Locus 2472

Sequence ID X_DroMel_CAF1
Location 6,589,217 – 6,589,456
Length 239
Max. P 0.956919
window4036 window4037 window4038 window4039

overview

Window 6

Location 6,589,217 – 6,589,336
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.34
Mean single sequence MFE -31.21
Consensus MFE -24.95
Energy contribution -26.32
Covariance contribution 1.37
Combinations/Pair 1.10
Mean z-score -1.52
Structure conservation index 0.80
SVM decision value 0.12
SVM RNA-class probability 0.592076
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6589217 119 + 22224390
AAAAAUAUGUAAGAAAAAAAAUGAAUUGGU-UUGGUGUCAGCGCAUUUUCUGGCCGGCCAAUUCGACGUGUUGAUUUCCACCAGCCAGAAUUGCGCCGCAAACACCAUUAACACGACCGC
...........................(((-((((((((.(((((..(((((((.((.....((((....))))......)).))))))).))))).)...)))))).......)))).. ( -34.31)
>DroSec_CAF1 4796 118 + 1
A-AAAUAUGUAAGAAAAAAAAUGAAUUGGU-UGGGUGUCAGCGCAUUUUCUGGCCGUCCAAUUCGACGUGUUGAUUUCCACCAGCCAGAAUUGCGCCGCAAACACCAUUAACACGACCGC
.-.........................(((-((((((((.(((((..(((((((.(((......)))(((........)))..))))))).))))).)...))))).......))))).. ( -33.11)
>DroEre_CAF1 4855 114 + 1
A-AAAUAUGUAAGAAAAAA-----AUUGGUGUUGAAGUAAACGCAUUUUCUGGCCGGCCAAUUCGGCGUGUUGAUUUCUACCAGCCAGAAUUGCGCCGCAAACACCAUUAGCACGACCGC
.-.................-----..(((((((...((...((((..(((((((.((.....((((....))))......)).))))))).))))..)).)))))))............. ( -29.70)
>DroYak_CAF1 3917 117 + 1
A-AAAUAUGUAAGAAAAAAA--GAAUUGGUUUCGGUGCAAACGCAUUUUCUGGCCGGCCAAUUGGACGUGUUGAUUUCUACCAGCCAGAAUUGCGCCGCCAACACCGUUAACACGACCGC
.-..................--...((((((.(((((....((((..(((((((.((..(((..(.....)..)))....)).))))))).)))).......)))))..))).))).... ( -27.70)
>consensus
A_AAAUAUGUAAGAAAAAAA__GAAUUGGU_UUGGUGUAAACGCAUUUUCUGGCCGGCCAAUUCGACGUGUUGAUUUCCACCAGCCAGAAUUGCGCCGCAAACACCAUUAACACGACCGC
.........................(((((..((((((..(((((..(((((((.((.....((((....))))......)).))))))).))))).....))))))...)).))).... (-24.95 = -26.32 +   1.37)

alignment

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secondary structure

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Window 7

Location 6,589,217 – 6,589,336
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.34
Mean single sequence MFE -36.60
Consensus MFE -31.76
Energy contribution -32.13
Covariance contribution 0.37
Combinations/Pair 1.14
Mean z-score -2.15
Structure conservation index 0.87
SVM decision value 1.43
SVM RNA-class probability 0.953578
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6589217 119 - 22224390
GCGGUCGUGUUAAUGGUGUUUGCGGCGCAAUUCUGGCUGGUGGAAAUCAACACGUCGAAUUGGCCGGCCAGAAAAUGCGCUGACACCAA-ACCAAUUCAUUUUUUUUCUUACAUAUUUUU
......(.(((..((((((...(((((((.(((((((((((.((..((........)).)).)))))))))))..))))))))))))))-)))........................... ( -39.50)
>DroSec_CAF1 4796 118 - 1
GCGGUCGUGUUAAUGGUGUUUGCGGCGCAAUUCUGGCUGGUGGAAAUCAACACGUCGAAUUGGACGGCCAGAAAAUGCGCUGACACCCA-ACCAAUUCAUUUUUUUUCUUACAUAUUU-U
..(((.(.......(((((...(((((((.(((((((((((....))))...((((......)))))))))))..))))))))))))).-))).........................-. ( -37.31)
>DroEre_CAF1 4855 114 - 1
GCGGUCGUGCUAAUGGUGUUUGCGGCGCAAUUCUGGCUGGUAGAAAUCAACACGCCGAAUUGGCCGGCCAGAAAAUGCGUUUACUUCAACACCAAU-----UUUUUUCUUACAUAUUU-U
(((....)))...(((((((...((((((.(((((((((((..((.((........)).)).)))))))))))..))))))......)))))))..-----.................-. ( -34.50)
>DroYak_CAF1 3917 117 - 1
GCGGUCGUGUUAACGGUGUUGGCGGCGCAAUUCUGGCUGGUAGAAAUCAACACGUCCAAUUGGCCGGCCAGAAAAUGCGUUUGCACCGAAACCAAUUC--UUUUUUUCUUACAUAUUU-U
..(((.((....))(((((....((((((.(((((((((((...(((...........))).)))))))))))..)))))).)))))...))).....--..................-. ( -35.10)
>consensus
GCGGUCGUGUUAAUGGUGUUUGCGGCGCAAUUCUGGCUGGUAGAAAUCAACACGUCGAAUUGGCCGGCCAGAAAAUGCGCUGACACCAA_ACCAAUUC__UUUUUUUCUUACAUAUUU_U
..(((........((((((...(((((((.(((((((((((.((...............)).)))))))))))..)))))))))))))..)))........................... (-31.76 = -32.13 +   0.37)

