Locus 2719

Sequence ID dm3.chr2L
Location 21,502,919 – 21,502,974
Length 55
Max. P 0.999888
window3732 window3733

overview

Window 2

Location 21,502,919 – 21,502,974
Length 55
Sequences 11
Columns 70
Reading direction forward
Mean pairwise identity 58.69
Shannon entropy 0.83541
G+C content 0.47896
Mean single sequence MFE -19.95
Consensus MFE -12.49
Energy contribution -13.75
Covariance contribution 1.25
Combinations/Pair 1.33
Mean z-score -2.24
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.72
SVM RNA-class probability 0.999888
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 21502919 55 + 23011544
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUA--UUGUCCGCA---UUCGCAGGAGAAAA----------
.((((((((((....)))))).....((((..--..))))...---...)))).......---------- ( -20.10, z-score =  -2.58, R)
>droSim1.chrU 5518301 55 - 15797150
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUG--UUGUCCGCA---UUCGCAGGAGCCAA----------
.....((((((....))))))(((((((((..--..))))((.---...)).)))))...---------- ( -21.60, z-score =  -2.34, R)
>droSec1.super_91 112088 55 + 125313
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUG--UUGUCCGCA---UUCGCAGGAGCCAA----------
.....((((((....))))))(((((((((..--..))))((.---...)).)))))...---------- ( -21.60, z-score =  -2.34, R)
>droYak2.chr2R_random 60460 58 - 67238
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUA--AUGUCCGCAGCAUUCGUAGGAACAAA----------
.((((((((((....))))))(((.(((((..--..))))).)))..........)))).---------- ( -23.20, z-score =  -3.62, R)
>droEre2.scaffold_4845 19574780 55 - 22589142
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUU--UUGUCCGCA---CUCGCAGGAGGAAA----------
..(((((((((....)))))).....((((..--..)))))))---(((....)))....---------- ( -21.40, z-score =  -2.38, R)
>droAna3.scaffold_13030 44769 54 - 47400
GUUGUGGCCCUGAAAAGGGCCUUUUUGGAUCA--UUCUGCCCA----GCAAGCGAGCAAU----------
((((.((((((....)))))).....(((...--.)))...))----))...........---------- ( -17.50, z-score =  -0.99, R)
>droWil1.scaffold_181036 1021 60 + 110856
AUUGUGGCCCUGAAAAGGGCUUUUUUUUUAAA--AGGAAGCGUGUGUUUAAGCUAGGGACAU--------
.((.(((((((....)))((((((((.....)--)))))))..........)))).))....-------- ( -14.80, z-score =  -0.85, R)
>droVir3.scaffold_13047 1603366 66 + 19223366
UUUGUGGCCCUGAAAAGGGCCUUUUGCUUUU----GUUUGCUUCCCGUACAAUGCACAUCUAGCUGAAUU
.....((((((....))))))(((.(((...----((.(((............))).))..))).))).. ( -18.20, z-score =  -1.84, R)
>droMoj3.scaffold_6540 26857080 64 - 34148556
UUUGUGGCCCUGAAAAGGGCCUUUUGCUUCU------UCUUUUGGAAUUCUGCAUACACCGAGGUAAGAU
.....((((((....))))))(((((((((.------.....((.(....).))......))))))))). ( -20.80, z-score =  -2.43, R)
>droGri2.scaffold_14978 520668 60 + 1124632
UUUGUGGCCCUGAAAAGGGCCUUUUGCUGCUAGCUGCUCGCUGGUAUUUCUGCCUGCAAU----------
.((((((((((....))))))......(((((((.....))))))).........)))).---------- ( -23.60, z-score =  -2.79, R)
>anoGam1.chr2R 47876183 55 + 62725911
UUUGUGGUCCUGAAAAGGACCGAUUUGAGAGA--ACGAAGCCAAUCAUUUCAGUGGC-------------
(((((((((((....))))))...((....))--)))))((((..........))))------------- ( -16.60, z-score =  -2.43, R)
>consensus
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUA__UUGUCCCCA___UUCGCAGGAGCAAA__________
