Locus 7553

Sequence ID X_DroMel_CAF1
Location 18,822,606 – 18,822,747
Length 141
Max. P 0.998666
window12388 window12389 window12390 window12391

overview

Window 8

Location 18,822,606 – 18,822,726
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.11
Mean single sequence MFE -35.03
Consensus MFE -32.76
Energy contribution -32.39
Covariance contribution -0.37
Combinations/Pair 1.07
Mean z-score -3.09
Structure conservation index 0.94
SVM decision value 2.48
SVM RNA-class probability 0.994483
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18822606 120 + 22224390
UCACUGUUUUCAUUAUCUGUGAUUUGCCCUUAUAGUCGCCUUGCCGGCAGCUCAUCCUUAAUUGCGAUUGUUGCAAGGACUUGCAGAAUUUUGCAUAUUUGAUGAGCCUGGCUCUUUCUC
..................((((((.........))))))...(((((..(((((((......(((((...((((((....))))))....))))).....))))))))))))........ ( -33.10)
>DroSec_CAF1 59657 118 + 1
UCACUGUUUUCAUUAUCUGUGAUUUGC-CUUAUAGUCGCCUCGCCGGCAGCUCAUCCUUAAUUGCGAUUGUUGCAAGGACUUGCAGAAU-UUGCAUAUUUGAUGAGCCUGGCUCUCCCUC
..................((((((...-.....))))))...(((((..(((((((......(((((...((((((....))))))...-))))).....))))))))))))........ ( -34.90)
>DroEre_CAF1 57588 115 + 1
UCACUGUUUUCAUUAUCUGUGAUUUGC-CUUAUUGCCGCCUCGCCGGCAGCUCAUCCUUAAUUGCGAUUGUUGCAAGGACUUGCAGAAUUUUGCAUAUUUGAUGAGCCUGGCUCU----C
((((..............))))...((-(....(((((......)))))(((((((......(((((...((((((....))))))....))))).....)))))))..)))...----. ( -35.44)
>DroYak_CAF1 58566 115 + 1
UCACUGUUUUCAUUAUCUGUGAUUUGC-CUUGUAGUCGCCUCGCCGGCAGCUCAUCCUUAAUUGCAAUUGCUGCAAGGACUUGCAGAAUUUUGCAUAUUUGAUGAGCCUGGCUCU----C
..................((((((...-.....))))))...(((((..(((((((......(((((...((((((....))))))....))))).....))))))))))))...----. ( -36.70)
>consensus
UCACUGUUUUCAUUAUCUGUGAUUUGC_CUUAUAGUCGCCUCGCCGGCAGCUCAUCCUUAAUUGCGAUUGUUGCAAGGACUUGCAGAAUUUUGCAUAUUUGAUGAGCCUGGCUCU____C
((((..............))))....................(((((..(((((((......(((((...((((((....))))))....))))).....))))))))))))........ (-32.76 = -32.39 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,822,606 – 18,822,726
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.11
Mean single sequence MFE -33.02
Consensus MFE -27.26
Energy contribution -27.26
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.67
Structure conservation index 0.83
SVM decision value 1.12
SVM RNA-class probability 0.918035
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18822606 120 - 22224390
GAGAAAGAGCCAGGCUCAUCAAAUAUGCAAAAUUCUGCAAGUCCUUGCAACAAUCGCAAUUAAGGAUGAGCUGCCGGCAAGGCGACUAUAAGGGCAAAUCACAGAUAAUGAAAACAGUGA
........(((.((((((((.....(((.......(((((....)))))......)))......))))))))(((.....))).........)))...((((..............)))) ( -30.86)
>DroSec_CAF1 59657 118 - 1
GAGGGAGAGCCAGGCUCAUCAAAUAUGCAA-AUUCUGCAAGUCCUUGCAACAAUCGCAAUUAAGGAUGAGCUGCCGGCGAGGCGACUAUAAG-GCAAAUCACAGAUAAUGAAAACAGUGA
........(((.((((((((.....(((..-....(((((....)))))......)))......))))))))(((.....)))........)-))...((((..............)))) ( -31.64)
>DroEre_CAF1 57588 115 - 1
G----AGAGCCAGGCUCAUCAAAUAUGCAAAAUUCUGCAAGUCCUUGCAACAAUCGCAAUUAAGGAUGAGCUGCCGGCGAGGCGGCAAUAAG-GCAAAUCACAGAUAAUGAAAACAGUGA
.----...(((.((((((((.....(((.......(((((....)))))......)))......))))))))((((......)))).....)-))...((((..............)))) ( -32.86)
>DroYak_CAF1 58566 115 - 1
G----AGAGCCAGGCUCAUCAAAUAUGCAAAAUUCUGCAAGUCCUUGCAGCAAUUGCAAUUAAGGAUGAGCUGCCGGCGAGGCGACUACAAG-GCAAAUCACAGAUAAUGAAAACAGUGA
.----...(((.((((((((.....(((((....((((((....))))))...)))))......))))))))(((.....)))........)-))...((((..............)))) ( -36.74)
>consensus
G____AGAGCCAGGCUCAUCAAAUAUGCAAAAUUCUGCAAGUCCUUGCAACAAUCGCAAUUAAGGAUGAGCUGCCGGCGAGGCGACUAUAAG_GCAAAUCACAGAUAAUGAAAACAGUGA
