Locus 14282

Sequence ID	dm3.chrX
Location	12,324,222 – 12,324,332
Length	110
Max. P	0.971723

overview

Window 4

Location	12,324,222 – 12,324,332
Length	110
Sequences	8
Columns	137
Reading direction	forward
Mean pairwise identity	67.33
Shannon entropy	0.57009
G+C content	0.48033
Mean single sequence MFE	-32.39
Consensus MFE	-14.92
Energy contribution	-15.12
Covariance contribution	0.20
Combinations/Pair	1.24
Mean z-score	-1.19
Structure conservation index	0.46
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.18
SVM RNA-class probability	0.583332
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12324222 110 + 22422827
---------------------------AAAUCCUUGCAGCAUGCAAUCUCCGCCAUCUUGAUGCAUUCUUAUAAUUCGCAUGGCAUGCAACCGACAUUUGUUGGAUGCCACACGAAUCCUUUCGUCCAGGAUACAUA
---------------------------..(((((.((((.(((((.((...........))))))).))....(((((..((((((.((((........)))).))))))..)))))......))..)))))..... ( -28.80, z-score =  -1.88, R)
>droSim1.chrX_random 259012 108 + 5698898
---------------------------AAAUCCUUGCAGCAUGCAAUCUCCGCCAUCUUGAUGCAUUCUUAUAAUUCGCAUGGCAUGCAACCGACAUUUGUUGGAUGCCACACGAAUCCUUUCGUCCAGGAUACA--
---------------------------..(((((.((((.(((((.((...........))))))).))....(((((..((((((.((((........)))).))))))..)))))......))..)))))...-- ( -28.80, z-score =  -1.91, R)
>droSec1.super_21 83346 108 + 1102487
---------------------------AAAUCCUUGCAGCAUGCAAUCUCCGCCAUCUUGAUGCAUUCUUAUAAUUCGCAUGGCAUGCAACCGACAUUUGUUGGAUGCCACACGAAUCCUUUCGUCCAGGAUACA--
---------------------------..(((((.((((.(((((.((...........))))))).))....(((((..((((((.((((........)))).))))))..)))))......))..)))))...-- ( -28.80, z-score =  -1.91, R)
>droYak2.chrX 6601839 108 + 21770863
---------------------------AAAUCCUUGCAGCAUGCAAUCUCCGCCAUCUUGAUGCACUCUUAUAAUUCGCAUGGCAUGCAACCGACAUUUGUUGGAUGCCACACGAAUCCUUUCGUCCAGGAUACA--
---------------------------..(((((.((.((((.(((...........))))))).........(((((..((((((.((((........)))).))))))..)))))......))..)))))...-- ( -27.90, z-score =  -1.76, R)
>droEre2.scaffold_4690 4216650 107 - 18748788
---------------------------AAAUCCUUGCAGCAUGCAAUCUUCGCCAUCUUGAUGCAUUCUUAUAAUUCGCAUGGCAUGCAACCGGCAUUUGUUGGAUGCCACACGA-UUCUUUCGUCCAGGAUACA--
---------------------------..(((((.((((.(((((.((...........))))))).))......(((..((((((.((((........)))).))))))..)))-.......))..)))))...-- ( -27.20, z-score =  -0.85, R)
>droAna3.scaffold_13335 2308401 91 - 3335858
---------------------------AAAUCCUUGCAACAUGCAACCGGCAGCAUCCU------UUAUUUUUUCUGGCAUGGCAUGCAACUGAUAUUUGUCGGUUGCCACAU----------CUCAGAGAUAC---
---------------------------....((((((.....))))..)).........------......(((((((.(((....(((((((((....)))))))))..)))----------.)))))))...--- ( -23.80, z-score =  -1.57, R)
>dp4.chrXL_group1a 3059431 137 + 9151740
AAAUCUAUGCAGCAUGCAAGCGGCUAGGGACAGGGCCAGUGCAGGCCAGGCAGCACCUUGAUGCGUUCCCAUAACUCGCGUGGCAUCCAGCCGGCAUUUGUUACAUGCCACACGAACCGCACAUGCAAGGAUGCACA
.......(((((((((...((((...(((((..((((......))))..(((.(.....).))))))))......(((.(((((((..(((........)))..))))))).))).)))).))))).....)))).. ( -46.90, z-score =   0.19, R)
>droPer1.super_12 2194453 137 - 2414086
AAAUCUAUGCAGCAUGCAAGCGGCUAGGGACAGGGCCAGUGCAGGCCAGGCAGCACCUUGAUGCGUUCCCAUAACUCGCGUGGCAUCCAGCCGGCAUUUGUUACAUGCCACACGAACCGCACAUGCAAGGAUGCACA
.......(((((((((...((((...(((((..((((......))))..(((.(.....).))))))))......(((.(((((((..(((........)))..))))))).))).)))).))))).....)))).. ( -46.90, z-score =   0.19, R)
>consensus
___________________________AAAUCCUUGCAGCAUGCAAUCUCCGCCAUCUUGAUGCAUUCUUAUAAUUCGCAUGGCAUGCAACCGACAUUUGUUGGAUGCCACACGAAUCCUUUCGUCCAGGAUACA__
.................................((((.....)))).............................(((..((((((.((((........)))).))))))..)))...................... (-14.92 = -15.12 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	12,324,222 – 12,324,332
