Locus 14831

Sequence ID dm3.chrX
Location 15,716,494 – 15,716,654
Length 160
Max. P 0.999055
window20421 window20422 window20423 window20424

overview

Window 1

Location 15,716,494 – 15,716,614
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.36
Shannon entropy 0.20494
G+C content 0.43937
Mean single sequence MFE -36.95
Consensus MFE -23.65
Energy contribution -23.53
Covariance contribution -0.12
Combinations/Pair 1.24
Mean z-score -2.85
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.31
SVM RNA-class probability 0.925146
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15716494 120 + 22422827
CACUAACGUAGACACCUCUUUGAAUGAGAUUUCGAAUCCUCGGAGGCUUUUGGGUGUCCAUAAGUACGCAACGAAGAAUAUGGCAUAUUCGAGAUAUUCUAUAGCAUACUUUUGGACACU
........((((..((((((((((......)))))......)))))..))))((((((((.(((((.((.....(((((((..(......)..)))))))...)).))))).)))))))) ( -32.50, z-score =  -2.53, R)
>droEre2.scaffold_4690 7422442 118 - 18748788
CACU--CGUAGACACCUCUUUGAAUGUGAUUUCGCGUCCUCGGAGGCUGUAAGGUGUCCGAAAGUAUGCAGUGAAGAACAUGGCAUGGUCAAGAUAUUCUAUAGCAUACUUUCAGACAGU
..((--..(((...(((((..(.(((((....))))).)..))))))))..)).((((.((((((((((.(((((...(.((((...)))).)...))).)).)))))))))).)))).. ( -37.50, z-score =  -2.29, R)
>droSec1.super_37 297444 120 + 454039
CACUAACGUAGACACCUCUUUGAAUGAGAUUUCGAAUCCUCGUAGGCUUUUGGGUGUCCGUGAGUACGCAACGAAGAAUAUGGCAUAGCCGCCAUAUUCUGUAGCAUACUUUUGGACACU
..(((.((..((......((((((......))))))))..))))).......((((((((.(((((.((.((..((((((((((......)))))))))))).)).))))).)))))))) ( -40.50, z-score =  -3.79, R)
>droSim1.chrU 78422 120 + 15797150
CACUAACGUAGCCACCUCUUGGAAUGAGAUUUCGAAUCCUCGCAGGCUUUUGGGUGUCCGUAAGUACGCAACGAAUAAUAUGGCAUAGCCGAGAUAUUCUGUAGCAUACUUUUGGACACU
..((((...((((.((....))...(((..........)))...)))).))))(((((((.(((((.((.(((((((.(.((((...)))).).))))).)).)).))))).))))))). ( -37.30, z-score =  -2.78, R)
>consensus
CACUAACGUAGACACCUCUUUGAAUGAGAUUUCGAAUCCUCGGAGGCUUUUGGGUGUCCGUAAGUACGCAACGAAGAAUAUGGCAUAGCCGAGAUAUUCUAUAGCAUACUUUUGGACACU
..............(((((..(.((..(....)..)).)..)))))......((((((((.(((((.((.(((((.....((((...)))).....))).)).)).))))).)))))))) (-23.65 = -23.53 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,716,494 – 15,716,614
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.36
Shannon entropy 0.20494
G+C content 0.43937
Mean single sequence MFE -37.80
Consensus MFE -26.60
Energy contribution -27.73
Covariance contribution 1.12
Combinations/Pair 1.18
Mean z-score -3.71
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.88
SVM RNA-class probability 0.996067
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15716494 120 - 22422827
AGUGUCCAAAAGUAUGCUAUAGAAUAUCUCGAAUAUGCCAUAUUCUUCGUUGCGUACUUAUGGACACCCAAAAGCCUCCGAGGAUUCGAAAUCUCAUUCAAAGAGGUGUCUACGUUAGUG
