Locus 15285

Sequence ID dm3.chrX
Location 18,269,474 – 18,269,617
Length 143
Max. P 0.999060
window21053 window21054 window21055 window21056

overview

Window 3

Location 18,269,474 – 18,269,580
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.61
Shannon entropy 0.35983
G+C content 0.46381
Mean single sequence MFE -35.38
Consensus MFE -20.72
Energy contribution -21.32
Covariance contribution 0.60
Combinations/Pair 1.23
Mean z-score -2.21
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.905495
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18269474 106 + 22422827
AAAUCGAACUGGAAUCGAGGG-UCUAUCAAAUUGAAGUUAUCGAGUUAUCGAGCUGAAUGUAGGCGAUGAAUCAGCG-------------UCCAUGGAACUGCUUCAUCGCCUAACUGCA
...((((....((.((((...-.((.((.....))))...)))).)).))))((......(((((((((((.(((..-------------((....)).))).)))))))))))...)). ( -31.50, z-score =  -1.71, R)
>droEre2.scaffold_4690 8590196 119 + 18748788
AAAUCGAACUGGAAUCGAGGGGUCUUUCAACUUUAAGUUCUCAAGUUCUCGAGCUGGAUUUAGGCGAUGAAUCUGCGGC-ACGUGGCGCAUUCAUGGGACUUAUUCAUCGUCUAUCUACA
.....((((((((((..((((.........))))..)))))..)))))....(.((((..((((((((((((.((((.(-....).)))).((....))...))))))))))))))))). ( -31.80, z-score =  -0.90, R)
>droYak2.chrX 16897467 113 + 21770863
AAAUCGAACUAGAAUCGAGGGGUCCUUCAACUUGAAGUUCCCAUGCUG-------GGAUUUAGACGAUGAAUCAGCGGCCACUUGGAGCAUUAGUGGAACUGCUUCAUCGUCUAGCUUCA
...((((.......)))).(((..((((.....))))..)))......-------(((.((((((((((((.(((...(((((.........)))))..))).)))))))))))).))). ( -41.50, z-score =  -3.32, R)
>droSec1.super_8 578967 106 + 3762037
AAAUCGAACUGGAAUCGAGGG-UCUAACAACUUGAAGUUAUCGAGUUAUCGAGCUGAAUGUGGGCGAUGAAUCAGCG-------------UCCAUGGAACUGCUUCAUCGCCUACCUGCA
...((((..((((........-))))..(((((((.....))))))).))))((.....((((((((((((.(((..-------------((....)).))).))))))))))))..)). ( -35.90, z-score =  -2.74, R)
>droSim1.chrX 14087622 106 + 17042790
AAAUCGAACUGGAAUCGGGGG-UCUAUCAACUUGAAGUUAUCGAGUUAUCGAGCUGAAUGUGGGCGAUGAAUCAGCG-------------UCCAUGGAACUGCUUCAUCGCCUACCUGCA
...((((.(((....)))...-......(((((((.....))))))).))))((.....((((((((((((.(((..-------------((....)).))).))))))))))))..)). ( -36.20, z-score =  -2.40, R)
>consensus
AAAUCGAACUGGAAUCGAGGG_UCUAUCAACUUGAAGUUAUCGAGUUAUCGAGCUGAAUGUAGGCGAUGAAUCAGCG_____________UCCAUGGAACUGCUUCAUCGCCUACCUGCA
...((((.......))))..........(((((((.....)))))))............((((((((((((.(((........................))).))))))))))))..... (-20.72 = -21.32 +   0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,269,474 – 18,269,580
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.61
Shannon entropy 0.35983
G+C content 0.46381
Mean single sequence MFE -31.44
Consensus MFE -18.15
Energy contribution -19.31
Covariance contribution 1.16
Combinations/Pair 1.11
Mean z-score -2.48
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.61
SVM RNA-class probability 0.954703
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18269474 106 - 22422827
