Locus 4687

Sequence ID dm3.chr2R
Location 15,049,336 – 15,049,393
Length 57
Max. P 0.825915
window6436 window6437

overview

Window 6

Location 15,049,336 – 15,049,393
Length 57
Sequences 6
Columns 59
Reading direction forward
Mean pairwise identity 88.90
Shannon entropy 0.21203
G+C content 0.49117
Mean single sequence MFE -19.48
Consensus MFE -12.85
Energy contribution -13.27
Covariance contribution 0.42
Combinations/Pair 1.10
Mean z-score -2.21
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.644457
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15049336 57 + 21146708
UUCGAUG--AUCGAAGCUCGCAACAUUGCCAGAAUGUUGACGAUCGAUCGACGAGGUGA
((((.((--(((((...((((((((((.....))))))).)))))))))).)))).... ( -21.30, z-score =  -2.71, R)
>droAna3.scaffold_13266 8375625 55 - 19884421
UUCGGAGGUAUCGAAGCUCGCAACAUUUCUAGAAUGUUGACGUUCGAUGUGGGCG----
(((((.....)))))(((((((.........(((((....)))))..))))))).---- ( -13.80, z-score =  -0.56, R)
>droEre2.scaffold_4845 9249348 57 + 22589142
UUCGAUG--AUCGAAGCUCGCAACAUUGCCAGAAUGUUGACGAUCGAUCGACGAAGCGA
((((.((--(((((...((((((((((.....))))))).)))))))))).)))).... ( -21.60, z-score =  -3.00, R)
>droYak2.chr2R 7008836 57 - 21139217
UUCAAUG--AUCGAAGCUCGCAACAUUGCCAGAAUGUUGACGAUCGAUCGACGAGGCGA
(((..((--(((((...((((((((((.....))))))).))))))))))..))).... ( -17.60, z-score =  -1.56, R)
>droSec1.super_1 12562322 57 + 14215200
UUCGAUG--AUCGAAGCUCGCAACAUUGCCAGAAUGUUGACGAUCGAUCGACGAGGUGA
((((.((--(((((...((((((((((.....))))))).)))))))))).)))).... ( -21.30, z-score =  -2.71, R)
>droSim1.chr2R 13753842 57 + 19596830
UUCGAUG--AUCGAAGCUCGCAACAUUGCCAGAAUGUUGACGAUCGAUCGACGAGGUGA
((((.((--(((((...((((((((((.....))))))).)))))))))).)))).... ( -21.30, z-score =  -2.71, R)
>consensus
UUCGAUG__AUCGAAGCUCGCAACAUUGCCAGAAUGUUGACGAUCGAUCGACGAGGUGA
((((.((..(((((...((((((((((.....))))))).)))))))))).)))).... (-12.85 = -13.27 +   0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 15,049,336 – 15,049,393
Length 57
Sequences 6
Columns 59
Reading direction reverse
Mean pairwise identity 88.90
Shannon entropy 0.21203
G+C content 0.49117
Mean single sequence MFE -18.20
Consensus MFE -12.53
Energy contribution -12.92
Covariance contribution 0.39
Combinations/Pair 1.06
Mean z-score -2.35
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.82
SVM RNA-class probability 0.825915
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15049336 57 - 21146708
UCACCUCGUCGAUCGAUCGUCAACAUUCUGGCAAUGUUGCGAGCUUCGAU--CAUCGAA
.....(((..(((((((((.(((((((.....))))))))))...)))))--)..))). ( -19.90, z-score =  -2.80, R)
>droAna3.scaffold_13266 8375625 55 + 19884421
----CGCCCACAUCGAACGUCAACAUUCUAGAAAUGUUGCGAGCUUCGAUACCUCCGAA
----.......((((((((.(((((((.....)))))))))...))))))......... ( -11.90, z-score =  -1.90, R)
>droEre2.scaffold_4845 9249348 57 - 22589142
UCGCUUCGUCGAUCGAUCGUCAACAUUCUGGCAAUGUUGCGAGCUUCGAU--CAUCGAA
.....(((..(((((((((.(((((((.....))))))))))...)))))--)..))). ( -20.00, z-score =  -2.25, R)
>droYak2.chr2R 7008836 57 + 21139217
UCGCCUCGUCGAUCGAUCGUCAACAUUCUGGCAAUGUUGCGAGCUUCGAU--CAUUGAA
.....(((..(((((((((.(((((((.....))))))))))...)))))--)..))). ( -17.60, z-score =  -1.53, R)
>droSec1.super_1 12562322 57 - 14215200
UCACCUCGUCGAUCGAUCGUCAACAUUCUGGCAAUGUUGCGAGCUUCGAU--CAUCGAA
.....(((..(((((((((.(((((((.....))))))))))...)))))--)..))). ( -19.90, z-score =  -2.80, R)
>droSim1.chr2R 13753842 57 - 19596830
UCACCUCGUCGAUCGAUCGUCAACAUUCUGGCAAUGUUGCGAGCUUCGAU--CAUCGAA
.....(((..(((((((((.(((((((.....))))))))))...)))))--)..))). ( -19.90, z-score =  -2.80, R)
>consensus
UCACCUCGUCGAUCGAUCGUCAACAUUCUGGCAAUGUUGCGAGCUUCGAU__CAUCGAA
.....(((...((((((((.(((((((.....))))))))))...))))).....))). (-12.53 = -12.92 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:34:05 2011