Locus 2505

Sequence ID dm3.chr2L
Location 19,573,774 – 19,573,864
Length 90
Max. P 0.999352
window3449 window3450

overview

Window 9

Location 19,573,774 – 19,573,864
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 73.67
Shannon entropy 0.48806
G+C content 0.38440
Mean single sequence MFE -23.00
Consensus MFE -14.48
Energy contribution -16.16
Covariance contribution 1.68
Combinations/Pair 1.19
Mean z-score -3.14
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.81
SVM RNA-class probability 0.999352
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19573774 90 + 23011544
AUGCCAACGUCGAUGUCGUCGAUUUUUUCAAAAAAUCACAAACAUCGAUGUUUUUCGAGGAAUCAUCGAUGUUUCUCCACCUCUAAUAAG
.....(((((((((((.((.((((((.....))))))))..)))))))))))....(((((((.......)))))))............. ( -21.50, z-score =  -2.68, R)
>droAna3.scaffold_12911 2449433 89 + 5364042
AUGUUAACAUCGAUGUCAUCGAUGUUUUGAAAACAUCGUUGACAUCGAUGUUUGGCAAGCCAACAUCGAUGUUUAUC-AUCUCUAACGAG
(((..(((((((((((((.(((((((.....))))))).)))))))((((((.((....))))))))))))))...)-))(((....))) ( -37.90, z-score =  -6.63, R)
>droSec1.super_7 3188050 90 + 3727775
AUCGCAACAUCGAUGUCAUCGAUGUUUUCGGAAAAUCACAAACAUCGAUGUUUUUUGAGGAAUCAUCGAUCUUUCUCCGCCUCUAAUGUG
..((((...((((...(((((((((((...(.....)..)))))))))))....))))(((..............)))........)))) ( -19.24, z-score =  -0.51, R)
>droSim1.chr2L 19261859 90 + 22036055
AUAGCAACAUCGAUGUCAUCGAUGUUUUCGCAAAAUCACAAACAUCGAUGUUUUUUGAGGAAUCAUCGAUCUUUCUCCGCCUCUAAUGUG
...(((((((((((((....(((...........)))....)))))))))))....((((((.........)))))).)).......... ( -18.80, z-score =  -1.12, R)
>droWil1.scaffold_181130 7972083 75 - 16660200
-----AACAUCGAUGUUUUG-----CUUAAAAACAUCUAAAACAUCGAUAGC-----AGCAAACAUCGAUGUUUCUCCACCUCUAACCGA
-----(((((((((((((((-----((......................)))-----)..)))))))))))))................. ( -17.55, z-score =  -4.78, R)
>consensus
AUGGCAACAUCGAUGUCAUCGAUGUUUUCAAAAAAUCACAAACAUCGAUGUUUUUCGAGGAAUCAUCGAUGUUUCUCCACCUCUAAUGAG
.....((((((((((.(((((((((((............))))))))))).............))))))))))................. (-14.48 = -16.16 +   1.68)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,573,774 – 19,573,864
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 73.67
Shannon entropy 0.48806
G+C content 0.38440
Mean single sequence MFE -25.08
Consensus MFE -14.20
Energy contribution -14.68
Covariance contribution 0.48
Combinations/Pair 1.33
Mean z-score -2.42
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.59
SVM RNA-class probability 0.993133
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19573774 90 - 23011544
CUUAUUAGAGGUGGAGAAACAUCGAUGAUUCCUCGAAAAACAUCGAUGUUUGUGAUUUUUUGAAAAAAUCGACGACAUCGACGUUGGCAU
...((((..((((......))))..)))).....(...(((.((((((((..(((((((.....)))))))..)))))))).)))..).. ( -22.30, z-score =  -1.10, R)
>droAna3.scaffold_12911 2449433 89 - 5364042
CUCGUUAGAGAU-GAUAAACAUCGAUGUUGGCUUGCCAAACAUCGAUGUCAACGAUGUUUUCAAAACAUCGAUGACAUCGAUGUUAACAU
(((....)))..-....((((((((((((((....)).))))))(((((((.(((((((.....))))))).)))))))))))))..... ( -36.90, z-score =  -6.26, R)
>droSec1.super_7 3188050 90 - 3727775
CACAUUAGAGGCGGAGAAAGAUCGAUGAUUCCUCAAAAAACAUCGAUGUUUGUGAUUUUCCGAAAACAUCGAUGACAUCGAUGUUGCGAU
.(((((.((((((..((....))..))...))))......(((((((((((.((......)).))))))))))).....)))))...... ( -22.70, z-score =  -0.96, R)
>droSim1.chr2L 19261859 90 - 22036055
CACAUUAGAGGCGGAGAAAGAUCGAUGAUUCCUCAAAAAACAUCGAUGUUUGUGAUUUUGCGAAAACAUCGAUGACAUCGAUGUUGCUAU
.......((((((..((....))..))...))))....((((((((((((..((((.((.....)).))))..))))))))))))..... ( -23.30, z-score =  -1.54, R)
>droWil1.scaffold_181130 7972083 75 + 16660200
UCGGUUAGAGGUGGAGAAACAUCGAUGUUUGCU-----GCUAUCGAUGUUUUAGAUGUUUUUAAG-----CAAAACAUCGAUGUU-----
...............(((((((((((((.....-----)).))))))))))).((((((((....-----.))))))))......----- ( -20.20, z-score =  -2.23, R)
>consensus
CACAUUAGAGGUGGAGAAACAUCGAUGAUUCCUCAAAAAACAUCGAUGUUUGUGAUUUUUUGAAAACAUCGAUGACAUCGAUGUUGCCAU
......................................((((((((((((..((((.((.....)).))))..))))))))))))..... (-14.20 = -14.68 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:52:33 2011