Locus 1507

Sequence ID dm3.chr2L
Location 11,679,650 – 11,679,781
Length 131
Max. P 0.670248
window2058 window2059

overview

Window 8

Location 11,679,650 – 11,679,781
Length 131
Sequences 6
Columns 142
Reading direction forward
Mean pairwise identity 83.37
Shannon entropy 0.30860
G+C content 0.47128
Mean single sequence MFE -36.85
Consensus MFE -19.99
Energy contribution -21.77
Covariance contribution 1.78
Combinations/Pair 1.10
Mean z-score -2.25
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.39
SVM RNA-class probability 0.670248
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11679650 131 + 23011544
CAUUUUGGCAUUGGCCAAAAUCAAACACAUUUAACAAGUCAUUUAAAAC-GCACCCAGCCACCCACUUG-GCCAUCAAUCCCCAUUGGGAUAGAGUCCCCAAGAGGA---------UCACCCAUUUGCCAGGCCAAAAUGGA
(((((((((.(((((..................................-((.....))...((.((((-(...((.(((((....))))).))....))))).)).---------..........)))))))))))))).. ( -37.30, z-score =  -2.81, R)
>droSim1.chr2L 11489117 131 + 22036055
CAUUUUGGCAUUGGCCAAAAUCAAACACAUUUAACAAGUCAUUUAAAAC-GCACCCCGCCGCCCACUUG-GCCAUCAAUCCCCAUUGGGAUAGAGUCCCCAAGAGGA---------UCACCCAGUUGCCAGGCCAAAAUGGA
(((((((((.(((((..................................-((.....))...((.((((-(...((.(((((....))))).))....))))).)).---------..........)))))))))))))).. ( -37.30, z-score =  -2.22, R)
>droSec1.super_3 7071585 131 + 7220098
CAUUUUGGCAUUGGCCAAAAUCAAACACAUUUAACAAGUCAUUUAAAUC-GCACCCUGCCGCCCACUUG-GCCAUCAAUCCCCAUUGGGAUAGAGUCCCCAAGAGGA---------UCACCCAGUUGCCAGGCCAAAAUGGA
(((((((((.(((((..................................-((.....))...((.((((-(...((.(((((....))))).))....))))).)).---------..........)))))))))))))).. ( -37.60, z-score =  -2.00, R)
>droYak2.chr2L 8102470 131 + 22324452
CAUUUUGGCAUUGGCCAAAAUCAAACACAUUUAACAAGUCAUUUAAAAC-GCACCCAGCCGCCCACUUG-GCCAUCAAUCCCCAUUGGGAUAGCGUUCCCAAGAGGA---------UCACCCGGUUCCCAGGCCAAAAUGGA
(((((((((..(((((((...........(((((........)))))..-((.....)).......)))-))))...((((...((((((......))))))..)))---------)..............))))))))).. ( -36.40, z-score =  -1.76, R)
>droEre2.scaffold_4929 12910569 131 - 26641161
CAUUCUGGCAUUGGCCAAAAUCAAACACAUUUAACAAGUCAUUUAAAAC-GCACCCAGCCGCCCACUUG-GCCAUCAAUCCCCAUUGGGAUAGAGUCGCCAAGAGGA---------UCACCCAGUUUCCAGGCCAAACUGGA
...((..(..((((((.................................-((.....))...((.((((-((..((.(((((....))))).))...)))))).)).---------..............)))))).)..)) ( -34.90, z-score =  -1.82, R)
>droAna3.scaffold_12916 9397040 142 - 16180835
CAAUUAAACUUUGGCCAAGAUCAAACACAAUUAACUAGUCAUUUGAAACUGAAAUCUACCGCCCCUUUGAGCCAUCAAUUUUGGAAAAGGACUUUCCCCAAAGAAGAGGCGGUAGCCUCUCCAGACUACUGGCCAAAAUAGU
.........((((((((...(((((.((.........))..)))))..(((....(((((((((((((...(((.......))).))))).((((.......)))).))))))))......))).....))))))))..... ( -37.60, z-score =  -2.93, R)
>consensus
CAUUUUGGCAUUGGCCAAAAUCAAACACAUUUAACAAGUCAUUUAAAAC_GCACCCAGCCGCCCACUUG_GCCAUCAAUCCCCAUUGGGAUAGAGUCCCCAAGAGGA_________UCACCCAGUUGCCAGGCCAAAAUGGA
(((((((((..(((((((...........(((((........)))))...((.....)).......))).))))......((..(((((........)))))..)).........................))))))))).. (-19.99 = -21.77 +   1.78)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,679,650 – 11,679,781
