Locus 11037

Sequence ID dm3.chr3R
Location 18,201,571 – 18,201,677
Length 106
Max. P 0.924825
window15163 window15164

overview

Window 3

Location 18,201,571 – 18,201,671
Length 100
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 88.00
Shannon entropy 0.19537
G+C content 0.33513
Mean single sequence MFE -24.45
Consensus MFE -16.70
Energy contribution -17.70
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.74
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.31
SVM RNA-class probability 0.924825
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18201571 100 - 27905053
AAUUAGAAUUUCGCCAUUCCUCAUCAUGUGGUGAAAUCACUUGCAUACGAUUAAUAUCGAAUAUUUCAUUAUCUUCAUCAUGUGGUGAAAUCAAUUGUAG
.....((.(((((((((..........)))))))))))...((((..((((....))))...((((((((((.........))))))))))....)))). ( -20.40, z-score =  -1.47, R)
>droYak2.chr3R 19045879 97 - 28832112
---AACUAUUUCGCCAUUCCUCAUGUUGUGGUGAAAUCAGUUGCAGACGAUUAAUUUCAAAAAGUUGAUAUUCCUCAUCUUGUGGUGAAAUCAAUCGUAA
---((((((((((((((..(....)..)))))))))).))))....((((((.((((((..(((.(((......))).)))....)))))).)))))).. ( -29.80, z-score =  -4.90, R)
>droSec1.super_0 18557485 100 - 21120651
AAUUAGAAUUUCGCCAUUCCUCAUGUUGUGGUGAAAUCACUUGCAGACGAUUAAUAUCGAACAUUUCAUAUUCUUCAUCAAGUGGUGAAAUCAAUUGUAG
.....((.(((((((((..(....)..)))))))))))...(((((.((((....))))...(((((((...(((....)))..)))))))...))))). ( -23.30, z-score =  -2.04, R)
>droSim1.chr3R 18010570 100 - 27517382
AAUUAGAAUUUCGCCAUUCCUCAUGUUGUGGUGAAAUUACUUGCAGACGAUUAAUAUCGAACAUUUCAUAUUCUUCAUCAAGUGGUGAAAUCAAUUGUAG
......(((((((((((..(....)..)))))))))))...(((((.((((....))))...(((((((...(((....)))..)))))))...))))). ( -24.30, z-score =  -2.54, R)
>consensus
AAUUAGAAUUUCGCCAUUCCUCAUGUUGUGGUGAAAUCACUUGCAGACGAUUAAUAUCGAACAUUUCAUAUUCUUCAUCAAGUGGUGAAAUCAAUUGUAG
.......((((((((((..(....)..))))))))))....(((...((((....))))..............((((((....)))))).......))). (-16.70 = -17.70 +   1.00)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 18,201,581 – 18,201,677
Length 96
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 70.04
Shannon entropy 0.57815
G+C content 0.34908
Mean single sequence MFE -19.97
Consensus MFE -9.69
Energy contribution -10.22
Covariance contribution 0.53
Combinations/Pair 1.25
Mean z-score -0.99
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.563773
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18201581 96 - 27905053
UGGGAGAAU--UAGAAUUUCGCCAUUCCUCAUCAUGUGGUGAAAUCA-CUUGCAUACGAUUAAUAUCGAAUAUUUCAUUAUCUUCAUCAUGUGGUGAAA
(((((((..--.....)))).)))....(((((((((((((((....-........((((....)))).(((......))).))))))))))))))).. ( -23.00, z-score =  -1.35, R)
>droEre2.scaffold_4820 594319 72 + 10470090
UGAGAUAAU--U---AUUUCACCAUUCCUCAUCUUGUGGUGAAAUCA-AUUGUAGACGAUUAAUAUAGAAAAGUUGGU---------------------
....(((((--(---((((((((((..........)))))))))).)-)))))...(((((..........)))))..--------------------- ( -14.60, z-score =  -1.36, R)
>droYak2.chr3R 19045889 93 - 28832112
UGAGAGAAC--U---AUUUCGCCAUUCCUCAUGUUGUGGUGAAAUCA-GUUGCAGACGAUUAAUUUCAAAAAGUUGAUAUUCCUCAUCUUGUGGUGAAA
......(((--(---((((((((((..(....)..)))))))))).)-)))...((..((((((((....))))))))..)).(((((....))))).. ( -22.70, z-score =  -1.64, R)
>droSec1.super_0 18557495 96 - 21120651
UGGGAGAAU--UAGAAUUUCGCCAUUCCUCAUGUUGUGGUGAAAUCA-CUUGCAGACGAUUAAUAUCGAACAUUUCAUAUUCUUCAUCAAGUGGUGAAA
...((((..--..((.(((((((((..(....)..))))))))))).-........((((....))))....))))......((((((....)))))). ( -22.50, z-score =  -0.95, R)
>droSim1.chr3R 18010580 96 - 27517382
UGGGAGAAU--UAGAAUUUCGCCAUUCCUCAUGUUGUGGUGAAAUUA-CUUGCAGACGAUUAAUAUCGAACAUUUCAUAUUCUUCAUCAAGUGGUGAAA
...((((..--...(((((((((((..(....)..))))))))))).-........((((....))))....))))......((((((....)))))). ( -23.50, z-score =  -1.52, R)
>droMoj3.scaffold_6496 7775451 97 + 26866924
UGGGACACUGGUCGAAUUUCAAUAAUACUCAACUCAUGAUGAGAUAAGAAUGCAGCUGG-CGACAUCGUAUA-UUCACUUUAUAUAUUCAGGCUUAAAU
((((...((((((..............((((.(....).))))........((.....)-))))...(((((-(.......)))))).))).))))... ( -13.50, z-score =   0.90, R)
>consensus
UGGGAGAAU__UAGAAUUUCGCCAUUCCUCAUCUUGUGGUGAAAUCA_CUUGCAGACGAUUAAUAUCGAAAAUUUCAUAUUCUUCAUCAAGUGGUGAAA
...............((((((((((..........)))))))))).....................................((((((....)))))). ( -9.69 = -10.22 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:35:10 2011