Locus 944

Sequence ID dm3.chr2L
Location 6,921,119 – 6,921,170
Length 51
Max. P 0.973703
window1282 window1283

overview

Window 2

Location 6,921,119 – 6,921,170
Length 51
Sequences 6
Columns 51
Reading direction forward
Mean pairwise identity 88.50
Shannon entropy 0.22752
G+C content 0.28105
Mean single sequence MFE -6.15
Consensus MFE -4.53
Energy contribution -4.50
Covariance contribution -0.03
Combinations/Pair 1.43
Mean z-score -1.74
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.17
SVM RNA-class probability 0.576127
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 6921119 51 + 23011544
UUUCCACCCAUCAAAGUGGAAAAUUUCAUAUUUUUAUACAUACAUACGAAA
(((((((........)))))))............................. (  -7.50, z-score =  -2.87, R)
>droSim1.chr2L 6717561 51 + 22036055
UUUCCACCCAUCAAAGUGGAAAAUUUCAUAUUUUUAUACAUACAUACGAAA
(((((((........)))))))............................. (  -7.50, z-score =  -2.87, R)
>droSec1.super_3 2454788 51 + 7220098
UUUCCACCCAUCAAAGUGGAAAAUUUCAUAUUUUUAUACAUACAUACGAAA
(((((((........)))))))............................. (  -7.50, z-score =  -2.87, R)
>droYak2.chr2L 16336002 51 - 22324452
UUUCCACCCAUGAAAGUGGAAAAUUUCAUAUUUUUAUACAUACAUACGAAA
(((((((........)))))))............................. (  -7.50, z-score =  -2.03, R)
>droEre2.scaffold_4929 15836088 51 + 26641161
UUUCAACCCAUCAAAGUGGAAAAUUUCAUAUUUUUAUACAUACAUACGAAA
.(((...((((....))))(((((.....))))).............))). (  -3.00, z-score =  -0.17, R)
>anoGam1.chr3L 39278587 51 - 41284009
UUCGUACCCAGUAACGCGUAAGAUUUCAAACUAUUGUACAUACUAAUGAAA
...((((..(((....(....).......)))...))))............ (  -3.90, z-score =   0.36, R)
>consensus
UUUCCACCCAUCAAAGUGGAAAAUUUCAUAUUUUUAUACAUACAUACGAAA
(((((((........)))))))............................. ( -4.53 =  -4.50 +  -0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 6,921,119 – 6,921,170
Length 51
Sequences 6
Columns 51
Reading direction reverse
Mean pairwise identity 88.50
Shannon entropy 0.22752
G+C content 0.28105
Mean single sequence MFE -11.08
Consensus MFE -9.36
Energy contribution -10.12
Covariance contribution 0.75
Combinations/Pair 1.19
Mean z-score -2.34
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.89
SVM RNA-class probability 0.973703
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 6921119 51 - 23011544
UUUCGUAUGUAUGUAUAAAAAUAUGAAAUUUUCCACUUUGAUGGGUGGAAA
((((((((............)))))))).(((((((((....))))))))) ( -13.50, z-score =  -3.57, R)
>droSim1.chr2L 6717561 51 - 22036055
UUUCGUAUGUAUGUAUAAAAAUAUGAAAUUUUCCACUUUGAUGGGUGGAAA
((((((((............)))))))).(((((((((....))))))))) ( -13.50, z-score =  -3.57, R)
>droSec1.super_3 2454788 51 - 7220098
UUUCGUAUGUAUGUAUAAAAAUAUGAAAUUUUCCACUUUGAUGGGUGGAAA
((((((((............)))))))).(((((((((....))))))))) ( -13.50, z-score =  -3.57, R)
>droYak2.chr2L 16336002 51 + 22324452
UUUCGUAUGUAUGUAUAAAAAUAUGAAAUUUUCCACUUUCAUGGGUGGAAA
((((((((............)))))))).(((((((((....))))))))) ( -13.50, z-score =  -3.40, R)
>droEre2.scaffold_4929 15836088 51 - 26641161
UUUCGUAUGUAUGUAUAAAAAUAUGAAAUUUUCCACUUUGAUGGGUUGAAA
((((((((............)))))))).((((.((((....)))).)))) (  -7.00, z-score =  -0.69, R)
>anoGam1.chr3L 39278587 51 + 41284009
UUUCAUUAGUAUGUACAAUAGUUUGAAAUCUUACGCGUUACUGGGUACGAA
(((((..(.(((.....))).).)))))((.(((.((....)).))).)). (  -5.50, z-score =   0.74, R)
>consensus
UUUCGUAUGUAUGUAUAAAAAUAUGAAAUUUUCCACUUUGAUGGGUGGAAA
((((((((............))))))))..((((((((....)))))))). ( -9.36 = -10.12 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:22:33 2011