Length 131
Sequences 6
Columns 142
Reading direction reverse
Mean pairwise identity 83.37
Shannon entropy 0.30860
G+C content 0.47128
Mean single sequence MFE -46.14
Consensus MFE -27.74
Energy contribution -28.08
Covariance contribution 0.34
Combinations/Pair 1.27
Mean z-score -1.84
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.02
SVM RNA-class probability 0.505140
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11679650 131 - 23011544
UCCAUUUUGGCCUGGCAAAUGGGUGA---------UCCUCUUGGGGACUCUAUCCCAAUGGGGAUUGAUGGC-CAAGUGGGUGGCUGGGUGC-GUUUUAAAUGACUUGUUAAAUGUGUUUGAUUUUGGCCAAUGCCAAAAUG
..(((((((((.((((.....(((.(---------(((.(((((...(((.(((((....))))).)).).)-)))).)))).)))(((..(-((((.............)))))..))).......))))..))))))))) ( -45.82, z-score =  -1.87, R)
>droSim1.chr2L 11489117 131 - 22036055
UCCAUUUUGGCCUGGCAACUGGGUGA---------UCCUCUUGGGGACUCUAUCCCAAUGGGGAUUGAUGGC-CAAGUGGGCGGCGGGGUGC-GUUUUAAAUGACUUGUUAAAUGUGUUUGAUUUUGGCCAAUGCCAAAAUG
(((((((.((((.(....).....((---------(((((((((((......)))))).)))))))...)))-)))))))).((((((...(-((.....))).))))))...........((((((((....)))))))). ( -44.00, z-score =  -0.88, R)
>droSec1.super_3 7071585 131 - 7220098
UCCAUUUUGGCCUGGCAACUGGGUGA---------UCCUCUUGGGGACUCUAUCCCAAUGGGGAUUGAUGGC-CAAGUGGGCGGCAGGGUGC-GAUUUAAAUGACUUGUUAAAUGUGUUUGAUUUUGGCCAAUGCCAAAAUG
..((((((((((((....).))..((---------(((((((((((......)))))).)))))))..((((-(((.(..(((.((....((-((.((....)).))))....)))))..)...)))))))..))))))))) ( -44.10, z-score =  -0.98, R)
>droYak2.chr2L 8102470 131 - 22324452
UCCAUUUUGGCCUGGGAACCGGGUGA---------UCCUCUUGGGAACGCUAUCCCAAUGGGGAUUGAUGGC-CAAGUGGGCGGCUGGGUGC-GUUUUAAAUGACUUGUUAAAUGUGUUUGAUUUUGGCCAAUGCCAAAAUG
..(((((((((((((...))))..((---------(((((((((((......)))))).)))))))..((((-(((.(..(((((.....))-(((......)))..........)))..)...)))))))..))))))))) ( -46.80, z-score =  -1.73, R)
>droEre2.scaffold_4929 12910569 131 + 26641161
UCCAGUUUGGCCUGGAAACUGGGUGA---------UCCUCUUGGCGACUCUAUCCCAAUGGGGAUUGAUGGC-CAAGUGGGCGGCUGGGUGC-GUUUUAAAUGACUUGUUAAAUGUGUUUGAUUUUGGCCAAUGCCAGAAUG
.((((((..(((((....).))))(.---------(((.((((((.(.((.(((((....))))).))).))-)))).))))))))))(..(-((((.............)))))..)...((((((((....)))))))). ( -46.52, z-score =  -2.07, R)
>droAna3.scaffold_12916 9397040 142 + 16180835
ACUAUUUUGGCCAGUAGUCUGGAGAGGCUACCGCCUCUUCUUUGGGGAAAGUCCUUUUCCAAAAUUGAUGGCUCAAAGGGGCGGUAGAUUUCAGUUUCAAAUGACUAGUUAAUUGUGUUUGAUCUUGGCCAAAGUUUAAUUG
...(((((((((((....((((((...(((((((((((..(((((..((.....))..))))).((((....))))))))))))))).))))))..((((((.((.........))))))))..)))))))))))....... ( -49.60, z-score =  -3.49, R)
>consensus
UCCAUUUUGGCCUGGCAACUGGGUGA_________UCCUCUUGGGGACUCUAUCCCAAUGGGGAUUGAUGGC_CAAGUGGGCGGCUGGGUGC_GUUUUAAAUGACUUGUUAAAUGUGUUUGAUUUUGGCCAAUGCCAAAAUG
..(((((((((........................(((((((((((......)))))).)))))....((((.((((..(((.((.....)).)))((((((.((.........)))))))).))))))))..))))))))) (-27.74 = -28.08 +   0.34)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:33:17 2011