Locus 7006

Sequence ID dm3.chr3L
Location 11,422,835 – 11,422,968
Length 133
Max. P 0.950147
window9642 window9643

overview

Window 2

Location 11,422,835 – 11,422,936
Length 101
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 83.14
Shannon entropy 0.27501
G+C content 0.37934
Mean single sequence MFE -24.78
Consensus MFE -18.66
Energy contribution -18.26
Covariance contribution -0.40
Combinations/Pair 1.09
Mean z-score -2.27
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.56
SVM RNA-class probability 0.950147
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11422835 101 + 24543557
CCCCGAAUGCGAUCCUAUAAUAUCAAUUAGGAUAUACCGUGGAAACACAAGGUGAAGGCCAUUGCUUUCACAUUUCUAAAGAAUAUCUUAAUUACCUGCCA------------
........(((((........)))(((((((((((...(((....)))...((((((((....))))))))...........)))))))))))....))..------------ ( -27.10, z-score =  -3.66, R)
>droEre2.scaffold_4784 11429390 98 + 25762168
CCCA---UGAGAUCCCAUAAUAUCAAUUAGGAUAUACCGUGGAAUAACAAGGUGAAGGCCGUUGCUUUCAAAUUCUUAAGGCAUAUUUUAAUUACCUGCUG------------
....---.................(((((((((((.((..(((((.......(((((((....))))))).)))))...)).)))))))))))........------------ ( -19.20, z-score =  -0.42, R)
>droYak2.chr3L 11462029 113 + 24197627
CCCAAAAUGAGAUCCUAUAAUAUCAAUUAGGAUAUACCGUGGAAAAGCAAGGUGAAGGCCGUUGCCUUCAAAAUCUUAAAGCAUAUUUUAAUUACCUGCCAAUAUCUCAUAUA
......(((((((((....(((((......))))).....)))...(((.(((((((((....))))))......((((((....))))))..)))))).....))))))... ( -26.10, z-score =  -2.61, R)
>droSec1.super_0 3631830 99 + 21120651
--CCCAUUGCGAUCCUAUAAUAUCAAUUAGGAUAUACCGUGGAAUCGCAAGGUGAAGGCCGUUGCUUUCACAUUUCUAAAGAAUAUCUUAAUUAGCUGCCA------------
--......(((((........)))(((((((((((.(..(((((.(....)((((((((....))))))))..)))))..).))))))))))).)).....------------ ( -27.00, z-score =  -2.68, R)
>droSim1.chr3L 10817111 99 + 22553184
--CCCAAUGCGAUCCUACAAUAUCAAUUAGGAUAUACCGUGGAAUCGCAAGGUGAAGGCCGUUGCUUUCAAAUUUCUAAAGAAUAUCUUAAUUAGCUGCCA------------
--.....((((((.((((.(((((......)))))...)))).)))))).(((((((((....)))))).........(((.....)))........))).------------ ( -24.50, z-score =  -2.01, R)
>consensus
CCCCCAAUGCGAUCCUAUAAUAUCAAUUAGGAUAUACCGUGGAAUCGCAAGGUGAAGGCCGUUGCUUUCAAAUUUCUAAAGAAUAUCUUAAUUACCUGCCA____________
........................((((((((((((((.((......)).)))((((((....)))))).............))))))))))).................... (-18.66 = -18.26 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,422,873 – 11,422,968
Length 95
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 65.19
Shannon entropy 0.53829
G+C content 0.35325
Mean single sequence MFE -19.06
Consensus MFE -9.96
Energy contribution -9.40
Covariance contribution -0.56
Combinations/Pair 1.33
Mean z-score -1.44
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.93
SVM RNA-class probability 0.855774
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11422873 95 + 24543557
GUGGAAACACAAGGUGAAGGCCAUUGCUUUCACAUUUCUAAAGAAUAUCUUAAUUACCUGCCAAUGC--------------------AAGAAAUUAGUGUGUGAAAGCAUGAAAC
(((....)))..(((....)))..(((((((((((..((((((.....))).....(.(((....))--------------------).)....))).)))))))))))...... ( -26.60, z-score =  -3.19, R)
>droEre2.scaffold_4784 11429425 95 + 25762168
GUGGAAUAACAAGGUGAAGGCCGUUGCUUUCAAAUUCUUAAGGCAUAUUUUAAUUACCUGCUGAU--------------------UAUAUAAAUGACAGUGUAAAAAAAUGAAAU
......(((.((..(((((((....)))))))..)).))).....((((((..((((..((((.(--------------------(((....)))))))))))).)))))).... ( -14.40, z-score =   0.11, R)
>droYak2.chr3L 11462067 115 + 24197627
GUGGAAAAGCAAGGUGAAGGCCGUUGCCUUCAAAAUCUUAAAGCAUAUUUUAAUUACCUGCCAAUAUCUCAUAUAACUACUGUAUUAUACAAAUGAGAGUGUGAGAACAUGAAAU
(((.....(((.(((((((((....))))))......((((((....))))))..)))))).....((((((((..((..((((...))))....)).)))))))).)))..... ( -23.70, z-score =  -1.42, R)
>droSec1.super_0 3631866 73 + 21120651
GUGGAAUCGCAAGGUGAAGGCCGUUGCUUUCACAUUUCUAAAGAAUAUCUUAAUUAGCUGCCAAUCU--------------------AUAAAC----------------------
(((((...(((..((((((((....)))))))).......(((.....))).......)))...)))--------------------))....---------------------- ( -16.30, z-score =  -1.68, R)
>droSim1.chr3L 10817147 73 + 22553184
GUGGAAUCGCAAGGUGAAGGCCGUUGCUUUCAAAUUUCUAAAGAAUAUCUUAAUUAGCUGCCAAUCU--------------------AUAAAC----------------------
((((((((....)))...(((.((((.((......(((....)))......)).)))).)))..)))--------------------))....---------------------- ( -14.30, z-score =  -1.05, R)
>consensus
GUGGAAUCGCAAGGUGAAGGCCGUUGCUUUCAAAUUUCUAAAGAAUAUCUUAAUUACCUGCCAAUCU____________________AAAAAAU_A__GUGU_A_A__AUGAAA_
(((....)))..(((((((((....)))))).........(((.....)))........)))..................................................... ( -9.96 =  -9.40 +  -0.56)

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 23:18:38 2011