Locus 7229

Sequence ID X_DroMel_CAF1
Location 18,069,571 – 18,069,851
Length 280
Max. P 0.818109
window11822 window11823 window11824 window11825 window11826 window11827

overview

Window 2

Location 18,069,571 – 18,069,691
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.77
Mean single sequence MFE -39.27
Consensus MFE -36.63
Energy contribution -36.97
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.93
SVM decision value 0.67
SVM RNA-class probability 0.818109
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18069571 120 + 22224390
UGGCAGCAAAUCAAUGGAUGGACUUAAAACCACCUGAAUUAGGUGCCUAAGGCUCCCAGUGCCACCCUGCUGUGUCCUGCAUGCCUCGUCCUUAGUUAUUAUUGACUGGUAGGACGACUU
.(((((((.(((....)))((((.......((((((...)))))).....(((.......)))..........))))))).))))(((((((((((((....))))))..)))))))... ( -39.20)
>DroSec_CAF1 7311 119 + 1
UGGCAGCAAAUCAAUGGAAGGACUUAAAACCACCUGAAUUAGGUGCCUAAGGC-CCCAGUGCCACCCUGCUGUGUGCUGCAUGCCUCGUCCUUAGUUAUUAUUGACUGGAAGGACGACUU
..((((((.....((((.(((.........((((((...)))))).....(((-......)))..))).)))).)))))).....(((((((((((((....))))))..)))))))... ( -39.30)
>DroSim_CAF1 11873 119 + 1
UGGCAGCAAAUCAAUGGAAGGACUUAAAACCACCUGAAUUAGGUGCCUAAGGC-CCCAGUGCCACCCUGCUGUGUGCUGCAUGCCUCGUCCUUAGUUAUUAUUGACUGGAAGGACGACUU
..((((((.....((((.(((.........((((((...)))))).....(((-......)))..))).)))).)))))).....(((((((((((((....))))))..)))))))... ( -39.30)
>consensus
UGGCAGCAAAUCAAUGGAAGGACUUAAAACCACCUGAAUUAGGUGCCUAAGGC_CCCAGUGCCACCCUGCUGUGUGCUGCAUGCCUCGUCCUUAGUUAUUAUUGACUGGAAGGACGACUU
.(((((((.....((((.(((.........((((((...)))))).....(((.......)))..))).))))....))).))))(((((((((((((....))))))..)))))))... (-36.63 = -36.97 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,069,571 – 18,069,691
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.77
Mean single sequence MFE -40.53
Consensus MFE -35.73
Energy contribution -36.07
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 0.88
SVM decision value 0.42
SVM RNA-class probability 0.729311
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18069571 120 - 22224390
AAGUCGUCCUACCAGUCAAUAAUAACUAAGGACGAGGCAUGCAGGACACAGCAGGGUGGCACUGGGAGCCUUAGGCACCUAAUUCAGGUGGUUUUAAGUCCAUCCAUUGAUUUGCUGCCA
...(((((((...(((........))).)))))))((((.(((((.((.....((((((.(((..(((((......((((.....)))))))))..)))))))))..)).))))))))). ( -41.20)
>DroSec_CAF1 7311 119 - 1
AAGUCGUCCUUCCAGUCAAUAAUAACUAAGGACGAGGCAUGCAGCACACAGCAGGGUGGCACUGGG-GCCUUAGGCACCUAAUUCAGGUGGUUUUAAGUCCUUCCAUUGAUUUGCUGCCA
...((((((((..(((........)))))))))))((((.(((((.....))..(((((....(((-((...((.(((((.....))))).))....))))).)))))....))))))). ( -40.20)
>DroSim_CAF1 11873 119 - 1
AAGUCGUCCUUCCAGUCAAUAAUAACUAAGGACGAGGCAUGCAGCACACAGCAGGGUGGCACUGGG-GCCUUAGGCACCUAAUUCAGGUGGUUUUAAGUCCUUCCAUUGAUUUGCUGCCA
...((((((((..(((........)))))))))))((((.(((((.....))..(((((....(((-((...((.(((((.....))))).))....))))).)))))....))))))). ( -40.20)
>consensus
AAGUCGUCCUUCCAGUCAAUAAUAACUAAGGACGAGGCAUGCAGCACACAGCAGGGUGGCACUGGG_GCCUUAGGCACCUAAUUCAGGUGGUUUUAAGUCCUUCCAUUGAUUUGCUGCCA
...((((((((..(((........)))))))))))((((.((((..(((......))).((.((((...(((((((((((.....)))))..))))))....)))).))..)))))))). (-35.73 = -36.07 +   0.33)

