Locus 2666

Sequence ID dm3.chr2L
Location 20,915,636 – 20,915,766
Length 130
Max. P 0.904059
window3655 window3656 window3657

overview

Window 5

Location 20,915,636 – 20,915,744
Length 108
Sequences 7
Columns 119
Reading direction forward
Mean pairwise identity 70.40
Shannon entropy 0.55557
G+C content 0.43106
Mean single sequence MFE -27.33
Consensus MFE -12.23
Energy contribution -14.97
Covariance contribution 2.74
Combinations/Pair 1.20
Mean z-score -1.69
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.96
SVM RNA-class probability 0.863147
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20915636 108 + 23011544
UGUGCAACGCGACGUUGACUUAUUGAAAUCGAUUGAUUCUGAUUCCAGUCGGUCAGCUUUGGACU------UACAUUUU-----CUGGCUGACUCGCCUGCCGGAUCUGUAUCUAUAUA
.............(((((((.((((.((((((.....)).)))).)))).)))))))..((((..------((((...(-----(((((.(......).))))))..)))))))).... ( -28.50, z-score =  -1.48, R)
>droAna3.scaffold_12943 1219981 109 - 5039921
----UAAGCUUAUGGUGACUUAUUGAAAUCGAUUGAUUCUGAUUCCAGUCUGUCGGCUUUGGUUUCUAUUCCAUUUUUUUUACCCUAGACGACUUGCCUGCCGGAUCUGUAAA------
----...((...(((((((..((((.((((((.....)).)))).))))..)))(((...((((((((.................)))).)))).))).)))).....))...------ ( -20.73, z-score =  -0.30, R)
>droEre2.scaffold_4845 19038025 102 - 22589142
UGUGCAACGCGACGUUGACUUAUUGAAAUCGAUUGAUUCUGAUUCCAGUCGGUCAGCUUUGGAUU------UACUUUUU-----CUGGCUGGCUCGCUGGCCGGAUCUGUAUA------
((((((...(((.(((((((.((((.((((((.....)).)))).)))).))))))).)))....------.......(-----(((((..(....)..))))))..))))))------ ( -34.40, z-score =  -3.18, R)
>droYak2.chr2R 19304075 102 - 21139217
UGUGCAACGCGACGUUGACUUAUUGAAAUCGAUUGAUUCUGAUUUCAUUCGGUCAGCUUUGGAUU------UACUUUUU-----CUGGCUGGUUCGCUGGCCGGAUCUGUAUA------
((((((...(((.(((((((...(((((((((.....)).)))))))...))))))).)))....------.......(-----(((((..(....)..))))))..))))))------ ( -35.60, z-score =  -4.35, R)
>droSec1.super_18 849398 108 + 1342155
UGUGCAACGCGACGUUGACUUAUUAAAAUCGAUUGAUUCUGAUUCCAGUCGGUCAGCUUUGGACU------UACUUUUU-----CUGGCUGACUCGCCUGCCGGAUCUGUAUCUGUAUA
((((((...(((..((((....))))..)))...(((...((((((((.(((((((((..(((..------......))-----).))))))).)).)))..)))))...))))))))) ( -28.10, z-score =  -1.57, R)
>droSim1.chr2L 20530877 107 + 22036055
UGUGCAACGCGACGUUGACUUAUUAAA-UCGAUUGAUUCUGAUUCCAGUCGGUCAGCUUUGGACU------UACUUUUU-----CUGGCUGACUCGCCUGCCGGAUCUGUAUCUGUAUA
((((((...(((.(((((((.(((.((-((((.....)).))))..))).))))))).)))....------(((....(-----(((((.(......).))))))...)))..)))))) ( -26.40, z-score =  -0.99, R)
>droWil1.scaffold_180708 8934112 89 + 12563649
--------------------AAUUGAAAGCGACAUUGACUUAUUGCCGAUAUUCAGAUUGAUAUU----UCUGUCUGCUG----UCUGCAGUUGCAUUUGCCGGAUCUAUAAUCGUG--
--------------------........((((...((....(((((.((((..(((((.((....----)).))))).))----)).)))))..)).))))................-- ( -17.60, z-score =   0.05, R)
>consensus
UGUGCAACGCGACGUUGACUUAUUGAAAUCGAUUGAUUCUGAUUCCAGUCGGUCAGCUUUGGAUU______UACUUUUU_____CUGGCUGACUCGCCUGCCGGAUCUGUAUA__U___
.........(((.(((((((.((((.(((((........))))).)))).))))))).))).......................(((((.(......).)))))............... (-12.23 = -14.97 +   2.74)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,915,675 – 20,915,766
Length 91
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 91.39
Shannon entropy 0.14130
G+C content 0.44712
