Locus 10619

Sequence ID dm3.chr3R
Location 15,120,837 – 15,120,973
Length 136
Max. P 0.968865
window14603 window14604 window14605

overview

Window 3

Location 15,120,837 – 15,120,942
Length 105
Sequences 10
Columns 105
Reading direction reverse
Mean pairwise identity 90.36
Shannon entropy 0.21719
G+C content 0.35321
Mean single sequence MFE -29.22
Consensus MFE -22.93
Energy contribution -22.73
Covariance contribution -0.20
Combinations/Pair 1.19
Mean z-score -2.56
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.81
SVM RNA-class probability 0.968865
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 15120837 105 - 27905053
CGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCGUUGAGGGCUUUUCCAUUUAGCGCAGAUAGACAUU
..........(((((((((((((((((((((((((.........))))))))))))))).((((((((((......))))........))).))))))))))))) ( -31.40, z-score =  -3.22, R)
>droSim1.chr3R 21156319 105 + 27517382
CGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCGUUGAGGGCUUUUCCAUUUAGCGCAGAUAGACAUU
..........(((((((((((((((((((((((((.........))))))))))))))).((((((((((......))))........))).))))))))))))) ( -31.40, z-score =  -3.22, R)
>droSec1.super_25 180979 105 + 827797
CGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCGUUGAGGGCUUUUCCAUUUAGCGCAGAUAGACAUU
..........(((((((((((((((((((((((((.........))))))))))))))).((((((((((......))))........))).))))))))))))) ( -31.40, z-score =  -3.22, R)
>droYak2.chr3R 3832822 105 - 28832112
CGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCGUUGAGGGCUUUUCCAUUUAGCGCAGAUAGACAUU
..........(((((((((((((((((((((((((.........))))))))))))))).((((((((((......))))........))).))))))))))))) ( -31.40, z-score =  -3.22, R)
>droEre2.scaffold_4770 11234439 105 + 17746568
CGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCGUUGAGGGCUUUUCCAUUUAGCGCAGAUAGACAUU
..........(((((((((((((((((((((((((.........))))))))))))))).((((((((((......))))........))).))))))))))))) ( -31.40, z-score =  -3.22, R)
>droAna3.scaffold_13340 8431990 105 + 23697760
AACAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUGUUGAGGGCUUUUCCAUUUGGCGCAGAUAGACGUU
.............((((((((((((((((((((((.........)))))))))))))))..(((.(((((......)))))........)))...)))))))... ( -28.10, z-score =  -1.95, R)
>dp4.chr2 29576364 102 - 30794189
CGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAACUUGUAAUUGCAAAUGUUUGCCUAAGCUGUUGAGGGCUUUUCCAUUUAGCGUAGA-AGCCA--
.(((((((((....))))))(((((((((((((((.........))))))))))))))).))).............(((((((.(.......).)))-)))).-- ( -26.60, z-score =  -1.53, R)
>droPer1.super_6 4948393 102 - 6141320
CGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUGUUGAGGGCUUUUCCAUUUAGCGUAGA-AGCCA--
.(((((((((....))))))(((((((((((((((.........))))))))))))))).))).............(((((((.(.......).)))-)))).-- ( -26.60, z-score =  -1.68, R)
>droVir3.scaffold_13047 2704644 103 + 19223366
CGGAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCCAAGCUGUUAAGGGCUUUACU-CGCAGC-UAAACCUUCAAC
.((.((((((....))))))(((((((((((((((.........)))))))))))))))....)).((((((...(((.....))-))))))-)........... ( -26.50, z-score =  -2.13, R)
>droGri2.scaffold_15116 346024 105 + 1808639
CGGCGAUAAAAUUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUGUAAAGGGCUUUACUCUCAGAUACUGGCACACACA
....((((((....))))))..(((((((((((((.........)))))))))))))((.((((....(((...((((.....))))))).....)))).))... ( -27.40, z-score =  -2.20, R)
>consensus
CGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCGUUGAGGGCUUUUCCAUUUAGCGCAGAUAGACAUU
....((((((....))))))..(((((((((((((.........)))))))))))))(((((((((((((......)))))........)).))))))....... (-22.93 = -22.73 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,120,871 – 15,120,973
