Locus 1547

Sequence ID dm3.chr2L
Location 11,972,444 – 11,972,581
Length 137
Max. P 0.985373
window2116 window2117 window2118

overview

Window 6

Location 11,972,444 – 11,972,551
Length 107
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 86.33
Shannon entropy 0.23807
G+C content 0.51577
Mean single sequence MFE -32.06
Consensus MFE -22.25
Energy contribution -23.77
Covariance contribution 1.52
Combinations/Pair 1.07
Mean z-score -1.95
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.623513
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11972444 107 + 23011544
UGCUUAACGGAAGCGGUCGCAACCGUUAGACGCUGCAUCCAAAGCUAUAU-----GCAGCUAUAGCUGCAUCUGAAUCCCAGCUCUCGACGGCGAUCCCAACCAAAUGCAAU
(((.....((..(.((((((...(((((((.((((.......((....((-----(((((....)))))))))......))))))).)))))))))).)..))....))).. ( -32.72, z-score =  -2.04, R)
>droSim1.chr2L 11779485 107 + 22036055
UGCUUAACGGAAGCGGUCGCAACCGUUAGACGCUGCAUCCAAAGCUAUAU-----GCAGCUAUAGCUGCAUCUGAAUCCCAACUCUUGCCGGCGAUCCCAACCAAAUGCAAU
((((((((((..((....))..))))))).(((((((...........((-----(((((....)))))))..((........)).)).))))).............))).. ( -29.70, z-score =  -1.46, R)
>droSec1.super_16 171775 107 + 1878335
UGCUUAACGGAAGCGGUCGCAACCGUUAGACGCUGCAUCCAAAGCUAUAU-----GCAGCUAUAGCUGCAUCUGAAUCCCAACUCUUGCCGGCGAUCCCAACCAAAUGCAAU
((((((((((..((....))..))))))).(((((((...........((-----(((((....)))))))..((........)).)).))))).............))).. ( -29.70, z-score =  -1.46, R)
>droYak2.chr2L 8394788 112 + 22324452
UGCUUAACGGAAGCGUUCGCCACCGUUAGACGCUGGAUCCAAAGCUAUACUCUAAGCAGCUAUAGCUGCAUCUGAAUCCCAGCUCUUGCCGGCGAUCCCAGCCAAAUGCAAU
((((((((((..((....))..)))))))..(((((...................(((((....)))))......(((((.((....)).)).))).))))).....))).. ( -35.40, z-score =  -2.19, R)
>droAna3.scaffold_12943 2768097 93 - 5039921
UGCUUAACGGAAGCGGUCGCAACCGUUAGACGCUGGAUCCGAAGCUAUA---------------GCUGAA----GAGCUGAGCUGUUGCCACCGAUCCCAGCCAAAUGCAAU
((((((((((..((....))..)))))))..((((((((.(..((.(((---------------(((.(.----....).)))))).))..).))).))))).....))).. ( -32.80, z-score =  -2.62, R)
>consensus
UGCUUAACGGAAGCGGUCGCAACCGUUAGACGCUGCAUCCAAAGCUAUAU_____GCAGCUAUAGCUGCAUCUGAAUCCCAGCUCUUGCCGGCGAUCCCAACCAAAUGCAAU
((((((((((..((....))..))))))).(((((....(((((((.........(((((....)))))...........)))).))).))))).............))).. (-22.25 = -23.77 +   1.52)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,972,444 – 11,972,551
Length 107
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 86.33
Shannon entropy 0.23807
G+C content 0.51577
Mean single sequence MFE -42.00
Consensus MFE -33.46
Energy contribution -35.30
Covariance contribution 1.84
Combinations/Pair 1.08
Mean z-score -2.67
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.20
SVM RNA-class probability 0.985373
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11972444 107 - 23011544
AUUGCAUUUGGUUGGGAUCGCCGUCGAGAGCUGGGAUUCAGAUGCAGCUAUAGCUGC-----AUAUAGCUUUGGAUGCAGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCA
.((((((((((((((((((.(((.(....).))))))))..(((((((....)))))-----)).)))))..)))))))).(..((((((..((....))..))))))..). ( -42.90, z-score =  -2.56, R)
>droSim1.chr2L 11779485 107 - 22036055
AUUGCAUUUGGUUGGGAUCGCCGGCAAGAGUUGGGAUUCAGAUGCAGCUAUAGCUGC-----AUAUAGCUUUGGAUGCAGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCA
