Locus 1532

Sequence ID 2L_DroMel_CAF1
Location 4,138,851 – 4,138,983
Length 132
Max. P 0.994442
window2477 window2478 window2479

overview

Window 7

Location 4,138,851 – 4,138,953
Length 102
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 90.20
Mean single sequence MFE -41.73
Consensus MFE -35.49
Energy contribution -37.05
Covariance contribution 1.56
Combinations/Pair 1.14
Mean z-score -2.17
Structure conservation index 0.85
SVM decision value 0.97
SVM RNA-class probability 0.891865
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4138851 102 + 22407834
GCCUGCCAAAGGACACUUGGCAUCCUGGCAGCGCAGGACUCGAUGCCCGGGACUUGUAGCCCAGGACUCUCGAGUGUCCCGCAUGUGUGGCAUGUGCAACAA
(((((((...((((((((((..((((((..(((((((.((((.....)))).))))).))))))))...)))))))))).((....)))))).).))..... ( -43.60)
>DroSec_CAF1 268286 102 + 1
GCCUGCCAAAUGACACUUGGCAUCCUGGCAGCGCAGGACUCGAAGCCCGGGACUUGUAGCCCAGGACUCUCGAGUGUCCCGCAUGUGUGGCAUGUGCAACAA
((((((((.(((((((((((..((((((..(((((((.((((.....)))).))))).))))))))...)))))))))....))...))))).).))..... ( -40.20)
>DroSim_CAF1 271926 102 + 1
GCCUGCCAAAGGACACUUGGCAUCCUGGCAGCGCAGGACUCGAAGCCCGGGACUUGUAGCCCAGGACUCUCGAGUGUCCCGCAUGUGUGGCAUGUGCAACAA
(((((((...((((((((((..((((((..(((((((.((((.....)))).))))).))))))))...)))))))))).((....)))))).).))..... ( -43.60)
>DroEre_CAF1 282282 102 + 1
GCCUGCCAAAGGACACUUGGCGUCCUGGCAGCGUAGGACUCGAAGCCCGGGACUUGUAGCCCAGGACUCUCGAGUGUCCCGCAUGUGUGGCAUGUGCAACAA
(((((((...((((((((((.((((((((.(((.((..((((.....)))).))))).).))))))).).))))))))).((....)))))).).))..... ( -43.80)
>DroYak_CAF1 286869 102 + 1
GCCUGCCAAAGGACACUUGGCGUCCUGGCAGCACAGGACUCGCAGCCCGGGACUUGUAGCCCAGGACUCUCGAGUGUCCCGCAUGUGUGGCAUGUGCAACAA
(((((((...((((((((((.(((((((..(((((((.((((.....)))).))))).))))))))).).))))))))).((....)))))).).))..... ( -47.10)
>DroAna_CAF1 315863 87 + 1
GCCUGCCAAAGGACACUUAGCAUCCUGGCAGGCCAGGACUCU---------------UGGUCGGGACUCUCGAGUGUCUCGCAUGUGUGGCAUGUGCAACAA
((((((((..(((.........)))))))))))...(((...---------------..)))(((((........)))))(((((((...)))))))..... ( -32.10)
>consensus
GCCUGCCAAAGGACACUUGGCAUCCUGGCAGCGCAGGACUCGAAGCCCGGGACUUGUAGCCCAGGACUCUCGAGUGUCCCGCAUGUGUGGCAUGUGCAACAA
(((((((...((((((((((..((((((..(((((((.((((.....)))).))))).))))))))...)))))))))).((....)))))).).))..... (-35.49 = -37.05 +   1.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,138,851 – 4,138,953
Length 102
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 90.20
Mean single sequence MFE -43.55
Consensus MFE -37.13
Energy contribution -39.63
Covariance contribution 2.50
Combinations/Pair 1.05
Mean z-score -2.55
Structure conservation index 0.85
SVM decision value 1.52
SVM RNA-class probability 0.960695
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4138851 102 - 22407834
UUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCAUCGAGUCCUGCGCUGCCAGGAUGCCAAGUGUCCUUUGGCAGGC
.(((.((....)).)))...(((((((..((((..((((.((((.....)))).)))).))))))))))).((((((((((((...))))))..)))))).. ( -46.70)
>DroSec_CAF1 268286 102 - 1
UUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCUUCGAGUCCUGCGCUGCCAGGAUGCCAAGUGUCAUUUGGCAGGC
.(((.((....)).)))...(((((((..((((.(((((.((((.....)))).)))))))))))))))).((((((.(((((...)))))...)))))).. ( -45.40)
>DroSim_CAF1 271926 102 - 1
UUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCUUCGAGUCCUGCGCUGCCAGGAUGCCAAGUGUCCUUUGGCAGGC
