Locus 12568

Sequence ID dm3.chrX
Location 950,834 – 951,008
Length 174
Max. P 0.968905
window17283 window17284 window17285

overview

Window 3

Location 950,834 – 950,945
Length 111
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 94.59
Shannon entropy 0.07446
G+C content 0.36857
Mean single sequence MFE -17.73
Consensus MFE -17.25
Energy contribution -17.69
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -0.97
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.15
SVM RNA-class probability 0.566212
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 950834 111 - 22422827
UGCAACUAUGUUGAUAAUUCUUGCUGUAACGCAUAAAUAAAGCCCAAAUUACAAAUUGGAUGCGAACGUAUGGAUUACUCGUACCUAAAACACAACCUCUCCCAAAAAGUG
.(((.(((..(((.(((((...(((...............)))...))))))))..))).)))....((((((.....))))))........................... ( -13.66, z-score =   0.30, R)
>droSim1.chrX 769715 109 - 17042790
UGCAACUAUGUUGGUAAUUCUUGCUGUAACGCAUAAAUAAAGCCCAAAUUACUAAUUGGAUGCGAACGUAUGAAUUACUCGUACCUGAAACACAACCAAUCCCAAAAUG--
.(((.(((.((((((((((...(((...............)))...))))))))))))).)))....((((((.....)))))).........................-- ( -19.76, z-score =  -1.81, R)
>droSec1.super_10 786650 111 - 3036183
UGCAACUAUGUUGGUAAUUCUUGCUGUAACGCAUAAAUAAAGCCCAAAUUACUAAUUGGAUGCGAACGUAUGAAUUACUCGUACCUGAAACACAACCAAUCCCAAAAAGUG
.(((.(((.((((((((((...(((...............)))...))))))))))))).)))....((((((.....))))))........................... ( -19.76, z-score =  -1.39, R)
>consensus
UGCAACUAUGUUGGUAAUUCUUGCUGUAACGCAUAAAUAAAGCCCAAAUUACUAAUUGGAUGCGAACGUAUGAAUUACUCGUACCUGAAACACAACCAAUCCCAAAAAGUG
.(((.(((.((((((((((...(((...............)))...))))))))))))).)))....((((((.....))))))........................... (-17.25 = -17.69 +   0.45)

alignment

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secondary structure

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dotplot

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Window 4

Location 950,905 – 951,008
Length 103
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 68.45
Shannon entropy 0.51628
G+C content 0.35428
Mean single sequence MFE -21.88
Consensus MFE -11.26
Energy contribution -10.45
Covariance contribution -0.81
Combinations/Pair 1.43
Mean z-score -2.05
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.81
SVM RNA-class probability 0.968905
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 950905 103 + 22422827
UUAUUUAUGCGUUACAGCAAGAAUUAUCAACAUAGUUGCACUCAUUAUGGUCGAUAAUGCUCGUAACUUAUCGUAAGAUAAGUUCAACAGCACAUGCAGUAAU
..........(((((.(((...((((((..((((((.......))))))...))))))(((.((((((((((....))))))))..)))))...))).))))) ( -26.20, z-score =  -3.15, R)
>droSim1.chrX 769784 103 + 17042790
UUAUUUAUGCGUUACAGCAAGAAUUACCAACAUAGUUGCACUCAUUAUGGUCGAUAAUGCUCGUAACUUAUCGUAAGAUAAGUUAAACAGCACAUACAGUAAU
.......(((......)))...(((((...((((((.......))))))........((((..(((((((((....)))))))))...))))......))))) ( -23.20, z-score =  -2.61, R)
>droSec1.super_10 786721 103 + 3036183
UUAUUUAUGCGUUACAGCAAGAAUUACCAACAUAGUUGCACUCAUUAUGGUCGAUAAUGCUCGUAACUUAUCGCAAGAUAAGUUAAACAGCACAUACAGUAAU
.......(((......)))...(((((...((((((.......))))))........((((..(((((((((....)))))))))...))))......))))) ( -24.20, z-score =  -3.00, R)
>droVir3.scaffold_12726 1198845 81 - 2840439
------GUAUAAUCAAGUUGGAAGAGGCUACA--GUUGCCCCAAGCGAAAUUUAGAUUUUUCGAGCUUUGUC-UGAAACAAGCUGAACAG-------------
------......(((((((.((((((.(((..--.((((.....))))....))).)))))).))))((((.-....))))..)))....------------- ( -13.90, z-score =   0.56, R)
>consensus
UUAUUUAUGCGUUACAGCAAGAAUUACCAACAUAGUUGCACUCAUUAUGGUCGAUAAUGCUCGUAACUUAUCGUAAGAUAAGUUAAACAGCACAUACAGUAAU
........(((((((.((.........((((...))))...........)).).))))))....((((((((....))))))))................... (-11.26 = -10.45 +  -0.81)

alignment

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secondary structure

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dotplot

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Window 5

Location 950,905 – 951,008
Length 103
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 68.45
Shannon entropy 0.51628
G+C content 0.35428
Mean single sequence MFE -22.07
Consensus MFE -10.66
Energy contribution -13.78
Covariance contribution 3.13
Combinations/Pair 1.27
Mean z-score -1.51
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.720004
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 950905 103 - 22422827
AUUACUGCAUGUGCUGUUGAACUUAUCUUACGAUAAGUUACGAGCAUUAUCGACCAUAAUGAGUGCAACUAUGUUGAUAAUUCUUGCUGUAACGCAUAAAUAA
.........(((((.((((((((((((....)))))))).((((.(((((((((.(((.((....))..)))))))))))).))))...)))))))))..... ( -25.50, z-score =  -2.43, R)
>droSim1.chrX 769784 103 - 17042790
AUUACUGUAUGUGCUGUUUAACUUAUCUUACGAUAAGUUACGAGCAUUAUCGACCAUAAUGAGUGCAACUAUGUUGGUAAUUCUUGCUGUAACGCAUAAAUAA
.....(((.(((((.((((((((((((....)))))))))((((.(((((((((.(((.((....))..)))))))))))).))))....)))))))).))). ( -24.60, z-score =  -1.98, R)
>droSec1.super_10 786721 103 - 3036183
AUUACUGUAUGUGCUGUUUAACUUAUCUUGCGAUAAGUUACGAGCAUUAUCGACCAUAAUGAGUGCAACUAUGUUGGUAAUUCUUGCUGUAACGCAUAAAUAA
.....(((.(((((.((((((((((((....)))))))))((((.(((((((((.(((.((....))..)))))))))))).))))....)))))))).))). ( -24.60, z-score =  -1.63, R)
>droVir3.scaffold_12726 1198845 81 + 2840439
-------------CUGUUCAGCUUGUUUCA-GACAAAGCUCGAAAAAUCUAAAUUUCGCUUGGGGCAAC--UGUAGCCUCUUCCAACUUGAUUAUAC------
-------------...(((((((((((...-))).))))).))).((((............(((((...--....))))).........))))....------ ( -13.60, z-score =   0.02, R)
>consensus
AUUACUGUAUGUGCUGUUUAACUUAUCUUACGAUAAGUUACGAGCAUUAUCGACCAUAAUGAGUGCAACUAUGUUGGUAAUUCUUGCUGUAACGCAUAAAUAA
.........(((((.((((((((((((....)))))))).((((.((((((((((((.....))).......))))))))).))))...)))))))))..... (-10.66 = -13.78 +   3.13)

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 01:04:46 2011