Locus 14274

Sequence ID dm3.chrX
Location 12,300,592 – 12,300,789
Length 197
Max. P 0.951097
window19653 window19654 window19655

overview

Window 3

Location 12,300,592 – 12,300,712
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.94
Shannon entropy 0.42178
G+C content 0.47917
Mean single sequence MFE -41.56
Consensus MFE -15.75
Energy contribution -16.98
Covariance contribution 1.23
Combinations/Pair 1.28
Mean z-score -3.02
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.57
SVM RNA-class probability 0.951097
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12300592 120 - 22422827
CCAUUCGACCCUAUCAUUUGAUCAAAAGUGGUAGGGUCCUUAUGCUAACGGCCAAUCAAGUUAAUGCACUUACUCAAAAAGGCAAGGAAAAGGUGGGCAUUACGUUUAUCGCCAGGAUGG
(((((((((((((((((((......)))))))))))))...........(((............(((.(((.......)))))).......(((((((.....)))))))))).)))))) ( -39.80, z-score =  -3.61, R)
>droSim1.chrX 9459323 120 - 17042790
CCAUUCGACCCUAUCAUUUGAUCAAAAGUGGUAGGGUCAUUAUACUAACGGCCAAACAAGCUGAAGCACUCACUCAAAAAUGCAAUAAAAAGGUGGGCAUUCAGUUUAUCGCCAGGAUGG
(((((((((((((((((((......)))))))))))))...........(((.....((((((((...((((((.................))))))..))))))))...))).)))))) ( -44.53, z-score =  -6.27, R)
>droSec1.super_21 56978 120 - 1102487
CCAUUCGGCCCUAUCAUUUGAUCAAAAGUGGUAGGGUCAUUAUACUAACGGCCAAACAAGCUAAAGCACUCACUCAAAAAUGCAAUAAAAAUGUGGGCAUUCAGUUUAUCGCCAGGAUGG
(((((((((((((((((((......)))))))))))))...........(((.((((..((....)).(((((...................)))))......))))...))).)))))) ( -38.11, z-score =  -4.52, R)
>droEre2.scaffold_4690 4194725 120 + 18748788
CCAUUCGACCCUUUGAUUUGAUCAAAAGUGGCAGGGUCAUUAUGCUAACGGCCAAUCAAGUGGAUGCACUUACUCAAAAGGGCAAGGAGAAGGUGGGCAUUCAGUUUGUGGCCAUGAUGG
(((((.((((((.(.((((......)))).).))))))...........(((((...((.(((((((((((.(((...........))).))))..))))))).))..)))))..))))) ( -40.00, z-score =  -1.96, R)
>droYak2.chrX 6575873 120 - 21770863
CCACUCGACCCCAUGAUUUGAUCAAAAGUGGUAGGGUCAUUAUGCUAACCGCGAAUCAAGUGGAUGCAUUCACUCAAAGGGGCACGCAGAAUGUGCGCAUUCAGUUUGUGGCCAUGAUGG
((....(((((.((.((((......)))).)).)))))((((((....((((((((....(((((((.....((.....))(((((.....)))))))))))))))))))).)))))))) ( -38.80, z-score =  -1.33, R)
>droAna3.scaffold_13335 2282168 120 + 3335858
CCCGACGCCCUCUGAAGCUUCUGAGGAGCGGGCGUGCCAUUAUCCUGACCGCCGAUCAGGUGGAGGGGCUGACCCAGAACGGCAUGGAGAUGGUGGGCAUCCAGAUCUCCGUCAAGAUGG
.(((.(((((((.((....)).)))).)))((((((((..........(((((.....))))).(((.....))).....)))))((((((..(((....))).)))))))))....))) ( -48.10, z-score =  -0.41, R)
>consensus
CCAUUCGACCCUAUCAUUUGAUCAAAAGUGGUAGGGUCAUUAUGCUAACGGCCAAUCAAGUGGAUGCACUCACUCAAAAAGGCAAGGAAAAGGUGGGCAUUCAGUUUAUCGCCAGGAUGG