.((((((((((((((((((.(((((....))))))))))..(((((((....)))))-----)).)))))..)))))))).(..((((((..((....))..))))))..). ( -44.30, z-score =  -3.30, R)
>droSec1.super_16 171775 107 - 1878335
AUUGCAUUUGGUUGGGAUCGCCGGCAAGAGUUGGGAUUCAGAUGCAGCUAUAGCUGC-----AUAUAGCUUUGGAUGCAGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCA
.((((((((((((((((((.(((((....))))))))))..(((((((....)))))-----)).)))))..)))))))).(..((((((..((....))..))))))..). ( -44.30, z-score =  -3.30, R)
>droYak2.chr2L 8394788 112 - 22324452
AUUGCAUUUGGCUGGGAUCGCCGGCAAGAGCUGGGAUUCAGAUGCAGCUAUAGCUGCUUAGAGUAUAGCUUUGGAUCCAGCGUCUAACGGUGGCGAACGCUUCCGUUAAGCA
..........(((((((((.(((((....)))))))))).((((((((....)))))((((((.....)))))))))))))(..((((((.(((....))).))))))..). ( -45.30, z-score =  -2.48, R)
>droAna3.scaffold_12943 2768097 93 + 5039921
AUUGCAUUUGGCUGGGAUCGGUGGCAACAGCUCAGCUC----UUCAGC---------------UAUAGCUUCGGAUCCAGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCA
..........((((((.((((((....))(((.((((.----...)))---------------)..))).)))).))))))(..((((((..((....))..))))))..). ( -33.20, z-score =  -1.71, R)
>consensus
AUUGCAUUUGGUUGGGAUCGCCGGCAAGAGCUGGGAUUCAGAUGCAGCUAUAGCUGC_____AUAUAGCUUUGGAUGCAGCGUCUAACGGUUGCGACCGCUUCCGUUAAGCA
.((((((((((((((((((.(((((....))))))))))....(((((....)))))........)))))..)))))))).(..((((((..((....))..))))))..). (-33.46 = -35.30 +   1.84)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,972,484 – 11,972,581
Length 97
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 85.40
Shannon entropy 0.23613
G+C content 0.48777
Mean single sequence MFE -36.55
Consensus MFE -31.55
Energy contribution -33.55
Covariance contribution 2.00
Combinations/Pair 1.06
Mean z-score -1.97
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.51
SVM RNA-class probability 0.945375
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11972484 97 - 23011544
AGCAGCAGCUGCAGUUUGUUGCUGCAACUAAUUGCAUUUGGUUGGGAUCGCCGUCGAGAGCUGGGAUUCAGAUGCAGCUAUAGCUGCAUAUAGCUUU
.((((((((........))))))))((((((......)))))).(((((.(((.(....).))))))))..(((((((....)))))))........ ( -38.40, z-score =  -2.05, R)
>droSim1.chr2L 11779525 97 - 22036055
AGCAGCAGCUGCAGUUUGUUGCUGCAACUAAUUGCAUUUGGUUGGGAUCGCCGGCAAGAGUUGGGAUUCAGAUGCAGCUAUAGCUGCAUAUAGCUUU
.((((((((........))))))))((((((......)))))).(((((.(((((....))))))))))..(((((((....)))))))........ ( -39.80, z-score =  -2.74, R)
>droSec1.super_16 171815 97 - 1878335
AGCAGCAGCUGCAGUUUGUUGCUGCAACUAAUUGCAUUUGGUUGGGAUCGCCGGCAAGAGUUGGGAUUCAGAUGCAGCUAUAGCUGCAUAUAGCUUU
.((((((((........))))))))((((((......)))))).(((((.(((((....))))))))))..(((((((....)))))))........ ( -39.80, z-score =  -2.74, R)
>droAna3.scaffold_12943 2768137 83 + 5039921
GGCAGCAGCUGCAGUUUGUUGCUGCAACUAAUUGCAUUUGGCUGGGAUCGGUGGCAACAGCUCAGCUC----UUCAGCUAUAGCUUC----------
.((((((((........))))))))........((...((((((((...(.((((....)).)).)..----))))))))..))...---------- ( -28.20, z-score =  -0.35, R)
>consensus
AGCAGCAGCUGCAGUUUGUUGCUGCAACUAAUUGCAUUUGGUUGGGAUCGCCGGCAAGAGCUGGGAUUCAGAUGCAGCUAUAGCUGCAUAUAGCUUU
.((((((((........))))))))((((((......)))))).(((((.(((((....))))))))))..(((((((....)))))))........ (-31.55 = -33.55 +   2.00)

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 21:34:06 2011