Locus 15224

Sequence ID	dm3.chrX
Location	18,031,612 – 18,031,743
Length	131
Max. P	0.997005

overview

Window 1

Location	18,031,612 – 18,031,674
Length	62
Sequences	5
Columns	66
Reading direction	forward
Mean pairwise identity	89.20
Shannon entropy	0.18523
G+C content	0.38972
Mean single sequence MFE	-11.94
Consensus MFE	-11.68
Energy contribution	-11.68
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.98
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.37
SVM RNA-class probability	0.932496
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18031612 62 + 22422827
AAGCCAACAAAAUGAUUUGCAUCGGUGUUGGUUCUCACU-UGCUCUCUUUGCUUUUCUCAAAA---
.((((((((...((((....)))).))))))))......-.((.......))...........--- ( -11.80, z-score =  -1.47, R)
>droSim1.chrX_random 149054 62 + 5698898
AAGCCAACAAAAUGAUUUGCAUCGGUGUUGGUUCUCACU-UGCUCUCUUUGCUUUUCUCAAAA---
.((((((((...((((....)))).))))))))......-.((.......))...........--- ( -11.80, z-score =  -1.47, R)
>droSec1.super_8 341333 63 + 3762037
AAGCCAACAAAAUGAUUUGCAUCGGUGUUGGUUCUCACU-UGCUCUCUUUGCUUUUUCUCAAAA--
.((((((((...((((....)))).))))))))......-.((.......))............-- ( -11.80, z-score =  -1.43, R)
>droYak2.chrX 16654665 61 + 21770863
AAGCCAACAAAAUGAUUUGCAUCGGUGUUGGUUCUCUUGGUGCUCUCUUUGCUUUUCUAAA-----
.((((((((...((((....)))).))))))))...((((.((.......))....)))).----- ( -13.10, z-score =  -1.76, R)
>droEre2.scaffold_4690 8359681 65 + 18748788
CAGCCAACAAAAUGAUUUGCAUCGGUGUUGGUUCUCACU-UGCUCUCUUCGCUUUUUCCAAAAAAA
.((((((((...((((....)))).))))))))......-.((.......)).............. ( -11.20, z-score =  -0.99, R)
>consensus
AAGCCAACAAAAUGAUUUGCAUCGGUGUUGGUUCUCACU_UGCUCUCUUUGCUUUUCUCAAAA___
.((((((((...((((....)))).))))))))........((.......)).............. (-11.68 = -11.68 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	18,031,674 – 18,031,743
Length	69
Sequences	6
Columns	74
Reading direction	reverse
Mean pairwise identity	75.09
Shannon entropy	0.45447
G+C content	0.47065
Mean single sequence MFE	-26.63
Consensus MFE	-17.71
Energy contribution	-16.94
Covariance contribution	-0.77
Combinations/Pair	1.60
Mean z-score	-2.60
Structure conservation index	0.67
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.02
SVM RNA-class probability	0.997005
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18031674 69 - 22422827
GCAAACAUGCGCACACA-----CUUUCACGCACACUUGACUCCACUGUGCGAGCGCGUGUGUGUGUGUGUUAUU
...((((((((((((((-----(...(.((((((..((....)).)))))).)...)))))))))))))))... ( -30.20, z-score =  -2.78, R)
>droEre2.scaffold_4690 8359746 74 - 18748788
GCAAACAGGCGCACGCAGCUCUCUUUCACACACACUUUACUUCACUGUGCGAGCGCGCGUGUGUGUGUGUUUUU
..(((((.((((((((.((.(((...((((...............)))).))).))..)))))))).))))).. ( -25.26, z-score =  -1.17, R)
>droYak2.chrX 16654726 74 - 21770863
ACAAGCAGGCGCACGCAGCUCUCUUUCGCACACACUUUACUUCACUGUGCGAGCGUGUGUGUGUGUGUUAUUUU
...((((.(((((((((((((......(((((.............))))))))).))))))))).))))..... ( -27.82, z-score =  -2.26, R)
>droSec1.super_8 341396 69 - 3762037
ACAAACAUGCGCACACA-----CUUUCACGCACACUUCACUCCACUGUGCGAGCGUGUGUGUGUGUGUGUUAUU
...((((((((((((((-----(...(.((((((...........)))))).)...)))))))))))))))... ( -30.20, z-score =  -3.23, R)
>droSim1.chrX_random 149116 67 - 5698898
ACAAACAUGCGCACACA-----CUUUCACGCACACUUCACUCCACUGUGCGAGCGUGUGUGUGUGUGUUAUU--
...((((((((((((((-----(...(.((((((...........)))))).).)))))))))))))))...-- ( -28.80, z-score =  -3.45, R)
>droGri2.scaffold_15081 3201122 69 + 4274704
GCUAUUAUUUACAUACA-----UAUUUAUGCAUAUUUCGUAAAUGUGUCCGUGUAUGUGUGUGUGUGUAUUUUU
.....(((.((((((((-----(((....(((((((.....)))))))....))))))))))).)))....... ( -17.50, z-score =  -2.72, R)
>consensus
ACAAACAUGCGCACACA_____CUUUCACGCACACUUCACUCCACUGUGCGAGCGUGUGUGUGUGUGUGUUUUU
....(((((((((((((.....(((.((((...............)))).)))..)))))))))))))...... (-17.71 = -16.94 +  -0.77)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:55:16 2011