Locus 8540

Sequence ID 3R_DroMel_CAF1
Location 22,811,065 – 22,811,202
Length 137
Max. P 0.992653
window13721 window13722 window13723 window13724

overview

Window 1

Location 22,811,065 – 22,811,171
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 89.34
Mean single sequence MFE -23.44
Consensus MFE -17.54
Energy contribution -18.66
Covariance contribution 1.12
Combinations/Pair 1.18
Mean z-score -1.54
Structure conservation index 0.75
SVM decision value -0.01
SVM RNA-class probability 0.529555
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22811065 106 + 27905053
UUUUAUCAACUAACACAAUUUAGGUUAAGUUUUAGGGGACCCUCUAGUCGAGAGUCUUCGAUCAAUCGAUAUUUCAUUGAUAGUUUUCACUAUCCUAGCUUAGUGA
.............(((((.(((((...(((....((((((.(((.....))).)))))).((((((.((....)))))))).......)))..))))).)).))). ( -23.00)
>DroSec_CAF1 20066 105 + 1
UU-UAUCAUCUAACCCAAUGUAGGUUAAGUUUUAGGGGACCCUCUAUUCGAGAGUCCUCGAUCAAUCGAUAUUUCAUUGAUAGUCUUCACUAUCCUAGCUUAGUGA
..-.......(((((.......))))).......((((((.(((.....))).)))))).((((((.((....)))))))).....((((((........)))))) ( -26.30)
>DroSim_CAF1 20371 106 + 1
UUUUAUCAACUAACCCAAUGCAGGUUAAGUUUUAGGGGACCCUCUAGUCGAGAGUCCUCGAUCAAUCGAUAUUUCAUUGAUAGUUUUCACUAUCCUAGCUUAGUGA
.......((((((((.......)))).))))...((((((.(((.....))).)))))).((((((.((....)))))))).....((((((........)))))) ( -27.20)
>DroEre_CAF1 19993 106 + 1
UUUUAUCAACUAACCCAAUAUAGGUUAAGCUUUAGAGGUGCCUCUGGUCGAGAGUACUUGAUCAAUCGAUAUUUCAUUGAUAUUUUUCAACUUGCUAGCGUAGUGA
.....(((..(((((.......))))).(((...((((((((((.....))).))))...((((((.((....)))))))).........)))...)))....))) ( -20.90)
>DroYak_CAF1 20139 106 + 1
UUUUAUCAACUAACCCAAUUUAGGUUAAGUUUUAAGGGUCCCUCUAAUCGAGAGUCCUUGAUCGAUCGAUAUUUAAUUGAUAUUUUUCACUUUCCUAGCGUAGUGA
........((((.......(((((..((((.(((((((.(.(((.....))).))))))))..((..((((((.....))))))..)))))).)))))..)))).. ( -19.80)
>consensus
UUUUAUCAACUAACCCAAUGUAGGUUAAGUUUUAGGGGACCCUCUAGUCGAGAGUCCUCGAUCAAUCGAUAUUUCAUUGAUAGUUUUCACUAUCCUAGCUUAGUGA
..........(((((.......))))).......((((((.(((.....))).)))))).((((((.((....)))))))).....((((((........)))))) (-17.54 = -18.66 +   1.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 22,811,065 – 22,811,171
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 89.34
Mean single sequence MFE -25.81
Consensus MFE -21.04
Energy contribution -23.04
Covariance contribution 2.00
Combinations/Pair 1.07
Mean z-score -2.53
Structure conservation index 0.82
SVM decision value 2.34
SVM RNA-class probability 0.992653
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22811065 106 - 27905053
UCACUAAGCUAGGAUAGUGAAAACUAUCAAUGAAAUAUCGAUUGAUCGAAGACUCUCGACUAGAGGGUCCCCUAAAACUUAACCUAAAUUGUGUUAGUUGAUAAAA
