Locus 2998

Sequence ID dm3.chr2R
Location 990,139 – 990,244
Length 105
Max. P 0.997142
window4113 window4114

overview

Window 3

Location 990,139 – 990,244
Length 105
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 73.21
Shannon entropy 0.48164
G+C content 0.55082
Mean single sequence MFE -36.53
Consensus MFE -22.10
Energy contribution -21.27
Covariance contribution -0.83
Combinations/Pair 1.36
Mean z-score -1.22
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.734661
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 990139 105 + 21146708
GAGUGUGACUAGUGAUAUACAGCAGCCUUAAAGUUCCAGGAAAAGUUGAUUAUUCGGUC------CGAUAGGUACUCCGCAGCCUGCCAAAGCAGGGCGGACUACAAAUUG
......((((((((((...((((..(((.........)))....)))))))))).))))------((((..(((.(((((..(((((....)))))))))).)))..)))) ( -28.70, z-score =  -1.06, R)
>droSim1.chr2h_random 1002769 111 + 3178526
GAGUGUGGCUAGUGAUAUACAGCAGCCUCAAAGUUCCAAGGUAAGUGGAUUACUCGGUCAGAAUCCGAUUGGUACUCCGCAGCCUGCCAAAGCAGGGCAGACUACAAAUUC
(((.((.(((.(((...)))))).)))))..((((.........(((((.(((.(((((.......)))))))).)))))..(((((....)))))...))))........ ( -31.20, z-score =  -0.65, R)
>droSec1.super_60 143709 109 - 163194
--GUGUGGCUAGUGAUAUACAGCAGCCUCAAAGUUCCAAGGAAAGUGGAUUACUCGGUCAGAAUUCGAGUGGUACUCCGCAGCCUGCCAUAGCAGGGCAGACUACAAAUUC
--.((.((((.((........)))))).))...(((....))).(((((((((((((.......))))))))...)))))((.(((((.......))))).))........ ( -32.00, z-score =  -1.00, R)
>droYak2.chr2L_random 1913381 111 + 4064425
GAGUGUGGCUGGUGAUCGGCAGCGGCCACAGACUCCGAAGGAAAGUGGAACAGCCGCCAGGAAAGCGGCAAGUAACCUGCAGCCCGCAGCAACGGGGCAGCUUACGGAAUC
...((((((((.((.....)).))))))))((.(((................(((((.......)))))..((((.((((..((((......)))))))).))))))).)) ( -44.10, z-score =  -1.51, R)
>droEre2.scaffold_4845 974651 111 + 22589142
GAAUGUGGCUGGUGAUCGGCAGCGGCCACAGACUCCGAAGGAAAGUGGAACAGCCGCCAGGAAAGCGGCAAGUAAACUGCAGCCCGCAGCAACGAGGCAGCUUACGGACUC
...((((((((.((.....)).))))))))((.(((((((....(..(.((.(((((.......)))))..))...)..).(((((......)).)))..))).)))).)) ( -40.00, z-score =  -1.01, R)
>droAna3.scaffold_13417 6855903 111 + 6960332
GAGUGUGGCUGGUGAUCGGCAGCGGCCACAGACUCCGAAGGAAAGUGGAACAGCCGCCAGGAAAGCGGCAAGUAACCUGCAGCCCGAAGCAAGGGGGCAGAUUACAGACCC
(((((((((((.((.....)).)))))))..))))....((...........(((((.......)))))..((((.((((..(((.......))).)))).))))...)). ( -43.20, z-score =  -2.07, R)
>consensus
GAGUGUGGCUAGUGAUAGACAGCAGCCACAAACUCCCAAGGAAAGUGGAACAGCCGCCAGGAAAGCGACAAGUAAUCCGCAGCCCGCAACAACAGGGCAGACUACAAAUUC
...((.((((.((........)))))).))..............((((....(((((.......))))).......((((..((((......)))))))).))))...... (-22.10 = -21.27 +  -0.83)

