Locus 9083

Sequence ID dm3.chr3R
Location 3,987,719 – 3,987,769
Length 50
Max. P 0.996333
window12461 window12462

overview

Window 1

Location 3,987,719 – 3,987,769
Length 50
Sequences 7
Columns 54
Reading direction forward
Mean pairwise identity 84.36
Shannon entropy 0.29233
G+C content 0.39663
Mean single sequence MFE -9.27
Consensus MFE -6.36
Energy contribution -6.79
Covariance contribution 0.43
Combinations/Pair 1.00
Mean z-score -3.32
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.92
SVM RNA-class probability 0.996333
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3987719 50 + 27905053
-UCCCCCAUUCACUCAUUUAAUGACGCCACUAAAUGGGCUUCAUU---AUUUCG
-.................((((((.(((.(.....)))).)))))---)..... (  -9.60, z-score =  -3.34, R)
>dp4.chr2 17711328 51 - 30794189
UCUUUUGCUCAACUCAUUUAAUGACGCCACUAAAUGGGCUUCAUU---AUUUCG
..................((((((.(((.(.....)))).)))))---)..... (  -9.60, z-score =  -3.50, R)
>droAna3.scaffold_13340 21442312 50 + 23697760
-UUUUUUCUCAACUCAUUUAAUGACGCCACUAAAUGGGCUUCAUU---AUUUCG
-.................((((((.(((.(.....)))).)))))---)..... (  -9.60, z-score =  -4.50, R)
>droEre2.scaffold_4770 153594 50 - 17746568
-UCCCCCAUUCACUCAUUUAAUGACGCCACUAAAUGGGCUUCAUU---AUUUCG
-.................((((((.(((.(.....)))).)))))---)..... (  -9.60, z-score =  -3.34, R)
>droYak2.chr3R 8060585 50 + 28832112
-AGCCCCAUUCACUCAUUUAAUGACGCCACUAAAUGGGCUUCAUU---AUUUCG
-.................((((((.(((.(.....)))).)))))---)..... (  -9.60, z-score =  -2.67, R)
>droSec1.super_0 3279852 50 - 21120651
-UCCCCUAUUCACUCAUUUAAUGACGCCACUAAAUGGGCUUCAUU---AUUUCG
-.................((((((.(((.(.....)))).)))))---)..... (  -9.60, z-score =  -3.61, R)
>droSim1.chr3R 10246465 52 - 27517382
-UCUCCUAUUCACGUCUUUA-UGACGCCACUAAAUGGGCUUAUCUCAUAUUUCG
-...((((((..((((....-.))))......))))))................ (  -7.30, z-score =  -2.26, R)
>consensus
_UCCCCCAUUCACUCAUUUAAUGACGCCACUAAAUGGGCUUCAUU___AUUUCG
...................(((((.(((.(.....)))).)))))......... ( -6.36 =  -6.79 +   0.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 3,987,719 – 3,987,769
Length 50
Sequences 7
Columns 54
Reading direction reverse
Mean pairwise identity 84.36
Shannon entropy 0.29233
G+C content 0.39663
Mean single sequence MFE -9.46
Consensus MFE -7.24
Energy contribution -7.67
Covariance contribution 0.43
Combinations/Pair 1.00
Mean z-score -1.44
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.653294
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3987719 50 - 27905053
CGAAAU---AAUGAAGCCCAUUUAGUGGCGUCAUUAAAUGAGUGAAUGGGGGA-
......---.......((((((((....(((......)))..))))))))...- (  -9.50, z-score =  -0.90, R)
>dp4.chr2 17711328 51 + 30794189
CGAAAU---AAUGAAGCCCAUUUAGUGGCGUCAUUAAAUGAGUUGAGCAAAAGA
......---..((.(((.(((((((((....))))))))).)))...))..... ( -10.30, z-score =  -2.29, R)
>droAna3.scaffold_13340 21442312 50 - 23697760
CGAAAU---AAUGAAGCCCAUUUAGUGGCGUCAUUAAAUGAGUUGAGAAAAAA-
.....(---(((((.((((.....).))).)))))).................- (  -9.40, z-score =  -2.60, R)
>droEre2.scaffold_4770 153594 50 + 17746568
CGAAAU---AAUGAAGCCCAUUUAGUGGCGUCAUUAAAUGAGUGAAUGGGGGA-
......---.......((((((((....(((......)))..))))))))...- (  -9.50, z-score =  -0.90, R)
>droYak2.chr3R 8060585 50 - 28832112
CGAAAU---AAUGAAGCCCAUUUAGUGGCGUCAUUAAAUGAGUGAAUGGGGCU-
......---.....(((((((((((((....)))))))).........)))))- ( -10.50, z-score =  -1.08, R)
>droSec1.super_0 3279852 50 + 21120651
CGAAAU---AAUGAAGCCCAUUUAGUGGCGUCAUUAAAUGAGUGAAUAGGGGA-
.....(---(((((.((((.....).))).)))))).................- (  -9.40, z-score =  -1.26, R)
>droSim1.chr3R 10246465 52 + 27517382
CGAAAUAUGAGAUAAGCCCAUUUAGUGGCGUCA-UAAAGACGUGAAUAGGAGA-
................((.((((....(((((.-....))))))))).))...- (  -7.60, z-score =  -1.03, R)
>consensus
CGAAAU___AAUGAAGCCCAUUUAGUGGCGUCAUUAAAUGAGUGAAUAGGGGA_
...............((.(((((((((....))))))))).))........... ( -7.24 =  -7.67 +   0.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:57:42 2011