Locus 3394

Sequence ID 2L_DroMel_CAF1
Location 9,828,786 – 9,828,908
Length 122
Max. P 0.761733
window5368 window5369

overview

Window 8

Location 9,828,786 – 9,828,885
Length 99
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 76.90
Mean single sequence MFE -28.78
Consensus MFE -19.94
Energy contribution -20.26
Covariance contribution 0.32
Combinations/Pair 1.13
Mean z-score -1.56
Structure conservation index 0.69
SVM decision value 0.50
SVM RNA-class probability 0.761733
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9828786 99 + 22407834
GCAGGCGGAGG--AACU--GGCAGUG---GAAGUGGAUGGCAAGAGCUGCGAGAAGUAGCAGCUGGAGAACUCAAGUGGCAACACACACUUCAAGGCCCGACUCGA
.......(((.--..(.--(((....---((((((.........((((((........))))))...........(((....))).))))))...))).).))).. ( -33.10)
>DroPse_CAF1 39383 82 + 1
-------AAGG--------AGAAGUGGGAGAAGUG----GCAAGCAUGGCGAGAGCAAGAAGUAGAAGUACUCAAGUGGCAGCACACACUUCAAGGC-----UCGU
-------...(--------((.....((((..(((----((..((...((....))..((.(((....))))).....)).)).))).))))....)-----)).. ( -17.80)
>DroSec_CAF1 37142 101 + 1
GCAGGCGGAGGAGAGCU--GGUAGUG---GAAGUGGAUGGCAAGAGCUGCGAGAAGUAGCAGCUGGAGAACUCAAGUGGCAACACACACUUCAAGGCCCGACUCGA
............((((.--(((....---((((((.........((((((........))))))...........(((....))).))))))...))).).))).. ( -32.90)
>DroSim_CAF1 40410 101 + 1
GCAGGCGGAGGAGAGCU--GGUAGUG---GAAGUGGAUGGCAAGAGCUGCGAGAAGUAGCAGCUGGAGAACUCAAGUGGCAACACACACUUCAAGGCCCGACUCGA
............((((.--(((....---((((((.........((((((........))))))...........(((....))).))))))...))).).))).. ( -32.90)
>DroEre_CAF1 39833 86 + 1
-----------------GAGGAACUG---GUAGUGGAAGGCAAGAGCUGCGAGAAGUAGCAGCUGGAGAACUCAAGUGGCAACACACACUUCAAGGCCCGACUCGA
-----------------(((...(.(---((....((((.....((((((........))))))...........(((....)))...))))...))).).))).. ( -27.20)
>consensus
GCAGGCGGAGG__A_CU__GGAAGUG___GAAGUGGAUGGCAAGAGCUGCGAGAAGUAGCAGCUGGAGAACUCAAGUGGCAACACACACUUCAAGGCCCGACUCGA
.............................((((((.........((((((........))))))...........(((....))).)))))).............. (-19.94 = -20.26 +   0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,828,815 – 9,828,908
Length 93
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 90.97
Mean single sequence MFE -27.00
Consensus MFE -24.17
Energy contribution -24.48
Covariance contribution 0.31
Combinations/Pair 1.13
Mean z-score -1.23
Structure conservation index 0.90
SVM decision value 0.06
SVM RNA-class probability 0.565125
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9828815 93 - 22407834
AAAGUAUCUCUUUGGCAGCCAAGUCGAGUCGGGCCUUGAAGUGUGUGUUGCCACUUGAGUUCUCCAGCUGCUACUUCUCGCAGCUCUUGCCAU
..((...(((..(((((((((..(((((......)))))....)).)))))))...)))..))..((((((........))))))........ ( -28.30)
>DroPse_CAF1 39403 85 - 1
AAAAUAUCUCUUUGGCUGCCAAGACGA-----GCCUUGAAGUGUGUGCUGCCACUUGAGUACUUCUACUUCUUGCUCUCGCCAUGCUUGC---
............((((......((.((-----((...((((((.(((((........)))))...))))))..)))))))))).......--- ( -20.50)
>DroSec_CAF1 37173 93 - 1
AAAGUAUCUCUUUGGCAGCCAAGUCGAGUCGGGCCUUGAAGUGUGUGUUGCCACUUGAGUUCUCCAGCUGCUACUUCUCGCAGCUCUUGCCAU
..((...(((..(((((((((..(((((......)))))....)).)))))))...)))..))..((((((........))))))........ ( -28.30)
>DroSim_CAF1 40441 93 - 1
AAAGUAUCUCUUUGGCAGCCAAGUCGAGUCGGGCCUUGAAGUGUGUGUUGCCACUUGAGUUCUCCAGCUGCUACUUCUCGCAGCUCUUGCCAU
..((...(((..(((((((((..(((((......)))))....)).)))))))...)))..))..((((((........))))))........ ( -28.30)
>DroEre_CAF1 39849 93 - 1
AAAGUAUCUCUUUGGCAGCCAAGUCGAGUCGGGCCUUGAAGUGUGUGUUGCCACUUGAGUUCUCCAGCUGCUACUUCUCGCAGCUCUUGCCUU
..((...(((..(((((((((..(((((......)))))....)).)))))))...)))..))..((((((........))))))........ ( -28.30)
>DroYak_CAF1 38306 93 - 1
AAAGUAUCUCUUUGGCAGCCAAGUCGAGUCGGGCCUUGAAGUGUGUGUUGCCACUUGAGUUCUCCAGCUGCUACUUCUCGCAGCUCUUGCCUU
..((...(((..(((((((((..(((((......)))))....)).)))))))...)))..))..((((((........))))))........ ( -28.30)
>consensus
AAAGUAUCUCUUUGGCAGCCAAGUCGAGUCGGGCCUUGAAGUGUGUGUUGCCACUUGAGUUCUCCAGCUGCUACUUCUCGCAGCUCUUGCCAU
.......(((..(((((((((..(((((......)))))....)).)))))))...)))......((((((........))))))........ (-24.17 = -24.48 +   0.31)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:23 2006