Locus 162

Sequence ID 3R_DroMel_CAF1
Location 818,835 – 818,995
Length 160
Max. P 0.939511
window267 window268 window269 window270

overview

Window 7

Location 818,835 – 818,955
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 74.44
Mean single sequence MFE -25.73
Consensus MFE -15.11
Energy contribution -15.90
Covariance contribution 0.79
Combinations/Pair 1.15
Mean z-score -1.88
Structure conservation index 0.59
SVM decision value 0.88
SVM RNA-class probability 0.874070
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 818835 120 + 27905053
AGGUUAAUAAUGCAAAGUAAUAGUACAGUAAUUUAUAACUUCAGUUUACAUCAGGCUAGUGAUUAUGCUAUGCAACCCUGCGCCUGAUAAUUACAAAAGUAAUUGAAGGCAAUGAUAGGA
..........(((...(((....)))............((((.......(((((((((((......)))).(((....))))))))))((((((....)))))))))))))......... ( -25.60)
>DroSim_CAF1 5991 105 + 1
GUUGUA---------------UGUAGAGUAAUUUAUAACUUCAGUUUUCAUCAGGCUAGUGAUUAUGCUAUGCAACCCUGCGCCAGAUAAUUACAAAAGUAAUUGAAGGCAAUGAUAGGA
(((((.---------------((((((....)))))).((((.......(((.(((((((......)))).(((....)))))).)))((((((....)))))))))))))))....... ( -23.30)
>DroYak_CAF1 9296 109 + 1
A-----AAGCUUCAAAGUAAUAGUGCAGUAAUUUAUAACUUUAGUUUGUAUCAGGCUGGUGAUUACGCU------UCAUGUGCCUGAUAAUUACAAAAGUUACUGAAGGCAAUAAUAGGA
.-----...(((((..(((....))).........(((((((.((...((((((((..((((.......------))))..))))))))...)).))))))).)))))............ ( -28.30)
>consensus
A___UAA___U_CAAAGUAAUAGUACAGUAAUUUAUAACUUCAGUUUACAUCAGGCUAGUGAUUAUGCUAUGCAACCCUGCGCCUGAUAAUUACAAAAGUAAUUGAAGGCAAUGAUAGGA
................................((((..(((((((....(((((((((((......)))).((......)))))))))...(((....))))))))))...))))..... (-15.11 = -15.90 +   0.79)

alignment

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secondary structure

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Window 8

Location 818,835 – 818,955
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.44
Mean single sequence MFE -20.45
Consensus MFE -15.21
Energy contribution -15.67
Covariance contribution 0.45
Combinations/Pair 1.18
Mean z-score -1.53
Structure conservation index 0.74
SVM decision value 1.30
SVM RNA-class probability 0.939511
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 818835 120 - 27905053
UCCUAUCAUUGCCUUCAAUUACUUUUGUAAUUAUCAGGCGCAGGGUUGCAUAGCAUAAUCACUAGCCUGAUGUAAACUGAAGUUAUAAAUUACUGUACUAUUACUUUGCAUUAUUAACCU
..........((((..((((((....))))))...))))...(((((((.(((........))))).(((((((((.((((((.(((......)))))).))).)))))))))..))))) ( -23.10)
>DroSim_CAF1 5991 105 - 1
UCCUAUCAUUGCCUUCAAUUACUUUUGUAAUUAUCUGGCGCAGGGUUGCAUAGCAUAAUCACUAGCCUGAUGAAAACUGAAGUUAUAAAUUACUCUACA---------------UACAAC
............(((((.((((....))))(((((.(((..(((((((.......))))).)).))).)))))....))))).................---------------...... ( -17.30)
>DroYak_CAF1 9296 109 - 1
UCCUAUUAUUGCCUUCAGUAACUUUUGUAAUUAUCAGGCACAUGA------AGCGUAAUCACCAGCCUGAUACAAACUAAAGUUAUAAAUUACUGCACUAUUACUUUGAAGCUU-----U
..........((.((((((((((((.((...((((((((...(((------.......)))...))))))))...)).))))))))....................))))))..-----. ( -20.95)
>consensus
UCCUAUCAUUGCCUUCAAUUACUUUUGUAAUUAUCAGGCGCAGGGUUGCAUAGCAUAAUCACUAGCCUGAUGAAAACUGAAGUUAUAAAUUACUGUACUAUUACUUUG_A___UUA___U
.................((.(((((.((...((((((((....(((((.......)))))....))))))))...)).))))).)).................................. (-15.21 = -15.67 +   0.45)

