Locus 8383

Sequence ID 3R_DroMel_CAF1
Location 22,355,433 – 22,355,569
Length 136
Max. P 0.999819
window13502 window13503 window13504 window13505

overview

Window 2

Location 22,355,433 – 22,355,539
Length 106
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 89.53
Mean single sequence MFE -36.88
Consensus MFE -29.50
Energy contribution -28.86
Covariance contribution -0.64
Combinations/Pair 1.12
Mean z-score -1.80
Structure conservation index 0.80
SVM decision value 0.83
SVM RNA-class probability 0.862602
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22355433 106 + 27905053
UGUUGCUUUUGUUGUUGUUGCCGAUGUUGG-----UGUAGCUGGCAUUGCAGGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGAGUUGA
.....(((((((((((.((((((((((..(-----.....)..)))))...((((...((((((....))))))...))))))))).)))..))))))))........... ( -41.60)
>DroSec_CAF1 63103 95 + 1
UGUUGCUUUUGUUGCUG---------UUGG-----UGUAGCUGGC--UGCGAGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGAGUUGA
....((((..((..((.---------(..(-----(...((((((--((....))(((((((((....)))))).)))))))))....))..)...))..))..))))... ( -34.70)
>DroSim_CAF1 62236 97 + 1
UGUUGCUUUUGUUGCUG---------UUGG-----UGUAGCUGGCAUUGCGAGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGAGUUGA
....((((..((..((.---------(..(-----(...((((((..((....))(((((((((....)))))).)))))))))....))..)...))..))..))))... ( -35.30)
>DroEre_CAF1 65381 100 + 1
UGUUGCUUUUGUUGUUGCUG------UUGA-----UGUAGCUGGCAGUGCAGGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGACUUGA
.((((((((((((...((((------((..-----.......))))))((.((((...((((((....))))))...)))).))........))))))))...)))).... ( -35.00)
>DroYak_CAF1 64872 105 + 1
UGUUGCCUUUGUUGUUGCUG------UUGUUGAUGUGUAGCUGGCAGUGCAGGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGAGUUGA
....((((((......((((------((((((.....)))).))))))((.((((...((((((....))))))...)))).))............))))))......... ( -37.80)
>consensus
UGUUGCUUUUGUUGUUG_UG______UUGG_____UGUAGCUGGCAGUGCAGGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGAGUUGA
....((((((.((((((......................(((.((...)).))).(((((((((....)))))).)))..))))))..........))))))......... (-29.50 = -28.86 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,355,433 – 22,355,539
Length 106
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 89.53
Mean single sequence MFE -26.24
Consensus MFE -22.02
Energy contribution -21.62
Covariance contribution -0.40
Combinations/Pair 1.12
Mean z-score -2.42
Structure conservation index 0.84
SVM decision value 2.52
SVM RNA-class probability 0.994873
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22355433 106 - 27905053
UCAACUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCCUGCAAUGCCAGCUACA-----CCAACAUCGGCAACAACAACAAAAGCAACA
.........((................((.((((((.(((((......))))))).)))).))..((((.......-----........))))............)).... ( -27.86)
>DroSec_CAF1 63103 95 - 1
UCAACUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCUCGCA--GCCAGCUACA-----CCAA---------CAGCAACAAAAGCAACA
.........((................((.((((((.(((((......))))))).)))).)).--....(((...-----....---------.))).......)).... ( -24.10)
>DroSim_CAF1 62236 97 - 1
UCAACUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCUCGCAAUGCCAGCUACA-----CCAA---------CAGCAACAAAAGCAACA
.........((................((.((((((.(((((......))))))).)))).)).......(((...-----....---------.))).......)).... ( -24.10)
>DroEre_CAF1 65381 100 - 1
UCAAGUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCCUGCACUGCCAGCUACA-----UCAA------CAGCAACAACAAAAGCAACA
.........((................((.((((((.(((((......))))))).)))).)).......(((...-----....------.)))..........)).... ( -26.00)
>DroYak_CAF1 64872 105 - 1
UCAACUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCCUGCACUGCCAGCUACACAUCAACAA------CAGCAACAACAAAGGCAACA
.........((((..............((.((((((.(((((......))))))).)))).)).......(((............------.)))........)))).... ( -29.12)
>consensus
UCAACUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCCUGCAAUGCCAGCUACA_____CCAA______CA_CAACAACAAAAGCAACA
