Locus 6388

Sequence ID dm3.chr3L
Location 6,257,661 – 6,257,819
Length 158
Max. P 0.993324
window8790 window8791

overview

Window 0

Location 6,257,661 – 6,257,779
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.56
Shannon entropy 0.36470
G+C content 0.40405
Mean single sequence MFE -34.56
Consensus MFE -19.95
Energy contribution -19.67
Covariance contribution -0.28
Combinations/Pair 1.26
Mean z-score -3.06
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.61
SVM RNA-class probability 0.993324
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6257661 118 + 24543557
UCAAA-CUACAAUUGUAAAUCUGAAUAGUUUUCAAGAUUUACUGGCGCCAUCUAG-GGCCUUAUACUUGAGCCAGUUGCGCUUAUAAAAAAUGCCGCUAGGGGCGCUAAAAAGCAAUGUG
.....-.((((...(((((((((((.....))).))))))))(((((((.(((((-(((........((((((....).)))))........))).))))))))))))........)))) ( -38.09, z-score =  -3.40, R)
>droEre2.scaffold_4784 8946846 119 + 25762168
UAAAAUCUACAAUUGUAAAUGUUCGUAAUUUUUAAAAGAUAGUGGCGGCCUCUAG-UGUCAUAAGCGAAAAUCAGUUGAGCUUAUAAAAACUGCCGCUAGGAGCGCUAAUAAGCAAUGUG
.......((((.........((((...((((.....))))..(((((((....((-(...((((((..((.....))..))))))....)))))))))).))))(((....)))..)))) ( -23.50, z-score =  -0.08, R)
>droYak2.chr3L 6838064 119 + 24197627
UAAAAUCUGCAAUUGUAAAUUCUCAUCAUUUAUAAGAGAUACUGGCGCCCUCUAG-GGUCGCUUCCAUAAACCAGUUGCGCUUUCAAAAACUGCCGCUAGGGGCGCUAGAAAGCAGUGUG
......((((..((((((((.......))))))))......(((((((((.((((-((......))......(((((...........)))))...)))))))))))))...)))).... ( -36.30, z-score =  -2.48, R)
>droSec1.super_2 6223428 119 + 7591821
UCAAA-CUACAAUUGUAAAUCAUAAUAAUUUUCAAGAGAUACUAGCGCCAUCUAGCGGCCUUUUUCCUAAUACAGUUCCGCUUAUGAAAACUGCCGCUAGAGGCGCUAGAAAACAAUGUG
.....-.((((.((((...............((....))..((((((((.(((((((((..(((((.(((...........))).)))))..)))))))))))))))))...)))))))) ( -38.30, z-score =  -5.99, R)
>droSim1.chr3L 5751474 119 + 22553184
UCAAA-CAACAAUUGUAAAUCUUAAUUAUUUUCAAGAGAUACUGGCGCCAUCUAGCGGCCUCUUGCUUAAUACAGUUGCGCCUUUGAUAACUGCCGCUAGGGGCGCUAGAAAACAAUGUG
.....-..(((.((((..(((((............))))).((((((((.(((((((((..............(((((((....)).))))))))))))))))))))))...))))))). ( -36.63, z-score =  -3.37, R)
>consensus
UCAAA_CUACAAUUGUAAAUCUUAAUAAUUUUCAAGAGAUACUGGCGCCAUCUAG_GGCCUUUUGCUUAAAACAGUUGCGCUUAUAAAAACUGCCGCUAGGGGCGCUAGAAAGCAAUGUG
........(((.((((((((.......))))..........((((((((.(((((.(((.................................))).)))))))))))))...))))))). (-19.95 = -19.67 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 6,257,700 – 6,257,819
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.95
Shannon entropy 0.37027
G+C content 0.44556
Mean single sequence MFE -36.74
Consensus MFE -21.59
Energy contribution -20.59
Covariance contribution -1.00
Combinations/Pair 1.36
Mean z-score -1.79
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.47
SVM RNA-class probability 0.707029
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6257700 119 + 24543557
ACUGGCGCCAUCUAG-GGCCUUAUACUUGAGCCAGUUGCGCUUAUAAAAAAUGCCGCUAGGGGCGCUAAAAAGCAAUGUGUAGAAUACAUUUGACGUGUAGAAGACAAGUUAUUGCAGUG
..(((((((.(((((-(((........((((((....).)))))........))).))))))))))))....(((((((((....(((((.....)))))....)))...)))))).... ( -38.49, z-score =  -2.02, R)
>droEre2.scaffold_4784 8946886 119 + 25762168
AGUGGCGGCCUCUAG-UGUCAUAAGCGAAAAUCAGUUGAGCUUAUAAAAACUGCCGCUAGGAGCGCUAAUAAGCAAUGUGUAGAAUAUAUUUGACGUGUAGAAGAGAGGAGGCUAUGAUG
.(((((..(((((..-..((((((((..((.....))..)))))).....(((((((.....))(((....)))...).)))).................))..)))))..))))).... ( -28.60, z-score =  -0.19, R)
>droYak2.chr3L 6838104 119 + 24197627
ACUGGCGCCCUCUAG-GGUCGCUUCCAUAAACCAGUUGCGCUUUCAAAAACUGCCGCUAGGGGCGCUAGAAAGCAGUGUGUAGAAUAUAUUUUACGUGUAGAGUAAAGUUGGCUAUAAUG
.(((((((((.((((-((......))......(((((...........)))))...))))))))))))).........(((((.....(((((((.......)))))))...)))))... ( -36.10, z-score =  -0.98, R)
>droSec1.super_2 6223467 120 + 7591821
ACUAGCGCCAUCUAGCGGCCUUUUUCCUAAUACAGUUCCGCUUAUGAAAACUGCCGCUAGAGGCGCUAGAAAACAAUGUGUAGAAUACGUUUGACGUGUAGAAGACAAGUUAUUGCAGUA
.((((((((.(((((((((..(((((.(((...........))).)))))..)))))))))))))))))....((((((((...(((((.....))))).....)))...)))))..... ( -42.20, z-score =  -4.22, R)
>droSim1.chr3L 5751513 120 + 22553184
ACUGGCGCCAUCUAGCGGCCUCUUGCUUAAUACAGUUGCGCCUUUGAUAACUGCCGCUAGGGGCGCUAGAAAACAAUGUGUAGAAUACAUUUGACGUGUAGAAGACAAGUUAUUGCAGUA
.((((((((.(((((((((..............(((((((....)).))))))))))))))))))))))....((((((((....(((((.....)))))....)))...)))))..... ( -38.33, z-score =  -1.56, R)
>consensus
ACUGGCGCCAUCUAG_GGCCUUUUGCUUAAAACAGUUGCGCUUAUAAAAACUGCCGCUAGGGGCGCUAGAAAGCAAUGUGUAGAAUACAUUUGACGUGUAGAAGACAAGUUAUUGCAGUG
.((((((((.(((((.(((.................................))).))))))))))))).....(((((((...))))))).....(((((...........)))))... (-21.59 = -20.59 +  -1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:06:48 2011