Locus 3738

Sequence ID X_DroMel_CAF1
Location 9,952,527 – 9,952,684
Length 157
Max. P 0.925769
window6130 window6131 window6132

overview

Window 0

Location 9,952,527 – 9,952,644
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 89.32
Mean single sequence MFE -28.10
Consensus MFE -20.98
Energy contribution -21.35
Covariance contribution 0.37
Combinations/Pair 1.13
Mean z-score -1.68
Structure conservation index 0.75
SVM decision value 0.22
SVM RNA-class probability 0.639756
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9952527 117 + 22224390
AAUGAUCAUUGGAAAUUCUUAAAAAUUUUCUUGGGAAAAUCGCGUGCCUCACGCGUGAAUAUCGAAUGAGUACACAACUUGCCAUCGAUUCAUUACGAUACCAAGUUGAAGUCGAGA
..((((((((.((.((((......((((((....))))))((((((...)))))).)))).)).))))).....(((((((..((((........))))..)))))))...)))... ( -31.10)
>DroSec_CAF1 15139 117 + 1
AAUGAUCAUUGGAAAUUCUUUAAAAUUUCCUUGCGAAAAUCGCGUGCCUCACGCGUGAGUAUCGAAUGAGUACACAACUCGCCAUCGAUUCAUUACGAUUCCAAGUUGAAGUCGGGG
(((((((...(((((((......)))))))..((((...(((((((.....)))))))...))....((((.....))))))....)).))))).(((((.(.....).)))))... ( -28.10)
>DroEre_CAF1 15133 117 + 1
AAUUAUCAUUGAAAAUUCUUAAACAUUUUCUUGGGAAAAUCGCGUGCCCCACGCGUGAAUAUCGAAUGAGUACACAACUUGCCAUCGAUUCAUUACGACUGAGAGUUAAAGUCAAGA
........((((.((((((((...((((((....)))))).(((((...)))))((((..(((((.((.(((.......))))))))))...))))...))))))))....)))).. ( -24.70)
>DroYak_CAF1 14912 117 + 1
GAUUAUCAUUGAAAAUUCUUUAAAAUUUCCUUGGGAAAAUCGCGUGCCUCACGCGUGAAUAUCGAACGAGUACACAACUCGCCAUCGAUUCAUUACGAUUCCAAGUUAAUGCCAUGA
........................(((..(((((((.....(((((...)))))((((..(((((.(((((.....)))))...)))))...))))..)))))))..)))....... ( -28.50)
>consensus
AAUGAUCAUUGAAAAUUCUUAAAAAUUUCCUUGGGAAAAUCGCGUGCCUCACGCGUGAAUAUCGAAUGAGUACACAACUCGCCAUCGAUUCAUUACGAUUCCAAGUUAAAGUCAAGA
.........................((..(((((...(((((((((...)))))((((..(((((.(((((.....)))))...)))))...)))))))))))))..))........ (-20.98 = -21.35 +   0.37)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,952,527 – 9,952,644
Length 117
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 89.32
Mean single sequence MFE -30.65
Consensus MFE -28.19
Energy contribution -27.50
Covariance contribution -0.69
Combinations/Pair 1.19
Mean z-score -1.82
Structure conservation index 0.92
SVM decision value 1.17
SVM RNA-class probability 0.925769
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9952527 117 - 22224390
UCUCGACUUCAACUUGGUAUCGUAAUGAAUCGAUGGCAAGUUGUGUACUCAUUCGAUAUUCACGCGUGAGGCACGCGAUUUUCCCAAGAAAAUUUUUAAGAAUUUCCAAUGAUCAUU
.....((..(((((((.(((((........))))).))))))).))..(((((.((.((((.((((((...))))))((((((....))))))......)))).)).)))))..... ( -33.90)
>DroSec_CAF1 15139 117 - 1
CCCCGACUUCAACUUGGAAUCGUAAUGAAUCGAUGGCGAGUUGUGUACUCAUUCGAUACUCACGCGUGAGGCACGCGAUUUUCGCAAGGAAAUUUUAAAGAAUUUCCAAUGAUCAUU
