Locus 3088

Sequence ID dm3.chr2R
Location 2,115,330 – 2,115,497
Length 167
Max. P 0.797112
window4238 window4239

overview

Window 8

Location 2,115,330 – 2,115,497
Length 167
Sequences 3
Columns 167
Reading direction forward
Mean pairwise identity 77.82
Shannon entropy 0.30989
G+C content 0.32552
Mean single sequence MFE -38.77
Consensus MFE -17.80
Energy contribution -18.70
Covariance contribution 0.90
Combinations/Pair 1.16
Mean z-score -2.63
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.723306
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2115330 167 + 21146708
AUUAACAGCAAUCAUAGUUAGUAAGUGAAAAUAUGAAAUCGAUAGGGUUCGGUUGAGUAGGAGUUUGAUGUAGGUUACCAUCUAUUUUCAAGAAAGAAAAAAUAUACAUAUGUAAAUUAUGUAUGCACUAUUGUGCUCUUUAAAAACAAAUACAAACCCAACGAAUC
.....((((..(((((.(((.....)))...)))))...(((......))))))).((.((.(((((..((((((....)))))).......(((((......(((((((.......)))))))((((....)))))))))...........))))))).))..... ( -31.90, z-score =  -1.11, R)
>droSim1.chr2R 1012183 162 + 19596830
AUUGAUUCCAAUCAUAUUUAGUAAUUGAAAAUAUGAAAUCAAUAGGGUUCGGUUGGGUAGGAGUUUGGAUUAGGCUUCCAUCU----UCCAAGCCCAGUAUUUUCAAGAAAGUAGAA-ACAUAGAAACAUGUGGGCUAUAUAAAAUCCAAUACAAACCCAACGAAUU
(((((((....((((((((.........))))))))))))))).(((((..(((((((.((((..((((.......))))..)----))).(((((..((((((....))))))...-((((......))))))))).......)))))))...)))))........ ( -45.00, z-score =  -3.65, R)
>droSec1.super_26 757949 154 + 826190
AUUGAUUCCAAUCAUAUUUAGUAAUUGAAAAUAUGAAAUCAAUAGGGUUCGGUUGAGUAGGAGUUUGGAUUAGGCUUCCAUCU----UCCAAGCCCAGUAUUUUCAAGAAAGUAGAA-ACAUA--------UGGGCUAUAUAAAAUCCAAUACAAACCCAACGAAUC
(((((((....((((((((.........))))))))))))))).(((((..((((....((((..((((.......))))..)----))).((((((....((((.........)))-)....--------))))))..........))))...)))))........ ( -39.40, z-score =  -3.12, R)
>consensus
AUUGAUUCCAAUCAUAUUUAGUAAUUGAAAAUAUGAAAUCAAUAGGGUUCGGUUGAGUAGGAGUUUGGAUUAGGCUUCCAUCU____UCCAAGCCCAGUAUUUUCAAGAAAGUAGAA_ACAUA___AC___UGGGCUAUAUAAAAUCCAAUACAAACCCAACGAAUC
(((((((....((((((((.........))))))))))))))).(((((..((((....((((((((...)))))).))............((((((.((((((....))))))(....)...........))))))..........))))...)))))........ (-17.80 = -18.70 +   0.90)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,115,330 – 2,115,497
Length 167
Sequences 3
Columns 167
Reading direction reverse
Mean pairwise identity 77.82
Shannon entropy 0.30989
G+C content 0.32552
Mean single sequence MFE -36.18
Consensus MFE -19.63
Energy contribution -19.98
Covariance contribution 0.35
Combinations/Pair 1.17
Mean z-score -2.41
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.72
SVM RNA-class probability 0.797112
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2115330 167 - 21146708
GAUUCGUUGGGUUUGUAUUUGUUUUUAAAGAGCACAAUAGUGCAUACAUAAUUUACAUAUGUAUAUUUUUUCUUUCUUGAAAAUAGAUGGUAACCUACAUCAAACUCCUACUCAACCGAACCCUAUCGAUUUCAUAUUUUCACUUACUAACUAUGAUUGCUGUUAAU
((.(((..(((((((....(((((((((.((((((....))))(((((((.......)))))))..........)))))))))))((((........))))...............)))))))...)))..))..............((((..........)))).. ( -33.50, z-score =  -2.80, R)
>droSim1.chr2R 1012183 162 - 19596830
AAUUCGUUGGGUUUGUAUUGGAUUUUAUAUAGCCCACAUGUUUCUAUGU-UUCUACUUUCUUGAAAAUACUGGGCUUGGA----AGAUGGAAGCCUAAUCCAAACUCCUACCCAACCGAACCCUAUUGAUUUCAUAUUUUCAAUUACUAAAUAUGAUUGGAAUCAAU
........(((((((..((((.........((((((....((((.....-............))))....)))))).(((----...((((.......))))...)))...)))).))))))).(((((((((((((((.........))))))))....))))))) ( -37.43, z-score =  -1.91, R)
>droSec1.super_26 757949 154 - 826190
GAUUCGUUGGGUUUGUAUUGGAUUUUAUAUAGCCCA--------UAUGU-UUCUACUUUCUUGAAAAUACUGGGCUUGGA----AGAUGGAAGCCUAAUCCAAACUCCUACUCAACCGAACCCUAUUGAUUUCAUAUUUUCAAUUACUAAAUAUGAUUGGAAUCAAU
(((((...(((((((..((((.........((((((--------....(-(((.........))))....)))))).(((----...((((.......))))...)))...)))).)))))))........((((((((.........))))))))...)))))... ( -37.60, z-score =  -2.51, R)
>consensus
GAUUCGUUGGGUUUGUAUUGGAUUUUAUAUAGCCCA___GU___UAUGU_UUCUACUUUCUUGAAAAUACUGGGCUUGGA____AGAUGGAAGCCUAAUCCAAACUCCUACUCAACCGAACCCUAUUGAUUUCAUAUUUUCAAUUACUAAAUAUGAUUGGAAUCAAU
..((((((((((..((.(((((((.......(((((..................................))))).............((...)).)))))))))....)))))).))))....(((((((((((((((.........))))))))....))))))) (-19.63 = -19.98 +   0.35)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:03:25 2011