Locus 8126

Sequence ID dm3.chr3L
Location 20,430,232 – 20,430,330
Length 98
Max. P 0.999111
window11179 window11180

overview

Window 9

Location 20,430,232 – 20,430,330
Length 98
Sequences 5
Columns 121
Reading direction forward
Mean pairwise identity 63.59
Shannon entropy 0.59014
G+C content 0.30300
Mean single sequence MFE -20.26
Consensus MFE -11.14
Energy contribution -12.18
Covariance contribution 1.04
Combinations/Pair 1.24
Mean z-score -2.65
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.65
SVM RNA-class probability 0.999111
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20430232 98 + 24543557
UUCCAAAAGUGUCACAGAAAUAUCUUUCAAUUACAUUGCUCGAAGAUCGAAUUUCCUUUCUUAAGAUUGCUGUGACACUUUCAUUUGCCUUUCUUUUU-----------------------
.....((((((((((((....(((((.............(((.....)))............)))))..)))))))))))).................----------------------- ( -22.41, z-score =  -3.55, R)
>droSim1.chr3L 19786033 98 + 22553184
UUCCAAAAGUGUCACAGAAAUAUUUUUCAAUUAUAUUGCCCGAAGAUCGAAUUUCCCAUCUUAAGAUUGCUGUGACACUUUCACUUGCUUUUCUUUUU-----------------------
.....((((((((((((.(((((.........))))).....(((((.(......).))))).......)))))))))))).................----------------------- ( -19.30, z-score =  -2.92, R)
>droSec1.super_11 325382 98 + 2888827
UUCCAAAAGUGUCACAGAAAUAUUUUUAAAUUAUAUUGCCUGAGGAUCGAAUUUCCCAUCUUAAGAUUGCUGUGACACUUUCAGUUGCUUUUCUUUUU-----------------------
.....((((((((((((.(((((.........)))))..((.(((((.(......).))))).))....)))))))))))).................----------------------- ( -20.20, z-score =  -2.13, R)
>droEre2.scaffold_4784 20131901 85 + 25762168
UUCAAAAAGUGUCACAGAAGUAUCUUUCAAUUAUAUUGC---AACAUU----------UCUUAAGAUUACUGUGACACUUUUAGUUAGCUUUCUUUUU-----------------------
....(((((((((((((....(((((.............---......----------....)))))..)))))))))))))................----------------------- ( -19.60, z-score =  -3.45, R)
>droAna3.scaffold_13337 10797660 120 + 23293914
UUUUAGGAGUGUCACAAAAAUCACUUUAAAAUAUGCUUUUU-UGUAAAGAUUUAAAACUAACAAUACUGUAAAAAGAGACUCGUUGAUUUUUAUGUGACACCUCUCGCAAUAAUUCCUUUU
....((..(((((((((((((((.((((((...(((.....-.)))....))))))....(((....)))..............)))))))..))))))))..))................ ( -19.80, z-score =  -1.18, R)
>consensus
UUCCAAAAGUGUCACAGAAAUAUCUUUCAAUUAUAUUGCCCGAAGAUCGAAUUUCCCAUCUUAAGAUUGCUGUGACACUUUCAGUUGCUUUUCUUUUU_______________________
.....((((((((((((....(((((....................................)))))..))))))))))))........................................ (-11.14 = -12.18 +   1.04)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,430,232 – 20,430,330
Length 98
Sequences 5
Columns 121
Reading direction reverse
Mean pairwise identity 63.59
Shannon entropy 0.59014
G+C content 0.30300
Mean single sequence MFE -22.84
Consensus MFE -12.10
Energy contribution -11.50
Covariance contribution -0.60
Combinations/Pair 1.44
Mean z-score -2.57
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.43
SVM RNA-class probability 0.998644
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20430232 98 - 24543557
-----------------------AAAAAGAAAGGCAAAUGAAAGUGUCACAGCAAUCUUAAGAAAGGAAAUUCGAUCUUCGAGCAAUGUAAUUGAAAGAUAUUUCUGUGACACUUUUGGAA
-----------------------................(((((((((((((..(((((...........((((.....))))((((...)))).)))))....))))))))))))).... ( -23.10, z-score =  -2.17, R)
>droSim1.chr3L 19786033 98 - 22553184
-----------------------AAAAAGAAAAGCAAGUGAAAGUGUCACAGCAAUCUUAAGAUGGGAAAUUCGAUCUUCGGGCAAUAUAAUUGAAAAAUAUUUCUGUGACACUUUUGGAA
-----------------------................(((((((((((((...(((.(((((.((....)).))))).))).......(((....)))....))))))))))))).... ( -24.60, z-score =  -3.06, R)
>droSec1.super_11 325382 98 - 2888827
-----------------------AAAAAGAAAAGCAACUGAAAGUGUCACAGCAAUCUUAAGAUGGGAAAUUCGAUCCUCAGGCAAUAUAAUUUAAAAAUAUUUCUGUGACACUUUUGGAA
-----------------------..............(..((((((((((((..(((....)))((((.......)))).........................))))))))))))..).. ( -24.40, z-score =  -3.23, R)
>droEre2.scaffold_4784 20131901 85 - 25762168
-----------------------AAAAAGAAAGCUAACUAAAAGUGUCACAGUAAUCUUAAGA----------AAUGUU---GCAAUAUAAUUGAAAGAUACUUCUGUGACACUUUUUGAA
-----------------------..............(.(((((((((((((..(((((..((----------.((((.---...))))..))..)))))....))))))))))))).).. ( -20.10, z-score =  -3.24, R)
>droAna3.scaffold_13337 10797660 120 - 23293914
AAAAGGAAUUAUUGCGAGAGGUGUCACAUAAAAAUCAACGAGUCUCUUUUUACAGUAUUGUUAGUUUUAAAUCUUUACA-AAAAAGCAUAUUUUAAAGUGAUUUUUGUGACACUCCUAAAA
...((((.......(....)((((((((..(((((((..((((..((((((...(((..(............)..))).-))))))...)))).....))))))))))))))))))).... ( -22.00, z-score =  -1.14, R)
>consensus
_______________________AAAAAGAAAAGCAAAUGAAAGUGUCACAGCAAUCUUAAGAUGGGAAAUUCGAUCUUCAAGCAAUAUAAUUGAAAGAUAUUUCUGUGACACUUUUGGAA
.......................................(((((((((((((...((....))...........................(((....)))....))))))))))))).... (-12.10 = -11.50 +  -0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:39:55 2011