Locus 10806

Sequence ID dm3.chr3R
Location 16,611,667 – 16,611,762
Length 95
Max. P 0.933342
window14848 window14849

overview

Window 8

Location 16,611,667 – 16,611,762
Length 95
Sequences 7
Columns 105
Reading direction forward
Mean pairwise identity 59.59
Shannon entropy 0.77537
G+C content 0.52697
Mean single sequence MFE -22.76
Consensus MFE -5.31
Energy contribution -9.21
Covariance contribution 3.90
Combinations/Pair 1.37
Mean z-score -2.00
Structure conservation index 0.23
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.69
SVM RNA-class probability 0.788381
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16611667 95 + 27905053
UGCAAGAUACGCCGCUCCCCAUUCUAUCGUGGAUAUA------UAUGUUCAU---ACGUUAGCCCCACUAUUCCCCCUAGAAUC-CAAUGCAAUUGAGCGGCGCC
.........((((((((...........((((.....------.((((....---)))).....)))).((((......)))).-..........)))))))).. ( -22.50, z-score =  -2.04, R)
>droSim1.chr3R 22666437 92 - 27517382
UGCAAGAUACGCCGCUCCCCAUUCUAUCGUGAAUAUAUG----UACAUACG-------UUAGCCCCACUAUUCCCC-UAGAAUC-CAAUGCAAUUGAGCGGCGCC
.........((((((((...((((......)))).....----........-------...((......((((...-..)))).-....))....)))))))).. ( -19.30, z-score =  -1.76, R)
>droSec1.super_27 675098 101 - 799419
UGCAAGAUACGCCGCUCCCCAUUCUAUCGUGGAUAUACAUACGUAUGUACAU---ACGUUGGCCCCACUAUUCCCCCUAGAAUC-CAAUGCAAUUGAGCGGCGCC
.........((((((((.((((......))))((((((....))))))....---.((((((.......((((......)))))-))))).....)))))))).. ( -27.41, z-score =  -2.35, R)
>droYak2.chr3R 5404402 102 + 28832112
UGCAAGAUACGCCGCUCCCCAUUCCAUCGUGGAUAUAUGCACAUCCAUACGCC--ACAUAAGCCCCACGAUUCCCCCUAGAAUC-CAAUGCAAUUGAGCGGCGCC
.........((((((((...........((((...((((......))))..))--))....((.....(((((......)))))-....))....)))))))).. ( -28.80, z-score =  -3.75, R)
>droEre2.scaffold_4770 12694555 97 - 17746568
UGCAAGAUACGCCGCUCCCCAUUUUAUCGUGGAUAUAUGUAUGUACAUAUG-------UAAGCCCCUCGAUUCCCCCUAGAAUC-CAAUGCAAUUGAGCGGCGCC
.........((((((((.((((......))))((((((((....)))))))-------)..((.....(((((......)))))-....))....)))))))).. ( -29.50, z-score =  -3.90, R)
>droAna3.scaffold_13340 10726419 73 - 23697760
--------------------------UACAAGAUACCCGC---UCAACACAAG--AGUCCUUUACCGUUACUGCUCCCCACAUG-CGAUGCAAUUGAGCGGCGCC
--------------------------..........((((---((((.....(--(((..............))))......((-(...))).)))))))).... ( -14.54, z-score =  -1.06, R)
>droVir3.scaffold_13047 7125703 81 - 19223366
------------------------AGCUAGAUACACCCGGCGUCAAGUAUAGCCCAGCCCCCUAUCCCCCCAUCCCCCAACCUGGCGCUGGAAUUGAGCGGCGCC
------------------------..............((((((...((....(((((.((......................)).)))))...))...)))))) ( -17.25, z-score =   0.82, R)
>consensus
UGCAAGAUACGCCGCUCCCCAUUCUAUCGUGGAUAUACG____UACAUACA____AC_UUAGCCCCACUAUUCCCCCUAGAAUC_CAAUGCAAUUGAGCGGCGCC
