Locus 8282

Sequence ID dm3.chr3L
Location 21,656,196 – 21,656,283
Length 87
Max. P 0.967656
window11382 window11383

overview

Window 2

Location 21,656,196 – 21,656,283
Length 87
Sequences 7
Columns 93
Reading direction forward
Mean pairwise identity 73.07
Shannon entropy 0.53662
G+C content 0.67294
Mean single sequence MFE -39.40
Consensus MFE -17.58
Energy contribution -19.07
Covariance contribution 1.49
Combinations/Pair 1.30
Mean z-score -2.21
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.79
SVM RNA-class probability 0.967656
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21656196 87 + 24543557
CUGGAGCACACGGAACUUCUCGCCGCCUCCGGCUGCCAUGCUGGCCAGGCGCAAUCAGCUGCUCCAGG---CGGAGGAACCUCCUCCGCG---
(((((((((...((.....))((.(((((((((......)))))..)))))).....).))))))))(---((((((.....))))))).--- ( -44.90, z-score =  -3.63, R)
>droAna3.scaffold_13337 3980390 93 + 23293914
CUGGAGCAUACGGAGCUGCUAGCCGCCUCCGGUUGUGGCUCCGGACAGGCUCCUCCUACAGCACCACAGACUGCCGGAGCAGGAGCAGCACCC
..((.((...((((((..(.(((((....))))))..)))))).....((((((.((.(.(((........))).).)).)))))).)).)). ( -41.00, z-score =  -1.54, R)
>droWil1.scaffold_180698 10321159 84 - 11422946
CUGGAGCACACGGAAAUUAUGGCCACCCAGAGUACAACUCCGGGUCAGGCUCCU---GCCUC-CCAUGGGCCAGCCAAUUCCCAUUCG-----
...........((((....(((((((((.(((.....))).)))).((((....---)))).-.....))))).....))))......----- ( -27.90, z-score =  -1.34, R)
>droSec1.super_11 1576113 87 + 2888827
CUGGAGCACACGGAACUUCUCGCCGCCUCGGGAUGCCAUGCUGGCCAGGCGCAAUCAGCUGCCCCAGG---CGGAGGAACUUCCUCCGCG---
((((((((...((....(((((......)))))..)).))))(((..(((.......))))))))))(---((((((.....))))))).--- ( -36.40, z-score =  -1.01, R)
>droSim1.chr3L 20999155 87 + 22553184
CUGGAGCACACGGAACUUCUCGCCGCCUCGGGCUGCCAUGGUGGCCAGGCGCAAUCAGCUGCCCCAGG---CGGAGGAACUUCCUCCGCG---
((((.((((...((.....))((.((((..(((..(....)..))))))))).....).))).))))(---((((((.....))))))).--- ( -41.70, z-score =  -2.03, R)
>droEre2.scaffold_4784 21312719 87 + 25762168
CUGGAGCACACGGAACUUCUCGCCGCCUCGGGCUGCCAUUCCGGCCAGGCCCAAUCCGCUGCCCCAGG---CGGAGGAACCUCCUCCGCG---
((((.(((..((((.......(......)((((((((.....)))..)))))..)))).))).))))(---((((((.....))))))).--- ( -40.70, z-score =  -2.53, R)
>droYak2.chr3L 5341880 84 - 24197627
CUGGAGCACACGGAACUUCUCGCCGCCUCGGGCUGCCAUUCUGGGCAGGCUCAA---GCUGCUCCAGG---CGGAGGAACCUCCUCCGCG---
(((((((((.(((.........)))....((((((((......)))).))))..---).))))))))(---((((((.....))))))).--- ( -43.20, z-score =  -3.37, R)
>consensus
CUGGAGCACACGGAACUUCUCGCCGCCUCGGGCUGCCAUGCUGGCCAGGCGCAAUCAGCUGCCCCAGG___CGGAGGAACCUCCUCCGCG___
((((.((....((.........))((((..(((((......)))))))))..........)).))))....((((((.....))))))..... (-17.58 = -19.07 +   1.49)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 21,656,196 – 21,656,283