(((((.((((((((.((((......)))).))))))))............(((......((....))...(((...................)))))).................))))) (-15.75 = -16.98 +   1.23)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,300,632 – 12,300,752
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.39
Shannon entropy 0.43197
G+C content 0.43889
Mean single sequence MFE -31.87
Consensus MFE -15.59
Energy contribution -16.45
Covariance contribution 0.86
Combinations/Pair 1.36
Mean z-score -1.95
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.763498
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12300632 120 - 22422827
ACGAUAUCCUAUACCGGAAAACCAUUUGAUAUUAAGAAGUCCAUUCGACCCUAUCAUUUGAUCAAAAGUGGUAGGGUCCUUAUGCUAACGGCCAAUCAAGUUAAUGCACUUACUCAAAAA
......(((......)))......(((((...((((..........(((((((((((((......)))))))))))))....(((((((..........))))..))))))).))))).. ( -28.60, z-score =  -2.61, R)
>droSim1.chrX 9459363 120 - 17042790
ACGAUAUCCUAUACUGGAAAACCCUUUGAUAUUAAGCAGUCCAUUCGACCCUAUCAUUUGAUCAAAAGUGGUAGGGUCAUUAUACUAACGGCCAAACAAGCUGAAGCACUCACUCAAAAA
......(((......)))......(((((......((.........(((((((((((((......)))))))))))))..........((((.......))))..))......))))).. ( -31.00, z-score =  -3.47, R)
>droSec1.super_21 57018 120 - 1102487
ACGAUAUCCUAUACUGGAAAACCCUUUGAUAUUAAGCAGUCCAUUCGGCCCUAUCAUUUGAUCAAAAGUGGUAGGGUCAUUAUACUAACGGCCAAACAAGCUAAAGCACUCACUCAAAAA
......(((......)))......(((((......((.........(((((((((((((......)))))))))))))...........(((.......)))...))......))))).. ( -27.90, z-score =  -2.38, R)
>droEre2.scaffold_4690 4194765 120 + 18748788
ACAAUAUCCUAUACCGGAAGUGCCUACGAUAUUAAGAGGUCCAUUCGACCCUUUGAUUUGAUCAAAAGUGGCAGGGUCAUUAUGCUAACGGCCAAUCAAGUGGAUGCACUUACUCAAAAG
......(((......)))(((((((.(........)))(((((((.((((((.(.((((......)))).).)))))).....((.....))......)))))))))))).......... ( -27.50, z-score =  -0.54, R)
>droYak2.chrX 6575913 120 - 21770863
ACGAUAUCCUAUACCGGAAGUCCCUACGAUAUUAAGAAGUCCACUCGACCCCAUGAUUUGAUCAAAAGUGGUAGGGUCAUUAUGCUAACCGCGAAUCAAGUGGAUGCAUUCACUCAAAGG
..(((.(((......))).)))(((..((.........(((((((.(((((.((.((((......)))).)).)))))....(((.....))).....)))))))........))..))) ( -29.53, z-score =  -1.12, R)
>droAna3.scaffold_13335 2282208 120 + 3335858
AUCAUCUCCUACACGGGACAGGGCUACGAUUUGCGGAACACCCGACGCCCUCUGAAGCUUCUGAGGAGCGGGCGUGCCAUUAUCCUGACCGCCGAUCAGGUGGAGGGGCUGACCCAGAAC
.(((.(((((...(((((...(((.(((.....(((.....))).(((((((.((....)).)))).)))..))))))....))))).(((((.....)))))))))).)))........ ( -46.70, z-score =  -1.55, R)
>consensus
ACGAUAUCCUAUACCGGAAAACCCUACGAUAUUAAGAAGUCCAUUCGACCCUAUCAUUUGAUCAAAAGUGGUAGGGUCAUUAUGCUAACGGCCAAUCAAGUGGAUGCACUCACUCAAAAA
......(((......)))............................((((((((.((((......)))).))))))))....(((...((((.......))))..)))............ (-15.59 = -16.45 +   0.86)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,300,672 – 12,300,789