UGCAGUUAGGCGAUGAAGCAGUUCCAUGGA-------------CGCUGAUUCAUCGCCUACAUUCAGCUCGAUAACUCGAUAACUUCAAUUUGAUAGA-CCCUCGAUUCCAGUUCGAUUU
((.((((((((((((((.((((((....))-------------.)))).)))))))))..........((((....))))))))).))..........-...((((.......))))... ( -30.00, z-score =  -2.46, R)
>droEre2.scaffold_4690 8590196 119 - 18748788
UGUAGAUAGACGAUGAAUAAGUCCCAUGAAUGCGCCACGU-GCCGCAGAUUCAUCGCCUAAAUCCAGCUCGAGAACUUGAGAACUUAAAGUUGAAAGACCCCUCGAUUCCAGUUCGAUUU
......(((.((((((((..((..((((.........)))-)..))..)))))))).)))((((....((((....))))(((((...((((((........))))))..))))))))). ( -24.90, z-score =  -1.24, R)
>droYak2.chrX 16897467 113 - 21770863
UGAAGCUAGACGAUGAAGCAGUUCCACUAAUGCUCCAAGUGGCCGCUGAUUCAUCGUCUAAAUCC-------CAGCAUGGGAACUUCAAGUUGAAGGACCCCUCGAUUCUAGUUCGAUUU
(((((.(((((((((((.((((.(((((.........)))))..)))).)))))))))))..(((-------(.....)))).)))))((((((.(....).))))))............ ( -39.20, z-score =  -3.73, R)
>droSec1.super_8 578967 106 - 3762037
UGCAGGUAGGCGAUGAAGCAGUUCCAUGGA-------------CGCUGAUUCAUCGCCCACAUUCAGCUCGAUAACUCGAUAACUUCAAGUUGUUAGA-CCCUCGAUUCCAGUUCGAUUU
....(((.(((((((((.((((((....))-------------.)))).))))))))).........((.(((((((.((.....)).))))))))))-)).((((.......))))... ( -32.50, z-score =  -2.66, R)
>droSim1.chrX 14087622 106 - 17042790
UGCAGGUAGGCGAUGAAGCAGUUCCAUGGA-------------CGCUGAUUCAUCGCCCACAUUCAGCUCGAUAACUCGAUAACUUCAAGUUGAUAGA-CCCCCGAUUCCAGUUCGAUUU
....(((.(((((((((.((((((....))-------------.)))).))))))))).....((((((.((.............)).))))))...)-))..(((.......))).... ( -30.62, z-score =  -2.30, R)
>consensus
UGCAGGUAGGCGAUGAAGCAGUUCCAUGGA_____________CGCUGAUUCAUCGCCUACAUUCAGCUCGAUAACUCGAUAACUUCAAGUUGAUAGA_CCCUCGAUUCCAGUUCGAUUU
......(((((((((((.((((......................)))).)))))))))))................((((..(((...((((((........))))))..)))))))... (-18.15 = -19.31 +   1.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,269,513 – 18,269,617
Length 104
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 79.55
Shannon entropy 0.31586
G+C content 0.44533
Mean single sequence MFE -37.50
Consensus MFE -28.89
Energy contribution -28.82
Covariance contribution -0.06
Combinations/Pair 1.24
Mean z-score -3.73
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.62
SVM RNA-class probability 0.999060
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18269513 104 + 22422827
UCGAGUUAUCGAGCUGAAUGUAGGCGAUGAAUCAGCG------------UCCAUGGAACUGCUUCAUCGCCUAACUGCAGCAUAUGGACUCAAAUGAUUGUAAUUGAUAACUUUGA
..((((((((((((((....(((((((((((.(((..------------((....)).))).)))))))))))....)))).((..(.(......).)..)).))))))))))... ( -40.30, z-score =  -5.18, R)
>droEre2.scaffold_4690 8590236 108 + 18748788
UCAAGUUCUCGAGCUGGAUUUAGGCGAUGAAUCUGCGGCACGUGGCGCAUUCAUGGGACUUAUUCAUCGUCUAUCUACAGCAUGCAG---CAUAUA-----AAUUGAUCAUUUUGA
(((((...((((((((....((((((((((((.((((.(....).)))).((....))...))))))))))))....))))(((...---)))...-----..))))....))))) ( -29.30, z-score =  -0.83, R)