.....((((((....))))))................................................. (-12.49 = -13.75 +   1.25)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 21,502,919 – 21,502,974
Length 55
Sequences 11
Columns 70
Reading direction reverse
Mean pairwise identity 58.69
Shannon entropy 0.83541
G+C content 0.47896
Mean single sequence MFE -15.70
Consensus MFE -11.22
Energy contribution -11.15
Covariance contribution -0.07
Combinations/Pair 1.17
Mean z-score -1.74
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.13
SVM RNA-class probability 0.999648
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 21502919 55 - 23011544
----------UUUUCUCCUGCGAA---UGCGGACAA--UAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
----------.......((((...---.))))....--...........((((((....))))))..... ( -15.70, z-score =  -2.52, R)
>droSim1.chrU 5518301 55 + 15797150
----------UUGGCUCCUGCGAA---UGCGGACAA--CAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
----------(((..(((.((...---.)))))...--)))........((((((....))))))..... ( -16.30, z-score =  -1.62, R)
>droSec1.super_91 112088 55 - 125313
----------UUGGCUCCUGCGAA---UGCGGACAA--CAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
----------(((..(((.((...---.)))))...--)))........((((((....))))))..... ( -16.30, z-score =  -1.62, R)
>droYak2.chr2R_random 60460 58 + 67238
----------UUUGUUCCUACGAAUGCUGCGGACAU--UAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
----------(((((....)))))......(((...--...))).....((((((....))))))..... ( -15.40, z-score =  -2.01, R)
>droEre2.scaffold_4845 19574780 55 + 22589142
----------UUUCCUCCUGCGAG---UGCGGACAA--AAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
----------.......((((...---.))))....--...........((((((....))))))..... ( -15.70, z-score =  -1.81, R)
>droAna3.scaffold_13030 44769 54 + 47400
----------AUUGCUCGCUUGC----UGGGCAGAA--UGAUCCAAAAAGGCCCUUUUCAGGGCCACAAC
----------.(((((((.....----)))))))..--...........((((((....))))))..... ( -18.10, z-score =  -1.59, R)
>droWil1.scaffold_181036 1021 60 - 110856
--------AUGUCCCUAGCUUAAACACACGCUUCCU--UUUAAAAAAAAAGCCCUUUUCAGGGCCACAAU
--------.(((....(((..........)))....--............(((((....))))).))).. (  -8.00, z-score =  -0.71, R)
>droVir3.scaffold_13047 1603366 66 - 19223366
AAUUCAGCUAGAUGUGCAUUGUACGGGAAGCAAAC----AAAAGCAAAAGGCCCUUUUCAGGGCCACAAA
......(((...(((((...)))))...)))....----..........((((((....))))))..... ( -18.30, z-score =  -1.74, R)
>droMoj3.scaffold_6540 26857080 64 + 34148556
AUCUUACCUCGGUGUAUGCAGAAUUCCAAAAGA------AGAAGCAAAAGGCCCUUUUCAGGGCCACAAA
....(((....)))..(((....(((.....))------)...)))...((((((....))))))..... ( -15.10, z-score =  -1.13, R)
>droGri2.scaffold_14978 520668 60 - 1124632
----------AUUGCAGGCAGAAAUACCAGCGAGCAGCUAGCAGCAAAAGGCCCUUUUCAGGGCCACAAA
----------.((((.((.(....).))(((.....)))....))))..((((((....))))))..... ( -20.30, z-score =  -2.35, R)
>anoGam1.chr2R 47876183 55 - 62725911
-------------GCCACUGAAAUGAUUGGCUUCGU--UCUCUCAAAUCGGUCCUUUUCAGGACCACAAA
-------------((((..........)))).....--...........((((((....))))))..... ( -13.50, z-score =  -2.00, R)
>consensus
__________UUUGCUCCUGCGAA___UGCGGACAA__UAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
.................................................((((((....))))))..... (-11.22 = -11.15 +  -0.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:56:32 2011