alignment

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secondary structure

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Window 4

Location 18,069,611 – 18,069,731
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -41.10
Consensus MFE -41.13
Energy contribution -41.13
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 1.00
SVM decision value 0.13
SVM RNA-class probability 0.598482
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18069611 120 + 22224390
AGGUGCCUAAGGCUCCCAGUGCCACCCUGCUGUGUCCUGCAUGCCUCGUCCUUAGUUAUUAUUGACUGGUAGGACGACUUCAUUGUGCACUCGGCUAAUUGCCCAAAACAGUGCGGCCGA
.(((((.((((((...(((.(.(((......))).))))...)))(((((((((((((....))))))..))))))).....))).)))))(((((.((((.......))))..))))). ( -40.10)
>DroSec_CAF1 7351 119 + 1
AGGUGCCUAAGGC-CCCAGUGCCACCCUGCUGUGUGCUGCAUGCCUCGUCCUUAGUUAUUAUUGACUGGAAGGACGACUUCAUUGUGCACUCGGCUAAUUGCCCAAAACAGUGCGGCCGA
.(((((.((((((-..(((..(((......)).)..)))...)))(((((((((((((....))))))..))))))).....))).)))))(((((.((((.......))))..))))). ( -41.60)
>DroSim_CAF1 11913 119 + 1
AGGUGCCUAAGGC-CCCAGUGCCACCCUGCUGUGUGCUGCAUGCCUCGUCCUUAGUUAUUAUUGACUGGAAGGACGACUUCAUUGUGCACUCGGCUAAUUGCCCAAAACAGUGCGGCCGA
.(((((.((((((-..(((..(((......)).)..)))...)))(((((((((((((....))))))..))))))).....))).)))))(((((.((((.......))))..))))). ( -41.60)
>consensus
AGGUGCCUAAGGC_CCCAGUGCCACCCUGCUGUGUGCUGCAUGCCUCGUCCUUAGUUAUUAUUGACUGGAAGGACGACUUCAUUGUGCACUCGGCUAAUUGCCCAAAACAGUGCGGCCGA
.(((((.((((((...(((..(((......)).)..)))...)))(((((((((((((....))))))..))))))).....))).)))))(((((.((((.......))))..))))). (-41.13 = -41.13 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,069,611 – 18,069,731
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -43.17
Consensus MFE -41.33
Energy contribution -42.00
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.96
SVM decision value 0.43
SVM RNA-class probability 0.733121
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18069611 120 - 22224390
UCGGCCGCACUGUUUUGGGCAAUUAGCCGAGUGCACAAUGAAGUCGUCCUACCAGUCAAUAAUAACUAAGGACGAGGCAUGCAGGACACAGCAGGGUGGCACUGGGAGCCUUAGGCACCU
...(((((.(((((.(((((.....)))...((((...((...(((((((...(((........))).)))))))..))))))...)).))))).)))))...(((.(((...))).))) ( -40.50)
>DroSec_CAF1 7351 119 - 1
UCGGCCGCACUGUUUUGGGCAAUUAGCCGAGUGCACAAUGAAGUCGUCCUUCCAGUCAAUAAUAACUAAGGACGAGGCAUGCAGCACACAGCAGGGUGGCACUGGG-GCCUUAGGCACCU
...(((((.(((((...(((.....)))..((((...(((...((((((((..(((........)))))))))))..)))...))))..))))).)))))...(((-(((...))).))) ( -44.50)
>DroSim_CAF1 11913 119 - 1
UCGGCCGCACUGUUUUGGGCAAUUAGCCGAGUGCACAAUGAAGUCGUCCUUCCAGUCAAUAAUAACUAAGGACGAGGCAUGCAGCACACAGCAGGGUGGCACUGGG-GCCUUAGGCACCU
...(((((.(((((...(((.....)))..((((...(((...((((((((..(((........)))))))))))..)))...))))..))))).)))))...(((-(((...))).))) ( -44.50)
>consensus
UCGGCCGCACUGUUUUGGGCAAUUAGCCGAGUGCACAAUGAAGUCGUCCUUCCAGUCAAUAAUAACUAAGGACGAGGCAUGCAGCACACAGCAGGGUGGCACUGGG_GCCUUAGGCACCU
...(((((.(((((...(((.....)))..((((...(((...((((((((..(((........)))))))))))..)))...))))..))))).)))))...(((.(((...))).))) (-41.33 = -42.00 +   0.67)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,069,651 – 18,069,771
