Locus 8571

Sequence ID 3R_DroMel_CAF1
Location 22,895,839 – 22,895,974
Length 135
Max. P 0.999999
window13769 window13770

overview

Window 9

Location 22,895,839 – 22,895,943
Length 104
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 84.14
Mean single sequence MFE -42.67
Consensus MFE -28.06
Energy contribution -28.50
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -1.57
Structure conservation index 0.66
SVM decision value -0.01
SVM RNA-class probability 0.526805
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22895839 104 + 27905053
CCCAAACAAUUGCUCAGUGCUUAAGUGCAGCUUUAAGCUAGCUUGCGAGAGUGUGAGCGGGAGCGGGCGCUGUGCGCGAGCGAGACGCCG-CCGGUCAGAGGCGG
.........((((((.((((...(((((.(((((......(((..((....))..))).)))))..)))))..))))))))))....(((-((.......))))) ( -43.40)
>DroSec_CAF1 12968 101 + 1
GCCACACAAUUGCUCGGUGCUUAAGUGCAGCUUUAAGCUAGCUUGCGAGAGUGCGAGCGAGAGCGGGCGCUGAGCGCUAGCGAGUC---G-CCGGGCGGCGGCGG
.((......(((((.((((((((.((((.(((((......(((((((....))))))).)))))..)))))))))))))))))(((---(-((....)))))))) ( -49.20)
>DroSim_CAF1 13838 100 + 1
GCCA-ACAAUUGCUCGGUGCUUAAGUGCAGCUUUAAGCUAGCUUGCGAGAGUGCGAGCGAGAGCGGACGCUGAGCGCGAGCGAGUC---G-CCGGGCAGAAGCGG
....-....(((((((((((((.....((((.....(((.(((((((....)))))))...)))....)))).((....))))).)---)-))))))))...... ( -42.30)
>DroYak_CAF1 13362 99 + 1
C-CAAACAAUUGCUGCGCGCUUAAGUGCAGCUUUAAGCUAGUUGGCGAGAGUGCGAGCGGGAGAGGGCGCUGUGCGCGAGCGAGAC---GAACUGCCUGGGU--G
(-(........(((.(((((((..((.(((((.......)))))))..))))))))))(((..((..((((.(((....))))).)---)..)).)))))..--. ( -35.80)
>consensus
CCCAAACAAUUGCUCGGUGCUUAAGUGCAGCUUUAAGCUAGCUUGCGAGAGUGCGAGCGAGAGCGGGCGCUGAGCGCGAGCGAGAC___G_CCGGGCAGAGGCGG
.........((((((.((((...((((((((.....))).(((((((....)))))))........)))))..))))))))))...................... (-28.06 = -28.50 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,895,875 – 22,895,974
Length 99
Sequences 3
Columns 100
Reading direction forward
Mean pairwise identity 68.29
Mean single sequence MFE -37.33
Consensus MFE -27.26
Energy contribution -27.60
Covariance contribution 0.34
Combinations/Pair 1.10
Mean z-score -2.80
Structure conservation index 0.73
SVM decision value 6.82
SVM RNA-class probability 0.999999
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22895875 99 + 27905053
GCUAGCUUGCGAGAGUGUGAGCGGGAGCGGGCGCUGUGCGCGAGCGAGACGCCGCCGGUCAGAGGCGGUGGAA-GCGGGAUGGGUAGUGAGCGCGAGGGU
(((.((((((((.(((((..((....))..))))).).)))))))....(((((((.......)))))))..)-))....((.((.....)).))..... ( -43.10)
>DroSec_CAF1 13004 87 + 1
GCUAGCUUGCGAGAGUGCGAGCGAGAGCGGGCGCUGAGCGCUAGCGAGUC---GCCGGGCGGCGGCGGCGAGAAGCGGGAUUGGUAG-AGA---------
(((.(((.(((..(((((..((....))..)))))...))).)))..(((---((((.....)))))))....)))...........-...--------- ( -37.90)
>DroSim_CAF1 13873 87 + 1
GCUAGCUUGCGAGAGUGCGAGCGAGAGCGGACGCUGAGCGCGAGCGAGUC---GCCGGGCAGAAGCGGCGGAANNNNNNNNNNNNNN-NNN---------
(((.(((((((..((((...((....))...))))...))))))).)))(---((((........))))).................-...--------- ( -31.00)
>consensus
GCUAGCUUGCGAGAGUGCGAGCGAGAGCGGGCGCUGAGCGCGAGCGAGUC___GCCGGGCAGAGGCGGCGGAA_GCGGGAU_GGUAG_____________
.((.(((((((..(((((..((....))..)))))...))))))).)).....((((........))))............................... (-27.26 = -27.60 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:22 2006