Locus 15134

Sequence ID	dm3.chrX
Location	17,539,036 – 17,539,140
Length	104
Max. P	0.857871

overview

Window 3

Location	17,539,036 – 17,539,126
Length	90
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	81.93
Shannon entropy	0.27598
G+C content	0.49451
Mean single sequence MFE	-25.35
Consensus MFE	-18.70
Energy contribution	-18.70
Covariance contribution	-0.00
Combinations/Pair	1.18
Mean z-score	-1.89
Structure conservation index	0.74
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.84
SVM RNA-class probability	0.832895
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17539036 90 + 22422827
-----------GAUUUGCUUUUUAGCAGGGG-UCGUGGGUCGGAGACCAUGGCAACAUGGCUAUAUGGUGGACAUGGGCACACGGAAUAUAUAUACAUAAAC
-----------..((((((....))))))..-(((((.(((..((.(((((....))))))).((((.....))))))).)))))................. ( -25.70, z-score =  -2.99, R)
>droSim1.chrX 3612425 88 - 17042790
-----------GAUUUGCUUUUUAGCCGGGG-UCGUGGGUCGGGGACCAUGGCAACAUGGCUACAUGGUGGACAUGGGCACACGGAAUAUAUA--CAUAAAC
-----------....((((...((((((..(-((((((........)))))))....))))))((((.....)))))))).............--....... ( -26.30, z-score =  -2.16, R)
>droSec1.super_17 1381779 88 + 1527944
-----------GAUUUGCUUUUUAGCCGGGG-UCGUGGGUCGGGAACCAUGGCAACAUGGCUACAUGGUGGACAUGGGCACACGGAAUAUAUA--CAUAAAC
-----------....((((...((((((..(-((((((........)))))))....))))))((((.....)))))))).............--....... ( -26.30, z-score =  -2.27, R)
>droYak2.chrX 16166309 94 + 21770863
UUUGGCAUUUGCAUUUGGAUUUUGGCCGGGGGUCGUGGGUCGGGCACCAUGGCGACAUGGACAAAU------CGUGGGCACAUGGAAUAUAUA--CAUAAAC
.....(((.(((...(((..((((.((((..(((((((........)))))))..).))).)))))------))...))).))).........--....... ( -23.10, z-score =  -0.13, R)
>consensus
___________GAUUUGCUUUUUAGCCGGGG_UCGUGGGUCGGGGACCAUGGCAACAUGGCUACAUGGUGGACAUGGGCACACGGAAUAUAUA__CAUAAAC
................................(((((.(((.....(((((....)))))...((((.....))))))).)))))................. (-18.70 = -18.70 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	17,539,043 – 17,539,140
Length	97
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	85.88
Shannon entropy	0.22809
G+C content	0.51080
Mean single sequence MFE	-28.00
Consensus MFE	-21.50
Energy contribution	-22.25
Covariance contribution	0.75
Combinations/Pair	1.12
Mean z-score	-2.03
Structure conservation index	0.77
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.94
SVM RNA-class probability	0.857871
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17539043 97 + 22422827
----UUUUUAGCAGGGGUCGUGGGUCGGAGACCAUGGCAACAUGGCUAUAUGGUGGACAUGGGCACACGGAAUAUAUAUACAUAAACAGCAUUACUGGCAG
----......((.....(((((.(((..((.(((((....))))))).((((.....))))))).)))))................(((.....))))).. ( -25.10, z-score =  -1.96, R)
>droSim1.chrX 3612432 95 - 17042790
----UUUUUAGCCGGGGUCGUGGGUCGGGGACCAUGGCAACAUGGCUACAUGGUGGACAUGGGCACACGGAAUAUAU--ACAUAAACAGCGUUACUGGCAG
----......(((((..(((((.(((..((.(((((....))))))).((((.....))))))).))))).......--.....(((...))).))))).. ( -30.70, z-score =  -2.64, R)
>droSec1.super_17 1381786 95 + 1527944
----UUUUUAGCCGGGGUCGUGGGUCGGGAACCAUGGCAACAUGGCUACAUGGUGGACAUGGGCACACGGAAUAUAU--ACAUAAACAGCGUUACUGGCAG
----......(((((..(((((.(((.....(((((....)))))...((((.....))))))).))))).......--.....(((...))).))))).. ( -29.30, z-score =  -2.26, R)
>droYak2.chrX 16166324 93 + 21770863
UGGAUUUUGGCCGGGGGUCGUGGGUCGGGCACCAUGGCGACAUGGACAAAU------CGUGGGCACAUGGAAUAUAU--ACAUAAACAGCUUUACUGGCAG
........((((...))))((.(((..(((.(((((....))))).....(------((((....))))).......--.........)))..))).)).. ( -26.90, z-score =  -1.25, R)
>consensus
____UUUUUAGCCGGGGUCGUGGGUCGGGGACCAUGGCAACAUGGCUACAUGGUGGACAUGGGCACACGGAAUAUAU__ACAUAAACAGCGUUACUGGCAG
..........(((((..(((((.(((.....(((((....)))))...((((.....))))))).)))))..(((......)))..........))))).. (-21.50 = -22.25 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:53:38 2011