Locus 2017

Sequence ID	dm3.chr2L
Location	15,547,025 – 15,547,127
Length	102
Max. P	0.875850

overview

Window 0

Location	15,547,025 – 15,547,127
Length	102
Sequences	7
Columns	114
Reading direction	forward
Mean pairwise identity	81.89
Shannon entropy	0.34915
G+C content	0.40365
Mean single sequence MFE	-26.96
Consensus MFE	-18.64
Energy contribution	-19.11
Covariance contribution	0.47
Combinations/Pair	1.20
Mean z-score	-1.83
Structure conservation index	0.69
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.02
SVM RNA-class probability	0.875850
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15547025 102 + 23011544
GGGAGAGACAGCAUUUCCG----------UUUGCGGCUGGCCAAAUAUUUGCAUUAAAUUUGGCCAAGUGGCAACGUUUAUUUUGCUAUUAUACAUUUUUUCUGUUCUGUCC--
.(((.((((((.....(((----------....))).(((((((((...........)))))))))((((((((........))))))))...........))).))).)))-- ( -29.50, z-score =  -2.46, R)
>droPer1.super_10 2169345 114 - 3432795
GGGAAGAACAACAUUCCAGGCCUCCUUCUUUUGCGGUUGGCCAAAUAUUUGCAUUAAAUUUGGCCAAGUGGCAACGUUUAUUCUGCUAUAAUAUAUUUCUUCUCCUCUGCUCGG
((((((((..........((((..((.(....).))..))))..(((((.(((.(((((...(((....)))...)))))...)))...)))))..)))))))).......... ( -28.70, z-score =  -1.63, R)
>droSim1.chr2L 15305011 102 + 22036055
GGGAGAGACAGCAUUUCCG----------UUUGCGGCUGGCCAAAUAUUUGCAUUAAAUUUGGCCAAGUGGCAACGUUUAUUCUGCUAUUAUACAUUUUUUCUGUUCUGCCC--
(((((((.(((.....(((----------....))).(((((((((...........)))))))))(((((((..........)))))))...........))))))).)))-- ( -28.00, z-score =  -1.53, R)
>droSec1.super_3 1801955 102 + 7220098
GGGAGAGACAGCAUUUCCG----------UUUGCGGCUGGCCAAAUAUUUGCAUUAAAUUUGGCCAAGUGGCAACGUUUAUUCUGCUAUUAUACAUUUUUUCUGUUUUGCCC--
(((..((((((.....(((----------....))).(((((((((...........)))))))))(((((((..........)))))))...........))))))..)))-- ( -30.00, z-score =  -2.26, R)
>droYak2.chr2L 2546222 102 - 22324452
GGGAGAGACAACAUUUCCG----------UUUGCGGCUGGCCAAAUAUUUGCAUUAAAUUUGGCCAAGUGGCAACGUUUAUUCUGAUAUUAUACAUUUUUUCUGUUCUGCCG--
((.((((.((.......((----------((.((.(((((((((((...........)))))))).))).))))))........((..............)))))))).)).-- ( -26.44, z-score =  -1.71, R)
>droEre2.scaffold_4929 7295405 102 + 26641161
GGGAGAGACAACAUUUCCG----------UUUGCGGCUGGCCAAAUAUUUGCAUUAAAUUUGGCCAAGUGGCAACGUUUAUUCUGCUAUUAUACAUUUUUUCUGUUCCGCCG--
((((.(((........(((----------....))).(((((((((...........)))))))))(((((((..........)))))))..........))).))))....-- ( -27.20, z-score =  -1.70, R)
>droVir3.scaffold_12963 12246859 81 + 20206255
----------GCCUUUUCU----------UUUGUGGUUGGCCAAAUAUUUGCAUUAAAUUUGGCCAAGUGGCAACAUUUUUUUCGUUUU------UUUUUCCAGGAA-------
----------.........----------(((.(((((((((((((...........))))))))))(((....)))............------.....))).)))------- ( -18.90, z-score =  -1.54, R)
>consensus
GGGAGAGACAGCAUUUCCG__________UUUGCGGCUGGCCAAAUAUUUGCAUUAAAUUUGGCCAAGUGGCAACGUUUAUUCUGCUAUUAUACAUUUUUUCUGUUCUGCCC__
.(((((.......)))))............((((.(((((((((((...........)))))))).))).))))........................................ (-18.64 = -19.11 +   0.47)

