Locus 7204

Sequence ID dm3.chr3L
Location 12,968,650 – 12,968,745
Length 95
Max. P 0.866998
window9913 window9914

overview

Window 3

Location 12,968,650 – 12,968,745
Length 95
Sequences 8
Columns 100
Reading direction forward
Mean pairwise identity 88.79
Shannon entropy 0.20290
G+C content 0.33840
Mean single sequence MFE -8.38
Consensus MFE -7.71
Energy contribution -7.52
Covariance contribution -0.19
Combinations/Pair 1.07
Mean z-score -1.14
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.45
SVM RNA-class probability 0.700097
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12968650 95 + 24543557
GCCACCAUUUUGCUCAAUUUAUUUCCAACAUCAAGCUCUC----UCGUUUCCUUUUUUUUUUUAAUUU-AACACAAAAUUUUCGUGUAAUGUUUGGCUUU
((((.((((.......................((((....----..))))..................-.((((.........))))))))..))))... (  -8.30, z-score =  -0.77, R)
>droSim1.chr3L 12351371 91 + 22553184
GCCACCAUUUUGCUCAAUUUAUUUCCAACAUCAAGCUCUC----UCGUUCCCUUUUUUU----AAUUU-AACACACAAUUUUCGUGUAAUGUUUGGCUUU
((((.((((..(((...................)))....----...............----.....-...((((.......))))))))..))))... (  -8.61, z-score =  -1.27, R)
>droSec1.super_0 5140261 91 + 21120651
GCCACCAUUUUGCUCAAUUUAUUUCCAACAUCAAGCUCUC----UCGUUCCCUUUUUUU----AAUUU-AACACACAAUUUUCGUGUAAUGUUUGGCUUU
((((.((((..(((...................)))....----...............----.....-...((((.......))))))))..))))... (  -8.61, z-score =  -1.27, R)
>droYak2.chr3L 13046303 90 + 24197627
GCCACCAUUUUGCUCAAUUUAUUUCCAACAUCAAGCUCCC----UCGUUCCCUUUUUU-----AAUUU-AACACACAAUUUUCGUGUAAUGUUUGGCUUU
((((.((((..(((...................)))....----..............-----.....-...((((.......))))))))..))))... (  -8.61, z-score =  -1.18, R)
>droEre2.scaffold_4784 12975245 90 + 25762168
GCCACCAUUUUGCUCAAUUUAUUUCCAACAUCAAGCUCCC----UCGUUCCCUUUUUU-----AAUUU-AACACACAAUUUUCGUGUAAUGUUUGGCUUU
((((.((((..(((...................)))....----..............-----.....-...((((.......))))))))..))))... (  -8.61, z-score =  -1.18, R)
>droAna3.scaffold_13337 6503340 88 - 23293914
GCCACCAUUUUGCUCAAUUUAUUUCCAACAUCAAGCUCCC----A---UUCCUUUUUUU----AAUUU-UACACACAAUUUUCGUGUAAUGUUUGGCUUU
((((.......(((...................)))....----.---...........----(((.(-(((((.........)))))).)))))))... (  -9.51, z-score =  -1.85, R)
>dp4.chrXR_group6 4339785 100 + 13314419
GCCACCAUUUUGCUCAAUUUAUUUCCAACAUCAAGUCCUCGCUCACUCCUCUUUUCUUUUUUUAAUUUCAACACAAAAUUUUCGUGUAAUGUUUGGCUUU
((((.((((........................(((....)))...........................((((.........))))))))..))))... (  -7.40, z-score =  -0.80, R)
>droPer1.super_9 2629056 100 + 3637205
GCCACCAUUUUGCUCAAUUUAUUUCCAACAUCAAGUCCUCGCUCACUCCUCUUUUCUUUUUUUAAUUUCAACACAAAAUUUUCGUGUAAUGUUUGGCUUU
((((.((((........................(((....)))...........................((((.........))))))))..))))... (  -7.40, z-score =  -0.80, R)
>consensus
GCCACCAUUUUGCUCAAUUUAUUUCCAACAUCAAGCUCUC____UCGUUCCCUUUUUUU____AAUUU_AACACACAAUUUUCGUGUAAUGUUUGGCUUU
((((.((((..(((...................)))..................................((((.........))))))))..))))... ( -7.71 =  -7.52 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,968,650 – 12,968,745
