Locus 1487

Sequence ID dm3.chr2L
Location 11,487,561 – 11,487,695
Length 134
Max. P 0.993012
window2027 window2028 window2029 window2030

overview

Window 7

Location 11,487,561 – 11,487,667
Length 106
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 95.09
Shannon entropy 0.08614
G+C content 0.50082
Mean single sequence MFE -40.60
Consensus MFE -34.64
Energy contribution -34.52
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -2.74
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.78
SVM RNA-class probability 0.967141
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11487561 106 + 23011544
CAAAGUGGGUGGUGGCCAAAGGGUGAACC-----ACCCAAGCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUUGCGGGAAUUUGUUUUUGCGUCGCU
.....((((((((.(((....)))..)))-----)))))(((((((....))))(((((...((((..((.(((((.......))))).))...)))).....)))))))) ( -41.40, z-score =  -3.36, R)
>droSim1.chr2L 11301884 106 + 22036055
CAUAGUGGGUGGUGGCCAAAGGGUGACCC-----ACCCAAGCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUUGCGGGAAUUUGUUUUUGCGUCGCU
.....((((((((.(((....))).).))-----)))))(((((((....))))(((((...((((..((.(((((.......))))).))...)))).....)))))))) ( -40.30, z-score =  -2.90, R)
>droSec1.super_3 6882610 106 + 7220098
CAAAGUGGGUGGUGGCCAAAGGGUGACCC-----ACCCAAGCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUUGCGGGAAUUUGUUUUUGCGUCGCU
.....((((((((.(((....))).).))-----)))))(((((((....))))(((((...((((..((.(((((.......))))).))...)))).....)))))))) ( -40.30, z-score =  -2.79, R)
>droYak2.chr2L 7893942 111 + 22324452
GAAAGUGGGUGGUGGCCAAAGGGUGACCCGAGCCACCCAAGCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUUGCGGGAAUUUGUUUUUGCGUCGCU
.....((((((((.......((....))...))))))))(((((((....))))(((((...((((..((.(((((.......))))).))...)))).....)))))))) ( -41.40, z-score =  -2.36, R)
>droEre2.scaffold_4929 12695257 106 - 26641161
GUGGGUGGGUGGUGGUUAAAGGGUGACCC-----ACCCAAGCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUUGCGGGAAUUUGUUUUUGCGUCGCU
.(((((((((.(...........).))))-----)))))(((((((....))))(((((...((((..((.(((((.......))))).))...)))).....)))))))) ( -39.60, z-score =  -2.28, R)
>consensus
CAAAGUGGGUGGUGGCCAAAGGGUGACCC_____ACCCAAGCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUUGCGGGAAUUUGUUUUUGCGUCGCU
.....((((((((.(((....))).)))......)))))(((((((....))))(((((...((((..((.(((((.......))))).))...)))).....)))))))) (-34.64 = -34.52 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,487,561 – 11,487,667
Length 106
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 95.09
Shannon entropy 0.08614
G+C content 0.50082
Mean single sequence MFE -40.29
Consensus MFE -34.98
Energy contribution -35.22
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -3.30
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.58
SVM RNA-class probability 0.993012
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11487561 106 - 23011544
AGCGACGCAAAAACAAAUUCCCGCAAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGCUUGGGU-----GGUUCACCCUUUGGCCACCACCCACUUUG
((((((((.....(((((..((((((((.......)))))))).)))))...))))).(((....))).)))(((((-----(((...((....))..))))))))..... ( -39.20, z-score =  -3.35, R)
>droSim1.chr2L 11301884 106 - 22036055
AGCGACGCAAAAACAAAUUCCCGCAAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGCUUGGGU-----GGGUCACCCUUUGGCCACCACCCACUAUG
((((((((.....(((((..((((((((.......)))))))).)))))...))))).(((....))).)))(((((-----((((((.....))))..)))))))..... ( -39.40, z-score =  -3.01, R)
>droSec1.super_3 6882610 106 - 7220098
