Locus 6024

Sequence ID 3L_DroMel_CAF1
Location 16,066,818 – 16,067,018
Length 200
Max. P 0.929987
window9639 window9640 window9641 window9642

overview

Window 9

Location 16,066,818 – 16,066,938
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -29.36
Consensus MFE -28.42
Energy contribution -28.87
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.80
Structure conservation index 0.97
SVM decision value 0.57
SVM RNA-class probability 0.785834
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16066818 120 - 23771897
UUCCCUGAUCCAACACUGAUUUUCCGCGUAGAAAAUCAGGAGCUUCCUUGGUGUAAGUGCCCUCCUCAUUCACAAAACACUUUACAGGAAUUUUCUGGGUCAGACUAACAAGGAAAUCUU
((((((((((((...(((((((((......)))))))))(((.(((((.(((((..(((...........)))...)))))....)))))..)))))))))))........))))..... ( -32.10)
>DroSim_CAF1 1884 120 - 1
UUCCCUGAUCCAACACUGAUUUUCCGCGUAGAAAAUCAGGAGCUUCCGUGGUGUAAGUGCCCUCCUCAUUCACAAAACAUUUUACAGGAAUUUUCUGGGUCAGACUAACAAGGAAAUCUU
((((((((((((...(((((((((......)))))))))(((.((((...(((.(((((..................)))))))).))))..)))))))))))........))))..... ( -29.37)
>DroYak_CAF1 1946 120 - 1
UUCCCUGAUCCAACACUGAUUGUCCGCGUAGAAAAUCAGGAGCUUCCUUGGUGUAAGUGCCCUCCUCAUUCACAAAACAUUUAACAGGAAUUUUUUGGGUCAGACUAACAAGGAAAUCUU
(((((((((((((..((((((.((......)).))))))....(((((.(((((..(((...........)))...)))))....)))))....)))))))))........))))..... ( -26.60)
>consensus
UUCCCUGAUCCAACACUGAUUUUCCGCGUAGAAAAUCAGGAGCUUCCUUGGUGUAAGUGCCCUCCUCAUUCACAAAACAUUUUACAGGAAUUUUCUGGGUCAGACUAACAAGGAAAUCUU
((((((((((((...(((((((((......)))))))))....(((((.(((((..(((...........)))...)))))....))))).....))))))))........))))..... (-28.42 = -28.87 +   0.45)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,066,858 – 16,066,978
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -37.03
Consensus MFE -37.27
Energy contribution -36.83
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -1.36
Structure conservation index 1.01
SVM decision value 0.14
SVM RNA-class probability 0.602657
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16066858 120 + 23771897
GUGUUUUGUGAAUGAGGAGGGCACUUACACCAAGGAAGCUCCUGAUUUUCUACGCGGAAAAUCAGUGUUGGAUCAGGGAAAUUCCCUAGUCCUCGACCGCAUAGCAGAGGAUGUAGUCCA
.((((.((((..((((((.((((((.......(((.....)))((((((((....)))))))))))))).....((((.....))))..))))))..)))).))))..((((...)))). ( -39.20)
>DroSim_CAF1 1924 120 + 1
AUGUUUUGUGAAUGAGGAGGGCACUUACACCACGGAAGCUCCUGAUUUUCUACGCGGAAAAUCAGUGUUGGAUCAGGGAAAUUCCCUAAUCCUCGACCGCAUAGCAGAGGAUGUAGUCCA
.((((.((((..((((((((.........))..((((..(((((((((...((((.(.....).)))).)))))))))...))))....))))))..)))).))))..((((...)))). ( -39.00)
>DroYak_CAF1 1986 120 + 1
AUGUUUUGUGAAUGAGGAGGGCACUUACACCAAGGAAGCUCCUGAUUUUCUACGCGGACAAUCAGUGUUGGAUCAGGGAAAUUCCCUAGUCCUUGAACGCAUAGCAGAGGAUGUGGUUCA
.((((.((((..((((((((.........))..((((..(((((((((...((((.(.....).)))).)))))))))...))))....))))))..)))).)))).............. ( -32.90)
>consensus
AUGUUUUGUGAAUGAGGAGGGCACUUACACCAAGGAAGCUCCUGAUUUUCUACGCGGAAAAUCAGUGUUGGAUCAGGGAAAUUCCCUAGUCCUCGACCGCAUAGCAGAGGAUGUAGUCCA
.((((.((((..((((((((.........))..((((..(((((((((...((((.(.....).)))).)))))))))...))))....))))))..)))).))))..((((...)))). (-37.27 = -36.83 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,066,898 – 16,067,018