>droSec1.super_8 579006 104 + 3762037
UCGAGUUAUCGAGCUGAAUGUGGGCGAUGAAUCAGCG------------UCCAUGGAACUGCUUCAUCGCCUACCUGCAGCAUAUGAACUCAAAUGCUUGUAAUUGAUCACUUUGA
..((((.(((((.......((((((((((((.(((..------------((....)).))).)))))))))))).((((((((.((....)).)))).)))).))))).))))... ( -38.30, z-score =  -4.02, R)
>droSim1.chrX 14087661 104 + 17042790
UCGAGUUAUCGAGCUGAAUGUGGGCGAUGAAUCAGCG------------UCCAUGGAACUGCUUCAUCGCCUACCUGCAGCAUAUGAACUCAAAUGCUUGUAAUCGAUCACUUCGA
((((((.(((((.......((((((((((((.(((..------------((....)).))).)))))))))))).((((((((.((....)).)))).)))).))))).)).)))) ( -42.10, z-score =  -4.88, R)
>consensus
UCGAGUUAUCGAGCUGAAUGUAGGCGAUGAAUCAGCG____________UCCAUGGAACUGCUUCAUCGCCUACCUGCAGCAUAUGAACUCAAAUGCUUGUAAUUGAUCACUUUGA
((((((.(((((((((...((((((((((((.(((.......................))).))))))))))))...)))).(((........))).......))))).)).)))) (-28.89 = -28.82 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,269,513 – 18,269,617
Length 104
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 79.55
Shannon entropy 0.31586
G+C content 0.44533
Mean single sequence MFE -33.48
Consensus MFE -23.59
Energy contribution -26.40
Covariance contribution 2.81
Combinations/Pair 1.04
Mean z-score -3.07
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.79
SVM RNA-class probability 0.995300
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18269513 104 - 22422827
UCAAAGUUAUCAAUUACAAUCAUUUGAGUCCAUAUGCUGCAGUUAGGCGAUGAAGCAGUUCCAUGGA------------CGCUGAUUCAUCGCCUACAUUCAGCUCGAUAACUCGA
....(((((((.....(((....))).........((((.((((((((((((((.((((((....))------------.)))).))))))))))).)))))))..)))))))... ( -37.40, z-score =  -5.14, R)
>droEre2.scaffold_4690 8590236 108 - 18748788
UCAAAAUGAUCAAUU-----UAUAUG---CUGCAUGCUGUAGAUAGACGAUGAAUAAGUCCCAUGAAUGCGCCACGUGCCGCAGAUUCAUCGCCUAAAUCCAGCUCGAGAACUUGA
...............-----......---......((((.(..(((.((((((((..((..((((.........))))..))..)))))))).)))..).))))((((....)))) ( -21.10, z-score =   0.24, R)
>droSec1.super_8 579006 104 - 3762037
UCAAAGUGAUCAAUUACAAGCAUUUGAGUUCAUAUGCUGCAGGUAGGCGAUGAAGCAGUUCCAUGGA------------CGCUGAUUCAUCGCCCACAUUCAGCUCGAUAACUCGA
.....((((....))))......(((((((.....((((...((.(((((((((.((((((....))------------.)))).))))))))).))...)))).....))))))) ( -36.50, z-score =  -3.67, R)
>droSim1.chrX 14087661 104 - 17042790
UCGAAGUGAUCGAUUACAAGCAUUUGAGUUCAUAUGCUGCAGGUAGGCGAUGAAGCAGUUCCAUGGA------------CGCUGAUUCAUCGCCCACAUUCAGCUCGAUAACUCGA
((((.((.(((((.....(((((.((....)).)))))((..((.(((((((((.((((((....))------------.)))).))))))))).)).....))))))).)))))) ( -38.90, z-score =  -3.71, R)
>consensus
UCAAAGUGAUCAAUUACAAGCAUUUGAGUCCAUAUGCUGCAGGUAGGCGAUGAAGCAGUUCCAUGGA____________CGCUGAUUCAUCGCCCACAUUCAGCUCGAUAACUCGA
........................((((((.....((((...((((((((((((.((((.....................)))).))))))))))))...)))).....)))))). (-23.59 = -26.40 +   2.81)

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 01:56:25 2011