Locus 6281

Sequence ID 3R_DroMel_CAF1
Location 16,391,769 – 16,392,008
Length 239
Max. P 0.930477
window10243 window10244 window10245 window10246

overview

Window 3

Location 16,391,769 – 16,391,889
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -44.30
Consensus MFE -38.92
Energy contribution -39.37
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.22
Structure conservation index 0.88
SVM decision value 0.47
SVM RNA-class probability 0.748718
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16391769 120 - 27905053
UACCGAGAGUUGAGAGCUCGACGAGAUGCUUUUGGCUUUUUGGCUUGGUCAGUUGGCUAAUAGUCGAGUCGCGGCUUUCUGGACUGCAUUGGCCGCUAGUAAUCGUAGUUGGCAGUGGUA
((((((((((((.((.((((((.....(((.((((((.........))))))..))).....)))))))).))))))))...(((((...(((..(.(....).)..))).))))))))) ( -42.30)
>DroSec_CAF1 12888 120 - 1
UACCGAGAGUUGAGAGCUCGACGAGAUGCUUUUGGCUUUUUGGCUUGGUCAGUUGGCUAAUAGUCGAGUCGCGGCUUUCUGGACUGCAUUGGCCGCUAGCAAUCGUAGUUGGCAGUGCUA
..((((((((((.((.((((((.....(((.((((((.........))))))..))).....)))))))).)))))))).))...((((((.(.((((.......)))).).)))))).. ( -44.00)
>DroEre_CAF1 13417 120 - 1
UACCGAGAGCUGAGAGCUCGACGAGAUGCUUUUGGCUUUUUGGCUUGGUCAGUUGGCUAAUAGGCGAGUCGAGGCUUUCUGGACUGCAUUGGCCGCUAGUAAUGGUAGUUGGCAGUGGUA
((((.......(((((((((((....(((((((((((..(((((...)))))..)))))).))))).))))).))))))...(((((...(((..(((....)))..))).))))))))) ( -46.60)
>consensus
UACCGAGAGUUGAGAGCUCGACGAGAUGCUUUUGGCUUUUUGGCUUGGUCAGUUGGCUAAUAGUCGAGUCGCGGCUUUCUGGACUGCAUUGGCCGCUAGUAAUCGUAGUUGGCAGUGGUA
..((((((((((.((.((((((.....(((.((((((.........))))))..))).....)))))))).)))))))).))(((((...(((..(........)..))).))))).... (-38.92 = -39.37 +   0.45)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,391,809 – 16,391,929
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -41.33
Consensus MFE -39.65
Energy contribution -39.77
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.29
Structure conservation index 0.96
SVM decision value 1.21
SVM RNA-class probability 0.930477
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16391809 120 - 27905053
CGACUGCAAUCGACUUUUUGGCUUGCACAAUUUUUUUGGGUACCGAGAGUUGAGAGCUCGACGAGAUGCUUUUGGCUUUUUGGCUUGGUCAGUUGGCUAAUAGUCGAGUCGCGGCUUUCU
.(.((((..((((((..((((((.((.(((.....))).(.(((((((((..(((((((.....)).)))))..)))......))))))).)).)))))).))))))...)))))..... ( -40.70)
>DroSec_CAF1 12928 120 - 1
CGACUGCAAUCGACUUUUUGGCUUGCACAAUUUUUUUGGGUACCGAGAGUUGAGAGCUCGACGAGAUGCUUUUGGCUUUUUGGCUUGGUCAGUUGGCUAAUAGUCGAGUCGCGGCUUUCU
.(.((((..((((((..((((((.((.(((.....))).(.(((((((((..(((((((.....)).)))))..)))......))))))).)).)))))).))))))...)))))..... ( -40.70)
>DroEre_CAF1 13457 119 - 1
CGACUGCAAUCGACUUUUUGGCUUGCACAAUUU-UUUGGGUACCGAGAGCUGAGAGCUCGACGAGAUGCUUUUGGCUUUUUGGCUUGGUCAGUUGGCUAAUAGGCGAGUCGAGGCUUUCU
.((..((..(((((((...(.((.((.(((((.-.(..(((...((((((..(((((((.....)).)))))..))))))..)))..)..)))))))....)).)))))))).))..)). ( -42.60)
>consensus
CGACUGCAAUCGACUUUUUGGCUUGCACAAUUUUUUUGGGUACCGAGAGUUGAGAGCUCGACGAGAUGCUUUUGGCUUUUUGGCUUGGUCAGUUGGCUAAUAGUCGAGUCGCGGCUUUCU
.((..((...((((((...((((.((.(((((...(..(((...((((((..(((((((.....)).)))))..))))))..)))..)..)))))))....))))))))))..))..)). (-39.65 = -39.77 +   0.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,391,849 – 16,391,969
