Locus 6138

Sequence ID	dm3.chr3L
Location	3,997,382 – 3,997,512
Length	130
Max. P	0.996325

overview

Window 2

Location	3,997,382 – 3,997,482
Length	100
Sequences	12
Columns	112
Reading direction	reverse
Mean pairwise identity	68.99
Shannon entropy	0.63764
G+C content	0.51814
Mean single sequence MFE	-27.57
Consensus MFE	-17.52
Energy contribution	-17.44
Covariance contribution	-0.08
Combinations/Pair	1.06
Mean z-score	-0.10
Structure conservation index	0.64
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.07
SVM RNA-class probability	0.530165
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3997382 100 - 24543557
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCACCGCGGGAGAA---------GUCAGAGCCGACCAGGC-CAAAUAGAUUCGC--AGGCCGAUAA
((((((.(((((.(((((.......)))))))))))))).)).......(((((((.(..---------..).(.(((.....)))-).......)))))--.))....... ( -27.60, z-score =   0.67, R)
>droSim1.chr3L 3540930 100 - 22553184
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCACCGCGGGAGAA---------GUCAGAGCCGACCAGGC-CAAAUAGAUUCGC--AGGCCGAUAA
((((((.(((((.(((((.......)))))))))))))).)).......(((((((.(..---------..).(.(((.....)))-).......)))))--.))....... ( -27.60, z-score =   0.67, R)
>droSec1.super_2 3989935 100 - 7591821
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCACCGCGGGAGAA---------GUCAGAGCCGACCAGGU-CAAAUAGAUUCGC--AGGCCGAUAA
((((((.(((((.(((((.......)))))))))))))).))....((.....)).....---------(((.(.(((...(..((-(.....)))..).--.))))))).. ( -26.90, z-score =   0.76, R)
>droYak2.chr3L 4561732 100 - 24197627
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCACCGCGGGAGAA---------UUCAGAACCGACCAGGC-CAAAUAGAUUCGC--AGGCCGAUAA
((((((.(((((.(((((.......)))))))))))))).))..........(((.....---------.......)))....(((-(............--.))))..... ( -27.22, z-score =   0.36, R)
>droEre2.scaffold_4784 6699103 100 - 25762168
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCACCGCGGGAGAA---------GUCAGAAACGACCAGGC-CAAAUAGAUUCGC--AGGCCGAUAA
((((((.(((((.(((((.......)))))))))))))).))....((.....)).....---------(((......)))..(((-(............--.))))..... ( -27.22, z-score =   0.34, R)
>droAna3.scaffold_13337 1844456 111 - 23293914
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCUCCGCAGGGAAGUCUGUC-CUGCCGGGCCGGACCCGGUACAAAUAGAUUCCCCAUGGCCGAUAA
((((((.(((((.(((((.......)))))))))))))).))......((.((.(((.(((((((.-.(((((((.....)))))))...))))))).)))...)).))... ( -43.90, z-score =  -2.02, R)
>dp4.chrXR_group8 645966 109 - 9212921
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCUUC-AAUGCGAUGAAGAAGAAGGUAGCUCCAACCGAA--UAUGUAGAUGCCACACUGGCGAUAA
((((((.(((((.(((((.......)))))))))))))).)).((((((((-....(......)..))))))))...........--........((((.....)))).... ( -30.80, z-score =  -0.78, R)
>droPer1.super_32 153808 109 + 992631
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCUUC-AAUGCGAUGAAGAAGAAGGUAGCUCCAACCGAA--UAUGUAGAUGCCACACUGGCGAUAA
((((((.(((((.(((((.......)))))))))))))).)).((((((((-....(......)..))))))))...........--........((((.....)))).... ( -30.80, z-score =  -0.78, R)
>droWil1.scaffold_180698 8766572 91 - 11422946
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCCGCAAUUACCUUC-AAUCCGAAACAGCUUGAAAUAGAUUUCACUUUA--GUGAUAA------------------
((((((.(((((.(((((.......)))))))))))).))))......(((-((..(......).))))).......((((....--))))...------------------ ( -21.40, z-score =  -0.49, R)
>droVir3.scaffold_12758 5256 90 + 972128
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCGGCAAUUACCUUC-AAUCCAAAACAGCU-CCAACAGAUUCAUCAGUU--CCGAUAA------------------
((((((.(((((.(((((.......)))))))))))))((......))...-........)))...-...........(((....--..)))..------------------ ( -17.80, z-score =   0.61, R)
>droMoj3.scaffold_6680 22746199 82 + 24764193
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCGGCAAUUACCUUUGGCUCCAA----------GGGAGAUUCAUCCAUU--GCGAUAA------------------
..((((.(((((.(((((.......))))))))))))))(((((..((((((....)))----------))).((....)).)))--)).....------------------ ( -27.40, z-score =  -1.10, R)
>droGri2.scaffold_15110 545794 92 - 24565398
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCGGCAAUUACCUUUGAAUCCGAAACAGCUAGAAACAGAUUCAUCCGCU--GCGAUAA------------------
........((((.(((((.......)))))))))(((((((.......((((....)))).......(((.....)))....)))--))))...------------------ ( -22.20, z-score =   0.61, R)
>consensus
UGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCUCCGCAGGCGAA_________GUCAGAUCCGACCAGG__CAAAUAGAUUCGC__AGGCCGAUAA
((((((.(((((.(((((.......)))))))))))))).))...................................................................... (-17.52 = -17.44 +  -0.08)

