Locus 322

Sequence ID dm3.chr2L
Location 2,287,927 – 2,287,986
Length 59
Max. P 0.988628
window439 window440

overview

Window 9

Location 2,287,927 – 2,287,986
Length 59
Sequences 7
Columns 62
Reading direction forward
Mean pairwise identity 72.70
Shannon entropy 0.54790
G+C content 0.49500
Mean single sequence MFE -15.29
Consensus MFE -6.34
Energy contribution -6.77
Covariance contribution 0.43
Combinations/Pair 1.27
Mean z-score -2.02
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.14
SVM RNA-class probability 0.898803
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2287927 59 + 23011544
AUCGAUCCGGGUGCAGUUCAUGUUUUCGCAUUUAUUGCCACCACCAGC---CGCACCCGAAU
.......(((((((.(((..((.....(((.....)))...))..)))---.)))))))... ( -18.10, z-score =  -3.12, R)
>droWil1.scaffold_180708 2252056 55 + 12563649
CUCACCCCUUCUGCAGUGUGCGU-----CACCAAUCGAUAUUGUCGAGU--UAAAUUCGAAA
........(((.(((((((.((.-----.......))))))))).))).--........... (  -8.00, z-score =  -0.55, R)
>droSim1.chr2L 2248341 59 + 22036055
AUCGAUCCGGGUGCAGUUCAUGUUUUCGCAUUUAUUGCCACCACCAGC---CGCAACCAAAU
.........((((((((..((((....))))..)))).))))......---........... ( -11.30, z-score =  -0.61, R)
>droSec1.super_5 462539 59 + 5866729
AUCGAUCCGGGUGCAGUUCAUGUUUUCGCAUUUAUUGCCACCACCAGC---CGCACCCAAAU
........((((((.(((..((.....(((.....)))...))..)))---.)))))).... ( -16.30, z-score =  -2.85, R)
>droEre2.scaffold_4929 2324861 59 + 26641161
AUCGAUCCGGGUGCAGUGCAUGUUUUCGCAUUUAUGGCCACCAGCUGC---CGCACCCAAAU
........(((((((((((........)))))...(((........))---))))))).... ( -20.60, z-score =  -1.99, R)
>droYak2.chr2L 2269306 62 + 22324452
AUCGAUCUGGGUGCAGUUCAUGUUUUCGCAUUUAUUGCCACCAGCAGCAGCCGCACCCAAAU
.......(((((((.(((..((((...(((.....)))....))))..))).)))))))... ( -19.80, z-score =  -2.97, R)
>droAna3.scaffold_12916 10001554 61 - 16180835
AUCGAUCCAAAGGCAGUGCAUGUUUUUGCAUUUAUUGCCAUCACGACCA-CCACAUUCCAGU
...........(((((((.((((....)))).)))))))..........-............ ( -12.90, z-score =  -2.02, R)
>consensus
AUCGAUCCGGGUGCAGUUCAUGUUUUCGCAUUUAUUGCCACCACCAGC___CGCACCCAAAU
.........((((((((..(((......)))..)))).)))).................... ( -6.34 =  -6.77 +   0.43)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 0

Location 2,287,927 – 2,287,986
Length 59
Sequences 7
Columns 62
Reading direction reverse
Mean pairwise identity 72.70
Shannon entropy 0.54790
G+C content 0.49500
Mean single sequence MFE -19.19
Consensus MFE -10.27
Energy contribution -10.34
Covariance contribution 0.07
Combinations/Pair 1.67
Mean z-score -2.06
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.33
SVM RNA-class probability 0.988628
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2287927 59 - 23011544
AUUCGGGUGCG---GCUGGUGGUGGCAAUAAAUGCGAAAACAUGAACUGCACCCGGAUCGAU
(((((((((((---(.(.(((.(.(((.....))).)...))).).)))))))))))).... ( -26.50, z-score =  -4.49, R)
>droWil1.scaffold_180708 2252056 55 - 12563649
UUUCGAAUUUA--ACUCGACAAUAUCGAUUGGUG-----ACGCACACUGCAGAAGGGGUGAG
..((((.....--..))))...........(...-----.)...((((.(....).)))).. (  -8.40, z-score =   0.26, R)
>droSim1.chr2L 2248341 59 - 22036055
AUUUGGUUGCG---GCUGGUGGUGGCAAUAAAUGCGAAAACAUGAACUGCACCCGGAUCGAU
((((((.((((---(.(.(((.(.(((.....))).)...))).).))))).)))))).... ( -17.90, z-score =  -1.56, R)
>droSec1.super_5 462539 59 - 5866729
AUUUGGGUGCG---GCUGGUGGUGGCAAUAAAUGCGAAAACAUGAACUGCACCCGGAUCGAU
(((((((((((---(.(.(((.(.(((.....))).)...))).).)))))))))))).... ( -24.50, z-score =  -4.04, R)
>droEre2.scaffold_4929 2324861 59 - 26641161
AUUUGGGUGCG---GCAGCUGGUGGCCAUAAAUGCGAAAACAUGCACUGCACCCGGAUCGAU
(((((((((((---(..((((.(.((.......)).)...)).)).)))))))))))).... ( -21.50, z-score =  -1.57, R)
>droYak2.chr2L 2269306 62 - 22324452
AUUUGGGUGCGGCUGCUGCUGGUGGCAAUAAAUGCGAAAACAUGAACUGCACCCAGAUCGAU
((((((((((((.(((((....)))))....(((......)))...)))))))))))).... ( -21.80, z-score =  -2.52, R)
>droAna3.scaffold_12916 10001554 61 + 16180835
ACUGGAAUGUGG-UGGUCGUGAUGGCAAUAAAUGCAAAAACAUGCACUGCCUUUGGAUCGAU
.(..((....((-..((((((...(((.....))).....)))).))..))))..)...... ( -13.70, z-score =  -0.53, R)
>consensus
AUUUGGGUGCG___GCUGGUGGUGGCAAUAAAUGCGAAAACAUGAACUGCACCCGGAUCGAU
(((((((((((...........(.(((.....))).)..........))))))))))).... (-10.27 = -10.34 +   0.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:10:46 2011