Locus 2327

Sequence ID dm3.chr2L
Location 17,972,379 – 17,972,499
Length 120
Max. P 0.735258
window3205 window3206

overview

Window 5

Location 17,972,379 – 17,972,499
Length 120
Sequences 11
Columns 120
Reading direction forward
Mean pairwise identity 82.47
Shannon entropy 0.36608
G+C content 0.57121
Mean single sequence MFE -44.47
Consensus MFE -23.03
Energy contribution -23.21
Covariance contribution 0.17
Combinations/Pair 1.38
Mean z-score -2.12
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.735258
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17972379 120 + 23011544
GAUAGGAAAAAGGCUCGUAGGGCCAACGAGGCCUUCAGGCAGCUGGAAAAGCUAAGGGAUAAGAUCCGAAAGGAUCGAAAGAAGGGCUUGCUUGUCACGGAUCCGACGCAGCUGCCGCCG
...........(((..(.((((((.....))))))).((((((((...(((((.........(((((....)))))........)))))....(((........))).))))))))))). ( -49.93, z-score =  -3.40, R)
>droSim1.chr2L 17650841 120 + 22036055
GAUAGGAAGAAGGCUCGUAGGGCCAACGAGGCCUUCAGGCAGCUGGAAAAGCUAAGGGAUAAGAUCCGAAAAGAUCGAAAGAAGGGCUUGCUUGUCACGGAUCCGACGCAGCUGCCGCCG
....((..((((((((((.......)))).)))))).((((((((((.((((.(((((((...)))).......((....))....))))))).)).((....))...)))))))).)). ( -46.30, z-score =  -2.44, R)
>droSec1.super_7 1607276 120 + 3727775
GAUAGGAAGAAGGCUCGUAGGGCCAACGAGGCCUUCAGGCAGCUGGAAAAGCUAAGGGAUAAGAUCCGAAAGGAUCGAAAGAAGGGCUUGCUUGUCACGGAUCCGACGCAGCUGCCGCCG
....((..((((((((((.......)))).)))))).((((((((...(((((.........(((((....)))))........)))))....(((........))).)))))))).)). ( -51.03, z-score =  -3.52, R)
>droYak2.chr2R 18015212 120 - 21139217
GAUAGAAAGAAGGCUCGUCGAGCCAACGAGGCCUUCAGGCAGCUGGAAAAGCUAAGGGAUAAGAUCCGAAAGGAUCGAAAGAAGGGCUUGCUUGUCACGGAUCCGACCCAGCUGCCGCCG
........((((((((((.......)))).)))))).(((((((((..(((((.........(((((....)))))........)))))........((....))..))))))))).... ( -51.13, z-score =  -3.78, R)
>droEre2.scaffold_4845 16294959 120 - 22589142
GAUAGAAAGAAGGCGCGUAGAGCCAACGAGGCCUUCAGGCAGCUGGAAAAGCUAAGGGAUAAGAUCCGAAAGGAUCGAAAGAAGGGCUUGCUUGUCACGGAUCCAACGCAGCUGCCGCCG
........((((((.(((.......)))..)))))).((((((((((.(((((.........(((((....)))))........))))).....)).((.......)))))))))).... ( -45.63, z-score =  -2.80, R)
>dp4.chr4_group3 1281054 120 - 11692001
GACAGAAAGAAGGCGCGGAGGGCGAACGAGGCCUUCCGGCAGCUCGAGAAGCUGCGCGACAAGAUACGCAAGGACCGCAAGAAGGGACUCCUGGUGACCGAUCCCUCACAGCUCCCGCCC
...........((((((((((((.......))))))))((((((.....))))))(((........)))..(((..((....(((((.((..(....).)))))))....))))))))). ( -45.00, z-score =  -0.92, R)
>droPer1.super_8 2342200 120 - 3966273
GACAGAAAGAAGGCGCGGAGGGCGAACGAGGCCUUCCGGCAGCUCGAGAAGCUGCGCGACAAGAUACGCAAGGACCGCAAGAAGGGACUCCUGGUGACCGAUCCCUCACAGCUCCCGCCC
...........((((((((((((.......))))))))((((((.....))))))(((........)))..(((..((....(((((.((..(....).)))))))....))))))))). ( -45.00, z-score =  -0.92, R)
>droWil1.scaffold_180764 3516351 120 - 3949147
GAUCGUAAAAAGGCCAGAAGAGCGAAUGAGGCCUUCCGGCAAUUGGAAAAGUUACGUGACAAAAUACGCAAAGAGCGGAAAAAGGGUCUCUUGGUAACAGAUCCCACACAAUUGCCGCCG