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 99.44
Mean single sequence MFE -35.40
Consensus MFE -35.40
Energy contribution -35.40
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 1.00
SVM decision value 0.32
SVM RNA-class probability 0.685531
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18069651 120 + 22224390
AUGCCUCGUCCUUAGUUAUUAUUGACUGGUAGGACGACUUCAUUGUGCACUCGGCUAAUUGCCCAAAACAGUGCGGCCGAAACGCCAAUGAAAAUUGAUGCCUAAUUGCCCUAAGCCCGG
..((.(((((((((((((....))))))..))))))).(((((((.((..((((((.((((.......))))..))))))...)))))))))......................)).... ( -35.40)
>DroSec_CAF1 7390 120 + 1
AUGCCUCGUCCUUAGUUAUUAUUGACUGGAAGGACGACUUCAUUGUGCACUCGGCUAAUUGCCCAAAACAGUGCGGCCGAAACGCCAAUGAAAAUUGAUGCCUAAUUGCCCUAAGCCCGG
..((.(((((((((((((....))))))..))))))).(((((((.((..((((((.((((.......))))..))))))...)))))))))......................)).... ( -35.40)
>DroSim_CAF1 11952 120 + 1
AUGCCUCGUCCUUAGUUAUUAUUGACUGGAAGGACGACUUCAUUGUGCACUCGGCUAAUUGCCCAAAACAGUGCGGCCGAAACGCCAAUGAAAAUUGAUGCCUAAUUGCCCUAAGCCCGG
..((.(((((((((((((....))))))..))))))).(((((((.((..((((((.((((.......))))..))))))...)))))))))......................)).... ( -35.40)
>consensus
AUGCCUCGUCCUUAGUUAUUAUUGACUGGAAGGACGACUUCAUUGUGCACUCGGCUAAUUGCCCAAAACAGUGCGGCCGAAACGCCAAUGAAAAUUGAUGCCUAAUUGCCCUAAGCCCGG
..((.(((((((((((((....))))))..))))))).(((((((.((..((((((.((((.......))))..))))))...)))))))))......................)).... (-35.40 = -35.40 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,069,731 – 18,069,851
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -47.23
Consensus MFE -45.37
Energy contribution -45.70
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.96
SVM decision value 0.17
SVM RNA-class probability 0.618651
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18069731 120 - 22224390
ACCCCUUUGACUUGGCCUUUUGGGUGGCGGUGCCUUGGCUACGCUGCGCUCCGAGUGGAUUGCUCUGGCCGGGACAAUCGCCGGGCUUAGGGCAAUUAGGCAUCAAUUUUCAUUGGCGUU
((.((..(((....(((........)))(((((((......((((.((...))))))(((((((((((((.((.(....))).))).))))))))))))))))).....)))..)).)). ( -44.80)
>DroSec_CAF1 7470 120 - 1
ACCCCUUUGACUUGGCCUUUUGGGUGGCGGUGCCUUGGCUACGCUCCGCUCCGAGUGGAUUGCUCUGGCCGGGACAAUCGCCGGGCUUAGGGCAAUUAGGCAUCAAUUUUCAUUGGCGUU
((.((..(((....(((........)))(((((((......(((((......)))))(((((((((((((.((.(....))).))).))))))))))))))))).....)))..)).)). ( -47.40)
>DroSim_CAF1 12032 120 - 1
ACCCCUUUGACUUGGCCUUUUGGGUGGCGGUGCCUUGGCUACGCUCCGCUCCGAGUGGAUUGCUCUGGCCUGGACAAUCGCCGGGCUUAGGGCAAUUAGGCAUCAAUUUUCAUUGGCGUU
((.((..(((....(((........)))(((((((......(((((......)))))((((((((((((((((.(....))))))).))))))))))))))))).....)))..)).)). ( -49.50)
>consensus
ACCCCUUUGACUUGGCCUUUUGGGUGGCGGUGCCUUGGCUACGCUCCGCUCCGAGUGGAUUGCUCUGGCCGGGACAAUCGCCGGGCUUAGGGCAAUUAGGCAUCAAUUUUCAUUGGCGUU
((.((..(((....(((........)))(((((((......(((((......)))))(((((((((((((.((.(....))).))).))))))))))))))))).....)))..)).)). (-45.37 = -45.70 +   0.33)

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 12:33:34 2006