Locus 8060

Sequence ID dm3.chr3L
Location 19,883,225 – 19,883,339
Length 114
Max. P 0.865123
window11092 window11093

overview

Window 2

Location 19,883,225 – 19,883,339
Length 114
Sequences 5
Columns 143
Reading direction forward
Mean pairwise identity 63.12
Shannon entropy 0.52962
G+C content 0.39717
Mean single sequence MFE -28.08
Consensus MFE -9.74
Energy contribution -11.02
Covariance contribution 1.28
Combinations/Pair 1.15
Mean z-score -2.35
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.97
SVM RNA-class probability 0.865123
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19883225 114 + 24543557
UGUAAACGAUGCAACGGCAACUAUAC-CGAAGUACAAGCAUAGAAAAUCGUUUA----------------------AGGAUCA------GCUCCAUCGUUUACAAACCACUUGAAUUAAGUUUUGCUUGUUGUUACAUUGUUU
...((((((((.((((....).....-......(((((((.(((.....(((((----------------------(((((..------.....)))(((....)))..)))))))....)))))))))).))).)))))))) ( -21.00, z-score =  -0.14, R)
>droSim1.chr3L 19177832 94 + 22553184
---------------------UGUAAACGAAGUACAAUCCUAGCAAAUCGCCCA----------------------AGGAGCA------GCUGCAUCGUUUACAAACAACUUGAAUUAAGUUUUGCCUGUUGUUACAUUGUUG
---------------------(((((((((.((((..((((.((.....))...----------------------))))...------).))).)))))))))((((((.((((......))))...))))))......... ( -21.00, z-score =  -1.24, R)
>droSec1.super_29 528540 94 + 700605
---------------------UGUAAACGAAGUACAAUCCUAGCAAAUCGGCCA----------------------AGGAGCA------GCUGCAUCGUUUACAAACAACUUGAAUUAAGUUUUGCCUGUUGUUACAUUGUUU
---------------------(((((((((.((((..((((.((......))..----------------------))))...------).))).)))))))))((((((.((((......))))...))))))......... ( -21.60, z-score =  -1.12, R)
>droYak2.chr3L 3503550 117 - 24197627
---------------------UGUGAACGA--UGAAGCGGCAACAAGUCCGAAAUUGAAGCCUAAGAAAUCGGCUCAGGAGCUUAUAUCGCUUCAUCGUUUACAAACAACUUGAAUUAGGUUUUGCCUGUU---AUAUUGUUC
---------------------(((((((((--(((((((((..(((........)))..)))...((.((.((((....)))).)).)))))))))))))))))(((((..(((..((((.....))))))---)..))))). ( -41.70, z-score =  -5.24, R)
>droEre2.scaffold_4784 19621389 96 + 25762168
---------------------UGUAAACGA--UGCAGCGGCAGCGAGUCCAAAGU--------------------CAGGAGCUUACAUCGCU-CAUCGUUUACAAACGAUGUGAAUUAGGUUUGACCUGUU---AUGUUGUUC
---------------------(((((((((--((.(((((..(..(((((.....--------------------..))).))..).)))))-)))))))))))((((((((((..((((.....))))))---)))))))). ( -35.10, z-score =  -4.00, R)
>consensus
_____________________UGUAAACGAAGUACAACCCUAGCAAAUCGGAAA______________________AGGAGCA______GCUGCAUCGUUUACAAACAACUUGAAUUAAGUUUUGCCUGUUGUUACAUUGUUC
.....................(((((((((..((......))...................................(.(((.......))).).)))))))))(((((..(((..((((.....))))...)))..))))). ( -9.74 = -11.02 +   1.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 19,883,225 – 19,883,339
Length 114
Sequences 5
Columns 143
Reading direction reverse
Mean pairwise identity 63.12
Shannon entropy 0.52962
G+C content 0.39717
Mean single sequence MFE -27.16
Consensus MFE -8.38
Energy contribution -8.34
Covariance contribution -0.04
Combinations/Pair 1.36
Mean z-score -2.20
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.594641
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19883225 114 - 24543557
AAACAAUGUAACAACAAGCAAAACUUAAUUCAAGUGGUUUGUAAACGAUGGAGC------UGAUCCU----------------------UAAACGAUUUUCUAUGCUUGUACUUCG-GUAUAGUUGCCGUUGCAUCGUUUACA
((((.(((((((.((((((...((((.....)))).)))))).(((.((((((.------.((((..----------------------.....))))))))))...(((((....-))))))))...))))))).))))... ( -28.10, z-score =  -2.01, R)
>droSim1.chr3L 19177832 94 - 22553184
CAACAAUGUAACAACAGGCAAAACUUAAUUCAAGUUGUUUGUAAACGAUGCAGC------UGCUCCU----------------------UGGGCGAUUUGCUAGGAUUGUACUUCGUUUACA---------------------
.((((((........((......))........))))))((((((((((((((.------...((((----------------------..(((.....))))))))))))..)))))))))--------------------- ( -20.09, z-score =  -0.17, R)
>droSec1.super_29 528540 94 - 700605
AAACAAUGUAACAACAGGCAAAACUUAAUUCAAGUUGUUUGUAAACGAUGCAGC------UGCUCCU----------------------UGGCCGAUUUGCUAGGAUUGUACUUCGUUUACA---------------------
(((((((........((......))........)))))))(((((((((((((.------...((((----------------------.(((......))))))))))))..)))))))).--------------------- ( -22.09, z-score =  -1.09, R)
>droYak2.chr3L 3503550 117 + 24197627
GAACAAUAU---AACAGGCAAAACCUAAUUCAAGUUGUUUGUAAACGAUGAAGCGAUAUAAGCUCCUGAGCCGAUUUCUUAGGCUUCAAUUUCGGACUUGUUGCCGCUUCA--UCGUUCACA---------------------
(((((((..---...(((.....))).......)))))))((.((((((((((((..(((((.(((((((((.........))).))).....))))))))...)))))))--))))).)).--------------------- ( -37.30, z-score =  -4.62, R)
>droEre2.scaffold_4784 19621389 96 - 25762168
GAACAACAU---AACAGGUCAAACCUAAUUCACAUCGUUUGUAAACGAUG-AGCGAUGUAAGCUCCUG--------------------ACUUUGGACUCGCUGCCGCUGCA--UCGUUUACA---------------------
.........---...(((.....))).............(((((((((((-((((..(..((.(((..--------------------.....)))))..)...)))).))--)))))))))--------------------- ( -28.20, z-score =  -3.13, R)
>consensus
AAACAAUGUAACAACAGGCAAAACUUAAUUCAAGUUGUUUGUAAACGAUGCAGC______UGCUCCU______________________UGGCCGAUUUGCUACGAUUGUACUUCGUUUACA_____________________
(((((((........(((.....))).......)))))))(((((((((((((........((....................................)).....)))))..))))))))...................... ( -8.38 =  -8.34 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:38:40 2011