Locus 8481

Sequence ID dm3.chr3L
Location 23,372,361 – 23,372,425
Length 64
Max. P 0.999519
window11647 window11648

overview

Window 7

Location 23,372,361 – 23,372,425
Length 64
Sequences 6
Columns 66
Reading direction forward
Mean pairwise identity 60.22
Shannon entropy 0.74286
G+C content 0.50599
Mean single sequence MFE -15.15
Consensus MFE -7.60
Energy contribution -7.38
Covariance contribution -0.22
Combinations/Pair 1.29
Mean z-score -0.94
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.51
SVM RNA-class probability 0.945651
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23372361 64 + 24543557
UGAACA-AGGCUCACUAAUCUGCGGGACGCAGAUCUUGAGG-GGGGAGGAGUUAAGAACCCUCUUC
......-...((((...(((((((...)))))))..)))).-(((((((.((.....))))))))) ( -20.50, z-score =  -1.32, R)
>droSim1.chr3L 2988948 54 - 22553184
CUUACCUAGGCUACUUAGUCUGCGGGGCGCAGAUCAUAAAG-GGGCAGGAGUUAA-----------
....(((..((..(((.(((((((...)))))))....)))-..)))))......----------- ( -15.10, z-score =  -0.84, R)
>droYak2.chr3h_random 334991 60 - 911842
-CGCCUAAGGCUUUCUGAUCUGUGGGACACAGAUCUUGUGAUGGGGAGGAGUUAACGACUU-----
-..((((..((.....((((((((...))))))))..))..))))(((..(....)..)))----- ( -16.00, z-score =  -0.80, R)
>droAna3.scaffold_13099 1688301 56 - 3324263
---CAUUCUGCCAAUUUAUCUGCGAGACGCAGAAUUUAAGAGGGGGAGGUUUUAUCACC-------
---..((((.((..((..((((((...))))))....))..)).))))...........------- ( -13.10, z-score =  -1.38, R)
>droWil1.scaffold_181148 2074492 53 - 5435427
------UGUACACCCUAAUCUGCGCGACGCAGAUCCUCGGAGUGGGAGGAGUUAACACC-------
------(((.........((((((...))))))(((((.......)))))....)))..------- ( -13.80, z-score =  -0.35, R)
>droMoj3.scaffold_6498 3059478 57 + 3408170
UGGACAUAUGCACCCUGAUCUGCGGGACGCAGAUAUUUAGAUGGGGAAGAGUUAAGA---------
............((((.(((((((...)))))))........))))...........--------- ( -12.40, z-score =  -0.95, R)
>consensus
___ACAUAGGCUCCCUAAUCUGCGGGACGCAGAUCUUAAGA_GGGGAGGAGUUAACA_C_______
.................(((((((...)))))))................................ ( -7.60 =  -7.38 +  -0.22)

alignment

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secondary structure

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dotplot

Postscript

Window 8

Location 23,372,361 – 23,372,425
Length 64
Sequences 6
Columns 66
Reading direction reverse
Mean pairwise identity 60.22
Shannon entropy 0.74286
G+C content 0.50599
Mean single sequence MFE -14.29
Consensus MFE -8.11
Energy contribution -8.42
Covariance contribution 0.31
Combinations/Pair 1.25
Mean z-score -2.09
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.97
SVM RNA-class probability 0.999519
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 23372361 64 - 24543557
GAAGAGGGUUCUUAACUCCUCCCC-CCUCAAGAUCUGCGUCCCGCAGAUUAGUGAGCCU-UGUUCA
(((.(((((((...(((.......-......((((((((...)))))))))))))))))-).))). ( -20.41, z-score =  -2.96, R)
>droSim1.chr3L 2988948 54 + 22553184
-----------UUAACUCCUGCCC-CUUUAUGAUCUGCGCCCCGCAGACUAAGUAGCCUAGGUAAG
-----------......(((((..-(((...(.((((((...))))))).)))..))..))).... ( -12.30, z-score =  -1.81, R)
>droYak2.chr3h_random 334991 60 + 911842
-----AAGUCGUUAACUCCUCCCCAUCACAAGAUCUGUGUCCCACAGAUCAGAAAGCCUUAGGCG-
-----..........................((((((((...)))))))).....(((...))).- ( -13.50, z-score =  -2.80, R)
>droAna3.scaffold_13099 1688301 56 + 3324263
-------GGUGAUAAAACCUCCCCCUCUUAAAUUCUGCGUCUCGCAGAUAAAUUGGCAGAAUG---
-------(((......)))((..((........((((((...))))))......))..))...--- ( -11.34, z-score =  -1.94, R)
>droWil1.scaffold_181148 2074492 53 + 5435427
-------GGUGUUAACUCCUCCCACUCCGAGGAUCUGCGUCGCGCAGAUUAGGGUGUACA------
-------((.(....).))...(((.((...((((((((...)))))))).)))))....------ ( -17.00, z-score =  -1.14, R)
>droMoj3.scaffold_6498 3059478 57 - 3408170
---------UCUUAACUCUUCCCCAUCUAAAUAUCUGCGUCCCGCAGAUCAGGGUGCAUAUGUCCA
---------..............(((((....(((((((...)))))))..))))).......... ( -11.20, z-score =  -1.90, R)
>consensus
_______G_UGUUAACUCCUCCCC_UCUCAAGAUCUGCGUCCCGCAGAUUAGGGAGCAUAAGU___
...............................((((((((...))))))))................ ( -8.11 =  -8.42 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:46:24 2011