Locus 14825

Sequence ID dm3.chrX
Location 15,708,203 – 15,708,351
Length 148
Max. P 0.638151
window20413 window20414

overview

Window 3

Location 15,708,203 – 15,708,292
Length 89
Sequences 11
Columns 89
Reading direction forward
Mean pairwise identity 89.58
Shannon entropy 0.21559
G+C content 0.52227
Mean single sequence MFE -28.67
Consensus MFE -24.23
Energy contribution -24.78
Covariance contribution 0.55
Combinations/Pair 1.08
Mean z-score -1.42
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.638151
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15708203 89 + 22422827
AAAAAAAGCUGGCUGCAUGAAAAACAUCACCAGCUCGAGCACUUGCAGCACUGGGCUGCUGCAAUUGCAGAACAACCUGAGCUGCAGCG
...........(((((.(((......)))..(((((..(((.((((((((......)))))))).)))((......)))))))))))). ( -32.40, z-score =  -1.96, R)
>droEre2.scaffold_4690 7414369 89 - 18748788
AAAAAAAGCUGGCUGCAUGAAAAACAUCACCAGCUCGAGCACUUGCAGCACCGGGCUGCUGCAAUUGCAGAACAACCUGAGCUGCAGCG
...........(((((.(((......)))..(((((..(((.((((((((......)))))))).)))((......)))))))))))). ( -32.40, z-score =  -2.10, R)
>droYak2.chrX 9907202 89 + 21770863
AGAAAAAGCUGGCUGCAUGAAAAACAUCACCAGCUCGAGCACUUGCAGCACCGGGCUGCUGCAAUUGCAGAACAACCUGAGCUGCAGCG
...........(((((.(((......)))..(((((..(((.((((((((......)))))))).)))((......)))))))))))). ( -32.40, z-score =  -1.74, R)
>droSec1.super_37 289379 89 + 454039
AAGAAAAGCUGGCUGCAUGAAAAACAUCACCAGCUCGAGCACUUGCAGCACCGGGCUGCUGCAAUUGCAGAACAACCUGAGCUGCAGCG
...........(((((.(((......)))..(((((..(((.((((((((......)))))))).)))((......)))))))))))). ( -32.40, z-score =  -1.74, R)
>droSim1.chrX_random 4067191 89 + 5698898
AAGAAAAGCUGGCUGCAUGAAAAACAUCACCAGCUCGAGCACUUGCAGCACCGGGCUGCUGCAAUUGCAGAACAACCUGAGCUGCAGCG
...........(((((.(((......)))..(((((..(((.((((((((......)))))))).)))((......)))))))))))). ( -32.40, z-score =  -1.74, R)
>droMoj3.scaffold_6473 7342772 89 - 16943266
GUAAAAAGCUGGCUGCAUGAAAAACAUCACCAGCUCAAGCACUUGCGGCACGGGGCUGCUGCAAUUGCAGAACAAUCUCAGCAACAGCG
......((((((.((.(((.....)))))))))))...(((.((((((((......)))))))).)))............((....)). ( -27.80, z-score =  -1.27, R)
>droVir3.scaffold_12970 11642609 89 + 11907090
AAUAAAAGCUGGCUGCAUGAAAAACAUCACCAGCUCAAGCACUUGCGGCACGGGGCUGCUGCAAUUGCAGAACAAUCUCAGCAACAGCG
......((((((.((.(((.....)))))))))))...(((.((((((((......)))))))).)))............((....)). ( -27.80, z-score =  -1.56, R)
>droGri2.scaffold_15203 3615191 84 + 11997470
-----AAACUGGCUGCAUGAAAAACAUCACCAGCUCAAGCACUUGCGGCACGGGGCUGCUGCAAUUGCAGAACAAUCUCAGCAACAGCG
-----...((((((((((((......)))...((....))...)))))).))).((((.(((...((.(((....)))))))).)))). ( -23.90, z-score =  -0.76, R)
>droWil1.scaffold_181096 6000290 84 + 12416693