alignment

secondary structure

dotplot

Window 3

Location	3,997,418 – 3,997,512
Length	94
Sequences	11
Columns	108
Reading direction	reverse
Mean pairwise identity	77.81
Shannon entropy	0.45045
G+C content	0.48246
Mean single sequence MFE	-31.15
Consensus MFE	-21.52
Energy contribution	-21.24
Covariance contribution	-0.28
Combinations/Pair	1.10
Mean z-score	-2.50
Structure conservation index	0.69
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.92
SVM RNA-class probability	0.996325
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3997418 94 - 24543557
--UAUCUCCAU--CUCUGUCCAUU-UUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCACCGCGGGAGAAGUCA---------
--..(((((..--...(((((((.-...)))))))((((((.(((((.(((((.......)))))))))))))).))............))))).....--------- ( -34.70, z-score =  -3.19, R)
>droSim1.chr3L 3540966 94 - 22553184
--UAUCUCCAU--CUCUGUCCAUU-UUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCACCGCGGGAGAAGUCA---------
--..(((((..--...(((((((.-...)))))))((((((.(((((.(((((.......)))))))))))))).))............))))).....--------- ( -34.70, z-score =  -3.19, R)
>droSec1.super_2 3989971 94 - 7591821
--UAUCUCCAU--CUCUGUCCAUU-UUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCACCGCGGGAGAAGUCA---------
--..(((((..--...(((((((.-...)))))))((((((.(((((.(((((.......)))))))))))))).))............))))).....--------- ( -34.70, z-score =  -3.19, R)
>droYak2.chr3L 4561768 96 - 24197627
--UAUCUCCAUCUCUCUGUCCAUU-UUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCACCGCGGGAGAAUUCA---------
--........(((((((((((((.-...)))))))((((((.(((((.(((((.......)))))))))))))).))...........)))))).....--------- ( -34.80, z-score =  -3.42, R)
>droEre2.scaffold_4784 6699139 96 - 25762168
--UAUCUCCAUCUCUCUGUCCAUU-UUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCACCGCGGGAGAAGUCA---------
--........(((((((((((((.-...)))))))((((((.(((((.(((((.......)))))))))))))).))...........)))))).....--------- ( -34.80, z-score =  -3.17, R)
>droAna3.scaffold_13337 1844495 104 - 23293914
--UAUCUCUCCAUCUCUGUUCAUU-UUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCUCCGCAGGGAAGUCUGUCCUGCCG-
--..............(((((((.-...)))))))((((((.(((((.(((((.......)))))))))))))).)).........((((((.......))))))..- ( -31.80, z-score =  -1.81, R)
>dp4.chrXR_group8 646003 102 - 9212921
----UAUCUCCCUGUCUGUCCAUU-UUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCUUC-AAUGCGAUGAAGAAGAAGGUA
----............(((((((.-...)))))))((((((.(((((.(((((.......)))))))))))))).))..(((((((-....(......)..))))))) ( -33.60, z-score =  -2.73, R)
>droPer1.super_32 153845 102 + 992631
----UAUCUCCCUGUCUGUCCAUU-UUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCUUC-AAUGCGAUGAAGAAGAAGGUA
----............(((((((.-...)))))))((((((.(((((.(((((.......)))))))))))))).))..(((((((-....(......)..))))))) ( -33.60, z-score =  -2.73, R)
>droWil1.scaffold_180698 8766607 89 - 11422946
--UAUCUUACACUCUUUAUCUAUUCUUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCCGCAAUUACCUUC-AAUCC----------------
--................(((((.....)))))..((((((.(((((.(((((.......)))))))))))).)))).........-.....---------------- ( -19.90, z-score =  -1.49, R)
>droVir3.scaffold_12758 5290 82 + 972128
--------GCACAUGCUAUCUAUU-UUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCGGCAAUUACCUUC-AAUCC----------------
--------(((((((((((.....-...)))).)))))))(((((((.(((((.......)))))))))).))((......))...-.....---------------- ( -25.70, z-score =  -2.11, R)
>droGri2.scaffold_15110 545829 91 - 24565398
CAUUCAUAUCCGGGGCUAUCUAUU-UUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCGGCAAUUACCUUUGAAUCC----------------
.(((((.....((.(((.(((((.-...))))).....(((.(((((.(((((.......)))))))))))))))).....))..)))))..---------------- ( -24.40, z-score =  -0.51, R)
>consensus
__UAUCUCCCUCUCUCUGUCCAUU_UUUAUGGACAUGUGCGUAAGCGAUCCGUGCGAAAAAUGGGCGCUUCGCAGCAAUUACCUCCGCAGGAGAAGUCA_________
..................(((((.....)))))..((((((.(((((.(((((.......))))))))))))).)))............................... (-21.52 = -21.24 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:01:57 2011