Locus 14803

Sequence ID	dm3.chrX
Location	15,575,336 – 15,575,449
Length	113
Max. P	0.999417

overview

Window 3

Location	15,575,336 – 15,575,449
Length	113
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	59.45
Shannon entropy	0.64902
G+C content	0.40404
Mean single sequence MFE	-24.35
Consensus MFE	-9.76
Energy contribution	-11.20
Covariance contribution	1.44
Combinations/Pair	1.48
Mean z-score	-1.27
Structure conservation index	0.40
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.43
SVM RNA-class probability	0.692157
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15575336 113 + 22422827
AAAAAAUGGCAUGGGAAGGAACAUUGAAUGGCCAAAAAUUAGCAUCUUUUACAUUCGAAAAUGUCAAAAGAAGAUGCAUCAA-AGCGGCGGCAUGAUUUCAAUAUAAUCCCCGA
............((((......((((((..(((........((((((((((((((....)))))....))))))))).((..-...)).))).....))))))....))))... ( -23.60, z-score =  -0.47, R)
>droSim1.chrX 12069617 101 + 17042790
-------------GAUGGGAACCUUAAACCGCCAAAAAUUAGCAUCUUCUCCAUUCGAAAAUGUCCAAAGAAGAUGCAUCGGCGGCGGCGGCAUGAUUUCAAUAUAAUCCCAGA
-------------..(((((........(((((........(((((((((.((((....)))).....)))))))))...(....))))))..((....))......))))).. ( -27.80, z-score =  -1.75, R)
>droSec1.super_37 153540 100 + 454039
-------------GAUGGGAACCUUAAACCGCCAGAAAUUAGCAUCUUCUCCAUUCGAAAAUGUCCAAAGAAGAUGCAUCAA-GGCGGCGGCAUGAUUUCAAUAUAAUCCCAGA
-------------..(((((........(((((........(((((((((.((((....)))).....))))))))).....-...)))))..((....))......))))).. ( -27.69, z-score =  -2.34, R)
>droWil1.scaffold_181150 3375737 103 - 4952429
-------AAGUAAAACAGGUGCGUUAAUGAGUCGAAAAUGGACUUUCAAUCAAUUGACAUAUAUUUCAC--AGGUUUAAGGUGGGCAAACCUUAGAAACUAACAGCAAAGCG--
-------............(((((((((..((.((((......)))).))..))))))...........--...((((((((......))))))))........))).....-- ( -18.30, z-score =  -0.50, R)
>consensus
_____________GAUAGGAACCUUAAACCGCCAAAAAUUAGCAUCUUCUCCAUUCGAAAAUGUCCAAAGAAGAUGCAUCAA_GGCGGCGGCAUGAUUUCAAUAUAAUCCCAGA
...............(((((........(((((........(((((((((..................))))))))).........)))))..((....))......))))).. ( -9.76 = -11.20 +   1.44)

alignment

secondary structure

dotplot

Window 4

Location	15,575,336 – 15,575,449
Length	113
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	59.45
Shannon entropy	0.64902
G+C content	0.40404
Mean single sequence MFE	-28.61
Consensus MFE	-19.08
Energy contribution	-18.96
Covariance contribution	-0.12
Combinations/Pair	1.58
Mean z-score	-2.24
Structure conservation index	0.67
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.87
SVM RNA-class probability	0.999417
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15575336 113 - 22422827
UCGGGGAUUAUAUUGAAAUCAUGCCGCCGCU-UUGAUGCAUCUUCUUUUGACAUUUUCGAAUGUAAAAGAUGCUAAUUUUUGGCCAUUCAAUGUUCCUUCCCAUGCCAUUUUUU
..(((((..(((((((....(((..((((..-.....(((((((......(((((....)))))..))))))).......))))))))))))))...)))))............ ( -26.94, z-score =  -1.66, R)
>droSim1.chrX 12069617 101 - 17042790
UCUGGGAUUAUAUUGAAAUCAUGCCGCCGCCGCCGAUGCAUCUUCUUUGGACAUUUUCGAAUGGAGAAGAUGCUAAUUUUUGGCGGUUUAAGGUUCCCAUC-------------
..(((((......((....)).(((...((((((((.(((((((((..(..(......)..)..)))))))))......))))))))....))))))))..------------- ( -36.10, z-score =  -3.22, R)
>droSec1.super_37 153540 100 - 454039
UCUGGGAUUAUAUUGAAAUCAUGCCGCCGCC-UUGAUGCAUCUUCUUUGGACAUUUUCGAAUGGAGAAGAUGCUAAUUUCUGGCGGUUUAAGGUUCCCAUC-------------
..(((((......((....)).(((((((((-..((.(((((((((..(..(......)..)..))))))))).....)).))))))....))))))))..------------- ( -33.50, z-score =  -2.86, R)
>droWil1.scaffold_181150 3375737 103 + 4952429
--CGCUUUGCUGUUAGUUUCUAAGGUUUGCCCACCUUAAACCU--GUGAAAUAUAUGUCAAUUGAUUGAAAGUCCAUUUUCGACUCAUUAACGCACCUGUUUUACUU-------
--....................(((((((.......)))))))--((((((((..(((....((((((((((....))))))).))).....)))..))))))))..------- ( -17.90, z-score =  -1.22, R)
>consensus
UCUGGGAUUAUAUUGAAAUCAUGCCGCCGCC_UCGAUGCAUCUUCUUUGGACAUUUUCGAAUGGAGAAGAUGCUAAUUUUUGGCGGUUUAAGGUUCCCAUC_____________
..(((((..((((((((......((((((........((((((((((((............)))))))))))).......)))))))))))))))))))............... (-19.08 = -18.96 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:46:59 2011