alignment

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secondary structure

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Window 8

Location 6,589,256 – 6,589,376
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.47
Mean single sequence MFE -40.92
Consensus MFE -35.08
Energy contribution -34.34
Covariance contribution -0.75
Combinations/Pair 1.15
Mean z-score -1.43
Structure conservation index 0.86
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6589256 120 - 22224390
CAAACUCAUUUAUUUGUAGCCAAGGCACUGUGGUACGUUUGCGGUCGUGUUAAUGGUGUUUGCGGCGCAAUUCUGGCUGGUGGAAAUCAACACGUCGAAUUGGCCGGCCAGAAAAUGCGC
..................(((.(((((((((..((((........))))...)))))))))..)))(((.(((((((((((.((..((........)).)).)))))))))))..))).. ( -40.40)
>DroSec_CAF1 4834 120 - 1
UAAACUCAUUUACUUGUAGCUAAGGCACUGCGGUACGUUUGCGGUCGUGUUAAUGGUGUUUGCGGCGCAAUUCUGGCUGGUGGAAAUCAACACGUCGAAUUGGACGGCCAGAAAAUGCGC
((((((((((.((.....((....))(((((((.....)))))))...)).))))).)))))..(((((.(((((((((((....))))...((((......)))))))))))..))))) ( -39.70)
>DroEre_CAF1 4889 120 - 1
AAAACUCAUUUACUUGUAGCCAGGGCAUUGCGGUACGUUUGCGGUCGUGCUAAUGGUGUUUGCGGCGCAAUUCUGGCUGGUAGAAAUCAACACGCCGAAUUGGCCGGCCAGAAAAUGCGU
....(.((..((((..((((.(.(((...((((.....)))).))).)))))..))))..)).)(((((.(((((((((((..((.((........)).)).)))))))))))..))))) ( -40.50)
>DroYak_CAF1 3954 120 - 1
CAAACUCAUUUACUUGUAGCCAGGGCACUGCGGUACGUUUGCGGUCGUGUUAACGGUGUUGGCGGCGCAAUUCUGGCUGGUAGAAAUCAACACGUCCAAUUGGCCGGCCAGAAAAUGCGU
..................(((((.(((((((((.....)))))))(((....))))).))))).(((((.(((((((((((...(((...........))).)))))))))))..))))) ( -43.10)
>consensus
CAAACUCAUUUACUUGUAGCCAAGGCACUGCGGUACGUUUGCGGUCGUGUUAAUGGUGUUUGCGGCGCAAUUCUGGCUGGUAGAAAUCAACACGUCGAAUUGGCCGGCCAGAAAAUGCGC
..............(((.(((..(((((.((.(((....))).)).)))))...)))....)))(((((.(((((((((((.((...............)).)))))))))))..))))) (-35.08 = -34.34 +  -0.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,589,336 – 6,589,456
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.08
Mean single sequence MFE -30.90
Consensus MFE -26.72
Energy contribution -25.91
Covariance contribution -0.81
Combinations/Pair 1.24
Mean z-score -2.28
Structure conservation index 0.86
SVM decision value 1.47
SVM RNA-class probability 0.956919
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6589336 120 + 22224390
AAACGUACCACAGUGCCUUGGCUACAAAUAAAUGAGUUUGAAUACGAUUUAAGUGGCAAUUUUCGGAAAAUAACUUUCUAGGCACAUGCACUCACCGGAAACGUGGAACGAAAAAGAAAG
...(((.((((.((((((..(((((...(((((..((......)).))))).))))).......(((((.....)))))))))))...........(....))))).))).......... ( -31.00)
>DroSec_CAF1 4914 120 + 1
AAACGUACCGCAGUGCCUUAGCUACAAGUAAAUGAGUUUAAAUACGAUUUAAGUGACAAAUUUCGGAAAAUAACUUUCUGGGCACAUGCACUCACCGGAAACGUGGAACGAAAAAGAAAG
...(((.((((((((((.......((..(((((..((......)).)))))..))........((((((.....))))))))))).)))......((....)).)).))).......... ( -29.60)
>DroEre_CAF1 4969 120 + 1
AAACGUACCGCAAUGCCCUGGCUACAAGUAAAUGAGUUUUGAAACGUUUUAAGUGGCAAUUUACGGAAAAUAACUCGCUGGGCACAUGCACUCACCGGAAACGUGGAACGAAAAAGAAAG
...(((.(((((.(((((.(((((....))...(((((......(((...((((....)))))))......)))))))))))))..)))......((....)).)).))).......... ( -29.00)
>DroYak_CAF1 4034 120 + 1
AAACGUACCGCAGUGCCCUGGCUACAAGUAAAUGAGUUUGGAAACGUUUAAAGUGGCAAUUUACGGAAAAUAACUCGCUGGGCACAUGCACUCACCGGAAACGUGGAACGAAAAAGAAAG
...(((.(((((((((((..(((((...((((((..........))))))..)))))......(((........)))..)))))).)))......((....)).)).))).......... ( -34.00)
>consensus
AAACGUACCGCAGUGCCCUGGCUACAAGUAAAUGAGUUUGAAAACGAUUUAAGUGGCAAUUUACGGAAAAUAACUCGCUGGGCACAUGCACUCACCGGAAACGUGGAACGAAAAAGAAAG
...(((.((((.((((((.(((...........(((((......(((...............)))......))))))))))))))...........(....))))).))).......... (-26.72 = -25.91 +  -0.81)

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 10:35:36 2006