Locus 7117

Sequence ID dm3.chr3L
Location 12,326,965 – 12,327,029
Length 64
Max. P 0.997682
window9801 window9802

overview

Window 1

Location 12,326,965 – 12,327,029
Length 64
Sequences 10
Columns 64
Reading direction forward
Mean pairwise identity 83.01
Shannon entropy 0.37002
G+C content 0.51914
Mean single sequence MFE -23.53
Consensus MFE -12.61
Energy contribution -13.37
Covariance contribution 0.76
Combinations/Pair 1.15
Mean z-score -2.78
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.96
SVM RNA-class probability 0.976929
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12326965 64 + 24543557
CUCCUUGCUCCAUUGGCAGCACAUGUCAUGAUAAUUUCGCAGCGACAUGUGCCGCCAUCACGUA
.............((((.(((((((((.((.........))..))))))))).))))....... ( -21.90, z-score =  -2.99, R)
>droSim1.chr3L 11705285 64 + 22553184
CUCCUUGCUCCAUUGGCAGCACAUGUCAUGAUAAUUUCGCAGCGACAUGUGCCGCCAUCACGUA
.............((((.(((((((((.((.........))..))))))))).))))....... ( -21.90, z-score =  -2.99, R)
>droSec1.super_0 4511823 64 + 21120651
CUCCCUGCUCCAUUGGCAGCACAUGUCAUGAUAAUUUCGCAGCAACAUGUGCCGCCAUCACGUA
.............((((.((((((((..((.........))...)))))))).))))....... ( -18.30, z-score =  -2.05, R)
>droYak2.chr3L 12381725 64 + 24197627
CUCCUCGCUCCAUUGGCAGCACAUGUCAUGAUAAUUUCGCAGCGACAUGUGCUGCCAUCACGUA
.............((((((((((((((.((.........))..))))))))))))))....... ( -26.50, z-score =  -4.66, R)
>droEre2.scaffold_4784 12322775 64 + 25762168
CUCCUUGCUCCAUUGGCAGCACAUGUCAUGAUAAUUUCGCAGCGACAUGUGCUGCCGUCACGUA
..............(((((((((((((.((.........))..)))))))))))))........ ( -25.80, z-score =  -3.97, R)
>droAna3.scaffold_13337 21971410 64 - 23293914
GUCCUUGCGCCAGUGGCAGCACAUGUCAUGAUAAUUUCGCUGCGACAUGUGCUGCCAGCACGUA
.....((((....((((((((((((((.(((.....)))....))))))))))))))...)))) ( -28.10, z-score =  -3.02, R)
>dp4.chrXR_group6 2683588 63 + 13314419
UUCCUGGCACUGUGG-CAGCACAUGUCAUGAUAAUUUUGCAGCGACAUGUGCUGCCAUCACGUA
......((...((((-(((((((((((.((.........))..)))))))))))))))...)). ( -28.00, z-score =  -3.78, R)
>droPer1.super_9 979720 63 + 3637205
UUCCUGGCACUGUGG-CAGCACAUGUCAUGAUAAUUUUGCAGCGACAUGUGCUGCCAUCACGUA
......((...((((-(((((((((((.((.........))..)))))))))))))))...)). ( -28.00, z-score =  -3.78, R)
>droWil1.scaffold_180949 2265781 64 - 6375548
CUCGCAGCAUCGGGGGCAGCACAUGCCAUGAUAAUUUUGCAGCAACAUAUGCUGCCAUCACGUA
......((((((..((((.....)))).))))......((((((.....))))))......)). ( -17.50, z-score =  -0.24, R)
>droMoj3.scaffold_6680 5935054 60 + 24764193
CUUCAUGCUUCAUUCGCGUCCUGC----UGAUGCUUGUGCAGCGGCACAUGCUGCCAGCACGUA
.....(((.......(((((....----.)))))..((((.(((((....)))))..))))))) ( -19.30, z-score =  -0.34, R)
>consensus
CUCCUUGCUCCAUUGGCAGCACAUGUCAUGAUAAUUUCGCAGCGACAUGUGCUGCCAUCACGUA
