Locus 1083

Sequence ID 3L_DroMel_CAF1
Location 3,172,131 – 3,172,254
Length 123
Max. P 0.906771
window1675 window1676 window1677

overview

Window 5

Location 3,172,131 – 3,172,223
Length 92
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 89.31
Mean single sequence MFE -19.95
Consensus MFE -13.61
Energy contribution -13.80
Covariance contribution 0.19
Combinations/Pair 1.08
Mean z-score -2.42
Structure conservation index 0.68
SVM decision value 0.41
SVM RNA-class probability 0.724942
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3172131 92 - 23771897
UACCGAAUCGAGUACGGAUUCUACUACCUCUGCAAUUAGUACCGAAUCUAGUACGGACUCAACUACAUCUGAAGUUACUACCAAUUCGAGUA
((((((((...(((((((((((((((..........)))))..)))))).))))((....((((.(....).))))....)).))))).))) ( -18.60)
>DroSec_CAF1 9305 92 - 1
UACCGAAUCGAGUACGGAUUCUACUACUUCUGAAAUUAGUACCGAAUCGAGUACGGACUCAACUACUUCUGAACUUACUACUGAUUCGAGUA
(((((((((.((((.(((((((((((.((....)).)))))..)))))((((.((((..........)))).)))).))))))))))).))) ( -21.60)
>DroSim_CAF1 9316 92 - 1
UACCGAAUCGAGUACGGAUUCUACUACUUCUGAAAUUAGUACCGAAUCGAGUACGGACUCAACUACUUCUGAACUUACUACUGAUUCGAGUA
(((((((((.((((.(((((((((((.((....)).)))))..)))))((((.((((..........)))).)))).))))))))))).))) ( -21.60)
>DroEre_CAF1 8999 92 - 1
UACCGAAUCCACUACAGAUUCUACUACUUCAGAAAUUAGUACCGAAUCUAGUACAGAUUCAACUCCAUCUGAAAUUAGUACCGAAUCCACUA
................((((((((((.((((((....(((...((((((.....)))))).)))...))))))..)))))..)))))..... ( -18.00)
>consensus
UACCGAAUCGAGUACGGAUUCUACUACUUCUGAAAUUAGUACCGAAUCGAGUACGGACUCAACUACAUCUGAACUUACUACCGAUUCGAGUA
...((((((.((((..((((((((((..........)))))..))))).....((((..........))))....))))...)))))).... (-13.61 = -13.80 +   0.19)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,172,161 – 3,172,254
Length 93
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 91.76
Mean single sequence MFE -25.40
Consensus MFE -21.14
Energy contribution -21.82
Covariance contribution 0.69
Combinations/Pair 1.06
Mean z-score -2.13
Structure conservation index 0.83
SVM decision value 1.05
SVM RNA-class probability 0.906771
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3172161 93 + 23771897
UUGAGUCCGUACUAGAUUCGGUACUAAUUGCAGAGGUAGUAGAAUCCGUACUCGAUUCGGUACUAAUUUCAGAAGUAGUAGAAUCUGUACUCG
........((((.((((((..(((((....(.((((((((((((((.......)))))..)))).))))).)...)))))))))))))))... ( -22.20)
>DroSec_CAF1 9335 93 + 1
UUGAGUCCGUACUCGAUUCGGUACUAAUUUCAGAAGUAGUAGAAUCCGUACUCGAUUCGGUACUAAUAUCAGAAGUAGUAGAAUCUGUACUCG
........((((..(((((..(((((.((((.((..((((((((((.......)))))..)))))...)).)))))))))))))).))))... ( -21.50)
>DroSim_CAF1 9346 93 + 1
UUGAGUCCGUACUCGAUUCGGUACUAAUUUCAGAAGUAGUAGAAUCCGUACUCGAUUCGGUACUUAUUUCAGAAGUAGUUGAGUCCGUACUCG
..((((.((.((((((((........(((((.((((((((((((((.......)))))..))).)))))).))))))))))))).)).)))). ( -25.40)
>DroEre_CAF1 9029 93 + 1
UUGAAUCUGUACUAGAUUCGGUACUAAUUUCUGAAGUAGUAGAAUCUGUAGUGGAUUCGGUACUAAUUUCAGAAGUAGUAGAAUCUGUACUAG
........((((.((((((..(((((.((((((((((((((((((((.....))))))..)))).)))))))))))))))))))))))))... ( -32.50)
>consensus
UUGAGUCCGUACUAGAUUCGGUACUAAUUUCAGAAGUAGUAGAAUCCGUACUCGAUUCGGUACUAAUUUCAGAAGUAGUAGAAUCUGUACUCG
........((((.((((((...((((.((((.((((((((((((((.......)))))..)))).))))).)))))))).))))))))))... (-21.14 = -21.82 +   0.69)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,172,161 – 3,172,254
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 91.76
Mean single sequence MFE -24.22
Consensus MFE -16.80
Energy contribution -18.30
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -3.42
Structure conservation index 0.69
SVM decision value 0.15
SVM RNA-class probability 0.608527
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3172161 93 - 23771897
CGAGUACAGAUUCUACUACUUCUGAAAUUAGUACCGAAUCGAGUACGGAUUCUACUACCUCUGCAAUUAGUACCGAAUCUAGUACGGACUCAA
.((((.(.((((((((((.((....)).)))))..)))))..(((((((((((((((..........)))))..)))))).))))).)))).. ( -22.50)
>DroSec_CAF1 9335 93 - 1
CGAGUACAGAUUCUACUACUUCUGAUAUUAGUACCGAAUCGAGUACGGAUUCUACUACUUCUGAAAUUAGUACCGAAUCGAGUACGGACUCAA
.((((.((((..........))))......(((((((.(((.((((...(((..........)))....))))))).))).))))..)))).. ( -24.20)
>DroSim_CAF1 9346 93 - 1
CGAGUACGGACUCAACUACUUCUGAAAUAAGUACCGAAUCGAGUACGGAUUCUACUACUUCUGAAAUUAGUACCGAAUCGAGUACGGACUCAA
.((((.((.((((...(((((.......)))))..((.(((.((((...(((..........)))....))))))).)))))).)).)))).. ( -22.90)
>DroEre_CAF1 9029 93 - 1
CUAGUACAGAUUCUACUACUUCUGAAAUUAGUACCGAAUCCACUACAGAUUCUACUACUUCAGAAAUUAGUACCGAAUCUAGUACAGAUUCAA
...(((((((((((((((.(((((((..(((((..(((((.......)))))))))).)))))))..)))))..)))))).))))........ ( -27.30)
>consensus
CGAGUACAGAUUCUACUACUUCUGAAAUUAGUACCGAAUCGAGUACGGAUUCUACUACUUCUGAAAUUAGUACCGAAUCGAGUACGGACUCAA
...(((((((((((((((.(((.((...(((((..(((((.......))))))))))..)).)))..)))))..)))))).))))........ (-16.80 = -18.30 +   1.50)

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 09:58:36 2006