Locus 3292

Sequence ID dm3.chr2R
Location 4,147,014 – 4,147,170
Length 156
Max. P 0.747443
window4534 window4535

overview

Window 4

Location 4,147,014 – 4,147,134
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.89
Shannon entropy 0.39272
G+C content 0.56528
Mean single sequence MFE -44.52
Consensus MFE -31.28
Energy contribution -30.93
Covariance contribution -0.35
Combinations/Pair 1.39
Mean z-score -1.35
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.747443
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4147014 120 - 21146708
UAAGAUCACGAGGAGCACCCUGCAUGUACACAGAAUCCAGAUGAUGGAGGGCCAAGAAGCUCUUCACCAGGAUGCGGGGUGGUCGGGUUGAUUGCGCCGGGGUCUUAAUCCUCGCGUCGG
...((.(.((((((.((((((((.((....))..((((...((.((((((((......)))))))).)))))))))))))).((((((.....)).))))........)))))).))).. ( -46.20, z-score =  -1.50, R)
>droSec1.super_1 1793264 120 - 14215200
UAAGAUCACGAGGAGCACCCUGCAUGUACACAGAAUCCAGAUGAUGGAGGGCCAAGAAGCUCUUCACCAGGAUGCGGGGUGGUCGGGUUGACUGCGCCGGGGUCUUAAUCCUCGCGUCGG
...((.(.((((((.((((((((.((....))..((((...((.((((((((......)))))))).)))))))))))))).((((((.....)).))))........)))))).))).. ( -46.20, z-score =  -1.30, R)
>droSim1.chr2R 2813328 120 - 19596830
UAAGAUCACGGGGAGCACCCUGCAUGUACACAGAAUCCAGAUGGUGGAGGGCCAAGAAGCUCUUCACCAGGAUGCGGGGUGGUCGGGUUGACUGCGCCGGGGUCUUAAUCCUCGCGUCGG
...((.(.((((((.((((((((.((....))..((((...(((((((((((......))))))))))))))))))))))).((((((.....)).))))........)))))).))).. ( -51.90, z-score =  -2.36, R)
>droYak2.chr2L 16798658 120 - 22324452
UAAGAUCGCGAGGAGCACCCUGCAUAUAAACAGAAUCCAGAUGAUGGAGGGCCAGGAAGCUCUUCACCAGUAUGCGGGGUGGUCGGGAUGACUGCUCUGGGAUCUUCAUCCUGGCGUCGG
...((.(((...((.((((((((((((.....(....)...((.((((((((......)))))))).)))))))))))))).))(((((((...(.....)....))))))).))))).. ( -47.10, z-score =  -1.85, R)
>droEre2.scaffold_4929 8155379 120 + 26641161
UAAGAUCACGAGGAGCACCCUGCAUAUAAACAGAGUCCAGAUGAUGGAGGGCCAAGAAGCUCUUCACCAGAAUACGGGGUGGUCGGGCUGACUGCGCUGGGGUCUUAAUCCUUGCGUCGG
...((.(.((((((((.....))........(((.(((((.((.((((((((......)))))))).)).........(..(((.....)))..).))))).)))...)))))).))).. ( -39.00, z-score =  -0.21, R)
>droAna3.scaffold_13266 18041571 120 + 19884421
UAAACUCGAUCGACACCUCUCGCAUAUACGACGAGUUAAUUUGAUUCAAGGCCUUGAAGCUUCUGAUUAGCAGCCGUGGCGGCUUCGUUGUCUCUGCCCGGGAGAAGGUCCUCCGAUCCG
.......(((((..((((((((((.(.((((((((((((((.(((((((....)))))...)).)))))))(((((...)))))))))))).).)))....))).))))....))))).. ( -36.70, z-score =  -0.88, R)
>consensus
UAAGAUCACGAGGAGCACCCUGCAUAUACACAGAAUCCAGAUGAUGGAGGGCCAAGAAGCUCUUCACCAGGAUGCGGGGUGGUCGGGUUGACUGCGCCGGGGUCUUAAUCCUCGCGUCGG
............((.((((((((((.........(((.....)))(((((((......)))))))......)))))))))).)).....(((.(((..(((((....))))))))))).. (-31.28 = -30.93 +  -0.35)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,147,054 – 4,147,170
