Locus 10878

Sequence ID dm3.chr3R
Location 17,282,463 – 17,282,588
Length 125
Max. P 0.846025
window14947 window14948 window14949

overview

Window 7

Location 17,282,463 – 17,282,565
Length 102
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 79.68
Shannon entropy 0.38501
G+C content 0.46389
Mean single sequence MFE -20.24
Consensus MFE -13.63
Energy contribution -14.66
Covariance contribution 1.03
Combinations/Pair 1.14
Mean z-score -1.33
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.619848
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17282463 102 + 27905053
GACUGGCCAAUGGCCAGGCAAUGUGAUUAAGCCACAGAUACACAGAUAUCUACGAGAUACAAGACACACACUCGUUCGAAUACAUGUUCAUACACAACACAC
..((((((...))))))....((((..........(((((......)))))(((((..............)))))..((((....))))...))))...... ( -20.74, z-score =  -1.95, R)
>droSim1.chr3R 23329854 102 - 27517382
GACUGGCCAAUGGCCAGGCAAUGUGAUUAAGCCACAGAUACACAGAUAUCUACGAGAUACAAGACACACACUCGUUCGAAUACAUGUUCAUACACACCACAC
..((((((...))))))....((((..........(((((......)))))(((((..............)))))..((((....))))...))))...... ( -20.44, z-score =  -1.71, R)
>droSec1.super_6 152272 102 - 4358794
GACUGGCCAAUGGCCAGGCAAUGUGAUUAAGCCACAGAUACACAGAUAUCUACGAGAUACAAGACACACACUCGUUCGAAUACAUGUUCAUACACACCACAC
..((((((...))))))....((((..........(((((......)))))(((((..............)))))..((((....))))...))))...... ( -20.44, z-score =  -1.71, R)
>droYak2.chr3R 6114270 99 + 28832112
GACUGGCCAAUGGCCAGGCAAUGUGAUUAAGCCACAGAUACACAGAUAUCUACGAGAUACGAGACACACACCCGUUCGAAUGCAUGUACAUAUACUUCC---
..((((((...))))))(((..(((.......)))(((((......))))).(((...(((.(........)))))))..)))................--- ( -19.00, z-score =  -0.54, R)
>droEre2.scaffold_4770 13361798 93 - 17746568
GACUGGCCAAUGGCCAGGCAAUGUGAUUAAGCCACAGAUACACAGAUAUCUACGAGAUACAAGACACACACUCGUUCGAAUGCAUGUAUAUUU---------
..((((((...))))))(((.(((((((........))).))))....((.(((((..............)))))..)).)))..........--------- ( -20.24, z-score =  -1.35, R)
>droAna3.scaffold_13340 17625554 88 + 23697760
GCCUGGCCAAUGGCCAAGCAAUGUGAUUAAC------ACACACAAUCUCCUGGAAGCCCAGACACUCACGCGCACACAGACACAUGGCCCCAUA--------
((((((((...))))).((..((((.....)------))).........((((....))))........))..............)))......-------- ( -20.60, z-score =  -0.74, R)
>consensus
GACUGGCCAAUGGCCAGGCAAUGUGAUUAAGCCACAGAUACACAGAUAUCUACGAGAUACAAGACACACACUCGUUCGAAUACAUGUUCAUACACA_CA___
..((((((...))))))...(((((..........(((((......)))))(((((..............))))).....)))))................. (-13.63 = -14.66 +   1.03)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,282,463 – 17,282,565
Length 102
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 79.68
Shannon entropy 0.38501
G+C content 0.46389
Mean single sequence MFE -30.28
Consensus MFE -19.59
Energy contribution -19.93
Covariance contribution 0.34
Combinations/Pair 1.45
Mean z-score -1.72
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.89
SVM RNA-class probability 0.846025
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17282463 102 - 27905053
GUGUGUUGUGUAUGAACAUGUAUUCGAACGAGUGUGUGUCUUGUAUCUCGUAGAUAUCUGUGUAUCUGUGGCUUAAUCACAUUGCCUGGCCAUUGGCCAGUC
(((((....(((..((((..(((((....)))))..))).)..))).((((((((((....))))))))))......)))))...((((((...)))))).. ( -28.60, z-score =  -1.48, R)
>droSim1.chr3R 23329854 102 + 27517382
GUGUGGUGUGUAUGAACAUGUAUUCGAACGAGUGUGUGUCUUGUAUCUCGUAGAUAUCUGUGUAUCUGUGGCUUAAUCACAUUGCCUGGCCAUUGGCCAGUC
..(..(((((((..((((..(((((....)))))..))).)..))..((((((((((....))))))))))......)))))..)((((((...)))))).. ( -32.80, z-score =  -2.50, R)
>droSec1.super_6 152272 102 + 4358794