AGCGACGCAAAAACAAAUUCCCGCAAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGCUUGGGU-----GGGUCACCCUUUGGCCACCACCCACUUUG
((((((((.....(((((..((((((((.......)))))))).)))))...))))).(((....))).)))(((((-----((((((.....))))..)))))))..... ( -39.40, z-score =  -2.92, R)
>droYak2.chr2L 7893942 111 - 22324452
AGCGACGCAAAAACAAAUUCCCGCAAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGCUUGGGUGGCUCGGGUCACCCUUUGGCCACCACCCACUUUC
((((((((.....(((((..((((((((.......)))))))).)))))...))))).(((....))).)))(((((((....(((((.....))))).)))))))..... ( -43.30, z-score =  -3.32, R)
>droEre2.scaffold_4929 12695257 106 + 26641161
AGCGACGCAAAAACAAAUUCCCGCAAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGCUUGGGU-----GGGUCACCCUUUAACCACCACCCACCCAC
((((((((.....(((((..((((((((.......)))))))).)))))...))))).(((....))).)))(((((-----((((...............))))))))). ( -40.16, z-score =  -3.89, R)
>consensus
AGCGACGCAAAAACAAAUUCCCGCAAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGCUUGGGU_____GGGUCACCCUUUGGCCACCACCCACUUUG
((((((((.....(((((..((((((((.......)))))))).)))))...))))).(((....))).)))(((((......(((((.....)))))...)))))..... (-34.98 = -35.22 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,487,596 – 11,487,695
Length 99
Sequences 7
Columns 109
Reading direction forward
Mean pairwise identity 73.22
Shannon entropy 0.50776
G+C content 0.43520
Mean single sequence MFE -24.67
Consensus MFE -8.59
Energy contribution -8.84
Covariance contribution 0.25
Combinations/Pair 1.25
Mean z-score -2.73
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.50
SVM RNA-class probability 0.944174
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11487596 99 + 23011544
GCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUU-GCGG-GAAUUUGUUUUUGCGUCGCUCACUUUUCUUGCUACUUCUUUUUCUUCU--------
((((((....))))(((((...((((..((.(((((.......))))-).))-...)))).....))))))).............................-------- ( -22.40, z-score =  -2.91, R)
>droSim1.chr2L 11301919 99 + 22036055
GCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUU-GCGG-GAAUUUGUUUUUGCGUCGCUCACUUUUCUUGCUGCUUCUUUUUCUUCU--------
(((((((....((.(((((...((((..((.(((((.......))))-).))-...)))).....))))))).........))))))).............-------- ( -27.12, z-score =  -3.91, R)
>droSec1.super_3 6882645 99 + 7220098
GCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUU-GCGG-GAAUUUGUUUUUGCGUCGCUCACUUUUCUUGCUGCUUCUUUUUCUUCU--------
(((((((....((.(((((...((((..((.(((((.......))))-).))-...)))).....))))))).........))))))).............-------- ( -27.12, z-score =  -3.91, R)
>droYak2.chr2L 7893982 96 + 22324452
GCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUU-GCGG-GAAUUUGUUUUUGCGUCGCUCACUUUUCUUGCUGCUUCUUCUUUU-----------
(((((((....((.(((((...((((..((.(((((.......))))-).))-...)))).....))))))).........)))))))..........----------- ( -27.12, z-score =  -3.76, R)
>droEre2.scaffold_4929 12695292 102 - 26641161
GCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUU-GCGG-GAAUUUGUUUUUGCGUCGCUCACUUUUCUUGCUGCCUCUGCUUCUUCUUUU-----
(((((((....((.(((((...((((..((.(((((.......))))-).))-...)))).....))))))).........)))))))................----- ( -26.72, z-score =  -2.99, R)
>droAna3.scaffold_12916 12187683 98 - 16180835
---------GGGGCAACAUUG-CUGGUGCCACAAGCACAUUUAGUUU-GCGGGGAACUUGUUGUUGCCUCGCUCAGAUCCGCCACUUUCCUUAAAAUGUGUUAUUUUCC
---------(((((((((..(-(.(((.((.(((((.......))))-).))...))).)))))))))))((........))(((............)))......... ( -25.10, z-score =  -0.06, R)