.(((.((....)).)))...(((((((..((((.(((((.((((.....)))).)))))))))))))))).((((((((((((...))))))..)))))).. ( -47.70)
>DroEre_CAF1 282282 102 - 1
UUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCUUCGAGUCCUACGCUGCCAGGACGCCAAGUGUCCUUUGGCAGGC
..(((.(.((((.....)))).).)))((((((.(((((.((((.....)))).)))))))))))......((((((((((((...))))))..)))))).. ( -45.60)
>DroYak_CAF1 286869 102 - 1
UUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCUGCGAGUCCUGUGCUGCCAGGACGCCAAGUGUCCUUUGGCAGGC
.(((.((....)).)))...(((((((..(((..(((((.((((.....)))).))))).)))))))))).((((((((((((...))))))..)))))).. ( -46.90)
>DroAna_CAF1 315863 87 - 1
UUGUUGCACAUGCCACACAUGCGAGACACUCGAGAGUCCCGACCA---------------AGAGUCCUGGCCUGCCAGGAUGCUAAGUGUCCUUUGGCAGGC
..((..(.((((.....)))).)..))((((..(.((....))).---------------.))))....((((((((((((((...))))))..)))))))) ( -29.00)
>consensus
UUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCUUCGAGUCCUGCGCUGCCAGGAUGCCAAGUGUCCUUUGGCAGGC
.(((.((....)).)))...(((((((..((((.(((((.((((.....)))).)))))))))))))))).((((((((((((...))))))..)))))).. (-37.13 = -39.63 +   2.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,138,881 – 4,138,983
Length 102
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 91.05
Mean single sequence MFE -39.95
Consensus MFE -34.81
Energy contribution -36.62
Covariance contribution 1.81
Combinations/Pair 1.08
Mean z-score -2.93
Structure conservation index 0.87
SVM decision value 2.48
SVM RNA-class probability 0.994442
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4138881 102 - 22407834
GGCAGCCAAGUCUCAUGUGCAUAAUUCAAGUUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCAUCGAGUCCUGCGC
.((......((..((((((((((((....)))).))))))))..))....(((((((..((((..((((.((((.....)))).)))).))))))))))))) ( -42.90)
>DroSec_CAF1 268316 102 - 1
GGCAGCCAAGUCUCAUGUGCAUAAUUCAAGUUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCUUCGAGUCCUGCGC
.((......((..((((((((((((....)))).))))))))..))....(((((((..((((.(((((.((((.....)))).)))))))))))))))))) ( -43.90)
>DroSim_CAF1 271956 102 - 1
GGCAGCCAAGUCUCAUGUGCAUAAUUCAAGUUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCUUCGAGUCCUGCGC
.((......((..((((((((((((....)))).))))))))..))....(((((((..((((.(((((.((((.....)))).)))))))))))))))))) ( -43.90)
>DroEre_CAF1 282312 102 - 1
GGCAGCCAAGUCUCAUGUGCAUAAUUCAAGUUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCUUCGAGUCCUACGC
.(((.....((..((((((((((((....)))).))))))))..))...)))(((((..((((.(((((.((((.....)))).)))))))))))))).... ( -39.50)
>DroYak_CAF1 286899 102 - 1
GGCAGCCAAGUCUCAUGUGCAUAAUUCAAGUUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCUGCGAGUCCUGUGC
.((......((..((((((((((((....)))).))))))))..))....(((((((..(((..(((((.((((.....)))).))))).)))))))))))) ( -40.30)
>DroAna_CAF1 315893 87 - 1
GCCAGCCAAGUCUCAUGUGCAUAAUUCAAGUUGUUGCACAUGCCACACAUGCGAGACACUCGAGAGUCCCGACCA---------------AGAGUCCUGGCC
(((((....((((((((((((((((....)))).)))))))((.......)))))))((((..(.((....))).---------------.)))).))))). ( -29.20)
>consensus
GGCAGCCAAGUCUCAUGUGCAUAAUUCAAGUUGUUGCACAUGCCACACAUGCGGGACACUCGAGAGUCCUGGGCUACAAGUCCCGGGCUUCGAGUCCUGCGC
.((((....((((((((((((((((....)))).)))))))((.......)))))))((((((.(((((.((((.....)))).))))))))))).)))).. (-34.81 = -36.62 +   1.81)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:52 2006