Locus 13917

Sequence ID dm3.chrX
Location 9,985,311 – 9,985,389
Length 78
Max. P 0.656775
window19143 window19144

overview

Window 3

Location 9,985,311 – 9,985,389
Length 78
Sequences 5
Columns 84
Reading direction forward
Mean pairwise identity 66.19
Shannon entropy 0.55136
G+C content 0.46069
Mean single sequence MFE -18.40
Consensus MFE -7.56
Energy contribution -9.36
Covariance contribution 1.80
Combinations/Pair 1.27
Mean z-score -1.55
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.23
SVM RNA-class probability 0.601761
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9985311 78 + 22422827
-----UUCGCUGGCGUGUGAAAAGCUGACGGAUAAACACAAA-CCAGUAGCUUUUCCCGCCUUUUUUUCCCAAUAUCGAGUGUG
-----..((((((((.(.(((((((((..((...........-))..)))))))))))))).........(......))))).. ( -19.90, z-score =  -1.90, R)
>droEre2.scaffold_4690 13626205 62 - 18748788
------UCGCUGGCGUGUGAAAAGCUGACGGAUAAACACACA-CCAGUAGCUUUUC---------------AAUAUCGAGUGUG
------.((((.(....((((((((((..((...........-))..)))))))))---------------)....).)))).. ( -18.30, z-score =  -1.96, R)
>droYak2.chrX 18575052 72 + 21770863
------GCGCUGGCGUGUGAAAAGCCGGCGGAUAAACACAAA-CCAGUAGCUUUUCCCGCCGUUUUUC---AAUAUCGAGUG--
------.((((.(....((((((((.(((((..((((((...-...)).).)))..))))))))))))---)....).))))-- ( -22.40, z-score =  -1.80, R)
>droSec1.super_15 701571 75 + 1954846
------UCGCUGGCGUGUGAAAAGCUGACGGAUAAACACAAA-CCAGUAGCUUUUCCCGCCUUUUUUUC--AAUAUCGAAUGUG
------.(((.((((.(.(((((((((..((...........-))..)))))))))))))).....(((--......))).))) ( -20.00, z-score =  -2.27, R)
>droWil1.scaffold_181130 904321 69 - 16660200
UGAGGCUUAAAGACCUAUGAGCAACUAGUAGAUCAACCCUCGUCCAGUUGUUUUCUU---------------GCAACAAGUUUG
.((((.((...((.((((.((...)).)))).)))).)))).....(((((......---------------)))))....... ( -11.40, z-score =   0.17, R)
>consensus
______UCGCUGGCGUGUGAAAAGCUGACGGAUAAACACAAA_CCAGUAGCUUUUCCCGCC_UUUUU____AAUAUCGAGUGUG
...........((((...(((((((((..((............))..))))))))).))))....................... ( -7.56 =  -9.36 +   1.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 9,985,311 – 9,985,389
Length 78
Sequences 5
Columns 84
Reading direction reverse
Mean pairwise identity 66.19
Shannon entropy 0.55136
G+C content 0.46069
Mean single sequence MFE -18.65
Consensus MFE -9.22
Energy contribution -10.70
Covariance contribution 1.48
Combinations/Pair 1.33
Mean z-score -1.22
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.35
SVM RNA-class probability 0.656775
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9985311 78 - 22422827
CACACUCGAUAUUGGGAAAAAAAGGCGGGAAAAGCUACUGG-UUUGUGUUUAUCCGUCAGCUUUUCACACGCCAGCGAA-----
....((((....)))).......((((.((((((((((.((-(........))).)).))))))))...))))......----- ( -21.90, z-score =  -1.68, R)
>droEre2.scaffold_4690 13626205 62 + 18748788
CACACUCGAUAUU---------------GAAAAGCUACUGG-UGUGUGUUUAUCCGUCAGCUUUUCACACGCCAGCGA------
.............---------------.........((((-((((((.................))))))))))...------ ( -15.33, z-score =  -1.20, R)
>droYak2.chrX 18575052 72 - 21770863
--CACUCGAUAUU---GAAAAACGGCGGGAAAAGCUACUGG-UUUGUGUUUAUCCGCCGGCUUUUCACACGCCAGCGC------
--...........---.......((((.((((((((..(((-...........)))..))))))))...)))).....------ ( -20.40, z-score =  -0.97, R)
>droSec1.super_15 701571 75 - 1954846
CACAUUCGAUAUU--GAAAAAAAGGCGGGAAAAGCUACUGG-UUUGUGUUUAUCCGUCAGCUUUUCACACGCCAGCGA------
.............--........((((.((((((((((.((-(........))).)).))))))))...)))).....------ ( -20.60, z-score =  -1.85, R)
>droWil1.scaffold_181130 904321 69 + 16660200
CAAACUUGUUGC---------------AAGAAAACAACUGGACGAGGGUUGAUCUACUAGUUGCUCAUAGGUCUUUAAGCCUCA
....((.((((.---------------.......)))).))..((((.((((....(((........)))....)))).)))). ( -15.00, z-score =  -0.41, R)
>consensus
CACACUCGAUAUU____AAAAA_GGCGGGAAAAGCUACUGG_UUUGUGUUUAUCCGUCAGCUUUUCACACGCCAGCGA______
.......................((((.((((((((..(((............)))..))))))))...))))........... ( -9.22 = -10.70 +   1.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:30:12 2011