Locus 15227

Sequence ID	dm3.chrX
Location	18,043,125 – 18,043,274
Length	149
Max. P	0.683088

overview

Window 5

Location	18,043,125 – 18,043,220
Length	95
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	90.07
Shannon entropy	0.16000
G+C content	0.50277
Mean single sequence MFE	-26.48
Consensus MFE	-19.58
Energy contribution	-19.18
Covariance contribution	-0.40
Combinations/Pair	1.10
Mean z-score	-2.08
Structure conservation index	0.74
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.29
SVM RNA-class probability	0.628266
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18043125 95 + 22422827
GUGUCGGGCACAACGAUUGAGAUUCUCAUUUUUAUACUCAUUCCCGGGGGGCAUCGAUUUU-UGUCCCCACCUCUCC-----------GCUAGUCCAACA---UUCUCCA
((((.((((.....((.((((...............)))).))...(((((((........-)))))))........-----------....)))).)))---)...... ( -25.06, z-score =  -1.78, R)
>droSim1.chrX_random 161141 95 + 5698898
GUGUCGGGCACAACGAUUGAGAUUCUCAUUUUUAUACUCAUUCCCGGGGGGCAUCGAUUUU-UGUCUCCACCUCCCC-----------GCUAGUCCAACA---UUCUCCA
((((.((((.....((.((((...............)))).)).(((((((....(((...-.))).....))))))-----------)...)))).)))---)...... ( -24.56, z-score =  -1.60, R)
>droSec1.super_8 353058 94 + 3762037
GUGUCGGGCACAACGAUUGAGAUUCUCAUUUUUAUACUCAUUCCCGGGGG-CAUCGAUUUU-UGUCUCCACCUCCCC-----------GCUAGUCCAACA---UUCUCCA
((((.((((.....((.((((...............)))).))..(((((-((........-)))))))........-----------....)))).)))---)...... ( -22.36, z-score =  -1.44, R)
>droYak2.chrX 16665953 109 + 21770863
GUGUCGGGCGCAACGAUUGAGAUUCUCAUUUUUAUACUCAUUCCCGGGGG-CAUCGAUUUUGUGUCCCCACCUCCCAACGUUCUCCUAGCUAGCCCAACAACGUUCUCCA
.(((.((((((...((.((((...............)))).))..(((((-(((.......))))))))...................))..)))).))).......... ( -28.16, z-score =  -1.69, R)
>droEre2.scaffold_4690 8372133 94 + 18748788
GUGUCGGGCGCAGCGAUUGAGAUUCUCAUUUUUAUACUCAUUCCCGGGGG-CAUCGAUUUU-UGUCCCCACCUCCCC-----------GCUAGCCCAACA---UUCUCUA
((((.((((..(((((.((((...............)))).))..(((((-((........-)))))))........-----------))).)))).)))---)...... ( -32.26, z-score =  -3.91, R)
>consensus
GUGUCGGGCACAACGAUUGAGAUUCUCAUUUUUAUACUCAUUCCCGGGGG_CAUCGAUUUU_UGUCCCCACCUCCCC___________GCUAGUCCAACA___UUCUCCA
.(((.((((.....((.((((...............)))).))..(((((.....(((.....))).....)))))................)))).))).......... (-19.58 = -19.18 +  -0.40)

alignment

secondary structure

dotplot

Window 6

Location	18,043,183 – 18,043,274
Length	91
Sequences	3
Columns	91
Reading direction	reverse
Mean pairwise identity	80.69
Shannon entropy	0.25228
G+C content	0.54179
Mean single sequence MFE	-25.77
Consensus MFE	-22.77
Energy contribution	-22.00
Covariance contribution	-0.77
Combinations/Pair	1.21
Mean z-score	-1.17
Structure conservation index	0.88
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.41
SVM RNA-class probability	0.683088
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18043183 91 - 22422827
UUUCUCCUAUCCCCCACCAUCUCCCCCCCCCCCUCGUGAACCUCAAAAACUCCCUGGAGAAUGUUGGACUAGCGGAGAGGUGGGGACAAAA
...........(((((((.(((((......((..((((.....).....(((....))).)))..))......))))))))))))...... ( -28.10, z-score =  -1.51, R)
>droSim1.chrX_random 161199 77 - 5698898
--------------UUUCUGCUCCUCCCCCCUCCUGUGAACCUCAAAAACUCCCUGGAGAAUGUUGGACUAGCGGGGAGGUGGAGACAAAA
--------------..(((.(.((((((((.(((..((.....))....(((....)))......)))...).))))))).).)))..... ( -24.60, z-score =  -1.00, R)
>droSec1.super_8 353115 77 - 3762037
--------------UUUCUGCUCCUCCCCCCUCCUGUGAACCUCAAAAACUCCCUGGAGAAUGUUGGACUAGCGGGGAGGUGGAGACAAAA
--------------..(((.(.((((((((.(((..((.....))....(((....)))......)))...).))))))).).)))..... ( -24.60, z-score =  -1.00, R)
>consensus
______________UUUCUGCUCCUCCCCCCUCCUGUGAACCUCAAAAACUCCCUGGAGAAUGUUGGACUAGCGGGGAGGUGGAGACAAAA
.......................((((.((.((((((.....((((...(((....)))....))))....)))))).)).))))...... (-22.77 = -22.00 +  -0.77)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:55:19 2011