alignment

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secondary structure

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dotplot

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Window 9

Location 818,875 – 818,995
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.39
Mean single sequence MFE -32.80
Consensus MFE -21.94
Energy contribution -24.50
Covariance contribution 2.56
Combinations/Pair 1.05
Mean z-score -2.39
Structure conservation index 0.67
SVM decision value 0.21
SVM RNA-class probability 0.635783
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 818875 120 + 27905053
UCAGUUUACAUCAGGCUAGUGAUUAUGCUAUGCAACCCUGCGCCUGAUAAUUACAAAAGUAAUUGAAGGCAAUGAUAGGAGGCAGUUCCAUCCUGUGCCUCGUUAUUAUUUUGUAAAAGC
...((((..(((((((((((......)))).(((....))))))))))..(((((((((((((.((.((((..(((.((((....)))))))...)))))))))))..)))))))))))) ( -34.40)
>DroSim_CAF1 6016 120 + 1
UCAGUUUUCAUCAGGCUAGUGAUUAUGCUAUGCAACCCUGCGCCAGAUAAUUACAAAAGUAAUUGAAGGCAAUGAUAGGAGGCAGUUCCAUCCUGUGCCUCGUUAUUAUUUUGUAAAAGC
...(((((((((.(((((((......)))).(((....)))))).)))((((((....))))))))))))((((((((((((((...........)))))).)))))))).......... ( -31.00)
>DroYak_CAF1 9331 112 + 1
UUAGUUUGUAUCAGGCUGGUGAUUACGCU------UCAUGUGCCUGAUAAUUACAAAAGUUACUGAAGGCAAUAAUAGGAGGCAGUUCCAAGCUGU--CUUGUUAUUAUUUUGUAAAAGG
........((((((((..((((.......------))))..)))))))).(((((((((((......)))((((((..((((((((.....)))))--))))))))).)))))))).... ( -33.00)
>consensus
UCAGUUUACAUCAGGCUAGUGAUUAUGCUAUGCAACCCUGCGCCUGAUAAUUACAAAAGUAAUUGAAGGCAAUGAUAGGAGGCAGUUCCAUCCUGUGCCUCGUUAUUAUUUUGUAAAAGC
.........(((((((((((......)))).((......)))))))))..(((((((((((((...(((((..(((.((((....)))))))...))))).)))))..)))))))).... (-21.94 = -24.50 +   2.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 818,875 – 818,995
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.39
Mean single sequence MFE -28.90
Consensus MFE -23.41
Energy contribution -25.53
Covariance contribution 2.12
Combinations/Pair 1.11
Mean z-score -2.48
Structure conservation index 0.81
SVM decision value 0.95
SVM RNA-class probability 0.887588
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 818875 120 - 27905053
GCUUUUACAAAAUAAUAACGAGGCACAGGAUGGAACUGCCUCCUAUCAUUGCCUUCAAUUACUUUUGUAAUUAUCAGGCGCAGGGUUGCAUAGCAUAAUCACUAGCCUGAUGUAAACUGA
....((((((((((((...((((((...((((((......))).)))..))))))..)))).)))))))).((((((((..(((((((.......))))).)).))))))))........ ( -34.20)
>DroSim_CAF1 6016 120 - 1
GCUUUUACAAAAUAAUAACGAGGCACAGGAUGGAACUGCCUCCUAUCAUUGCCUUCAAUUACUUUUGUAAUUAUCUGGCGCAGGGUUGCAUAGCAUAAUCACUAGCCUGAUGAAAACUGA
....((((((((((((...((((((...((((((......))).)))..))))))..)))).))))))))(((((.(((..(((((((.......))))).)).))).)))))....... ( -31.20)
>DroYak_CAF1 9331 112 - 1
CCUUUUACAAAAUAAUAACAAG--ACAGCUUGGAACUGCCUCCUAUUAUUGCCUUCAGUAACUUUUGUAAUUAUCAGGCACAUGA------AGCGUAAUCACCAGCCUGAUACAAACUAA
....((((((((......((((--....)))).............((((((....)))))).)))))))).((((((((...(((------.......)))...))))))))........ ( -21.30)
>consensus
GCUUUUACAAAAUAAUAACGAGGCACAGGAUGGAACUGCCUCCUAUCAUUGCCUUCAAUUACUUUUGUAAUUAUCAGGCGCAGGGUUGCAUAGCAUAAUCACUAGCCUGAUGAAAACUGA
....((((((((((((...((((((...((((((......))).)))..))))))..)))).)))))))).((((((((....(((((.......)))))....))))))))........ (-23.41 = -25.53 +   2.12)

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 09:35:25 2006