Locus 8513

Sequence ID dm3.chr3L
Location 24,272,292 – 24,272,356
Length 64
Max. P 0.998935
window11693 window11694

overview

Window 3

Location 24,272,292 – 24,272,356
Length 64
Sequences 6
Columns 68
Reading direction forward
Mean pairwise identity 57.55
Shannon entropy 0.77657
G+C content 0.50194
Mean single sequence MFE -14.73
Consensus MFE -7.64
Energy contribution -7.17
Covariance contribution -0.47
Combinations/Pair 1.71
Mean z-score -0.72
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.46
SVM RNA-class probability 0.940551
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24272292 64 + 24543557
--UGAACAAGGCUCACUAAUCUGCG-GGACGCAGAU-CUUGAGGGGGGAGGAGUUAAGAACCCUCUUC
--.........((((...(((((((-...)))))))-..)))).(((((((.((.....))))))))) ( -20.50, z-score =  -1.32, R)
>droSim1.chr3L 2988948 54 - 22553184
-CUUACCUAGGCUACUUAGUCUGCG-GGGCGCAGAU-CAUAAAGGGGCAGGAGUUAA-----------
-....(((..((..(((.(((((((-...)))))))-....)))..)))))......----------- ( -15.10, z-score =  -0.84, R)
>droAna3.scaffold_13082 1758569 59 - 3919855
-CACAUUUCUGUUAAUUGAUCUGCG-GGACGCAGACUUUUAGAGGGGGAGGAGUUAUCACC-------
-..(.(..((.((((..(.((((((-...)))))))..)))).))..).)...........------- ( -12.40, z-score =  -0.56, R)
>droWil1.scaffold_181154 4133291 53 + 4610121
-------CCUUUACCAUAAUCUGCG-GGAUGCAGAUCUCUGGAGGGGGAGGAGUUAACACC-------
-------((((..(((..((((((.-....))))))...)))..)))).............------- ( -15.00, z-score =  -0.70, R)
>droMoj3.scaffold_6498 3059478 57 + 3408170
-UGGACAUAUGCACCCUGAUCUGCG-GGACGCAGAUAUUUAGAUGGGGAAGAGUUAAGA---------
-............((((.(((((((-...)))))))........))))...........--------- ( -12.40, z-score =  -0.95, R)
>droGri2.scaffold_14906 13489288 68 + 14172833
GAAACAAGAUUCUACAUCGCGUCCGAGGACGUCCGCAUUUAAAGGGGGAGGAGUUAACAUCCAUCAUC
.......((((((.(...(((((....)))))((.(.......).))).))))))............. ( -13.00, z-score =   0.06, R)
>consensus
__AGAAAUAUGCUACAUAAUCUGCG_GGACGCAGAU_UUUAAAGGGGGAGGAGUUAACA_C_______
..................(((((((....)))))))................................ ( -7.64 =  -7.17 +  -0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 24,272,292 – 24,272,356
Length 64
Sequences 6
Columns 68
Reading direction reverse
Mean pairwise identity 57.55
Shannon entropy 0.77657
G+C content 0.50194
Mean single sequence MFE -13.50
Consensus MFE -7.45
Energy contribution -7.28
Covariance contribution -0.16
Combinations/Pair 1.57
Mean z-score -1.76
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.56
SVM RNA-class probability 0.998935
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24272292 64 - 24543557
GAAGAGGGUUCUUAACUCCUCCCCCCUCAAG-AUCUGCGUCC-CGCAGAUUAGUGAGCCUUGUUCA--
(((.(((((((...(((.............(-(((((((...-)))))))))))))))))).))).-- ( -20.41, z-score =  -2.96, R)
>droSim1.chr3L 2988948 54 + 22553184
-----------UUAACUCCUGCCCCUUUAUG-AUCUGCGCCC-CGCAGACUAAGUAGCCUAGGUAAG-
-----------......(((((..(((...(-.((((((...-))))))).)))..))..)))....- ( -12.30, z-score =  -1.81, R)
>droAna3.scaffold_13082 1758569 59 + 3919855
-------GGUGAUAACUCCUCCCCCUCUAAAAGUCUGCGUCC-CGCAGAUCAAUUAACAGAAAUGUG-
-------((........)).............(((((((...-)))))))......(((....))).- ( -10.70, z-score =  -2.47, R)
>droWil1.scaffold_181154 4133291 53 - 4610121
-------GGUGUUAACUCCUCCCCCUCCAGAGAUCUGCAUCC-CGCAGAUUAUGGUAAAGG-------
-------((.(....).))....((((((..(((((((....-.))))))).)))...)))------- ( -14.30, z-score =  -1.85, R)
>droMoj3.scaffold_6498 3059478 57 - 3408170
---------UCUUAACUCUUCCCCAUCUAAAUAUCUGCGUCC-CGCAGAUCAGGGUGCAUAUGUCCA-
---------..............(((((....(((((((...-)))))))..)))))..........- ( -11.20, z-score =  -1.90, R)
>droGri2.scaffold_14906 13489288 68 - 14172833
GAUGAUGGAUGUUAACUCCUCCCCCUUUAAAUGCGGACGUCCUCGGACGCGAUGUAGAAUCUUGUUUC
...((.(((((((..(................)..)))))))))(((((.(((.....))).))))). ( -12.09, z-score =   0.43, R)
>consensus
_______G_UGUUAACUCCUCCCCCUCUAAA_AUCUGCGUCC_CGCAGAUUAAGGAGCAUAGGUCA__
................................(((((((....))))))).................. ( -7.45 =  -7.28 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:47:02 2011