Locus 7368

Sequence ID X_DroMel_CAF1
Location 18,365,652 – 18,365,769
Length 117
Max. P 0.965449
window12071 window12072 window12073 window12074

overview

Window 1

Location 18,365,652 – 18,365,742
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -23.38
Consensus MFE -20.72
Energy contribution -21.12
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.05
Structure conservation index 0.89
SVM decision value 1.58
SVM RNA-class probability 0.965449
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18365652 90 + 22224390
AAAAAAGGACCGAUGAUAGUCCUGCGGCUGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAU
.........(((....((((((((((((((......)))))))..)))))))(((.........)))...)))((((.(....))))).. ( -23.50)
>DroSec_CAF1 10287 90 + 1
AAAAAAGGACCGAUGAUAGUCCUGCGGCUGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAU
.........(((....((((((((((((((......)))))))..)))))))(((.........)))...)))((((.(....))))).. ( -23.50)
>DroSim_CAF1 11147 90 + 1
AAAAAAGGACCGAUGAUAGUCCUGCGGCUGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAU
.........(((....((((((((((((((......)))))))..)))))))(((.........)))...)))((((.(....))))).. ( -23.50)
>DroEre_CAF1 9437 90 + 1
AAAAAAGGACCGAUGAUAGUCCUGCGGCAGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAU
.........(((....(((((((.((((((.........)))))))))))))(((.........)))...)))((((.(....))))).. ( -23.20)
>DroYak_CAF1 9422 90 + 1
UAAAAAGGACCGAUGAUAGUCCUGCGGCAGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAU
.........(((....(((((((.((((((.........)))))))))))))(((.........)))...)))((((.(....))))).. ( -23.20)
>consensus
AAAAAAGGACCGAUGAUAGUCCUGCGGCUGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAU
.........(((....((((((((((((((......)))))))..)))))))(((.........)))...)))................. (-20.72 = -21.12 +   0.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,365,652 – 18,365,742
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -16.94
Consensus MFE -15.70
Energy contribution -15.70
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.93
SVM decision value 0.93
SVM RNA-class probability 0.883561
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18365652 90 - 22224390
AUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCAGCCGCAGGACUAUCAUCGGUCCUUUUUU
...........((..........(((.........)))..(((...))).((((......)))).))((((((......))))))..... ( -16.50)
>DroSec_CAF1 10287 90 - 1
AUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCAGCCGCAGGACUAUCAUCGGUCCUUUUUU
...........((..........(((.........)))..(((...))).((((......)))).))((((((......))))))..... ( -16.50)
>DroSim_CAF1 11147 90 - 1
AUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCAGCCGCAGGACUAUCAUCGGUCCUUUUUU
...........((..........(((.........)))..(((...))).((((......)))).))((((((......))))))..... ( -16.50)
>DroEre_CAF1 9437 90 - 1
AUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCUGCCGCAGGACUAUCAUCGGUCCUUUUUU
....................................(((((.....(((....)))....)))))..((((((......))))))..... ( -17.60)
>DroYak_CAF1 9422 90 - 1
AUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCUGCCGCAGGACUAUCAUCGGUCCUUUUUA
....................................(((((.....(((....)))....)))))..((((((......))))))..... ( -17.60)
>consensus
AUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCAGCCGCAGGACUAUCAUCGGUCCUUUUUU
...........((...........((.........))(((((........)))))..........))((((((......))))))..... (-15.70 = -15.70 +   0.00)