.........((((((((...((((......))))...........................((.....(((((......))))).....))....)))))))).. ( -5.31 =  -9.21 +   3.90)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,611,667 – 16,611,762
Length 95
Sequences 7
Columns 105
Reading direction reverse
Mean pairwise identity 59.59
Shannon entropy 0.77537
G+C content 0.52697
Mean single sequence MFE -31.53
Consensus MFE -10.34
Energy contribution -13.41
Covariance contribution 3.07
Combinations/Pair 1.37
Mean z-score -1.69
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.38
SVM RNA-class probability 0.933342
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16611667 95 - 27905053
GGCGCCGCUCAAUUGCAUUG-GAUUCUAGGGGGAAUAGUGGGGCUAACGU---AUGAACAUA------UAUAUCCACGAUAGAAUGGGGAGCGGCGUAUCUUGCA
.(((((((((.....((((.-.(((((....))))).(((((......((---((....)))------)...))))).....))))..)))))))))........ ( -28.30, z-score =  -1.16, R)
>droSim1.chr3R 22666437 92 + 27517382
GGCGCCGCUCAAUUGCAUUG-GAUUCUA-GGGGAAUAGUGGGGCUAA-------CGUAUGUA----CAUAUAUUCACGAUAGAAUGGGGAGCGGCGUAUCUUGCA
.(((((((((.....(....-)((((((-..(((((((((..((...-------.)).....----))).))))).)..))))))...)))))))))........ ( -28.20, z-score =  -1.63, R)
>droSec1.super_27 675098 101 + 799419
GGCGCCGCUCAAUUGCAUUG-GAUUCUAGGGGGAAUAGUGGGGCCAACGU---AUGUACAUACGUAUGUAUAUCCACGAUAGAAUGGGGAGCGGCGUAUCUUGCA
.(((((((((.....((((.-.(((((....))))).(((((....((((---((((....))))))))...))))).....))))..)))))))))........ ( -36.30, z-score =  -2.30, R)
>droYak2.chr3R 5404402 102 - 28832112
GGCGCCGCUCAAUUGCAUUG-GAUUCUAGGGGGAAUCGUGGGGCUUAUGU--GGCGUAUGGAUGUGCAUAUAUCCACGAUGGAAUGGGGAGCGGCGUAUCUUGCA
.(((((((((.(((.((((.-((((((....))))))(((((...(((((--(.(((....)))))))))..))))))))).)))...)))))))))........ ( -42.70, z-score =  -3.45, R)
>droEre2.scaffold_4770 12694555 97 + 17746568
GGCGCCGCUCAAUUGCAUUG-GAUUCUAGGGGGAAUCGAGGGGCUUA-------CAUAUGUACAUACAUAUAUCCACGAUAAAAUGGGGAGCGGCGUAUCUUGCA
.(((((((((....((.((.-((((((....)))))).))..))...-------.((((((....)))))).((((........)))))))))))))........ ( -33.30, z-score =  -3.12, R)
>droAna3.scaffold_13340 10726419 73 + 23697760
GGCGCCGCUCAAUUGCAUCG-CAUGUGGGGAGCAGUAACGGUAAAGGACU--CUUGUGUUGA---GCGGGUAUCUUGUA--------------------------
.((.((((((.(((((..(.-(....).)..)))))..........(((.--.....)))))---))))))........-------------------------- ( -20.40, z-score =   0.17, R)
>droVir3.scaffold_13047 7125703 81 + 19223366
GGCGCCGCUCAAUUCCAGCGCCAGGUUGGGGGAUGGGGGGAUAGGGGGCUGGGCUAUACUUGACGCCGGGUGUAUCUAGCU------------------------
....((.((((.(((((((.....)))))))..)))).))......(((((((.((((((((....)))))))))))))))------------------------ ( -31.50, z-score =  -0.31, R)
>consensus
GGCGCCGCUCAAUUGCAUUG_GAUUCUAGGGGGAAUAGUGGGGCUAA_GU____UGUAUGUA____CAUAUAUCCACGAUAGAAUGGGGAGCGGCGUAUCUUGCA
.(((((((((............(((((....))))).(((((..............................)))))...........)))))))))........ (-10.34 = -13.41 +   3.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:30:48 2011