Locus 4327

Sequence ID 2R_DroMel_CAF1
Location 14,218,274 – 14,218,403
Length 129
Max. P 0.854572
window6936 window6937 window6938

overview

Window 6

Location 14,218,274 – 14,218,379
Length 105
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 80.11
Mean single sequence MFE -49.82
Consensus MFE -31.76
Energy contribution -31.90
Covariance contribution 0.14
Combinations/Pair 1.29
Mean z-score -2.07
Structure conservation index 0.64
SVM decision value 0.80
SVM RNA-class probability 0.854572
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14218274 105 + 20766785
AGUAC------GGGAUGUGCUGGUGGUUCUAUCACCAGAGGCACUUCAGCAGCCAGCGAAGGAGCAGCAGCGGCCGCUGCCGCUAACCAACCUCUAGACCUGUCCAUGGAU
.(.((------(((.......((((((...))))))(((((..((((.((.....)))))).(((.(((((....))))).)))......)))))...))))).)...... ( -37.70)
>DroPse_CAF1 44172 111 + 1
ACCACAGGCAGCGGCAGUGGCGGUGGCUCCAUUACACGCGGCACAUCGGCGGCAAGCGAAGGAGCGGCUGCUGCUGCAGCUGCCAAUCAGCCGCUGGAUCUGUCCAUGGAU
......((((((.((((..(((((.(((((.(..(..((.((......)).))..)..).))))).)))))..)))).))))))......(((.((((....))))))).. ( -58.20)
>DroEre_CAF1 36879 105 + 1
AGUAC------CGGUGGUGCUGGUGGUUCCAUCACCAGGGGCACUUCAGCCGCCAGCGAAGGGGCAGCGGCGGCCGCCGCUGCCAAUCAGCCUCUGGACCUGUCCAUGGAU
(((((------(...))))))((((....)))).((((((((.((((.((.....)))))).(((((((((....))))))))).....)))))))).((.......)).. ( -53.40)
>DroYak_CAF1 37704 105 + 1
AGUAC------CGGUGGUGCUGGUGGUUCCAUCACCAGGGGCACUUCGGCCGCCAGCGAAGGAGCGGCAGCGGCUGCCGCUGCCAAUCAACCUCUUGACUUGUCCAUGGAU
....(------((.((((.((((((((...)))))))).(((......))))))).)...(((..((((((((...))))))))..((((....))))....)))..)).. ( -43.30)
>DroAna_CAF1 38869 105 + 1
AGCAC------UGGCGGUGGCGGUGGCUCCAUUACCCGGGGCACUUCGGCGGCCAGCGAAGGAGCUGCAGCUGCGGCGGCUGCCAAUCAGCCCCUGGACUUGUCCAUGGAC
..(((------((.(...).)))))..(((((.....(((((.....(((((((..(....).(((((....)))))))))))).....))))).(((....)))))))). ( -48.10)
>DroPer_CAF1 43819 111 + 1
ACCACAGGCAGCGGCAGUGGCGGUGGCUCCAUUACACGCGGCACAUCGGCGGCAAGCGAAGGAGCGGCUGCUGCUGCAGCUGCCAAUCAGCCGCUGGAUCUGUCCAUGGAU
......((((((.((((..(((((.(((((.(..(..((.((......)).))..)..).))))).)))))..)))).))))))......(((.((((....))))))).. ( -58.20)
>consensus
AGCAC______CGGCGGUGCCGGUGGCUCCAUCACCAGGGGCACUUCGGCGGCCAGCGAAGGAGCGGCAGCGGCUGCAGCUGCCAAUCAGCCUCUGGACCUGUCCAUGGAU
.((((...........)))).......((((......(((((.((((.((.....))))))..((((((((....))))))))......)))))((((....)))))))). (-31.76 = -31.90 +   0.14)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,218,274 – 14,218,379
Length 105
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 80.11
Mean single sequence MFE -45.10
Consensus MFE -30.66
Energy contribution -30.08
Covariance contribution -0.58
Combinations/Pair 1.36
Mean z-score -1.18
Structure conservation index 0.68
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14218274 105 - 20766785
AUCCAUGGACAGGUCUAGAGGUUGGUUAGCGGCAGCGGCCGCUGCUGCUCCUUCGCUGGCUGCUGAAGUGCCUCUGGUGAUAGAACCACCAGCACAUCCC------GUACU
....((((.(((..((((.((..((..(((((((((....))))))))))).)).))))...)))..((((...(((((.......)))))))))...))------))... ( -39.30)
>DroPse_CAF1 44172 111 - 1
AUCCAUGGACAGAUCCAGCGGCUGAUUGGCAGCUGCAGCAGCAGCCGCUCCUUCGCUUGCCGCCGAUGUGCCGCGUGUAAUGGAGCCACCGCCACUGCCGCUGCCUGUGGU
........((((...(((((((....((((.(((((....))))).(((((...((.(((.((......)).))).))...)))))....))))..))))))).))))... ( -47.00)
>DroEre_CAF1 36879 105 - 1
AUCCAUGGACAGGUCCAGAGGCUGAUUGGCAGCGGCGGCCGCCGCUGCCCCUUCGCUGGCGGCUGAAGUGCCCCUGGUGAUGGAACCACCAGCACCACCG------GUACU
