Locus 4490

Sequence ID 3L_DroMel_CAF1
Location 12,977,428 – 12,977,558
Length 130
Max. P 0.998971
window7009 window7010 window7011

overview

Window 9

Location 12,977,428 – 12,977,518
Length 90
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.23
Mean single sequence MFE -32.88
Consensus MFE -25.35
Energy contribution -26.16
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -1.74
Structure conservation index 0.77
SVM decision value 1.04
SVM RNA-class probability 0.904824
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12977428 90 + 23771897
AAUGGG------------------------------AUUGGGGGCCGGGGCGAUAAAAAUGCGUGUUAAUGUUUAUGCCGCCGGCAAGCGAGGACAAUUGUCCUGCGGGGCGUCAAGCCG
....((------------------------------.((((.(((((((((.((((....((((....))))))))))).)))))..((.(((((....)))))))....).)))).)). ( -34.50)
>DroSec_CAF1 94825 90 + 1
UAUGGG------------------------------AUUGGAAGCCGGGGCGAUAAAAAUGCGUGUUAAUGUUUCUGCCGCCGGCAAGCGAGGACAAUUGUCCUGCGGGGCGCCAAGCCG
....((------------------------------.((((..((((((((((.......((((....)))).)).))).)))))..((.(((((....)))))))......)))).)). ( -34.00)
>DroSim_CAF1 104460 90 + 1
UAUGGG------------------------------AUUGGAAGCCGGGGCGAUAAAAAUGCGUGUUAAUGUUUAUGCCGCCGGCAAGCGAGGACAAUUGUCCUGCGGGGCGCCAAGCCU
...(((------------------------------.((((..((((((((.((((....((((....))))))))))).)))))..((.(((((....)))))))......)))).))) ( -35.40)
>DroEre_CAF1 100540 120 + 1
AAUGGGAAUGGGAAUGGGAAUGGGUAUGGGUAUGGGAAUGGAAGGUGUGGCGAUAAAAAUGCGUGUUAAUGUUUAUGCCGCCGGCGAGCGAGGACAAUUGUCCUGCGGGGCGCCAAGCCG
.........((.....((....((((((..(((....(((.(...(((....)))....).)))....)))..)))))).))((((.((.(((((....)))))))....))))...)). ( -31.50)
>DroYak_CAF1 98829 86 + 1
AAUGGGAAUGGG------------------------AAUGGAAGGUGUGGCGAUAAAAA----------UGUUUAUGCCGCCGGCAAGCGAGGACAAUUGUCCUGCGGGGCGCCAAGCCG
....((..(((.------------------------..........(((((.(((((..----------..))))))))))((.(..((.(((((....)))))))..).)))))..)). ( -29.00)
>consensus
AAUGGG______________________________AUUGGAAGCCGGGGCGAUAAAAAUGCGUGUUAAUGUUUAUGCCGCCGGCAAGCGAGGACAAUUGUCCUGCGGGGCGCCAAGCCG
...........................................((((((((.(((((.((........)).)))))))).)))))..((.(((((....)))))))..(((.....))). (-25.35 = -26.16 +   0.81)

