Locus 11136

Sequence ID	dm3.chr3R
Location	18,873,319 – 18,873,430
Length	111
Max. P	0.737482

overview

Window 5

Location	18,873,319 – 18,873,429
Length	110
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	64.88
Shannon entropy	0.57239
G+C content	0.42955
Mean single sequence MFE	-28.85
Consensus MFE	-14.07
Energy contribution	-18.07
Covariance contribution	4.00
Combinations/Pair	1.17
Mean z-score	-1.09
Structure conservation index	0.49
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.29
SVM RNA-class probability	0.631927
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18873319 110 - 27905053
GGGCUAACAAAUGGCUGCAAUGAGCGUCUGGCAAAUGAGCCAUUAAUAAGGCUA---GUCAGAUGCACAUCAGA-CAUGGAUGCACUUAGAAAAUGCAGUCGCAUUUCAUGUUA
.(((((.....)))))...(((.(((((((((.....((((........)))).---))))))))).)))..((-((((((((((((((.....)).))).))).)))))))). ( -36.00, z-score =  -2.48, R)
>droYak2.chr3R 19737193 110 - 28832112
GUGCUAACAAAUGGCUGCAAUGAACGCCUGGCAAAUGAGCCAUUAAUAAGGCUA---GUCAGAUACACAUCGGA-CUUGGAUGCACUCGGAAAAUGCAGUAUGCUUUCACGUUA
((((...(((.(((((((.......)).((((......)))).......)))))---(((.(((....))).))-))))...)))).((((((..((.....)))))).))... ( -24.40, z-score =   0.71, R)
>droSim1.chr3R 18683953 98 - 27517382
GGGCUAACAAAUGGCUGCAAUGAGCGUCUGGCAAAUGAGCCAUUAAUAAGGCUA---GUCAGAUGCACAUCAGA-CAUGGAUGCACUUAGAAAAUGCAGUCU------------
............(((((((....(((((((((.....((((........)))).---))))))))).((((...-....))))...........))))))).------------ ( -32.70, z-score =  -2.68, R)
>droGri2.scaffold_15074 3685347 111 - 7742996
AUGCGAGUAAA--ACUGUAUUGAAAGCUUUACCUAUAAG-CAUUACAGCGUAUACAUAUCUUAUACAAAUAGGAGUGUGAGAGAGAGAGAGAGGGGGAGUUGGUUGCUGUACUA
.....((((..--...(((.....(((((..(((....(-(......)).........((((((((........)))))))).........)))..)))))...)))..)))). ( -22.30, z-score =   0.10, R)
>consensus
GGGCUAACAAAUGGCUGCAAUGAACGCCUGGCAAAUGAGCCAUUAAUAAGGCUA___GUCAGAUACACAUCAGA_CAUGGAUGCACUUAGAAAAUGCAGUCGG_UUUCAUGUUA
............(((((((....(((((((((.....((((........))))....))))))))).((((........))))...........)))))))............. (-14.07 = -18.07 +   4.00)

alignment

secondary structure

dotplot

Window 6

Location	18,873,320 – 18,873,430
Length	110
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	64.58
Shannon entropy	0.57843
G+C content	0.43548
Mean single sequence MFE	-29.34
Consensus MFE	-14.07
Energy contribution	-18.07
Covariance contribution	4.00
Combinations/Pair	1.17
Mean z-score	-1.23
Structure conservation index	0.48
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.55
SVM RNA-class probability	0.737482
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18873320 110 - 27905053
GGGGCUAACAAAUGGCUGCAAUGAGCGUCUGGCAAAUGAGCCAUUAAUAAGGCUA---GUCAGAUGCACAUCAGA-CAUGGAUGCACUUAGAAAAUGCAGUCGCAUUUCAUGUU
(.(((((.....))))).).(((.(((((((((.....((((........)))).---))))))))).)))..((-((((((((((((((.....)).))).))).)))))))) ( -37.40, z-score =  -2.88, R)
>droYak2.chr3R 19737194 110 - 28832112
CGUGCUAACAAAUGGCUGCAAUGAACGCCUGGCAAAUGAGCCAUUAAUAAGGCUA---GUCAGAUACACAUCGGA-CUUGGAUGCACUCGGAAAAUGCAGUAUGCUUUCACGUU
((((..(.((....((((((.....((....(((....((((........))))(---(((.(((....))).))-))....)))...)).....)))))).)).)..)))).. ( -25.60, z-score =   0.37, R)
>droSim1.chr3R 18683953 99 - 27517382
GGGGCUAACAAAUGGCUGCAAUGAGCGUCUGGCAAAUGAGCCAUUAAUAAGGCUA---GUCAGAUGCACAUCAGA-CAUGGAUGCACUUAGAAAAUGCAGUCU-----------
.............(((((((....(((((((((.....((((........)))).---))))))))).((((...-....))))...........))))))).----------- ( -32.70, z-score =  -2.58, R)
>droGri2.scaffold_15074 3685348 111 - 7742996
UAUGCGAGUAAA--ACUGUAUUGAAAGCUUUACCUAUAAG-CAUUACAGCGUAUACAUAUCUUAUACAAAUAGGAGUGUGAGAGAGAGAGAGAGGGGGAGUUGGUUGCUGUACU
..(((.(((((.--...........(((((..(((....(-(......)).........((((((((........)))))))).........)))..)))))..)))))))).. ( -21.64, z-score =   0.17, R)
>consensus
GGGGCUAACAAAUGGCUGCAAUGAACGCCUGGCAAAUGAGCCAUUAAUAAGGCUA___GUCAGAUACACAUCAGA_CAUGGAUGCACUUAGAAAAUGCAGUCGG_UUUCAUGUU
.............(((((((....(((((((((.....((((........))))....))))))))).((((........))))...........)))))))............ (-14.07 = -18.07 +   4.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:37:08 2011