alignment

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secondary structure

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dotplot

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Window 4

Location 990,139 – 990,244
Length 105
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 73.21
Shannon entropy 0.48164
G+C content 0.55082
Mean single sequence MFE -38.83
Consensus MFE -28.31
Energy contribution -25.90
Covariance contribution -2.41
Combinations/Pair 1.55
Mean z-score -2.37
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.05
SVM RNA-class probability 0.997142
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 990139 105 - 21146708
CAAUUUGUAGUCCGCCCUGCUUUGGCAGGCUGCGGAGUACCUAUCG------GACCGAAUAAUCAACUUUUCCUGGAACUUUAAGGCUGCUGUAUAUCACUAGUCACACUC
......(((.((((((((((....)))))..))))).))).....(------..(((...((......))...)))..).....(((((.((.....)).)))))...... ( -26.40, z-score =  -0.76, R)
>droSim1.chr2h_random 1002769 111 - 3178526
GAAUUUGUAGUCUGCCCUGCUUUGGCAGGCUGCGGAGUACCAAUCGGAUUCUGACCGAGUAAUCCACUUACCUUGGAACUUUGAGGCUGCUGUAUAUCACUAGCCACACUC
......((((((((((.......))))))))))(((((.((((((((.......))))((((.....)))).)))).)))))..(((((.((.....)).)))))...... ( -36.50, z-score =  -2.52, R)
>droSec1.super_60 143709 109 + 163194
GAAUUUGUAGUCUGCCCUGCUAUGGCAGGCUGCGGAGUACCACUCGAAUUCUGACCGAGUAAUCCACUUUCCUUGGAACUUUGAGGCUGCUGUAUAUCACUAGCCACAC--
((((((((((((((((.......)))))))))).(((.....)))))))))...(((((.((......)).)))))........(((((.((.....)).)))))....-- ( -36.50, z-score =  -2.99, R)
>droYak2.chr2L_random 1913381 111 - 4064425
GAUUCCGUAAGCUGCCCCGUUGCUGCGGGCUGCAGGUUACUUGCCGCUUUCCUGGCGGCUGUUCCACUUUCCUUCGGAGUCUGUGGCCGCUGCCGAUCACCAGCCACACUC
((((((((((.(((((((((....)))))..)))).))))..((((((.....))))))................))))))((((((.(.((.....)).).))))))... ( -46.80, z-score =  -3.10, R)
>droEre2.scaffold_4845 974651 111 - 22589142
GAGUCCGUAAGCUGCCUCGUUGCUGCGGGCUGCAGUUUACUUGCCGCUUUCCUGGCGGCUGUUCCACUUUCCUUCGGAGUCUGUGGCCGCUGCCGAUCACCAGCCACAUUC
((.(((((((((((((((((....)))))..)))))))))..((((((.....))))))................))).))((((((.(.((.....)).).))))))... ( -44.40, z-score =  -2.64, R)
>droAna3.scaffold_13417 6855903 111 - 6960332
GGGUCUGUAAUCUGCCCCCUUGCUUCGGGCUGCAGGUUACUUGCCGCUUUCCUGGCGGCUGUUCCACUUUCCUUCGGAGUCUGUGGCCGCUGCCGAUCACCAGCCACACUC
.(((..(((((((((.(((.......)))..)))))))))..)))(((....(((((((.((..((..((((...))))..))..)).)))))))......)))....... ( -42.40, z-score =  -2.21, R)
>consensus
GAAUCUGUAAUCUGCCCCGCUGCGGCAGGCUGCAGAGUACCUGCCGCUUUCCGACCGACUAAUCCACUUUCCUUCGAACUCUGAGGCCGCUGCAGAUCACCAGCCACACUC
((.((((((.((((((((((....)))))..))))).)))..(((((.......)))))................))).))...(((.(.((.....)).).)))...... (-28.31 = -25.90 +  -2.41)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:01:43 2011