...........(((..((((.((.......)))))).(((((((((........)(((........(((.....)))......((((((.........))))))))).))))))))))). ( -32.30, z-score =  -1.31, R)
>droMoj3.scaffold_6500 22055376 120 + 32352404
GAUAGAAAGAAGGCGCGACGCGCCAAUGAGGCGUUCCGGCAGCUGGAGAAGCUACGUGAUAAGAUACGCAAGGAGCGCAAGAAGGGUCUCCUGGUGACUGAUCCCACACAACUGCCGCCC
...........((((.((.(((((.....))))))))(((((((.....))))..(((....(((.(((.((((((.(.....).).))))).)))....)))...)))....)))))). ( -37.10, z-score =  -0.16, R)
>droGri2.scaffold_15252 14472686 120 + 17193109
GAUCGGAAGAAGGCGCGACGUGCGAAUGAGGCAUUCAGGCAGCUGGAGAAGCUGCGCGAUAAGAUACGCAAGGAGCGCAAGAAGGGACUCCUGGUGACGGAUGCUACGCAAUUGCCGCAU
..((....))..((((((..((((.....(((((((..((((((.....))))))(((........))).((((((.(.....).).)))))(....)))))))).)))).))).))).. ( -43.60, z-score =  -2.03, R)
>droVir3.scaffold_12963 17038579 120 + 20206255
GAUCGAAAGAAGGCGAGACGCGCCAACGAGGCGUUCCGGCAGCUGGAAAAGCUACGUGAUAAGAUACGCAAGGAGCGUAAGAAGGGUCUCCUGGUGACUGAUCCCACACAAUUGCCGCCC
..((....)).((((.((.(((((.....))))))))(((((((.....))))..(((......(((((.....)))))....(((((....(....).)))))..)))....)))))). ( -42.20, z-score =  -2.06, R)
>consensus
GAUAGAAAGAAGGCGCGUAGGGCCAACGAGGCCUUCAGGCAGCUGGAAAAGCUACGGGAUAAGAUACGCAAGGAUCGAAAGAAGGGCCUCCUGGUCACGGAUCCCACACAGCUGCCGCCG
...........(((.....((((.......))))...((((((((.....................(((.....)))................(((........))).))))))))))). (-23.03 = -23.21 +   0.17)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,972,379 – 17,972,499
Length 120
Sequences 11
Columns 120
Reading direction reverse
Mean pairwise identity 82.47
Shannon entropy 0.36608
G+C content 0.57121
Mean single sequence MFE -40.85
Consensus MFE -26.16
Energy contribution -25.09
Covariance contribution -1.07
Combinations/Pair 1.52
Mean z-score -1.43
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.07
SVM RNA-class probability 0.527261
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17972379 120 - 23011544
CGGCGGCAGCUGCGUCGGAUCCGUGACAAGCAAGCCCUUCUUUCGAUCCUUUCGGAUCUUAUCCCUUAGCUUUUCCAGCUGCCUGAAGGCCUCGUUGGCCCUACGAGCCUUUUUCCUAUC
.(((((((((((.((((......))))(((((((.....)))..(((((....)))))..........))))...))))))))....((((.....))))......)))........... ( -39.80, z-score =  -1.95, R)
>droSim1.chr2L 17650841 120 - 22036055
CGGCGGCAGCUGCGUCGGAUCCGUGACAAGCAAGCCCUUCUUUCGAUCUUUUCGGAUCUUAUCCCUUAGCUUUUCCAGCUGCCUGAAGGCCUCGUUGGCCCUACGAGCCUUCUUCCUAUC
.((.((((((((.((((......))))(((((((.......(((((.....)))))........))).))))...)))))))).((((((.((((.......))))))))))..)).... ( -40.46, z-score =  -2.08, R)
>droSec1.super_7 1607276 120 - 3727775
CGGCGGCAGCUGCGUCGGAUCCGUGACAAGCAAGCCCUUCUUUCGAUCCUUUCGGAUCUUAUCCCUUAGCUUUUCCAGCUGCCUGAAGGCCUCGUUGGCCCUACGAGCCUUCUUCCUAUC
.((.((((((((.((((......))))(((((((.....)))..(((((....)))))..........))))...)))))))).((((((.((((.......))))))))))..)).... ( -41.10, z-score =  -2.27, R)
