Locus 3460

Sequence ID X_DroMel_CAF1
Location 9,277,261 – 9,277,386
Length 125
Max. P 0.995131
window5662 window5663 window5664 window5665

overview

Window 2

Location 9,277,261 – 9,277,353
Length 92
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 78.32
Mean single sequence MFE -29.56
Consensus MFE -17.68
Energy contribution -18.08
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.60
SVM decision value 0.02
SVM RNA-class probability 0.542320
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9277261 92 + 22224390
AGGAUGCUCAGGAUGUU--------UCGGGAUGCUGAGUAUGGUAAGGCAGUGUAAUUGCCGCCGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUG
...((((((((.((.(.--------...).)).)))))))).....((((((...))))))(((((.((((((.......))..)))))))))....... ( -31.60)
>DroSec_CAF1 59692 91 + 1
AGG---------AUGUUCAGGAUGCUGAGCAUGCUGAGGAUGGUAAGGCAGUGUAAUUGCCGCCGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUG
((.---------((((((((....)))))))).))...........((((((...))))))(((((.((((((.......))..)))))))))....... ( -32.20)
>DroSim_CAF1 57046 100 + 1
AGGAUGCUCAGGAUGUUCAGGAUGCUGAGCAUGCUGGGGAUGGUAAGGCAGUGUAAUUGCCGCCGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUG
...((.(((((.((((((((....)))))))).))))).)).....((((((...))))))(((((.((((((.......))..)))))))))....... ( -40.40)
>DroEre_CAF1 66187 82 + 1
UAGAUGCUCAGGAUGUU------------------CGCGAUGGUAAGGCAGUGUAAUUGCCGCCGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUG
............((((.------------------.((((((((..((((((...)))))))))..((((((....))))))..)))))..))))..... ( -23.90)
>DroYak_CAF1 58221 77 + 1
-----GCUCAGGAUGGU------------------AAGGAUGGCAAGGCAGUGUAAUUGCCACAGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUG
-----((.(((......------------------...........((((((...))))))(((..((((((....)))))).)))..)))))....... ( -19.70)
>consensus
AGGAUGCUCAGGAUGUU________U__G_AUGCUGAGGAUGGUAAGGCAGUGUAAUUGCCGCCGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUG
..............................................((((((...))))))(((((.((((((.......))..)))))))))....... (-17.68 = -18.08 +   0.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,277,261 – 9,277,353
Length 92
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 78.32
Mean single sequence MFE -17.98
Consensus MFE -11.70
Energy contribution -11.74
Covariance contribution 0.04
Combinations/Pair 1.08
Mean z-score -1.52
Structure conservation index 0.65
SVM decision value -0.04
SVM RNA-class probability 0.515458
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9277261 92 - 22224390
CAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCGGCGGCAAUUACACUGCCUUACCAUACUCAGCAUCCCGA--------AACAUCCUGAGCAUCCU
.......(((.(((...(((.......))).)))..)))((((.......))))........(((((.((.....--------...)).)))))...... ( -17.80)
>DroSec_CAF1 59692 91 - 1
CAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCGGCGGCAAUUACACUGCCUUACCAUCCUCAGCAUGCUCAGCAUCCUGAACAU---------CCU
.......(((.(((...(((.......))).)))..)))((((.......)))).........((((.((((...)))).))))....---------... ( -20.50)
>DroSim_CAF1 57046 100 - 1
CAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCGGCGGCAAUUACACUGCCUUACCAUCCCCAGCAUGCUCAGCAUCCUGAACAUCCUGAGCAUCCU
.......(((.(((...(((.......))).)))..)))((((.......))))...........((.((((((((.((.......)).)))))))).)) ( -24.00)
>DroEre_CAF1 66187 82 - 1
CAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCGGCGGCAAUUACACUGCCUUACCAUCGCG------------------AACAUCCUGAGCAUCUA
.......((((((.....)).......(((.((...(((((........)))))....)).))).------------------.......)).))..... ( -16.00)
>DroYak_CAF1 58221 77 - 1
CAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCUGUGGCAAUUACACUGCCUUGCCAUCCUU------------------ACCAUCCUGAGC-----
.......(((((......(((.(......).)))...(((((((..........)))))))....------------------......))).))----- ( -11.60)
>consensus
CAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCGGCGGCAAUUACACUGCCUUACCAUCCUCAGCAU_C__A________AACAUCCUGAGCAUCCU
