Locus 12005

Sequence ID dm3.chr3R
Location 25,042,904 – 25,043,006
Length 102
Max. P 0.998860
window16501 window16502

overview

Window 1

Location 25,042,904 – 25,043,006
Length 102
Sequences 12
Columns 120
Reading direction forward
Mean pairwise identity 94.73
Shannon entropy 0.10543
G+C content 0.42500
Mean single sequence MFE -36.37
Consensus MFE -35.14
Energy contribution -35.14
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -4.04
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.52
SVM RNA-class probability 0.998860
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25042904 102 + 27905053
-----------------UUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUG-GUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAGCACA
-----------------..(((((((.((((.((.(((((.((((((((((((.(((((..-..............))))))))))).)))))).))))).)).)))).))))))).... ( -37.39, z-score =  -4.28, R)
>droSim1.chr3R 24713800 102 + 27517382
-----------------UUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUG-GUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAGCACA
-----------------..(((((((.((((.((.(((((.((((((((((((.(((((..-..............))))))))))).)))))).))))).)).)))).))))))).... ( -37.39, z-score =  -4.28, R)
>droSec1.super_4 3905697 102 + 6179234
-----------------UUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUG-GUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAGCACA
-----------------..(((((((.((((.((.(((((.((((((((((((.(((((..-..............))))))))))).)))))).))))).)).)))).))))))).... ( -37.39, z-score =  -4.28, R)
>droYak2.chr3R 7377586 102 - 28832112
-----------------UUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUG-GUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAGCACU
-----------------..(((((((.((((.((.(((((.((((((((((((.(((((..-..............))))))))))).)))))).))))).)).)))).))))))).... ( -37.39, z-score =  -4.32, R)
>droEre2.scaffold_4820 7482567 102 - 10470090
-----------------UUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUG-GUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAGCACU
-----------------..(((((((.((((.((.(((((.((((((((((((.(((((..-..............))))))))))).)))))).))))).)).)))).))))))).... ( -37.39, z-score =  -4.32, R)
>droAna3.scaffold_13340 9498697 102 - 23697760
-----------------UUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUG-UUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAGCACA
-----------------..(((((((.((((.((.(((((.((((((((((((.(((((..-((........))..))))))))))).)))))).))))).)).)))).))))))).... ( -37.40, z-score =  -4.50, R)
>droPer1.super_7 2047033 102 + 4445127
-----------------CUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUU-GUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAACACA
-----------------...((((((.((((.((.(((((.((((((((((((.(((((..-..............))))))))))).)))))).))))).)).)))).))))))..... ( -35.19, z-score =  -4.02, R)
>dp4.chr2 1883620 102 + 30794189
-----------------CUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUU-GUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAACACA
-----------------...((((((.((((.((.(((((.((((((((((((.(((((..-..............))))))))))).)))))).))))).)).)))).))))))..... ( -35.19, z-score =  -4.02, R)
>droWil1.scaffold_181108 1735992 120 + 4707319
UUCUAUGUGGCAGCGUCUCUUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUUUGUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAGCACA
.....((((..........(((((((.((((.((.(((((.((((((((((((.(((((.................))))))))))).)))))).))))).)).)))).))))))))))) ( -36.13, z-score =  -2.09, R)
>droVir3.scaffold_12822 2333413 102 + 4096053
-----------------CUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUU-GUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAACACA
-----------------...((((((.((((.((.(((((.((((((((((((.(((((..-..............))))))))))).)))))).))))).)).)))).))))))..... ( -35.19, z-score =  -4.02, R)
>droMoj3.scaffold_6540 26449283 102 + 34148556
-----------------CUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUU-GUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAAUACA
-----------------...((((((.((((.((.(((((.((((((((((((.(((((..-..............))))))))))).)))))).))))).)).)))).))))))..... ( -35.19, z-score =  -4.25, R)
>droGri2.scaffold_14624 3251573 102 + 4233967
-----------------UUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUU-GUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAACACA
-----------------...((((((.((((.((.(((((.((((((((((((.(((((..-..............))))))))))).)))))).))))).)).)))).))))))..... ( -35.19, z-score =  -4.10, R)
>consensus
_________________UUCUGACUCUAUUUUGUCGGCGAACAUGGAUCUAGUGCACGGUG_GUUCAUGAUUAAGUUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAGCACA
....................((((((.((((.((.(((((.((((((((((((.(((((.................))))))))))).)))))).))))).)).)))).))))))..... (-35.14 = -35.14 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 25,042,904 – 25,043,006