>droWil1.scaffold_181038 383564 78 - 637489
--------------GACGCUAUCAAACGCCACAAACACAUUUAGUUUUGCGGCGAAUUUGUUUUUGCAGCGUUGGCCUUUUCCUCUAUCCUU-----------------
--------------((((((......((((.((((.((.....)))))).)))).....((....))))))))...................----------------- ( -17.10, z-score =  -1.52, R)
>consensus
GCGGCAACAUUGCUGACGCUAUCAAACACCACAAACACAUUUAGUUU_GCGG_GAAUUUGUUUUUGCGUCGCUCACUUUUCUUGCUGCUUCUUUUUCUUCU________
..............(((((...((((..((.(((((.......)))).).))....)))).....)))))....................................... ( -8.59 =  -8.84 +   0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,487,596 – 11,487,695
Length 99
Sequences 7
Columns 109
Reading direction reverse
Mean pairwise identity 73.22
Shannon entropy 0.50776
G+C content 0.43520
Mean single sequence MFE -26.77
Consensus MFE -13.38
Energy contribution -13.53
Covariance contribution 0.15
Combinations/Pair 1.28
Mean z-score -2.26
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.03
SVM RNA-class probability 0.979713
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11487596 99 - 23011544
--------AGAAGAAAAAGAAGUAGCAAGAAAAGUGAGCGACGCAAAAACAAAUUC-CCGC-AAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGC
--------.............((((((......(....)(((((.....(((((..-((((-((((.......)))))))).)))))...))))).....))))))... ( -25.50, z-score =  -2.39, R)
>droSim1.chr2L 11301919 99 - 22036055
--------AGAAGAAAAAGAAGCAGCAAGAAAAGUGAGCGACGCAAAAACAAAUUC-CCGC-AAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGC
--------.............((((((......(....)(((((.....(((((..-((((-((((.......)))))))).)))))...))))).....))))))... ( -27.50, z-score =  -2.60, R)
>droSec1.super_3 6882645 99 - 7220098
--------AGAAGAAAAAGAAGCAGCAAGAAAAGUGAGCGACGCAAAAACAAAUUC-CCGC-AAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGC
--------.............((((((......(....)(((((.....(((((..-((((-((((.......)))))))).)))))...))))).....))))))... ( -27.50, z-score =  -2.60, R)
>droYak2.chr2L 7893982 96 - 22324452
-----------AAAAGAAGAAGCAGCAAGAAAAGUGAGCGACGCAAAAACAAAUUC-CCGC-AAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGC
-----------..........((((((......(....)(((((.....(((((..-((((-((((.......)))))))).)))))...))))).....))))))... ( -27.50, z-score =  -2.57, R)
>droEre2.scaffold_4929 12695292 102 + 26641161
-----AAAAGAAGAAGCAGAGGCAGCAAGAAAAGUGAGCGACGCAAAAACAAAUUC-CCGC-AAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGC
-----...............(((((((......(....)(((((.....(((((..-((((-((((.......)))))))).)))))...))))).....))))))).. ( -31.70, z-score =  -3.16, R)
>droAna3.scaffold_12916 12187683 98 + 16180835
GGAAAAUAACACAUUUUAAGGAAAGUGGCGGAUCUGAGCGAGGCAACAACAAGUUCCCCGC-AAACUAAAUGUGCUUGUGGCACCAG-CAAUGUUGCCCC---------
((...(((((((((((..((....((((.(((.((......(....)....)).)))))))-...))))))))).))))((((.((.-...)).))))))--------- ( -25.60, z-score =  -0.52, R)
>droWil1.scaffold_181038 383564 78 + 637489
-----------------AAGGAUAGAGGAAAAGGCCAACGCUGCAAAAACAAAUUCGCCGCAAAACUAAAUGUGUUUGUGGCGUUUGAUAGCGUC--------------
-----------------.........((......)).((((((((((........(((((((((((.....)).))))))))))))).)))))).-------------- ( -22.10, z-score =  -2.01, R)
>consensus
________AGAAGAAAAAGAAGCAGCAAGAAAAGUGAGCGACGCAAAAACAAAUUC_CCGC_AAACUAAAUGUGUUUGUGGUGUUUGAUAGCGUCAGCAAUGUUGCCGC
.......................................(((((.....(((((...((((.((((.......)))))))).)))))...))))).............. (-13.38 = -13.53 +   0.15)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:32:52 2011