Locus 10339

Sequence ID	dm3.chr3R
Location	13,164,621 – 13,164,731
Length	110
Max. P	0.903730

overview

Window 8

Location	13,164,621 – 13,164,731
Length	110
Sequences	10
Columns	113
Reading direction	reverse
Mean pairwise identity	63.01
Shannon entropy	0.74352
G+C content	0.43197
Mean single sequence MFE	-22.69
Consensus MFE	-9.90
Energy contribution	-10.44
Covariance contribution	0.54
Combinations/Pair	1.22
Mean z-score	-1.06
Structure conservation index	0.44
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.17
SVM RNA-class probability	0.903730
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13164621 110 - 27905053
CACAAAACGCAGUUGGGCAAGGGGGAAAAAGAAGAA-AAAAAAAUUGCGAAAAACUUGCUGAACUAAAAAUCCA--UUCGGCAUCGAUGCUGGUGCCGAGAUAACAAAAUGUU
.(((......((((.((((((...............-.................)))))).)))).........--((((((((((....)))))))))).........))). ( -25.55, z-score =  -1.98, R)
>droSim1.chr3R 19210008 109 + 27517382
CACAAAACGCAGUUGGGCGGGGGGGAAAAAGC-AAA-AAAAAAAUUGCGAAAAACUUGCUGAACUAAAAAUCCA--UUCGGCAUCGAUGCUGGUGCCGAGAUAACAAAAUGUU
.(((......((((.((((((.........((-((.-.......))))......)))))).)))).........--((((((((((....)))))))))).........))). ( -28.66, z-score =  -2.37, R)
>droSec1.super_12 1140956 110 + 2123299
CACAAAACGCAGUUGGGCAGGGGGGAAAAAGCAAAA-AAAAAAAUUGCGAAAAACUUGCUGAACUAAAAAUCCA--UUCGGCAUCGAUGCUGGUGCCGAGAUAACAAAAUGUU
.(((......((((.((((((.........((((..-.......))))......)))))).)))).........--((((((((((....)))))))))).........))). ( -28.66, z-score =  -2.59, R)
>droYak2.chr3R 17255854 111 - 28832112
CACAAAACGCAGUUGGUGGGUGGCGAGGGGGUAAAAGAAAAAAAUUGCGAAAAACUUGCUGAACUAAAAAUCCA--UUCGGCAUCGAUGCUGGUGCCGAGAUAACAAAAUGUU
...........((((((((((((((((...((((..........))))......)))))).........)))))--)(((((((((....)))))))))..))))........ ( -24.90, z-score =  -0.49, R)
>droEre2.scaffold_4770 9283502 105 + 17746568
CACAAAACGCAGUUGGGCGGGGGGAGGAAAA------GAAAAAAUUGCGAAAAACUUGCUGAACUAAAAAUCCA--UUCGGCAUCGAUGCUGGUGCCGAGAUAACAAAAUGUU
.(((......((((.((((((..........------.................)))))).)))).........--((((((((((....)))))))))).........))). ( -24.63, z-score =  -1.17, R)
>droAna3.scaffold_13340 10377955 86 - 23697760
------------------CAAAACGCAAUGGUGGA--GGAAAAAU-----AAAAAUUGCUGAACUAAAAAUCCA--UUCGGCAUCGAUGCUGGUUCCGAGAUAACAAAAUGUU
------------------.....(((....)))..--((((....-----......(((((((...........--)))))))..........))))................ ( -12.95, z-score =   0.23, R)
>dp4.chr2 21530843 87 + 30794189
------------------------CAGAACGCAGCCAUGGCAGGGAGGGGGGAACAUAGAGAACUAAAAAUCCA--UUCGGCAUCGAUGCUGGUGCCGAGAUAACAAAAUGUU
------------------------......(((((....))..(((...(....).(((....)))....))).--((((((((((....)))))))))).........))). ( -19.60, z-score =  -0.30, R)
>droPer1.super_0 8752202 84 + 11822988
------------------------CAGAACGCAGCCAUGGAAG---GGGGGGGAAAUAGAGAACUAAAAAUCCA--UUCGGCAUCGAUGCUGGUGCCGAGAUAACAAAAUGUU
------------------------.....(.(..((......)---).).)(((..(((....)))....))).--((((((((((....))))))))))............. ( -18.00, z-score =  -0.32, R)
>droVir3.scaffold_13047 14256584 93 - 19223366
--------------------CACAGUGAACACAGCUGGGCAAAAGCAAUGCGCAGAAUAAGCGCUGAAAACUGAAUAUCGCAAUCGAUGCUGGCGUCGAGAUAACAAAAUGUU
--------------------..(((((.......(((.(((.......))).)))......))))).........((((....((((((....)))))))))).......... ( -22.52, z-score =  -0.48, R)
>droMoj3.scaffold_6540 17684622 92 - 34148556
---------------------ACAGUAAACACUACUGGGCGCUGCCAGUGUGCAGAACAAGAAGUGAAAACUGAAUAUCGCUAUCGAUGCUAACGUCGAGAUAACAAAAUGUU
---------------------.((((...((((.((..(..((((......))))..).)).))))...))))..((((....((((((....)))))))))).......... ( -21.40, z-score =  -1.11, R)
>consensus
____________________GGGGGAAAAAGCAGAA_AAAAAAAUUGCGAAAAACUUGCUGAACUAAAAAUCCA__UUCGGCAUCGAUGCUGGUGCCGAGAUAACAAAAUGUU
.............................................................................(((((((((....))))))))).............. ( -9.90 = -10.44 +   0.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:22:04 2011