Locus 2448

Sequence ID dm3.chr2L
Location 19,143,153 – 19,143,263
Length 110
Max. P 0.545232
window3368 window3369

overview

Window 8

Location 19,143,153 – 19,143,263
Length 110
Sequences 8
Columns 115
Reading direction forward
Mean pairwise identity 65.74
Shannon entropy 0.67785
G+C content 0.47516
Mean single sequence MFE -29.33
Consensus MFE -13.38
Energy contribution -12.67
Covariance contribution -0.70
Combinations/Pair 1.43
Mean z-score -0.68
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.545232
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19143153 110 + 23011544
CAAAGGCCCCUGGGAGAAUGAGAGGUCGCCUCUUUGCCAGGUUCAGUUCAAAGAACUUCCCACAUCUGAUUAAAGAAAUA-----AUCAAGGGGUGUGCGAAUUAUGCUGAGGGG
......(((((.((...((((...((((((((((((..((((((........))))))..)).....(((((......))-----))))))))))).))...)))).)).))))) ( -31.40, z-score =  -0.23, R)
>droSim1.chr2L 18840032 109 + 22036055
CAAAGGCCCCUGGGAGAAUGAGAGGUCGC-UCUUUGCCAGGUUCAGUUCAAAGAACUUCCCACAUCUGAUUAAAGAAAUA-----AUCAAGGGGCGUGCGAAUUAUGCUGAGGGG
......(((((.((...((((....((((-....((((.((...(((((...)))))..)).....((((((......))-----))))...)))).)))).)))).)).))))) ( -32.40, z-score =  -0.65, R)
>droSec1.super_7 2772681 109 + 3727775
CAAAGGCCCCUGGGAGAAUGAGAGGUCGU-UCUUUGCCAGGUUCAGUUCAAAGAACUUCCCACAUCUGAUUAAAGAAAUA-----AUCAAGGGGUGUGCGAAUUAUGCUGAGGGG
......(((((.(((((((((....))))-)))))..(((((((........))))(((.((((((((((((......))-----)))...))))))).))).....)))))))) ( -32.20, z-score =  -0.94, R)
>droYak2.chr2R 5658184 99 + 21139217
CAAAGGCCCCUGGGAGAAUG----------------CUGAGCUCAGUUCAAAGAACUUCCCACAUCUGAUUAAAGAAAUUUGUACAUCUGGGGGUGUGCGAAUCAUGUUUAGGGG
......((((((((((....----------------.(((((...)))))......)))))((((((......))).(((((((((((....)))))))))))..)))..))))) ( -29.30, z-score =  -1.02, R)
>droEre2.scaffold_4845 17459223 108 - 22589142
CAAAGGCCCCUGGGAGAAUGAGAGGUCGC-UCUUUGCUGAGUUCAGUUCAAAGAACUUCCCACAUCUGAUUAAAGAAAUA-----AUCUGGGG-UGUGCGAAUCAUGUUGAGGGG
......(((((.((...((((....((((-(((((((((....)))..))))))((.(((((.....(((((......))-----))))))))-.)))))).)))).)).))))) ( -33.70, z-score =  -1.29, R)
>droAna3.scaffold_12916 10896218 94 - 16180835
CAAUGCCCUCCGGGAGAAGGAGGAGAACU--UGAACUCGAACUCGGUUCAAAGAACUUCCCACAUCUGAUUAAAGAAAAAA----AUCAAGGGGUGUGCG---------------
....(((((((..((...((.((((..((--(((((.((....)))))).)))..))))))...(((......))).....----.))..)))).).)).--------------- ( -24.50, z-score =  -0.74, R)
>dp4.chr4_group4 224740 101 - 6586962
----GACUCUCAGGGGAGCAAGCGGUUG---------CAGGCCCAGUUAAAAUAACUUCC-AGAUCUCAUUGGGGAAAUAAUAAGAAUGGCGUGCGAAUUGAGAACGCUGGAGAG
----..(((((((.(...(((....(((---------((.(((.(((((...)))))(((-((......)))))..............))).))))).)))....).)).))))) ( -26.30, z-score =  -0.45, R)
>droPer1.super_16 530629 101 + 1990440
----GACUCUCAGGGGAGCAAGCGGUUG---------CAGGCCCAGUUAAAAUAACUUCC-AGAUCUCAUUGGGGAAAUAAUAAGAAUGGUGUGCGAAUUGAGAACGCUGGAGAG
----..(((((((.(...(((....(((---------((.(((.(((((...)))))(((-((......)))))..............))).))))).)))....).)).))))) ( -24.80, z-score =  -0.11, R)
>consensus
CAAAGGCCCCUGGGAGAAUGAGAGGUCG___CUUUGCCAGGCUCAGUUCAAAGAACUUCCCACAUCUGAUUAAAGAAAUA_____AUCAAGGGGUGUGCGAAUUAUGCUGAGGGG
......(((((((((((((.....................))))(((((...)))))))))...(((......)))..................................))))) (-13.38 = -12.67 +  -0.70)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,143,153 – 19,143,263
