Locus 10308

Sequence ID dm3.chr3R
Location 12,888,011 – 12,888,145
Length 134
Max. P 0.756472
window14174 window14175

overview

Window 4

Location 12,888,011 – 12,888,105
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.70
Shannon entropy 0.35316
G+C content 0.42796
Mean single sequence MFE -28.32
Consensus MFE -15.49
Energy contribution -16.22
Covariance contribution 0.73
Combinations/Pair 1.31
Mean z-score -2.09
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.59
SVM RNA-class probability 0.753280
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12888011 94 + 27905053
-------------CCUCUGGAGA----UCGGCUACAGAUACAUAUUUAUGCUGGCA-UAUUUGC---GCU----GGUCGAAAUCGUUUCGGGAC-UAUUUAAUGAUUUCGAUGGAGGGAA
-------------(((((...((----(((((..((((((......))).)))(((-....)))---)))----))))(((((((((.......-.....)))))))))...)))))... ( -30.00, z-score =  -2.94, R)
>droSim1.chr3R 18934155 94 - 27517382
-------------CCUCUGGAGA----UCGUCUACAGAUACAUAUUUAUGCUGGCA-UAUUUGC---GCU----GGUCGAAAUCGUUUCGGGAC-UAUUUAAUGAUUUCGAUGGAGGGAA
-------------(((((.....----.......(((...((....((((....))-))..)).---.))----)((((((((((((.......-.....)))))))))))))))))... ( -24.50, z-score =  -1.05, R)
>droSec1.super_12 855525 94 - 2123299
-------------CCUCUGGAGA----UCGUCUACAGAUACAUAUUUAUGCUGGCA-UAUUUGC---GCU----GGUCGAAAUCGUUUCGGGAC-UAUUUAAUGAUUUCGAUGGAGGGAA
-------------(((((.....----.......(((...((....((((....))-))..)).---.))----)((((((((((((.......-.....)))))))))))))))))... ( -24.50, z-score =  -1.05, R)
>droYak2.chr3R 17336621 94 - 28832112
-------------CCUCUGAAGA----UCGGCUACAGAUACAUAUUUAUGCUGGCA-UAUUUGC---GCU----GGUCGAAAUCGUUUCGGGAC-UAUUUAAUGAUUUCGAUGGAGGCAA
-------------(((((...((----(((((..((((((......))).)))(((-....)))---)))----))))(((((((((.......-.....)))))))))...)))))... ( -29.10, z-score =  -2.77, R)
>droEre2.scaffold_4770 9003942 94 - 17746568
-------------CCUCUGGAGA----UCGGCUACAGAUACAUAUUUAUGCUGGCA-UAUUUGC---GCU----GGUCGAAAUCGUUUCGGGAC-UAUUUAAUGAUUUCGAUGGAGGCAA
-------------(((((...((----(((((..((((((......))).)))(((-....)))---)))----))))(((((((((.......-.....)))))))))...)))))... ( -29.10, z-score =  -2.57, R)
>droAna3.scaffold_13340 16681992 117 - 23697760
UUUAUGGAGACUGGCUCCGAAGACACAUCUUCAACACAUACAGAUAUAAGAAUACAAUAUCUAUAGGGCUCUGGGGCCUAAAUUGUUUUGGGGCCUAGUCGAUGGCAUUAAAGGGAA---
........(((((((((((((((....)))))((((.....((((((.........))))))...(((((....)))))....))))..)))))).)))).................--- ( -32.70, z-score =  -2.14, R)
>consensus
_____________CCUCUGGAGA____UCGGCUACAGAUACAUAUUUAUGCUGGCA_UAUUUGC___GCU____GGUCGAAAUCGUUUCGGGAC_UAUUUAAUGAUUUCGAUGGAGGGAA
.............(((((.........(((((...((((....))))..))))).....................((((((((((((.............)))))))))))))))))... (-15.49 = -16.22 +   0.73)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,888,044 – 12,888,145
Length 101
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 81.00
Shannon entropy 0.33212
G+C content 0.42330
Mean single sequence MFE -27.88
Consensus MFE -19.03
Energy contribution -19.03
Covariance contribution 0.00
Combinations/Pair 1.38
Mean z-score -1.72
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.60
SVM RNA-class probability 0.756472
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12888044 101 + 27905053
-----------CUGGCAUAUUUGC---GCU----GGUCGAAAUCGUUUCGGGACUAUUUAAUGAUUUCGAUGGAGGGAACUUGACUAAUUACGUUGUAUGCCUGGAAUAGCAUGGAGUU
-----------..(((((((..((---(..----.((((((((((((............)))))))))))).(((....))).........))).)))))))................. ( -26.90, z-score =  -1.67, R)
>droSim1.chr3R 18934188 101 - 27517382
-----------CUGGCAUAUUUGC---GCU----GGUCGAAAUCGUUUCGGGACUAUUUAAUGAUUUCGAUGGAGGGAACUUGACUAAUUACGUUGUAUGCCUGGCAUGGCAUGGAGUU
-----------..(((((((..((---(..----.((((((((((((............)))))))))))).(((....))).........))).)))))))................. ( -26.90, z-score =  -1.22, R)
>droSec1.super_12 855558 101 - 2123299
-----------CUGGCAUAUUUGC---GCU----GGUCGAAAUCGUUUCGGGACUAUUUAAUGAUUUCGAUGGAGGGAACUUGACUAAUUACGUUGUAUGCCUGGAAUAGCAUGGAGUU
-----------..(((((((..((---(..----.((((((((((((............)))))))))))).(((....))).........))).)))))))................. ( -26.90, z-score =  -1.67, R)
>droYak2.chr3R 17336654 101 - 28832112
-----------CUGGCAUAUUUGC---GCU----GGUCGAAAUCGUUUCGGGACUAUUUAAUGAUUUCGAUGGAGGCAACUUGACUAAUUACGUUGUAUGCUUCGAAUAGCACGGAGUU
-----------((((((....)))---(((----(((((((((((((............)))))))))))).((((((...((((.......))))..))))))...)))).))).... ( -29.30, z-score =  -2.33, R)
>droEre2.scaffold_4770 9003975 101 - 17746568
-----------CUGGCAUAUUUGC---GCU----GGUCGAAAUCGUUUCGGGACUAUUUAAUGAUUUCGAUGGAGGCAACUUGACUAAUUACGUUGUAUGCUUGGGAUAGCAUGGAGUU
-----------...(((....)))---(((----.((((((((((((............))))))))))))...)))((((((((.......))).((((((......))))))))))) ( -26.20, z-score =  -1.47, R)
>droAna3.scaffold_13340 16682032 115 - 23697760
CAGAUAUAAGAAUACAAUAUCUAUAGGGCUCUGGGGCCUAAAUUGUUUUGGGGCC--UAGUCGAUGGCAUUAAAGGGAACUUGACUAAUUAUGUUGU-CGGUUAGAA-AGCAUCAAUGU
.((((((.........)))))).....((((((((.((((((....)))))).))--)))((((..((((..(((....)))........))))..)-)))......-)))........ ( -31.10, z-score =  -1.95, R)
>consensus
___________CUGGCAUAUUUGC___GCU____GGUCGAAAUCGUUUCGGGACUAUUUAAUGAUUUCGAUGGAGGGAACUUGACUAAUUACGUUGUAUGCCUGGAAUAGCAUGGAGUU
.............(((((((..((...........((((((((((((............)))))))))))).(((....)))..........)).)))))))................. (-19.03 = -19.03 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:21:28 2011