GUGUGGUGUGUAUGAACAUGUAUUCGAACGAGUGUGUGUCUUGUAUCUCGUAGAUAUCUGUGUAUCUGUGGCUUAAUCACAUUGCCUGGCCAUUGGCCAGUC
..(..(((((((..((((..(((((....)))))..))).)..))..((((((((((....))))))))))......)))))..)((((((...)))))).. ( -32.80, z-score =  -2.50, R)
>droYak2.chr3R 6114270 99 - 28832112
---GGAAGUAUAUGUACAUGCAUUCGAACGGGUGUGUGUCUCGUAUCUCGUAGAUAUCUGUGUAUCUGUGGCUUAAUCACAUUGCCUGGCCAUUGGCCAGUC
---..(((((((((.((((((((((....))))))))))..)))))..(((((((((....)))))))))))))...........((((((...)))))).. ( -29.40, z-score =  -1.20, R)
>droEre2.scaffold_4770 13361798 93 + 17746568
---------AAAUAUACAUGCAUUCGAACGAGUGUGUGUCUUGUAUCUCGUAGAUAUCUGUGUAUCUGUGGCUUAAUCACAUUGCCUGGCCAUUGGCCAGUC
---------..(((.((((((((((....))))))))))..)))...((((((((((....))))))))))..............((((((...)))))).. ( -25.70, z-score =  -1.56, R)
>droAna3.scaffold_13340 17625554 88 - 23697760
--------UAUGGGGCCAUGUGUCUGUGUGCGCGUGAGUGUCUGGGCUUCCAGGAGAUUGUGUGU------GUUAAUCACAUUGCUUGGCCAUUGGCCAGGC
--------.........(((((.....(..((((..(...(((((....)))))...)..)))).------.)....))))).((((((((...)))))))) ( -32.40, z-score =  -1.07, R)
>consensus
___UG_UGUAUAUGAACAUGUAUUCGAACGAGUGUGUGUCUUGUAUCUCGUAGAUAUCUGUGUAUCUGUGGCUUAAUCACAUUGCCUGGCCAUUGGCCAGUC
.........(((((((((..(((((....)))))..))).))))))..(((((((((....)))))))))...............((((((...)))))).. (-19.59 = -19.93 +   0.34)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,282,495 – 17,282,588
Length 93
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 75.52
Shannon entropy 0.46434
G+C content 0.46732
Mean single sequence MFE -21.81
Consensus MFE -12.61
Energy contribution -12.95
Covariance contribution 0.34
Combinations/Pair 1.50
Mean z-score -1.16
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.537645
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17282495 93 - 27905053
CUUCGCAGUGUCCCUGUGUGUAUGUGUGUUGUGUAUGAACAUGUAUUCGAACGAGUGUGUGUCUUGUAUCUCGUAGAUAUCUGUGUAUCUGUG
...(((((((..(..((((.((((.(......(((..((((..(((((....)))))..))).)..)))).)))).))))..)..)).))))) ( -20.50, z-score =  -1.56, R)
>droSim1.chr3R 23329886 93 + 27517382
CUUCGCAGUGUCCCUGUGUGUGUGUGUGGUGUGUAUGAACAUGUAUUCGAACGAGUGUGUGUCUUGUAUCUCGUAGAUAUCUGUGUAUCUGUG
...(((((.....))))).(((..((.(((((.((((((((..(((((....)))))..)))........))))).)))))))..)))..... ( -21.20, z-score =  -1.47, R)
>droSec1.super_6 152304 93 + 4358794
CUUCGCAGUAUCCCUGUGUGUGUGUGUGGUGUGUAUGAACAUGUAUUCGAACGAGUGUGUGUCUUGUAUCUCGUAGAUAUCUGUGUAUCUGUG
...(((((.....))))).(((..((.(((((.((((((((..(((((....)))))..)))........))))).)))))))..)))..... ( -21.20, z-score =  -1.36, R)
>droYak2.chr3R 6114302 90 - 28832112
CUUCGCAGUGCCCCUGUGUGUGUG---GAAGUAUAUGUACAUGCAUUCGAACGGGUGUGUGUCUCGUAUCUCGUAGAUAUCUGUGUAUCUGUG
..(((.(((((...((((..((((---....))))..)))).))))))))(((((((..(((((((.....)).))))....)..))))))). ( -23.90, z-score =  -0.92, R)
>droEre2.scaffold_4770 13361830 84 + 17746568
CUUCGCAGUGUCCCUGUGUGUGU---------AAAUAUACAUGCAUUCGAACGAGUGUGUGUCUUGUAUCUCGUAGAUAUCUGUGUAUCUGUG
...(((((((((..(((((((((---------....))))))))).....(((((..............))))).)))).)))))........ ( -20.14, z-score =  -1.88, R)
>droAna3.scaffold_13340 17625583 80 - 23697760
CUUCGGAGACUCCGAGCGUCU----------UAUGGGGCCAUGUGUCUGUGUGCGCGUGAGUGUCUGGGCUUCCAGGAGAUUGUGUGUGU---
...((.((((.(...((.((.----------...)).))...).)))).)).(((((..(...(((((....)))))...)..)))))..--- ( -23.90, z-score =   0.22, R)
>consensus
CUUCGCAGUGUCCCUGUGUGUGUG___G_UGUAUAUGAACAUGUAUUCGAACGAGUGUGUGUCUUGUAUCUCGUAGAUAUCUGUGUAUCUGUG
...(((((.....)))))..............(((((((((..(((((....)))))..))).))))))....(((((((....))))))).. (-12.61 = -12.95 +   0.34)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:32:12 2011