Locus 7702

Sequence ID dm3.chr3L
Location 16,691,257 – 16,691,398
Length 141
Max. P 0.973173
window10601 window10602 window10603

overview

Window 1

Location 16,691,257 – 16,691,365
Length 108
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 78.81
Shannon entropy 0.38668
G+C content 0.52681
Mean single sequence MFE -33.40
Consensus MFE -22.91
Energy contribution -22.42
Covariance contribution -0.50
Combinations/Pair 1.26
Mean z-score -1.72
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.15
SVM RNA-class probability 0.900417
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16691257 108 + 24543557
-CUUUUAGUCCAGCAUGGACCACUGUUGGUUGGCCAAGUGGAAUCGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCUGU---GGAGCACUCUUC
-.......(((.....)))(((((..(((....))))))))....(((((((((((.((((((..(....)..)))))).)))).)))..((((...---.))))))))... ( -38.20, z-score =  -1.79, R)
>droAna3.scaffold_13337 9383256 98 - 23293914
CUUCUAUGUCUUCCUCAGACCACUGUACU--------------CCAAGUGGAAUGGAGUUGUCCCCACCAGAAGACAACACUGUUUCUGUUCUCAGUUCCAGUACCAGUACC
......(((((((....(((.(((.((.(--------------((....))).)).))).))).......)))))))..((((...(((....)))...))))......... ( -23.70, z-score =  -0.73, R)
>droEre2.scaffold_4784 8619403 104 - 25762168
-CUUUUAGACCAGCAUGGACCACUGUUGC----CGAAGUGGAAUGAAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCUGAGCUCGGC---GGAACCCUCUUC
-......(.(((((.(((((((((....(----(.....)).....))))).((((.((((((..(....)..)))))).)))).)))).))).)))---............ ( -28.60, z-score =  -0.20, R)
>droYak2.chr3L 6813962 104 - 24197627
-CUUUUAGUCCAGCAUGGACCACUGUUGC----CCAAGUGGAAUGAAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCGGA---GAAACCCUCUUC
-.......((((((.(((((((((.....----((....)).....))))).((((.((((((..(....)..)))))).)))).)))).))).)))---............ ( -32.90, z-score =  -2.12, R)
>droSec1.super_0 8763791 104 + 21120651
-CUUUUUGUCCAGCAUGGACCACUGUUGC----CCAAGUGGAAUGGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCAAGCUCGCU---GGAGUCCACUUC
-.......((((((.....(((((.....----...)))))....(((((((((((.((((((..(....)..)))))).)))).)))..)))))))---)))......... ( -38.50, z-score =  -2.74, R)
>droSim1.chr3L 16018255 104 + 22553184
-CUUUUUGUCCAGCAUGGACCACUGUUGC----CCAAGUGGAAUGGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCAAGCUCGCU---GGAGUCCACUUC
-.......((((((.....(((((.....----...)))))....(((((((((((.((((((..(....)..)))))).)))).)))..)))))))---)))......... ( -38.50, z-score =  -2.74, R)
>consensus
_CUUUUAGUCCAGCAUGGACCACUGUUGC____CCAAGUGGAAUGAAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCGGU___GGAACCCUCUUC
...........(((.(((((((((......................))))).((((.((((((..(....)..)))))).)))).)))).)))................... (-22.91 = -22.42 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,691,257 – 16,691,365
Length 108
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 78.81
Shannon entropy 0.38668
G+C content 0.52681
Mean single sequence MFE -37.62
Consensus MFE -22.84
Energy contribution -23.15
Covariance contribution 0.31
Combinations/Pair 1.09
Mean z-score -2.10
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.36
SVM RNA-class probability 0.931600
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16691257 108 - 24543557
GAAGAGUGCUCC---ACAGAGCUCGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCGAUUCCACUUGGCCAACCAACAGUGGUCCAUGCUGGACUAAAAG-
...((((((((.---...))))..(((.((((.(((((((((....))))))))).)))))))))))...(((((.((((((........))).))).).)))).......- ( -40.40, z-score =  -2.75, R)
>droAna3.scaffold_13337 9383256 98 + 23293914
GGUACUGGUACUGGAACUGAGAACAGAAACAGUGUUGUCUUCUGGUGGGGACAACUCCAUUCCACUUGG--------------AGUACAGUGGUCUGAGGAAGACAUAGAAG
..(((((.(((((...(((....)))...))))).(((((((....)))))))((((((.......)))--------------))).)))))((((.....))))....... ( -30.90, z-score =  -0.82, R)
>droEre2.scaffold_4784 8619403 104 + 25762168
GAAGAGGGUUCC---GCCGAGCUCAGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUUCAUUCCACUUCG----GCAACAGUGGUCCAUGCUGGUCUAAAAG-