alignment

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secondary structure

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Window 0

Location 12,977,428 – 12,977,518
Length 90
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.23
Mean single sequence MFE -27.36
Consensus MFE -20.71
Energy contribution -22.16
Covariance contribution 1.45
Combinations/Pair 1.00
Mean z-score -2.81
Structure conservation index 0.76
SVM decision value 2.91
SVM RNA-class probability 0.997677
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12977428 90 - 23771897
CGGCUUGACGCCCCGCAGGACAAUUGUCCUCGCUUGCCGGCGGCAUAAACAUUAACACGCAUUUUUAUCGCCCCGGCCCCCAAU------------------------------CCCAUU
.(((.....)))..(((((((....))))).))..(((((.((((((((.((........)).))))).)))))))).......------------------------------...... ( -28.80)
>DroSec_CAF1 94825 90 - 1
CGGCUUGGCGCCCCGCAGGACAAUUGUCCUCGCUUGCCGGCGGCAGAAACAUUAACACGCAUUUUUAUCGCCCCGGCUUCCAAU------------------------------CCCAUA
.((.((((......(((((((....))))).))..(((((.(((.((....................))))))))))..)))).------------------------------)).... ( -28.75)
>DroSim_CAF1 104460 90 - 1
AGGCUUGGCGCCCCGCAGGACAAUUGUCCUCGCUUGCCGGCGGCAUAAACAUUAACACGCAUUUUUAUCGCCCCGGCUUCCAAU------------------------------CCCAUA
.((.((((......(((((((....))))).))..(((((.((((((((.((........)).))))).))))))))..)))).------------------------------)).... ( -31.00)
>DroEre_CAF1 100540 120 - 1
CGGCUUGGCGCCCCGCAGGACAAUUGUCCUCGCUCGCCGGCGGCAUAAACAUUAACACGCAUUUUUAUCGCCACACCUUCCAUUCCCAUACCCAUACCCAUUCCCAUUCCCAUUCCCAUU
.(((.(((((...((.(((((....)))))))..)))))(((...............))).........)))................................................ ( -24.46)
>DroYak_CAF1 98829 86 - 1
CGGCUUGGCGCCCCGCAGGACAAUUGUCCUCGCUUGCCGGCGGCAUAAACA----------UUUUUAUCGCCACACCUUCCAUU------------------------CCCAUUCCCAUU
.((..(((.(((..(((((((....))))).)).....)))((((((((..----------..))))).)))............------------------------.)))..)).... ( -23.80)
>consensus
CGGCUUGGCGCCCCGCAGGACAAUUGUCCUCGCUUGCCGGCGGCAUAAACAUUAACACGCAUUUUUAUCGCCCCGGCUUCCAAU______________________________CCCAUU
.(((.....)))..(((((((....))))).))..(((((.((((((((.((........)).))))).))))))))........................................... (-20.71 = -22.16 +   1.45)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,977,438 – 12,977,558
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.17
Mean single sequence MFE -39.67
Consensus MFE -35.29
Energy contribution -36.74
Covariance contribution 1.45
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.89
SVM decision value 3.31
SVM RNA-class probability 0.998971
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12977438 120 - 23771897
UCGCCAUUGCAGUUGUCCAUAAUGGUUUCGGCCAUAAGCUCGGCUUGACGCCCCGCAGGACAAUUGUCCUCGCUUGCCGGCGGCAUAAACAUUAACACGCAUUUUUAUCGCCCCGGCCCC
..((....((((((((((...(((((....)))))..((..(((.....)))..)).))))))))))....))..(((((.((((((((.((........)).))))).))))))))... ( -43.30)
>DroSec_CAF1 94835 120 - 1
UCGCCAUUGCAGUUGUCCAUAAUGGUUUCGGCCAUAAGCUCGGCUUGGCGCCCCGCAGGACAAUUGUCCUCGCUUGCCGGCGGCAGAAACAUUAACACGCAUUUUUAUCGCCCCGGCUUC
..((....((((((((((...(((((....)))))..((..(((.....)))..)).))))))))))....))..(((((.(((.((....................))))))))))... ( -41.35)
>DroSim_CAF1 104470 120 - 1
UCGCCAUUGCAGUUGUCCAUAAUGGUUUCGGCCAUAAGCUAGGCUUGGCGCCCCGCAGGACAAUUGUCCUCGCUUGCCGGCGGCAUAAACAUUAACACGCAUUUUUAUCGCCCCGGCUUC
..((....((((((((((...(((((....)))))..((..(((.....)))..)).))))))))))....))..(((((.((((((((.((........)).))))).))))))))... ( -44.00)
>DroEre_CAF1 100580 120 - 1
UCGCCAUUGCAGUUGUCCAUAAUGGUUUCGGCCAUAAGCUCGGCUUGGCGCCCCGCAGGACAAUUGUCCUCGCUCGCCGGCGGCAUAAACAUUAACACGCAUUUUUAUCGCCACACCUUC
..(((...((((((((((...(((((....)))))..((..(((.....)))..)).))))))))))....(....).)))((((((((.((........)).))))).)))........ ( -34.50)
>DroYak_CAF1 98845 110 - 1
UCGCCAUUGCAGUUGUCCAUAAUGGUUUCGGCCAUAAGCUCGGCUUGGCGCCCCGCAGGACAAUUGUCCUCGCUUGCCGGCGGCAUAAACA----------UUUUUAUCGCCACACCUUC
..(((...((((((((((...(((((....)))))..((..(((.....)))..)).))))))))))....(....).)))((((((((..----------..))))).)))........ ( -35.20)
>consensus
UCGCCAUUGCAGUUGUCCAUAAUGGUUUCGGCCAUAAGCUCGGCUUGGCGCCCCGCAGGACAAUUGUCCUCGCUUGCCGGCGGCAUAAACAUUAACACGCAUUUUUAUCGCCCCGGCUUC
..((....((((((((((...(((((....)))))..((..(((.....)))..)).))))))))))....))..(((((.((((((((.((........)).))))).))))))))... (-35.29 = -36.74 +   1.45)

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 11:24:46 2006