Locus 8406

Sequence ID X_DroMel_CAF1
Location 20,879,747 – 20,879,892
Length 145
Max. P 0.848977
window13801 window13802 window13803

overview

Window 1

Location 20,879,747 – 20,879,852
Length 105
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 79.20
Mean single sequence MFE -35.05
Consensus MFE -24.03
Energy contribution -24.37
Covariance contribution 0.34
Combinations/Pair 1.13
Mean z-score -1.84
Structure conservation index 0.69
SVM decision value 0.74
SVM RNA-class probability 0.837598
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20879747 105 + 22224390
AAGUAGCCGCAGCCCAAUUCGAAAUGCUAAUGAUAACGAAAAUCUGGUUGGGUGAAUCACCCAGUGAUUCAGUGGGGCUUGAC------GAGGAUCGCCUCCUAGCCAGAU
......((((.(((((((..((....................))..)))))))(((((((...))))))).))))((((....------((((....))))..)))).... ( -33.25)
>DroSec_CAF1 7325 101 + 1
----AGCCGCAACCCAAUUCGAAAUGCUAAUGAUAACGAAUGUCUGGUUGGGUGAAUCACCCGGUGAUUCAGUGGGGCUCGGC------GAGGAUCGCCUCCUAGCCAGAU
----..((((.(((((((..((....(..........)....))..)))))))(((((((...))))))).))))((((.((.------((((....)))))))))).... ( -35.80)
>DroEre_CAF1 7397 111 + 1
AAGUAACAUUAGACCGACACGAAACAGUAAUGAUAAGGAAAGUCUGGGUGGGUGAAUCACCCAGUGAUUCAGUGGGGCUUGGCUCCACACAGGAUCCACCCCUGGCCAGAU
........................((....))....((..((...(((((((((((((((...))))))).(((((((...))))))).....))))))))))..)).... ( -36.10)
>consensus
AAGUAGCCGCAGCCCAAUUCGAAAUGCUAAUGAUAACGAAAGUCUGGUUGGGUGAAUCACCCAGUGAUUCAGUGGGGCUUGGC______GAGGAUCGCCUCCUAGCCAGAU
.........................................((((((((((.((((((((...))))))))..(((((..................))))))))))))))) (-24.03 = -24.37 +   0.34)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,879,784 – 20,879,892
Length 108
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 84.52
Mean single sequence MFE -38.90
Consensus MFE -28.09
Energy contribution -27.76
Covariance contribution -0.33
Combinations/Pair 1.12
Mean z-score -1.94
Structure conservation index 0.72
SVM decision value 0.21
SVM RNA-class probability 0.633283
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20879784 108 + 22224390
GAAAAUCUGGUUGGGUGAAUCACCCAGUGAUUCAGUGGGGCUUGAC------GAGGAUCGCCUCCUAGCCAGAUCAGUUAAAAGUCCCCCACUGAAACUGACCACUUCUUGCGA
.......((((((((((...)))))(((..((((((((((...(((------((((....)))).((((.......))))...))))))))))))))))))))).......... ( -37.60)
>DroSec_CAF1 7358 108 + 1
GAAUGUCUGGUUGGGUGAAUCACCCGGUGAUUCAGUGGGGCUCGGC------GAGGAUCGCCUCCUAGCCAGAUCUGAUUAAAGUCCCCCACUGAAACUGACCACUUCUUGUGA
.......((((((((((...)))))(((..((((((((((...(((------.((((.....)))).))).((.((......)))))))))))))))))))))).......... ( -40.50)
>DroEre_CAF1 7434 113 + 1
GAAAGUCUGGGUGGGUGAAUCACCCAGUGAUUCAGUGGGGCUUGGCUCCACACAGGAUCCACCCCUGGCCAGAUCAGAUUAAAGUCC-CCACAGAACCUGACCAUUUCUUGCGG
(.(((..(((..(((((((((((...))))))).(((((((((((.(((.....))).))....((((.....))))....))).))-))))...))))..)))...))).).. ( -38.60)
>consensus
GAAAGUCUGGUUGGGUGAAUCACCCAGUGAUUCAGUGGGGCUUGGC______GAGGAUCGCCUCCUAGCCAGAUCAGAUUAAAGUCCCCCACUGAAACUGACCACUUCUUGCGA
(((.(((.(((((((((...))))))....((((((((((...(((.........((((..((...))...))))........)))))))))))))))))))...)))...... (-28.09 = -27.76 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,879,784 – 20,879,892
Length 108
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 84.52
Mean single sequence MFE -41.17
Consensus MFE -28.98
Energy contribution -28.77
Covariance contribution -0.21
Combinations/Pair 1.13
Mean z-score -2.47
Structure conservation index 0.70
SVM decision value 0.78
SVM RNA-class probability 0.848977
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20879784 108 - 22224390
UCGCAAGAAGUGGUCAGUUUCAGUGGGGGACUUUUAACUGAUCUGGCUAGGAGGCGAUCCUC------GUCAAGCCCCACUGAAUCACUGGGUGAUUCACCCAACCAGAUUUUC
((....))..((((..(.(((((((((((((........).))((((.((((.....)))).------))))..)))))))))).)..((((((...))))))))))....... ( -40.00)
>DroSec_CAF1 7358 108 - 1
UCACAAGAAGUGGUCAGUUUCAGUGGGGGACUUUAAUCAGAUCUGGCUAGGAGGCGAUCCUC------GCCGAGCCCCACUGAAUCACCGGGUGAUUCACCCAACCAGACAUUC
.(((.....)))(((.(.((((((((((((......)).....((((.((((.....)))).------))))..)))))))))).)...(((((...))))).....))).... ( -41.40)
>DroEre_CAF1 7434 113 - 1
CCGCAAGAAAUGGUCAGGUUCUGUGG-GGACUUUAAUCUGAUCUGGCCAGGGGUGGAUCCUGUGUGGAGCCAAGCCCCACUGAAUCACUGGGUGAUUCACCCACCCAGACUUUC
.(....)...((((((((((....(.-...)........))))))))))(((((((.(((.....))).))..))))).........(((((((.......)))))))...... ( -42.10)
>consensus
UCGCAAGAAGUGGUCAGUUUCAGUGGGGGACUUUAAUCUGAUCUGGCUAGGAGGCGAUCCUC______GCCAAGCCCCACUGAAUCACUGGGUGAUUCACCCAACCAGACUUUC
............(((.(.(((((((((((((........).))((((.((((.....)))).......))))..)))))))))).)...(((((...))))).....))).... (-28.98 = -28.77 +  -0.21)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:03:08 2006