Locus 2492

Sequence ID dm3.chr2L
Location 19,472,032 – 19,472,157
Length 125
Max. P 0.985598
window3425 window3426

overview

Window 5

Location 19,472,032 – 19,472,123
Length 91
Sequences 9
Columns 120
Reading direction reverse
Mean pairwise identity 75.82
Shannon entropy 0.42623
G+C content 0.44323
Mean single sequence MFE -28.22
Consensus MFE -15.41
Energy contribution -16.30
Covariance contribution 0.89
Combinations/Pair 1.29
Mean z-score -2.59
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.21
SVM RNA-class probability 0.985598
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19472032 91 - 23011544
---------------ACACCGCAGCUCGCUUUUUUCGGGCCAAAAUCAAAUUCGACCAAUUUGUAAUGGCCCGGAGUCG----------CAGGCG----AAGGCAAAUGUCUUCAUAUGC
---------------.....(((((..((...((((((((((....((((((.....))))))...))))))))))..)----------)..))(----(((((....))))))...))) ( -35.80, z-score =  -4.33, R)
>droEre2.scaffold_4845 17764239 87 + 22589142
---------------ACACCGCAGCUCGCUUUUU---GGCCCAAAUCAAAUUCAACCAAUUUGUAAUGG-CCGGAGUCG----------CAGGCG----AAGGCAAAUGUCUUCAUAUGC
---------------.....(((((..((.((((---((((.....((((((.....))))))....))-))))))..)----------)..))(----(((((....))))))...))) ( -28.70, z-score =  -2.74, R)
>droYak2.chr2R 5970199 90 - 21139217
---------------ACACCGCAGCUCGCUUUUUU-GGGCCAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCGGAGUCG----------CAGGCG----AAGGCAAAUGUCUUCAUUUGC
---------------.....(((((..((..((((-((((((....((((((.....))))))...))))))))))..)----------)..))(----(((((....))))))...))) ( -35.00, z-score =  -4.33, R)
>droSec1.super_7 3087394 91 - 3727775
---------------ACACCGCAGCUCGCUUUUUUCGGGCCAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCGGAGUCG----------CAGGCG----AAGGCAAAUGUCUUCAUAUGC
---------------.....(((((..((...((((((((((....((((((.....))))))...))))))))))..)----------)..))(----(((((....))))))...))) ( -35.80, z-score =  -4.83, R)
>dp4.chr4_group4 578888 87 + 6586962
-------------------AGACCACAGUUCUUUUUGGGGCAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCGGAAUUG----------AAGGAA----AAGGCAAAUGUCUUCAUAUGC
-------------------...((.(((((((.....((((.....((((((.....)))))).....)))))))))))----------..))..----(((((....)))))....... ( -20.40, z-score =  -0.82, R)
>droPer1.super_16 886178 87 - 1990440
-------------------AGACCACAGUUCUUUUUGGGGCAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCGGAAUUG----------AAGGAA----AAGGCAAAUGUCUUCAUAUGC
-------------------...((.(((((((.....((((.....((((((.....)))))).....)))))))))))----------..))..----(((((....)))))....... ( -20.40, z-score =  -0.82, R)
>droAna3.scaffold_12916 4073164 105 + 16180835
ACACCGCAGAAUGAGUCGAAGAGUUUGGUUUUUUUCGUAACAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCGGAGU-G----------AAGGCA----GAGGCAAAUGUCUUCAUAUGU
...(((..............((((((((((((.........))))))))))))..(((........)))..))).((-(----------((((((----........))))))))).... ( -24.90, z-score =  -1.09, R)
>droSim1.chr2L 19153839 91 - 22036055
---------------ACACCGCAGCUCGCUUUUUUCGGGCCAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCGGAGUCG----------CAGGCG----AAGGCAAAUGUCUUCAUAUGC
---------------.....(((((..((...((((((((((....((((((.....))))))...))))))))))..)----------)..))(----(((((....))))))...))) ( -35.80, z-score =  -4.83, R)
>droWil1.scaffold_180772 7201517 96 - 8906247
------------------------AUGAAAGCUUUUAGGGCAAAAUCAAAUUCAAGCUAUUUGUAAUGCUACGGAAAUAGGAAUGGGCCAAGACAAGGCAAGGCAAAUGUCUUCAUAUGC
------------------------(((((.(((((...(((..(.((...(((.(((..........)))...)))....)).)..))).....)))))..(((....)))))))).... ( -17.20, z-score =   0.48, R)
