Locus 1126

Sequence ID dm3.chr2L
Location 8,470,383 – 8,470,502
Length 119
Max. P 0.987682
window1543 window1544

overview

Window 3

Location 8,470,383 – 8,470,502
Length 119
Sequences 5
Columns 143
Reading direction forward
Mean pairwise identity 70.43
Shannon entropy 0.46490
G+C content 0.50200
Mean single sequence MFE -42.67
Consensus MFE -22.55
Energy contribution -25.55
Covariance contribution 3.00
Combinations/Pair 1.13
Mean z-score -2.51
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.29
SVM RNA-class probability 0.987682
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8470383 119 + 23011544
UGGCCAAGGGUGUGCAAUUGCAUUGGCCAUAUCCACAUUCACAUCCACAUCCAUGGACA------------UAGCCAUGGCCAUAGCC------------GUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUC
.....(((((.(((((((((((.(((......)))........((((......))))..------------..((((((((((.(((.------------...)))...))))))))))...))))))))))).))))).... ( -44.70, z-score =  -3.13, R)
>droSim1.chr2L 8247872 107 + 22036055
UGGCCAAGGGUGUGCAAUUGCAUUGGCCAUAUCCACAUCCACAUCCAU------------------------GGACAUGGCCAUAGCC------------GUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUC
.....(((((.(((((((((((.(((((((.((((............)------------------------))).)))))))..(((------------((.(((....))).)))))...))))))))))).))))).... ( -43.40, z-score =  -3.44, R)
>droSec1.super_3 3957641 107 + 7220098
UGGCCAAGGGUGUGCAAUUGCAUUGGCCAUAUCCACAUCCACAUCCAU------------------------GGACAUGGCCAUAGCC------------GUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUC
.....(((((.(((((((((((.(((((((.((((............)------------------------))).)))))))..(((------------((.(((....))).)))))...))))))))))).))))).... ( -43.40, z-score =  -3.44, R)
>droEre2.scaffold_4929 9056873 143 + 26641161
UGACCAAGGGUGUGCAGUUGCUUUGGCCACAUCCACAUCCACAUCCAUAUCCAUGGCCAAAGCCACAUCCAUGGCCAUAGCCAUAGCCAUUGCCAUUGCCGUAGCUCUUGGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUC
.......(((((((.....((((((((((........................)))))))))))))))))(((((....))))).((.(((((.((((((((.(((....))).)))))))).))))).))............ ( -54.86, z-score =  -3.70, R)
>droVir3.scaffold_13049 16074427 108 - 25233164
CAGUCAGGGACAACAAGUUG----GGCCACGUCCACAUUCACGUCCAAGUCCA------------------CGUCCAUGUCCAUGUCCA----------CGUUGCACGCUGGUCAAAGCGAAGGC---UGCGUUUUGUUUGCC
(((.((((((((.......(----(((...))))((((..((((........)------------------)))..))))...)))))(----------(((.((.((((......))))...))---.)))).))).))).. ( -27.00, z-score =   1.14, R)
>consensus
UGGCCAAGGGUGUGCAAUUGCAUUGGCCAUAUCCACAUCCACAUCCAU_UCCA___________________GGCCAUGGCCAUAGCC____________GUAGCUCUUUGGCCAUGGCAAUUGCGAUUGCAUUUUCUUUAUC
.....(((((.((((((((((...((......)).......................................((((((((((.(((................)))...))))))))))....)))))))))).))))).... (-22.55 = -25.55 +   3.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 8,470,383 – 8,470,502
Length 119
Sequences 5
Columns 143
Reading direction reverse
Mean pairwise identity 70.43
Shannon entropy 0.46490
G+C content 0.50200
Mean single sequence MFE -44.14
Consensus MFE -20.78
Energy contribution -23.34
Covariance contribution 2.56
Combinations/Pair 1.23
Mean z-score -2.06
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.99
SVM RNA-class probability 0.869453
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8470383 119 - 23011544
GAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUAC------------GGCUAUGGCCAUGGCUA------------UGUCCAUGGAUGUGGAUGUGAAUGUGGAUAUGGCCAAUGCAAUUGCACACCCUUGGCCA
............(((.((((....((((((((((...(((...------------.))).))))))))))..------------.((((((....)))))))))).))).....((((((((((....))).....))))))) ( -50.90, z-score =  -4.01, R)
>droSim1.chr2L 8247872 107 - 22036055
GAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUAC------------GGCUAUGGCCAUGUCC------------------------AUGGAUGUGGAUGUGGAUAUGGCCAAUGCAAUUGCACACCCUUGGCCA
............(((((....)))))..(((((((..(((...------------.))).(((((((((((------------------------(((........)))))))))))))).(((....))).....))))))) ( -42.50, z-score =  -2.85, R)
>droSec1.super_3 3957641 107 - 7220098
GAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUAC------------GGCUAUGGCCAUGUCC------------------------AUGGAUGUGGAUGUGGAUAUGGCCAAUGCAAUUGCACACCCUUGGCCA
............(((((....)))))..(((((((..(((...------------.))).(((((((((((------------------------(((........)))))))))))))).(((....))).....))))))) ( -42.50, z-score =  -2.85, R)
>droEre2.scaffold_4929 9056873 143 - 26641161
GAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCCAAGAGCUACGGCAAUGGCAAUGGCUAUGGCUAUGGCCAUGGAUGUGGCUUUGGCCAUGGAUAUGGAUGUGGAUGUGGAUGUGGCCAAAGCAACUGCACACCCUUGGUCA
(((.(((....((((..((((....((((((((....(((((..((.((....)).))..)))))..)))))))).))))((((((((((((..((((........))))..))))))))))))...))))....))).))). ( -57.80, z-score =  -2.42, R)
>droVir3.scaffold_13049 16074427 108 + 25233164
GGCAAACAAAACGCA---GCCUUCGCUUUGACCAGCGUGCAACG----------UGGACAUGGACAUGGACG------------------UGGACUUGGACGUGAAUGUGGACGUGGCC----CAACUUGUUGUCCCUGACUG
(((((.(((.(((..---((...((((......)))).))..))----------)((.((((..((((.(((------------------(........))))...))))..))))..)----)...))))))))........ ( -27.00, z-score =   1.82, R)
>consensus
GAUAAAGAAAAUGCAAUCGCAAUUGCCAUGGCCAAAGAGCUAC____________GGCUAUGGCCAUGGCC___________________UGGA_AUGGAUGUGGAUGUGGAUAUGGCCAAUGCAAUUGCACACCCUUGGCCA
...........((((.(((((.((((((((((((...((((..............)))).))))))))))...........................)).))))).))))....((((((((((....))).....))))))) (-20.78 = -23.34 +   2.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:26:09 2011