Locus 1044

Sequence ID dm3.chr2L
Location 7,844,698 – 7,844,823
Length 125
Max. P 0.988799
window1421 window1422 window1423

overview

Window 1

Location 7,844,698 – 7,844,792
Length 94
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 90.48
Shannon entropy 0.17024
G+C content 0.44437
Mean single sequence MFE -31.00
Consensus MFE -21.43
Energy contribution -21.60
Covariance contribution 0.17
Combinations/Pair 1.12
Mean z-score -2.56
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.86
SVM RNA-class probability 0.838468
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7844698 94 - 23011544
------GUCCGUA--CUG--UUCCUGCCAUUUGGCUGGAAUGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUUGACGUUUUAUAGAUAGAGACAUGUGCGAUA
------...((((--(.(--((((.(((....))).))))).((((((((((........)))))))))).......(((((.......)))))..)))))... ( -29.60, z-score =  -2.63, R)
>droSim1.chr2L 7641970 94 - 22036055
------GUCCGUA--CUG--UUCCUGCCAUUUGGCUGGAACGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUUGACGUUUUAUAGAUAGAGACAUGUGCGAUA
------...((((--(.(--((((.(((....))).))))).((((((((((........)))))))))).......(((((.......)))))..)))))... ( -31.70, z-score =  -3.11, R)
>droSec1.super_3 3359026 94 - 7220098
------GUCCGCA--CUG--UUCCUGCCAUUUGGCUGGAACGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUUGACGUUUUAUAGAUAGAGACAUGUGCGAUA
------...((((--(.(--((((.(((....))).))))).((((((((((........)))))))))).......(((((.......)))))..)))))... ( -33.70, z-score =  -3.41, R)
>droYak2.chr2L 17272157 94 + 22324452
------GUCCGUG--CUG--UUCCUGCCAUUUGGCUGGAACGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUUGACGUUUUAUAGAUAGAGACAUGUGCGAUA
------...((..--(.(--((((.(((....))).))))).((((((((((........)))))))))).......(((((.......)))))..)..))... ( -30.90, z-score =  -2.59, R)
>droEre2.scaffold_4929 16766316 100 - 26641161
GUCUGUACUCGCA--CAG--UUCCUGCCAUUUGGCUGGAACGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUUGACGUUUUAUAGAUAGAGACAUGUGCGAUA
........(((((--(((--((((.(((....))).))))).((((((((((........)))))))))).......(((((.......))))).))))))).. ( -36.60, z-score =  -3.68, R)
>droAna3.scaffold_12943 3579432 98 + 5039921
------GUUUGUAGUCUGGCUUGCUGGCUUCUCGCUGGAAUGUUAUUUGCCUCAGUUGUUGGGCAAAUAAAGUUGACGUUUUAUAGAUAGAGACAUGUGCCAUA
------..........((((...(..((.....))..)(((.((((((((((........)))))))))).)))...(((((.......)))))....)))).. ( -23.50, z-score =   0.05, R)
>consensus
______GUCCGUA__CUG__UUCCUGCCAUUUGGCUGGAACGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUUGACGUUUUAUAGAUAGAGACAUGUGCGAUA
.........((((.......((((.(((....))).))))..((((((((((........)))))))))).......(((((.......)))))...))))... (-21.43 = -21.60 +   0.17)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,844,728 – 7,844,823
Length 95
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 75.91
Shannon entropy 0.43872
G+C content 0.47244
Mean single sequence MFE -25.29
Consensus MFE -12.37
Energy contribution -12.73
Covariance contribution 0.36
Combinations/Pair 1.07
Mean z-score -2.35
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.46
SVM RNA-class probability 0.940322
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7844728 95 + 23011544
AACUUUAUUUGCCCGACAACUGAGGCAAACAACAUUCCAGCCAAAUGGCAGGAA--CAG--UACGGACCACAGUAUG--GUCCU---UCAUAUGUAGACCGAAU
.......((((((((.....)).))))))..(((((((.(((....))).))))--...--...((((((.....))--)))).---.....)))......... ( -25.30, z-score =  -2.37, R)
>droSim1.chr2L 7642000 97 + 22036055
AACUUUAUUUGCCCGACAACUGAGGCAAACAACGUUCCAGCCAAAUGGCAGGAA--CAG--UACGGACCAUAGUAUGUAGUCCU---CCAUAUGUAGACCGAGU
.(((...((((((((.....)).))))))....(((((.(((....))).))))--)))--).(((......(((((.......---.))))).....)))... ( -25.30, z-score =  -1.85, R)
>droSec1.super_3 3359056 97 + 7220098
AACUUUAUUUGCCCGACAACUGAGGCAAACAACGUUCCAGCCAAAUGGCAGGAA--CAG--UGCGGACCACAGUAUGUAGUCCU---CCAUAUGUACACCGAGU
