 0.939974
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22276868 120 - 23771897
UCCUGCUUCUUGCCUCCGACUGCGCUUUAAGUGGUCGCUUGGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUACGCCUGUCUGCAUGUGGAUAUAAAUGCGGACGAGGAUGGGA
(((((((((.((((..((((..(.......)..))))...))))((((((((((((.(((.....))).))))..((((((..((....))))))))....)))))))).)))).))))) ( -43.20)
>DroSec_CAF1 35240 120 - 1
UCCUUCUUCUUGCCUCCGACUGCGCUUUAAGUGGUCGCUUGGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUACGCCUAUCUGCAUGUGGAUAUAAAUGCGGACGGGGAUGUGG
..........((((..((((..(.......)..))))...))))..((((((((((.(((.....))).))))........((..(((((((..........)))))))..)))))))). ( -41.30)
>DroSim_CAF1 26844 120 - 1
UCCUUCUUCUUGCCUCCGACUGCGCUUUAAGUGGUCGCUUGGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUCCGCCUGUCUGCAUGUGGAUAUAAAUGCGGACGGGGAUGUGG
..........((((..((((..(.......)..))))...))))..((((((((((.(((.....))).))))........(((((((((((..........))))))))))))))))). ( -46.10)
>DroEre_CAF1 34058 120 - 1
UCCUGCUGCUUGCCACCGACCGAGCUUUAAGUGGUCGCUUGGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUACGCCUGUCUGCAUGAGGAUAUAAAUGCGGAUGGGGAUGCGG
..........(((((.((((((.........))))))..)))))..((((((((((.(((.....))).))))........(((((((((((..........))))))))))))))))). ( -44.10)
>DroYak_CAF1 89 120 - 1
UCCUCCUCCUUGCCUCCGACUGAGCUUUAAGUGGUCGCUUGGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUACGCCUGUCUGCAUGUGGAUAGAAAUGCGGAUGGGGAUGCGG
..........((((..(((((..((.....)))))))...))))..((((((((((.(((.....))).))))........(((((((((((..........))))))))))))))))). ( -41.70)
>consensus
UCCUGCUUCUUGCCUCCGACUGCGCUUUAAGUGGUCGCUUGGCAUUCGCAUUGGCUCCCAGUUCAUGGCAGCUCCUCUACGCCUGUCUGCAUGUGGAUAUAAAUGCGGACGGGGAUGCGG
..........((((..(((((((.......)))))))...)))).(((((((((((.(((.....))).))))........(((((((((((..........)))))))))))))))))) (-41.36 = -41.72 +   0.36)

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 13:16:27 2006