Locus 6319

Sequence ID dm3.chr3L
Location 5,518,351 – 5,518,507
Length 156
Max. P 0.889364
window8689 window8690 window8691

overview

Window 9

Location 5,518,351 – 5,518,453
Length 102
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 71.42
Shannon entropy 0.49968
G+C content 0.42399
Mean single sequence MFE -24.40
Consensus MFE -10.48
Energy contribution -10.80
Covariance contribution 0.32
Combinations/Pair 1.29
Mean z-score -1.85
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.735651
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5518351 102 - 24543557
UCACUAAUCUGACGCAAGGGAAACCUAGUCAAUUGUUGAUGUCUUUAGCAACUGUCAUCAACGAAU----------AAAAAACACCCAUCUGGUCUAGACAGCUCUAGGCCC
.........((((...(((....))).)))).(((((((((.(..........).)))))))))..----------...............((((((((....)))))))). ( -30.90, z-score =  -3.99, R)
>droSim1.chr3L 5034012 102 - 22553184
UCACUAAUCUGACGCAAAGGAAACCUAGUCAAUUGUUGAUGUCUUUAGCAACUGUCAUCAACGAAU----------AAAAAACACCCAUCUGGUCUAGACAGUUCCAGGCCC
.........((((.....(....)...)))).(((((((((.(..........).)))))))))..----------...............(((((.((....)).))))). ( -21.10, z-score =  -1.23, R)
>droSec1.super_2 5454626 102 - 7591821
UCACUAAUCUGACGCAAAGGAAACCUGGUCAAUUGUUGAUGUCUUUAGCAACUGUCAUCAACGAAU----------AAAAAACACCCAUCUGGUCUAGACAGUUCCAGGCCC
.........((((.((..(....).)))))).(((((((((.(..........).)))))))))..----------...............(((((.((....)).))))). ( -21.80, z-score =  -0.86, R)
>droYak2.chr3L 6081474 94 - 24197627
------------------GCGAAACUACUAAUUUGUUGAUGUCUUUAGCAACUGUCAUCAACGACUUGAUGUGCUGAACAGACAUUGAUCAGAUCUAGACACUUUCAGGCUC
------------------..((((...(((((((((..((((((((((((.....((((((....))))))))))))..))))))..).))))).)))....))))...... ( -24.40, z-score =  -1.86, R)
>droEre2.scaffold_4784 8202723 102 - 25762168
GCACUUAAUUGUCCCGAAGGCAAAACUACUAGUUGUUGAUGUCUUCAACGACUUGAUUUGCUCAGU----------AAAAAACACCCAUCAGGUCUAGACAGAUCCAGGCUC
((......(((((..(((((((.(((........)))..)))))))...((((((((((((...))----------)).........))))))))..)))))......)).. ( -23.80, z-score =  -1.32, R)
>consensus
UCACUAAUCUGACGCAAAGGAAACCUAGUCAAUUGUUGAUGUCUUUAGCAACUGUCAUCAACGAAU__________AAAAAACACCCAUCUGGUCUAGACAGUUCCAGGCCC
................................(((((((((.(..........).)))))))))...........................(((((.((....)).))))). (-10.48 = -10.80 +   0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 5,518,388 – 5,518,486
Length 98
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 65.05
Shannon entropy 0.62210
G+C content 0.38446
Mean single sequence MFE -22.20
Consensus MFE -8.52
Energy contribution -8.76
Covariance contribution 0.24
Combinations/Pair 1.57
Mean z-score -1.82
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.889364
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5518388 98 - 24543557
UCACAAUUAAAUAUUUAUGGUGACCCACGUCAGUCACUAA--UCUGACGCAAGGGAAACCUAGUCAAUUGUUGAUGUCUUUAGCAACUGUCAUCAACGAA
.................(((((((........))))))).--..((((...(((....))).)))).(((((((((.(..........).))))))))). ( -28.30, z-score =  -3.55, R)
>droSim1.chr3L 5034049 98 - 22553184
UCACAAUUAAAUAUUUAUGGUGACCCACGUCAGUCACUAA--UCUGACGCAAAGGAAACCUAGUCAAUUGUUGAUGUCUUUAGCAACUGUCAUCAACGAA
