Locus 2612

Sequence ID dm3.chr2L
Location 20,502,796 – 20,502,928
Length 132
Max. P 0.988994
window3588 window3589

overview

Window 8

Location 20,502,796 – 20,502,888
Length 92
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 74.92
Shannon entropy 0.46167
G+C content 0.64587
Mean single sequence MFE -41.05
Consensus MFE -27.71
Energy contribution -29.80
Covariance contribution 2.09
Combinations/Pair 1.19
Mean z-score -2.08
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.35
SVM RNA-class probability 0.988994
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20502796 92 + 23011544
UCCGGGAGGCGUCCCUUGUGGUGACGCUUGAUUGAAAUGCCUGGUAGGCCAGGCAGCGAUCCCGGC------------CACUCCCACUCGCAGCCCGGAGCAAC
((((((..(((......((((.((.(((.(((((...(((((((....))))))).)))))..)))------------...)))))).)))..))))))..... ( -44.70, z-score =  -2.95, R)
>droSim1.chr2L 20073120 104 + 22036055
UCCGGGAGGCGUCCCUUGUGGCGACGCUUGAUUGAAAUGCCUGGUAGGCCAGGCAGCGAUCCCGGCCACUCCCACUUCCACUCCCACUCGCAGCCCGGAGCAAC
((((((..(((((((....)).)))(((.(((((...(((((((....))))))).)))))..))).......................))..))))))..... ( -43.80, z-score =  -2.03, R)
>droSec1.super_18 380878 104 + 1342155
UCCGGGAGGCGUCCCUUGUGGCGACGCUUGAUUGAAAUGCCUGGUAGGCCAGGCAGCGAUCCCGGCCACUCCCACUUCCACUCCCACUCGCAGCCCGGAGCAAC
((((((..(((((((....)).)))(((.(((((...(((((((....))))))).)))))..))).......................))..))))))..... ( -43.80, z-score =  -2.03, R)
>droYak2.chr2R 6858298 104 + 21139217
CCCGGGAGGCAUCCCUUGUGGCAACGCUUGAUUGAAAUGCCUGGCAGGCCAGGCAGCGAUCCCAGCAACUCCCACUUCCACUCCCACUCGCCGCCCGGAGCAAC
.(((((.(((.........(....)(((.(((((...(((((((....))))))).)))))..))).......................))).)))))...... ( -41.50, z-score =  -2.31, R)
>droEre2.scaffold_4845 18649687 90 - 22589142
-GCCGGGGGCGUCCCUUGUGGCGACGCUUGAUUGAAAUGCCUGGCAGGCCAGGCAGCGAUCC-GGC------------CACGCCCACUCGCAGCCCGGGGCAAC
-(((..((((......((.((((..(((.(((((...(((((((....))))))).))))).-)))------------..))))))......))))..)))... ( -46.30, z-score =  -1.84, R)
>droAna3.scaffold_12916 7000249 75 + 16180835
ACUGGAGCUCGUCUCUUGAGGCGGUGCUUGAUUGAAAUGCCUGGUAGGCAUUGCCUGGCUUU----------------CACCCCGAGCUAC-------------
.....((((((.......((((((((((((...(......)...))))))))))))((....----------------..)).))))))..------------- ( -26.20, z-score =  -1.33, R)
>consensus
UCCGGGAGGCGUCCCUUGUGGCGACGCUUGAUUGAAAUGCCUGGUAGGCCAGGCAGCGAUCCCGGC____________CACUCCCACUCGCAGCCCGGAGCAAC
.((((((((((((((....)).)))))))(((((...(((((((....))))))).)))))................................)))))...... (-27.71 = -29.80 +   2.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 20,502,833 – 20,502,928
Length 95
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 81.13
Shannon entropy 0.34058
G+C content 0.57816
Mean single sequence MFE -41.30
Consensus MFE -30.91
Energy contribution -33.63
Covariance contribution 2.72
Combinations/Pair 1.04
Mean z-score -1.43
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.58
SVM RNA-class probability 0.750127
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20502833 95 - 23011544
AAAACUAAUUAAGCCAACUUAAGUGCGGAGCAGCUUGGCAGUUGCUCCGGGCUGCG------------AGUGGGAGUGGCCGGGAUCGCUGCCUGGCCUACCAGGCA
............(((.((((.(((.((((((((((....)))))))))).)))..)------------)))((....(((((((.......)))))))..)).))). ( -46.90, z-score =  -3.05, R)
>droSim1.chr2L 20073157 106 - 22036055
-AAAAUAAUUAAGCCAACUUAAGUGCGGAGCAGCUUGGCAGUUGCUCCGGGCUGCGAGUGGGAGUGGAAGUGGGAGUGGCCGGGAUCGCUGCCUGGCCUACCAGGCA
-...........(((.((((.(((.((((((((((....)))))))))).)))..))))...........(((....(((((((.......)))))))..)))))). ( -47.80, z-score =  -2.39, R)
>droSec1.super_18 380915 107 - 1342155
AAAACUAAUUAAGCCAACUUAAGUGCGGAGCAGCUUGGCAGUUGCUCCGGGCUGCGAGUGGGAGUGGAAGUGGGAGUGGCCGGGAUCGCUGCCUGGCCUACCAGGCA
............(((.((((.(((.((((((((((....)))))))))).)))..))))...........(((....(((((((.......)))))))..)))))). ( -47.80, z-score =  -2.06, R)
>droYak2.chr2R 6858335 107 - 21139217
AAAACUAAUUAAGCCAACUUAAGUGCGGAGCAGCUUGCCAGUUGCUCCGGGCGGCGAGUGGGAGUGGAAGUGGGAGUUGCUGGGAUCGCUGCCUGGCCUGCCAGGCA
.............((.((((..((.((((((((((....)))))))))).))...)))).))(((((.((..(...)..))....)))))((((((....)))))). ( -43.10, z-score =  -0.46, R)
>droEre2.scaffold_4845 18649723 94 + 22589142
AAAACUAAUUAAGCCAACUUAAGUGCGGACCAGCUUGCCAGUUGCCCCGGGCUGCG------------AGUGGGCGUGGCC-GGAUCGCUGCCUGGCCUGCCAGGCA
............(((.((((.(((.(((..(((((....)))))..))).)))..)------------))).((((.((((-((........)))))))))).))). ( -39.60, z-score =  -0.54, R)
>droAna3.scaffold_12916 7000286 78 - 16180835
AAAACUAAUUAAGCCAACUUAAGUGCGGAGCAUCUUGGCAGUAGCUCGGG-------------------GUGAAA---GCCAG-------GCAAUGCCUACCAGGCA
............(((((.....((((...)))).)))))....((..(((-------------------((....---)))((-------((...)))).))..)). ( -22.60, z-score =  -0.09, R)
>consensus
AAAACUAAUUAAGCCAACUUAAGUGCGGAGCAGCUUGGCAGUUGCUCCGGGCUGCG____________AGUGGGAGUGGCCGGGAUCGCUGCCUGGCCUACCAGGCA
............(((......(((.((((((((((....)))))))))).))).................(((....(((((((.......)))))))..)))))). (-30.91 = -33.63 +   2.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:54:33 2011