Locus 15709

Sequence ID	dm3.chrX
Location	20,536,612 – 20,536,708
Length	96
Max. P	0.998031

overview

Window 6

Location	20,536,612 – 20,536,708
Length	96
Sequences	4
Columns	100
Reading direction	forward
Mean pairwise identity	66.33
Shannon entropy	0.53611
G+C content	0.44917
Mean single sequence MFE	-20.16
Consensus MFE	-13.90
Energy contribution	-13.65
Covariance contribution	-0.25
Combinations/Pair	1.31
Mean z-score	-2.29
Structure conservation index	0.69
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.23
SVM RNA-class probability	0.998008
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20536612 96 + 22422827
UCCCAGUUCCCUGGGCUCUC--AUCGUCCUGCGUCCUGGGCUUGUAUAUUUUUUAUACUUUUCAUACUCCACCCCAGGACCUUGUUCGCAUUUCUUUA--
.(((((....))))).....--..((..(...((((((((...(((((.....)))))..............))))))))...)..))..........-- ( -23.73, z-score =  -3.50, R)
>droSim1.chrX 15760474 96 + 17042790
UCCCAGUUCCCUGGGCUCUC--AUCGUCCUGCGUCCUGGGCUUGUAUAUUUUUUACACUUUUCAUACUCCACCCCAGGACCUUGUUCGCAUUUCUUUA--
.(((((....))))).....--..((..(...((((((((...((((................)))).....))))))))...)..))..........-- ( -22.99, z-score =  -3.17, R)
>droSec1.super_8 2779331 96 + 3762037
UCCCAGUUCCCUGGGCUCUC--AUCGUCCUGCGUCCUGGGCUUGUAUAUUUUUUAUACUUUUCAUACUCCACCCCAGGACCUUCUUCGCAUUUCUUUA--
.(((((....))))).....--.......(((((((((((...(((((.....)))))..............)))))))).......)))........-- ( -22.54, z-score =  -3.51, R)
>droWil1.scaffold_180702 1767368 100 - 4511350
CCUCAAUCUAGUAAGUUCCUUGAGCAACUAAAAAUCAUGUUUUCCAUUUACUUUCCUGUACUUUCACUGCCUGCGAGAGGUGAUACCAAAGCUUUCAAAA
........((((..((((...)))).))))...(((((..........(((......)))(((((.(.....).))))))))))................ ( -11.40, z-score =   1.05, R)
>consensus
UCCCAGUUCCCUGGGCUCUC__AUCGUCCUGCGUCCUGGGCUUGUAUAUUUUUUACACUUUUCAUACUCCACCCCAGGACCUUGUUCGCAUUUCUUUA__
.(((((....))))).................((((((((................................)))))))).................... (-13.90 = -13.65 +  -0.25)

alignment

secondary structure

dotplot

Window 7

Location	20,536,612 – 20,536,708
Length	96
Sequences	4
Columns	100
Reading direction	reverse
Mean pairwise identity	66.33
Shannon entropy	0.53611
G+C content	0.44917
Mean single sequence MFE	-24.93
Consensus MFE	-18.30
Energy contribution	-19.24
Covariance contribution	0.94
Combinations/Pair	1.21
Mean z-score	-2.25
Structure conservation index	0.73
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.24
SVM RNA-class probability	0.998031
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20536612 96 - 22422827
--UAAAGAAAUGCGAACAAGGUCCUGGGGUGGAGUAUGAAAAGUAUAAAAAAUAUACAAGCCCAGGACGCAGGACGAU--GAGAGCCCAGGGAACUGGGA
--..........((..(...((((((((.(......(....)(((((.....))))).).))))))))...)..))..--.....(((((....))))). ( -28.60, z-score =  -3.71, R)
>droSim1.chrX 15760474 96 - 17042790
--UAAAGAAAUGCGAACAAGGUCCUGGGGUGGAGUAUGAAAAGUGUAAAAAAUAUACAAGCCCAGGACGCAGGACGAU--GAGAGCCCAGGGAACUGGGA
--..........((..(...((((((((.(......(....)(((((.....))))).).))))))))...)..))..--.....(((((....))))). ( -28.60, z-score =  -3.46, R)
>droSec1.super_8 2779331 96 - 3762037
--UAAAGAAAUGCGAAGAAGGUCCUGGGGUGGAGUAUGAAAAGUAUAAAAAAUAUACAAGCCCAGGACGCAGGACGAU--GAGAGCCCAGGGAACUGGGA
--..................((((((((.(......(....)(((((.....))))).).))))))))..........--.....(((((....))))). ( -28.10, z-score =  -3.84, R)
>droWil1.scaffold_180702 1767368 100 + 4511350
UUUUGAAAGCUUUGGUAUCACCUCUCGCAGGCAGUGAAAGUACAGGAAAGUAAAUGGAAAACAUGAUUUUUAGUUGCUCAAGGAACUUACUAGAUUGAGG
..........(((((((...(((.((((.....)))).((((...((((((..(((.....))).))))))...))))..)))....)))))))...... ( -14.40, z-score =   1.99, R)
>consensus
__UAAAGAAAUGCGAACAAGGUCCUGGGGUGGAGUAUGAAAAGUAUAAAAAAUAUACAAGCCCAGGACGCAGGACGAU__GAGAGCCCAGGGAACUGGGA
....................((((((((.(.(.((((..............)))).).).)))))))).................(((((....))))). (-18.30 = -19.24 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:04:24 2011