........(((.((((((((.....(((.......(((((....)))))......)))......))))))))(((.....)))........).))...((((..............)))) (-27.26 = -27.26 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,822,646 – 18,822,747
Length 101
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 90.83
Mean single sequence MFE -33.45
Consensus MFE -32.22
Energy contribution -31.79
Covariance contribution -0.44
Combinations/Pair 1.15
Mean z-score -3.71
Structure conservation index 0.96
SVM decision value 3.18
SVM RNA-class probability 0.998666
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18822646 101 + 22224390
UUGCCGGCAGCUCAUCCUUAAUUGCGAUUGUUGCAAGGACUUGCAGAAUUUUGCAUAUUUGAUGAGCCUGGCUCUUUCUC---ACUCCUCUGCCUGCCUGCAUA
.(((.(((((((((((......(((((...((((((....))))))....))))).....)))))))..(((........---........))))))).))).. ( -34.89)
>DroSec_CAF1 59696 103 + 1
UCGCCGGCAGCUCAUCCUUAAUUGCGAUUGUUGCAAGGACUUGCAGAAU-UUGCAUAUUUGAUGAGCCUGGCUCUCCCUCUCAACUCCUCCGCCUGCCUGCAUA
..((.(((((((((((......(((((...((((((....))))))...-))))).....)))))))..(((...................))))))).))... ( -34.41)
>DroEre_CAF1 57627 97 + 1
UCGCCGGCAGCUCAUCCUUAAUUGCGAUUGUUGCAAGGACUUGCAGAAUUUUGCAUAUUUGAUGAGCCUGGCUCU----C---AAUCCUCUGCCCGCAUGCAUA
..((.(((((((((((......(((((...((((((....))))))....))))).....)))))))..((....----.---...))..)))).))....... ( -31.00)
>DroYak_CAF1 58605 97 + 1
UCGCCGGCAGCUCAUCCUUAAUUGCAAUUGCUGCAAGGACUUGCAGAAUUUUGCAUAUUUGAUGAGCCUGGCUCU----C---ACUCCUCUGCCUGUUUGCAUA
..(((((..(((((((......(((((...((((((....))))))....))))).....))))))))))))...----.---.......(((......))).. ( -33.50)
>consensus
UCGCCGGCAGCUCAUCCUUAAUUGCGAUUGUUGCAAGGACUUGCAGAAUUUUGCAUAUUUGAUGAGCCUGGCUCU____C___ACUCCUCUGCCUGCCUGCAUA
..((.(((.(((((((......(((((...((((((....))))))....))))).....)))))))..(((...................))).))).))... (-32.22 = -31.79 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,822,646 – 18,822,747
Length 101
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 90.83
Mean single sequence MFE -32.18
Consensus MFE -27.62
Energy contribution -28.18
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.61
Structure conservation index 0.86
SVM decision value 1.89
SVM RNA-class probability 0.981714
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18822646 101 - 22224390
UAUGCAGGCAGGCAGAGGAGU---GAGAAAGAGCCAGGCUCAUCAAAUAUGCAAAAUUCUGCAAGUCCUUGCAACAAUCGCAAUUAAGGAUGAGCUGCCGGCAA
..(((.(((.(((........---........))).((((((((.....(((.......(((((....)))))......)))......))))))))))).))). ( -31.61)
>DroSec_CAF1 59696 103 - 1
UAUGCAGGCAGGCGGAGGAGUUGAGAGGGAGAGCCAGGCUCAUCAAAUAUGCAA-AUUCUGCAAGUCCUUGCAACAAUCGCAAUUAAGGAUGAGCUGCCGGCGA
..(((.(((((((((((...(((.....((((((...)))).)).......)))-.))))))..((((((((.......)))....)))))...))))).))). ( -33.10)
>DroEre_CAF1 57627 97 - 1
UAUGCAUGCGGGCAGAGGAUU---G----AGAGCCAGGCUCAUCAAAUAUGCAAAAUUCUGCAAGUCCUUGCAACAAUCGCAAUUAAGGAUGAGCUGCCGGCGA
......(((.(((...((...---.----....)).((((((((.....(((.......(((((....)))))......)))......))))))))))).))). ( -30.52)
>DroYak_CAF1 58605 97 - 1
UAUGCAAACAGGCAGAGGAGU---G----AGAGCCAGGCUCAUCAAAUAUGCAAAAUUCUGCAAGUCCUUGCAGCAAUUGCAAUUAAGGAUGAGCUGCCGGCGA
..(((.....(((....(.((---.----...))).((((((((.....(((((....((((((....))))))...)))))......))))))))))).))). ( -33.50)
>consensus
UAUGCAGGCAGGCAGAGGAGU___G____AGAGCCAGGCUCAUCAAAUAUGCAAAAUUCUGCAAGUCCUUGCAACAAUCGCAAUUAAGGAUGAGCUGCCGGCGA
..(((.(((.(((...................))).((((((((.....(((.......(((((....)))))......)))......))))))))))).))). (-27.62 = -28.18 +   0.56)

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 12:41:47 2006