Locus 5054

Sequence ID dm3.chr2R
Location 17,376,282 – 17,376,352
Length 70
Max. P 0.916497
window6938 window6939

overview

Window 8

Location 17,376,282 – 17,376,352
Length 70
Sequences 5
Columns 72
Reading direction forward
Mean pairwise identity 92.98
Shannon entropy 0.11756
G+C content 0.38261
Mean single sequence MFE -19.60
Consensus MFE -15.54
Energy contribution -15.66
Covariance contribution 0.12
Combinations/Pair 1.16
Mean z-score -2.57
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.25
SVM RNA-class probability 0.916497
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17376282 70 + 21146708
AAAUGGAGCCAUAAACACGCUGUAAAAUGGCGUUUAUAGGCCAACAU--GAGCUUAUGGGCUUUAAUUCAGU
...(((((((......(((((((...))))))).((((((((.....--).))))))))))))))....... ( -19.90, z-score =  -2.14, R)
>droSim1.chr2R 16035901 72 + 19596830
CAAUAGAGCCAUAAACACGCUGUAAACUGGCGUUUAUAGGCCAACAUAUGAGCUUAUAGGCUUUAAUUCAGU
...(((((((......(((((.......))))).(((((((((.....)).))))))))))))))....... ( -21.30, z-score =  -3.29, R)
>droSec1.super_9 706103 72 + 3197100
CAAUAGAGCCAUAAACACGCUGUAAAAUGGCGUUUAUAGGCCAACAUAUGAGCUUAUGGGCUUUAAUUCAGU
...(((((((......(((((((...))))))).(((((((((.....)).))))))))))))))....... ( -20.90, z-score =  -2.87, R)
>droYak2.chr2R 9335346 68 - 21139217
AAAUAGAGCCAUAAACACGUUGUAAAAUGGCGUUUAUAGGCCAACAU--G--CUUAUGGGCUUUAAUUCAGU
...(((((((......((((..(...)..)))).(((((((......--)--)))))))))))))....... ( -18.40, z-score =  -2.35, R)
>droEre2.scaffold_4845 11521073 68 + 22589142
AAAUAGAGCCAUAAACACGCUGUAAAAUGGCGUUUAUAGGCCAACAU--G--CUUAUGAGCUUUAAUUCAGU
.....(((((((..((.....))...)))))((((((((((......--)--)))))))))......))... ( -17.50, z-score =  -2.20, R)
>consensus
AAAUAGAGCCAUAAACACGCUGUAAAAUGGCGUUUAUAGGCCAACAU__GAGCUUAUGGGCUUUAAUUCAGU
...(((((((......(((((.......))))).(((((((..........))))))))))))))....... (-15.54 = -15.66 +   0.12)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 17,376,282 – 17,376,352
Length 70
Sequences 5
Columns 72
Reading direction reverse
Mean pairwise identity 92.98
Shannon entropy 0.11756
G+C content 0.38261
Mean single sequence MFE -17.16
Consensus MFE -13.12
Energy contribution -13.36
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -2.05
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.533681
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17376282 70 - 21146708
ACUGAAUUAAAGCCCAUAAGCUC--AUGUUGGCCUAUAAACGCCAUUUUACAGCGUGUUUAUGGCUCCAUUU
..........((((.((((((.(--.(((((((........))))....)))..).))))))))))...... ( -16.10, z-score =  -1.64, R)
>droSim1.chr2R 16035901 72 - 19596830
ACUGAAUUAAAGCCUAUAAGCUCAUAUGUUGGCCUAUAAACGCCAGUUUACAGCGUGUUUAUGGCUCUAUUG
..........((((.((((((.(...(((((((........))))....)))..).))))))))))...... ( -15.60, z-score =  -0.89, R)
>droSec1.super_9 706103 72 - 3197100
ACUGAAUUAAAGCCCAUAAGCUCAUAUGUUGGCCUAUAAACGCCAUUUUACAGCGUGUUUAUGGCUCUAUUG
..........((((.((((((.(...(((((((........))))....)))..).))))))))))...... ( -15.60, z-score =  -1.34, R)
>droYak2.chr2R 9335346 68 + 21139217
ACUGAAUUAAAGCCCAUAAG--C--AUGUUGGCCUAUAAACGCCAUUUUACAACGUGUUUAUGGCUCUAUUU
...((((...((((.(((((--(--((((((((........)))).......))))))))))))))..)))) ( -19.11, z-score =  -3.41, R)
>droEre2.scaffold_4845 11521073 68 - 22589142
ACUGAAUUAAAGCUCAUAAG--C--AUGUUGGCCUAUAAACGCCAUUUUACAGCGUGUUUAUGGCUCUAUUU
...((((...(((.((((((--(--((((((((........)))).......))))))))))))))..)))) ( -19.41, z-score =  -2.98, R)
>consensus
ACUGAAUUAAAGCCCAUAAGCUC__AUGUUGGCCUAUAAACGCCAUUUUACAGCGUGUUUAUGGCUCUAUUU
..........((((.((((((.(...(((((((........))))....)))..).))))))))))...... (-13.12 = -13.36 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:41:00 2011