Locus 5904

Sequence ID dm3.chr3L
Location 2,346,258 – 2,346,350
Length 92
Max. P 0.997291
window8119 window8120

overview

Window 9

Location 2,346,258 – 2,346,350
Length 92
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 70.14
Shannon entropy 0.57537
G+C content 0.41863
Mean single sequence MFE -26.62
Consensus MFE -12.14
Energy contribution -12.95
Covariance contribution 0.81
Combinations/Pair 1.35
Mean z-score -2.72
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.07
SVM RNA-class probability 0.997291
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2346258 92 + 24543557
GUUAGCGGACCGCGUUCAGCGGAAAAUUCCCAGUAACUUU-----CUAGUGC-AAAAUUAAAAGAGGGAAAGCCAAGUUGAACGGGUUCACCAAGGAU
......(((((.((((((((((....(((((.....((((-----.((((..-...)))))))).)))))..))..)))))))))))))......... ( -26.80, z-score =  -2.29, R)
>droAna3.scaffold_13337 394404 84 + 23293914
---------CUACUUGAGGCUUUAACUUUU--ACAGCCUUUUAACAAAAAUUUGAUGCCACAGCUUACAGGACU---UUAAAAGGGUUCGCUUGGGAU
---------......((((((.((.....)--).))))))..............((.(((.(((.....(((((---(.....)))))))))))).)) ( -14.90, z-score =  -0.03, R)
>droEre2.scaffold_4784 2359928 91 + 25762168
GUUAGCAAACCGCGUUCAGCGGAAAAUUCCCAGUAACUUU-----CUA--GUUAAAAUUAAAAGAGAGCAAGCCAAGUUGAACGGGUUCGCUAAGGAU
.(((((.((((.(((((((((((....)))......((((-----((.--.(((....))).))))))........)))))))))))).))))).... ( -28.10, z-score =  -3.80, R)
>droYak2.chr3L 14606296 96 - 24197627
GUUAGCGAACCGCGUUCAGCGGAAAAUUCCCAGUAACUUUAAAAGUUACUUUUAAAAUUAAAAGAGAGAAAGCAAAGUUGAACGGGUUUCC--AGGAU
....(.(((((.(((((((((((....))).(((((((.....)))))))..........................))))))))))))).)--..... ( -25.30, z-score =  -2.95, R)
>droSec1.super_2 2371156 93 + 7591821
GUUAGCGGACCGCGUUCAGCGGAAAAUUCCCAUUAACUUU-----UUGAAGUUAAAAUUAAAAGGGCCAAAGCCAAGUUGAAUGGGUUCGCCAAGGAU
....(((((((.(((((((((((....)))..(((((((.-----...))))))).........(((....)))..)))))))))))))))....... ( -31.90, z-score =  -3.56, R)
>droSim1.chr3L 1907891 93 + 22553184
GUUAGCGGACCGCGUUCAGCGGAAAAUUCCCAGUAACUUU-----UUGAAGUUAAAAUUAAAAGGGCCAAAGCCAAGUUGAACGGGUUCGCCAAGGAU
....(((((((.(((((((((((....)))...((((((.-----...))))))..........(((....)))..)))))))))))))))....... ( -32.70, z-score =  -3.71, R)
>consensus
GUUAGCGGACCGCGUUCAGCGGAAAAUUCCCAGUAACUUU_____UUAAAGUUAAAAUUAAAAGAGACAAAGCCAAGUUGAACGGGUUCGCCAAGGAU
......(((((.(((((((((((....)))......((((....................))))............)))))))))))))......... (-12.14 = -12.95 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 2,346,258 – 2,346,350
Length 92
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 70.14
Shannon entropy 0.57537
G+C content 0.41863
Mean single sequence MFE -23.70
Consensus MFE -10.58
Energy contribution -13.42
Covariance contribution 2.84
Combinations/Pair 1.32
Mean z-score -2.49
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.62
SVM RNA-class probability 0.993507
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2346258 92 - 24543557
AUCCUUGGUGAACCCGUUCAACUUGGCUUUCCCUCUUUUAAUUUU-GCACUAG-----AAAGUUACUGGGAAUUUUCCGCUGAACGCGGUCCGCUAAC
....((((((.(((((((((...(((..(((((.....(((((((-.......-----)))))))..)))))....))).)))))).))).)))))). ( -26.50, z-score =  -2.94, R)
>droAna3.scaffold_13337 394404 84 - 23293914
AUCCCAAGCGAACCCUUUUAA---AGUCCUGUAAGCUGUGGCAUCAAAUUUUUGUUAAAAGGCUGU--AAAAGUUAAAGCCUCAAGUAG---------
.......((.....((((((.---.........((((.(((((.........)))))...)))).)--))))).....)).........--------- ( -10.80, z-score =   0.72, R)
>droEre2.scaffold_4784 2359928 91 - 25762168
AUCCUUAGCGAACCCGUUCAACUUGGCUUGCUCUCUUUUAAUUUUAAC--UAG-----AAAGUUACUGGGAAUUUUCCGCUGAACGCGGUUUGCUAAC
....((((((((((((((((...(((.....((((...(((((((...--...-----)))))))..)))).....))).)))))).)))))))))). ( -28.70, z-score =  -4.36, R)
>droYak2.chr3L 14606296 96 + 24197627
AUCCU--GGAAACCCGUUCAACUUUGCUUUCUCUCUUUUAAUUUUAAAAGUAACUUUUAAAGUUACUGGGAAUUUUCCGCUGAACGCGGUUCGCUAAC
....(--((.((((((((((........(((((.....((((((((((((...))))))))))))..)))))........)))))).))))..))).. ( -22.89, z-score =  -2.88, R)
>droSec1.super_2 2371156 93 - 7591821
AUCCUUGGCGAACCCAUUCAACUUGGCUUUGGCCCUUUUAAUUUUAACUUCAA-----AAAGUUAAUGGGAAUUUUCCGCUGAACGCGGUCCGCUAAC
....((((((..((((........(((....))).........(((((((...-----.)))))))))))......((((.....))))..)))))). ( -25.30, z-score =  -2.39, R)
>droSim1.chr3L 1907891 93 - 22553184
AUCCUUGGCGAACCCGUUCAACUUGGCUUUGGCCCUUUUAAUUUUAACUUCAA-----AAAGUUACUGGGAAUUUUCCGCUGAACGCGGUCCGCUAAC
....((((((.(((((((((...(((......(((...(((((((........-----)))))))..)))......))).)))))).))).)))))). ( -28.00, z-score =  -3.07, R)
>consensus
AUCCUUGGCGAACCCGUUCAACUUGGCUUUCUCUCUUUUAAUUUUAACUUUAA_____AAAGUUACUGGGAAUUUUCCGCUGAACGCGGUCCGCUAAC
....((((((.(((((((((...(((......(((...(((((((.............)))))))..)))......))).)))))).))).)))))). (-10.58 = -13.42 +   2.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:57:28 2011