Locus 7456

Sequence ID dm3.chr3L
Location 14,953,285 – 14,953,335
Length 50
Max. P 0.988289
window10272 window10273

overview

Window 2

Location 14,953,285 – 14,953,335
Length 50
Sequences 5
Columns 52
Reading direction forward
Mean pairwise identity 87.40
Shannon entropy 0.22562
G+C content 0.34523
Mean single sequence MFE -10.90
Consensus MFE -8.50
Energy contribution -9.38
Covariance contribution 0.88
Combinations/Pair 1.15
Mean z-score -2.88
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.31
SVM RNA-class probability 0.988289
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14953285 50 + 24543557
AAACAA--UAAAGCAGAUAUCGGUUUAUUUACCAACCGACAUUUGUUCUGAG
......--...(((((((.((((((........)))))).)))))))..... ( -12.10, z-score =  -3.95, R)
>droAna3.scaffold_13337 19128445 52 - 23293914
AAACAAUGGUAAACAAAUCUGGGUUUAUUUACCAACCGUCAUUUGUUGUGAG
......(((((((.((((....)))).)))))))....((((.....)))). ( -10.50, z-score =  -0.99, R)
>droYak2.chr3L 15040809 50 + 24197627
AAACAA--AAAAAGAGAUAUCGGUUUAUUUACCAACCGCCAUUUGUUUCGAG
......--.....((((((.(((((........))))).....))))))... (  -7.90, z-score =  -1.83, R)
>droSec1.super_0 7069943 50 + 21120651
AAACAA--AAACACAGAUAUCGGUUUAUUUACCAACCGACAUUUGUUCUGAG
......--....((((((.((((((........)))))).))))))...... ( -11.20, z-score =  -3.52, R)
>droSim1.chr3L 14270076 50 + 22553184
AAACAA--GAACACAGAUAUCGGUUUAUUUACCAACCGACAUUUGUUCUGAG
.....(--(((((..(((.((((((........)))))).)))))))))... ( -12.80, z-score =  -4.11, R)
>consensus
AAACAA__AAAAACAGAUAUCGGUUUAUUUACCAACCGACAUUUGUUCUGAG
...........(((((((.((((((........)))))).)))))))..... ( -8.50 =  -9.38 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 14,953,285 – 14,953,335
Length 50
Sequences 5
Columns 52
Reading direction reverse
Mean pairwise identity 87.40
Shannon entropy 0.22562
G+C content 0.34523
Mean single sequence MFE -13.10
Consensus MFE -9.20
Energy contribution -10.96
Covariance contribution 1.76
Combinations/Pair 1.13
Mean z-score -3.14
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.28
SVM RNA-class probability 0.987492
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14953285 50 - 24543557
CUCAGAACAAAUGUCGGUUGGUAAAUAAACCGAUAUCUGCUUUA--UUGUUU
...(((.((.(((((((((........))))))))).)).))).--...... ( -12.20, z-score =  -3.02, R)
>droAna3.scaffold_13337 19128445 52 + 23293914
CUCACAACAAAUGACGGUUGGUAAAUAAACCCAGAUUUGUUUACCAUUGUUU
............((((((.((((((((((......)))))))))))))))). ( -12.40, z-score =  -2.08, R)
>droYak2.chr3L 15040809 50 - 24197627
CUCGAAACAAAUGGCGGUUGGUAAAUAAACCGAUAUCUCUUUUU--UUGUUU
....(((((((.((..((((((......))))))....))...)--)))))) (  -9.30, z-score =  -1.55, R)
>droSec1.super_0 7069943 50 - 21120651
CUCAGAACAAAUGUCGGUUGGUAAAUAAACCGAUAUCUGUGUUU--UUGUUU
...((((((.(((((((((........)))))))))...)))))--)..... ( -14.50, z-score =  -3.84, R)
>droSim1.chr3L 14270076 50 - 22553184
CUCAGAACAAAUGUCGGUUGGUAAAUAAACCGAUAUCUGUGUUC--UUGUUU
...((((((.(((((((((........)))))))))...)))))--)..... ( -17.10, z-score =  -5.19, R)
>consensus
CUCAGAACAAAUGUCGGUUGGUAAAUAAACCGAUAUCUGUUUUC__UUGUUU
...((((((.(((((((((........))))))))).))))))......... ( -9.20 = -10.96 +   1.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:27:20 2011