Length 102
Sequences 10
Columns 108
Reading direction forward
Mean pairwise identity 81.87
Shannon entropy 0.37395
G+C content 0.39274
Mean single sequence MFE -20.44
Consensus MFE -13.46
Energy contribution -13.32
Covariance contribution -0.14
Combinations/Pair 1.10
Mean z-score -1.36
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.15
SVM RNA-class probability 0.566013
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 15120871 102 + 27905053
CGGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUGCGACUGCUGUUCACUCUCGGUUCUCCACAGCAA------
..(((...(((....((((((((((.............))))))))))...((((((....)))))))))((..((((........))))..))...)))..------ ( -18.92, z-score =  -1.13, R)
>droSim1.chr3R 21156353 102 - 27517382
CGGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUGCGACUGCUGUUCACUCUCGGUUCUCCACAGCAA------
..(((...(((....((((((((((.............))))))))))...((((((....)))))))))((..((((........))))..))...)))..------ ( -18.92, z-score =  -1.13, R)
>droSec1.super_25 181013 102 - 827797
CGGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUGCGACUGCUGUUCACUCUCGGUUCUCCACAGCAA------
..(((...(((....((((((((((.............))))))))))...((((((....)))))))))((..((((........))))..))...)))..------ ( -18.92, z-score =  -1.13, R)
>droYak2.chr3R 3832856 108 + 28832112
CGGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUGCGGCUGCUGUUCACUCUCGGUUCUCCACAGCAAUGGCAA
..(((...((.....((((((((((.............))))))))))...((((((....))))))((.((..((((........))))...)).))))...))).. ( -22.02, z-score =  -0.74, R)
>droEre2.scaffold_4770 11234473 108 - 17746568
CGGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUGCGGCUGCUGUUCACUCUCGGUUCUCCACAGCAAUGCCAA
.(((....(((....((((((((((.............))))))))))...((((((....)))))))))...((((((........((....))))))))..))).. ( -24.22, z-score =  -1.67, R)
>dp4.chr2 29576395 91 + 30794189
CAGCUUAGGCAAACAUUUGCAAUUACAAGUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUGCGGCUGCUCCACCGACUGCGAC-----------------
(((((...(((....((((((((((...(.....)...))))))))))...((((((....))))))))))))))................----------------- ( -17.90, z-score =  -0.79, R)
>droPer1.super_6 4948424 91 + 6141320
CAGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUGCGGCUGCUCCACCGACUGCGAC-----------------
(((((...(((....((((((((((.............))))))))))...((((((....))))))))))))))................----------------- ( -17.32, z-score =  -1.16, R)
>droMoj3.scaffold_6540 21311424 101 - 34148556
CAGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCGCCGCUCGUUGCGCCG-CCAAGCAGCCCAGAACAA------
..((((.(((.....((((((((((.............))))))))))...((((((....))))))(.(((.....))).))-))))))............------ ( -24.22, z-score =  -2.25, R)
>droVir3.scaffold_13047 2704676 93 - 19223366
CAGCUUGGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUCCGCUCGCUGCGC---------UGCCAAGAACAA------
((((.(((((.....((((((((((.............))))))))))...((((((....))))))...)))))....))---------))..........------ ( -19.42, z-score =  -1.19, R)
>droGri2.scaffold_15116 346058 95 - 1808639
CAGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACAAUUUUAUCGCCGUUCGCUGCUC-------GCUGCCCAGAACAA------
.......(((.....((((((((((.............))))))))))...((((((....)))))))))((((...((..-------...))...))))..------ ( -22.52, z-score =  -2.43, R)
>consensus
CAGCUUAGGCAAACAUUUGCAAUUACAAUUUUAGCAUAUAAUUGCAAACAUGAUAAACACUUUUAUCUGCGGCUGCUGCUCACUCUCGGUUCUCCACAGCAA______
((((...........((((((((((.............))))))))))...((((((....)))))).......)))).............................. (-13.46 = -13.32 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,120,871 – 15,120,973
