Locus 6237

Sequence ID 3R_DroMel_CAF1
Location 16,291,002 – 16,291,162
Length 160
Max. P 0.917932
window10174 window10175 window10176

overview

Window 4

Location 16,291,002 – 16,291,122
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -25.20
Consensus MFE -24.40
Energy contribution -24.73
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.97
SVM decision value 1.12
SVM RNA-class probability 0.917932
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16291002 120 + 27905053
GAAAAUCAAAUAAUAAAUACGAAAUGUAAACUGAACAAUUAUGCUGCCAGUGUCAAGCAUAAAAGUGGCCGGCUGCAUCUUCGCAAAUGCAAAUGUAAAUUGCGAAAUGCAAAUUAUGCA
........................((((..(((..((.(((((((..........)))))))...))..))).(((((.(((((((.(((....)))..)))))))))))).....)))) ( -25.60)
>DroSec_CAF1 11641 120 + 1
GAAAAUCAAAUAAUAAAUACGAAAUGUAAACUGAACAAUUAUGCUGCCAGUGUCAAGCAUAAAAGUGGCCGGCUGCAUCUUCGCAAAUGCAAAUGUAAAUUGCGAAAUGCAAAUUAUGCA
........................((((..(((..((.(((((((..........)))))))...))..))).(((((.(((((((.(((....)))..)))))))))))).....)))) ( -25.60)
>DroSim_CAF1 3758 119 + 1
GAAAAUCAAAUAAUAAAUACGAAAUGUAAACUGAACAAUUAUGCUGCCAGUGUCAAGCAUAAAAGUGGCCGGCUGCAUCUUCGCA-ACGCAAAUGUAAAUUGCGAAAUGCAAAUUAUGCA
........................((((..(((..((.(((((((..........)))))))...))..))).(((((.((((((-(.((....))...)))))))))))).....)))) ( -24.40)
>consensus
GAAAAUCAAAUAAUAAAUACGAAAUGUAAACUGAACAAUUAUGCUGCCAGUGUCAAGCAUAAAAGUGGCCGGCUGCAUCUUCGCAAAUGCAAAUGUAAAUUGCGAAAUGCAAAUUAUGCA
........................((((..(((..((.(((((((..........)))))))...))..))).(((((.((((((..(((....)))...))))))))))).....)))) (-24.40 = -24.73 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,291,042 – 16,291,162
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -32.13
Consensus MFE -30.93
Energy contribution -31.27
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.96
SVM decision value 0.05
SVM RNA-class probability 0.560124
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16291042 120 + 27905053
AUGCUGCCAGUGUCAAGCAUAAAAGUGGCCGGCUGCAUCUUCGCAAAUGCAAAUGUAAAUUGCGAAAUGCAAAUUAUGCAUAUUUUGAUUGGGCCCAAAGUCAGCCGGAAGUGCUUAAAA
(((((..........)))))..(((((.((((((((...(((((((.(((....)))..)))))))(((((.....))))).......(((....))).).)))))))...))))).... ( -33.40)
>DroSec_CAF1 11681 120 + 1
AUGCUGCCAGUGUCAAGCAUAAAAGUGGCCGGCUGCAUCUUCGCAAAUGCAAAUGUAAAUUGCGAAAUGCAAAUUAUGCACAUUUUGAUUGGGGCCAAAGACAGCCGGAAGUGCUUAAAA
(((((..........)))))..(((((.((((((((...(((((((.(((....)))..))))))).((((.....))))........(((....))).).)))))))...))))).... ( -32.10)
>DroSim_CAF1 3798 119 + 1
AUGCUGCCAGUGUCAAGCAUAAAAGUGGCCGGCUGCAUCUUCGCA-ACGCAAAUGUAAAUUGCGAAAUGCAAAUUAUGCACAUUUUGAUUGGGCCCAAAGACAGCCGGAAGUGCUUAAAA
(((((..........)))))..(((((.((((((((...((((((-(.((....))...))))))).((((.....))))........(((....))).).)))))))...))))).... ( -30.90)
>consensus
AUGCUGCCAGUGUCAAGCAUAAAAGUGGCCGGCUGCAUCUUCGCAAAUGCAAAUGUAAAUUGCGAAAUGCAAAUUAUGCACAUUUUGAUUGGGCCCAAAGACAGCCGGAAGUGCUUAAAA
(((((..........)))))..(((((.((((((((...((((((..(((....)))...)))))).((((.....))))........(((....))).).)))))))...))))).... (-30.93 = -31.27 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,291,042 – 16,291,162
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -32.88
Consensus MFE -31.45
Energy contribution -31.57
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.13
Structure conservation index 0.96
SVM decision value 1.00
SVM RNA-class probability 0.897525
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16291042 120 - 27905053
UUUUAAGCACUUCCGGCUGACUUUGGGCCCAAUCAAAAUAUGCAUAAUUUGCAUUUCGCAAUUUACAUUUGCAUUUGCGAAGAUGCAGCCGGCCACUUUUAUGCUUGACACUGGCAGCAU
......((....(((((((....((....))(((.....(((((.....)))))(((((((.............)))))))))).))))))).........((((.......)))))).. ( -31.62)
>DroSec_CAF1 11681 120 - 1
UUUUAAGCACUUCCGGCUGUCUUUGGCCCCAAUCAAAAUGUGCAUAAUUUGCAUUUCGCAAUUUACAUUUGCAUUUGCGAAGAUGCAGCCGGCCACUUUUAUGCUUGACACUGGCAGCAU
......((....((((((((...((....))(((.....(((((.....)))))(((((((.............)))))))))))))))))).........((((.......)))))).. ( -32.92)
>DroSim_CAF1 3798 119 - 1
UUUUAAGCACUUCCGGCUGUCUUUGGGCCCAAUCAAAAUGUGCAUAAUUUGCAUUUCGCAAUUUACAUUUGCGU-UGCGAAGAUGCAGCCGGCCACUUUUAUGCUUGACACUGGCAGCAU
......((....((((((...(((((......)))))....((((..((((((...(((((.......))))).-)))))).)))))))))).........((((.......)))))).. ( -34.10)
>consensus
UUUUAAGCACUUCCGGCUGUCUUUGGGCCCAAUCAAAAUGUGCAUAAUUUGCAUUUCGCAAUUUACAUUUGCAUUUGCGAAGAUGCAGCCGGCCACUUUUAUGCUUGACACUGGCAGCAU
......((....(((((((((((((..............(((((.....)))))...((((.......)))).....)))))..)))))))).........((((.......)))))).. (-31.45 = -31.57 +   0.11)

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 12:16:24 2006