..............(((.((((((((..((.........))...)))))))).)))........ (-12.61 = -13.37 +   0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 12,326,965 – 12,327,029
Length 64
Sequences 10
Columns 64
Reading direction reverse
Mean pairwise identity 83.01
Shannon entropy 0.37002
G+C content 0.51914
Mean single sequence MFE -25.57
Consensus MFE -19.75
Energy contribution -19.83
Covariance contribution 0.08
Combinations/Pair 1.50
Mean z-score -2.95
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.15
SVM RNA-class probability 0.997682
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12326965 64 - 24543557
UACGUGAUGGCGGCACAUGUCGCUGCGAAAUUAUCAUGACAUGUGCUGCCAAUGGAGCAAGGAG
..(((..(((((((((((((((.((.........)))))))))))))))))))).......... ( -25.90, z-score =  -3.32, R)
>droSim1.chr3L 11705285 64 - 22553184
UACGUGAUGGCGGCACAUGUCGCUGCGAAAUUAUCAUGACAUGUGCUGCCAAUGGAGCAAGGAG
..(((..(((((((((((((((.((.........)))))))))))))))))))).......... ( -25.90, z-score =  -3.32, R)
>droSec1.super_0 4511823 64 - 21120651
UACGUGAUGGCGGCACAUGUUGCUGCGAAAUUAUCAUGACAUGUGCUGCCAAUGGAGCAGGGAG
..(((..((((((((((((((................))))))))))))))))).......... ( -23.29, z-score =  -2.38, R)
>droYak2.chr3L 12381725 64 - 24197627
UACGUGAUGGCAGCACAUGUCGCUGCGAAAUUAUCAUGACAUGUGCUGCCAAUGGAGCGAGGAG
..(((..(((((((((((((((.((.........))))))))))))))))).....)))..... ( -28.30, z-score =  -4.19, R)
>droEre2.scaffold_4784 12322775 64 - 25762168
UACGUGACGGCAGCACAUGUCGCUGCGAAAUUAUCAUGACAUGUGCUGCCAAUGGAGCAAGGAG
..(((...((((((((((((((.((.........)))))))))))))))).))).......... ( -26.00, z-score =  -3.49, R)
>droAna3.scaffold_13337 21971410 64 + 23293914
UACGUGCUGGCAGCACAUGUCGCAGCGAAAUUAUCAUGACAUGUGCUGCCACUGGCGCAAGGAC
...(((((((((((((((((((..............))))))))))))))...)))))...... ( -30.84, z-score =  -4.22, R)
>dp4.chrXR_group6 2683588 63 - 13314419
UACGUGAUGGCAGCACAUGUCGCUGCAAAAUUAUCAUGACAUGUGCUG-CCACAGUGCCAGGAA
(((.((.(((((((((((((((.((.........))))))))))))))-))))))))....... ( -27.80, z-score =  -3.71, R)
>droPer1.super_9 979720 63 - 3637205
UACGUGAUGGCAGCACAUGUCGCUGCAAAAUUAUCAUGACAUGUGCUG-CCACAGUGCCAGGAA
(((.((.(((((((((((((((.((.........))))))))))))))-))))))))....... ( -27.80, z-score =  -3.71, R)
>droWil1.scaffold_180949 2265781 64 + 6375548
UACGUGAUGGCAGCAUAUGUUGCUGCAAAAUUAUCAUGGCAUGUGCUGCCCCCGAUGCUGCGAG
..((.(..(((((((((((((................))))))))))))).))).......... ( -19.99, z-score =  -0.64, R)
>droMoj3.scaffold_6680 5935054 60 - 24764193
UACGUGCUGGCAGCAUGUGCCGCUGCACAAGCAUCA----GCAGGACGCGAAUGAAGCAUGAAG
..(.((((((..((.(((((....))))).)).)))----))).)..((.......))...... ( -19.90, z-score =  -0.53, R)
>consensus
UACGUGAUGGCAGCACAUGUCGCUGCGAAAUUAUCAUGACAUGUGCUGCCAAUGGAGCAAGGAG
........((((((((((((((..............)))))))))))))).............. (-19.75 = -19.83 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:20:50 2011