Locus 4858

Sequence ID 2L_DroMel_CAF1
Location 13,813,011 – 13,813,109
Length 98
Max. P 0.873052
window7706 window7707

overview

Window 6

Location 13,813,011 – 13,813,109
Length 98
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 79.25
Mean single sequence MFE -36.98
Consensus MFE -22.84
Energy contribution -24.15
Covariance contribution 1.31
Combinations/Pair 1.29
Mean z-score -2.05
Structure conservation index 0.62
SVM decision value 0.88
SVM RNA-class probability 0.873052
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13813011 98 + 22407834
CCAAAGCAGCCUUCUCCUUGCUCCUGACCAGCUCGAGUGCACGAUUCGCUCGGGCUUUGGCCAGCUGCAAUUCGAGAGGCGC-CUUUGGCAGGUUAAAA
((((((..((((.(((.((((..(((.((((((((((((.......)))))))))..))).)))..))))...)))))))..-)))))).......... ( -41.50)
>DroSec_CAF1 960 98 + 1
CCAAAGCAGCCUUCUGCUUGCUCCUGACCAGCUCGAGCUCCCGAUCCGCUCGGGCUUUGGCCAGCUGCAAUUCGAGAGGCGC-CUUGGGCAGGUUAAAA
((((.((.((((..((.((((..(((.(((((((((((.........))))))))..))).)))..))))..))..))))))-.))))........... ( -40.20)
>DroSim_CAF1 960 99 + 1
CCAAAGCAGCCUUCUGCUUGCUCCUGACCAGCUCGAGCUCCCGAUCCGCUCGGGCUUUGGCCAGCUGCAAUUCGAGAGGCGCCCUUGGGCAGGUUAAAA
((......((((..((.((((..(((.(((((((((((.........))))))))..))).)))..))))..))..))))(((....))).))...... ( -40.80)
>DroEre_CAF1 963 98 + 1
CCAAAGCAGCCUUCUGCUUGCUCCUGACCAGCUCGAUGGCCCGAUCCACUCGGGCUUUGGCCAGCUGCACUUCAAAAGGUGC-CUUGGGAACCCUAUAA
((((.(((.((((.((..(((..(((.((((......(((((((.....))))))))))).)))..)))...)).)))))))-.))))........... ( -35.30)
>DroYak_CAF1 961 98 + 1
CCAAAGCAGCCUUCUGCGUGCUCCUGACCAGCUCGAGGGCACGAUCCGCUCGGGCUUUGGCCAGCUGCACUUCAAAGGGCGC-CUUGGGCUGGCUGAAA
((((.((.(((((.((.((((..(((.((((((((((((......)).)))))))..))).)))..))))..)).)))))))-.))))........... ( -41.20)
>DroAna_CAF1 942 98 + 1
CCAAUGCCUUCUUUUGGUUGCUUGAGACCAUUUGACUGGCACGACUGGCCCGUUCUUCAGCAAGCUUUAUCUCAGUAGGAGU-UUUGGACAGGCUCCAA
....((((.((...(((((......)))))...))..)))).....((((.((((......(((((((.........)))))-)).)))).)))).... ( -22.90)
>consensus
CCAAAGCAGCCUUCUGCUUGCUCCUGACCAGCUCGAGGGCACGAUCCGCUCGGGCUUUGGCCAGCUGCAAUUCAAGAGGCGC_CUUGGGCAGGCUAAAA
(((..((.(((((.((..(((..(((.((((((((((...........))))))))..)).)))..)))...)).)))))))...)))........... (-22.84 = -24.15 +   1.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,813,011 – 13,813,109
Length 98
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 79.25
Mean single sequence MFE -39.00
Consensus MFE -22.81
Energy contribution -24.62
Covariance contribution 1.81
Combinations/Pair 1.27
Mean z-score -2.00
Structure conservation index 0.58
SVM decision value 0.63
SVM RNA-class probability 0.806684
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13813011 98 - 22407834
UUUUAACCUGCCAAAG-GCGCCUCUCGAAUUGCAGCUGGCCAAAGCCCGAGCGAAUCGUGCACUCGAGCUGGUCAGGAGCAAGGAGAAGGCUGCUUUGG
..........((((((-..(((((((...((((..(((((((..((.((((.(.......).)))).)))))))))..)))).))).))))..)))))) ( -38.90)
>DroSec_CAF1 960 98 - 1
UUUUAACCUGCCCAAG-GCGCCUCUCGAAUUGCAGCUGGCCAAAGCCCGAGCGGAUCGGGAGCUCGAGCUGGUCAGGAGCAAGCAGAAGGCUGCUUUGG
...........(((((-((((((.((...((((..(((((((..((.(((((.........))))).)))))))))..))))...)))))).))))))) ( -44.00)
>DroSim_CAF1 960 99 - 1
UUUUAACCUGCCCAAGGGCGCCUCUCGAAUUGCAGCUGGCCAAAGCCCGAGCGGAUCGGGAGCUCGAGCUGGUCAGGAGCAAGCAGAAGGCUGCUUUGG
...........((((((..((((.((...((((..(((((((..((.(((((.........))))).)))))))))..))))...))))))..)))))) ( -40.30)
>DroEre_CAF1 963 98 - 1
UUAUAGGGUUCCCAAG-GCACCUUUUGAAGUGCAGCUGGCCAAAGCCCGAGUGGAUCGGGCCAUCGAGCUGGUCAGGAGCAAGCAGAAGGCUGCUUUGG
...........(((((-((((((((((...(((..(((((((..((((((.....))))))........)))))))..)))..))))))).)))))))) ( -44.90)
>DroYak_CAF1 961 98 - 1
UUUCAGCCAGCCCAAG-GCGCCCUUUGAAGUGCAGCUGGCCAAAGCCCGAGCGGAUCGUGCCCUCGAGCUGGUCAGGAGCACGCAGAAGGCUGCUUUGG
...........(((((-(((.(((((...((((..(((((((..((.((((.((......)))))).)))))))))..))))...))))).)))))))) ( -45.80)
>DroAna_CAF1 942 98 - 1
UUGGAGCCUGUCCAAA-ACUCCUACUGAGAUAAAGCUUGCUGAAGAACGGGCCAGUCGUGCCAGUCAAAUGGUCUCAAGCAACCAAAAGAAGGCAUUGG
...(.((((((.(...-.(((.....)))....((....))...).)))))))....(((((..((...((((........))))...)).)))))... ( -20.10)
>consensus
UUUUAACCUGCCCAAG_GCGCCUCUCGAAUUGCAGCUGGCCAAAGCCCGAGCGGAUCGGGCCCUCGAGCUGGUCAGGAGCAAGCAGAAGGCUGCUUUGG
...........(((((.((((((.((...((((..(((((((..((((((.....))))))........)))))))..))))...)))))).))))))) (-22.81 = -24.62 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:29 2006