Locus 7406

Sequence ID X_DroMel_CAF1
Location 18,469,608 – 18,469,740
Length 132
Max. P 0.960773
window12139 window12140 window12141

overview

Window 9

Location 18,469,608 – 18,469,702
Length 94
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 90.80
Mean single sequence MFE -19.58
Consensus MFE -17.60
Energy contribution -18.72
Covariance contribution 1.12
Combinations/Pair 1.04
Mean z-score -2.08
Structure conservation index 0.90
SVM decision value 1.52
SVM RNA-class probability 0.960773
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18469608 94 - 22224390
AAAGGGGGAC-CAUCCACGUAUGUCCCCCGUGAAAAAAAGAACACCACACACAGUUGAAAUAUGUUGAUACUACAAUGAUUUUACUUAUUGAUAU
...(((((((-...........)))))))(((.............)))...((((((((((.(((((......)))))))))))...)))).... ( -18.92)
>DroSec_CAF1 13184 90 - 1
AAAGGGGGAC-CACCCACUUGUGUCCCCCGCGAAAAAA--AACACCA--CACAGUUUAAAUAUGUUGAUACUACAAUGAUUUUACUUAUUGAUAU
...(((((((-((......)).)))))))........(--(((....--....))))................((((((......)))))).... ( -19.40)
>DroSim_CAF1 10025 94 - 1
AAAGGGGGAA-CACCCACGUGUGUCCCCCGCGAAAAAAAAAACACCACACACAGUUGAAAUAUGUUGAUACUACAAUGAUUUUACUUAUUGAUAU
...(((((((-(((....)))).))))))......................((((((((((.(((((......)))))))))))...)))).... ( -20.40)
>DroEre_CAF1 10270 90 - 1
GAAGGGGGACCCACCCACGUAUGUCCCCCUCGAAAA-----ACACCACACACAGUUGAAAUAUGUUGAUACUACAAUGAUUUUACUUAUUGAUAU
((.(((((((..((....))..))))))))).....-----..........((((((((((.(((((......)))))))))))...)))).... ( -19.60)
>consensus
AAAGGGGGAC_CACCCACGUAUGUCCCCCGCGAAAAAA__AACACCACACACAGUUGAAAUAUGUUGAUACUACAAUGAUUUUACUUAUUGAUAU
...(((((((.(((....))).)))))))......................((((((((((.(((((......)))))))))))...)))).... (-17.60 = -18.72 +   1.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,469,637 – 18,469,740
Length 103
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 90.63
Mean single sequence MFE -25.27
Consensus MFE -19.50
Energy contribution -20.75
Covariance contribution 1.25
Combinations/Pair 1.04
Mean z-score -1.88
Structure conservation index 0.77
SVM decision value 0.46
SVM RNA-class probability 0.743580
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18469637 103 + 22224390
AACAUAUUUCAACUGUGUGUGGUGUUCUUUUUUUCACGGGGGACAUACGUGGAUG-GUCCCCCUUUCCCACUUUUCGCUUAACCGCUAAAACAUAAAUAAUUUA
.............(((((((((((..........)))(((((((...........-))))))).....))).....((......))....)))))......... ( -21.50)
>DroSec_CAF1 13213 99 + 1
AACAUAUUUAAACUGUG--UGGUGUU--UUUUUUCGCGGGGGACACAAGUGGGUG-GUCCCCCUUUCCCACUUUUCGCUUAACCGCUAAAACAUAAAUAAUUUA
..(((((.......)))--))(((((--((.....((((.((....(((((((.(-(....))...)))))))....))...)))).))))))).......... ( -25.90)
>DroSim_CAF1 10054 103 + 1
AACAUAUUUCAACUGUGUGUGGUGUUUUUUUUUUCGCGGGGGACACACGUGGGUG-UUCCCCCUUUCCCACUUUUCGCUUAACCGCUAAAACAUAAAUAAUUUA
.((((((.......)))))).(((((((.........((((((.((((....)))-))))))).............((......)).))))))).......... ( -25.30)
>DroEre_CAF1 10299 99 + 1
AACAUAUUUCAACUGUGUGUGGUGU-----UUUUCGAGGGGGACAUACGUGGGUGGGUCCCCCUUCCCCCCUUUUCGCUUAACUGCUAAAACAUAAAUAAUUUA
.((((((.......)))))).((((-----(((..(((((((((.(((....))).)))))))))...........((......)).))))))).......... ( -28.40)
>consensus
AACAUAUUUCAACUGUGUGUGGUGUU__UUUUUUCGCGGGGGACACACGUGGGUG_GUCCCCCUUUCCCACUUUUCGCUUAACCGCUAAAACAUAAAUAAUUUA
.((((((.......)))))).(((((...........(((((((.(((....))).))))))).............((......))...))))).......... (-19.50 = -20.75 +   1.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,469,637 – 18,469,740
Length 103
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 90.63
Mean single sequence MFE -26.48
Consensus MFE -21.99
Energy contribution -23.61
Covariance contribution 1.62
Combinations/Pair 1.04
Mean z-score -2.18
Structure conservation index 0.83
SVM decision value 1.20
SVM RNA-class probability 0.929068
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18469637 103 - 22224390
UAAAUUAUUUAUGUUUUAGCGGUUAAGCGAAAAGUGGGAAAGGGGGAC-CAUCCACGUAUGUCCCCCGUGAAAAAAAGAACACCACACACAGUUGAAAUAUGUU
.........(((((((((((.(.....).....((((....(((((((-...........)))))))((..........)).)))).....))))))))))).. ( -27.30)
>DroSec_CAF1 13213 99 - 1
UAAAUUAUUUAUGUUUUAGCGGUUAAGCGAAAAGUGGGAAAGGGGGAC-CACCCACUUGUGUCCCCCGCGAAAAAA--AACACCA--CACAGUUUAAAUAUGUU
((((((.....((((((.((((....(((..(((((((...((....)-).))))))).)))...)))).....))--))))...--...))))))........ ( -25.00)
>DroSim_CAF1 10054 103 - 1
UAAAUUAUUUAUGUUUUAGCGGUUAAGCGAAAAGUGGGAAAGGGGGAA-CACCCACGUGUGUCCCCCGCGAAAAAAAAAACACCACACACAGUUGAAAUAUGUU
.........(((((((((((.(.....).....((((....(((((((-(((....)))).))))))...............)))).....))))))))))).. ( -27.61)
>DroEre_CAF1 10299 99 - 1
UAAAUUAUUUAUGUUUUAGCAGUUAAGCGAAAAGGGGGGAAGGGGGACCCACCCACGUAUGUCCCCCUCGAAAA-----ACACCACACACAGUUGAAAUAUGUU
.........(((((((((((.(.....).....(((((((.((((......))).).....)))))))......-----............))))))))))).. ( -26.00)
>consensus
UAAAUUAUUUAUGUUUUAGCGGUUAAGCGAAAAGUGGGAAAGGGGGAC_CACCCACGUAUGUCCCCCGCGAAAAAA__AACACCACACACAGUUGAAAUAUGUU
.........(((((((((((.(.....).....((((....(((((((.(((....))).)))))))...............)))).....))))))))))).. (-21.99 = -23.61 +   1.62)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:06 2006