Locus 7842

Sequence ID dm3.chr3L
Location 17,765,881 – 17,766,064
Length 183
Max. P 0.901663
window10795 window10796 window10797

overview

Window 5

Location 17,765,881 – 17,765,992
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 95.59
Shannon entropy 0.07560
G+C content 0.45045
Mean single sequence MFE -30.71
Consensus MFE -28.04
Energy contribution -27.80
Covariance contribution -0.24
Combinations/Pair 1.09
Mean z-score -1.74
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.75
SVM RNA-class probability 0.807750
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17765881 111 + 24543557
GAAUGAAAUUUAAACCCGAAACUGAGCGGUAAUUACAUCAUACAUGGCUCGAUAGUUUUCCAAGUGGCGUCAGCUUCACCUCAUUAUCCUUUUGGGCAACCGCCAAGGAUG
.(((((...........((((((((((.((.............)).))))...))))))....(.(((....))).)...)))))((((((.(((....)))..)))))). ( -23.72, z-score =  -0.15, R)
>droEre2.scaffold_4784 9667833 111 - 25762168
GAAUGAAAUUUAAAUCCGAAACUGAGUGGUAAUUACAUCAUGCAAGGCUCGAUAGUUUUCCAAGUGGCGGCAGCUCCACCUCAUUAUCCUUGUGGGCAACCACCAAGGAUG
.(((((..........(((..((..(((((......)))))...))..)))............((((.(....).)))).)))))((((((((((....))).))))))). ( -30.80, z-score =  -1.50, R)
>droYak2.chr3L 7905893 111 - 24197627
GAAUGAAAUUUAAAUCCGAAACUGAGUGGUAAUUACAUCAUUCAUGGCUCGAUAGUUUUCCAAGUGGCGGCAGCUCCACCUCAUUAUCCUUGUGGGCAACCACCAAGGAUG
.(((((..........(((..(((((((((......)))))))).)..)))............((((.(....).)))).)))))((((((((((....))).))))))). ( -33.60, z-score =  -2.55, R)
>droSec1.super_0 9812971 111 + 21120651
GAAUGAAAUUUAAACCCGAAACUGAGCGGUAAUUACAUCAUACAUGGCUCGAUAGUUUUGCAAGUGGCGUCAGCUCCACCUCAUUAUCCUUGUGGGCAACCGCCAAGGAUG
.(((((..........(((((((((((.((.............)).))))...)))))))...((((.(....).)))).)))))((((((((((....))).))))))). ( -32.72, z-score =  -2.25, R)
>droSim1.chr3L 17103530 111 + 22553184
GAAUGAAAUUUAAACCCGAAACUGAGCGGUAAUUACAUCAUACAUGGCUCGAUAGUUUUGCAAGUGGCGUCAGCUCCACCUCAUUAUCCUUGUGGGCAACCGCCAAGGAUG
.(((((..........(((((((((((.((.............)).))))...)))))))...((((.(....).)))).)))))((((((((((....))).))))))). ( -32.72, z-score =  -2.25, R)
>consensus
GAAUGAAAUUUAAACCCGAAACUGAGCGGUAAUUACAUCAUACAUGGCUCGAUAGUUUUCCAAGUGGCGUCAGCUCCACCUCAUUAUCCUUGUGGGCAACCGCCAAGGAUG
.(((((...........((((((((((.((.............)).))))...))))))....((((.(....).)))).)))))((((((((((....))).))))))). (-28.04 = -27.80 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,765,920 – 17,766,028
Length 108
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 95.09
Shannon entropy 0.08646
G+C content 0.52037
Mean single sequence MFE -36.33
Consensus MFE -33.12
Energy contribution -32.76
Covariance contribution -0.36
Combinations/Pair 1.09
Mean z-score -1.96
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.16
SVM RNA-class probability 0.901663
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17765920 108 + 24543557
AUACAUGGCUCGAUAGUUUUCCAAGUGGCGUCAGCUUCACCUCAUUAUCCUUUUGGGCAACCGCCAAGGAUGUGGUGAUCCCAGUGGUCGCACCUCCACAUAUCAGCU
......((((.((((...........(((....)))(((((....(((((((.(((....)))..))))))).))))).....((((........)))).)))))))) ( -32.10, z-score =  -1.42, R)
>droEre2.scaffold_4784 9667872 108 - 25762168
AUGCAAGGCUCGAUAGUUUUCCAAGUGGCGGCAGCUCCACCUCAUUAUCCUUGUGGGCAACCACCAAGGAUGUGGUGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCU
......((((.((((.........(((((.((.....((((....(((((((((((....))).)))))))).))))......)).))))).........)))))))) ( -37.07, z-score =  -1.76, R)
>droYak2.chr3L 7905932 108 - 24197627
AUUCAUGGCUCGAUAGUUUUCCAAGUGGCGGCAGCUCCACCUCAUUAUCCUUGUGGGCAACCACCAAGGAUGUGGUGAUCCCAGCGGUCGCAUCUCUACAUAUCAGCU
