Locus 8669

Sequence ID 3L_DroMel_CAF1
Location 22,497,905 – 22,498,055
Length 150
Max. P 0.947161
window14207 window14208 window14209

overview

Window 7

Location 22,497,905 – 22,498,017
Length 112
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 93.45
Mean single sequence MFE -39.52
Consensus MFE -35.46
Energy contribution -36.40
Covariance contribution 0.94
Combinations/Pair 1.13
Mean z-score -1.67
Structure conservation index 0.90
SVM decision value 0.60
SVM RNA-class probability 0.794184
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22497905 112 + 23771897
GCUCCAGCACUUUCAGCUGCUUUUGAUUGCGUGAAGCAGCUUUCUCUUCAGCUUUCGGGCUUUGUUUUGUCGCCGGCUGAGUUUUUGGCCAGACGGAGCAGGGACUGAGAAG
(((..((.......(((((((((.........)))))))))....))..)))((((((.((((((((((((...(((..(....)..))).)))))))))))).)))))).. ( -39.80)
>DroSec_CAF1 6320 112 + 1
GCUCCAGCACUUUCAGCUGCUUUUGAUUGCGUGAAGCAGCUUUCUCUUCGGCUUUCUGGCUUUGUUUUGUCGCCGGCUGAGUUUUUAGCCAGACGACUGAGCGACUGAGGAG
((....))......(((((((((.........)))))))))..((((((((((....))))((((((.(((((.((((((....)))))).).)))).))))))..)))))) ( -40.10)
>DroSim_CAF1 6345 112 + 1
GCUCCAGCACUUUCAGCUGCUUUUGAUUGCGUGAAGCAGCUUUCUCUUCGGCUUUCUGGCUUUGUUUUGUCGCCGGCUGAGUUUUUAGCCAGACGACUGAGCGACCGAGGAG
((....))......(((((((((.........)))))))))..((((((((((....))).((((((.(((((.((((((....)))))).).)))).)))))).))))))) ( -41.60)
>DroEre_CAF1 8388 112 + 1
GCCCCAGCACUUUCAGCUGCUUUUGAUUGCGUGAAGCAGCUUUCUCUUCGGCUUUCAGGCUUUGUUGUGUCGCCGGCUGAGUUUUUAGCCAGACGGAGCAGCGACUGAGCAG
(((..((.......(((((((((.........)))))))))....))..))).(((((.(.(((((.((((...((((((....)))))).)))).))))).).)))))... ( -36.60)
>consensus
GCUCCAGCACUUUCAGCUGCUUUUGAUUGCGUGAAGCAGCUUUCUCUUCGGCUUUCUGGCUUUGUUUUGUCGCCGGCUGAGUUUUUAGCCAGACGAAGCAGCGACUGAGGAG
((....))......(((((((((.........)))))))))..((((((((((....))).((((((((((((.((((((....)))))).).))))))))))).))))))) (-35.46 = -36.40 +   0.94)

