Locus 15272

Sequence ID dm3.chrX
Location 18,207,763 – 18,207,904
Length 141
Max. P 0.842486
window21038 window21039

overview

Window 8

Location 18,207,763 – 18,207,871
Length 108
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 88.87
Shannon entropy 0.18151
G+C content 0.47760
Mean single sequence MFE -34.15
Consensus MFE -26.29
Energy contribution -27.60
Covariance contribution 1.31
Combinations/Pair 1.14
Mean z-score -1.76
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.542490
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18207763 108 + 22422827
CAAAAACGGAAUCUCGCGCAUACUUCCCCAGUAUUUCCGAUUUGGGGGAGUGGUAAUUGGGUUGCCAACUUCAAGCAUUGGAGGUCAUAAACCCGCGAGUCCCCAAAA
.......((...(((((((.(((((((((((..........)))))))))))))....(((((....(((((........)))))....))))))))))...)).... ( -40.20, z-score =  -3.28, R)
>droSim1.chrX 14029488 107 + 17042790
CGAAAACGGAAUCUCGCGCAUAUUUCCCCAGUAUUUCCGAUUUGGGGGAGUGGUAAUUGGGUUGCCAACUUCAAGCAUUGGAGGUCAUAAACCCAAGAUUCCCCCAA-
.......((((((....((.(((((((((((..........)))))))))))))..(((((((....(((((........)))))....))))))))))))).....- ( -36.10, z-score =  -2.17, R)
>droYak2.chrX 16842239 104 + 21770863
CGAAAAUGGAAUCUCG--CAUAUUUCCCCAGUAUUUCCGAUUUGGGGGAGUGGUAACUGGGUUGCCAACCUGAAGCUUUGGCGUUCAUAAACCAUCGUUUCUCGAA--
(((...((((((((.(--..(((((((((((..........)))))))))))....).))))).)))....(((((..(((..........)))..))))))))..-- ( -28.10, z-score =  -0.43, R)
>droSec1.super_8 519793 108 + 3762037
CGAAAACGGAAUCUCGCGCAUAUUUCCCCAGUAUUUCCGAUUUGGGGGAGUGGUAAUUCGGUUGCCAACUUCAAGCAUUGGAGGUCAUAAACCCGCGAUUCCCUCAAA
.......((((..(((((..(((((((((((..........))))))))))).......((((....(((((........)))))....)))))))))))))...... ( -32.20, z-score =  -1.16, R)
>consensus
CGAAAACGGAAUCUCGCGCAUAUUUCCCCAGUAUUUCCGAUUUGGGGGAGUGGUAAUUGGGUUGCCAACUUCAAGCAUUGGAGGUCAUAAACCCGCGAUUCCCCAAA_
.......((((((.......(((((((((((..........))))))))))).....((((((....(((((........)))))....)))))).))))))...... (-26.29 = -27.60 +   1.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,207,803 – 18,207,904
Length 101
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 73.37
Shannon entropy 0.42910
G+C content 0.38281
Mean single sequence MFE -24.93
Consensus MFE -16.58
Energy contribution -17.57
Covariance contribution 1.00
Combinations/Pair 1.14
Mean z-score -1.46
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.88
SVM RNA-class probability 0.842486
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 18207803 101 + 22422827
UUUGGGGGAGUGGUAAUUGGGUUGCCAACUUCAAGCAUUGGAGGUCAUAAACCCGCGAGUCCCCAAAAAAAAAACAGUGAAAA-AUCAAAAAACCCUAAGUA-------
....(((((.(.((....(((((....(((((........)))))....))))))).).)))))...................-..................------- ( -24.00, z-score =  -0.42, R)
>droSim1.chrX 14029528 97 + 17042790
UUUGGGGGAGUGGUAAUUGGGUUGCCAACUUCAAGCAUUGGAGGUCAUAAACCCAAGAUUCCCCCAAAAAAA----GUGAAAA-AUCAAAAUAUUUAAAAUA-------
(((((((((((.....(((((((....(((((........)))))....))))))).)))))))))))....----.......-..................------- ( -30.70, z-score =  -3.27, R)
>droYak2.chrX 16842277 91 + 21770863
UUUGGGGGAGUGGUAACUGGGUUGCCAACCUGAAGCUUUGGCGUUCAUAAACCAUCGUUUCUCGAAUAUAAAUAAUAUAAUGGUAUUAAUA------------------
((((((..((((((...((..(.(((((.........))))))..))...)))))..)..))))))......((((((....))))))...------------------ ( -20.50, z-score =  -0.68, R)
>droSec1.super_8 519833 105 + 3762037
UUUGGGGGAGUGGUAAUUCGGUUGCCAACUUCAAGCAUUGGAGGUCAUAAACCCGCGAUUCCCUCAAAAAAAA---GUGAAAA-AUCAAAAAACCUAAUAUAUUAAGUG
(((((((((((.((.....((((....(((((........)))))....)))).)).))))))))))).....---.......-......................... ( -24.50, z-score =  -1.47, R)
>consensus
UUUGGGGGAGUGGUAAUUGGGUUGCCAACUUCAAGCAUUGGAGGUCAUAAACCCGCGAUUCCCCAAAAAAAAA___GUGAAAA_AUCAAAAAACCUAAAAUA_______
(((((((((.(((((((...))))))).(((((.....)))))................)))))))))......................................... (-16.58 = -17.57 +   1.00)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:56:11 2011