...(((.(((.....))).))).(((((.(((...(((((((((((.(((((.((.......)).)))))..)))))))..))))..((((((((....))))))))..)))))))) ( -33.40)
>DroEre_CAF1 15133 117 - 1
UCUUGACUUUAACUCUCAGUCGUAAUGAAUCGAUGGCAAGUUGUGUACUCAUUCGAUAUUCACGCGUGGGGCACGCGAUUUUCCCAAGAAAAUGUUUAAGAAUUUUCAAUGAUAAUU
....((((.........)))).......((((.(((.(((((((((.(((((.((.......)).)))))..)))))))))..))).((((((........))))))..)))).... ( -24.60)
>DroYak_CAF1 14912 117 - 1
UCAUGGCAUUAACUUGGAAUCGUAAUGAAUCGAUGGCGAGUUGUGUACUCGUUCGAUAUUCACGCGUGAGGCACGCGAUUUUCCCAAGGAAAUUUUAAAGAAUUUUCAAUGAUAAUC
((((........(((((........((((((((..((((((.....)))))))))))..)))((((((...))))))......)))))(((((((....)))))))..))))..... ( -30.70)
>consensus
UCUCGACUUCAACUUGGAAUCGUAAUGAAUCGAUGGCAAGUUGUGUACUCAUUCGAUAUUCACGCGUGAGGCACGCGAUUUUCCCAAGAAAAUUUUAAAGAAUUUCCAAUGAUAAUU
.....((..(((((((..((((........))))..))))))).))..(((((.((.((((.((((((...))))))((((((....))))))......)))).)).)))))..... (-28.19 = -27.50 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,952,567 – 9,952,684
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 91.30
Mean single sequence MFE -28.93
Consensus MFE -25.80
Energy contribution -25.43
Covariance contribution -0.37
Combinations/Pair 1.13
Mean z-score -1.45
Structure conservation index 0.89
SVM decision value 0.25
SVM RNA-class probability 0.655007
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9952567 117 + 22224390
CGCGUGCCUCACGCGUGAAUAUCGAAUGAGUACACAACUUGCCAUCGAUUCAUUACGAUACCAAGUUGAAGUCGAGAAAAAAAGAAAACAAUUUCGUGACUGGCACUUGCUACUCCA
((((((...))))))............((((...(((((((..((((........))))..))))))).(((((.((((............)))).)))))(((....))))))).. ( -29.10)
>DroSec_CAF1 15179 115 + 1
CGCGUGCCUCACGCGUGAGUAUCGAAUGAGUACACAACUCGCCAUCGAUUCAUUACGAUUCCAAGUUGAAGUCGGGGAAAAA--GAAACAAUUUCGUGACUGGCACUUGCUACUCCA
.(((((((((((((((((..(((((.(((((.....)))))...)))))...))))).((((..(.......)..))))...--..........)))))..)))))..))....... ( -31.80)
>DroEre_CAF1 15173 117 + 1
CGCGUGCCCCACGCGUGAAUAUCGAAUGAGUACACAACUUGCCAUCGAUUCAUUACGACUGAGAGUUAAAGUCAAGAAAAAAAUGAAACAAUUUCGUGACUGGCACUUGCUACUCCA
.(((((((.((..(((((..(((((.((.(((.......))))))))))...)))))..))........(((((.((((............)))).))))))))))..))....... ( -26.30)
>DroYak_CAF1 14952 116 + 1
CGCGUGCCUCACGCGUGAAUAUCGAACGAGUACACAACUCGCCAUCGAUUCAUUACGAUUCCAAGUUAAUGCCAUGAAAAAAA-GAAACAAUUUCGUGACUGGCACUUGCUACUCCA
.(((((((((((((((((..(((((.(((((.....)))))...)))))...))))).(((...((....))...))).....-..........)))))..)))))..))....... ( -28.50)
>consensus
CGCGUGCCUCACGCGUGAAUAUCGAAUGAGUACACAACUCGCCAUCGAUUCAUUACGAUUCCAAGUUAAAGUCAAGAAAAAAA_GAAACAAUUUCGUGACUGGCACUUGCUACUCCA
.(((((((.....(((((..(((((.(((((.....)))))...)))))...)))))............(((((.((((............)))).))))))))))..))....... (-25.80 = -25.43 +  -0.37)

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 11:07:04 2006