Locus 11793

Sequence ID dm3.chr3R
Location 23,845,678 – 23,845,867
Length 189
Max. P 0.735082
window16210 window16211

overview

Window 0

Location 23,845,678 – 23,845,769
Length 91
Sequences 7
Columns 106
Reading direction forward
Mean pairwise identity 72.97
Shannon entropy 0.51960
G+C content 0.60686
Mean single sequence MFE -38.87
Consensus MFE -20.49
Energy contribution -20.80
Covariance contribution 0.31
Combinations/Pair 1.33
Mean z-score -1.11
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.571449
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23845678 91 + 27905053
GCAUGAGGGGGUGGUAGCCUG-------------GGGGCGCCC--CCCUCGAGGACGACCGCAGGCAGGCACCAGCUGGUGUCAAACUCAAAAGUGGUUUGUUCUC
....(((((((.(...(((..-------------..))).)))--)))))((((((((((((((...((((((....))))))...)).....)))).)))))))) ( -42.80, z-score =  -1.98, R)
>dp4.chr2 22554513 97 - 30794189
UCGGGAUGUGGCUAUGGCUGUGGGAUGU------GGGACGUCC---UGGGGGGGACGACCGCAGGCAGGCACCAGCUGGUGUCAGACUCAAAAGUGGUUUGUUCUC
..((((...((((((.....((((.(((------((..(((((---(....)))))).)))))....((((((....))))))...))))...))))))...)))) ( -37.70, z-score =  -1.27, R)
>droPer1.super_0 9747597 97 - 11822988
UCGGGAUGUGGCUGUGGCUGUGGGAUGU------GGGACGUCC---UGGGGGGGACGACCGCAGGCAGGCACCAGCUGGUGUCAGACUCAAAAGUGGUUUGUUCUC
..((((...(((((((.((((....(((------((..(((((---(....)))))).))))).)))).)).))))).....(((((.((....))))))).)))) ( -36.40, z-score =  -0.57, R)
>droWil1.scaffold_181108 1066238 99 + 4707319
GACUGAGAGGGAUAAAGCGAGAGGUUUGCAA---GGAACGAGC----AAGGGGUCUAACCACAGGCAGGAACCAGCUGGUGUCAAACUCAAAAGUGGUUGGCUCCC
..((....))(.((((.(....).)))))..---.........----..((((.((((((((.(((.(....).)))(((.....))).....)))))))))))). ( -25.10, z-score =   0.73, R)
>droSim1.chr3R 23547485 104 + 27517382
GCAUGAGGGGGUGGUAGCCUGAGGGCGGCGAUCAGGGGCGCCC--CCCUCGAGGACGACCGCAGGCAGGCACCAGCUGGUGUCAAACUCAAAAGUGGUUUGUUCUC
....(((((((..((..(((((.........))))).))..))--)))))((((((((((((((...((((((....))))))...)).....)))).)))))))) ( -47.00, z-score =  -1.55, R)
>droSec1.super_22 468330 102 + 1066717
--AUGAGGGGGUGGUAGCCUGAGGGCGGCGAUCAGGGGCGCCC--CCCUCGAGGACGACCGCAGGCAGGCACCAGCUGGUGUCAAACUCAAAAGUGGUUUGUUCUC
--..(((((((..((..(((((.........))))).))..))--)))))((((((((((((((...((((((....))))))...)).....)))).)))))))) ( -47.00, z-score =  -1.92, R)
>droAna3.scaffold_13340 21984827 97 + 23697760
-CAGAAAGGAGUAAAGGACGGCGGGU--------GGGUCGUCCGACCCCCUUGGACGACCACAGGCAGGCACCAGCUGGUGUCAAACUCAAAAGUGGUUUGUUCUU
-............((((((.((..((--------((.((((((((.....))))))))))))..)).((((((....))))))((((.((....)))))))))))) ( -36.10, z-score =  -1.25, R)
>consensus
GCAUGAGGGGGUGGUAGCCGGAGGGUGG______GGGACGCCC__CCCUCGAGGACGACCGCAGGCAGGCACCAGCUGGUGUCAAACUCAAAAGUGGUUUGUUCUC
........((((....))))..............................((((((((((((((...((((((....))))))...)).....)))))).)))))) (-20.49 = -20.80 +   0.31)