Length 110
Sequences 8
Columns 115
Reading direction reverse
Mean pairwise identity 65.74
Shannon entropy 0.67785
G+C content 0.47516
Mean single sequence MFE -25.73
Consensus MFE -9.56
Energy contribution -8.82
Covariance contribution -0.73
Combinations/Pair 1.47
Mean z-score -1.15
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.524009
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19143153 110 - 23011544
CCCCUCAGCAUAAUUCGCACACCCCUUGAU-----UAUUUCUUUAAUCAGAUGUGGGAAGUUCUUUGAACUGAACCUGGCAAAGAGGCGACCUCUCAUUCUCCCAGGGGCCUUUG
(((((..((....(((.((((....(((((-----((......))))))).)))).)))((((........))))...))..(((((...))))).........)))))...... ( -28.50, z-score =  -0.80, R)
>droSim1.chr2L 18840032 109 - 22036055
CCCCUCAGCAUAAUUCGCACGCCCCUUGAU-----UAUUUCUUUAAUCAGAUGUGGGAAGUUCUUUGAACUGAACCUGGCAAAGA-GCGACCUCUCAUUCUCCCAGGGGCCUUUG
.......((.......))..((((((((((-----((......)))))))...(((((.((((((((............))))))-))((....))....))))))))))..... ( -31.00, z-score =  -1.79, R)
>droSec1.super_7 2772681 109 - 3727775
CCCCUCAGCAUAAUUCGCACACCCCUUGAU-----UAUUUCUUUAAUCAGAUGUGGGAAGUUCUUUGAACUGAACCUGGCAAAGA-ACGACCUCUCAUUCUCCCAGGGGCCUUUG
.......((.......))...(((((((((-----((......)))))))...(((((.((((((((............))))))-))((....))....)))))))))...... ( -27.40, z-score =  -1.39, R)
>droYak2.chr2R 5658184 99 - 21139217
CCCCUAAACAUGAUUCGCACACCCCCAGAUGUACAAAUUUCUUUAAUCAGAUGUGGGAAGUUCUUUGAACUGAGCUCAG----------------CAUUCUCCCAGGGGCCUUUG
(((((......((...((...(((.((..((...(((....)))...))..)).))).(((((........)))))..)----------------)..))....)))))...... ( -19.70, z-score =   0.44, R)
>droEre2.scaffold_4845 17459223 108 + 22589142
CCCCUCAACAUGAUUCGCACA-CCCCAGAU-----UAUUUCUUUAAUCAGAUGUGGGAAGUUCUUUGAACUGAACUCAGCAAAGA-GCGACCUCUCAUUCUCCCAGGGGCCUUUG
(((((....(((((((.((((-.(...(((-----((......))))).).)))).)))((((((((..(((....)))))))))-))......))))......)))))...... ( -29.60, z-score =  -2.08, R)
>droAna3.scaffold_12916 10896218 94 + 16180835
---------------CGCACACCCCUUGAU----UUUUUUCUUUAAUCAGAUGUGGGAAGUUCUUUGAACCGAGUUCGAGUUCA--AGUUCUCCUCCUUCUCCCGGAGGGCAUUG
---------------.((...(((((((((----(.........))))))..).)))......(((((((((....)).)))))--))....(((((.......))))))).... ( -23.70, z-score =  -0.67, R)
>dp4.chr4_group4 224740 101 + 6586962
CUCUCCAGCGUUCUCAAUUCGCACGCCAUUCUUAUUAUUUCCCCAAUGAGAUCU-GGAAGUUAUUUUAACUGGGCCUG---------CAACCGCUUGCUCCCCUGAGAGUC----
(((((..(((.........)))...(((.(((((((........)))))))..)-)).(((((...)))))(((...(---------(((....))))..))).)))))..---- ( -22.80, z-score =  -1.21, R)
>droPer1.super_16 530629 101 - 1990440
CUCUCCAGCGUUCUCAAUUCGCACACCAUUCUUAUUAUUUCCCCAAUGAGAUCU-GGAAGUUAUUUUAACUGGGCCUG---------CAACCGCUUGCUCCCCUGAGAGUC----
(((((..(((.........)))...(((.(((((((........)))))))..)-)).(((((...)))))(((...(---------(((....))))..))).)))))..---- ( -23.10, z-score =  -1.69, R)
>consensus
CCCCUCAGCAUAAUUCGCACACCCCCUGAU_____UAUUUCUUUAAUCAGAUGUGGGAAGUUCUUUGAACUGAACCUGGCAAAG___CGACCUCUCAUUCUCCCAGGGGCCUUUG
(((((..................................(((......)))..((((.(((((...)))))...))))..........................)))))...... ( -9.56 =  -8.82 +  -0.73)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:51:25 2011