alignment

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secondary structure

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Window 3

Location 18,365,677 – 18,365,769
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.30
Mean single sequence MFE -29.17
Consensus MFE -23.99
Energy contribution -23.80
Covariance contribution -0.19
Combinations/Pair 1.09
Mean z-score -1.39
Structure conservation index 0.82
SVM decision value 0.14
SVM RNA-class probability 0.604675
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18365677 92 + 22224390
GGC---------------UGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAUGCGUUGCCGUUUCCACCCCCCCCCCCC-------------
((.---------------.(..((.((((((......))))))...........(((((((((...((((((.....))))))...)))))))))))..)..))...------------- ( -29.90)
>DroSec_CAF1 10312 84 + 1
GGC---------------UGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAUGCGUUGCCGCUUCCACCC--------C-------------
...---------------....((.((((((......))))))...........(((((.(((...((((((.....))))))...))).))))))).--------.------------- ( -25.00)
>DroAna_CAF1 13036 99 + 1
GGCAGAGGCUUCACUUUCUGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAUGCGUUGCCAUUUCCACUUU---------------------
(((((..(((((..........)))))..)))))..((....))..........(((((((((...((((((.....))))))...)))))))))....--------------------- ( -36.70)
>DroSim_CAF1 11172 85 + 1
GGC---------------UGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAUGCGUUGCCGCUUCCACCCC-------C-------------
...---------------....((.((((((......))))))...........(((((.(((...((((((.....))))))...))).)))))))..-------.------------- ( -25.00)
>DroEre_CAF1 9462 85 + 1
GGC---------------AGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAUGCGUUGCCGCUACCACUUCC--------------------
...---------------.(((((.((((((......)))))))..........(((...(((...((((((.....))))))...)))...))))))).-------------------- ( -23.20)
>DroYak_CAF1 9447 105 + 1
GGC---------------AGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAUGCGUUGCCGCUUCCACCCCCCUUUCCUGCCCAUACCCAUA
(((---------------((((((.((((((......))))))...........(((((.(((...((((((.....))))))...))).)))))....))))..))))).......... ( -35.20)
>consensus
GGC_______________UGAAGGAGCAGCUGCCGAGGGCUGCCAAUUAAUAGAUGGAAAUGGAUUUGCGUAAGAAAUAUGCGUUGCCGCUUCCACCCC_______C_____________
......................((.((((((......))))))...........(((((.(((...((((((.....))))))...))).)))))))....................... (-23.99 = -23.80 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,365,677 – 18,365,769
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.30
Mean single sequence MFE -27.78
Consensus MFE -20.41
Energy contribution -20.47
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -1.52
Structure conservation index 0.73
SVM decision value 0.16
SVM RNA-class probability 0.611504
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18365677 92 - 22224390
-------------GGGGGGGGGGGGUGGAAACGGCAACGCAUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCA---------------GCC
-------------(((((((((..(((((...(....)((.((.....)).))...)))))..))...........(((.(((...))).))).))))))).---------------... ( -31.50)
>DroSec_CAF1 10312 84 - 1
-------------G--------GGGUGGAAGCGGCAACGCAUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCA---------------GCC
-------------.--------(((((((((((....)))...........(......)..)))))))).......((((((........))))))......---------------... ( -22.80)
>DroAna_CAF1 13036 99 - 1
---------------------AAAGUGGAAAUGGCAACGCAUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCAGAAAGUGAAGCCUCUGCC
---------------------...((((((((((....((.((.....)).))....)))))))))).........(((((.....(((.(((..((.....)).)))...))).))))) ( -25.80)
>DroSim_CAF1 11172 85 - 1
-------------G-------GGGGUGGAAGCGGCAACGCAUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCA---------------GCC
-------------(-------(..(((((.(((....))).((.....))......)))))..))...........((((((........))))))......---------------... ( -26.10)
>DroEre_CAF1 9462 85 - 1
--------------------GGAAGUGGUAGCGGCAACGCAUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCU---------------GCC
--------------------((((((((..(((....))).((.....)).......))))))))...........(((((.....(((....)))....))---------------))) ( -24.90)
>DroYak_CAF1 9447 105 - 1
UAUGGGUAUGGGCAGGAAAGGGGGGUGGAAGCGGCAACGCAUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCU---------------GCC
..........(((((((...((..(((((.(((....))).((.....))......)))))..))...........((((((........))))))..))))---------------))) ( -35.60)
>consensus
_____________G_______GGGGUGGAAGCGGCAACGCAUAUUUCUUACGCAAAUCCAUUUCCAUCUAUUAAUUGGCAGCCCUCGGCAGCUGCUCCUUCA_______________GCC
......................(((((((((.((....((.((.....)).))....)).))))))))).......((((((........))))))........................ (-20.41 = -20.47 +   0.06)

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 12:37:09 2006