((((.((((((.---...)))))).(..((((.(((((((((....))))))))).))))..).))))...(((((..(----....)))))).((.....))........- ( -34.10, z-score =  -1.23, R)
>droYak2.chr3L 6813962 104 + 24197627
GAAGAGGGUUUC---UCCGAGCUCGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUUCAUUCCACUUGG----GCAACAGUGGUCCAUGCUGGACUAAAAG-
((((.((((((.---...))))))(((.((((.(((((((((....))))))))).))))))).))))..(((((.(((----((.......))))).).)))).......- ( -39.70, z-score =  -2.67, R)
>droSec1.super_0 8763791 104 - 21120651
GAAGUGGACUCC---AGCGAGCUUGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCCAUUCCACUUGG----GCAACAGUGGUCCAUGCUGGACAAAAAG-
.........(((---((((((..((((.((((.(((((((((....))))))))).)))))))))))....(((((..(----....)))))).....)))))).......- ( -40.30, z-score =  -2.56, R)
>droSim1.chr3L 16018255 104 - 22553184
GAAGUGGACUCC---AGCGAGCUUGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCCAUUCCACUUGG----GCAACAGUGGUCCAUGCUGGACAAAAAG-
.........(((---((((((..((((.((((.(((((((((....))))))))).)))))))))))....(((((..(----....)))))).....)))))).......- ( -40.30, z-score =  -2.56, R)
>consensus
GAAGAGGGCUCC___ACCGAGCUCGGAUAUGGCGUUGUCUUCUGGCGGGGACAACUCCAUUCCACUCCAUUCCACUUGG____GCAACAGUGGUCCAUGCUGGACAAAAAG_
..................(((...(((.((((.(((((((((....))))))))).))))))).))).........................((((.....))))....... (-22.84 = -23.15 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,691,296 – 16,691,398
Length 102
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 77.50
Shannon entropy 0.39809
G+C content 0.55271
Mean single sequence MFE -28.86
Consensus MFE -17.91
Energy contribution -17.47
Covariance contribution -0.44
Combinations/Pair 1.38
Mean z-score -2.30
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.88
SVM RNA-class probability 0.973173
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 16691296 102 + 24543557
GAAUCGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCUGU---GGAGCACUCUUCACCGCCCCUUCUUCCCCCCUUCA-CUUAGCGCAC
(((..(((((((((((.((((((..(....)..)))))).)))).)))..((((...---.)))))))))))..(((..................-....)))... ( -26.95, z-score =  -1.25, R)
>droAna3.scaffold_13337 9383288 94 - 23293914
------AGUGGAAUGGAGUUGUCCCCACCAGAAGACAACACUGUUUCUGUUCUCAGUUCCAGUACCAGUACCAGCCCCA------UUCCUCUUCAGUUUGGAGCAC
------...(((((((.((((((..(....)..))))))((((...(((....)))...)))).............)))------)))).((((.....))))... ( -25.00, z-score =  -1.44, R)
>droEre2.scaffold_4784 8619438 92 - 25762168
GAAUGAAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCUGAGCUCGGC---GGAACCCUCUUCUCCGC----------CCCCUUCA-CUUAGAGCAC
...(((((.((.((((.((((((..(....)..)))))).))))..........(((---(((.........)))))----------))))))))-.......... ( -29.90, z-score =  -2.40, R)
>droYak2.chr3L 6813997 92 - 24197627
GAAUGAAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCGGA---GAAACCCUCUUCUCCGC----------CCCCUUCA-CUUAGAGCAC
...(((((((((((((.((((((..(....)..)))))).)))).))))....((((---(((......))))))).----------...)))))-.......... ( -29.90, z-score =  -3.35, R)
>droSec1.super_0 8763826 93 + 21120651
GAAUGGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCAAGCUCGCU---GGAGUCCACUUCACCCCG---------CUUCUUCA-CUUAGCGCAC
...(((((((((((((.((((((..(....)..)))))).)))).((((.(....))---))).)))))))))...((---------((......-...))))... ( -32.20, z-score =  -2.94, R)
>droSim1.chr3L 16018290 93 + 22553184
GAAUGGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCAAGCUCGCU---GGAGUCCACUUCACCCCC---------CUUCUUCA-CUUAGCGCAC
...(((((((((((((.((((((..(....)..)))))).)))).((((.(....))---))).))))))))).....---------........-.......... ( -29.20, z-score =  -2.40, R)
>consensus
GAAUGGAGUGGAAUGGAGUUGUCCCCGCCAGAAGACAACGCCAUAUCCGAGCUCGGU___GGAACCCUCUUCACCCCC_________CCCCUUCA_CUUAGAGCAC
...(((((((((((((.((((((..(....)..)))))).)))).))))...........((((....))))..................)))))........... (-17.91 = -17.47 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:31:53 2011