......((((.((((((......((..(((((.(((.((((....(((((((((((....))).)))))))).)))).....))).)))))..))..)).)))))))) ( -38.30, z-score =  -2.66, R)
>droSec1.super_0 9813010 108 + 21120651
AUACAUGGCUCGAUAGUUUUGCAAGUGGCGUCAGCUCCACCUCAUUAUCCUUGUGGGCAACCGCCAAGGAUGUGGCGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCU
......((((.(((((..((((..((((.(....).))))..(((.((((((((((....))).))))))))))))))..)..((((........)))).)))))))) ( -38.10, z-score =  -2.28, R)
>droSim1.chr3L 17103569 108 + 22553184
AUACAUGGCUCGAUAGUUUUGCAAGUGGCGUCAGCUCCACCUCAUUAUCCUUGUGGGCAACCGCCAAGGAUGUGGUGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCU
......((((.((((..........(((.((((...((((......((((((((((....))).))))))))))))))).)))((((........)))).)))))))) ( -36.10, z-score =  -1.67, R)
>consensus
AUACAUGGCUCGAUAGUUUUCCAAGUGGCGUCAGCUCCACCUCAUUAUCCUUGUGGGCAACCGCCAAGGAUGUGGUGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCU
......((((.((((.........((((.(....).))))..(((.((((((((((....))).))))))))))((((((.....)))))).........)))))))) (-33.12 = -32.76 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,765,954 – 17,766,064
Length 110
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 83.12
Shannon entropy 0.32377
G+C content 0.52109
Mean single sequence MFE -34.98
Consensus MFE -22.48
Energy contribution -23.73
Covariance contribution 1.25
Combinations/Pair 1.26
Mean z-score -1.67
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.558656
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17765954 110 + 24543557
CUUCACCUCAUUAUCCUUUUGGGCAACCGCCAAGGAUGU--GGUGAUCCCAGUGGUCGCACCUCCACAUAUCAGCUUACCAAUA-AGAUGACUCCUGUCCUGGUUUCGGGCGU
..(((((....(((((((.(((....)))..))))))).--))))).(((.((((........))))..(((((((((....))-))..(((....))))))))...)))... ( -33.60, z-score =  -1.40, R)
>droAna3.scaffold_13337 14463836 108 + 23293914
----ACCCUAUUAUCCUUGUGGGUAAAGUGCUGGAAUUUUUGGUCAUUCCAGUGGUCACAUCGGCCCAUAUCGUGUUGCAAAUU-ACAAGGUUUCGGUCUUCAUCUCGGGCGU
----.(((..((((((....))))))...((((((((........)))))))).........((((...(((.(((........-))).)))...))))........)))... ( -26.80, z-score =  -0.42, R)
>droEre2.scaffold_4784 9667906 109 - 25762168
CUCCACCUCAUUAUCCUUGUGGGCAACCACCAAGGAUGU--GGUGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUG-AGAUGACUCCUGCCCU-GUUUCGGGCGU
...((.((((((((((((((((....))).))))))))(--(((((.....((((........))))........)))))))))-)).))......((((.-.....)))).. ( -38.32, z-score =  -2.43, R)
>droYak2.chr3L 7905966 111 - 24197627
CUCCACCUCAUUAUCCUUGUGGGCAACCACCAAGGAUGU--GGUGAUCCCAGCGGUCGCAUCUCUACAUAUCAGCUUACCAAUGGAGCUGACUUCUGCCCUGGUUUCGGGCGU
.((((((....(((((((((((....))).)))))))).--)))((..((((.(((.(........)...(((((((.......))))))).....)))))))..)))))... ( -39.90, z-score =  -2.28, R)
>droSec1.super_0 9813044 110 + 21120651
CUCCACCUCAUUAUCCUUGUGGGCAACCGCCAAGGAUGU--GGCGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUG-AGAUGACUCCUCCCCUUGUUUCGGGUGU
...((((((((.((((((((((....))).)))))))))--))(((..(.((.((...((((((...................)-)))))......)).)).)..))))))). ( -33.91, z-score =  -1.34, R)
>droSim1.chr3L 17103603 110 + 22553184
CUCCACCUCAUUAUCCUUGUGGGCAACCGCCAAGGAUGU--GGUGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUG-CGAUGACUCCUGCCCUUGUUUCGGGUGU
...((((....(((((((((((....))).)))))))).--)))).....(((.(((((((....................)))-)))).)))...((((.......)))).. ( -37.35, z-score =  -2.13, R)
>consensus
CUCCACCUCAUUAUCCUUGUGGGCAACCGCCAAGGAUGU__GGUGAUCCCAGUGGUCGCAUCUCCACAUAUCAGCUUACCAAUG_AGAUGACUCCUGCCCUGGUUUCGGGCGU
...((((....(((((((((((....))).))))))))...))))......((((........)))).............................((((.......)))).. (-22.48 = -23.73 +   1.25)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:34:34 2011