Locus 604

Sequence ID 3R_DroMel_CAF1
Location 2,250,700 – 2,250,828
Length 128
Max. P 0.575282
window957 window958

overview

Window 7

Location 2,250,700 – 2,250,799
Length 99
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 84.94
Mean single sequence MFE -27.08
Consensus MFE -20.62
Energy contribution -20.22
Covariance contribution -0.40
Combinations/Pair 1.15
Mean z-score -1.58
Structure conservation index 0.76
SVM decision value 0.08
SVM RNA-class probability 0.575282
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2250700 99 + 27905053
AAAGCA------------AUUGGGCAAA--AGAACCAAGUGAGACCUUGGAAAAAUGAGUAAUUACUAGUUGCCAGGGGCACUAAACCACUGCGAUUAGCUCAUGCGAAGUCU
...(((------------..(((((...--....(((((......)))))................(((((((.((((........)).)))))))))))))))))....... ( -25.40)
>DroSec_CAF1 41886 98 + 1
AAAGCA------------AUUGGGCAAA--AGAAACGGGCGAGACCUUGUA-AUAUGAGUUAUAACUAGUUGCCAGGGGCACUAAGCCACUGCGAUUAGCUCAUGCGAAGUCU
...(((------------..(((((...--......((......))(((((-((....))))))).(((((((.((.(((.....))).)))))))))))))))))....... ( -25.70)
>DroSim_CAF1 40003 98 + 1
AAAGCA------------AUUGGGCAAA--AGAACCGGGCGAGACCUUGGA-AUAUGAGUAAUAACUAGUUGCCAGGGGCACUAAACCACUGCGAUUAGCUCAUACAAAGUCU
...((.------------..(((.....--....))).)).((((.(((..-.((((((......((((((((.((((........)).))))))))))))))))))).)))) ( -24.60)
>DroEre_CAF1 39558 110 + 1
AAAGCCAAUGCUGAUUCUAUUGGCCAAA--AGAGCCGGGCGAGACCUUGGA-AAAUGAGUAAUAGCUAGUUGCCAGGGGCACUAAACCACUGCGAUUAGCUCAUGCGAAGUCU
...(((((((.......)))))))....--(((.(((((......))))).-......(((..((((((((((.((((........)).))))))))))))..)))....))) ( -30.50)
>DroYak_CAF1 36429 112 + 1
AAAGCAAAUGCUGAUUUAAUUGGGCAAAAAAAAACCGGGUGAGACCUUGGA-AAAUGAGUAAUAACUAGUUGCCAGGGGCACUAAAUCACUGCGAUUAGAUCAUGCGAAGUCU
........((((((((((((((((..........)).((((...((((((.-.....(((....))).....)))))).)))).........))))))))))).)))...... ( -29.20)
>consensus
AAAGCA____________AUUGGGCAAA__AGAACCGGGCGAGACCUUGGA_AAAUGAGUAAUAACUAGUUGCCAGGGGCACUAAACCACUGCGAUUAGCUCAUGCGAAGUCU
.....................((((.........(((((......)))))....(((((......((((((((.((((........)).))))))))))))))).....)))) (-20.62 = -20.22 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,250,719 – 2,250,828
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.30
Mean single sequence MFE -35.36
Consensus MFE -23.30
Energy contribution -24.26
Covariance contribution 0.96
Combinations/Pair 1.09
Mean z-score -2.09
Structure conservation index 0.66
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2250719 109 + 27905053
ACCAAGUGAGACCUUGGAAAAAUGAGUAAUUACUAGUUGCCAGGGGCACUAAACCACUGCGAUUAGCUCAUGCGAAGUCUUCUAACCAGCGGGGAGC-----------UGAACAAGCCCA
....((((...((((((...(((.(((....))).))).)))))).))))........((..(((((((.(((...((......))..)))..))))-----------)))....))... ( -29.70)
>DroSec_CAF1 41905 108 + 1
AACGGGCGAGACCUUGUA-AUAUGAGUUAUAACUAGUUGCCAGGGGCACUAAGCCACUGCGAUUAGCUCAUGCGAAGUCUUCUAACCAGCGGGGAGC-----------UGAACAAGCCCA
...(((((((((.((((.-..(((((......((((((((.((.(((.....))).))))))))))))))))))).))))).....((((.....))-----------)).....)))). ( -40.10)
>DroSim_CAF1 40022 108 + 1
ACCGGGCGAGACCUUGGA-AUAUGAGUAAUAACUAGUUGCCAGGGGCACUAAACCACUGCGAUUAGCUCAUACAAAGUCUUCUAACCAGCGGGGAGC-----------UGAACAAGCCCA
...(((((((((.(((..-.((((((......((((((((.((((........)).))))))))))))))))))).))))).....((((.....))-----------)).....)))). ( -37.10)
>DroEre_CAF1 39589 119 + 1
GCCGGGCGAGACCUUGGA-AAAUGAGUAAUAGCUAGUUGCCAGGGGCACUAAACCACUGCGAUUAGCUCAUGCGAAGUCUUCUAACCAGCGGGGAGCUGGUUACAAGCUGAACAAGCCCA
...((((...........-......(((..((((((((((.((((........)).))))))))))))..)))..((.(((.((((((((.....)))))))).)))))......)))). ( -44.00)
>DroYak_CAF1 36462 103 + 1
ACCGGGUGAGACCUUGGA-AAAUGAGUAAUAACUAGUUGCCAGGGGCACUAAAUCACUGCGAUUAGAUCAUGCGAAGUCUUCUAACCAGCGGGGAGC-----------UGAACAA-----
.((.((((...((((((.-.....(((....))).....)))))).))))......((((..(((((..((.....))..)))))...))))))...-----------.......----- ( -25.90)
>consensus
ACCGGGCGAGACCUUGGA_AAAUGAGUAAUAACUAGUUGCCAGGGGCACUAAACCACUGCGAUUAGCUCAUGCGAAGUCUUCUAACCAGCGGGGAGC___________UGAACAAGCCCA
...(((((((((.(((.....(((((......((((((((.((((........)).))))))))))))))).))).)))))((..((...))..))...................)))). (-23.30 = -24.26 +   0.96)

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 09:47:10 2006