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -36.80
Consensus MFE -35.55
Energy contribution -35.67
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.97
SVM decision value 0.61
SVM RNA-class probability 0.800299
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16066898 120 + 23771897
CCUGAUUUUCUACGCGGAAAAUCAGUGUUGGAUCAGGGAAAUUCCCUAGUCCUCGACCGCAUAGCAGAGGAUGUAGUCCACUCCUCAAAGCUGGAACAUUCCUAUCCUAUUGAUUGGCGC
.((((((((((....))))))))))....((((.((((.....)))).)))).....(((....(((((((((...((((((......)).)))).......)))))).)))....))). ( -37.10)
>DroSim_CAF1 1964 120 + 1
CCUGAUUUUCUACGCGGAAAAUCAGUGUUGGAUCAGGGAAAUUCCCUAAUCCUCGACCGCAUAGCAGAGGAUGUAGUCCACUCCUCCAAGCUGGAACAUUCCUAUCCCAUUGAUUGGCGC
.((((((((((....))))))))))....((((.((((.....)))).)))).....(((..(((.(((((.((.....)))))))...)))(((....)))..............))). ( -35.80)
>DroYak_CAF1 2026 120 + 1
CCUGAUUUUCUACGCGGACAAUCAGUGUUGGAUCAGGGAAAUUCCCUAGUCCUUGAACGCAUAGCAGAGGAUGUGGUUCACUCCUCCAAGCUGGAGCAUUCCUAUCCCAUAGAUUGGCGU
...........((((...(((((.(((((((((.((((.....)))).))))...)))))......(.(((((.((....((((........))))....))))))))...))))))))) ( -37.50)
>consensus
CCUGAUUUUCUACGCGGAAAAUCAGUGUUGGAUCAGGGAAAUUCCCUAGUCCUCGACCGCAUAGCAGAGGAUGUAGUCCACUCCUCCAAGCUGGAACAUUCCUAUCCCAUUGAUUGGCGC
.((((((((((....))))))))))....((((.((((.....)))).)))).....(((..(((.(((((.((.....)))))))...)))(((....)))..............))). (-35.55 = -35.67 +   0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,066,898 – 16,067,018
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.89
Mean single sequence MFE -44.27
Consensus MFE -37.59
Energy contribution -37.70
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -3.20
Structure conservation index 0.85
SVM decision value 1.20
SVM RNA-class probability 0.929987
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16066898 120 - 23771897
GCGCCAAUCAAUAGGAUAGGAAUGUUCCAGCUUUGAGGAGUGGACUACAUCCUCUGCUAUGCGGUCGAGGACUAGGGAAUUUCCCUGAUCCAACACUGAUUUUCCGCGUAGAAAAUCAGG
.((((.............(((....)))(((...(((((.((.....))))))).)))....)).)).(((.(((((.....))))).)))....(((((((((......))))))))). ( -39.70)
>DroSim_CAF1 1964 120 - 1
GCGCCAAUCAAUGGGAUAGGAAUGUUCCAGCUUGGAGGAGUGGACUACAUCCUCUGCUAUGCGGUCGAGGAUUAGGGAAUUUCCCUGAUCCAACACUGAUUUUCCGCGUAGAAAAUCAGG
.((((.......((((((....))))))(((..((((((.((.....)))))))))))....)).)).(((((((((.....)))))))))....(((((((((......))))))))). ( -47.30)
>DroYak_CAF1 2026 120 - 1
ACGCCAAUCUAUGGGAUAGGAAUGCUCCAGCUUGGAGGAGUGAACCACAUCCUCUGCUAUGCGUUCAAGGACUAGGGAAUUUCCCUGAUCCAACACUGAUUGUCCGCGUAGAAAAUCAGG
.......((((((((((((((((((...(((..(((((((((...))).)))))))))..))))))..(((.(((((.....))))).)))........)))))).))))))........ ( -45.80)
>consensus
GCGCCAAUCAAUGGGAUAGGAAUGUUCCAGCUUGGAGGAGUGGACUACAUCCUCUGCUAUGCGGUCGAGGACUAGGGAAUUUCCCUGAUCCAACACUGAUUUUCCGCGUAGAAAAUCAGG
.(((..............(((....)))(((...((((((((...))).))))).)))..))).....(((.(((((.....))))).)))....(((((((((......))))))))). (-37.59 = -37.70 +   0.11)

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 12:07:11 2006