Length	110
Sequences	8
Columns	137
Reading direction	reverse
Mean pairwise identity	67.33
Shannon entropy	0.57009
G+C content	0.48033
Mean single sequence MFE	-38.58
Consensus MFE	-24.54
Energy contribution	-24.47
Covariance contribution	-0.06
Combinations/Pair	1.42
Mean z-score	-1.35
Structure conservation index	0.64
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.86
SVM RNA-class probability	0.971723
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12324222 110 - 22422827
UAUGUAUCCUGGACGAAAGGAUUCGUGUGGCAUCCAACAAAUGUCGGUUGCAUGCCAUGCGAAUUAUAAGAAUGCAUCAAGAUGGCGGAGAUUGCAUGCUGCAAGGAUUU---------------------------
.....(((((...(....)((((((((((((((.((((........)))).))))))))))))))...((.(((((((...........)).))))).))...)))))..--------------------------- ( -34.60, z-score =  -1.65, R)
>droSim1.chrX_random 259012 108 - 5698898
--UGUAUCCUGGACGAAAGGAUUCGUGUGGCAUCCAACAAAUGUCGGUUGCAUGCCAUGCGAAUUAUAAGAAUGCAUCAAGAUGGCGGAGAUUGCAUGCUGCAAGGAUUU---------------------------
--...(((((...(....)((((((((((((((.((((........)))).))))))))))))))...((.(((((((...........)).))))).))...)))))..--------------------------- ( -34.60, z-score =  -1.68, R)
>droSec1.super_21 83346 108 - 1102487
--UGUAUCCUGGACGAAAGGAUUCGUGUGGCAUCCAACAAAUGUCGGUUGCAUGCCAUGCGAAUUAUAAGAAUGCAUCAAGAUGGCGGAGAUUGCAUGCUGCAAGGAUUU---------------------------
--...(((((...(....)((((((((((((((.((((........)))).))))))))))))))...((.(((((((...........)).))))).))...)))))..--------------------------- ( -34.60, z-score =  -1.68, R)
>droYak2.chrX 6601839 108 - 21770863
--UGUAUCCUGGACGAAAGGAUUCGUGUGGCAUCCAACAAAUGUCGGUUGCAUGCCAUGCGAAUUAUAAGAGUGCAUCAAGAUGGCGGAGAUUGCAUGCUGCAAGGAUUU---------------------------
--...(((((...(....)((((((((((((((.((((........)))).))))))))))))))...((.(((((((...........)).))))).))...)))))..--------------------------- ( -34.90, z-score =  -1.60, R)
>droEre2.scaffold_4690 4216650 107 + 18748788
--UGUAUCCUGGACGAAAGAA-UCGUGUGGCAUCCAACAAAUGCCGGUUGCAUGCCAUGCGAAUUAUAAGAAUGCAUCAAGAUGGCGAAGAUUGCAUGCUGCAAGGAUUU---------------------------
--...(((((...(....)..-(((((((((((.((((........)))).)))))))))))..........((((.((.....((((...)))).)).)))))))))..--------------------------- ( -31.80, z-score =  -1.21, R)
>droAna3.scaffold_13335 2308401 91 + 3335858
---GUAUCUCUGAG----------AUGUGGCAACCGACAAAUAUCAGUUGCAUGCCAUGCCAGAAAAAAUAA------AGGAUGCUGCCGGUUGCAUGUUGCAAGGAUUU---------------------------
---(((((((((.(----------.(((((((..((((........))))..))))))))))))........------..)))))..((...(((.....))).))....--------------------------- ( -21.90, z-score =   0.07, R)
>dp4.chrXL_group1a 3059431 137 - 9151740
UGUGCAUCCUUGCAUGUGCGGUUCGUGUGGCAUGUAACAAAUGCCGGCUGGAUGCCACGCGAGUUAUGGGAACGCAUCAAGGUGCUGCCUGGCCUGCACUGGCCCUGUCCCUAGCCGCUUGCAUGCUGCAUAGAUUU
((((((.....((((((((((((((((((((((.((.(........).)).))))))))))).....((((..((((....)))).....((((......))))...))))..)))))..))))))))))))..... ( -58.10, z-score =  -1.54, R)
>droPer1.super_12 2194453 137 + 2414086
UGUGCAUCCUUGCAUGUGCGGUUCGUGUGGCAUGUAACAAAUGCCGGCUGGAUGCCACGCGAGUUAUGGGAACGCAUCAAGGUGCUGCCUGGCCUGCACUGGCCCUGUCCCUAGCCGCUUGCAUGCUGCAUAGAUUU
((((((.....((((((((((((((((((((((.((.(........).)).))))))))))).....((((..((((....)))).....((((......))))...))))..)))))..))))))))))))..... ( -58.10, z-score =  -1.54, R)
>consensus
__UGUAUCCUGGACGAAAGGAUUCGUGUGGCAUCCAACAAAUGUCGGUUGCAUGCCAUGCGAAUUAUAAGAAUGCAUCAAGAUGGCGGAGAUUGCAUGCUGCAAGGAUUU___________________________
.....((((..........((((((((((((((.((((........)))).))))))))))))))..........................((((.....))))))))............................. (-24.54 = -24.47 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:37:19 2011