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.69
Shannon entropy 0.40224
G+C content 0.47318
Mean single sequence MFE -33.35
Consensus MFE -22.77
Energy contribution -22.70
Covariance contribution -0.07
Combinations/Pair 1.39
Mean z-score -1.28
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.679738
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4147054 116 - 21146708
----UUCUCUCGUUUUUCCAGCUUGACAUAAAAUAGUCUCUAAGAUCACGAGGAGCACCCUGCAUGUACACAGAAUCCAGAUGAUGGAGGGCCAAGAAGCUCUUCACCAGGAUGCGGGGU
----(((.(((((..((..((...(((........))).))..))..)))))))).(((((((.((....))..((((...((.((((((((......)))))))).))))))))))))) ( -35.30, z-score =  -1.23, R)
>droSec1.super_1 1793304 116 - 14215200
----UUUUCUCGUUCUUCCAGCUCGACAUAAAAUAGUCUCUAAGAUCACGAGGAGCACCCUGCAUGUACACAGAAUCCAGAUGAUGGAGGGCCAAGAAGCUCUUCACCAGGAUGCGGGGU
----.((((((((((((..((...(((........))).))))))..)))))))).(((((((.((....))..((((...((.((((((((......)))))))).))))))))))))) ( -36.20, z-score =  -1.52, R)
>droSim1.chr2R 2813368 116 - 19596830
----UUUUCUCGUUCUUCCAGCUCGACAUAAAAUAGUCUCUAAGAUCACGGGGAGCACCCUGCAUGUACACAGAAUCCAGAUGGUGGAGGGCCAAGAAGCUCUUCACCAGGAUGCGGGGU
----.((((((((((((..((...(((........))).))))))..)))))))).(((((((.((....))..((((...(((((((((((......)))))))))))))))))))))) ( -41.90, z-score =  -2.59, R)
>droYak2.chr2L 16798698 116 - 22324452
----UUUUUGCGUUUUUCCAGCUUGACAUAAAAAAGUCUCUAAGAUCGCGAGGAGCACCCUGCAUAUAAACAGAAUCCAGAUGAUGGAGGGCCAGGAAGCUCUUCACCAGUAUGCGGGGU
----((((((((.((((..(((((.........))).))..)))).))))))))..(((((((((((.....(....)...((.((((((((......)))))))).))))))))))))) ( -36.50, z-score =  -1.96, R)
>droEre2.scaffold_4929 8155419 116 + 26641161
----UCUUCGCGUUCUUCCAGUUUGACAUAAAAAAGUCCCUAAGAUCACGAGGAGCACCCUGCAUAUAAACAGAGUCCAGAUGAUGGAGGGCCAAGAAGCUCUUCACCAGAAUACGGGGU
----((((((.(.((((..((...(((........))).)))))).).))))))..((((((..........(....)...((.((((((((......)))))))).)).....)))))) ( -28.50, z-score =  -0.26, R)
>droAna3.scaffold_13266 18041611 120 + 19884421
UGAAUUUACAACCACUUCCAUUUCGAUAAGAAUUGAUCACUAAACUCGAUCGACACCUCUCGCAUAUACGACGAGUUAAUUUGAUUCAAGGCCUUGAAGCUUCUGAUUAGCAGCCGUGGC
...........((((......(((((...(..(((((((...((((((.(((................)))))))))....))).))))..).)))))(((.......)))....)))). ( -21.69, z-score =  -0.15, R)
>consensus
____UUUUCUCGUUCUUCCAGCUCGACAUAAAAUAGUCUCUAAGAUCACGAGGAGCACCCUGCAUAUACACAGAAUCCAGAUGAUGGAGGGCCAAGAAGCUCUUCACCAGGAUGCGGGGU
...........(((((((...((.(((........)))....)).....)))))))(((((((((.........(((.....)))(((((((......)))))))......))))))))) (-22.77 = -22.70 +  -0.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:07:32 2011