Length 95
Sequences 8
Columns 100
Reading direction reverse
Mean pairwise identity 88.79
Shannon entropy 0.20290
G+C content 0.33840
Mean single sequence MFE -16.11
Consensus MFE -13.77
Energy contribution -14.02
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.80
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.98
SVM RNA-class probability 0.866998
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12968650 95 - 24543557
AAAGCCAAACAUUACACGAAAAUUUUGUGUU-AAAUUAAAAAAAAAAAGGAAACGA----GAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGC
...((((..((((((((((.....)))))).-................(....)..----....(((..((..(....)...))..)))..)))).)))) ( -18.30, z-score =  -2.92, R)
>droSim1.chr3L 12351371 91 - 22553184
AAAGCCAAACAUUACACGAAAAUUGUGUGUU-AAAUU----AAAAAAAGGGAACGA----GAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGC
...((((..((((((((((...))))))...-.....----...............----....(((..((..(....)...))..)))..)))).)))) ( -16.70, z-score =  -2.17, R)
>droSec1.super_0 5140261 91 - 21120651
AAAGCCAAACAUUACACGAAAAUUGUGUGUU-AAAUU----AAAAAAAGGGAACGA----GAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGC
...((((..((((((((((...))))))...-.....----...............----....(((..((..(....)...))..)))..)))).)))) ( -16.70, z-score =  -2.17, R)
>droYak2.chr3L 13046303 90 - 24197627
AAAGCCAAACAUUACACGAAAAUUGUGUGUU-AAAUU-----AAAAAAGGGAACGA----GGGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGC
...((((..((((((((((...))))))...-.....-----..............----....(((..((..(....)...))..)))..)))).)))) ( -16.70, z-score =  -1.94, R)
>droEre2.scaffold_4784 12975245 90 - 25762168
AAAGCCAAACAUUACACGAAAAUUGUGUGUU-AAAUU-----AAAAAAGGGAACGA----GGGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGC
...((((..((((((((((...))))))...-.....-----..............----....(((..((..(....)...))..)))..)))).)))) ( -16.70, z-score =  -1.94, R)
>droAna3.scaffold_13337 6503340 88 + 23293914
AAAGCCAAACAUUACACGAAAAUUGUGUGUA-AAAUU----AAAAAAAGGAA---U----GGGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGC
...((((....(((((((.......))))))-)....----...........---.----....(((..((..(....)...))..))).......)))) ( -16.80, z-score =  -2.53, R)
>dp4.chrXR_group6 4339785 100 - 13314419
AAAGCCAAACAUUACACGAAAAUUUUGUGUUGAAAUUAAAAAAAGAAAAGAGGAGUGAGCGAGGACUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGC
...((((..((((((((((.....))))))......................((((........))))..((((.((......)).)))).)))).)))) ( -13.50, z-score =  -0.38, R)
>droPer1.super_9 2629056 100 - 3637205
AAAGCCAAACAUUACACGAAAAUUUUGUGUUGAAAUUAAAAAAAGAAAAGAGGAGUGAGCGAGGACUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGC
...((((..((((((((((.....))))))......................((((........))))..((((.((......)).)))).)))).)))) ( -13.50, z-score =  -0.38, R)
>consensus
AAAGCCAAACAUUACACGAAAAUUGUGUGUU_AAAUU____AAAAAAAGGAAACGA____GAGAGCUUGAUGUUGGAAAUAAAUUGAGCAAAAUGGUGGC
...((((..(((((((((.......)))))..................................(((..((..(....)...))..)))..)))).)))) (-13.77 = -14.02 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:22:24 2011