.(((((((.((((((((...(((((((..(......)..))))))).....)))))))).)))))))......(((((...((((..(....)..))))...)))))............. ( -33.50, z-score =  -3.42, R)
>droEre2.scaffold_4690 7422442 118 + 18748788
ACUGUCUGAAAGUAUGCUAUAGAAUAUCUUGACCAUGCCAUGUUCUUCACUGCAUACUUUCGGACACCUUACAGCCUCCGAGGACGCGAAAUCACAUUCAAAGAGGUGUCUACG--AGUG
(((....((((((((((...(((((((............))))))).....))))))))))(((((((((...((.((....)).))(((......)))...)))))))))...--))). ( -36.50, z-score =  -3.36, R)
>droSec1.super_37 297444 120 - 454039
AGUGUCCAAAAGUAUGCUACAGAAUAUGGCGGCUAUGCCAUAUUCUUCGUUGCGUACUCACGGACACCCAAAAGCCUACGAGGAUUCGAAAUCUCAUUCAAAGAGGUGUCUACGUUAGUG
.((((((...(((((((.(((((((((((((....)))))))))))..)).)))))))...))))))......((..(((.((((.....(((((.......))))))))).)))..)). ( -43.80, z-score =  -5.04, R)
>droSim1.chrU 78422 120 - 15797150
AGUGUCCAAAAGUAUGCUACAGAAUAUCUCGGCUAUGCCAUAUUAUUCGUUGCGUACUUACGGACACCCAAAAGCCUGCGAGGAUUCGAAAUCUCAUUCCAAGAGGUGGCUACGUUAGUG
.((((((..((((((((.((.(((((....(((...)))....))))))).))))))))..)))))).....((((..((......))..(((((.......)))))))))......... ( -37.40, z-score =  -3.01, R)
>consensus
AGUGUCCAAAAGUAUGCUACAGAAUAUCUCGACUAUGCCAUAUUCUUCGUUGCGUACUUACGGACACCCAAAAGCCUCCGAGGAUUCGAAAUCUCAUUCAAAGAGGUGUCUACGUUAGUG
.(((((((.((((((((...(((((((..((....))..))))))).....)))))))).)))))))......((..(((.((((.....(((((.......))))))))).)))..)). (-26.60 = -27.73 +   1.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,716,534 – 15,716,654
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.92
Shannon entropy 0.21068
G+C content 0.44273
Mean single sequence MFE -35.88
Consensus MFE -25.59
Energy contribution -25.40
Covariance contribution -0.19
Combinations/Pair 1.21
Mean z-score -2.09
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.47
SVM RNA-class probability 0.707465
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15716534 120 + 22422827
CGGAGGCUUUUGGGUGUCCAUAAGUACGCAACGAAGAAUAUGGCAUAUUCGAGAUAUUCUAUAGCAUACUUUUGGACACUUUGUUGAUGAAGGGAUUUUCGAUCUAUCGCACCCGUGUAU
(((..((....(((((((((.(((((.((.....(((((((..(......)..)))))))...)).))))).))))))))).......((..(((((...))))).))))..)))..... ( -34.20, z-score =  -2.05, R)
>droEre2.scaffold_4690 7422480 117 - 18748788
CGGAGGCUGUAAGGUGUCCGAAAGUAUGCAGUGAAGAACAUGGCAUGGUCAAGAUAUUCUAUAGCAUACUUUCAGACAGUCUGUUGAA---GGGAUUUUCGAGCUAUCGCACCCAUGUAU
.((..((.((((((((((.((((((((((.(((((...(.((((...)))).)...))).)).)))))))))).)))).))).(((((---(....))))))..))).))..))...... ( -32.60, z-score =  -1.08, R)
>droSec1.super_37 297484 117 + 454039
CGUAGGCUUUUGGGUGUCCGUGAGUACGCAACGAAGAAUAUGGCAUAGCCGCCAUAUUCUGUAGCAUACUUUUGGACACUUUGUUGAA---GGGAUUUUCGAUCUAUCGCACCCGUGUAU
.(((.((....(((((((((.(((((.((.((..((((((((((......)))))))))))).)).))))).))))))))).......---(((.....(((....)))..))))).))) ( -41.70, z-score =  -3.44, R)
