Locus 11354

Sequence ID dm3.chr3R
Location 20,501,331 – 20,501,405
Length 74
Max. P 0.980906
window15611 window15612

overview

Window 1

Location 20,501,331 – 20,501,405
Length 74
Sequences 14
Columns 74
Reading direction forward
Mean pairwise identity 88.05
Shannon entropy 0.29668
G+C content 0.37589
Mean single sequence MFE -17.63
Consensus MFE -13.64
Energy contribution -14.96
Covariance contribution 1.32
Combinations/Pair 1.14
Mean z-score -2.43
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.06
SVM RNA-class probability 0.980906
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20501331 74 + 27905053
AUUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCG
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.73, R)
>anoGam1.chr2R 44155550 62 + 62725911
------------UUCACAUACAGCUGGAAAACUCUGGCGAUCCACUAGAGUUCAAUAAUCCGCAACAGCUCUCA
------------.........(((((...((((((((.......)))))))).............))))).... ( -11.99, z-score =  -1.58, R)
>apiMel3.GroupUn 14476131 74 + 399230636
AUGUUCAUAUUAUGUGAUUACAGCUUGAAAACUCAGGGGACCCGUUCGAGUUCACGAACCCUCAACAGCUUUCG
.(((((((.....))))..)))((((((....)))((((....(((((......)))))))))...)))..... ( -12.80, z-score =   0.25, R)
>droSim1.chr3R 20343957 74 + 27517382
AUUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCG
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.73, R)
>droSec1.super_0 20835804 74 + 21120651
AUUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCG
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.73, R)
>droYak2.chr3R 2836515 74 - 28832112
AUUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCG
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.73, R)
>droEre2.scaffold_4820 2913228 74 - 10470090
AUUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCG
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.73, R)
>droAna3.scaffold_13340 19023573 74 - 23697760
AUUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCG
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.73, R)
>dp4.chr2 29060159 74 - 30794189
AUUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCG
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.73, R)
>droPer1.super_7 2557692 74 - 4445127
AUUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCG
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.73, R)
>droWil1.scaffold_181089 2772547 74 - 12369635
AUUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCC
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.71, R)
>droVir3.scaffold_13047 799371 74 + 19223366
AAUUGCAUUUUCUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCC
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.53, R)
>droMoj3.scaffold_6540 4800240 74 + 34148556
AAUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCU
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.85, R)
>droGri2.scaffold_14906 8666472 74 - 14172833
AAUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCC
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. ( -18.50, z-score =  -2.71, R)
>consensus
AUUUGCAUUUACUUAAAAUUUAGCUGGAGAACUCUGGCGAUCCGCUGGAUUUUAAUAAUGCUCAUCGUUUAUCG
....(((((...((((((((((((.(((...(....)...))))))))))))))).)))))............. (-13.64 = -14.96 +   1.32)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,501,331 – 20,501,405
Length 74
Sequences 14
Columns 74
Reading direction reverse
Mean pairwise identity 88.05
Shannon entropy 0.29668
G+C content 0.37589
Mean single sequence MFE -15.38
Consensus MFE -10.71
Energy contribution -11.88
Covariance contribution 1.16
Combinations/Pair 1.15
Mean z-score -1.92
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.80
SVM RNA-class probability 0.820697
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20501331 74 - 27905053
CGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAAU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -2.24, R)
>anoGam1.chr2R 44155550 62 - 62725911
UGAGAGCUGUUGCGGAUUAUUGAACUCUAGUGGAUCGCCAGAGUUUUCCAGCUGUAUGUGAA------------
.(((((((.(.((((.((((((.....)))))).)))).).)))))))..............------------ ( -14.60, z-score =  -0.50, R)
>apiMel3.GroupUn 14476131 74 - 399230636
CGAAAGCUGUUGAGGGUUCGUGAACUCGAACGGGUCCCCUGAGUUUUCAAGCUGUAAUCACAUAAUAUGAACAU
.(((((((...(.(((..(((........)))..))).)..))))))).......................... ( -17.10, z-score =  -0.56, R)
>droSim1.chr3R 20343957 74 - 27517382
CGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAAU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -2.24, R)
>droSec1.super_0 20835804 74 - 21120651
CGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAAU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -2.24, R)
>droYak2.chr3R 2836515 74 + 28832112
CGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAAU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -2.24, R)
>droEre2.scaffold_4820 2913228 74 + 10470090
CGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAAU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -2.24, R)
>droAna3.scaffold_13340 19023573 74 + 23697760
CGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAAU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -2.24, R)
>dp4.chr2 29060159 74 + 30794189
CGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAAU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -2.24, R)
>droPer1.super_7 2557692 74 + 4445127
CGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAAU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -2.24, R)
>droWil1.scaffold_181089 2772547 74 + 12369635
GGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAAU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -1.94, R)
>droVir3.scaffold_13047 799371 74 - 19223366
GGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGAAAAUGCAAUU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -1.78, R)
>droMoj3.scaffold_6540 4800240 74 - 34148556
AGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAUU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -2.32, R)
>droGri2.scaffold_14906 8666472 74 + 14172833
GGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAUU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... ( -15.30, z-score =  -1.83, R)
>consensus
CGAUAAACGAUGAGCAUUAUUAAAAUCCAGCGGAUCGCCAGAGUUCUCCAGCUAAAUUUUAAGUAAAUGCAAAU
.............(((((.(((((((..((((((..((....))..))).)))..)))))))...))))).... (-10.71 = -11.88 +   1.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:41:24 2011