Locus 1375

Sequence ID dm3.chr2L
Location 10,698,987 – 10,699,087
Length 100
Max. P 0.561500
window1874 window1875

overview

Window 4

Location 10,698,987 – 10,699,087
Length 100
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 87.60
Shannon entropy 0.21869
G+C content 0.56026
Mean single sequence MFE -34.20
Consensus MFE -26.30
Energy contribution -27.46
Covariance contribution 1.16
Combinations/Pair 1.09
Mean z-score -1.61
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.540556
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10698987 100 + 23011544
CAGGAAAAGCGCAGCUGAGCGUAGCUGAGCUCCACCCAAAUGCAAAUGGCAAGACAAUGUGGGCUAAGAGCCCAAGAAACUAUAGCUGGCGGAAGGUCGG
..(((...((.((((((....)))))).)))))..((...(((.....))).(((....(((((.....)))))...............(....)))))) ( -29.10, z-score =   0.02, R)
>droSim1.chr2L 10497711 100 + 22036055
CAGGAAAAGCGCAGCUGAGCGCAGCUGAGCUCCACCCAAAUGCAAAUGGCAAGACAAUGUGGGCUAAGAGCCCAAGAAAGUGGAGCUGGCGGAAGGUUGG
........((((......)))).(((.((((((((.....(((.....)))........(((((.....))))).....))))))))))).......... ( -36.40, z-score =  -1.64, R)
>droSec1.super_3 6116634 100 + 7220098
CAGGAAAAGAGCAGCUGAGCGCAGUUGAGCUCCACCCAAAUGCAAAUGGCAAGACAAUGUGGGCUAAGAGCCCAAGAAAGUGGAGCUGGCGGAGGGUGGG
.......((..((((((....))))))..))((((((...(((....(((....((...(((((.....)))))......))..))).)))..)))))). ( -34.80, z-score =  -1.81, R)
>droYak2.chr2L 7101869 92 + 22324452
CCGGAAAAGCGCAGCUGAGCAGUGCUGAGCUCCACCCAAAUGCAAAUGGAGAGACAAUGUGGGCUAAGAGCCCCAGAACGUGGAGCUGGCGG--------
(((....(((((.((...)).))))).(((((((((((........)))........((.((((.....))))))....))))))))..)))-------- ( -33.60, z-score =  -1.82, R)
>droEre2.scaffold_4929 11908063 92 - 26641161
CAGGAAAAGCGCAGCUGAGCAGAGCUGAGCUCCACCCAAAUGCAAAUGGCAAGACAAUGUGGGCUAAGAGCCCAAGGAAGUGGAGCUGCCUG--------
((((.......(((((......)))))((((((((((...(((.....)))........(((((.....))))).))..)))))))).))))-------- ( -37.10, z-score =  -2.81, R)
>consensus
CAGGAAAAGCGCAGCUGAGCGCAGCUGAGCUCCACCCAAAUGCAAAUGGCAAGACAAUGUGGGCUAAGAGCCCAAGAAAGUGGAGCUGGCGGA_GGU_GG
...........((((((....))))))(((((((((((........)))..........(((((.....))))).....))))))))............. (-26.30 = -27.46 +   1.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,698,987 – 10,699,087
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 87.60
Shannon entropy 0.21869
G+C content 0.56026
Mean single sequence MFE -30.96
Consensus MFE -25.44
Energy contribution -26.08
Covariance contribution 0.64
Combinations/Pair 1.05
Mean z-score -1.41
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.561500
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10698987 100 - 23011544
CCGACCUUCCGCCAGCUAUAGUUUCUUGGGCUCUUAGCCCACAUUGUCUUGCCAUUUGCAUUUGGGUGGAGCUCAGCUACGCUCAGCUGCGCUUUUCCUG
..........(((((((...((...(((((((((..(((((...(((..........)))..))))))))))))))..))....))))).))........ ( -29.80, z-score =  -0.91, R)
>droSim1.chr2L 10497711 100 - 22036055
CCAACCUUCCGCCAGCUCCACUUUCUUGGGCUCUUAGCCCACAUUGUCUUGCCAUUUGCAUUUGGGUGGAGCUCAGCUGCGCUCAGCUGCGCUUUUCCUG
..........((.((((((((.....(((((.....)))))..........(((........)))))))))))..)).((((......))))........ ( -33.90, z-score =  -2.25, R)
>droSec1.super_3 6116634 100 - 7220098
CCCACCCUCCGCCAGCUCCACUUUCUUGGGCUCUUAGCCCACAUUGUCUUGCCAUUUGCAUUUGGGUGGAGCUCAACUGCGCUCAGCUGCUCUUUUCCUG
..........((.((((((((.....(((((.....)))))..........(((........))))))))))).....))((......)).......... ( -27.20, z-score =  -1.13, R)
>droYak2.chr2L 7101869 92 - 22324452
--------CCGCCAGCUCCACGUUCUGGGGCUCUUAGCCCACAUUGUCUCUCCAUUUGCAUUUGGGUGGAGCUCAGCACUGCUCAGCUGCGCUUUUCCGG
--------(((..((((((((....((((((.....)))).))........(((........)))))))))))((((........))))........))) ( -30.60, z-score =  -1.09, R)
>droEre2.scaffold_4929 11908063 92 + 26641161
--------CAGGCAGCUCCACUUCCUUGGGCUCUUAGCCCACAUUGUCUUGCCAUUUGCAUUUGGGUGGAGCUCAGCUCUGCUCAGCUGCGCUUUUCCUG
--------((((.(((..........(((((.....)))))................(((.(((((..((((...))))..))))).))))))...)))) ( -33.30, z-score =  -1.64, R)
>consensus
CC_ACC_UCCGCCAGCUCCACUUUCUUGGGCUCUUAGCCCACAUUGUCUUGCCAUUUGCAUUUGGGUGGAGCUCAGCUCCGCUCAGCUGCGCUUUUCCUG
.............((((((((......((((.....))))...........(((........)))))))))))(((((......)))))........... (-25.44 = -26.08 +   0.64)

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 21:30:45 2011