Locus 9817

Sequence ID dm3.chr3R
Location 9,295,873 – 9,295,970
Length 97
Max. P 0.956602
window13472 window13473

overview

Window 2

Location 9,295,873 – 9,295,970
Length 97
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 81.72
Shannon entropy 0.31007
G+C content 0.49352
Mean single sequence MFE -22.24
Consensus MFE -14.72
Energy contribution -16.12
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.97
SVM RNA-class probability 0.863508
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9295873 97 + 27905053
UUCUUAAUAAUGUGGCCUGGAGUCCGUAGUCCGGACAAUCCGGACAACCCCUGCACAC-----GCACAUCUCAUAUAUAUCUCCAUAUCCACAUCCACCUGU
.........((((((..(((((...(((((((((.....))))))......(((....-----))).........)))..)))))...))))))........ ( -27.50, z-score =  -3.78, R)
>droSim1.chr3R 15381440 88 - 27517382
UUCUUAAUAAUGUGGCCUGGAGUCCGGAGUCCGGACAA---------CCCCAGCACAC-----GCACAUCGCAUAUAUAUCUCCAUAUCCACAUCCACCUGU
.........((((((..((((((((((...))))))..---------...........-----((.....)).........))))...))))))........ ( -22.40, z-score =  -2.12, R)
>droSec1.super_0 8411256 88 - 21120651
UUCUUAAUAAUGUGGCCUGGAGUCCGGAGUCCGGACAA---------CCCCAGCACAC-----GCACAUCGCAUAUAUAUCUCCAUGUCCACAUCCACCUGU
.........(((((((.((((((((((...))))))..---------...........-----((.....)).........)))).).))))))........ ( -23.90, z-score =  -2.13, R)
>droYak2.chr3R 13603988 102 + 28832112
UUCUUAAUAAUGUGGCCGGGAGUCCGGACUCCGGAAAACCCCUGCAACAACAACACGCACAUCGCAUAUAUCGCAUAUAUCUCCAUAUCCACAGCCACCUGU
.........(((((((.(((..(((((...)))))....))).))...........((.....))......)))))..............((((....)))) ( -21.40, z-score =  -0.88, R)
>droEre2.scaffold_4770 5401678 81 - 17746568
UUCUUAAUAAUGUGGCCUGGAGUCCG-------GACAA---------CACCAGCACAC-----GCACAUCGCAUAUACAUCUCCAUAUCCACAUCCACCUGU
.........((((((..(((((...(-------(....---------..)).......-----((.....))........)))))...))))))........ ( -16.00, z-score =  -1.53, R)
>consensus
UUCUUAAUAAUGUGGCCUGGAGUCCGGAGUCCGGACAA_________CCCCAGCACAC_____GCACAUCGCAUAUAUAUCUCCAUAUCCACAUCCACCUGU
.........((((((..(((((((((.....)))))...........................((.....)).........))))...))))))........ (-14.72 = -16.12 +   1.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,295,873 – 9,295,970
Length 97
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 81.72
Shannon entropy 0.31007
G+C content 0.49352
Mean single sequence MFE -33.26
Consensus MFE -21.30
Energy contribution -21.78
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -2.53
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956602
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9295873 97 - 27905053
ACAGGUGGAUGUGGAUAUGGAGAUAUAUAUGAGAUGUGC-----GUGUGCAGGGGUUGUCCGGAUUGUCCGGACUACGGACUCCAGGCCACAUUAUUAAGAA
.......(((((((...(((((............(.(((-----....))).).((.((((((.....)))))).))...)))))..)))))))........ ( -33.70, z-score =  -2.47, R)
>droSim1.chr3R 15381440 88 + 27517382
ACAGGUGGAUGUGGAUAUGGAGAUAUAUAUGCGAUGUGC-----GUGUGCUGGGG---------UUGUCCGGACUCCGGACUCCAGGCCACAUUAUUAAGAA
.......(((((((...(((((...(((((((.....))-----)))))((((((---------((.....)))))))).)))))..)))))))........ ( -34.10, z-score =  -2.96, R)
>droSec1.super_0 8411256 88 + 21120651
ACAGGUGGAUGUGGACAUGGAGAUAUAUAUGCGAUGUGC-----GUGUGCUGGGG---------UUGUCCGGACUCCGGACUCCAGGCCACAUUAUUAAGAA
.......(((((((...(((((...(((((((.....))-----)))))((((((---------((.....)))))))).)))))..)))))))........ ( -34.10, z-score =  -2.72, R)
>droYak2.chr3R 13603988 102 - 28832112
ACAGGUGGCUGUGGAUAUGGAGAUAUAUGCGAUAUAUGCGAUGUGCGUGUUGUUGUUGCAGGGGUUUUCCGGAGUCCGGACUCCCGGCCACAUUAUUAAGAA
....(((((((.......(((((....(((((((.(((((.....)))))...))))))).....)))))(((((....))))))))))))........... ( -35.60, z-score =  -1.96, R)
>droEre2.scaffold_4770 5401678 81 + 17746568
ACAGGUGGAUGUGGAUAUGGAGAUGUAUAUGCGAUGUGC-----GUGUGCUGGUG---------UUGUC-------CGGACUCCAGGCCACAUUAUUAAGAA
.......(((((((...(((((..((((((((.....))-----))))))(((..---------....)-------))..)))))..)))))))........ ( -28.80, z-score =  -2.54, R)
>consensus
ACAGGUGGAUGUGGAUAUGGAGAUAUAUAUGCGAUGUGC_____GUGUGCUGGGG_________UUGUCCGGACUCCGGACUCCAGGCCACAUUAUUAAGAA
.......(((((((...(((((.............(..(.......)..).................((((.....)))))))))..)))))))........ (-21.30 = -21.78 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:11:45 2011