Locus 6720

Sequence ID 2L_DroMel_CAF1
Location 18,761,016 – 18,761,134
Length 118
Max. P 0.865983
window10730 window10731

overview

Window 0

Location 18,761,016 – 18,761,110
Length 94
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 78.65
Mean single sequence MFE -28.52
Consensus MFE -17.15
Energy contribution -16.77
Covariance contribution -0.38
Combinations/Pair 1.44
Mean z-score -1.64
Structure conservation index 0.60
SVM decision value 0.30
SVM RNA-class probability 0.676488
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18761016 94 + 22407834
CGAUUCACUGUUCUCACCCUUUAGAAAGCCAAAUGGUAGUUUCUGAUCAAAGGCGGAAACGGGAGAAGUGAUCUCCGGACCACCGCAACCCAAA
.(((.((((.(((((..(((((((((((((....)))..)))))))....))).(....)))))).)))))))..(((....)))......... ( -24.30)
>DroSec_CAF1 24332 94 + 1
CGAUUCACAGUUCUCACCCUUCAGAAAGCCAAAUGGUAGUUUCUGAUCAAAGGCGGAAACGGGUGAGGUGAUUUCCGGGCCACCGCAACCCAAA
.((.((((....(((((((.((((((((((....)))..)))))))........(....))))))))))))..)).(((.........)))... ( -30.60)
>DroSim_CAF1 22864 94 + 1
CGAUUCACAGUUCUCACCCUUCAGAAAGCCAAAUGGUAGUUUCUGAUCAAAGGCGGAAACGGGUGAGGUGAUUUCCGGACCACCGCAACCCAAG
.((.((((....(((((((.((((((((((....)))..)))))))........(....))))))))))))..))(((....)))......... ( -29.20)
>DroEre_CAF1 24853 94 + 1
GGACUCACUGUUCUCACCGUUUAGGAAGCCAAAUGGCAGUUUCUGAUCAAAUGUGGAAACGGGAGAGGUGAUUUCGGGACCACCGCAGCCCAAA
(((.(((((..((((.(((.((((((((((....)))..))))))).)......(....)))))))))))).)))(((..........)))... ( -28.50)
>DroWil_CAF1 1515 89 + 1
--UUUCGCGAUUCUCCAUCUUG---AGGCCAAACUGCAACUGCUGGCGAUAGGCUGCAGUGGGUGAGCUUAAAGGCGGAAUACUGCAGCCCAUA
--..((((...((((......)---))).....(.((....)).)))))..((((((((((.....(((....)))....)))))))))).... ( -30.00)
>DroYak_CAF1 24720 94 + 1
CGACUCACUGUUUUCACCAUUCAGAAAGCCAAAUGGCAGUUUCUGAUCAAAUGCGGAAACGGGAGAAGUGAUUUCGGGUCCACCGCAGCCCAAA
...(((.((((((((.(...((((((((((....)))..)))))))......).)))))))))))..........((((........))))... ( -28.50)
>consensus
CGAUUCACUGUUCUCACCCUUCAGAAAGCCAAAUGGCAGUUUCUGAUCAAAGGCGGAAACGGGAGAGGUGAUUUCCGGACCACCGCAACCCAAA
.........(((.((..(((((((((((((....)))..)))))))....)))..)))))(((...((((..........))))....)))... (-17.15 = -16.77 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,761,041 – 18,761,134
Length 93
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 69.33
Mean single sequence MFE -31.18
Consensus MFE -17.29
Energy contribution -16.52
Covariance contribution -0.77
Combinations/Pair 1.55
Mean z-score -1.61
Structure conservation index 0.55
SVM decision value 0.85
SVM RNA-class probability 0.865983
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18761041 93 + 22407834
--AAGCCAAAUGGUAGUUUCUGAUCAAAGGCGGAAACGGGAGAAGUGAUCUCCGGACCACCGCAACCCAAAUCCAU---GGGAUUUUUCGAGAAAAAC
--..(((....)))..(((((((......((((...(.(((((.....))))).)....))))..((((......)---))).....)).)))))... ( -25.30)
>DroPse_CAF1 33935 92 + 1
CCAGGGCGAAGGG---AUGAUGGCGGAAGGCGGCAUUGGGCGAGGUCAUGGGCGGCAUGCCGCAGCCCAUGUCCAU---CGGUGGCUUCGGAAAGAAG
((..(((.....(---(((.((.(....).)).)))).(.(((((.(((((((.((.....)).))))))).)).)---)).).)))..))....... ( -37.40)
>DroSec_CAF1 24357 93 + 1
--AAGCCAAAUGGUAGUUUCUGAUCAAAGGCGGAAACGGGUGAGGUGAUUUCCGGGCCACCGCAACCCAAAUCCAU---GGGAUUUUUCGAGAAAAAC
--..(((....))).(((((((........)))))))((((..((((..........))))...))))((((((..---.))))))............ ( -25.40)
>DroSim_CAF1 22889 93 + 1
--AAGCCAAAUGGUAGUUUCUGAUCAAAGGCGGAAACGGGUGAGGUGAUUUCCGGACCACCGCAACCCAAGUCCAU---GGGAUUUUUCGAGAAAAAC
--..(((....))).(((((((........)))))))((((..((((.((....)).))))...))))((((((..---.))))))............ ( -25.60)
>DroWil_CAF1 1535 96 + 1
--AGGCCAAACUGCAACUGCUGGCGAUAGGCUGCAGUGGGUGAGCUUAAAGGCGGAAUACUGCAGCCCAUAUCCAAUUGCGGAUGCUUGGGAAACAUG
--...((((...(((.(((((((..((.((((((((((.....(((....)))....)))))))))).))..)))...)))).)))))))........ ( -36.00)
>DroPer_CAF1 33391 92 + 1
CCAGGGCGAAGGG---AUGAUGGCGGAAGGCGGCAUUGGGCGAGGUCAUGGGCGGCAUGCCGCAGCCCAUGUCCAU---CGGUGGCUUCGGAAAGAAG
((..(((.....(---(((.((.(....).)).)))).(.(((((.(((((((.((.....)).))))))).)).)---)).).)))..))....... ( -37.40)
>consensus
__AAGCCAAAUGGUAGUUGCUGACCAAAGGCGGAAACGGGUGAGGUGAUGGCCGGAACACCGCAACCCAAAUCCAU___CGGAUGCUUCGAAAAAAAC
...............(((((((.(....).)))))))((((..(((............)))...)))).(((((......)))))............. (-17.29 = -16.52 +  -0.77)

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 12:18:22 2006