Locus 9560

Sequence ID dm3.chr3R
Location 7,365,237 – 7,365,345
Length 108
Max. P 0.679081
window13117 window13118

overview

Window 7

Location 7,365,237 – 7,365,345
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.80
Shannon entropy 0.29536
G+C content 0.34777
Mean single sequence MFE -28.26
Consensus MFE -14.99
Energy contribution -15.55
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.36
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.679081
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7365237 108 + 27905053
AAAUCAAGCCUAUCAUAUCGGUUCUUGUCAUCAGUGUCAAUGGGCUUAAUUAAAAUAGAUGUGCAAUCGACCAUUGACACAUUGACAAAUUCGAAUGAUCUUGAAUGC------------
...(((((...(((((.((((...((((((...((((((((((..............(((.....)))..))))))))))..))))))..))))))))))))))....------------ ( -32.79, z-score =  -3.91, R)
>droEre2.scaffold_4770 3491090 118 - 17746568
UAGUUAAGCUUAUCGUAUCUGUUCUCGUCAUCAGUGUCAAUGGGUUUAAUUAAAA-AGCCGUGCGAUUGUC-AAUGACACAUUGACAAAUUUGAAUGCUCUUUAAUGCAGUCUCUGCACA
(((((((((((((.(...(((..........)))...).)))))))))))))...-....(((((.(((((-((((...)))))))))....((.(((........))).))..))))). ( -31.40, z-score =  -2.74, R)
>droYak2.chr3R 11400968 118 + 28832112
AAAUCAAGCUUAUCGUAUCUGUUCUUGUCAUCAGUGUCAAUGGGUUUAAUUAAAAUAC-CGUGCAAUUGGC-ACUGACACUUUGACAAAUUUGAAUGAUCUUUAAUGCAGUCUGUGCAUU
...........(((((.((.....((((((..(((((((...(((...........))-)((((.....))-))))))))).))))))....)))))))....((((((.....)))))) ( -28.40, z-score =  -1.84, R)
>droSec1.super_0 6521164 108 - 21120651
AAAUCAAGACUAUCAUAUCUGUUCUUGUCAUCAGUGUCAAUGGGUUUAAUUAAAAUAGACAUGCAAUCGACCAGUGACACAUUGACAAAUUCGAAUGAUCUUUAAUGC------------
.....((((...((((.((.(...((((((...((((((.((((((((.......)))))...(....).))).))))))..))))))...)))))))))))......------------ ( -20.80, z-score =  -0.43, R)
>droSim1.chr3R 13488862 108 - 27517382
AAAUCAAGCAUAUCAUAUCUGGUAUUGUCAUCAGUGUCAAUGGGUUUAAUUAAAAUAGACAUGCAAUCGACCAUUGACACAUUGACAAAUUCGAAUGAUCUUUAAUGC------------
.......(((((((((.((..((.((((((...(((((((((((((((.......)))))...(....).))))))))))..))))))))..))))))).....))))------------ ( -27.90, z-score =  -2.89, R)
>consensus
AAAUCAAGCCUAUCAUAUCUGUUCUUGUCAUCAGUGUCAAUGGGUUUAAUUAAAAUAGACGUGCAAUCGACCAUUGACACAUUGACAAAUUCGAAUGAUCUUUAAUGC____________
...........(((((.((.....((((((...((((((.(((...........................))).))))))..))))))....)))))))..................... (-14.99 = -15.55 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 7,365,237 – 7,365,345
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.80
Shannon entropy 0.29536
G+C content 0.34777
Mean single sequence MFE -26.23
Consensus MFE -17.28
Energy contribution -18.60
Covariance contribution 1.32
Combinations/Pair 1.10
Mean z-score -1.81
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.630315
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7365237 108 - 27905053
------------GCAUUCAAGAUCAUUCGAAUUUGUCAAUGUGUCAAUGGUCGAUUGCACAUCUAUUUUAAUUAAGCCCAUUGACACUGAUGACAAGAACCGAUAUGAUAGGCUUGAUUU
------------....(((((((((((((..(((((((..((((((((((.(.......................).))))))))))...)))))))...))).)))))...)))))... ( -30.50, z-score =  -3.01, R)
>droEre2.scaffold_4770 3491090 118 + 17746568
UGUGCAGAGACUGCAUUAAAGAGCAUUCAAAUUUGUCAAUGUGUCAUU-GACAAUCGCACGGCU-UUUUAAUUAAACCCAUUGACACUGAUGACGAGAACAGAUACGAUAAGCUUAACUA
.((((((...))))))((((((((........(((((((((...))))-))))).......)))-)))))........((((......))))............................ ( -23.16, z-score =  -0.61, R)
>droYak2.chr3R 11400968 118 - 28832112
AAUGCACAGACUGCAUUAAAGAUCAUUCAAAUUUGUCAAAGUGUCAGU-GCCAAUUGCACG-GUAUUUUAAUUAAACCCAUUGACACUGAUGACAAGAACAGAUACGAUAAGCUUGAUUU
((((((.....))))))..((((((..(...(((((((.(((((((((-((.....))))(-((...........)))...)))))))..)))))))..(......)....)..)))))) ( -28.60, z-score =  -2.63, R)
>droSec1.super_0 6521164 108 + 21120651
------------GCAUUAAAGAUCAUUCGAAUUUGUCAAUGUGUCACUGGUCGAUUGCAUGUCUAUUUUAAUUAAACCCAUUGACACUGAUGACAAGAACAGAUAUGAUAGUCUUGAUUU
------------..(((((..(((((((...(((((((..((((((.(((..(((((...........)))))....))).))))))...)))))))....)).)))))....))))).. ( -21.70, z-score =  -0.34, R)
>droSim1.chr3R 13488862 108 + 27517382
------------GCAUUAAAGAUCAUUCGAAUUUGUCAAUGUGUCAAUGGUCGAUUGCAUGUCUAUUUUAAUUAAACCCAUUGACACUGAUGACAAUACCAGAUAUGAUAUGCUUGAUUU
------------((((.....(((((((....((((((..((((((((((..(((((...........)))))....))))))))))...)))))).....)).)))))))))....... ( -27.20, z-score =  -2.44, R)
>consensus
____________GCAUUAAAGAUCAUUCGAAUUUGUCAAUGUGUCAAUGGUCGAUUGCACGUCUAUUUUAAUUAAACCCAUUGACACUGAUGACAAGAACAGAUAUGAUAAGCUUGAUUU
.....................(((((((...(((((((..((((((((((..(((((...........)))))....))))))))))...)))))))....)).)))))........... (-17.28 = -18.60 +   1.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:06:47 2011