.......(((.(((...(((.......))).)))..)))((((.......)))).............................................. (-11.70 = -11.74 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,277,293 – 9,277,386
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 96.99
Mean single sequence MFE -33.30
Consensus MFE -30.34
Energy contribution -30.98
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -1.94
Structure conservation index 0.91
SVM decision value 2.32
SVM RNA-class probability 0.992305
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9277293 93 + 22224390
UGGUAAGGCAGUGUAAUUGCCGCCGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUGUUGCAGUUAAAUGCCGCCAGCAAUCAGAACCGC
.(((..((((((...)))))))))((((((((....))))))..((((((((((........(((......))))))))))))).....)).. ( -34.90)
>DroSec_CAF1 59723 93 + 1
UGGUAAGGCAGUGUAAUUGCCGCCGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUGUUGCAGUUAAAUGCCGCCAGCAAUCAGAACCGC
.(((..((((((...)))))))))((((((((....))))))..((((((((((........(((......))))))))))))).....)).. ( -34.90)
>DroSim_CAF1 57086 93 + 1
UGGUAAGGCAGUGUAAUUGCCGCCGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUGUUGCAGUUAAAUGCCGCCAGCAAUCAGAACCGC
.(((..((((((...)))))))))((((((((....))))))..((((((((((........(((......))))))))))))).....)).. ( -34.90)
>DroEre_CAF1 66209 93 + 1
UGGUAAGGCAGUGUAAUUGCCGCCGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUGUUGCAGCUAAAUGCCGCAAGCAAUCAGAACAGC
.(((..((((((...)))))))))..((((((....)))))).....((((.....((((((((.((.....)).)).)))))).....)))) ( -28.80)
>DroYak_CAF1 58238 93 + 1
UGGCAAGGCAGUGUAAUUGCCACAGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUGUUGCAGUUAAAUGCCGCCAGCGAUCAGAACCGC
..((..((((((...))))))...((((((((....))))))..((((((((((........(((......))))))))))))).....)))) ( -33.00)
>consensus
UGGUAAGGCAGUGUAAUUGCCGCCGGGCAGCGCUAAUGUUGCAUGUUGCUGGCGUAAUUGUUGCAGUUAAAUGCCGCCAGCAAUCAGAACCGC
.(((..((((((...)))))))))((((((((....))))))..((((((((((........(((......))))))))))))).....)).. (-30.34 = -30.98 +   0.64)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,277,293 – 9,277,386
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 96.99
Mean single sequence MFE -29.36
Consensus MFE -26.08
Energy contribution -26.72
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -2.20
Structure conservation index 0.89
SVM decision value 2.54
SVM RNA-class probability 0.995131
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9277293 93 - 22224390
GCGGUUCUGAUUGCUGGCGGCAUUUAACUGCAACAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCGGCGGCAAUUACACUGCCUUACCA
(((((.((((((((((((((((......)))........)))))))).........))))).)))))..(((((........)))))...... ( -30.50)
>DroSec_CAF1 59723 93 - 1
GCGGUUCUGAUUGCUGGCGGCAUUUAACUGCAACAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCGGCGGCAAUUACACUGCCUUACCA
(((((.((((((((((((((((......)))........)))))))).........))))).)))))..(((((........)))))...... ( -30.50)
>DroSim_CAF1 57086 93 - 1
GCGGUUCUGAUUGCUGGCGGCAUUUAACUGCAACAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCGGCGGCAAUUACACUGCCUUACCA
(((((.((((((((((((((((......)))........)))))))).........))))).)))))..(((((........)))))...... ( -30.50)
>DroEre_CAF1 66209 93 - 1
GCUGUUCUGAUUGCUUGCGGCAUUUAGCUGCAACAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCGGCGGCAAUUACACUGCCUUACCA
((.((..((((((((((((((.....)))))))......((((.(((...(((.......))).)))..))))))))))).)).))....... ( -29.30)
>DroYak_CAF1 58238 93 - 1
GCGGUUCUGAUCGCUGGCGGCAUUUAACUGCAACAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCUGUGGCAAUUACACUGCCUUGCCA
(((((.(((((.((((((((((......)))........)))))))..........))))).)))))....((((((..........)))))) ( -26.00)
>consensus
GCGGUUCUGAUUGCUGGCGGCAUUUAACUGCAACAAUUACGCCAGCAACAUGCAACAUUAGCGCUGCCCGGCGGCAAUUACACUGCCUUACCA
(((((.((((((((((((((((......)))........)))))))).........))))).)))))..(((((........)))))...... (-26.08 = -26.72 +   0.64)

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 10:59:58 2006