Locus 13889

Sequence ID dm3.chrX
Location 9,786,286 – 9,786,404
Length 118
Max. P 0.951678
window19109 window19110

overview

Window 9

Location 9,786,286 – 9,786,404
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.42
Shannon entropy 0.48144
G+C content 0.38156
Mean single sequence MFE -27.29
Consensus MFE -12.96
Energy contribution -13.04
Covariance contribution 0.08
Combinations/Pair 1.26
Mean z-score -2.28
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.57
SVM RNA-class probability 0.951678
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9786286 118 + 22422827
UAGUUCCCAAGAGCAGAAUUCCUAAAACACUUGAAAUUCAUUUAGCUUUUUGCCUGCA-GAUAUGCUGUAGCAUACUCACAGGCACUUCAAA-AAAGUUUUCUAAUCCUUGAGGAUUUUU
....(((((((....(((((.(..........).)))))....(((((((((((((..-(((((((....))))).)).))))))......)-))))))........)))).)))..... ( -25.90, z-score =  -1.48, R)
>droEre2.scaffold_4690 13417469 113 - 18748788
------UGCCAAGCUGAGUUUUUAGAGCACUUGAAAUUCAUUUAGCUUUCUGCCUGCGCAAUAUUCUGUUGCAUACUCUCAGGCAGUUCGAA-AAAGUUUUCUAAUCCUCAGACAUUUCC
------......((((((...((((((.(((((.....)..........(((((((.(((((.....))))).......)))))))......-.)))).))))))..))))).)...... ( -26.00, z-score =  -1.20, R)
>droYak2.chrX 18378386 99 + 21770863
-------------------UUCCAAAUCACUUGAAAUUCAUAUAGCUUUCUGCCUGCG-GAUAAGCUGUAGCAAACUUUCAGUUACUUCAAA-CUGGUUUUCCAAUCCUCGAGGAUCAUU
-------------------......(((.(((((......((((((((((((....))-)).))))))))........((((((......))-))))...........)))))))).... ( -22.70, z-score =  -2.42, R)
>droSec1.super_15 546786 116 + 1954846
---UAGUUCCAUGCAGAGUUCGUAAAACGCUUGAAAUUCAUUUAGCUUUUUGCCUGCG-GAUAUGCUGUAGCAUACUCUCAGGCACUUCAAAACAAGUUUUCUAAUUCUCGAGGAUUUUU
---....(((.((.((((((.(.((((((((.((......)).)))....((((((.(-..(((((....)))))..).))))))...........)))))).)))))))).)))..... ( -31.60, z-score =  -2.80, R)
>droSim1.chrX 7789053 105 + 17042790
---UAGUUCCACGCAGAGUUC-----------GAAAUUCAUUUAGCUUUUUGCCUGCG-GAUAUGCUGUAGCAUACUCUCAGGCACUUCAAAACAAGUUUUCUAAUUCUCGAGGAUUUUU
---....(((.((.((((((.-----------((((..............((((((.(-..(((((....)))))..).)))))).............)))).)))))))).)))..... ( -30.23, z-score =  -3.52, R)
>consensus
___U__UUCCAAGCAGAGUUCCUAAAACACUUGAAAUUCAUUUAGCUUUUUGCCUGCG_GAUAUGCUGUAGCAUACUCUCAGGCACUUCAAA_CAAGUUUUCUAAUCCUCGAGGAUUUUU
..................................................((((((.....(((((....)))))....)))))).........((((((((........)))))))).. (-12.96 = -13.04 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 9,786,286 – 9,786,404
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.42
Shannon entropy 0.48144
G+C content 0.38156
Mean single sequence MFE -27.88
Consensus MFE -12.74
Energy contribution -13.14
Covariance contribution 0.40
Combinations/Pair 1.21
Mean z-score -1.63
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.20
SVM RNA-class probability 0.589390
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9786286 118 - 22422827
AAAAAUCCUCAAGGAUUAGAAAACUUU-UUUGAAGUGCCUGUGAGUAUGCUACAGCAUAUC-UGCAGGCAAAAAGCUAAAUGAAUUUCAAGUGUUUUAGGAAUUCUGCUCUUGGGAACUA
.....(((.(((((.((((...(((((-...)))))((((((..((((((....)))))).-.))))))......))))..(((((((..........)))))))...)))))))).... ( -34.60, z-score =  -2.81, R)
>droEre2.scaffold_4690 13417469 113 + 18748788
GGAAAUGUCUGAGGAUUAGAAAACUUU-UUCGAACUGCCUGAGAGUAUGCAACAGAAUAUUGCGCAGGCAGAAAGCUAAAUGAAUUUCAAGUGCUCUAAAAACUCAGCUUGGCA------
......(.(((((..(((((..(((..-......(((((((.((((((........))))).).))))))).........((.....)))))..)))))...))))))......------ ( -27.10, z-score =  -0.46, R)
>droYak2.chrX 18378386 99 - 21770863
AAUGAUCCUCGAGGAUUGGAAAACCAG-UUUGAAGUAACUGAAAGUUUGCUACAGCUUAUC-CGCAGGCAGAAAGCUAUAUGAAUUUCAAGUGAUUUGGAA-------------------
.....(((....(((((((....))))-))).((((.(((..(((((((.((.(((((.((-.(....).))))))).)))))))))..))).))))))).------------------- ( -19.30, z-score =   0.22, R)
>droSec1.super_15 546786 116 - 1954846
AAAAAUCCUCGAGAAUUAGAAAACUUGUUUUGAAGUGCCUGAGAGUAUGCUACAGCAUAUC-CGCAGGCAAAAAGCUAAAUGAAUUUCAAGCGUUUUACGAACUCUGCAUGGAACUA---
.....(((..((((.((..(((((..(((((....((((((.(..(((((....)))))..-).)))))).)))))....((.....))...)))))...)).))).)..)))....--- ( -28.60, z-score =  -1.85, R)
>droSim1.chrX 7789053 105 - 17042790
AAAAAUCCUCGAGAAUUAGAAAACUUGUUUUGAAGUGCCUGAGAGUAUGCUACAGCAUAUC-CGCAGGCAAAAAGCUAAAUGAAUUUC-----------GAACUCUGCGUGGAACUA---
.....(((.(((((.((.((((..(..(((.(...((((((.(..(((((....)))))..-).)))))).....).)))..).))))-----------.)).))).)).)))....--- ( -29.80, z-score =  -3.26, R)
>consensus
AAAAAUCCUCGAGGAUUAGAAAACUUG_UUUGAAGUGCCUGAGAGUAUGCUACAGCAUAUC_CGCAGGCAAAAAGCUAAAUGAAUUUCAAGUGUUUUAGGAACUCUGCUUGGAA__A___
........(((((....((....))...)))))..((((((...((((((....))))))....)))))).................................................. (-12.74 = -13.14 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:29:43 2011