Locus 4079

Sequence ID 3L_DroMel_CAF1
Location 11,884,405 – 11,884,541
Length 136
Max. P 0.896160
window6349 window6350

overview

Window 9

Location 11,884,405 – 11,884,505
Length 100
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 87.67
Mean single sequence MFE -30.36
Consensus MFE -25.78
Energy contribution -25.38
Covariance contribution -0.40
Combinations/Pair 1.08
Mean z-score -1.49
Structure conservation index 0.85
SVM decision value 0.30
SVM RNA-class probability 0.679424
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11884405 100 - 23771897
GCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCAACUGGAAAGUAUGAGUAGAUCUGCUGCAGUUGCAAGG----CUUUGCAAGUUUUUAAAUGUCGA
(((((((...........((((.(((....)))))))(((((((...((((.((.....)))))).)))))))..))----).))))................. ( -31.70)
>DroSec_CAF1 59611 100 - 1
GCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCAACUGGAAAGUAUGAGUAGAUCUGUUGCAGUUGCAAGG----CUUUGCAAGUUUUUAAAUUUCGA
(((((((...........((((.(((....)))))))(((((((.((.....((.....))..)).)))))))..))----).))))................. ( -29.40)
>DroSim_CAF1 60131 100 - 1
GCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCAACUGAAAAGUAUGAGUAGAUCUGUUGCAGUUGCAAGG----CUUUGCAAGUUUUUAAAUUUCGA
(((((((...........((((.(((....)))))))(((((((...((.((......))))....)))))))..))----).))))................. ( -28.10)
>DroEre_CAF1 61714 98 - 1
GCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCAACUGGAAAGUCUGAGUAGAUCCGCUGCAGUUGCAAGGUG------GCUGCUCCUGUAGUAUCGA
((((.((((((((.((((((((.(((....)))))))...(((....)))..)))).)))..)))).).))))..((((------.((((....)))))))).. ( -32.90)
>DroYak_CAF1 62186 104 - 1
GCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCAACUGGAAGGUCUGAGUAGAUCUGCUGCAGUUGCAAGGGAUACUCUACUUCACCUGAAAUAUCGA
((......))........((((.(((....)))))))(((((((..((((((....))))))....))))))).(((((.........)).))).......... ( -29.70)
>consensus
GCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCAACUGGAAAGUAUGAGUAGAUCUGCUGCAGUUGCAAGG____CUUUGCAAGUUUUUAAAUAUCGA
((((.((((((((.((((((((.(((....)))))))...(((....)))..)))).)))..)))).).))))............................... (-25.78 = -25.38 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,884,435 – 11,884,541
Length 106
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 86.50
Mean single sequence MFE -34.45
Consensus MFE -28.00
Energy contribution -29.45
Covariance contribution 1.45
Combinations/Pair 1.14
Mean z-score -2.76
Structure conservation index 0.81
SVM decision value 0.99
SVM RNA-class probability 0.896160
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11884435 106 - 23771897
----GAACAGGUGAGUGUUGCAUAAAUUUGCAAACAUUUUGCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCA-ACUGGAAAGUAUGAGUAGAUCUGCUGCAGU
----.....((..(((..(((....((((((((.....))))))))..)))...)))..))..(((.((((((..((.((-(((....))).)).))....))))))))). ( -37.20)
>DroSec_CAF1 59641 106 - 1
----GAACAGGUGAGUGUUGCAUAAAUUUGCAAACAUUUUGCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCA-ACUGGAAAGUAUGAGUAGAUCUGUUGCAGU
----.....((..(((..(((....((((((((.....))))))))..)))...)))..))..(((.((((((..((.((-(((....))).)).))....))))))))). ( -34.80)
>DroSim_CAF1 60161 106 - 1
----GAACAGGUGAGUGUUGCAUAAAUUUGCAAACAUUUUGCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCA-ACUGAAAAGUAUGAGUAGAUCUGUUGCAGU
----.....((..(((..(((....((((((((.....))))))))..)))...)))..))..(((.((((((..((.((-(((....))).)).))....))))))))). ( -34.80)
>DroEre_CAF1 61742 106 - 1
----GAACAGGUGAGUGUUGCAUAAAUUUGCAAGCAUUUUGCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCA-ACUGGAAAGUCUGAGUAGAUCCGCUGCAGU
----((.(((((((((((((((......))).))))))..((((((........)))))))))))))).(((((((..(.-(((((.....)).))).)..)))))))... ( -36.10)
>DroWil_CAF1 118551 103 - 1
UUCAGCUCAGAUGAGUGUUGCAUAAAUUUGCAAAUAUUUUGCAAGUCAGCAACA----GCCGCCUGCCAGCAAAUGCGCGCACCAUGAAUUCUUAC----UUCACGGCAGU
....((((....))))(((((....((((((((.....))))))))..))))).----((((..(((..((....))..)))...((((.......----))))))))... ( -27.50)
>DroYak_CAF1 62220 106 - 1
----GAGCAGGUGAGUGUUGCAUAAAUUUGCAAACAUUUUGCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCA-ACUGGAAGGUCUGAGUAGAUCUGCUGCAGU
----(.((((((..((((((.....((((((((.....))))))))))))))..)))))))..(((.((((((..((.((-(((....))).)).))....))))))))). ( -36.30)
>consensus
____GAACAGGUGAGUGUUGCAUAAAUUUGCAAACAUUUUGCAAGUCAGCAUCAACUUGCCAUCUGUCAGCAGUGGCGCA_ACUGGAAAGUAUGAGUAGAUCUGCUGCAGU
.........(((((((..(((....(((((((((...)))))))))..)))...)))))))..(((.((((((..((.((.(((....))).)).))....))))))))). (-28.00 = -29.45 +   1.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:00 2006