Locus 14589

Sequence ID dm3.chrX
Location 14,254,136 – 14,254,330
Length 194
Max. P 0.953791
window20085 window20086 window20087

overview

Window 5

Location 14,254,136 – 14,254,254
Length 118
Sequences 5
Columns 121
Reading direction reverse
Mean pairwise identity 81.42
Shannon entropy 0.32645
G+C content 0.41954
Mean single sequence MFE -30.22
Consensus MFE -20.52
Energy contribution -19.68
Covariance contribution -0.84
Combinations/Pair 1.32
Mean z-score -2.14
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.33
SVM RNA-class probability 0.927012
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 14254136 118 - 22422827
GAGAGUCCAGACUCAUCUG-GGCUUUCACAAUAGAUGCAAUCCACAUGAUCGCUGCUUACAUUUUGAGCAGCAAAAUCAUGACUUAAUAAUGCCAUUUUCU-CCAUGUACUCGUGGAUCC-
(((((((((((....))))-))))))).................((((((.((((((((.....))))))))...))))))...................(-(((((....))))))...- ( -40.20, z-score =  -4.88, R)
>droSim1.chrX 10948039 118 - 17042790
--GAGUACAGACUCAUCUG-GGCUUUCAGUAGAGAUGCAAUCCACAUGAUCGCUGCUUACAUCUUGAGCAGCAAAAUCAUGACUUAAUAAUGCCAUUUUCUUCCAUGUACUGGUGGACUCC
--((((.((((....))))-(((.....(((....)))......((((((.((((((((.....))))))))...))))))..........)))........((((......)))))))). ( -31.80, z-score =  -1.51, R)
>droSec1.super_20 856680 118 - 1148123
--GAGUACAGACUCAUCUG-GGCUUUCAGAAGAGAUGCAAUCCAUAUGAUCGCUGCUUACAUCUUGAGCAGCAAAAUCAUGACGUAAUAAUGCCAUUUUCUCCCAUGUACUCGUGGACUCC
--(((((((..(((.((((-(....))))).)))..........((((((.((((((((.....))))))))...))))))........................)))))))......... ( -32.40, z-score =  -1.88, R)
>droYak2.chrX 8497513 114 - 21770863
----AUACAGAUUCAUCUG-GCUUUUUAAAAUAGAUGCAAUUCACAUGAUCGCUGCUUACAUCUUGAGUAGCAAAAUCAUGACUUAAUAAUGCCUUUUUCG-CCAUGUACUUGUGGACCC-
----.(((((...((..((-((...........((......)).((((((.((((((((.....))))))))...))))))...................)-)))))...))))).....- ( -23.50, z-score =  -1.26, R)
>droEre2.scaffold_4690 6060012 104 + 18748788
--------------AUACGCUAUCUUUGAAGUAGAUGCCAUCCACAUGAUCGCUGCUCGCAUCUUGAGUGGCAAAAUCAUGACCUAAUAAUGCCUUUUUCU-CCAUGUACUUGUGGACC--
--------------....((.((((.......))))))......((((((.((..((((.....))))..))...))))))...................(-((((......)))))..-- ( -23.20, z-score =  -1.19, R)
>consensus
__GAGUACAGACUCAUCUG_GGCUUUCAAAAUAGAUGCAAUCCACAUGAUCGCUGCUUACAUCUUGAGCAGCAAAAUCAUGACUUAAUAAUGCCAUUUUCU_CCAUGUACUCGUGGACCC_
............................................((((((.((((((((.....))))))))...)))))).....................(((((....)))))..... (-20.52 = -19.68 +  -0.84)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,254,174 – 14,254,290
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.77
Shannon entropy 0.38579
G+C content 0.39021
Mean single sequence MFE -30.74
Consensus MFE -18.98
Energy contribution -17.50
Covariance contribution -1.48
Combinations/Pair 1.44
Mean z-score -2.20
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.60
SVM RNA-class probability 0.953791
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 14254174 116 - 22422827
AAGAUCUUUUAUUAUC----AUAAGUAGCUCAGAGAGAUAGAGAGUCCAGACUCAUCUGGGCUUUCACAAUAGAUGCAAUCCACAUGAUCGCUGCUUACAUUUUGAGCAGCAAAAUCAUG
...(((((((......----............))))))).(((((((((((....))))))))))).................((((((.((((((((.....))))))))...)))))) ( -35.37, z-score =  -3.47, R)
>droSim1.chrX 10948079 112 - 17042790
UAGAUCUUUUAUUAUC----AUAAGUAACUCAGUGAG----AGAGUACAGACUCAUCUGGGCUUUCAGUAGAGAUGCAAUCCACAUGAUCGCUGCUUACAUCUUGAGCAGCAAAAUCAUG
................----....(((.((((.((((----((....((((....))))..)))))).).))).)))......((((((.((((((((.....))))))))...)))))) ( -32.20, z-score =  -2.35, R)
