Locus 8435

Sequence ID dm3.chr3L
Location 22,724,911 – 22,725,030
Length 119
Max. P 0.966053
window11588 window11589

overview

Window 8

Location 22,724,911 – 22,725,004
Length 93
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 68.05
Shannon entropy 0.60173
G+C content 0.41019
Mean single sequence MFE -19.44
Consensus MFE -10.60
Energy contribution -11.33
Covariance contribution 0.73
Combinations/Pair 1.71
Mean z-score -0.61
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.554306
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22724911 93 + 24543557
-----GAAAUCAAUGCCUACCAAUUUUU---AUGAGGGAGCGUAAACUGUUUCAUCGACGAACGGUGGAACUGGCUGAUAGCCCCAAUAAUCAUUUCCUGA
-----.......................---....(((.((.((..(.(((((((((.....))))))))).)..))...)))))................ ( -19.60, z-score =  -0.26, R)
>droAna3.scaffold_13499 254431 99 - 1739075
AAAAUCGGCCUAACCACAAACAAUUUUUAAUUUGGGGUAAUGGGUGUUUUUUUUUCCACUUACAUCGAGUUUAUUUUCCACGUCCAAAAGAUCUUUUGU--
......((.....))(((((..((((((((((((..((((((((..........)))).))))..))))))...............))))))..)))))-- ( -12.56, z-score =   1.30, R)
>droEre2.scaffold_4784 22375410 94 + 25762168
-----GAAAUCAGUGCCUACCAAUUUUUU-UAUGAGCGGCCGUAAACUGUUUCACCGACGAACGGUGGUCUUGGCUAAUAGCCC-AAUAAUAAUGUCCUGA
-----....((((..(.............-...((((.(((((....((((.....)))).))))).).)))(((.....))).-.........)..)))) ( -17.60, z-score =   0.49, R)
>droYak2.chr3L 23212181 84 + 24197627
----------------CUACAAAAUUUUU-UAUGAGGGAGCAUAAACUGUUUCACCGAUGAACGGUGGAACUUUUUGAUAGCCCCAAUUAUCAUUUCCUGA
----------------.............-.....(((.((.((((..(((((((((.....)))))))))..))))...)))))................ ( -21.30, z-score =  -2.77, R)
>droSec1.super_11 2645793 93 + 2888827
-----GAAAUCAGUGCCUACCAAUUUUU---AUGAGGGAUCGUAAACUGUUUCGCCGACGAACGGUGGAACUGGCUUAUAGCCCCAAUAAACAUUUCCUGA
-----....((((............(((---((((....)))))))..(((((((((.....))))))))).(((.....)))..............)))) ( -22.10, z-score =  -1.11, R)
>droSim1.chr3L 22012052 93 + 22553184
-----GAAAUCAGUGCCUACCAAUUUUU---AUGAGGGAGCGUAAACUGUUUCGCCGACGAACGGUGGAACUGGCUUAUAGCCCCAAUAAACAUUUCCUGA
-----....((((.(......(((.(((---((..(((.((((((.(((((((((((.....))))))))).)).)))).))))).))))).))).))))) ( -23.50, z-score =  -1.33, R)
>consensus
_____GAAAUCAGUGCCUACCAAUUUUU___AUGAGGGAGCGUAAACUGUUUCACCGACGAACGGUGGAACUGGCUUAUAGCCCCAAUAAACAUUUCCUGA
...................................(((((........(((((((((.....))))))))).(((.....)))...........))))).. (-10.60 = -11.33 +   0.73)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 22,724,939 – 22,725,030
Length 91
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 65.05
Shannon entropy 0.67194
G+C content 0.40945
Mean single sequence MFE -25.35
Consensus MFE -10.16
Energy contribution -11.67
Covariance contribution 1.51
Combinations/Pair 1.54
Mean z-score -1.84
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.76
SVM RNA-class probability 0.966053
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22724939 91 + 24543557
GGAGCGUAAACUGUUUCAUCGACGAACGGUGGAACUGGCUGAUAGCCCCAAUAAUCAUUUCCUGAUUGUUGGAUAAACUCAAUUAGAGUCA-------------
.(((..((....(((((((((.....))))))))).(((.....)))((((((((((.....)))))))))).))..)))...........------------- ( -27.40, z-score =  -2.59, R)
>droAna3.scaffold_13499 254467 91 - 1739075
GUAAUGGGUGUUUUUUUUUCCACUUACAUCGAGUUUAUUUUCCACGUCCAA--AAGAUCUUUUGUCGGGUUGAGCGAUGAAUCUAUAAUUUUA-----------
((((((((..........)))).)))).(((.(((((....((.((..(((--((....))))).)))).)))))..))).............----------- ( -14.20, z-score =   0.30, R)
>droEre2.scaffold_4784 22375440 99 + 25762168
CGGCCGUAAACUGUUUCACCGACGAACGGUGGUCUUGGCUAAUAGCCC-AAUAAUAAUGUCCUGAUAAUUU--CAGGCUCAAU-AGAGCC-UAAAUUAGUACUA
.((.(((........((((((.....))))))....(((.....))).-.......))).))...((((((--.((((((...-.)))))-)))))))...... ( -26.40, z-score =  -2.01, R)
>droYak2.chr3L 23212200 103 + 24197627
GGAGCAUAAACUGUUUCACCGAUGAACGGUGGAACUUUUUGAUAGCCCCAAUUAUCAUUUCCUGAUUGUUGGAUAAACUCAAUUAGAGCC-CGUUUUAGUAAUA
((.((.((((..(((((((((.....)))))))))..))))......(((((.((((.....)))).)))))...............)))-)............ ( -26.80, z-score =  -2.69, R)
>droSec1.super_11 2645821 104 + 2888827
GGAUCGUAAACUGUUUCGCCGACGAACGGUGGAACUGGCUUAUAGCCCCAAUAAACAUUUCCUGAUUGUUGGAUAAACUCAAUUAGAGCCAUGUUUCAGCACUA
((..........(((((((((.....))))))))).(((.....)))))...((((((..((((((((..(......).))))))).)..))))))........ ( -26.50, z-score =  -1.51, R)
>droSim1.chr3L 22012080 104 + 22553184
GGAGCGUAAACUGUUUCGCCGACGAACGGUGGAACUGGCUUAUAGCCCCAAUAAACAUUUCCUGAUUGUUGGAUAAACUCACUUAGAGCCAUGUUUCAGCACUA
(((((((.....(((((((((.....))))))))).(((((......(((((((.((.....)).))))))).(((......)))))))))))))))....... ( -30.80, z-score =  -2.54, R)
>consensus
GGAGCGUAAACUGUUUCACCGACGAACGGUGGAACUGGCUUAUAGCCCCAAUAAACAUUUCCUGAUUGUUGGAUAAACUCAAUUAGAGCCAUGUUU_AG_ACUA
............(((((((((.....))))))))).(((.....)))(((((.((((.....)))).))))).....(((.....)))................ (-10.16 = -11.67 +   1.51)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:45:36 2011