Locus 12177

Sequence ID dm3.chr3R
Location 26,268,002 – 26,268,098
Length 96
Max. P 0.810530
window16747 window16748

overview

Window 7

Location 26,268,002 – 26,268,098
Length 96
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 82.09
Shannon entropy 0.31613
G+C content 0.36383
Mean single sequence MFE -17.70
Consensus MFE -11.74
Energy contribution -11.90
Covariance contribution 0.16
Combinations/Pair 1.06
Mean z-score -1.86
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.58
SVM RNA-class probability 0.751145
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26268002 96 + 27905053
CUAAUCGUCCAGCAGUUUCCAACAUUUUCA------AAUGCCUUCCGUCUUUGGCAGGCUAACAUGACAAAUGUGGUUAUACUAAUAUUUGAAUAUCCUUUU
....(((......(((..(((.((((((((------...((((.(((....))).)))).....))).))))))))....)))......))).......... ( -18.00, z-score =  -1.45, R)
>droEre2.scaffold_4820 8726468 102 - 10470090
UUAAUCGUUCGCCACUUUCCAAUAUUUUCAUAUCCAAAUGCCCUCCGUCUUUGGCAGGCUAACAUGACAAAUGUUGUUAUUUCAAUAUUUGAAUUUCCUUUU
......(((.(((........((((....))))(((((.((.....)).)))))..))).)))....(((((((((......)))))))))........... ( -17.80, z-score =  -2.51, R)
>droYak2.chr3R 27186270 84 + 28832112
UUAAUCGUCCAGCACUUGCCAAUAUUUUCAUAUCCAAAUGCCUUCCGUCUUUGGCAGGCUAACAUGACAAAUGU--UUAUUCUCUU----------------
...........((....)).(((((((((((........((((.(((....))).))))....)))).))))))--).........---------------- ( -12.60, z-score =  -1.02, R)
>droSec1.super_4 5092671 102 + 6179234
CUAAUCGUCCAACACUUUGGAACAUUUUCAUAUCCAAAUGCCUUCCGUCUUUGGCAGGCUAACAUGACAAAUGUGGUUAUUCUAAUAUUUGAAUAUCCUUUU
.......(((((....)))))((((((((((........((((.(((....))).))))....)))).))))))((.(((((........))))).)).... ( -23.00, z-score =  -2.96, R)
>droSim1.chr3R 25913909 98 + 27517382
CUAAUCGUCCAACACUUUCGAACAUUUUCAUAUCCAAAUGCCUUCCGUCUUUGGCAGGCUAACAUGACAAAUGUGGUUAUUCCAAUAUUUGAAUAUCC----
....(((...........)))((((((((((........((((.(((....))).))))....)))).))))))((.(((((........))))).))---- ( -17.10, z-score =  -1.36, R)
>consensus
CUAAUCGUCCAACACUUUCCAACAUUUUCAUAUCCAAAUGCCUUCCGUCUUUGGCAGGCUAACAUGACAAAUGUGGUUAUUCUAAUAUUUGAAUAUCCUUUU
.....................((((((((((........((((.(((....))).))))....)))).))))))............................ (-11.74 = -11.90 +   0.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 26,268,002 – 26,268,098
Length 96
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 82.09
Shannon entropy 0.31613
G+C content 0.36383
Mean single sequence MFE -23.06
Consensus MFE -13.62
Energy contribution -14.90
Covariance contribution 1.28
Combinations/Pair 1.11
Mean z-score -2.21
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.76
SVM RNA-class probability 0.810530
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26268002 96 - 27905053
AAAAGGAUAUUCAAAUAUUAGUAUAACCACAUUUGUCAUGUUAGCCUGCCAAAGACGGAAGGCAUU------UGAAAAUGUUGGAAACUGCUGGACGAUUAG
.................((((((...((((((((.(((.....((((.((......)).))))...------)))))))).)))....))))))........ ( -18.50, z-score =  -0.60, R)
>droEre2.scaffold_4820 8726468 102 + 10470090
AAAAGGAAAUUCAAAUAUUGAAAUAACAACAUUUGUCAUGUUAGCCUGCCAAAGACGGAGGGCAUUUGGAUAUGAAAAUAUUGGAAAGUGGCGAACGAUUAA
.........((((.....)))).......(.((((((((....((((.((......)).)))).(((.(((((....))))).))).)))))))).)..... ( -22.50, z-score =  -2.29, R)
>droYak2.chr3R 27186270 84 - 28832112
----------------AAGAGAAUAA--ACAUUUGUCAUGUUAGCCUGCCAAAGACGGAAGGCAUUUGGAUAUGAAAAUAUUGGCAAGUGCUGGACGAUUAA
----------------..........--.((((((((......((((.((......)).)))).....(((((....)))))))))))))............ ( -20.80, z-score =  -2.28, R)
>droSec1.super_4 5092671 102 - 6179234
AAAAGGAUAUUCAAAUAUUAGAAUAACCACAUUUGUCAUGUUAGCCUGCCAAAGACGGAAGGCAUUUGGAUAUGAAAAUGUUCCAAAGUGUUGGACGAUUAG
....((.(((((........))))).))....(((((......((((.((......)).)))).(((((((((....))).))))))......))))).... ( -26.60, z-score =  -3.02, R)
>droSim1.chr3R 25913909 98 - 27517382
----GGAUAUUCAAAUAUUGGAAUAACCACAUUUGUCAUGUUAGCCUGCCAAAGACGGAAGGCAUUUGGAUAUGAAAAUGUUCGAAAGUGUUGGACGAUUAG
----((.(((((........))))).))....(((((......((((.((......)).)))).(((((((((....))))))))).......))))).... ( -26.90, z-score =  -2.85, R)
>consensus
AAAAGGAUAUUCAAAUAUUAGAAUAACCACAUUUGUCAUGUUAGCCUGCCAAAGACGGAAGGCAUUUGGAUAUGAAAAUGUUGGAAAGUGCUGGACGAUUAG
................................(((((......((((.((......)).)))).(((.(((((....))))).))).......))))).... (-13.62 = -14.90 +   1.28)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:57:15 2011