>droSec1.super_20 856720 112 - 1148123
UAGACCUUUUAUUAUC----AUAAGCAGCUCAGUGAG----AGAGUACAGACUCAUCUGGGCUUUCAGAAGAGAUGCAAUCCAUAUGAUCGCUGCUUACAUCUUGAGCAGCAAAAUCAUG
................----....(((.(((..(..(----((((..((((....))))..))))).)..))).)))......((((((.((((((((.....))))))))...)))))) ( -31.70, z-score =  -1.80, R)
>droYak2.chrX 8497551 112 - 21770863
AAGAUCUUUUAUUAUU--UAAUAAGUAGCUCAGCG------AGAAUACAGAUUCAUCUGGCUUUUUAAAAUAGAUGCAAUUCACAUGAUCGCUGCUUACAUCUUGAGUAGCAAAAUCAUG
..((.......(((((--(..((((.(((.(((..------.((((....))))..)))))).)))))))))).......)).((((((.((((((((.....))))))))...)))))) ( -23.04, z-score =  -0.94, R)
>droEre2.scaffold_4690 6060049 105 + 18748788
AAGAUCUCUUACUUUUAAGUACGAGUAUCUCAG--------CGGGCAUACGCU-------AUCUUUGAAGUAGAUGCCAUCCACAUGAUCGCUGCUCGCAUCUUGAGUGGCAAAAUCAUG
.(((((((.((((....)))).))).))))...--------..(((((..(((-------........)))..))))).....((((((.((..((((.....))))..))...)))))) ( -31.40, z-score =  -2.44, R)
>consensus
AAGAUCUUUUAUUAUC____AUAAGUAGCUCAGUGAG____AGAGUACAGACUCAUCUGGGCUUUCAAAAUAGAUGCAAUCCACAUGAUCGCUGCUUACAUCUUGAGCAGCAAAAUCAUG
..........................................((((....)))).............................((((((.((((((((.....))))))))...)))))) (-18.98 = -17.50 +  -1.48)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,254,214 – 14,254,330
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.69
Shannon entropy 0.42253
G+C content 0.32879
Mean single sequence MFE -24.79
Consensus MFE -14.84
Energy contribution -15.48
Covariance contribution 0.64
Combinations/Pair 1.26
Mean z-score -1.54
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.747406
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 14254214 116 - 22422827
UUUAUUAAAUUGUGUGAAAACCAUUUACUUUGCAUUUCCCAAGAUCUUUUAUUAUC----AUAAGUAGCUCAGAGAGAUAGAGAGUCCAGACUCAUCUGGGCUUUCACAAUAGAUGCAAU
.....(((((.(.((....))))))))..((((((((......(((((((......----............))))))).(((((((((((....))))))))))).....)))))))). ( -28.17, z-score =  -2.46, R)
>droSim1.chrX 10948119 112 - 17042790
UUUAUUAAAUUGUGUGUAAACCAUUUACUUUGCAUUUCCCUAGAUCUUUUAUUAUC----AUAAGUAACUCAGUG----AGAGAGUACAGACUCAUCUGGGCUUUCAGUAGAGAUGCAAU
.....(((((.((......)).)))))..(((((((((................((----((..........)))----)(((((..((((....))))..)))))....))))))))). ( -23.90, z-score =  -1.07, R)
>droSec1.super_20 856760 112 - 1148123
AUUAUUAAAUUGUGUGUAAACCAUUUACUUUGCAUUUCCCUAGACCUUUUAUUAUC----AUAAGCAGCUCAGUG----AGAGAGUACAGACUCAUCUGGGCUUUCAGAAGAGAUGCAAU
.....(((((.((......)).)))))..(((((((((....((.(((((((....----))))).)).))....----.(((((..((((....))))..)))))....))))))))). ( -24.60, z-score =  -1.02, R)
>droYak2.chrX 8497591 112 - 21770863
UUUAUUAAAUGUUGUGAAAAGCAUGUAUUUUGCAUUUACCAAGAUCUUUUAUUAUU--UAAUAAGUAGCUCAG------CGAGAAUACAGAUUCAUCUGGCUUUUUAAAAUAGAUGCAAU
........(((((......))))).....(((((((((....((.((((((((...--.)))))).)).))..------.(((((..((((....))))..)))))....))))))))). ( -19.20, z-score =  -0.10, R)
>droEre2.scaffold_4690 6060089 105 + 18748788
UUUAUUAAAUUGUAGGGAAACCAUUUAUUUAGCAUUUGCCAAGAUCUCUUACUUUUAAGUACGAGUAUCUC--------AGCGGGCAUACGCU-------AUCUUUGAAGUAGAUGCCAU
.....(((((....((....))....)))))((((((((..(((((((.((((....)))).))).)))).--------((((......))))-------.........))))))))... ( -28.10, z-score =  -3.08, R)
>consensus
UUUAUUAAAUUGUGUGAAAACCAUUUACUUUGCAUUUCCCAAGAUCUUUUAUUAUC____AUAAGUAGCUCAG_G____AGAGAGUACAGACUCAUCUGGGCUUUCAAAAUAGAUGCAAU
.....(((((.((......)).)))))..(((((((((....((.(((((((........))))).)).)).........((((((.(((......))).))))))....))))))))). (-14.84 = -15.48 +   0.64)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:43:00 2011