...........................((.((((((.(((((......))))))).)))).)).......(((...............................))).... (-22.02 = -21.62 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,355,465 – 22,355,569
Length 104
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 97.31
Mean single sequence MFE -38.96
Consensus MFE -36.62
Energy contribution -36.62
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.94
SVM decision value 2.82
SVM RNA-class probability 0.997205
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22355465 104 + 27905053
UAGCUGGCAUUGCAGGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGAGUUGAAGGCAAUUGCCGAAGUAGGCAGGCAAGCGG
..(((.((.((((.((((...((((((....))))))...)))).))))..............((.(........)))..(((((......))))))).))).. ( -39.50)
>DroSec_CAF1 63126 102 + 1
UAGCUGGC--UGCGAGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGAGUUGAAGGCAAUUGCCGAAGUAGGCAGGCAAGCGG
..((((.(--(((((((.(((((((((....)))))).)))(....)................))))........(((....))).......)))).).))).. ( -38.10)
>DroSim_CAF1 62259 104 + 1
UAGCUGGCAUUGCGAGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGAGUUGAAGGCAAUUGCCGAAGUAGGCAGGCAAGCGG
......((.((((.....(((((((((....)))))).)))(((..(((...((((.........)))).)))..)))..(((((......))))))))))).. ( -37.50)
>DroEre_CAF1 65407 104 + 1
UAGCUGGCAGUGCAGGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGACUUGAAGGCAAUUGCCGAAGUAGGCAGGCAAGCGG
..(((.((..(((.((((...((((((....))))))...))))(((((...(((.....(((......))).....)))))))).......))).)).))).. ( -41.00)
>DroYak_CAF1 64903 104 + 1
UAGCUGGCAGUGCAGGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGAGUUGAAGGCAAUUGCCGAAGUAGGCAGGCAAGCGG
..(((.((..(((.(((((((((((((....)))))).)))(((..(((...((((.........)))).)))..)))...)))).......))).)).))).. ( -38.70)
>consensus
UAGCUGGCAGUGCAGGCGGUGGGCGCUAGAUGGCGCCACACGCCGGCGAAAAUUGAAUAAGAGGCUCGAGUUGAAGGCAAUUGCCGAAGUAGGCAGGCAAGCGG
..(((.((..........(((((((((....)))))).)))(((..(((...((((.........)))).)))..)))..(((((......))))))).))).. (-36.62 = -36.62 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 22,355,465 – 22,355,569
Length 104
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 97.31
Mean single sequence MFE -32.81
Consensus MFE -32.38
Energy contribution -32.14
Covariance contribution -0.24
Combinations/Pair 1.05
Mean z-score -2.39
Structure conservation index 0.99
SVM decision value 4.16
SVM RNA-class probability 0.999819
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22355465 104 - 27905053
CCGCUUGCCUGCCUACUUCGGCAAUUGCCUUCAACUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCCUGCAAUGCCAGCUA
..(((.((.((((......))))..................................((.((((((.(((((......))))))).)))).))...)).))).. ( -32.90)
>DroSec_CAF1 63126 102 - 1
CCGCUUGCCUGCCUACUUCGGCAAUUGCCUUCAACUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCUCGCA--GCCAGCUA
..(((.((.(((.......(((....)))........((((................(....)(((.(((((......)))))))).)))))))--)).))).. ( -32.20)
>DroSim_CAF1 62259 104 - 1
CCGCUUGCCUGCCUACUUCGGCAAUUGCCUUCAACUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCUCGCAAUGCCAGCUA
..(((.((.((((......))))(((((...........(((..................)))(((.(((((......)))))))).....))))))).))).. ( -31.07)
>DroEre_CAF1 65407 104 - 1
CCGCUUGCCUGCCUACUUCGGCAAUUGCCUUCAAGUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCCUGCACUGCCAGCUA
..(((.((..(((.((((.(((....)))...)))).).))................((.((((((.(((((......))))))).)))).))...)).))).. ( -35.00)
>DroYak_CAF1 64903 104 - 1
CCGCUUGCCUGCCUACUUCGGCAAUUGCCUUCAACUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCCUGCACUGCCAGCUA
..(((.((.((((......))))..................................((.((((((.(((((......))))))).)))).))...)).))).. ( -32.90)
>consensus
CCGCUUGCCUGCCUACUUCGGCAAUUGCCUUCAACUCGAGCCUCUUAUUCAAUUUUCGCCGGCGUGUGGCGCCAUCUAGCGCCCACCGCCUGCAAUGCCAGCUA
..(((.((.((((......))))..................................((.((((((.(((((......))))))).)))).))...)).))).. (-32.38 = -32.14 +  -0.24)

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 13:10:13 2006