alignment

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secondary structure

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dotplot

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Window 8

Location 22,497,905 – 22,498,017
Length 112
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 93.45
Mean single sequence MFE -32.70
Consensus MFE -26.44
Energy contribution -27.75
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -1.58
Structure conservation index 0.81
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22497905 112 - 23771897
CUUCUCAGUCCCUGCUCCGUCUGGCCAAAAACUCAGCCGGCGACAAAACAAAGCCCGAAAGCUGAAGAGAAAGCUGCUUCACGCAAUCAAAAGCAGCUGAAAGUGCUGGAGC
.............(((((....((((......(((((.(((...........))).....)))))......((((((((...........))))))))....).)))))))) ( -28.30)
>DroSec_CAF1 6320 112 - 1
CUCCUCAGUCGCUCAGUCGUCUGGCUAAAAACUCAGCCGGCGACAAAACAAAGCCAGAAAGCCGAAGAGAAAGCUGCUUCACGCAAUCAAAAGCAGCUGAAAGUGCUGGAGC
((((.((.((.(((.((((.((((((........))))))))))........((......))....)))..((((((((...........))))))))))...))..)))). ( -34.10)
>DroSim_CAF1 6345 112 - 1
CUCCUCGGUCGCUCAGUCGUCUGGCUAAAAACUCAGCCGGCGACAAAACAAAGCCAGAAAGCCGAAGAGAAAGCUGCUUCACGCAAUCAAAAGCAGCUGAAAGUGCUGGAGC
((((.(..((.(((.((((.((((((........))))))))))........((......))....)))..((((((((...........))))))))))..)....)))). ( -34.80)
>DroEre_CAF1 8388 112 - 1
CUGCUCAGUCGCUGCUCCGUCUGGCUAAAAACUCAGCCGGCGACACAACAAAGCCUGAAAGCCGAAGAGAAAGCUGCUUCACGCAAUCAAAAGCAGCUGAAAGUGCUGGGGC
...(((((.((((.(((((.((((((........))))))))..........((......))....)))..((((((((...........))))))))...))))))))).. ( -33.60)
>consensus
CUCCUCAGUCGCUCAGCCGUCUGGCUAAAAACUCAGCCGGCGACAAAACAAAGCCAGAAAGCCGAAGAGAAAGCUGCUUCACGCAAUCAAAAGCAGCUGAAAGUGCUGGAGC
....((((.((((..((((.((((((........))))))))))...........................((((((((...........))))))))...))))))))... (-26.44 = -27.75 +   1.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,497,939 – 22,498,055
Length 116
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 90.25
Mean single sequence MFE -44.88
Consensus MFE -41.69
Energy contribution -42.12
Covariance contribution 0.44
Combinations/Pair 1.16
Mean z-score -1.90
Structure conservation index 0.93
SVM decision value 1.37
SVM RNA-class probability 0.947161
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22497939 116 + 23771897
AGCAGCUUUCUCUUCAGCUUUCGGGCUUUGUUUUGUCGCCGGCUGAGUUUUUGGCCAGACGGAGCAGGGACUGAGAAGUUGCAUU-UCGAAGGGCCCGCCCG-GGGCCUCAAAUGAAA
.(((((((.(((.((((((....))))((((((((((...(((..(....)..))).)))))))))).))..)))))))))).((-(((..((((((.....-))))))....))))) ( -45.80)
>DroSec_CAF1 6354 118 + 1
AGCAGCUUUCUCUUCGGCUUUCUGGCUUUGUUUUGUCGCCGGCUGAGUUUUUAGCCAGACGACUGAGCGACUGAGGAGUUGCAUUUUCGAAGGGCCCACCCAAGGGCCUCAGAUGAAA
.(((((((.(((...((((....))))((((((.(((((.((((((....)))))).).)))).))))))..))))))))))..(((((..((((((......))))))....))))) ( -45.50)
>DroSim_CAF1 6379 118 + 1
AGCAGCUUUCUCUUCGGCUUUCUGGCUUUGUUUUGUCGCCGGCUGAGUUUUUAGCCAGACGACUGAGCGACCGAGGAGUUGCAUUUUCGAAGGGCCCGCCCAAGGGCCUCAGAUGAAA
.(((((((.(((...((((....))))((((((.(((((.((((((....)))))).).)))).))))))..))))))))))..(((((..((((((......))))))....))))) ( -46.50)
>DroEre_CAF1 8422 118 + 1
AGCAGCUUUCUCUUCGGCUUUCAGGCUUUGUUGUGUCGCCGGCUGAGUUUUUAGCCAGACGGAGCAGCGACUGAGCAGUUGCAUUUUCGAAGGACUCGCCCGAGGGUCUCGGAUGAAA
.......((((((..(((((((.(((..((((.((((...((((((....)))))).)))).))))((((((....))))))....((....))...))).)))))))..))).))). ( -41.70)
>consensus
AGCAGCUUUCUCUUCGGCUUUCUGGCUUUGUUUUGUCGCCGGCUGAGUUUUUAGCCAGACGAAGCAGCGACUGAGGAGUUGCAUUUUCGAAGGGCCCGCCCAAGGGCCUCAGAUGAAA
.(((((((.(((...((((....))))((((((((((((.((((((....)))))).).)))))))))))..))))))))))..(((((..((((((......))))))....))))) (-41.69 = -42.12 +   0.44)

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 13:21:53 2006