..................(((..((..((((((.......--.))))))....))..))).......(((((((((.(..........).))))))))). ( -23.30, z-score =  -2.28, R)
>droSec1.super_2 5454663 98 - 7591821
UCACAAUUAAAUAUUUAUGGUGACCCACGUCAGUCACUAA--UCUGACGCAAAGGAAACCUGGUCAAUUGUUGAUGUCUUUAGCAACUGUCAUCAACGAA
....................(((((..((((((.......--.))))))....(....)..))))).(((((((((.(..........).))))))))). ( -25.80, z-score =  -2.64, R)
>droEre2.scaffold_4784 8202762 96 - 25762168
UCCUAAUUAAAUAUUUAUGGUGACCAACGUCAGGCACUUA--AUUGUCCCGAAGGCAAAACUACUAGUUGUUGAUGUCUUCAACGACU-UGAUUUGCUC-
.................(((((((....))))((((....--..)))))))..((((((.(....(((((((((.....)))))))))-.).)))))).- ( -21.70, z-score =  -1.81, R)
>droAna3.scaffold_13337 10257876 99 + 23293914
CCGUUAUAAAUAAUUCAUGCUGGUUUACAAGAGCCAAGGACUACCAUAUCAAUUACGACGUAUAUCUUCAACGACUUUCAUUAGGGACAUGACUUGCUG-
..(((((.........((((((((((....)))))).((....))..............)))).(((..((.(.....).))..))).)))))......- ( -11.90, z-score =   1.19, R)
>consensus
UCACAAUUAAAUAUUUAUGGUGACCCACGUCAGUCACUAA__UCUGACGCAAAGGAAACCUAGUCAAUUGUUGAUGUCUUUAGCAACUGUCAUCAACGAA
.................(((((((........)))))))............................(((((((.....))))))).............. ( -8.52 =  -8.76 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 5,518,415 – 5,518,507
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 65.17
Shannon entropy 0.63928
G+C content 0.34498
Mean single sequence MFE -18.56
Consensus MFE -7.54
Energy contribution -8.14
Covariance contribution 0.60
Combinations/Pair 1.54
Mean z-score -1.34
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.60
SVM RNA-class probability 0.758935
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 5518415 92 + 24543557
CAACAAUUGACUAGGUUUCCCUUGCGUCAGAUUAGUGACUGACGUGGGUCACCAUAAAUAUUUAAUUGUGAAAAGAUAAUUACUUAUUUGAA
.............(((..(((..(((((((........))))))))))..))).((((((..(((((((......)))))))..)))))).. ( -25.10, z-score =  -3.38, R)
>droSim1.chr3L 5034076 92 + 22553184
CAACAAUUGACUAGGUUUCCUUUGCGUCAGAUUAGUGACUGACGUGGGUCACCAUAAAUAUUUAAUUGUGAAAAGAUAAUUACUCAUUUGAA
...(((.(((...(((..(((..(((((((........))))))))))..))).........(((((((......))))))).))).))).. ( -22.60, z-score =  -2.30, R)
>droSec1.super_2 5454690 92 + 7591821
CAACAAUUGACCAGGUUUCCUUUGCGUCAGAUUAGUGACUGACGUGGGUCACCAUAAAUAUUUAAUUGUGAAAAGAUAAUUACUUAUUUGAA
.............(((..(((..(((((((........))))))))))..))).((((((..(((((((......)))))))..)))))).. ( -23.40, z-score =  -2.67, R)
>droEre2.scaffold_4784 8202787 85 + 25762168
CAACAACUAGUAGUUUUGCCUUCGGGACAAUUAAGUGCCUGACGUUGGUCACCAUAAAUAUUUAAUUAGGAAAAGAUAAUUACCA-------
((((..(..(((.(((((((....)).)))..)).)))..)..))))...............((((((........))))))...------- ( -12.90, z-score =   0.39, R)
>droAna3.scaffold_13337 10257916 72 - 23293914
-----------GUCGUAAUUGAUAUGGUAG-UCCUUGGCUCUUGUAAACCAGCAUGAAUUAUUUAUAACGGACAAAUGAUCACA--------
-----------(((((((((.((.((((((-(.....))).......))))..)).))))))........)))...........-------- (  -8.81, z-score =   1.27, R)
>consensus
CAACAAUUGACUAGGUUUCCUUUGCGUCAGAUUAGUGACUGACGUGGGUCACCAUAAAUAUUUAAUUGUGAAAAGAUAAUUACUUAUUUGAA
.............(((..(((..(((((((........))))))))))..)))....................................... ( -7.54 =  -8.14 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:05:24 2011