Locus 1416

Sequence ID dm3.chr2L
Location 11,069,428 – 11,069,521
Length 93
Max. P 0.935601
window1930 window1931

overview

Window 0

Location 11,069,428 – 11,069,521
Length 93
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 87.72
Shannon entropy 0.19830
G+C content 0.57508
Mean single sequence MFE -34.80
Consensus MFE -30.77
Energy contribution -30.90
Covariance contribution 0.13
Combinations/Pair 1.08
Mean z-score -1.93
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.40
SVM RNA-class probability 0.935601
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11069428 93 + 23011544
AGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCAGAAAGGUGGGAGCGAGAAGGAGCUAAGCUGAGGAGAGGG----
..((((...(((((..((((((((.((.(((.....))).)).)).....((((......))))))))))...)))))..)))).........---- ( -33.50, z-score =  -1.88, R)
>droYak2.chr2L 7464792 96 + 22324452
AGCAGCAGAAGCUGCAUUUGCUGAGGUAGCUGAAGAAGCCGCGUCAGAAGCCCAGAA-GGUGGGAGCGAGAAGGGGCUGAGCUGCUGCGGGGAGAGG
.(((((((.((((.(.((((((((.(..(((.....)))..).)).....((((...-..))))))))))..).))))...)))))))......... ( -39.00, z-score =  -2.09, R)
>droSec1.super_3 6470908 97 + 7220098
AGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCAGAAAGGUGGGAGCGAGAAGGAGCUAUGCUGAGGGAGGGAGAAG
..(((((..(((((..((((((((.((.(((.....))).)).)).....((((......))))))))))...))))).)))))............. ( -36.10, z-score =  -2.72, R)
>droSim1.chr2L 10867677 93 + 22036055
AGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCAGAAAGGUGGGAGCGAGAAGGAGCUAGACUGAGGGGAGGG----
..(..(((.(((((..((((((((.((.(((.....))).)).)).....((((......))))))))))...)))))...)))..)......---- ( -30.60, z-score =  -1.04, R)
>consensus
AGCAGCAGAAGCUCAAUUCGCUGAGGUUGCUGAAGAAGCUGCGUCAGAAGCCCAGAAAGGUGGGAGCGAGAAGGAGCUAAGCUGAGGGGAGGA____
..((((...(((((..((((((((.((.(((.....))).)).)).....((((......))))))))))...)))))..))))............. (-30.77 = -30.90 +   0.13)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,069,428 – 11,069,521
Length 93
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 87.72
Shannon entropy 0.19830
G+C content 0.57508
Mean single sequence MFE -24.80
Consensus MFE -21.46
Energy contribution -22.02
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -1.28
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.596630
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11069428 93 - 23011544
----CCCUCUCCUCAGCUUAGCUCCUUCUCGCUCCCACCUUUCUGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCU
----.........((((..(((((....((((.((((......))))....(((.(..(((.....)))..).)))))))...)))))...)))).. ( -24.80, z-score =  -1.47, R)
>droYak2.chr2L 7464792 96 - 22324452
CCUCUCCCCGCAGCAGCUCAGCCCCUUCUCGCUCCCACC-UUCUGGGCUUCUGACGCGGCUUCUUCAGCUACCUCAGCAAAUGCAGCUUCUGCUGCU
.........(((((((...(((...........((((..-...))))...((((.(..(((.....)))..).))))........))).))))))). ( -26.60, z-score =  -0.92, R)
>droSec1.super_3 6470908 97 - 7220098
CUUCUCCCUCCCUCAGCAUAGCUCCUUCUCGCUCCCACCUUUCUGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCU
.............(((((.(((((....((((.((((......))))....(((.(..(((.....)))..).)))))))...)))))..))))).. ( -25.30, z-score =  -1.80, R)
>droSim1.chr2L 10867677 93 - 22036055
----CCCUCCCCUCAGUCUAGCUCCUUCUCGCUCCCACCUUUCUGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCU
----.........((((..(((((....((((.((((......))))....(((.(..(((.....)))..).)))))))...)))))...)))).. ( -22.50, z-score =  -0.93, R)
>consensus
____CCCCCCCCUCAGCUUAGCUCCUUCUCGCUCCCACCUUUCUGGGCUUCUGACGCAGCUUCUUCAGCAACCUCAGCGAAUUGAGCUUCUGCUGCU
.............((((..(((((....((((.((((......))))....(((.(..(((.....)))..).)))))))...)))))...)))).. (-21.46 = -22.02 +   0.56)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:31:30 2011