............((((((....)))))).......(((((((((((....(((((((.....))))))).......((............)))))))))))))... ( -25.40)
>DroSec_CAF1 20066 105 - 1
UCACUAAGCUAGGAUAGUGAAGACUAUCAAUGAAAUAUCGAUUGAUCGAGGACUCUCGAAUAGAGGGUCCCCUAAAACUUAACCUACAUUGGGUUAGAUGAUA-AA
(((((((.((..((((((....))))))((((.....((((....))))((((((((.....))))))))................)))))).)))).)))..-.. ( -29.80)
>DroSim_CAF1 20371 106 - 1
UCACUAAGCUAGGAUAGUGAAAACUAUCAAUGAAAUAUCGAUUGAUCGAGGACUCUCGACUAGAGGGUCCCCUAAAACUUAACCUGCAUUGGGUUAGUUGAUAAAA
............((((((....)))))).......(((((((((((.(.((((((((.....)))))))).)..........((......)))))))))))))... ( -32.80)
>DroEre_CAF1 19993 106 - 1
UCACUACGCUAGCAAGUUGAAAAAUAUCAAUGAAAUAUCGAUUGAUCAAGUACUCUCGACCAGAGGCACCUCUAAAGCUUAACCUAUAUUGGGUUAGUUGAUAAAA
(((....(((.....(((((.....((((((((....)).)))))).........))))).((((....))))..)))(((((((.....))))))).)))..... ( -18.04)
>DroYak_CAF1 20139 106 - 1
UCACUACGCUAGGAAAGUGAAAAAUAUCAAUUAAAUAUCGAUCGAUCAAGGACUCUCGAUUAGAGGGACCCUUAAAACUUAACCUAAAUUGGGUUAGUUGAUAAAA
(((((.(....)...)))))....(((((((................((((.(((((.....)))))..))))......((((((.....)))))))))))))... ( -23.00)
>consensus
UCACUAAGCUAGGAUAGUGAAAACUAUCAAUGAAAUAUCGAUUGAUCGAGGACUCUCGACUAGAGGGUCCCCUAAAACUUAACCUAAAUUGGGUUAGUUGAUAAAA
............((((((....)))))).......(((((((((((...((((((((.....))))))))............((......)))))))))))))... (-21.04 = -23.04 +   2.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,811,092 – 22,811,202
Length 110
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 91.00
Mean single sequence MFE -26.56
Consensus MFE -20.76
Energy contribution -21.28
Covariance contribution 0.52
Combinations/Pair 1.14
Mean z-score -1.87
Structure conservation index 0.78
SVM decision value 0.79
SVM RNA-class probability 0.851766
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22811092 110 + 27905053
AGUUUUAGGGGACCCUCUAGUCGAGAGUCUUCGAUCAAUCGAUAUUUCAUUGAUAGUUUUCACUAUCCUAGCUUAGUGAACUCGUGCCUCGAUAUCAAAUAUCUAAAAUG
.((((((((((((.(((.....))).))))))........((((((....(((((...(((((((........))))))).(((.....)))))))))))))))))))). ( -26.50)
>DroSec_CAF1 20092 110 + 1
AGUUUUAGGGGACCCUCUAUUCGAGAGUCCUCGAUCAAUCGAUAUUUCAUUGAUAGUCUUCACUAUCCUAGCUUAGUGAACUCGUGCCUCGAUAUCAAAUAUCUAAAAUG
.((((((((((((.(((.....))).))))))........((((((....(((((...(((((((........))))))).(((.....)))))))))))))))))))). ( -29.20)
>DroSim_CAF1 20398 110 + 1
AGUUUUAGGGGACCCUCUAGUCGAGAGUCCUCGAUCAAUCGAUAUUUCAUUGAUAGUUUUCACUAUCCUAGCUUAGUGAACUCGUGCCUCGAUAUCAAAUAUCUAAAAUG
.((((((((((((.(((.....))).))))))........((((((....(((((...(((((((........))))))).(((.....)))))))))))))))))))). ( -29.30)
>DroEre_CAF1 20020 110 + 1
AGCUUUAGAGGUGCCUCUGGUCGAGAGUACUUGAUCAAUCGAUAUUUCAUUGAUAUUUUUCAACUUGCUAGCGUAGUGAACUCGUGCCUCGAUAUCAAAUAUCAAAAAUG
