Locus 8528

Sequence ID dm3.chr3L
Location 24,496,289 – 24,496,459
Length 170
Max. P 0.908502
window11717 window11718

overview

Window 7

Location 24,496,289 – 24,496,459
Length 170
Sequences 4
Columns 170
Reading direction forward
Mean pairwise identity 52.10
Shannon entropy 0.79144
G+C content 0.41431
Mean single sequence MFE -44.00
Consensus MFE -8.85
Energy contribution -11.85
Covariance contribution 3.00
Combinations/Pair 1.48
Mean z-score -2.40
Structure conservation index 0.20
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.20
SVM RNA-class probability 0.908502
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24496289 170 + 24543557
CUGCAGGGCCAAAACCCCUCGCGGUGGUUCCACUAAAGAAACAAAUUUUCGUUUCUCGGCUUUCCCCUGAUCAAACAUCGUCUGAUGCAUUGUCUUAUAUACAAGACAAAACAAAAGCCCAUAAUAUAAAAGUGGAAAAAUGUAUCUUCUCUUACGCUAGGGACAUAUCA
((((((((.......)))).))))...(((((((..((((((........)))))).((((((............((((....))))..(((((((......)))))))....))))))...........)))))))..........(((((......)))))....... ( -41.80, z-score =  -2.77, R)
>droPer1.super_100 48496 146 - 203787
CCUAGGUGGCUAA-CCACUGGUGGGGAUCC-ACCAAAACGACAAGUUUUUGUUUCACGGCUGGCCCCUGACCACAUAACUAAUGAUGUAAUUGCUUUUACUCAAAGCUAAAUAAAAGCCGUGGGUUUAAAGGUGGAGAAGUUUAAGCA----------------------
..((((.(((((.-((..((((((....))-))))((((((.......))))))...)).))))))))).((((.....((((......))))((((.(((((..(((.......)))..)))))..)))))))).............---------------------- ( -41.00, z-score =  -0.51, R)
>dp4.Unknown_group_854 2336 153 - 3980
CUGUGGCGCCUAAGCCGCUGGUGGGAGUCCCACCAAAACGACAAGGUUUUGUUUCACGGUUUGCCCCUGACUUCACAUCUAAUGAUGUAAUUGCUUUUAUUCAAAGCAAAAUAAAUGCCGUGGGUAUAAAGGUGUUAUCGUUUAUGAUAAGAA-----------------
..(((((......)))))(((((((...)))))))((((((...(.((((((((((((((..............(((((....)))))..(((((((.....))))))).......)))))))).)))))).)....))))))..........----------------- ( -48.40, z-score =  -2.79, R)
>droMoj3.scaffold_6680 24022688 152 + 24764193
---------------CCUUAUCUGUCGUCUCUCCUCGAAAGCAAAUAUUUUUAUCUAGGCUUUCAUCUGAUACGACAUGUGAGGCAGUAUCUGCUUUUAUUGCAAGCAAGACUUCGGCUAAUGUUUUUA---UAUCGAAGUUUAGUUUUGCAACUCCGCGAGAAAUUGCU
---------------.(((((.((((((.((.....((((((..(((....)))....))))))....)).)))))).)))))(((((.(((((.....((((((((.(((((((((.(((.....)))---..))))))))).).)))))))....)).))).))))). ( -44.80, z-score =  -3.53, R)
>consensus
CUG_GG_GCCUAA_CCCCUGGCGGGGGUCCCACCAAAAAAACAAAUUUUUGUUUCACGGCUUGCCCCUGACCACACAUCUAAUGAUGUAAUUGCUUUUAUUCAAAGCAAAACAAAAGCCGAGGGUAUAAAGGUGGAAAAGUUUAUGUU__CAA_________________
....((((.......))))(((((.....)))))..................(((((((((.............(((((....)))))....((((.......))))........))))))))).............................................. ( -8.85 = -11.85 +   3.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 24,496,289 – 24,496,459
Length 170
Sequences 4
Columns 170
Reading direction reverse
Mean pairwise identity 52.10
Shannon entropy 0.79144
G+C content 0.41431
Mean single sequence MFE -43.97
Consensus MFE -8.10
Energy contribution -11.60
Covariance contribution 3.50
Combinations/Pair 1.40
Mean z-score -2.41
Structure conservation index 0.18
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.859372
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 24496289 170 - 24543557
UGAUAUGUCCCUAGCGUAAGAGAAGAUACAUUUUUCCACUUUUAUAUUAUGGGCUUUUGUUUUGUCUUGUAUAUAAGACAAUGCAUCAGACGAUGUUUGAUCAGGGGAAAGCCGAGAAACGAAAAUUUGUUUCUUUAGUGGAACCACCGCGAGGGGUUUUGGCCCUGCAG
......((((.(((..((((((..((........))..))))))..))).))))...(((.((((((((....)))))))).)))((((((...)))))).(((((.......(((((((((....)))))))))....((((((.((....))))))))..)))))... ( -50.60, z-score =  -2.58, R)
>droPer1.super_100 48496 146 + 203787
----------------------UGCUUAAACUUCUCCACCUUUAAACCCACGGCUUUUAUUUAGCUUUGAGUAAAAGCAAUUACAUCAUUAGUUAUGUGGUCAGGGGCCAGCCGUGAAACAAAAACUUGUCGUUUUGGU-GGAUCCCCACCAGUGG-UUAGCCACCUAGG
----------------------................(((......((((((((((((((((....)))))))))))(((((......))))).)))))..((((((.(((((....((((....))))....(((((-((....))))))))))-)).))).)))))) ( -40.50, z-score =  -1.32, R)
>dp4.Unknown_group_854 2336 153 + 3980
-----------------UUCUUAUCAUAAACGAUAACACCUUUAUACCCACGGCAUUUAUUUUGCUUUGAAUAAAAGCAAUUACAUCAUUAGAUGUGAAGUCAGGGGCAAACCGUGAAACAAAACCUUGUCGUUUUGGUGGGACUCCCACCAGCGGCUUAGGCGCCACAG
-----------------...(((((......)))))...............(((.......(((((((.....)))))))(((((((....)))))))..(((.((.....)).))).......(((.(((((..(((((((...))))))))))))..))).))).... ( -46.30, z-score =  -3.66, R)
>droMoj3.scaffold_6680 24022688 152 - 24764193
AGCAAUUUCUCGCGGAGUUGCAAAACUAAACUUCGAUA---UAAAAACAUUAGCCGAAGUCUUGCUUGCAAUAAAAGCAGAUACUGCCUCACAUGUCGUAUCAGAUGAAAGCCUAGAUAAAAAUAUUUGCUUUCGAGGAGAGACGACAGAUAAGG---------------
.((((((((....))))))))........((((((...---(((.....)))..)))))).((((((.......))))))......(((....((((((.((...(((((((..(((((....))))))))))))..))...))))))....)))--------------- ( -38.50, z-score =  -2.09, R)
>consensus
_________________UUG__AACAUAAACUUCUACACCUUUAAACCAACGGCUUUUAUUUUGCUUUGAAUAAAAGCAAAUACAUCAUUAGAUGUGUGAUCAGGGGAAAGCCGAGAAACAAAAACUUGUCGUUUUGGUGGGACCACCACCAGGGG_UUAGGC_CC_CAG
..................................................((((.......(((((((.....)))))))....................(((.((.....)).)))...........))))(((((((((.....)))))))))............... ( -8.10 = -11.60 +   3.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:47:21 2011