Locus 4052

Sequence ID 3L_DroMel_CAF1
Location 11,799,917 – 11,800,055
Length 138
Max. P 0.759011
window6313 window6314

overview

Window 3

Location 11,799,917 – 11,800,021
Length 104
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 70.83
Mean single sequence MFE -29.50
Consensus MFE -19.84
Energy contribution -22.19
Covariance contribution 2.35
Combinations/Pair 1.20
Mean z-score -1.25
Structure conservation index 0.67
SVM decision value 0.50
SVM RNA-class probability 0.759011
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11799917 104 - 23771897
CUGAGGGCGACUUUUCGCUUCUUGCAGAGCACGGUGUAUAAGAAAGAGUUGGAUUCGGCCUUGCUGGGUUUGGAACAACAAUAUAUACUGAGAUUAGGAAAAAG
(((.((((((....))))))....)))....(((((((((........(..((((((((...))))))))..)........))))))))).............. ( -26.69)
>DroSec_CAF1 9453 80 - 1
CUGAAGGCGACUUUUCGCCUCAUGCAGAGCGUGGUGGAUAGGGAAGAGUUGGAUUCAUCCUUCCU------------------------GAGCUCGGAUAGGAG
.((((..(((((((((.((((((((...)))))).)).....)))))))))..))))((((..((------------------------(....)))..)))). ( -27.50)
>DroSim_CAF1 9045 104 - 1
CUGAAGGCGACUUUUCGCCUCAUGCAGAGCGUGGUGGAUAGGGAAGAGUUGGAUUCAGCCUUCCUGGAUUUGCAACACCAAUAUUUACUGAGCUCGACUAGGAG
.(((.(((((....))))))))....((((..((((((((((((((.((((....))))))))))((..........))..))))))))..))))......... ( -34.30)
>consensus
CUGAAGGCGACUUUUCGCCUCAUGCAGAGCGUGGUGGAUAGGGAAGAGUUGGAUUCAGCCUUCCUGG_UUUG_AACA_CAAUAU_UACUGAGCUCGGAUAGGAG
..((.(((((....))))))).....((((.(((((((((((((((.((((....))))))))))................))))))))).))))......... (-19.84 = -22.19 +   2.35)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,799,941 – 11,800,055
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.06
Mean single sequence MFE -39.17
Consensus MFE -29.55
Energy contribution -29.90
Covariance contribution 0.35
Combinations/Pair 1.18
Mean z-score -1.48
Structure conservation index 0.75
SVM decision value 0.48
SVM RNA-class probability 0.752483
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11799941 114 - 23771897
------CCAUAUAAGCCCCGCUACGUCGUUCCAGGAAUGCCUGAGGGCGACUUUUCGCUUCUUGCAGAGCACGGUGUAUAAGAAAGAGUUGGAUUCGGCCUUGCUGGGUUUGGAACAACA
------...((((.(((..(((..(((((((((((....)))).))))))).....((.....))..)))..))).)))).......((((..((..((((....))))..))..)))). ( -35.50)
>DroSec_CAF1 9468 105 - 1
CACAGACCCUAUCAGCCCCACUAUGUCGUUCCAGGAAUGGCUGAAGGCGACUUUUCGCCUCAUGCAGAGCGUGGUGGAUAGGGAAGAGUUGGAUUCAUCCUUCCU---------------
......((((((.....((((((((((((((...)))))(((((.(((((....)))))))).))...))))))))))))))).......(((........))).--------------- ( -36.00)
>DroSim_CAF1 9069 120 - 1
CACAGACCCUAUCAGCCCCACCAUGUCGUUCCAGGAAUGGCUGAAGGCGACUUUUCGCCUCAUGCAGAGCGUGGUGGAUAGGGAAGAGUUGGAUUCAGCCUUCCUGGAUUUGCAACACCA
.......................(((...((((((((.(((((((..(((((((((.((((((((...)))))).)).....)))))))))..)))))))))))))))...)))...... ( -46.00)
>consensus
CACAGACCCUAUCAGCCCCACUAUGUCGUUCCAGGAAUGGCUGAAGGCGACUUUUCGCCUCAUGCAGAGCGUGGUGGAUAGGGAAGAGUUGGAUUCAGCCUUCCUGG_UUUG_AACA_CA
.................((((((((((((((...))))).(((.((((((....))))))....))).)))))))))...((((((.((((....))))))))))............... (-29.55 = -29.90 +   0.35)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:25 2006