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -41.37
Consensus MFE -41.67
Energy contribution -41.23
Covariance contribution -0.44
Combinations/Pair 1.05
Mean z-score -2.02
Structure conservation index 1.01
SVM decision value 1.18
SVM RNA-class probability 0.927051
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16391849 120 - 27905053
GCCAGGAUUGUGCAAUCCGCAAUCGGCAAUCCGCAGCUGACGACUGCAAUCGACUUUUUGGCUUGCACAAUUUUUUUGGGUACCGAGAGUUGAGAGCUCGACGAGAUGCUUUUGGCUUUU
.((((((((((((((.((....(((((........)))))(((......))).......)).))))))))))...)))).....((((((..(((((((.....)).)))))..)))))) ( -40.50)
>DroSec_CAF1 12968 120 - 1
GCCAGGAUUGUGCAAUCCGCAAUCGGCAAUCCGCAGCUGACGACUGCAAUCGACUUUUUGGCUUGCACAAUUUUUUUGGGUACCGAGAGUUGAGAGCUCGACGAGAUGCUUUUGGCUUUU
.((((((((((((((.((....(((((........)))))(((......))).......)).))))))))))...)))).....((((((..(((((((.....)).)))))..)))))) ( -40.50)
>DroEre_CAF1 13497 119 - 1
GCCAGGAUUGUGCAAUCCGCAAUCAGCAAUCCGCAGCUGACGACUGCAAUCGACUUUUUGGCUUGCACAAUUU-UUUGGGUACCGAGAGCUGAGAGCUCGACGAGAUGCUUUUGGCUUUU
.((((((((((((((.((....(((((........)))))(((......))).......)).)))))))))).-.)))).....((((((..(((((((.....)).)))))..)))))) ( -43.10)
>consensus
GCCAGGAUUGUGCAAUCCGCAAUCGGCAAUCCGCAGCUGACGACUGCAAUCGACUUUUUGGCUUGCACAAUUUUUUUGGGUACCGAGAGUUGAGAGCUCGACGAGAUGCUUUUGGCUUUU
.((((((((((((((.((....(((((........)))))(((......))).......)).))))))))))...)))).....((((((..(((((((.....)).)))))..)))))) (-41.67 = -41.23 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,391,889 – 16,392,008
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.04
Mean single sequence MFE -36.07
Consensus MFE -33.80
Energy contribution -34.13
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.94
SVM decision value 0.30
SVM RNA-class probability 0.677172
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16391889 119 - 27905053
CACACACACAC-AGCAGCAGCCAACGAACAGCAACAGGUUGCCAGGAUUGUGCAAUCCGCAAUCGGCAAUCCGCAGCUGACGACUGCAAUCGACUUUUUGGCUUGCACAAUUUUUUUGGG
...........-....((((((((....((((..(.(((((((..(((((((.....)))))))))))))).)..)))).(((......))).....))))).))).(((.....))).. ( -35.40)
>DroSec_CAF1 13008 112 - 1
CACACAC--------AGCAGCCAACGAACAGCAACAGGUUGCCAGGAUUGUGCAAUCCGCAAUCGGCAAUCCGCAGCUGACGACUGCAAUCGACUUUUUGGCUUGCACAAUUUUUUUGGG
.......--------.((((((((....((((..(.(((((((..(((((((.....)))))))))))))).)..)))).(((......))).....))))).))).(((.....))).. ( -35.40)
>DroEre_CAF1 13537 119 - 1
CACACACGCGCGUGCAGCAGCCAACCAACAGCAACAGGUUGCCAGGAUUGUGCAAUCCGCAAUCAGCAAUCCGCAGCUGACGACUGCAAUCGACUUUUUGGCUUGCACAAUUU-UUUGGG
...........(((((..((((((....((((..(.((((((...(((((((.....))))))).)))))).)..)))).(((......))).....))))))))))).....-...... ( -37.40)
>consensus
CACACAC_C_C__GCAGCAGCCAACGAACAGCAACAGGUUGCCAGGAUUGUGCAAUCCGCAAUCGGCAAUCCGCAGCUGACGACUGCAAUCGACUUUUUGGCUUGCACAAUUUUUUUGGG
................((((((((....((((..(.(((((((..(((((((.....)))))))))))))).)..)))).(((......))).....))))).))).(((.....))).. (-33.80 = -34.13 +   0.33)

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 12:17:35 2006