Locus 1304

Sequence ID dm3.chr2L
Location 9,975,542 – 9,975,649
Length 107
Max. P 0.989428
window1780 window1781

overview

Window 0

Location 9,975,542 – 9,975,649
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 55.14
Shannon entropy 0.64895
G+C content 0.40831
Mean single sequence MFE -28.00
Consensus MFE -10.75
Energy contribution -10.20
Covariance contribution -0.55
Combinations/Pair 1.27
Mean z-score -2.38
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.37
SVM RNA-class probability 0.989428
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 9975542 107 + 23011544
AAAUAAUUUAGCGGACUUUGACAGGGUGCCUGAUAUCGUAAAAUCGAUCAGGGAAUUCUCUGGAAAUCCAGCAGAAUUCGGGUCUUGGAAAAAGAGCGUUGAUAGAA
.......((((((..((((..(((((..(((((..(((......))))))))(((((((((((....)))).)))))))...)))))...))))..))))))..... ( -34.70, z-score =  -3.40, R)
>droAna3.scaffold_13034 1551495 94 - 2223656
-------------GACUUAGAUCGGGUACCAGAUAUAGUGAAGUGCAUGAAGGAAUUUUCGGGAAAGCCCACAGAAUUUAGUUCGUGGACAAAAACGGUAGAUCGAG
-------------......((((((...))...(((.((...((.((((((.(((((((.(((....)))..)))))))..)))))).))....)).)))))))... ( -21.30, z-score =  -1.18, R)
>droWil1.scaffold_180943 117849 98 + 149748
AGAUAAUUGGCAUGAGGUAGAUAAAGUUCCAGACUUAGUGAAAGGUCUAAAGGAAUUCUCUGGUAAUCCAGCAGAAUUUACAACUUGGUUCGCUUCAA---------
............(((((..(((.(((((..((((((......))))))....(((((((((((....)))).)))))))..))))).)))..))))).--------- ( -28.00, z-score =  -2.56, R)
>consensus
A_AUAAUU_____GACUUAGAUAGGGUACCAGAUAUAGUGAAAUGCAUAAAGGAAUUCUCUGGAAAUCCAGCAGAAUUUAGAUCUUGGAAAAAAACAGU_GAU_GA_
....................................................(((((((((((....)))).)))))))............................ (-10.75 = -10.20 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 9,975,542 – 9,975,649
Length 107
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 55.14
Shannon entropy 0.64895
G+C content 0.40831
Mean single sequence MFE -18.70
Consensus MFE -7.70
Energy contribution -7.37
Covariance contribution -0.33
Combinations/Pair 1.20
Mean z-score -1.24
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.712776
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 9975542 107 - 23011544
UUCUAUCAACGCUCUUUUUCCAAGACCCGAAUUCUGCUGGAUUUCCAGAGAAUUCCCUGAUCGAUUUUACGAUAUCAGGCACCCUGUCAAAGUCCGCUAAAUUAUUU
.........((..((((......(((..(((((((.((((....)))))))))))((((((((......)))..)))))......)))))))..))........... ( -23.70, z-score =  -2.33, R)
>droAna3.scaffold_13034 1551495 94 + 2223656
CUCGAUCUACCGUUUUUGUCCACGAACUAAAUUCUGUGGGCUUUCCCGAAAAUUCCUUCAUGCACUUCACUAUAUCUGGUACCCGAUCUAAGUC-------------
...((((((((......(((((((((.....))).))))))......(((......)))..................))))...))))......------------- ( -17.20, z-score =  -1.53, R)
>droWil1.scaffold_180943 117849 98 - 149748
---------UUGAAGCGAACCAAGUUGUAAAUUCUGCUGGAUUACCAGAGAAUUCCUUUAGACCUUUCACUAAGUCUGGAACUUUAUCUACCUCAUGCCAAUUAUCU
---------.(((((..............((((((.((((....))))))))))..(((((((..........))))))).)))))..................... ( -15.20, z-score =   0.13, R)
>consensus
_UC_AUC_ACCGUAUUUAUCCAAGAACUAAAUUCUGCUGGAUUUCCAGAGAAUUCCUUCAUACAUUUCACUAUAUCUGGAACCCUAUCUAAGUC_____AAUUAU_U
.............................((((((.((((....))))))))))..................................................... ( -7.70 =  -7.37 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:29:24 2011