Locus 3322

Sequence ID dm3.chr2R
Location 4,368,609 – 4,368,713
Length 104
Max. P 0.984863
window4577

overview

Window 7

Location 4,368,609 – 4,368,713
Length 104
Sequences 3
Columns 130
Reading direction forward
Mean pairwise identity 59.34
Shannon entropy 0.52911
G+C content 0.29581
Mean single sequence MFE -22.67
Consensus MFE -11.08
Energy contribution -11.87
Covariance contribution 0.79
Combinations/Pair 1.35
Mean z-score -2.28
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.18
SVM RNA-class probability 0.984863
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 4368609 104 + 21146708
---------------------AUCUUAAGACUGAAUUGUUUCAAAUGGUUUUAUAAAAGCCAUUAAUAACUAUUAA-----AUAUUAUUAAAAGUAAUUUCCUAUACCCGUUUUUAUCACGGUGUAUGCG
---------------------..........((((....))))((((((((.....))))))))....(((.((((-----......)))).))).......(((((((((.......)))).))))).. ( -16.30, z-score =  -1.44, R)
>droYak2.chr2L 17023208 103 + 22324452
--------------------------AUUAACCAGCUGUUUUAGAUUGUUUUAUUAAUAACACUGAAACUAGCUCAUUUUCAUCUUAGCGAAAGUGAUUUUUUUAACCCGCUUUC-UCGCGGUGUAUGCA
--------------------------........((((((((((..((((........))))))))))).)))((((((((........))))))))........((((((....-..)))).))..... ( -24.80, z-score =  -3.19, R)
>droSim1.chr2R_random 1482301 125 + 2996586
AUUCUGCGGGCAUUAAAAUCGAUUUUAAGACUGAAUUGUUUAAAAUGGUUUUAUGAAAGCCAUUAAAUACAAUUAA-----AUAGUAUUAAAAGUAACUUUCUUUACUCGUUUUAAUCGCGGUGUAUGCG
...(((((...(((((((.(((((((((.((((((((((....((((((((.....))))))))....))))))..-----.)))).))))))((((......)))))))))))))))))))........ ( -26.90, z-score =  -2.20, R)
>consensus
_____________________AU_UUAAGACUGAAUUGUUUAAAAUGGUUUUAUAAAAGCCAUUAAAAACAAUUAA_____AUAUUAUUAAAAGUAAUUUUCUUUACCCGUUUUAAUCGCGGUGUAUGCG
.................................((((((((..((((((((.....))))))))..))))))))..............................(((((((.......)))).))).... (-11.08 = -11.87 +   0.79)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:08:06 2011