.((((..((((((((.....)).))))))....(((((.(((....))).))))--).(--(((((((.((.....)).)))).---......))))...)))) ( -27.81, z-score =  -2.13, R)
>droYak2.chr2L 17272187 80 - 22324452
AACUUUAUUUGCCCGACAACUGAGGCAAACAACGUUCCAGCCAAAUGGCAGGAA--CAG--CACGGACCACGGU-------CCU---CCAUAGA----------
.......((((((((.....)).))))))....(((((.(((....))).))))--)..--...((((....))-------)).---.......---------- ( -26.00, z-score =  -3.48, R)
>droEre2.scaffold_4929 16766346 86 + 26641161
AACUUUAUUUGCCCGACAACUGAGGCAAACAACGUUCCAGCCAAAUGGCAGGAA--CUG--UGCGAGU-ACAGACCAUGGUCCU---CCAUAGA----------
.......((((((((.....)).))))))....(((((.(((....))).))))--)((--((.(((.-...(((....)))))---)))))..---------- ( -26.00, z-score =  -2.44, R)
>droAna3.scaffold_12943 3579462 104 - 5039921
AACUUUAUUUGCCCAACAACUGAGGCAAAUAACAUUCCAGCGAGAAGCCAGCAAGCCAGACUACAAACCAUACAAGGUACACAUGAGCAGAAUGUACUACGGUU
.....((((((((((.....)).))))))))((((((..((.........))..((((........(((......))).....)).)).))))))((....)). ( -21.32, z-score =  -1.84, R)
>consensus
AACUUUAUUUGCCCGACAACUGAGGCAAACAACGUUCCAGCCAAAUGGCAGGAA__CAG__UACGGACCACAGUAUGUAGUCCU___CCAUAUGUA_ACCGA_U
.......((((((((.....)).)))))).....((((.(((....))).)))).................................................. (-12.37 = -12.73 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,844,728 – 7,844,823
Length 95
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 75.91
Shannon entropy 0.43872
G+C content 0.47244
Mean single sequence MFE -32.05
Consensus MFE -17.41
Energy contribution -17.77
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -2.64
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.34
SVM RNA-class probability 0.988799
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7844728 95 - 23011544
AUUCGGUCUACAUAUGA---AGGAC--CAUACUGUGGUCCGUA--CUG--UUCCUGCCAUUUGGCUGGAAUGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUU
...(((.(((((((((.---.....--)))).))))).)))..--..(--((((.(((....))).))))).((((((((((........)))))))))).... ( -34.30, z-score =  -3.56, R)
>droSim1.chr2L 7642000 97 - 22036055
ACUCGGUCUACAUAUGG---AGGACUACAUACUAUGGUCCGUA--CUG--UUCCUGCCAUUUGGCUGGAACGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUU
...(((.(((..((((.---.......))))...))).)))..--..(--((((.(((....))).))))).((((((((((........)))))))))).... ( -31.80, z-score =  -2.33, R)
>droSec1.super_3 3359056 97 - 7220098
ACUCGGUGUACAUAUGG---AGGACUACAUACUGUGGUCCGCA--CUG--UUCCUGCCAUUUGGCUGGAACGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUU
....(((((.(....).---.(((((((.....))))))))))--))(--((((.(((....))).))))).((((((((((........)))))))))).... ( -38.60, z-score =  -3.73, R)
>droYak2.chr2L 17272187 80 + 22324452
----------UCUAUGG---AGG-------ACCGUGGUCCGUG--CUG--UUCCUGCCAUUUGGCUGGAACGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUU
----------.......---.((-------((....))))..(--(((--((((.(((....))).))))).((((((((((........))))))))))))). ( -31.40, z-score =  -3.25, R)
>droEre2.scaffold_4929 16766346 86 - 26641161
----------UCUAUGG---AGGACCAUGGUCUGU-ACUCGCA--CAG--UUCCUGCCAUUUGGCUGGAACGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUU
----------.((((((---....)))))).....-.......--..(--((((.(((....))).))))).((((((((((........)))))))))).... ( -30.00, z-score =  -2.31, R)
>droAna3.scaffold_12943 3579462 104 + 5039921
AACCGUAGUACAUUCUGCUCAUGUGUACCUUGUAUGGUUUGUAGUCUGGCUUGCUGGCUUCUCGCUGGAAUGUUAUUUGCCUCAGUUGUUGGGCAAAUAAAGUU
.((((((((((((.........))))))....))))))((.((((..((((....))))....)))).))..((((((((((........)))))))))).... ( -26.20, z-score =  -0.64, R)
>consensus
A_UCGGU_UACAUAUGG___AGGACUACAUACUGUGGUCCGUA__CUG__UUCCUGCCAUUUGGCUGGAACGUUGUUUGCCUCAGUUGUCGGGCAAAUAAAGUU
..................................................((((.(((....))).))))..((((((((((........)))))))))).... (-17.41 = -17.77 +   0.36)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:24:30 2011