Locus 989

Sequence ID X_DroMel_CAF1
Location 2,870,870 – 2,870,996
Length 126
Max. P 0.989029
window1599 window1600 window1601

overview

Window 9

Location 2,870,870 – 2,870,973
Length 103
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 89.70
Mean single sequence MFE -16.87
Consensus MFE -15.56
Energy contribution -15.80
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.84
Structure conservation index 0.92
SVM decision value 2.15
SVM RNA-class probability 0.989029
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2870870 103 + 22224390
ACCAUUUAACCCACUUUGGCCCCCUUAACCCAUCCACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAGCUAAACAUAAGUUAUGUGUGCAAAGCACAC------AC
.............(((((((.......................)).(((((((((..((((.((((....))))))))....)))))))))))))).....------.. ( -17.50)
>DroSec_CAF1 257806 109 + 1
CCCCUUUAACCCACUUUGGCCUCCCUAACCCAUCCACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAGCUAAACAUAAGUUAUGUGUGCAAAGCACACACACACAC
.............(((((((.......................)).(((((((((..((((.((((....))))))))....))))))))))))))............. ( -17.50)
>DroSim_CAF1 227776 109 + 1
CCCCUUUAACCCACUUUGGCCCUCUUAACCUAUCCACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAGCUAAACAUAAGUUAUGUGUGCAAAGCACACACACACAC
.............(((((((.......................)).(((((((((..((((.((((....))))))))....))))))))))))))............. ( -17.50)
>DroEre_CAF1 281005 98 + 1
CCCCUUUAACCCACUUUGGCCCCCUUA-A----ACACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAGCUAAACAUAAGUUAUGUGUGCAAAACACAC------AC
..........((.....))........-.----..........(((((((.......((((.((((....)))))))).......))))))).........------.. ( -15.54)
>DroYak_CAF1 265845 99 + 1
CCCCUUUAACCCACUUUGGCCCCCUUAAA----ACACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAUCUAAAUAUAAGUUAUGUGUGCAAAGCACAC------AC
.............(((((((.........----..........)).(((((((((.((((..(((......)))...)))).)))))))))))))).....------.. ( -16.31)
>consensus
CCCCUUUAACCCACUUUGGCCCCCUUAACC_AUCCACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAGCUAAACAUAAGUUAUGUGUGCAAAGCACAC______AC
.............(((((((.......................)).(((((((((..((((.((((....))))))))....))))))))))))))............. (-15.56 = -15.80 +   0.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,870,903 – 2,870,996
Length 93
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 92.08
Mean single sequence MFE -24.13
Consensus MFE -20.28
Energy contribution -21.12
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -2.01
Structure conservation index 0.84
SVM decision value 1.86
SVM RNA-class probability 0.980426
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2870903 93 + 22224390
CCACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAGCUAAACAUAAGUUAUGUGUGCAAAGCACAC------ACACAAAGAACAGUGACGGCGGGCU
.......(((((.(((((.......(((((....))))).............(((((((...))))))------)...........))).))))))).. ( -25.90)
>DroSec_CAF1 257839 99 + 1
CCACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAGCUAAACAUAAGUUAUGUGUGCAAAGCACACACACACACACAAAGAAGAGUGACGGCGGGCU
.......(((((.(((((.......(((((....))))).........((..(((((((...)))))))...))............))).))))))).. ( -26.00)
>DroSim_CAF1 227809 99 + 1
CCACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAGCUAAACAUAAGUUAUGUGUGCAAAGCACACACACACACACAAAGAAGAGUGACGGCGGGCU
.......(((((.(((((.......(((((....))))).........((..(((((((...)))))))...))............))).))))))).. ( -26.00)
>DroEre_CAF1 281033 93 + 1
ACACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAGCUAAACAUAAGUUAUGUGUGCAAAACACAC------ACACAAAGAAGAGUGACGGCGGUCU
.(.((((((((((((((.......((((.((((....)))))))).......))))))).........------.(.....)..)))))..)).).... ( -21.64)
>DroYak_CAF1 265874 89 + 1
ACACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAUCUAAAUAUAAGUUAUGUGUGCAAAGCACAC------ACACAAAGAAGAGUGACGGC----U
.....((((((((.(((((........))).)))))................(((((((...))))))------).........))))).....----. ( -21.10)
>consensus
CCACCCACUCGCACGCACAUAAAUUGUUGUAGUUGCAGCUAAACAUAAGUUAUGUGUGCAAAGCACAC______ACACAAAGAAGAGUGACGGCGGGCU
.......(((((.(((((((((..((((.((((....))))))))....))))))))).................(((........)))...))))).. (-20.28 = -21.12 +   0.84)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,870,903 – 2,870,996
Length 93
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 92.08
Mean single sequence MFE -29.64
Consensus MFE -22.98
Energy contribution -23.62
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -2.13
Structure conservation index 0.78
SVM decision value 1.05
SVM RNA-class probability 0.907613
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2870903 93 - 22224390
AGCCCGCCGUCACUGUUCUUUGUGU------GUGUGCUUUGCACACAUAACUUAUGUUUAGCUGCAACUACAACAAUUUAUGUGCGUGCGAGUGGGUGG
.((((((((.(((......((((((------((((.....))))))))))....(((((((......))).))))..........))))).)))))).. ( -30.00)
>DroSec_CAF1 257839 99 - 1
AGCCCGCCGUCACUCUUCUUUGUGUGUGUGUGUGUGCUUUGCACACAUAACUUAUGUUUAGCUGCAACUACAACAAUUUAUGUGCGUGCGAGUGGGUGG
...(((((..(((((..((..(..((..(((((((((...)))))))))...))..)..))..(((..((((........))))..))))))))))))) ( -32.20)
>DroSim_CAF1 227809 99 - 1
AGCCCGCCGUCACUCUUCUUUGUGUGUGUGUGUGUGCUUUGCACACAUAACUUAUGUUUAGCUGCAACUACAACAAUUUAUGUGCGUGCGAGUGGGUGG
...(((((..(((((..((..(..((..(((((((((...)))))))))...))..)..))..(((..((((........))))..))))))))))))) ( -32.20)
>DroEre_CAF1 281033 93 - 1
AGACCGCCGUCACUCUUCUUUGUGU------GUGUGUUUUGCACACAUAACUUAUGUUUAGCUGCAACUACAACAAUUUAUGUGCGUGCGAGUGGGUGU
....((((..(((((....((((((------((((.....)))))))))).............(((..((((........))))..)))))))))))). ( -27.80)
>DroYak_CAF1 265874 89 - 1
A----GCCGUCACUCUUCUUUGUGU------GUGUGCUUUGCACACAUAACUUAUAUUUAGAUGCAACUACAACAAUUUAUGUGCGUGCGAGUGGGUGU
.----(((..(((((....((((((------((((.....)))))))))).............(((..((((........))))..))))))))))).. ( -26.00)
>consensus
AGCCCGCCGUCACUCUUCUUUGUGU______GUGUGCUUUGCACACAUAACUUAUGUUUAGCUGCAACUACAACAAUUUAUGUGCGUGCGAGUGGGUGG
...(((((..(((((................((((((...)))))).................(((..((((........))))..))))))))))))) (-22.98 = -23.62 +   0.64)

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 09:58:47 2006