.....(((((....)))))((((((.((((...((((((.((....))))))))....((((...((....))...))))...))))))))))................. ( -25.40)
>DroYak_CAF1 20166 110 + 1
AGUUUUAAGGGUCCCUCUAAUCGAGAGUCCUUGAUCGAUCGAUAUUUAAUUGAUAUUUUUCACUUUCCUAGCGUAGUGAACUCGUGCCUCGAUAUUAAAUAUCAAAAAUG
....(((((((.(.(((.....))).))))))))......((((((((((........((((((..........)))))).(((.....))).))))))))))....... ( -22.40)
>consensus
AGUUUUAGGGGACCCUCUAGUCGAGAGUCCUCGAUCAAUCGAUAUUUCAUUGAUAGUUUUCACUAUCCUAGCUUAGUGAACUCGUGCCUCGAUAUCAAAUAUCUAAAAUG
.....(((((....)))))((((((.((...(((...((((((.....))))))....(((((((........))))))).))).))))))))................. (-20.76 = -21.28 +   0.52)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,811,092 – 22,811,202
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 91.00
Mean single sequence MFE -28.88
Consensus MFE -23.34
Energy contribution -24.78
Covariance contribution 1.44
Combinations/Pair 1.14
Mean z-score -2.57
Structure conservation index 0.81
SVM decision value 2.32
SVM RNA-class probability 0.992290
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22811092 110 - 27905053
CAUUUUAGAUAUUUGAUAUCGAGGCACGAGUUCACUAAGCUAGGAUAGUGAAAACUAUCAAUGAAAUAUCGAUUGAUCGAAGACUCUCGACUAGAGGGUCCCCUAAAACU
..((((((...((((((((((((((...((....))..)))..((((((....)))))).........)))))..))))))(((((((.....)))))))..)))))).. ( -32.30)
>DroSec_CAF1 20092 110 - 1
CAUUUUAGAUAUUUGAUAUCGAGGCACGAGUUCACUAAGCUAGGAUAGUGAAGACUAUCAAUGAAAUAUCGAUUGAUCGAGGACUCUCGAAUAGAGGGUCCCCUAAAACU
..((((((....(((((((((((((...((....))..)))..((((((....)))))).........)))))..)))))((((((((.....)))))))).)))))).. ( -32.40)
>DroSim_CAF1 20398 110 - 1
CAUUUUAGAUAUUUGAUAUCGAGGCACGAGUUCACUAAGCUAGGAUAGUGAAAACUAUCAAUGAAAUAUCGAUUGAUCGAGGACUCUCGACUAGAGGGUCCCCUAAAACU
..((((((....(((((((((((((...((....))..)))..((((((....)))))).........)))))..)))))((((((((.....)))))))).)))))).. ( -34.60)
>DroEre_CAF1 20020 110 - 1
CAUUUUUGAUAUUUGAUAUCGAGGCACGAGUUCACUACGCUAGCAAGUUGAAAAAUAUCAAUGAAAUAUCGAUUGAUCAAGUACUCUCGACCAGAGGCACCUCUAAAGCU
.....((((((((((((((((((((...((....))..))).....(((((......)))))......)))))..))))))))...))))..((((....))))...... ( -20.50)
>DroYak_CAF1 20166 110 - 1
CAUUUUUGAUAUUUAAUAUCGAGGCACGAGUUCACUACGCUAGGAAAGUGAAAAAUAUCAAUUAAAUAUCGAUCGAUCAAGGACUCUCGAUUAGAGGGACCCUUAAAACU
.....((((((((((((.(((.....))).((((((.(....)...))))))........))))))))))))......((((.(((((.....)))))..))))...... ( -24.60)
>consensus
CAUUUUAGAUAUUUGAUAUCGAGGCACGAGUUCACUAAGCUAGGAUAGUGAAAACUAUCAAUGAAAUAUCGAUUGAUCGAGGACUCUCGACUAGAGGGUCCCCUAAAACU
..((((((....(((((((((((((...((....))..)))..((((((....)))))).........)))))..)))))((((((((.....)))))))).)))))).. (-23.34 = -24.78 +   1.44)

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 13:13:38 2006