Locus 9926

Sequence ID dm3.chr3R
Location 9,830,171 – 9,830,264
Length 93
Max. P 0.975388
window13638 window13639

overview

Window 8

Location 9,830,171 – 9,830,264
Length 93
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 86.10
Shannon entropy 0.20373
G+C content 0.35614
Mean single sequence MFE -20.29
Consensus MFE -15.15
Energy contribution -15.15
Covariance contribution 0.00
Combinations/Pair 1.07
Mean z-score -2.62
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956213
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9830171 93 + 27905053
-----UCAACUUUUUACACUACAUCACAAAGAGCUGCCAGUCAUUCGUG-CAUUUGAUUAUUAUUAUUAUUAUUAGUUGUUCAAAAAUAUUGGCAGCUA
-----..........................((((((((((.......(-((.(((((...((....))..))))).)))........)))))))))). ( -18.36, z-score =  -2.27, R)
>droSim1.chr3R 15918562 88 - 27517382
-----UCAACUUUUUACACUACAUCACAAAGAGCUGCCAGUCAUUCGUGGCAUUCGAUUAUUAUUAUUA------GUUGUUCAUAAAUAUUGGCAGCUA
-----..........................((((((((((.(((..(((....((((((.......))------)))).)))..))))))))))))). ( -22.20, z-score =  -4.01, R)
>droYak2.chr3R 12230861 88 - 28832112
GCCGAUCAACUUUU-GCACUACAUCACAAAGAGCUGCCAGUCAUUCGUG-CAUUCGAUUAUUAUUUGU---------UGUUCAUAAAUACGGGCAGCUA
((.((......)).-))..............(((((((.((.(((..((-....((((........))---------))..))..))))).))))))). ( -18.50, z-score =  -0.95, R)
>droEre2.scaffold_4770 9373714 83 + 17746568
-----UCAACUUUU-GCACUACAUCACAAAGAGCUGCCAGUCAUUCGUG-CAUUCGAUUAUUAUUUGU---------UGUUCAUAAAUACUGGCAGCUA
-----.........-................((((((((((.(((..((-....((((........))---------))..))..))))))))))))). ( -22.10, z-score =  -3.24, R)
>consensus
_____UCAACUUUU_ACACUACAUCACAAAGAGCUGCCAGUCAUUCGUG_CAUUCGAUUAUUAUUAGU_________UGUUCAUAAAUACUGGCAGCUA
...............................((((((((((.(((..((................................))..))))))))))))). (-15.15 = -15.15 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 9,830,171 – 9,830,264
Length 93
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 88.26
Shannon entropy 0.17433
G+C content 0.35093
Mean single sequence MFE -20.04
Consensus MFE -16.37
Energy contribution -16.18
Covariance contribution -0.19
Combinations/Pair 1.11
Mean z-score -2.65
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.93
SVM RNA-class probability 0.975388
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9830171 93 + 27905053
--UCAACUUUUUACACUACAUCACAAAGAGCUGCCAGUCAUUCGUG-CAUUUGAUUAUUAUUAUUAUUAUUAGUUGUUCAAAAAUAUUGGCAGCUA
--..........................((((((((((.......(-((.(((((...((....))..))))).)))........)))))))))). ( -18.36, z-score =  -2.27, R)
>droSim1.chr3R 15918562 88 - 27517382
--UCAACUUUUUACACUACAUCACAAAGAGCUGCCAGUCAUUCGUGGCAUUCGAUUAUUAUUAUUA------GUUGUUCAUAAAUAUUGGCAGCUA
--..........................((((((((((.(((..(((....((((((.......))------)))).)))..))))))))))))). ( -22.20, z-score =  -4.01, R)
>droYak2.chr3R 12230864 85 - 28832112
GAUCAACUUUU-GCACUACAUCACAAAGAGCUGCCAGUCAUUCGUG-CAUUCGAUUAUUAUUU---------GUUGUUCAUAAAUACGGGCAGCUA
...........-................(((((((.((.(((..((-....((((........---------))))..))..))))).))))))). ( -17.50, z-score =  -1.09, R)
>droEre2.scaffold_4770 9373714 83 + 17746568
--UCAACUUUU-GCACUACAUCACAAAGAGCUGCCAGUCAUUCGUG-CAUUCGAUUAUUAUUU---------GUUGUUCAUAAAUACUGGCAGCUA
--.........-................((((((((((.(((..((-....((((........---------))))..))..))))))))))))). ( -22.10, z-score =  -3.24, R)
>consensus
__UCAACUUUU_ACACUACAUCACAAAGAGCUGCCAGUCAUUCGUG_CAUUCGAUUAUUAUUA_________GUUGUUCAUAAAUACUGGCAGCUA
............................((((((((((.(((..((.....((((.................))))..))..))))))))))))). (-16.37 = -16.18 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:14:02 2011