Locus 11402

Sequence ID dm3.chr3R
Location 20,870,545 – 20,870,619
Length 74
Max. P 0.950747
window15670 window15671

overview

Window 0

Location 20,870,545 – 20,870,619
Length 74
Sequences 6
Columns 77
Reading direction forward
Mean pairwise identity 85.33
Shannon entropy 0.27691
G+C content 0.39421
Mean single sequence MFE -19.35
Consensus MFE -13.06
Energy contribution -14.15
Covariance contribution 1.09
Combinations/Pair 1.12
Mean z-score -1.78
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.594347
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20870545 74 + 27905053
AACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAUAUGCG-AUUU--ACGCAUCGUGUA
..(((((.....(((((((((....))))))))).)))))....(((((....(((((-....--.))))).))))) ( -19.20, z-score =  -1.65, R)
>droAna3.scaffold_13340 6229584 69 - 23697760
------AGCCCAUAGAUACAUAUUUAUCUAUGUUAGCGGGCCC-CACAUAAAUAUGCGUAUUUGUACGCAUCGAGU-
------.(((((((((((......)))))))(....)))))..-.........(((((((....))))))).....- ( -18.60, z-score =  -2.47, R)
>droSec1.super_33 132284 74 + 478481
AACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAUAUGCG-AUUU--ACGCAUCGUGUA
..(((((.....(((((((((....))))))))).)))))....(((((....(((((-....--.))))).))))) ( -19.20, z-score =  -1.65, R)
>droSim1.chr3R 20697922 74 + 27517382
AACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAUAUGCG-AUUU--ACGCAUCGUGUA
..(((((.....(((((((((....))))))))).)))))....(((((....(((((-....--.))))).))))) ( -19.20, z-score =  -1.65, R)
>droEre2.scaffold_4820 3287885 74 - 10470090
GACUCGGAUUCGGAUACACAUAUCAAUGUAUGUCAGUGAGUCCAUACAUAAAUAUGCG-AUUU--ACGCAUCGUGUA
.....((((((.((((.((((....)))).))))...)))))).(((((....(((((-....--.))))).))))) ( -20.50, z-score =  -1.83, R)
>droYak2.chr3R 3204938 74 - 28832112
AGCUCGGAUUCGGUUAUACAUAUCUAUGUAUGUCAGUGGGUCCAUACAUAAAUAUGCG-AUUU--ACGCAUCGUGUA
.....(((((((.((((((((....)))))))..).))))))).(((((....(((((-....--.))))).))))) ( -19.40, z-score =  -1.44, R)
>consensus
AACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAUAUGCG_AUUU__ACGCAUCGUGUA
.....((.(((.(((((((((....)))))))))...))).)).(((((....(((((........))))).))))) (-13.06 = -14.15 +   1.09)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,870,545 – 20,870,619
Length 74
Sequences 6
Columns 77
Reading direction reverse
Mean pairwise identity 85.33
Shannon entropy 0.27691
G+C content 0.39421
Mean single sequence MFE -19.05
Consensus MFE -15.74
Energy contribution -15.97
Covariance contribution 0.22
Combinations/Pair 1.13
Mean z-score -1.98
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.56
SVM RNA-class probability 0.950747
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20870545 74 - 27905053
UACACGAUGCGU--AAAU-CGCAUAUUUAUGUAUGGGCCCAGUGACAUACAUAGAUAUGUAUAUCCGAAUCCGAGUU
.....(((.((.--....-.(((((((((((((((..........))))))))))))))).....)).)))...... ( -19.20, z-score =  -1.81, R)
>droAna3.scaffold_13340 6229584 69 + 23697760
-ACUCGAUGCGUACAAAUACGCAUAUUUAUGUG-GGGCCCGCUAACAUAGAUAAAUAUGUAUCUAUGGGCU------
-.....(((((((....))))))).........-.(((((......(((((((......))))))))))))------ ( -18.90, z-score =  -1.79, R)
>droSec1.super_33 132284 74 - 478481
UACACGAUGCGU--AAAU-CGCAUAUUUAUGUAUGGGCCCAGUGACAUACAUAGAUAUGUAUAUCCGAAUCCGAGUU
.....(((.((.--....-.(((((((((((((((..........))))))))))))))).....)).)))...... ( -19.20, z-score =  -1.81, R)
>droSim1.chr3R 20697922 74 - 27517382
UACACGAUGCGU--AAAU-CGCAUAUUUAUGUAUGGGCCCAGUGACAUACAUAGAUAUGUAUAUCCGAAUCCGAGUU
.....(((.((.--....-.(((((((((((((((..........))))))))))))))).....)).)))...... ( -19.20, z-score =  -1.81, R)
>droEre2.scaffold_4820 3287885 74 + 10470090
UACACGAUGCGU--AAAU-CGCAUAUUUAUGUAUGGACUCACUGACAUACAUUGAUAUGUGUAUCCGAAUCCGAGUC
.....(((.((.--....-((((((((.(((((((..........))))))).))))))))....)).)))...... ( -18.60, z-score =  -1.37, R)
>droYak2.chr3R 3204938 74 + 28832112
UACACGAUGCGU--AAAU-CGCAUAUUUAUGUAUGGACCCACUGACAUACAUAGAUAUGUAUAACCGAAUCCGAGCU
.....(((.((.--....-.(((((((((((((((..........))))))))))))))).....)).)))...... ( -19.20, z-score =  -3.32, R)
>consensus
UACACGAUGCGU__AAAU_CGCAUAUUUAUGUAUGGGCCCACUGACAUACAUAGAUAUGUAUAUCCGAAUCCGAGUU
....................(((((((((((((((..........)))))))))))))))................. (-15.74 = -15.97 +   0.22)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:42:15 2011