Locus 15740

Sequence ID dm3.chrX
Location 20,736,216 – 20,736,332
Length 116
Max. P 0.981478
window21684 window21685

overview

Window 4

Location 20,736,216 – 20,736,332
Length 116
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 80.35
Shannon entropy 0.26699
G+C content 0.61037
Mean single sequence MFE -38.32
Consensus MFE -22.49
Energy contribution -23.72
Covariance contribution 1.23
Combinations/Pair 1.19
Mean z-score -2.44
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.75
SVM RNA-class probability 0.805463
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20736216 116 + 22422827
CCCCAGUUACCCGGAACCAGGAUUCUGGAUCCUGGAUCCAGCGCCCAGUACCCAGGAUUCAGAAUCCAGAACCCAGAACCCAGAAUCCAGCCUCCACUUUGGGACCCUGUGUGCGC
.....((.((.(((.....((((((((((((((((.....((.....))..))))))))))))))))....((((((....((........))....))))))...))).)))).. ( -38.10, z-score =  -2.31, R)
>droEre2.scaffold_4690 17319215 95 + 18748788
CCCCAGUUACCCGGAACCAGGAUCCUGGAUCCUG--------------CGCCCAGGAU-------CCAGAAUCCGGAAUCCGGACUACAGCCUCCACUGUGGGACCAUGUGUGCGC
.(((......(((((.((.((((.((((((((((--------------....))))))-------)))).))))))..)))))...((((......)))))))............. ( -40.80, z-score =  -3.25, R)
>droSim1.chrX_random 382597 109 + 5698898
CCCCAGUUACCCGGAACCAGGAUCCUGGAUCCUGGAUCCAGCACCCAGCACCCAGGAU-------CCAGAGCCCAGAACCCAGAAUCCAGCCUCCACUUUGGGACCCUGUGUGCGC
............(((.((((((((...)))))))).)))........((((.((((.(-------((((((...((...............))...)))))))..)))).)))).. ( -36.06, z-score =  -1.77, R)
>consensus
CCCCAGUUACCCGGAACCAGGAUCCUGGAUCCUGGAUCCAGC_CCCAGCACCCAGGAU_______CCAGAACCCAGAACCCAGAAUCCAGCCUCCACUUUGGGACCCUGUGUGCGC
............(((.((((((((...)))))))).)))........((((.((((............(....)....((((((.............))))))..)))).)))).. (-22.49 = -23.72 +   1.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 20,736,216 – 20,736,332
Length 116
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 80.35
Shannon entropy 0.26699
G+C content 0.61037
Mean single sequence MFE -51.67
Consensus MFE -38.27
Energy contribution -39.14
Covariance contribution 0.87
Combinations/Pair 1.11
Mean z-score -2.67
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.08
SVM RNA-class probability 0.981478
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20736216 116 - 22422827
GCGCACACAGGGUCCCAAAGUGGAGGCUGGAUUCUGGGUUCUGGGUUCUGGAUUCUGAAUCCUGGGUACUGGGCGCUGGAUCCAGGAUCCAGAAUCCUGGUUCCGGGUAACUGGGG
.......(((...(((..(((....)))(((..(.((((((((((((((((((((.(..(((........)))..).)))))))))))))))))))).)..))))))...)))... ( -53.30, z-score =  -2.53, R)
>droEre2.scaffold_4690 17319215 95 - 18748788
GCGCACACAUGGUCCCACAGUGGAGGCUGUAGUCCGGAUUCCGGAUUCUGG-------AUCCUGGGCG--------------CAGGAUCCAGGAUCCUGGUUCCGGGUAACUGGGG
.............((((((((....)))))..((((((..(((((((((((-------((((((....--------------))))))))))))))).)).)))))).....))). ( -48.60, z-score =  -3.30, R)
>droSim1.chrX_random 382597 109 - 5698898
GCGCACACAGGGUCCCAAAGUGGAGGCUGGAUUCUGGGUUCUGGGCUCUGG-------AUCCUGGGUGCUGGGUGCUGGAUCCAGGAUCCAGGAUCCUGGUUCCGGGUAACUGGGG
.......((((((((......((((.(..((........))..).))))((-------(((((((((.(........).))))))))))).))))))))..(((((....))))). ( -53.10, z-score =  -2.18, R)
>consensus
GCGCACACAGGGUCCCAAAGUGGAGGCUGGAUUCUGGGUUCUGGGUUCUGG_______AUCCUGGGUGCUGGG_GCUGGAUCCAGGAUCCAGGAUCCUGGUUCCGGGUAACUGGGG
.......(((((((((.....)).))))....((((((..(.(((((((((.......(((((((((.(........).)))))))))))))))))).)..))))))...)))... (-38.27 = -39.14 +   0.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:04:56 2011