Locus 12590

Sequence ID dm3.chrX
Location 1,048,335 – 1,048,479
Length 144
Max. P 0.964693
window17313 window17314 window17315 window17316

overview

Window 3

Location 1,048,335 – 1,048,439
Length 104
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 97.43
Shannon entropy 0.03532
G+C content 0.44520
Mean single sequence MFE -29.77
Consensus MFE -28.31
Energy contribution -27.87
Covariance contribution -0.44
Combinations/Pair 1.08
Mean z-score -2.26
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.74
SVM RNA-class probability 0.964693
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1048335 104 + 22422827
GCGUGAGUAGGCUUAAAAUGUAUCUGCACAAAUUUCAAAUACGAACACAAGAGCACAGACACGCAGUGUUUGUGUGGCCAAAAGGGCCCAAAGUCGAAGAUAUA
((....))..........(((((((..((.......................((((((((((...))))))))))((((.....))))....))...))))))) ( -27.00, z-score =  -1.57, R)
>droSim1.chrX 838168 103 + 17042790
GCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACUUCAAAUACGAACACGAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGCC-AAAGUCGAAGAUAUA
((....))..........(((((((........(((......)))..(((..((((((((((...))))))))))((((.....))))-....))).))))))) ( -31.30, z-score =  -2.53, R)
>droSec1.super_10 878090 103 + 3036183
GCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACUUCAAAUACGAACACAAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGCC-AAAGUCGAAGAUAUA
..(((((...((.......))..)).)))...((((................((((((((((...))))))))))((((.....))))-......))))..... ( -31.00, z-score =  -2.67, R)
>consensus
GCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACUUCAAAUACGAACACAAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGCC_AAAGUCGAAGAUAUA
..(((((...((.......))..)).)))...((((................((((((((((...))))))))))((((.....)))).......))))..... (-28.31 = -27.87 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,048,335 – 1,048,439
Length 104
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 97.43
Shannon entropy 0.03532
G+C content 0.44520
Mean single sequence MFE -26.00
Consensus MFE -24.64
Energy contribution -24.53
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.48
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.59
SVM RNA-class probability 0.752778
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1048335 104 - 22422827
UAUAUCUUCGACUUUGGGCCCUUUUGGCCACACAAACACUGCGUGUCUGUGCUCUUGUGUUCGUAUUUGAAAUUUGUGCAGAUACAUUUUAAGCCUACUCACGC
..............((((((.....)))).))........(((((..((.(((..(((((..((((.........))))..))))).....))).))..))))) ( -23.70, z-score =  -1.04, R)
>droSim1.chrX 838168 103 - 17042790
UAUAUCUUCGACUUU-GGCCCUUUUGGCCACACAGACACUGCGUGUCUGUGCUCUCGUGUUCGUAUUUGAAGUUUGUGCAGAUACAUUUUAAGCCUACUCACGC
..............(-((((.....)))))(((((((((...)))))))))....((((...(((((((((((.(((....))).))))))))..))).)))). ( -27.50, z-score =  -1.79, R)
>droSec1.super_10 878090 103 - 3036183
UAUAUCUUCGACUUU-GGCCCUUUUGGCCACACAGACACUGCGUGUCUGUGCUCUUGUGUUCGUAUUUGAAGUUUGUGCAGAUACAUUUUAAGCCUACUCACGC
..............(-((((.....)))))(((((((((...)))))))))....(((((..((((.........))))..))))).................. ( -26.80, z-score =  -1.60, R)
>consensus
UAUAUCUUCGACUUU_GGCCCUUUUGGCCACACAGACACUGCGUGUCUGUGCUCUUGUGUUCGUAUUUGAAGUUUGUGCAGAUACAUUUUAAGCCUACUCACGC
................((((.....)))).(((((((((...)))))))))....((((...(((((((((((.(((....))).))))))))..))).)))). (-24.64 = -24.53 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,048,375 – 1,048,479
Length 104
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 97.43
Shannon entropy 0.03532
G+C content 0.52262
Mean single sequence MFE -32.61
Consensus MFE -31.34
Energy contribution -31.12
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.61
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.850746
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1048375 104 + 22422827
ACGAACACAAGAGCACAGACACGCAGUGUUUGUGUGGCCAAAAGGGCCCAAAGUCGAAGAUAUAGCCGCACUUUGCAAAUCGUGACUGGGCAAAGGCACUUACC
.(((........((((((((((...))))))))))((((.....)))).....)))...........((.((((((.............))))))))....... ( -29.92, z-score =  -0.92, R)
>droSim1.chrX 838208 103 + 17042790
ACGAACACGAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGCC-AAAGUCGAAGAUAUAGCCGCACUUUGCAAAUCGUGACUGGGCAAAGGCACCUACC
.....(((((..((((((((((...))))))))))((((.....))))-(((((((..........)).))))).....)))))...((((....)).)).... ( -34.30, z-score =  -1.98, R)
>droSec1.super_10 878130 103 + 3036183
ACGAACACAAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGCC-AAAGUCGAAGAUAUAGCCGCACUUUGCAAAUCGUGACUGGGCAAAGGCACCUACC
.(((........((((((((((...))))))))))((((.....))))-....)))......(((..((.((((((.............))))))))..))).. ( -33.62, z-score =  -1.95, R)
>consensus
ACGAACACAAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGCC_AAAGUCGAAGAUAUAGCCGCACUUUGCAAAUCGUGACUGGGCAAAGGCACCUACC
.(((........((((((((((...))))))))))((((.....)))).....)))...........((.((((((.............))))))))....... (-31.34 = -31.12 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,048,375 – 1,048,479
Length 104
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 97.43
Shannon entropy 0.03532
G+C content 0.52262
Mean single sequence MFE -33.30
Consensus MFE -31.53
Energy contribution -32.20
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.32
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.644235
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1048375 104 - 22422827
GGUAAGUGCCUUUGCCCAGUCACGAUUUGCAAAGUGCGGCUAUAUCUUCGACUUUGGGCCCUUUUGGCCACACAAACACUGCGUGUCUGUGCUCUUGUGUUCGU
(((....)))...((.(((.((((...((((((((.(((........)))))))))((((.....)))).......))...)))).))).))............ ( -28.10, z-score =   0.04, R)
>droSim1.chrX 838208 103 - 17042790
GGUAGGUGCCUUUGCCCAGUCACGAUUUGCAAAGUGCGGCUAUAUCUUCGACUUU-GGCCCUUUUGGCCACACAGACACUGCGUGUCUGUGCUCUCGUGUUCGU
.((((.(((((((((..(((....))).)))))).))).)))).....(((...(-((((.....)))))(((((((((...))))))))).........))). ( -35.90, z-score =  -1.98, R)
>droSec1.super_10 878130 103 - 3036183
GGUAGGUGCCUUUGCCCAGUCACGAUUUGCAAAGUGCGGCUAUAUCUUCGACUUU-GGCCCUUUUGGCCACACAGACACUGCGUGUCUGUGCUCUUGUGUUCGU
.((((.(((((((((..(((....))).)))))).))).)))).....(((...(-((((.....)))))(((((((((...))))))))).........))). ( -35.90, z-score =  -2.02, R)
>consensus
GGUAGGUGCCUUUGCCCAGUCACGAUUUGCAAAGUGCGGCUAUAUCUUCGACUUU_GGCCCUUUUGGCCACACAGACACUGCGUGUCUGUGCUCUUGUGUUCGU
.((((.(((((((((..(((....))).)))))).))).)))).....(((.....((((.....)))).(((((((((...))))))))).........))). (-31.53 = -32.20 +   0.67)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:05:12 2011