Locus 7733

Sequence ID dm3.chr3L
Location 16,964,869 – 16,964,963
Length 94
Max. P 0.718033
window10643 window10644

overview

Window 3

Location 16,964,869 – 16,964,963
Length 94
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 92.87
Shannon entropy 0.12104
G+C content 0.54852
Mean single sequence MFE -32.98
Consensus MFE -29.60
Energy contribution -29.80
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.718033
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16964869 94 + 24543557
GAGCCCACGCCCACGGCGGCCGCACACGAAAUUGUGCUGCGUGGGCAUAAUUGUGAAUUUGUAGCUCGCAGAUACAAAUAGAUAGCCCGGUGCU-------
.(((((.((((...))))((.(((((......))))).))..((((((.....((.((((((.....)))))).)).....)).)))))).)))------- ( -32.40, z-score =  -0.94, R)
>droEre2.scaffold_4784 8883836 93 - 25762168
GAGCCCACGCCCACGGCGGCCGCACACGAAAUUGUGCUGCGUGGGCGUAAU-GUGAAUUUGUAGCUCGCAGAUACAAAUAGAUAGUCCGAUGCU-------
..(((((((((...))).((.(((((......))))).))))))))(((.(-((((.........)))))..)))...................------- ( -31.40, z-score =  -0.99, R)
>droYak2.chr3L 7087222 101 - 24197627
GAGCCCACGCCCACGACGGCCGCACACGAAACUGUGCUGCGUGGGCGUAAUUGUGAAUUUGUAGCUCGCAGAUACAAAUAGAUACCCCGAUGCUCGUAAUU
((((..(((((((((.((((.(((........))))))))))))))))..((((..((((((.....))))))))))..............))))...... ( -35.20, z-score =  -2.83, R)
>droSec1.super_0 9026264 94 + 21120651
GAGCCCACGCCCACGGCGGCCGCACACGAAAUUGUGCUGCGUGGGCGUAAUUGUGAAUUUGUAGCUCGCAGAUACAAAUAGAUACGCCAGUGCU-------
..(((((((((...))).((.(((((......))))).))))))))(((.((((((.........)))))).)))....((.(((....)))))------- ( -33.10, z-score =  -1.14, R)
>droSim1.chr3L 16303642 94 + 22553184
GAGCCCACGCCCACGGCGGCCGCACACGAAAUUGUGCUGCGUGGGCGUAAUUGUGAAUUUGUAGCUCGCAGAUACAAAUAGAUACCCCAGUGCU-------
..(((((((((...))).((.(((((......))))).))))))))(((.((((((.........)))))).)))...................------- ( -32.80, z-score =  -1.65, R)
>consensus
GAGCCCACGCCCACGGCGGCCGCACACGAAAUUGUGCUGCGUGGGCGUAAUUGUGAAUUUGUAGCUCGCAGAUACAAAUAGAUACCCCGGUGCU_______
.(((..(((((((((.((((.(((........))))))))))))))))........(((((((.(.....).)))))))............)))....... (-29.60 = -29.80 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,964,869 – 16,964,963
Length 94
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 92.87
Shannon entropy 0.12104
G+C content 0.54852
Mean single sequence MFE -32.78
Consensus MFE -30.86
Energy contribution -30.70
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.18
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.35
SVM RNA-class probability 0.657183
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16964869 94 - 24543557
-------AGCACCGGGCUAUCUAUUUGUAUCUGCGAGCUACAAAUUCACAAUUAUGCCCACGCAGCACAAUUUCGUGUGCGGCCGCCGUGGGCGUGGGCUC
-------......(((((....(((((((.(.....).))))))).......(((((((((((.(((((......)))))....).))))))))))))))) ( -31.80, z-score =  -0.74, R)
>droEre2.scaffold_4784 8883836 93 + 25762168
-------AGCAUCGGACUAUCUAUUUGUAUCUGCGAGCUACAAAUUCAC-AUUACGCCCACGCAGCACAAUUUCGUGUGCGGCCGCCGUGGGCGUGGGCUC
-------(((............(((((((.(.....).)))))))....-.((((((((((((.(((((......)))))....).)))))))))))))). ( -31.00, z-score =  -1.15, R)
>droYak2.chr3L 7087222 101 + 24197627
AAUUACGAGCAUCGGGGUAUCUAUUUGUAUCUGCGAGCUACAAAUUCACAAUUACGCCCACGCAGCACAGUUUCGUGUGCGGCCGUCGUGGGCGUGGGCUC
......((((.(((((((((......)))))).)))...............((((((((((((.(((((......)))))....).))))))))))))))) ( -36.10, z-score =  -1.99, R)
>droSec1.super_0 9026264 94 - 21120651
-------AGCACUGGCGUAUCUAUUUGUAUCUGCGAGCUACAAAUUCACAAUUACGCCCACGCAGCACAAUUUCGUGUGCGGCCGCCGUGGGCGUGGGCUC
-------.(((...(((........)))...)))(((((.............(((((((((((.(((((......)))))....).))))))))))))))) ( -33.01, z-score =  -1.13, R)
>droSim1.chr3L 16303642 94 - 22553184
-------AGCACUGGGGUAUCUAUUUGUAUCUGCGAGCUACAAAUUCACAAUUACGCCCACGCAGCACAAUUUCGUGUGCGGCCGCCGUGGGCGUGGGCUC
-------.(((....(((((......))))))))(((((.............(((((((((((.(((((......)))))....).))))))))))))))) ( -32.01, z-score =  -0.87, R)
>consensus
_______AGCACCGGGGUAUCUAUUUGUAUCUGCGAGCUACAAAUUCACAAUUACGCCCACGCAGCACAAUUUCGUGUGCGGCCGCCGUGGGCGUGGGCUC
.......(((............(((((((.(.....).)))))))......((((((((((((.(((((......)))))....).)))))))))))))). (-30.86 = -30.70 +  -0.16)

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 23:32:27 2011