Length 87
Sequences 7
Columns 93
Reading direction reverse
Mean pairwise identity 73.07
Shannon entropy 0.53662
G+C content 0.67294
Mean single sequence MFE -42.97
Consensus MFE -19.10
Energy contribution -20.17
Covariance contribution 1.07
Combinations/Pair 1.38
Mean z-score -1.97
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.24
SVM RNA-class probability 0.914406
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21656196 87 - 24543557
---CGCGGAGGAGGUUCCUCCG---CCUGGAGCAGCUGAUUGCGCCUGGCCAGCAUGGCAGCCGGAGGCGGCGAGAAGUUCCGUGUGCUCCAG
---.(((((((.....))))))---)((((((((((.((...((((..(((.....))).(((...)))))))......)).)).)))))))) ( -44.30, z-score =  -1.93, R)
>droAna3.scaffold_13337 3980390 93 - 23293914
GGGUGCUGCUCCUGCUCCGGCAGUCUGUGGUGCUGUAGGAGGAGCCUGUCCGGAGCCACAACCGGAGGCGGCUAGCAGCUCCGUAUGCUCCAG
.((.(((((((((.((.(((((.(....).))))).)).)))(((((.(((((........))))).).)))))))))).))........... ( -41.00, z-score =  -0.13, R)
>droWil1.scaffold_180698 10321159 84 + 11422946
-----CGAAUGGGAAUUGGCUGGCCCAUGG-GAGGC---AGGAGCCUGACCCGGAGUUGUACUCUGGGUGGCCAUAAUUUCCGUGUGCUCCAG
-----...((((((((((..(((((.....-.((((---....)))).((((((((.....)))))))))))))))))))))))......... ( -36.80, z-score =  -2.16, R)
>droSec1.super_11 1576113 87 - 2888827
---CGCGGAGGAAGUUCCUCCG---CCUGGGGCAGCUGAUUGCGCCUGGCCAGCAUGGCAUCCCGAGGCGGCGAGAAGUUCCGUGUGCUCCAG
---.(((((((.....))))))---)(((((((((((..((((((((.(((.....)))......)))).))))..)))......)))))))) ( -42.20, z-score =  -1.67, R)
>droSim1.chr3L 20999155 87 - 22553184
---CGCGGAGGAAGUUCCUCCG---CCUGGGGCAGCUGAUUGCGCCUGGCCACCAUGGCAGCCCGAGGCGGCGAGAAGUUCCGUGUGCUCCAG
---.(((.(((((.((((.(((---(((.((((.((.....))((((((...))).))).)))).)))))).).))).)))).).)))..... ( -46.00, z-score =  -2.67, R)
>droEre2.scaffold_4784 21312719 87 - 25762168
---CGCGGAGGAGGUUCCUCCG---CCUGGGGCAGCGGAUUGGGCCUGGCCGGAAUGGCAGCCCGAGGCGGCGAGAAGUUCCGUGUGCUCCAG
---.(((((((.....))))))---)(((((((((((((((((((...(((.....))).))))))....((.....))))))).)))))))) ( -47.50, z-score =  -2.29, R)
>droYak2.chr3L 5341880 84 + 24197627
---CGCGGAGGAGGUUCCUCCG---CCUGGAGCAGC---UUGAGCCUGCCCAGAAUGGCAGCCCGAGGCGGCGAGAAGUUCCGUGUGCUCCAG
---.(((((((.....))))))---)((((((((.(---(((.((.((((......)))))).))))((((.........)))).)))))))) ( -43.00, z-score =  -2.92, R)
>consensus
___CGCGGAGGAGGUUCCUCCG___CCUGGGGCAGCUGAUUGAGCCUGGCCAGAAUGGCAGCCCGAGGCGGCGAGAAGUUCCGUGUGCUCCAG
.....((((((.....))))))....((((((((.........((((..................)))).(((........))).)))))))) (-19.10 = -20.17 +   1.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:42:45 2011