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.67
Shannon entropy 0.50068
G+C content 0.47664
Mean single sequence MFE -39.32
Consensus MFE -16.84
Energy contribution -17.90
Covariance contribution 1.06
Combinations/Pair 1.36
Mean z-score -2.37
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.57
SVM RNA-class probability 0.950870
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12300672 117 - 22422827
GACCUUGUGGUCAACGGGUGGCGAUGUCCC---CAAAAGUACGAUAUCCUAUACCGGAAAACCAUUUGAUAUUAAGAAGUCCAUUCGACCCUAUCAUUUGAUCAAAAGUGGUAGGGUCCU
((((....))))..(((((((.((((((..---.........)))))))))).)))...................(((.....)))(((((((((((((......))))))))))))).. ( -38.10, z-score =  -2.79, R)
>droSim1.chrX 9459403 117 - 17042790
GACUUUGUGGUCAACGGGUGGCGAUUAUCC---CAUAAGUACGAUAUCCUAUACUGGAAAACCCUUUGAUAUUAAGCAGUCCAUUCGACCCUAUCAUUUGAUCAAAAGUGGUAGGGUCAU
((((((...(((((.((((((.(.....))---)............(((......)))..)))).)))))....)).)))).....(((((((((((((......))))))))))))).. ( -38.50, z-score =  -3.31, R)
>droSec1.super_21 57058 117 - 1102487
GACUUUGUGGUCAACGGGUGGCGAUUCUCC---CAAAAGUACGAUAUCCUAUACUGGAAAACCCUUUGAUAUUAAGCAGUCCAUUCGGCCCUAUCAUUUGAUCAAAAGUGGUAGGGUCAU
((((((...(((((.((((((.(.....))---)............(((......)))..)))).)))))....)).)))).....(((((((((((((......))))))))))))).. ( -37.90, z-score =  -2.86, R)
>droEre2.scaffold_4690 4194805 117 + 18748788
GACCUUGUGGCCAAAGGCAGGCAAAUCCAC---CGGUAGUACAAUAUCCUAUACCGGAAGUGCCUACGAUAUUAAGAGGUCCAUUCGACCCUUUGAUUUGAUCAAAAGUGGCAGGGUCAU
((((((((.((...(((((((.....)).(---(((((.............))))))...))))).(((.((((((.((((.....)))).))))))))).......)).)))))))).. ( -40.42, z-score =  -3.21, R)
>droYak2.chrX 6575953 120 - 21770863
GACUUUGUGGCCAAAGGCUAGCAAUUCGCCUGGUGGUAGUACGAUAUCCUAUACCGGAAGUCCCUACGAUAUUAAGAAGUCCACUCGACCCCAUGAUUUGAUCAAAAGUGGUAGGGUCAU
((((((...((((.((((.........))))..)))).(((.(((.(((......))).)))..)))........)))))).....(((((.((.((((......)))).)).))))).. ( -34.70, z-score =  -1.29, R)
>droAna3.scaffold_13335 2282248 117 + 3335858
CAGCAUGUGGUCCUUGGAGGGCGACAGGCC---CGAGUGCAUCAUCUCCUACACGGGACAGGGCUACGAUUUGCGGAACACCCGACGCCCUCUGAAGCUUCUGAGGAGCGGGCGUGCCAU
..((((...(((((..(((((((...((((---(((.....))...((((....))))..)))))........(((.....))).)))))))..).((((.....))))))))))))... ( -46.30, z-score =  -0.73, R)
>consensus
GACCUUGUGGUCAACGGGUGGCGAUUCCCC___CAAAAGUACGAUAUCCUAUACCGGAAAACCCUACGAUAUUAAGAAGUCCAUUCGACCCUAUCAUUUGAUCAAAAGUGGUAGGGUCAU
((((..((.((((.....)))).)).....................(((......)))...................)))).....((((((((.((((......)))).)))))))).. (-16.84 = -17.90 +   1.06)

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 01:37:11 2011