Locus 9172

Sequence ID dm3.chr3R
Location 4,662,765 – 4,662,871
Length 106
Max. P 0.982153
window12575 window12576

overview

Window 5

Location 4,662,765 – 4,662,871
Length 106
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 72.33
Shannon entropy 0.38901
G+C content 0.50887
Mean single sequence MFE -39.57
Consensus MFE -23.80
Energy contribution -26.90
Covariance contribution 3.10
Combinations/Pair 1.21
Mean z-score -2.54
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.10
SVM RNA-class probability 0.982153
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 4662765 106 + 27905053
UGGCCAGAUCCGGCUGAUGCUGCUGCUGCUGCUGGGGCAGAAGAUUCAGACUGGAAUCGAAGAGAUUCUUCUGCAGCAGCAGCUCGUGGUAGUAGUAGGGAGUGGU
..((((..(((..(((.((((((..(.(((((((..((((((((.((...((........)).)).))))))))..)))))))..)..)))))).)))))).)))) ( -48.60, z-score =  -3.20, R)
>droSim1.chr3R 10882195 100 - 27517382
UGGCCAGAUCCGG------CUGCUGCUGCUGCUGGGGCAGAAGAUUGAGACUGGAAUCGAAGAGAUUCUUCUGCAGCAGGAGCUCGUGGUAGUAGUAGGGCGUGGU
..((((..(((.(------(((((((((((.(((..((((((((((((........))))......))))))))..))).)))....))))))))).)))..)))) ( -42.70, z-score =  -2.46, R)
>droWil1.scaffold_181089 6324798 95 + 12369635
-------UGCUGCUUGAGAUUAUUGUU-CUUCUCUUGCAGUAGAUUCAAACUUGAAUCGAAAACGUUCUUCUGGAGCAG---UUCAUGAUAGUAAUAGGGCGUGGU
-------((((((..((((........-..))))..))))))((((((....))))))....(((((((.(((...((.---....)).)))....)))))))... ( -27.40, z-score =  -1.95, R)
>consensus
UGGCCAGAUCCGG_UGA__CUGCUGCUGCUGCUGGGGCAGAAGAUUCAGACUGGAAUCGAAGAGAUUCUUCUGCAGCAG_AGCUCGUGGUAGUAGUAGGGCGUGGU
..((((..(((.((((..(((((.((((((((((...((((((((((......)))))(((....))))))))))))))))))..)))))..)))).)))..)))) (-23.80 = -26.90 +   3.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,662,765 – 4,662,871
Length 106
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 72.33
Shannon entropy 0.38901
G+C content 0.50887
Mean single sequence MFE -27.41
Consensus MFE -17.11
Energy contribution -18.53
Covariance contribution 1.42
Combinations/Pair 1.11
Mean z-score -1.96
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.19
SVM RNA-class probability 0.907001
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 4662765 106 - 27905053
ACCACUCCCUACUACUACCACGAGCUGCUGCUGCAGAAGAAUCUCUUCGAUUCCAGUCUGAAUCUUCUGCCCCAGCAGCAGCAGCAGCAUCAGCCGGAUCUGGCCA
.....................(((((((((((((.((((.....))))(((((......)))))...(((....)))))))))))))).)).((((....)))).. ( -39.20, z-score =  -3.82, R)
>droSim1.chr3R 10882195 100 + 27517382
ACCACGCCCUACUACUACCACGAGCUCCUGCUGCAGAAGAAUCUCUUCGAUUCCAGUCUCAAUCUUCUGCCCCAGCAGCAGCAGCAG------CCGGAUCUGGCCA
.....(((............((.(((.((((((((((.(((((.....)))))...)))........(((....)))))))))).))------))).....))).. ( -27.63, z-score =  -1.58, R)
>droWil1.scaffold_181089 6324798 95 - 12369635
ACCACGCCCUAUUACUAUCAUGAA---CUGCUCCAGAAGAACGUUUUCGAUUCAAGUUUGAAUCUACUGCAAGAGAAG-AACAAUAAUCUCAAGCAGCA-------
........................---(((((..(((.(((((....)).)))..((((...(((......)))...)-))).....)))..)))))..------- ( -15.40, z-score =  -0.50, R)
>consensus
ACCACGCCCUACUACUACCACGAGCU_CUGCUGCAGAAGAAUCUCUUCGAUUCCAGUCUGAAUCUUCUGCCCCAGCAGCAGCAGCAG__UCA_CCGGAUCUGGCCA
.......................((((((((((..((((.....))))(((((......)))))........))))))))))........................ (-17.11 = -18.53 +   1.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:59:18 2011