Locus 2020

Sequence ID dm3.chr2L
Location 15,555,511 – 15,555,649
Length 138
Max. P 0.692579
window2777 window2778

overview

Window 7

Location 15,555,511 – 15,555,617
Length 106
Sequences 7
Columns 114
Reading direction reverse
Mean pairwise identity 64.10
Shannon entropy 0.69731
G+C content 0.43661
Mean single sequence MFE -28.69
Consensus MFE -9.74
Energy contribution -11.23
Covariance contribution 1.48
Combinations/Pair 1.77
Mean z-score -1.25
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.517395
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15555511 106 - 23011544
-----GUGCGGUGAAAGCACUUUCCUUGGCCACA---AGUUUUGGGUCACAUUAUAAGGAGGUUGGCAAGUCAGGGUUGGCCUUUGGAUUAUGGUUUUUGAGGGCACAUACUUU
-----((((((((....))))..((((((((.((---.....)))))).(((.((..((((((..((........))..))))))..)).)))......))))))))....... ( -32.20, z-score =  -1.38, R)
>droAna3.scaffold_12984 234627 92 + 754457
----------------UCACUUUCUUUGACCACGCGUAGAUGUGAACGCGUUACUAAUAUGAUUAGUAAACUAAUAAAAAGAAUAGGCUGAUAA-UUUUGUG---ACAUUUU--
----------------((((.....((..((((((((........))))))(((((((...))))))).................))..))...-....)))---)......-- ( -15.90, z-score =  -0.89, R)
>droEre2.scaffold_4929 7304263 105 - 26641161
-----GUGCGGUAAAAGCACUUUCCUUGGCCACA---AGUUUUGGGUCACAAAUUAAGGAGGUUGACAAGUCAGGAUUGGCCUUUGGAUUAUGG-UUUUGCGGGCAGAGGCUUU
-----((.((.(((((.((...(((..(((((..---.(((((((((((..............))))...))))))))))))...)))...)).-))))))).))......... ( -26.84, z-score =   0.40, R)
>droYak2.chr2L 2554710 105 + 22324452
-----GUGCGGUAGAAGUACUUUCCUUGGCCACA---AGUUUUGGGUCACAUAAUAAGGAGGUUGGCAAGUCAGGGUUGGCUUUUGGAUUAUGG-UUUUAAGGGAAGACGCUUU
-----........(((((.((((((((((((.((---.....)))))).((((((..((((((..((........))..))))))..)))))).-....))))))))..))))) ( -32.60, z-score =  -2.63, R)
>droSec1.super_3 1817339 105 - 7220098
-----GUGCGGUGAAAGCACUUUCCUUGGCCACA---AGUUUUGGGUCACAUUAUAAGGAGGUUGGCAAGUCAGGGUUGGCCUUUGGAUUAUGG-UUUUGAGGGCACAUACUUU
-----((((((((....))))..((((((((.((---.....)))))).(((.((..((((((..((........))..))))))..)).))).-....))))))))....... ( -32.20, z-score =  -1.37, R)
>droSim1.chr2L 15313545 105 - 22036055
-----GUGCGGUGAAAGCACUUUCCUUGGCCACA---AGUUUUGGGUCACAUUAUAAGGAGGUUGGCAAGUCAGGGUUGGCCUUUGGAUUAUGG-UUUUGAGGGCACAUACUUU
-----((((((((....))))..((((((((.((---.....)))))).(((.((..((((((..((........))..))))))..)).))).-....))))))))....... ( -32.20, z-score =  -1.37, R)
>droVir3.scaffold_12963 12257884 109 - 20206255
UGAAGAUAUCCUAUGGAUAUGCUAAUGCGACAGG---AUAUUAAAAGGAGAUUUGCCGAGCUGCACUAAGUCUGCGUUAGACUUACCACUAUUGAUGGUGGGAGCAAAGGUC--
...((((.((((...(((((.((........)).---)))))...)))).))))(((..(((....((((((((...))))))))((((((....)))))).)))...))).-- ( -28.90, z-score =  -1.50, R)
>consensus
_____GUGCGGUAAAAGCACUUUCCUUGGCCACA___AGUUUUGGGUCACAUUAUAAGGAGGUUGGCAAGUCAGGGUUGGCCUUUGGAUUAUGG_UUUUGAGGGCACAUACUUU
.....((((.......))))..(((((((((.((........)))))).(((.....((((((..((........))..)))))).....)))......))))).......... ( -9.74 = -11.23 +   1.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,555,545 – 15,555,649