>consensus
_______________ACACCGCAGCUCGCUUUUUUCGGGCCAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCGGAGUCG__________CAGGCG____AAGGCAAAUGUCUUCAUAUGC
................................((((((((((....((((((.....))))))...))))))))))................(((....(((((....)))))....))) (-15.41 = -16.30 +   0.89)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,472,065 – 19,472,157
Length 92
Sequences 8
Columns 103
Reading direction reverse
Mean pairwise identity 65.66
Shannon entropy 0.65804
G+C content 0.46315
Mean single sequence MFE -20.65
Consensus MFE -9.46
Energy contribution -10.55
Covariance contribution 1.09
Combinations/Pair 1.27
Mean z-score -1.39
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.39
SVM RNA-class probability 0.934586
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19472065 92 - 23011544
--------CCCAAAGCCACCGAAGCCACCAUUC-GAAUA-GUGGACACCGCAGCUC-GCUUUUUUCGGGCCAAAAUCAAAUUCGACCAAUUUGUAAUGGCCCG
--------...(((((...((((.......)))-)....-((((...)))).....-)))))...(((((((....((((((.....))))))...))))))) ( -25.00, z-score =  -2.51, R)
>droEre2.scaffold_4845 17764272 85 + 22589142
--------CCGAAAGCCACCAAAGC---CAUUC-GAAUA-GUGGACACCGCAGCUC-GCUUUUU---GGCCCAAAUCAAAUUCAACCAAUUUGUAAUGGCCG-
--------.(....)........((---(((((-((((.-((((...)))).....-(((....---)))..................))))).))))))..- ( -16.50, z-score =  -0.45, R)
>droYak2.chr2R 5970232 91 - 21139217
--------CCGAAAGCCACCAAAGCUAGCAUUC-GAAUA-GUGGACACCGCAGCUC-GCUUUUUU-GGGCCAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCG
--------.(....).....(((((.(((((..-..)).-((((...)))).))).-)))))...-((((((....((((((.....))))))...)))))). ( -23.70, z-score =  -1.96, R)
>droSec1.super_7 3087427 82 - 3727775
------------------CCAAAGCCACCAUUC-GAAUA-GUGGACACCGCAGCUC-GCUUUUUUCGGGCCAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCG
------------------...............-(((.(-(((..(......)..)-)))...)))((((((....((((((.....))))))...)))))). ( -21.30, z-score =  -2.51, R)
>droPer1.super_16 886211 82 - 1990440
----------------CACCAGUACGGGGAGUAUCGGGGAGGGGAGACCACAGUUC-UUUUU----GGGGCAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCG
----------------..((.((((.....)))).))....((....)).(((...-...))----)((((.....((((((.....)))))).....)))). ( -21.90, z-score =  -0.55, R)
>droAna3.scaffold_12916 4073196 103 + 16180835
CCGGAACACUGCAAAUCAACGCGGCAGUGGACACCGCAGAAUGAGUCGAAGAGUUUGGUUUUUUUCGUAACAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCG
.(((..((.(((((((....((((.........)))).............((((((((((((.........)))))))))))).....))))))).))..))) ( -26.30, z-score =  -1.23, R)
>droSim1.chr2L 19153872 84 - 22036055
------------------CCAAAGCCACCAUUCUUAAUAUGUGGACACCGCAGCUC-GCUUUUUUCGGGCCAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCG
------------------..(((((..............(((((...)))))....-)))))...(((((((....((((((.....))))))...))))))) ( -20.67, z-score =  -2.45, R)
>droWil1.scaffold_180772 7201564 74 - 8906247
--------------------CCCACAUCUACU--GGCUAUAUAGAGAAUGAAA----GCUUUU---AGGGCAAAAUCAAAUUCAAGCUAUUUGUAAUGCUACG
--------------------.......(((..--((((..............)----)))..)---))((((....(((((.......)))))...))))... (  -9.84, z-score =   0.54, R)
>consensus
________________CACCAAAGCCACCAUUC_GAAUA_GUGGACACCGCAGCUC_GCUUUUUU_GGGCCAAAAUCAAAUUCAACCAAUUUGUAAUGGCCCG
........................................(((.....)))...............((((((....((((((.....))))))...)))))). ( -9.46 = -10.55 +   1.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:52:12 2011