Locus 7279

Sequence ID dm3.chr3L
Location 13,607,950 – 13,608,045
Length 95
Max. P 0.953251
window10017 window10018

overview

Window 7

Location 13,607,950 – 13,608,045
Length 95
Sequences 7
Columns 98
Reading direction forward
Mean pairwise identity 75.52
Shannon entropy 0.48651
G+C content 0.42912
Mean single sequence MFE -30.91
Consensus MFE -13.41
Energy contribution -15.57
Covariance contribution 2.16
Combinations/Pair 1.32
Mean z-score -1.98
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.782150
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 13607950 95 + 24543557
---CCACACACACACACACACCUUUAAUGUGGCCACAAUGUGAAAACGAGUAUGUGCUCGGGUGUGUGUGUGUAUGUGCUUCAUUAUUAUUAUGGUUG
---.((((.(((((((((((((((((...((....))...))))..(((((....)))))))))))))))))).)))).................... ( -36.40, z-score =  -2.88, R)
>droWil1.scaffold_180698 10807309 92 - 11422946
CACACAUAUACACUCACAUAGCUUUAAUGCAGACACAGCAUGU---UCAGUAUGU---UGUGUAUGUGUUUGUGUGUGCCACAUUAUUAUUAUUGGUG
((((((((.((((.......((......))..((((((((((.---....)))))---)))))..)))).))))))))...(((((.......))))) ( -29.00, z-score =  -1.57, R)
>droEre2.scaffold_4784 13608786 91 + 25762168
-------CCACACACACACACUUUUAAUGUGGCCACAAUGUGAAAACGAGUAUGUGCGCGAGUGUGUGUGUGUGUGCGCUUCAUUAUUAUUAUGGUUG
-------.(((((((((((((((........((((((.(((....)))....)))).)))))))))))))))))........................ ( -30.40, z-score =  -1.37, R)
>droYak2.chr3L 13700923 91 + 24197627
-----CCACACUCACACACACCUUUAAUGUGGCCACAAUGUGAAAACGAGUAUGUGCGCCAGUGU--GUGUGUGUGUGCUUCAUUAUUAUUAUGGUUG
-----.(((((.(((((((((........((((((((.(((....)))....)))).))))))))--))))).))))).................... ( -32.50, z-score =  -2.56, R)
>droSec1.super_0 5769649 93 + 21120651
-----CCACACACACACACACCUUUAAUGUGGCCACAAUGUGAAAACGAGUAUGUGCUCGGGUGUCUGUGUGUGUGUGCUUCAUUAUUAUUAUGGUUG
-----.((((((((((((((((((((...((....))...))))..(((((....))))))))))..))))))))))).................... ( -32.70, z-score =  -2.22, R)
>droSim1.chr3L 12991467 91 + 22553184
-----CCACACACACACACACCUUUAAUGUGGCCACAAUGUGAAAACGAGUAUGUGCUCGGGUGU--GUGUGUGUGUGCUUCAUUAUUAUUAUGGUUG
-----.((((((((((((((((((((...((....))...))))..(((((....))))))))))--))))))))))).................... ( -38.10, z-score =  -3.90, R)
>droMoj3.scaffold_6680 17243675 88 - 24764193
---------CCGCAGA-ACACCCACAAGGCAGCUAUGCUACACAUGUGUGUGUCUCUCCCUCUAUGUAUGUGUGUGUGCUUCAUUAUUAUUAUUGUUG
---------..(.((.-((((.((((.((((....))))(((((....)))))...............)))).)))).)).)................ ( -17.30, z-score =   0.62, R)
>consensus
_____CCACACACACACACACCUUUAAUGUGGCCACAAUGUGAAAACGAGUAUGUGCUCGGGUGUGUGUGUGUGUGUGCUUCAUUAUUAUUAUGGUUG
..........(((((((((((.....((.((..((((.(((....)))....))))..)).))....))))))))))).................... (-13.41 = -15.57 +   2.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 13,607,950 – 13,608,045
Length 95
Sequences 7
Columns 98
Reading direction reverse
Mean pairwise identity 75.52
Shannon entropy 0.48651
G+C content 0.42912
Mean single sequence MFE -29.12
Consensus MFE -13.46
Energy contribution -14.89
Covariance contribution 1.43
Combinations/Pair 1.19
Mean z-score -2.31
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.59
SVM RNA-class probability 0.953251
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 13607950 95 - 24543557
CAACCAUAAUAAUAAUGAAGCACAUACACACACACACCCGAGCACAUACUCGUUUUCACAUUGUGGCCACAUUAAAGGUGUGUGUGUGUGUGUGG---
....................((((((((((((((((((.(((......)))((..((((...))))..))......)))))))))))))))))).--- ( -37.70, z-score =  -4.23, R)
>droWil1.scaffold_180698 10807309 92 + 11422946
CACCAAUAAUAAUAAUGUGGCACACACAAACACAUACACA---ACAUACUGA---ACAUGCUGUGUCUGCAUUAAAGCUAUGUGAGUGUAUAUGUGUG
...............((((.....)))).((((((((((.---(((((((..---..((((.......))))...)).)))))..)))))..))))). ( -22.00, z-score =   0.02, R)
>droEre2.scaffold_4784 13608786 91 - 25762168
CAACCAUAAUAAUAAUGAAGCGCACACACACACACACUCGCGCACAUACUCGUUUUCACAUUGUGGCCACAUUAAAAGUGUGUGUGUGUGG-------
........................((((((((((((((.((.((((...............)))))).........)))))))))))))).------- ( -26.96, z-score =  -1.97, R)
>droYak2.chr3L 13700923 91 - 24197627
CAACCAUAAUAAUAAUGAAGCACACACACAC--ACACUGGCGCACAUACUCGUUUUCACAUUGUGGCCACAUUAAAGGUGUGUGUGAGUGUGG-----
....................(((((.(((((--((((((((.((((...............)))))))........)))))))))).))))).----- ( -30.56, z-score =  -2.63, R)
>droSec1.super_0 5769649 93 - 21120651
CAACCAUAAUAAUAAUGAAGCACACACACACAGACACCCGAGCACAUACUCGUUUUCACAUUGUGGCCACAUUAAAGGUGUGUGUGUGUGUGG-----
......................((((((((((.(((((.(((......)))((..((((...))))..))......))))).)))))))))).----- ( -31.70, z-score =  -2.82, R)
>droSim1.chr3L 12991467 91 - 22553184
CAACCAUAAUAAUAAUGAAGCACACACACAC--ACACCCGAGCACAUACUCGUUUUCACAUUGUGGCCACAUUAAAGGUGUGUGUGUGUGUGG-----
....................(((((((((((--(((((.(((......)))((..((((...))))..))......)))))))))))))))).----- ( -35.30, z-score =  -4.15, R)
>droMoj3.scaffold_6680 17243675 88 + 24764193
CAACAAUAAUAAUAAUGAAGCACACACACAUACAUAGAGGGAGAGACACACACAUGUGUAGCAUAGCUGCCUUGUGGGUGU-UCUGCGG---------
...................(((...((((...((((.(((.((.(..((((....))))..)....)).))))))).))))-..)))..--------- ( -19.60, z-score =  -0.36, R)
>consensus
CAACCAUAAUAAUAAUGAAGCACACACACACACACACCCGAGCACAUACUCGUUUUCACAUUGUGGCCACAUUAAAGGUGUGUGUGUGUGUGG_____
...................((((((((((((...........((((...............))))............))))))))))))......... (-13.46 = -14.89 +   1.43)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:23:51 2011