Length 104
Sequences 7
Columns 110
Reading direction forward
Mean pairwise identity 66.82
Shannon entropy 0.66944
G+C content 0.43352
Mean single sequence MFE -24.51
Consensus MFE -4.27
Energy contribution -5.40
Covariance contribution 1.13
Combinations/Pair 1.47
Mean z-score -2.65
Structure conservation index 0.17
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.43
SVM RNA-class probability 0.692579
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 15555545 104 + 23011544
CCAACCCUGACUUGCCA-ACCUCCUUA-UAAUGUGACCCAAA--ACUUGUGGCCAAGGAAAGUGCUUUCACCGCACU--UUAUAUAUUGGCCGAGGCAAUUCACUCGCUC
.......(((.(((((.-........(-(((.((........--))))))((((((..(((((((.......)))))--)).....))))))..))))).)))....... ( -28.80, z-score =  -3.35, R)
>droAna3.scaffold_12984 234655 91 - 754457
UUUUUAUUAGUUUACUA-AUCAUAUUAGUAACGCGUUCACAUCUACGCGUGGUCAAAGAAAGUGAAUUGGCCAAA------------------AAAAAAUUCAUUUUCUU
............(((((-((...)))))))((((((........)))))).....(((((((((((((.......------------------....))))))))))))) ( -22.70, z-score =  -4.48, R)
>droEre2.scaffold_4929 7304296 104 + 26641161
CCAAUCCUGACUUGUCA-ACCUCCUUA-AUUUGUGACCCAAA--ACUUGUGGCCAAGGAAAGUGCUUUUACCGCACU--UUAUAUAUUGGCCGAGGCAAUUCACCCGCUC
.......(((.(((((.-.........-.((((.....))))--.....(((((((..(((((((.......)))))--)).....))))))).))))).)))....... ( -26.20, z-score =  -2.44, R)
>droYak2.chr2L 2554743 104 - 22324452
CCAACCCUGACUUGCCA-ACCUCCUUA-UUAUGUGACCCAAA--ACUUGUGGCCAAGGAAAGUACUUCUACCGCACU--UUAUAUAUUGGCCAAGGCAAUUCACUCGCUC
.......(((.(((((.-.........-....((........--))...(((((((..(((((.(.......).)))--)).....))))))).))))).)))....... ( -22.30, z-score =  -1.77, R)
>droSec1.super_3 1817372 104 + 7220098
CCAACCCUGACUUGCCA-ACCUCCUUA-UAAUGUGACCCAAA--ACUUGUGGCCAAGGAAAGUGCUUUCACCGCACU--UUAUAUAUUGGCCGAGGCAAUUCACUCGCUC
.......(((.(((((.-........(-(((.((........--))))))((((((..(((((((.......)))))--)).....))))))..))))).)))....... ( -28.80, z-score =  -3.35, R)
>droSim1.chr2L 15313578 104 + 22036055
CCAACCCUGACUUGCCA-ACCUCCUUA-UAAUGUGACCCAAA--ACUUGUGGCCAAGGAAAGUGCUUUCACCGCACU--UUAUAUAUUGGCCGAGGCAAUUCACUCGCUC
.......(((.(((((.-........(-(((.((........--))))))((((((..(((((((.......)))))--)).....))))))..))))).)))....... ( -28.80, z-score =  -3.35, R)
>droVir3.scaffold_12963 12257916 102 + 20206255
CUAACGCAGACUUAGUGCAGCUCGGCA--AAUCUCCUUUUAAUAUCCUGUCGCAUUAGCAUAUCCAUAGGAUAUCUUCAUUAUCUAUCAUUUUAUGUAAAGCAC------
.....((.....((((((.((..((..--................)).)).))))))(((((......(((((.......))))).......)))))...))..------ ( -13.99, z-score =   0.22, R)
>consensus
CCAACCCUGACUUGCCA_ACCUCCUUA_UAAUGUGACCCAAA__ACUUGUGGCCAAGGAAAGUGCUUUCACCGCACU__UUAUAUAUUGGCCGAGGCAAUUCACUCGCUC
........((.(((((.......(........)..............(((((..((((......))))..)))))...................))))).))........ ( -4.27 =  -5.40 +   1.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:43:13 2011