Length 102
Sequences 10
Columns 108
Reading direction reverse
Mean pairwise identity 81.87
Shannon entropy 0.37395
G+C content 0.39274
Mean single sequence MFE -27.71
Consensus MFE -18.97
Energy contribution -18.65
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -1.91
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.33
SVM RNA-class probability 0.926831
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 15120871 102 - 27905053
------UUGCUGUGGAGAACCGAGAGUGAACAGCAGUCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCG
------(((((((.....((.....))..)))))))..(((((((((....))))))(((((((((((((((.........))))))))))))))).)))........ ( -26.10, z-score =  -1.81, R)
>droSim1.chr3R 21156353 102 + 27517382
------UUGCUGUGGAGAACCGAGAGUGAACAGCAGUCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCG
------(((((((.....((.....))..)))))))..(((((((((....))))))(((((((((((((((.........))))))))))))))).)))........ ( -26.10, z-score =  -1.81, R)
>droSec1.super_25 181013 102 + 827797
------UUGCUGUGGAGAACCGAGAGUGAACAGCAGUCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCG
------(((((((.....((.....))..)))))))..(((((((((....))))))(((((((((((((((.........))))))))))))))).)))........ ( -26.10, z-score =  -1.81, R)
>droYak2.chr3R 3832856 108 - 28832112
UUGCCAUUGCUGUGGAGAACCGAGAGUGAACAGCAGCCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCG
.(((..(((((((.....((.....))..)))))))..)))((((((....))))))(((((((((((((((.........)))))))))))))))............ ( -27.50, z-score =  -1.58, R)
>droEre2.scaffold_4770 11234473 108 + 17746568
UUGGCAUUGCUGUGGAGAACCGAGAGUGAACAGCAGCCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCG
..(((.(((((((.....((.....))..)))))))..(((((((((....))))))(((((((((((((((.........))))))))))))))).)))....))). ( -32.00, z-score =  -2.55, R)
>dp4.chr2 29576395 91 - 30794189
-----------------GUCGCAGUCGGUGGAGCAGCCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAACUUGUAAUUGCAAAUGUUUGCCUAAGCUG
-----------------....((((...(((.((((.....((((((....))))))(((((((((((((((.........)))))))))))))))))))))).)))) ( -24.50, z-score =  -1.17, R)
>droPer1.super_6 4948424 91 - 6141320
-----------------GUCGCAGUCGGUGGAGCAGCCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUG
-----------------....((((...(((.((((.....((((((....))))))(((((((((((((((.........)))))))))))))))))))))).)))) ( -24.50, z-score =  -1.43, R)
>droMoj3.scaffold_6540 21311424 101 + 34148556
------UUGUUCUGGGCUGCUUGG-CGGCGCAACGAGCGGCGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUG
------..((((((.(((((...)-)))).))..))))(((((((((....))))))(((((((((((((((.........)))))))))))))))..)))....... ( -34.00, z-score =  -2.63, R)
>droVir3.scaffold_13047 2704676 93 + 19223366
------UUGUUCUUGGCA---------GCGCAGCGAGCGGAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCCAAGCUG
------..........((---------((...((((((...((((((....))))))..(((((((((((((.........)))))))))))))))))))....)))) ( -28.20, z-score =  -2.19, R)
>droGri2.scaffold_15116 346058 95 + 1808639
------UUGUUCUGGGCAGC-------GAGCAGCGAACGGCGAUAAAAUUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCUG
------..........((((-------.....((((((...((((((....))))))..(((((((((((((.........)))))))))))))))))))....)))) ( -28.10, z-score =  -2.11, R)
>consensus
______UUGCUGUGGAGAACCGAGAGUGAACAGCAGCCGCAGAUAAAAGUGUUUAUCAUGUUUGCAAUUAUAUGCUAAAAUUGUAAUUGCAAAUGUUUGCCUAAGCCG
................................((((.....((((((....))))))(((((((((((((((.........)))))))))))))))))))........ (-18.97 = -18.65 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:27:24 2011