Locus 1020

Sequence ID 3L_DroMel_CAF1
Location 3,013,319 – 3,013,528
Length 209
Max. P 0.839949
window1574 window1575 window1576

overview

Window 4

Location 3,013,319 – 3,013,427
Length 108
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 95.43
Mean single sequence MFE -37.75
Consensus MFE -32.65
Energy contribution -32.90
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.86
SVM decision value 0.26
SVM RNA-class probability 0.657892
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3013319 108 - 23771897
GCGCUUAAGUCAAUUUGAGUUUGACUCGGGGAGCGAAAGCAGCCAGGACAUCGCAGGAUGUCUCAGAAUCACCGAG---GACAUCGAAGAGCGGCAAAGUUCAGCUGGCCA
...((..((((((.......))))))..))..((....)).(((((..........(((((((..(......)..)---))))))...((((......))))..))))).. ( -36.40)
>DroSec_CAF1 47546 108 - 1
GCGCUUAAGUCAAUUUGAGUUUGACUCGGCGAGCGAAAGCAGCCAGGACAUCGCAGGAUGUCUCAGAAUCACCGAG---GACAUCGCAGAGCGGCAAAGUUCAGCUGGCCA
.((((..((((((.......)))))).)))).((....)).(((((......((..(((((((..(......)..)---)))))))).((((......))))..))))).. ( -38.40)
>DroSim_CAF1 48183 108 - 1
GCGCUUAAGUCAAUUUGAGUUUGACUCGGCGAGCGAAAGCAGCCAGGACAUCGCAGGAUGUCUCAGAAUCACCGAG---GACAUCGCAGAGCAGCAAAGUUCAGCUGGCCA
.((((..((((((.......)))))).)))).((....)).(((((......((..(((((((..(......)..)---)))))))).((((......))))..))))).. ( -37.70)
>DroYak_CAF1 48844 111 - 1
GCGCUUAAGUCAAUUUGAGUUUGACUCGGAGAGCGAAGGCAGCCAGGACAUCGCAGGAUGUCUCAGAAUCACCGAGGAGGACAGCGCCGAGCAGCAAAGUUCAGCUGGCCA
(((((....((.....))((((..(((((.((((....)).....(((((((....))))))).....)).)))))..)))))))))....((((........)))).... ( -38.50)
>consensus
GCGCUUAAGUCAAUUUGAGUUUGACUCGGCGAGCGAAAGCAGCCAGGACAUCGCAGGAUGUCUCAGAAUCACCGAG___GACAUCGCAGAGCAGCAAAGUUCAGCUGGCCA
........((((......(((...(((((.((((....)).....(((((((....))))))).....)).)))))...)))...((.((((......)))).)))))).. (-32.65 = -32.90 +   0.25) 

alignment

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secondary structure

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dotplot

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Window 5

Location 3,013,350 – 3,013,462
Length 112
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 89.43
Mean single sequence MFE -34.23
Consensus MFE -27.92
Energy contribution -29.43
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.82
SVM decision value 0.57
SVM RNA-class probability 0.786015
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3013350 112 - 23771897
CUGACUAAUGAAAGUGGACAGGGGCGGCAGAAGAAGCGCUUAAGUCAAUUUGAGUUUGACUCGGGGAGCGAAAGCAGCCAGGACAUCGCAGGAUGUCUCAGAAUCACCGAG---G
(.((((.....((((.(((..(((((.(.......))))))..))).)))).)))).).(((((((.((....))..)).(((((((....)))))))........)))))---. ( -34.70)
>DroSec_CAF1 47577 112 - 1
GUGACAAAUGAAAGUGGACAGGGGCUGCAGAAGAAGCGCUUAAGUCAAUUUGAGUUUGACUCGGCGAGCGAAAGCAGCCAGGACAUCGCAGGAUGUCUCAGAAUCACCGAG---G
....(((((..((((.(((..((((.((.......))))))..))).))))..))))).(((((.((((....)).....(((((((....))))))).....)).)))))---. ( -39.10)
>DroSim_CAF1 48214 112 - 1
GUGACUAAUGAAAGUGGACAGGGGCGGCAGAAGAAGCGCUUAAGUCAAUUUGAGUUUGACUCGGCGAGCGAAAGCAGCCAGGACAUCGCAGGAUGUCUCAGAAUCACCGAG---G
..((((.....((((.(((..(((((.(.......))))))..))).)))).))))...(((((.((((....)).....(((((((....))))))).....)).)))))---. ( -35.10)
>DroYak_CAF1 48875 104 - 1
UGCACUAAUGAAAGUGGACG-----------AAAAGCGCUUAAGUCAAUUUGAGUUUGACUCGGAGAGCGAAGGCAGCCAGGACAUCGCAGGAUGUCUCAGAAUCACCGAGGAGG
..((((......))))....-----------......(((((((....)))))))....(((((.((((....)).....(((((((....))))))).....)).))))).... ( -28.00)
>consensus
GUGACUAAUGAAAGUGGACAGGGGCGGCAGAAGAAGCGCUUAAGUCAAUUUGAGUUUGACUCGGCGAGCGAAAGCAGCCAGGACAUCGCAGGAUGUCUCAGAAUCACCGAG___G
....(.(((..((((.(((..((((.((.......))))))..))).))))..))).).(((((.((((....)).....(((((((....))))))).....)).))))).... (-27.92 = -29.43 +   1.50) 

alignment

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secondary structure

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dotplot

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Window 6

Location 3,013,427 – 3,013,528
Length 101
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 92.74
Mean single sequence MFE -35.00
Consensus MFE -32.48
Energy contribution -32.27
Covariance contribution -0.21
Combinations/Pair 1.12
Mean z-score -1.98
Structure conservation index 0.93
SVM decision value 0.75
SVM RNA-class probability 0.839949
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3013427 101 - 23771897
CAGAAUCUUGAGUCCUGAGUUCUGGGCACUGAGCCCAGAACCAUCAGCACCUUCCCUUUCUCCUUUCUGACUAAUGAAAGUGGACAGGGGCGGCAGAAGAA
.....((((..((((((((((((((((.....)))))))))..)))).....(((((.((..(((((........)))))..)).))))).)))..)))). ( -40.10)
>DroSec_CAF1 47654 101 - 1
CAGAGUCUUGAGUCCUGAGUUCUGGGCACUGAGUCCUGAACCAUCAGCUCCUCCUCUCUCCCCUUUGUGACAAAUGAAAGUGGACAGGGGCUGCAGAAGAA
.....((((......((.((((.((((.....)))).)))))).((((((((((.((.((...((((...)))).)).)).)))..)))))))...)))). ( -27.30)
>DroSim_CAF1 48291 101 - 1
CAGAGUCUUGAGUCCUGAGUUCUGGGCACUGAGCCCAGAACCAUCAGCUCCUCCUCUCUCCCCUUUGUGACUAAUGAAAGUGGACAGGGGCGGCAGAAGAA
.....((((.....(((((((((((((.....)))))))))..))))((((.(((((.(((.((((((.....)).)))).))).))))).)).)))))). ( -37.60)
>consensus
CAGAGUCUUGAGUCCUGAGUUCUGGGCACUGAGCCCAGAACCAUCAGCUCCUCCUCUCUCCCCUUUGUGACUAAUGAAAGUGGACAGGGGCGGCAGAAGAA
.....((((..((((((((((((((((.....)))))))))..)))).....(((((.(((.((((..........)))).))).))))).)))..)))). (-32.48 = -32.27 +  -0.21) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:01 2006