>droYak2.chr2R 18015212 120 + 21139217
CGGCGGCAGCUGGGUCGGAUCCGUGACAAGCAAGCCCUUCUUUCGAUCCUUUCGGAUCUUAUCCCUUAGCUUUUCCAGCUGCCUGAAGGCCUCGUUGGCUCGACGAGCCUUCUUUCUAUC
....(((((((((((((......))))(((((((.....)))..(((((....)))))..........))))..))))))))).((((((.((((((...))))))))))))........ ( -46.20, z-score =  -2.76, R)
>droEre2.scaffold_4845 16294959 120 + 22589142
CGGCGGCAGCUGCGUUGGAUCCGUGACAAGCAAGCCCUUCUUUCGAUCCUUUCGGAUCUUAUCCCUUAGCUUUUCCAGCUGCCUGAAGGCCUCGUUGGCUCUACGCGCCUUCUUUCUAUC
.(((((((((((....(....)..((.(((((((.....)))..(((((....)))))..........)))).)))))))))).(.(((((.....))).)).)..)))........... ( -35.50, z-score =  -0.70, R)
>dp4.chr4_group3 1281054 120 + 11692001
GGGCGGGAGCUGUGAGGGAUCGGUCACCAGGAGUCCCUUCUUGCGGUCCUUGCGUAUCUUGUCGCGCAGCUUCUCGAGCUGCCGGAAGGCCUCGUUCGCCCUCCGCGCCUUCUUUCUGUC
(((((((((((((.((((((((.....((((((....))))))))))))))(((........))))))))))).((((..(((....)))))))..)))))................... ( -49.80, z-score =  -0.73, R)
>droPer1.super_8 2342200 120 + 3966273
GGGCGGGAGCUGUGAGGGAUCGGUCACCAGGAGUCCCUUCUUGCGGUCCUUGCGUAUCUUGUCGCGCAGCUUCUCGAGCUGCCGGAAGGCCUCGUUCGCCCUCCGCGCCUUCUUUCUGUC
(((((((((((((.((((((((.....((((((....))))))))))))))(((........))))))))))).((((..(((....)))))))..)))))................... ( -49.80, z-score =  -0.73, R)
>droWil1.scaffold_180764 3516351 120 + 3949147
CGGCGGCAAUUGUGUGGGAUCUGUUACCAAGAGACCCUUUUUCCGCUCUUUGCGUAUUUUGUCACGUAACUUUUCCAAUUGCCGGAAGGCCUCAUUCGCUCUUCUGGCCUUUUUACGAUC
((.(((((((((...(((.(((.......)))..)))............((((((........))))))......)))))))))(((((((..............)))))))...))... ( -34.04, z-score =  -1.83, R)
>droMoj3.scaffold_6500 22055376 120 - 32352404
GGGCGGCAGUUGUGUGGGAUCAGUCACCAGGAGACCCUUCUUGCGCUCCUUGCGUAUCUUAUCACGUAGCUUCUCCAGCUGCCGGAACGCCUCAUUGGCGCGUCGCGCCUUCUUUCUAUC
(((((((((((...(((((....)).)))(((((..((...(((((.....)))))...........))..))))))))))))((..((((.....))))..))..)))).......... ( -41.34, z-score =  -1.05, R)
>droGri2.scaffold_15252 14472686 120 - 17193109
AUGCGGCAAUUGCGUAGCAUCCGUCACCAGGAGUCCCUUCUUGCGCUCCUUGCGUAUCUUAUCGCGCAGCUUCUCCAGCUGCCUGAAUGCCUCAUUCGCACGUCGCGCCUUCUUCCGAUC
..(((((...((((((((....))....((((((.(......).)))))))))))).......((((((((.....))))))..(((((...)))))))..))))).............. ( -33.40, z-score =  -0.92, R)
>droVir3.scaffold_12963 17038579 120 - 20206255
GGGCGGCAAUUGUGUGGGAUCAGUCACCAGGAGACCCUUCUUACGCUCCUUGCGUAUCUUAUCACGUAGCUUUUCCAGCUGCCGGAACGCCUCGUUGGCGCGUCUCGCCUUCUUUCGAUC
(((((((((..((((((((...(((.......)))...))))))))...))))............((((((.....)))))).((..((((.....))))..)).))))).......... ( -37.90, z-score =  -0.68, R)
>consensus
CGGCGGCAGCUGCGUGGGAUCCGUCACCAGGAGGCCCUUCUUUCGAUCCUUGCGUAUCUUAUCCCGUAGCUUUUCCAGCUGCCUGAAGGCCUCGUUGGCCCUACGCGCCUUCUUUCUAUC
.(((((((((((.((((......))))..............(((((.....)))))...................))))))))....(((.......)))......)))........... (-26.16 = -25.09 +  -1.07)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:49:09 2011