>droSim1.chrU 78462 116 + 15797150
CGCAGGCUUUUGGGUGUCCGUAAGUACGCAACGAAUAAUAUGGCAUAGCCGAGAUAUUCUGUAGCAUACUUUUGGACACUUUGUUGA----GGGAUUUUCGAUCUAUCGCACCCGUGUAU
(((.((.....(((((((((.(((((.((.(((((((.(.((((...)))).).))))).)).)).))))).)))))))))(((.((----.(((((...))))).))))))).)))... ( -35.00, z-score =  -1.78, R)
>consensus
CGGAGGCUUUUGGGUGUCCGUAAGUACGCAACGAAGAAUAUGGCAUAGCCGAGAUAUUCUAUAGCAUACUUUUGGACACUUUGUUGAA___GGGAUUUUCGAUCUAUCGCACCCGUGUAU
....(((....(((((((((.(((((.((.(((((.....((((...)))).....))).)).)).))))).))))))))).)))......(((.....(((....)))..)))...... (-25.59 = -25.40 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,716,534 – 15,716,654
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.92
Shannon entropy 0.21068
G+C content 0.44273
Mean single sequence MFE -35.88
Consensus MFE -27.50
Energy contribution -27.88
Covariance contribution 0.38
Combinations/Pair 1.16
Mean z-score -4.34
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.62
SVM RNA-class probability 0.999055
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15716534 120 - 22422827
AUACACGGGUGCGAUAGAUCGAAAAUCCCUUCAUCAACAAAGUGUCCAAAAGUAUGCUAUAGAAUAUCUCGAAUAUGCCAUAUUCUUCGUUGCGUACUUAUGGACACCCAAAAGCCUCCG
.....((((.((....(((.(((......))))))......(((((((.((((((((...(((((((..(......)..))))))).....)))))))).)))))))......)).)))) ( -35.80, z-score =  -5.11, R)
>droEre2.scaffold_4690 7422480 117 + 18748788
AUACAUGGGUGCGAUAGCUCGAAAAUCCC---UUCAACAGACUGUCUGAAAGUAUGCUAUAGAAUAUCUUGACCAUGCCAUGUUCUUCACUGCAUACUUUCGGACACCUUACAGCCUCCG
......(((.((........(((......---))).......(((((((((((((((...(((((((............))))))).....))))))))))))))).......)).))). ( -32.90, z-score =  -3.59, R)
>droSec1.super_37 297484 117 - 454039
AUACACGGGUGCGAUAGAUCGAAAAUCCC---UUCAACAAAGUGUCCAAAAGUAUGCUACAGAAUAUGGCGGCUAUGCCAUAUUCUUCGUUGCGUACUCACGGACACCCAAAAGCCUACG
......(((..(((....))).....)))---.........((((((...(((((((.(((((((((((((....)))))))))))..)).)))))))...))))))............. ( -40.20, z-score =  -4.98, R)
>droSim1.chrU 78462 116 - 15797150
AUACACGGGUGCGAUAGAUCGAAAAUCCC----UCAACAAAGUGUCCAAAAGUAUGCUACAGAAUAUCUCGGCUAUGCCAUAUUAUUCGUUGCGUACUUACGGACACCCAAAAGCCUGCG
.....(((((..((..(((.....)))..----))......((((((..((((((((.((.(((((....(((...)))....))))))).))))))))..))))))......))))).. ( -34.60, z-score =  -3.67, R)
>consensus
AUACACGGGUGCGAUAGAUCGAAAAUCCC___UUCAACAAAGUGUCCAAAAGUAUGCUACAGAAUAUCUCGACUAUGCCAUAUUCUUCGUUGCGUACUUACGGACACCCAAAAGCCUCCG
......((((.(((....)))...)))).............(((((((.((((((((...(((((((..((....))..))))))).....)))))))).)))))))............. (-27.50 = -27.88 +   0.38)

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 01:47:40 2011