alignment

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secondary structure

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dotplot

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Window 1

Location 23,845,769 – 23,845,867
Length 98
Sequences 7
Columns 104
Reading direction reverse
Mean pairwise identity 77.23
Shannon entropy 0.45512
G+C content 0.30402
Mean single sequence MFE -18.91
Consensus MFE -9.38
Energy contribution -10.77
Covariance contribution 1.39
Combinations/Pair 1.35
Mean z-score -1.75
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.735082
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23845769 98 - 27905053
AAAUGUAAAGUUCAUGUUUAUAUUUUGGCUAAUG--UUUUUUCUAGUCGAGUAGUCGAGUGUGCUGGACAAAAUAAUAGAAA-AAGUGGCCGAGAAAAAAG---
...((((((.......))))))(((((((((...--(((((((((........(((.((....)).))).......))))))-))))))))))))......--- ( -22.26, z-score =  -2.79, R)
>droWil1.scaffold_181108 1066337 99 - 4707319
AAAUUUAAACUUUAUGUUUAUAUUUUGGCUAAU---GUUUUCUAUUUUCUAGAGCUGGGUUAUCCAACGACAACAACAAAAAAUGAAAGAUGGGUUAAAAAU--
...(((.(((((....(((((.(((((.....(---(((.((((.....))))(.(((.....))).)))))....))))).)))))....))))).)))..-- ( -13.10, z-score =   0.16, R)
>droSim1.chr3R 23547589 98 - 27517382
AAAUGUAAAGUUCAUGUUUAUAUUUUGGCUAAUG--UUUUUUCUAGUCGAGUAGUCGAGUGUGCUGGACAAAAUAAUAGAAA-AAGUGGCCGAGAAAAAAG---
...((((((.......))))))(((((((((...--(((((((((........(((.((....)).))).......))))))-))))))))))))......--- ( -22.26, z-score =  -2.79, R)
>droSec1.super_22 468432 98 - 1066717
AAAUGUAAAGUUCAUGUUUAUAUUUUGGCUAAUG--UUUUUUCUAGUCGAGUAGUCGAGUGUGCUGGACAAAAUAAUAGAAA-AAGUGGCCGAGAAAAAAG---
...((((((.......))))))(((((((((...--(((((((((........(((.((....)).))).......))))))-))))))))))))......--- ( -22.26, z-score =  -2.79, R)
>droYak2.chr3R 6179058 103 + 28832112
AAAUGUAAAGUUCAUGUUUAUAUUUUGGCUAAUGUUUUUUUUCUAGUCGAGCAGUCGAGUGUGCUGGACAAAAUAAUAGAAA-AAGUAGCUGAGAAAAAAAAAG
...((((((.......))))))(((..((((.....((((((((((((.((((........)))).))).......))))))-)))))))..)))......... ( -20.71, z-score =  -1.59, R)
>droEre2.scaffold_4820 6274706 98 + 10470090
AAAUGUAAAGUUCAUGUUUAUAUUUUGGCUAAUG--UUUUUUCUAGUCGAGUAGUCGAGUGUGCUGGACAAAAUAAUAGAAA-AAGUGGCCGAGAAAAAAG---
...((((((.......))))))(((((((((...--(((((((((........(((.((....)).))).......))))))-))))))))))))......--- ( -22.26, z-score =  -2.79, R)
>droMoj3.scaffold_6540 14918760 89 + 34148556
AAAUCGAAAGUUCAUGUUUAUAUUUUGGCUAAGG--GCUUUGCUAGUUGCAUCCACAA---------AAAAAAUAAUACAAAUAAAAUAACGAAAAUAUA----
...((((((((((..(((........)))...))--)))))((.....))........---------.......................))).......---- (  -9.50, z-score =   0.33, R)
>consensus
AAAUGUAAAGUUCAUGUUUAUAUUUUGGCUAAUG__UUUUUUCUAGUCGAGUAGUCGAGUGUGCUGGACAAAAUAAUAGAAA_AAGUGGCCGAGAAAAAAG___
......................(((((((((........((((((........(((.((....)).))).......))))))....)))))))))......... ( -9.38 = -10.77 +   1.39)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:49:48 2011