Locus 4096

Sequence ID 3R_DroMel_CAF1
Location 11,189,820 – 11,190,002
Length 182
Max. P 0.977987
window6558 window6559

overview

Window 8

Location 11,189,820 – 11,189,911
Length 91
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 66.35
Mean single sequence MFE -22.07
Consensus MFE -18.28
Energy contribution -18.17
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -0.91
Structure conservation index 0.83
SVM decision value 1.80
SVM RNA-class probability 0.977987
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11189820 91 - 27905053
---------------------AUACUCAAAUACAUACAUAUUCAGAGGUGCCAUGAGCAAGGCUCCACCAACCUAUCCAUAGAUCCGUGGGAUUGGAGCAUCCGUCUAUGGG
---------------------...(((.((((......))))..)))...(((((..(...((((((((.((..(((....)))..)).))..))))))....)..))))). ( -21.40)
>DroSim_CAF1 2313 112 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGUGCCAUGAGCAAGGCUCCACCAACCUAUCCAUAGAUCCUUGGGAUUGGAGCAGUAGUCUAUGGG
..................................................(((((..((..((((((((((...(((....)))..))))...))))))..).)..))))). ( -19.80)
>DroYak_CAF1 2346 88 - 1
---------------------AUACUCAAAUACAUACAUAUUCAGAGGUGCCAUGAGCAAGGCUCC---AACCUAUCCAUAGAUCCGUGGGAUUGGAGCAUCCGUCUCUGGG
---------------------....................((((((((((.....)))..(((((---(((((((..........))))).))))))).....))))))). ( -25.00)
>consensus
_____________________AUACUCAAAUACAUACAUAUUCAGAGGUGCCAUGAGCAAGGCUCCACCAACCUAUCCAUAGAUCCGUGGGAUUGGAGCAUCCGUCUAUGGG
.............................................((((.....((((...)))).....))))..((((((((..(((.........)))..)))))))). (-18.28 = -18.17 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 11,189,911 – 11,190,002
Length 91
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 64.35
Mean single sequence MFE -26.07
Consensus MFE -19.53
Energy contribution -19.87
Covariance contribution 0.34
Combinations/Pair 1.09
Mean z-score -0.98
Structure conservation index 0.75
SVM decision value 1.40
SVM RNA-class probability 0.949918
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11189911 91 + 27905053
-----------------------------GUAGUUACUGCAGCCUUAUCUGCGAGGCAGGGACACCGCCCAAGCCCCAGCCGACUGCAAUUAAGUCGCAUGGCACAUUCGUGAUACUGUC
-----------------------------(((.((((.((.(((((......))))).(((......)))..)).(((..(((((.......)))))..))).......))))))).... ( -25.30)
>DroSim_CAF1 2625 119 + 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGGGCAGGGACACUGCCCAAGCCCCAGCCGACUGCAAU-AAGUCGCAUGGCACAUUCGUGAUACUGUC
.....................................................((((((.....)))))).....(((..(((((.....-.)))))..)))(((....)))........ ( -23.80)
>DroYak_CAF1 2434 91 + 1
-----------------------------GUAGUUGCUGCAGCCUUAUCUGUGGGGUAGGGACACCGCCCAAGCCCCAACCGACUGCAAUUUAGUCGCAUGGCACAUUCGUGAUACUGUC
-----------------------------(((((((..((((......))))(((((.(((......)))..)))))...)))))))....((((..(((((.....)))))..)))).. ( -29.10)
>consensus
_____________________________GUAGUU_CUGCAGCCUUAUCUG_GGGGCAGGGACACCGCCCAAGCCCCAGCCGACUGCAAUUAAGUCGCAUGGCACAUUCGUGAUACUGUC
......................................((((......))))(((((.(((......)))..)))))...(((((.......)))))(((((.....)))))........ (-19.53 = -19.87 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:01 2006