..((.((((....))))(..((((...(((((((((....)))))))))((.((((..(.(((......))).)..)))).))......))))..)...)------).... ( -50.50)
>DroYak_CAF1 37704 105 - 1
AUCCAUGGACAAGUCAAGAGGUUGAUUGGCAGCGGCAGCCGCUGCCGCUCCUUCGCUGGCGGCCGAAGUGCCCCUGGUGAUGGAACCACCAGCACCACCG------GUACU
.....(((....((((.((((..((.(((((((((...))))))))).))))))..))))..))).((((((..(((((.(((.....))).)))))..)------))))) ( -46.40)
>DroAna_CAF1 38869 105 - 1
GUCCAUGGACAAGUCCAGGGGCUGAUUGGCAGCCGCCGCAGCUGCAGCUCCUUCGCUGGCCGCCGAAGUGCCCCGGGUAAUGGAGCCACCGCCACCGCCA------GUGCU
(((....))).((..(.(((((...(((((.(((...((....))(((......)))))).)))))...))))).(((..(((........)))..))).------)..)) ( -40.40)
>DroPer_CAF1 43819 111 - 1
AUCCAUGGACAGAUCCAGCGGCUGAUUGGCAGCUGCAGCAGCAGCCGCUCCUUCGCUUGCCGCCGAUGUGCCGCGUGUAAUGGAGCCACCGCCACUGCCGCUGCCUGUGGU
........((((...(((((((....((((.(((((....))))).(((((...((.(((.((......)).))).))...)))))....))))..))))))).))))... ( -47.00)
>consensus
AUCCAUGGACAGGUCCAGAGGCUGAUUGGCAGCGGCAGCAGCUGCCGCUCCUUCGCUGGCCGCCGAAGUGCCCCGGGUAAUGGAACCACCACCACCGCCG______GUACU
.((((((((....))).(((((...(((((.(((((....))))).((......)).....)))))...))))).....)))))........................... (-30.66 = -30.08 +  -0.58)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,218,299 – 14,218,403
Length 104
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 80.90
Mean single sequence MFE -45.95
Consensus MFE -31.96
Energy contribution -31.80
Covariance contribution -0.16
Combinations/Pair 1.33
Mean z-score -1.26
Structure conservation index 0.70
SVM decision value 0.02
SVM RNA-class probability 0.543587
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14218299 104 + 20766785
UCACCAGAGGCACUUCAGCAGCCAGCGAAGGAGCAGCAGCGGCCGCUGCCGCUAACCAACCUCUAGACCUGUCCAUGGAUGUUUGCGGCGGGGUAAUGGAUCAG
...(((((((..((((.((.....)))))).(((.(((((....))))).)))......)))))...((((((((........)).)))))).....))..... ( -36.60)
>DroPse_CAF1 44203 104 + 1
UUACACGCGGCACAUCGGCGGCAAGCGAAGGAGCGGCUGCUGCUGCAGCUGCCAAUCAGCCGCUGGAUCUGUCCAUGGAUGUCUGCGGCGGAGUCCACGGCGAG
.....(((((.(((((((((((...(....).((((((((....))))))))......))))))(((....)))...))))))))))((.(......).))... ( -46.70)
>DroEre_CAF1 36904 104 + 1
UCACCAGGGGCACUUCAGCCGCCAGCGAAGGGGCAGCGGCGGCCGCCGCUGCCAAUCAGCCUCUGGACCUGUCCAUGGAUGUUUGCGGCGGGGUAAUAGACCAG
...((((((((.((((.((.....)))))).(((((((((....))))))))).....)))))))).((((((((........)).))))))............ ( -52.50)
>DroYak_CAF1 37729 104 + 1
UCACCAGGGGCACUUCGGCCGCCAGCGAAGGAGCGGCAGCGGCUGCCGCUGCCAAUCAACCUCUUGACUUGUCCAUGGAUGUUUGCGGCGGGGGAAUGGACCAG
......((..((((((.(((((.(((.(((....((((((((...))))))))..((((....)))))))(((....)))))).))))).))))..))..)).. ( -40.90)
>DroAna_CAF1 38894 104 + 1
UUACCCGGGGCACUUCGGCGGCCAGCGAAGGAGCUGCAGCUGCGGCGGCUGCCAAUCAGCCCCUGGACUUGUCCAUGGACGUGUGUGGUGGCGCCAUGGAGCAG
...((.(((((.....(((((((..(....).(((((....)))))))))))).....))))).))...(((((((((.(((........)))))))))).)). ( -52.30)
>DroPer_CAF1 43850 104 + 1
UUACACGCGGCACAUCGGCGGCAAGCGAAGGAGCGGCUGCUGCUGCAGCUGCCAAUCAGCCGCUGGAUCUGUCCAUGGAUGUCUGCGGCGGAGUCCACGGCGAG
.....(((((.(((((((((((...(....).((((((((....))))))))......))))))(((....)))...))))))))))((.(......).))... ( -46.70)
>consensus
UCACCAGGGGCACUUCGGCGGCCAGCGAAGGAGCGGCAGCGGCUGCAGCUGCCAAUCAGCCUCUGGACCUGUCCAUGGAUGUUUGCGGCGGGGUAAUGGACCAG
......(((((.((((.((.....))))))..((((((((....))))))))......)))))....((((((((........)).))))))............ (-31.96 = -31.80 +  -0.16)

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 11:17:08 2006