-----AAACGGGCUGCAUGAAAAACAUUACCAGCUCAAGCACUUGCAGCACUGGCCUGCUGCAAUUGCAGAACAAUCUCAGCAGCAGCG
-----......((((((((.....))).....(((...(((.((((((((......)))))))).))).((......))))).))))). ( -27.30, z-score =  -1.38, R)
>droPer1.super_95 100261 84 + 176753
-----AAGCUGGCUGCAUGAAAAACAUAACCAGCUCGAGCACCUGCAGCACGGGGCUGCUGCAAUUGCAGAACAAUCUAAACAACAGGG
-----..((((((((.(((.....)))...)))))..))).((((((((.....))))((((....))))..............)))). ( -23.30, z-score =  -0.72, R)
>dp4.Unknown_group_9 52432 84 + 53872
-----AAGCUGGCUGCAUGAAAAACAUAACCAGCUCGAGCACCUGCAGCACGGGGCUGCUGCAAUUGCAGAACAAUCUAAACAACAGGG
-----..((((((((.(((.....)))...)))))..))).((((((((.....))))((((....))))..............)))). ( -23.30, z-score =  -0.72, R)
>consensus
AA_AAAAGCUGGCUGCAUGAAAAACAUCACCAGCUCGAGCACUUGCAGCACGGGGCUGCUGCAAUUGCAGAACAAUCUGAGCAGCAGCG
......((((((.((.(((.....)))))))))))...(((.((((((((......)))))))).)))............((....)). (-24.23 = -24.78 +   0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 15,708,292 – 15,708,351
Length 59
Sequences 5
Columns 67
Reading direction reverse
Mean pairwise identity 71.60
Shannon entropy 0.50493
G+C content 0.51377
Mean single sequence MFE -17.74
Consensus MFE -9.54
Energy contribution -9.78
Covariance contribution 0.24
Combinations/Pair 1.33
Mean z-score -1.09
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.519210
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15708292 59 - 22422827
-------GGUAAUUCGG-AUGGGCAACGGACCUGCCUGUUGUUCUGUCUUCUCGGCAACUUCCAACU
-------........((-(.(((((((((......)))))))))((((.....))))...))).... ( -16.20, z-score =  -1.20, R)
>droSec1.super_37 289468 59 - 454039
-------GGUGAUUUGG-AUGGGCAACGGACCUGCCUGUUGUUCUGUCUUCUCGGCAACUUCCAACU
-------......((((-(.(((((((((......)))))))))((((.....))))...))))).. ( -17.40, z-score =  -1.32, R)
>droYak2.chrX 9907291 67 - 21770863
AAUGAGGGGGAAUGGGGAAUGGGCAACGGACCUGCCUGUUGUUCUGUCUUCUCGGCAACUUCCAACU
....((..((((.(((((..(((((((((......)))))))))..)))))..(....)))))..)) ( -21.80, z-score =  -0.95, R)
>droEre2.scaffold_4690 7414458 65 + 18748788
GGUGAUUGGAAA--GGGAAUGGGCAACGGACCUGCCUGUUGUUCUGUCUUCUCGGCAACUUCCAACU
.....((((((.--(((((.(((((((((......)))))))))....)))))(....))))))).. ( -21.30, z-score =  -1.53, R)
>droMoj3.scaffold_6473 7342861 59 + 16943266
--------GAGAAAUGGUGUAAAUAACGCACCUGCUUCUGGUUUGCCAACAACAGCGACGUCCAAUU
--------.((((..(((((.......)))))...))))((.((((........))))...)).... ( -12.00, z-score =  -0.47, R)
>consensus
_______GGAAAUUGGG_AUGGGCAACGGACCUGCCUGUUGUUCUGUCUUCUCGGCAACUUCCAACU
...............((...(((((((((......)))))))))((((.....))))....)).... ( -9.54 =  -9.78 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:47:32 2011