alignment

secondary structure

dotplot

Window 1

Location	15,547,025 – 15,547,127
Length	102
Sequences	7
Columns	114
Reading direction	reverse
Mean pairwise identity	81.89
Shannon entropy	0.34915
G+C content	0.40365
Mean single sequence MFE	-24.34
Consensus MFE	-16.07
Energy contribution	-16.39
Covariance contribution	0.31
Combinations/Pair	1.27
Mean z-score	-1.64
Structure conservation index	0.66
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.46
SVM RNA-class probability	0.705837
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15547025 102 - 23011544
--GGACAGAACAGAAAAAAUGUAUAAUAGCAAAAUAAACGUUGCCACUUGGCCAAAUUUAAUGCAAAUAUUUGGCCAGCCGCAAA----------CGGAAAUGCUGUCUCUCCC
--(((.(((.(((......(((......))).......((((((...((((((((((...........))))))))))..)).))----------))......)))))).))). ( -26.80, z-score =  -2.83, R)
>droPer1.super_10 2169345 114 + 3432795
CCGAGCAGAGGAGAAGAAAUAUAUUAUAGCAGAAUAAACGUUGCCACUUGGCCAAAUUUAAUGCAAAUAUUUGGCCAACCGCAAAAGAAGGAGGCCUGGAAUGUUGUUCUUCCC
.........((.((((((..(((((...((..........((((...((((((((((...........))))))))))..)))).........))....)))))..)))))))) ( -28.11, z-score =  -1.43, R)
>droSim1.chr2L 15305011 102 - 22036055
--GGGCAGAACAGAAAAAAUGUAUAAUAGCAGAAUAAACGUUGCCACUUGGCCAAAUUUAAUGCAAAUAUUUGGCCAGCCGCAAA----------CGGAAAUGCUGUCUCUCCC
--(((.((((((.......)))...((((((.......((((((...((((((((((...........))))))))))..)).))----------))....)))))).)))))) ( -28.90, z-score =  -2.55, R)
>droSec1.super_3 1801955 102 - 7220098
--GGGCAAAACAGAAAAAAUGUAUAAUAGCAGAAUAAACGUUGCCACUUGGCCAAAUUUAAUGCAAAUAUUUGGCCAGCCGCAAA----------CGGAAAUGCUGUCUCUCCC
--(((....(((.......)))...((((((.......((((((...((((((((((...........))))))))))..)).))----------))....))))))....))) ( -25.90, z-score =  -1.75, R)
>droYak2.chr2L 2546222 102 + 22324452
--CGGCAGAACAGAAAAAAUGUAUAAUAUCAGAAUAAACGUUGCCACUUGGCCAAAUUUAAUGCAAAUAUUUGGCCAGCCGCAAA----------CGGAAAUGUUGUCUCUCCC
--.((.((((((.......))).........((...((((((.....((((((((((...........))))))))))(((....----------))).)))))).))))))). ( -22.40, z-score =  -1.19, R)
>droEre2.scaffold_4929 7295405 102 - 26641161
--CGGCGGAACAGAAAAAAUGUAUAAUAGCAGAAUAAACGUUGCCACUUGGCCAAAUUUAAUGCAAAUAUUUGGCCAGCCGCAAA----------CGGAAAUGUUGUCUCUCCC
--.((.(..((((......(((......))).......((((((...((((((((((...........))))))))))..)).))----------))......))))..).)). ( -24.50, z-score =  -1.13, R)
>droVir3.scaffold_12963 12246859 81 - 20206255
-------UUCCUGGAAAAA------AAAACGAAAAAAAUGUUGCCACUUGGCCAAAUUUAAUGCAAAUAUUUGGCCAACCACAAA----------AGAAAAGGC----------
-------............------.................(((..((((((((((...........))))))))))...(...----------.)....)))---------- ( -13.80, z-score =  -0.63, R)
>consensus
__GGGCAGAACAGAAAAAAUGUAUAAUAGCAGAAUAAACGUUGCCACUUGGCCAAAUUUAAUGCAAAUAUUUGGCCAGCCGCAAA__________CGGAAAUGCUGUCUCUCCC
...(((((.(((.......)))..................((((...((((((((((...........))))))))))..))))...................)))))...... (-16.07 = -16.39 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:43:08 2011