Length 102
Sequences 12
Columns 120
Reading direction reverse
Mean pairwise identity 94.73
Shannon entropy 0.10543
G+C content 0.42500
Mean single sequence MFE -27.52
Consensus MFE -27.21
Energy contribution -27.09
Covariance contribution -0.12
Combinations/Pair 1.04
Mean z-score -3.74
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.48
SVM RNA-class probability 0.998763
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25042904 102 - 27905053
UGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAC-CACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAA-----------------
....(((((...........(.((((((((..(((((((((((...............-...)))).))))))).)))))))).)...........)))))..----------------- ( -28.42, z-score =  -4.19, R)
>droSim1.chr3R 24713800 102 - 27517382
UGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAC-CACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAA-----------------
....(((((...........(.((((((((..(((((((((((...............-...)))).))))))).)))))))).)...........)))))..----------------- ( -28.42, z-score =  -4.19, R)
>droSec1.super_4 3905697 102 - 6179234
UGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAC-CACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAA-----------------
....(((((...........(.((((((((..(((((((((((...............-...)))).))))))).)))))))).)...........)))))..----------------- ( -28.42, z-score =  -4.19, R)
>droYak2.chr3R 7377586 102 + 28832112
AGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAC-CACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAA-----------------
....(((((...........(.((((((((..(((((((((((...............-...)))).))))))).)))))))).)...........)))))..----------------- ( -28.42, z-score =  -4.21, R)
>droEre2.scaffold_4820 7482567 102 + 10470090
AGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAC-CACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAA-----------------
....(((((...........(.((((((((..(((((((((((...............-...)))).))))))).)))))))).)...........)))))..----------------- ( -28.42, z-score =  -4.21, R)
>droAna3.scaffold_13340 9498697 102 + 23697760
UGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAA-CACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAA-----------------
....(((((...........(.((((((((..(((((((((((...............-...)))).))))))).)))))))).)...........)))))..----------------- ( -28.42, z-score =  -4.12, R)
>droPer1.super_7 2047033 102 - 4445127
UGUGUUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAC-AACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAG-----------------
....(((((...........(.((((((((..(((((((((((...............-...)))).))))))).)))))))).)...........)))))..----------------- ( -26.12, z-score =  -3.26, R)
>dp4.chr2 1883620 102 - 30794189
UGUGUUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAC-AACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAG-----------------
....(((((...........(.((((((((..(((((((((((...............-...)))).))))))).)))))))).)...........)))))..----------------- ( -26.12, z-score =  -3.26, R)
>droWil1.scaffold_181108 1735992 120 - 4707319
UGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAACAAACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAAGAGACGCUGCCACAUAGAA
((((................(.((((((((..(((((((((((...................)))).))))))).)))))))).).......(((.(((....))).))).))))..... ( -29.01, z-score =  -2.90, R)
>droVir3.scaffold_12822 2333413 102 - 4096053
UGUGUUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAC-AACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAG-----------------
....(((((...........(.((((((((..(((((((((((...............-...)))).))))))).)))))))).)...........)))))..----------------- ( -26.12, z-score =  -3.26, R)
>droMoj3.scaffold_6540 26449283 102 - 34148556
UGUAUUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAC-AACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAG-----------------
....(((((...........(.((((((((..(((((((((((...............-...)))).))))))).)))))))).)...........)))))..----------------- ( -26.22, z-score =  -3.84, R)
>droGri2.scaffold_14624 3251573 102 - 4233967
UGUGUUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAC-AACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAA-----------------
....(((((...........(.((((((((..(((((((((((...............-...)))).))))))).)))))))).)...........)))))..----------------- ( -26.12, z-score =  -3.29, R)
>consensus
UGUGCUGACCCAACUUAAUAGACGAGCAUGAAAUCUAGUCACGAACUUAAUCAUGAAC_AACCGUGCACUAGAUCCAUGUUCGCCGACAAAAUAGAGUCAGAA_________________
....(((((...........(.((((((((..(((((((((((...................)))).))))))).)))))))).)...........)))))................... (-27.21 = -27.09 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:53:52 2011