Mean single sequence MFE -23.50
Consensus MFE -20.73
Energy contribution -20.23
Covariance contribution -0.50
Combinations/Pair 1.13
Mean z-score -1.97
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.17
SVM RNA-class probability 0.904059
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20915675 91 + 23011544
UGAUUCCAGUCGGUCAGCUUUGGACUUACAUUUUCUGGCUGACUCGCCUGCCGGAUCUGUAUCUAUAUAUUGCACGACUGCUUUUUUUUUA
......((((((..(((...((((..((((...((((((.(......).))))))..))))))))....)))..))))))........... ( -23.50, z-score =  -2.67, R)
>droEre2.scaffold_4845 19038064 85 - 22589142
UGAUUCCAGUCGGUCAGCUUUGGAUUUACUUUUUCUGGCUGGCUCGCUGGCCGGAUCUGUAU------AUUGCUCGACAGCUUUUUUAUGA
.(((((((((.((((((((..(((........))).)))))))).)))))...)))).....------...(((....))).......... ( -23.90, z-score =  -1.39, R)
>droSec1.super_18 849437 91 + 1342155
UGAUUCCAGUCGGUCAGCUUUGGACUUACUUUUUCUGGCUGACUCGCCUGCCGGAUCUGUAUCUGUAUAUUGCACGACUGCUUUUUUAUGA
......(((((((((((((..(((........))).)))))))..((....(((((....)))))......)).))))))........... ( -23.30, z-score =  -1.90, R)
>droSim1.chr2L 20530915 91 + 22036055
UGAUUCCAGUCGGUCAGCUUUGGACUUACUUUUUCUGGCUGACUCGCCUGCCGGAUCUGUAUCUGUAUAUUGCACGACUGCUUUUUUAUGA
......(((((((((((((..(((........))).)))))))..((....(((((....)))))......)).))))))........... ( -23.30, z-score =  -1.90, R)
>consensus
UGAUUCCAGUCGGUCAGCUUUGGACUUACUUUUUCUGGCUGACUCGCCUGCCGGAUCUGUAUCUGUAUAUUGCACGACUGCUUUUUUAUGA
.((((((((.(((((((((..(((........))).))))))).)).)))..)))))..............(((....))).......... (-20.73 = -20.23 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,915,675 – 20,915,766
Length 91
Sequences 4
Columns 91
Reading direction reverse
Mean pairwise identity 91.39
Shannon entropy 0.14130
G+C content 0.44712
Mean single sequence MFE -17.64
Consensus MFE -17.61
Energy contribution -17.48
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -1.03
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.829652
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20915675 91 - 23011544
UAAAAAAAAAGCAGUCGUGCAAUAUAUAGAUACAGAUCCGGCAGGCGAGUCAGCCAGAAAAUGUAAGUCCAAAGCUGACCGACUGGAAUCA
..........(((....)))..............(((((((....((.((((((...................)))))))).)))).))). ( -18.51, z-score =  -1.32, R)
>droEre2.scaffold_4845 19038064 85 + 22589142
UCAUAAAAAAGCUGUCGAGCAAU------AUACAGAUCCGGCCAGCGAGCCAGCCAGAAAAAGUAAAUCCAAAGCUGACCGACUGGAAUCA
..........(((....)))...------.....(((....((((((.(.((((...................)))).))).)))).))). ( -15.01, z-score =  -0.45, R)
>droSec1.super_18 849437 91 - 1342155
UCAUAAAAAAGCAGUCGUGCAAUAUACAGAUACAGAUCCGGCAGGCGAGUCAGCCAGAAAAAGUAAGUCCAAAGCUGACCGACUGGAAUCA
..........(((....)))..............(((((((....((.((((((...................)))))))).)))).))). ( -18.51, z-score =  -1.17, R)
>droSim1.chr2L 20530915 91 - 22036055
UCAUAAAAAAGCAGUCGUGCAAUAUACAGAUACAGAUCCGGCAGGCGAGUCAGCCAGAAAAAGUAAGUCCAAAGCUGACCGACUGGAAUCA
..........(((....)))..............(((((((....((.((((((...................)))))))).)))).))). ( -18.51, z-score =  -1.17, R)
>consensus
UCAUAAAAAAGCAGUCGUGCAAUAUACAGAUACAGAUCCGGCAGGCGAGUCAGCCAGAAAAAGUAAGUCCAAAGCUGACCGACUGGAAUCA
..........(((....)))..............(((((((....((.((((((...................)))))))).)))).))). (-17.61 = -17.48 +  -0.13)

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 21:55:30 2011