Locus 8887

Sequence ID dm3.chr3R
Location 2,425,404 – 2,425,516
Length 112
Max. P 0.975450
window12193 window12194 window12195

overview

Window 3

Location 2,425,404 – 2,425,508
Length 104
Sequences 7
Columns 110
Reading direction forward
Mean pairwise identity 66.49
Shannon entropy 0.67244
G+C content 0.39551
Mean single sequence MFE -25.94
Consensus MFE -6.51
Energy contribution -6.59
Covariance contribution 0.07
Combinations/Pair 1.68
Mean z-score -1.98
Structure conservation index 0.25
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.585754
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2425404 104 + 27905053
CGCUUUGCGUGUUGCUCUUCUGAUGUCGUUUAACCAUUAU-GUGGCAUGA--AUUUGCC---AUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUU
.(((..(((.(((((((..........((((((.......-((((((...--...))))---))......))))))(((((.....)))))))).)))).))).)))... ( -34.52, z-score =  -3.74, R)
>droSec1.super_6 2519216 104 + 4358794
CGCUUUGCGUGUUGCUCUUCUGAUGCCGUUUAACCAUUAU-GUGGCAUGA--AUUUGCC---AUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUU
.(((..(((.(((((((..........((((((.......-((((((...--...))))---))......))))))(((((.....)))))))).)))).))).)))... ( -34.52, z-score =  -3.43, R)
>droSim1.chr3R 2454998 104 + 27517382
CGCUUUGCGUGUUGCUCUUCUGAUGCCGUUUAACCAUUAU-GUGGCAUGA--AUUUGCC---AUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUU
.(((..(((.(((((((..........((((((.......-((((((...--...))))---))......))))))(((((.....)))))))).)))).))).)))... ( -34.52, z-score =  -3.43, R)
>droYak2.chr3R 18341672 91 + 28832112
-------AGUUUUGC----GUGAUGUCGUUUAGCCAUUAU-GUGGCAUGA--AUUUGCC---ACUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGCCAACUC--UGAAUUC
-------.(((..((----(......)))..)))......-((((((...--...))))---)).((((.......(((((.....)))))(((....)))--))))... ( -25.70, z-score =  -1.65, R)
>droEre2.scaffold_4770 2668197 104 + 17746568
UGUUUUGCGUUUUGCUCUUCUGAUGUCGUUUAACCAUUAU-GUGGCAUGA--GUUUGCC---AUUUUCAUUUAAAUGGUUCUCUUGGCAGCGAGUCAACUCGUUGGCUUU
......((.....)).......((((((..((.....)).-.))))))((--(...(((---((((......))))))).)))..(.(((((((....))))))).)... ( -25.80, z-score =  -1.52, R)
>droAna3.scaffold_13340 13653739 83 + 23697760
UUUAUUGCGUAUGACUUUUCUGAUGUCGGUUAACCACUUU-UUGA-GUAA--AAGUGUC---AUUUCCAUUU---UACUCCAUUUGGUAAUGA-----------------
.(((((((....(((.........)))((.....((((((-(...-..))--)))))..---....))....---...........)))))))----------------- ( -13.70, z-score =  -0.66, R)
>droGri2.scaffold_14830 4714654 109 - 6267026
AGCUGUAUGUGUGAAUAUUGUCGAUUUAUUUAAUCUUCUUCGCAAUUUAAUAAUAUGUUUGAAUAUGCAUUUAGUUGAGCGUUUUUCCCUCUCUCCAAUUAUUAUUGCU-
((((((((.((((((....(..((((.....))))..)))))))((((((........)))))))))))..((((((((.(.........).)).)))))).....)))- ( -12.80, z-score =   0.56, R)
>consensus
CGCUUUGCGUGUUGCUCUUCUGAUGUCGUUUAACCAUUAU_GUGGCAUGA__AUUUGCC___AUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUU
.........(((((((.....(....(((((((..........((((........))))...........)))))))...)....))))))).................. ( -6.51 =  -6.59 +   0.07)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,425,412 – 2,425,516
Length 104
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 72.64
Shannon entropy 0.51959
G+C content 0.40256
Mean single sequence MFE -26.52
Consensus MFE -14.34
Energy contribution -14.52
Covariance contribution 0.18
Combinations/Pair 1.48
Mean z-score -1.79
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.58
SVM RNA-class probability 0.952477
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2425412 104 + 27905053
GUGUUGCUCUUCUGAUGUCGUUUAACCAUU------AUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGAC
..(((((((..........((((((.....------..((((((......))))))......))))))(((((.....)))))))).))))(((((((....))))))). ( -30.32, z-score =  -2.49, R)
>droSec1.super_6 2519224 104 + 4358794
GUGUUGCUCUUCUGAUGCCGUUUAACCAUU------AUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGAA
..(((((((..........((((((.....------..((((((......))))))......))))))(((((.....)))))))).))))(((((((....))))))). ( -30.62, z-score =  -2.28, R)
>droSim1.chr3R 2455006 104 + 27517382
GUGUUGCUCUUCUGAUGCCGUUUAACCAUU------AUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGAA
..(((((((..........((((((.....------..((((((......))))))......))))))(((((.....)))))))).))))(((((((....))))))). ( -30.62, z-score =  -2.28, R)
>droYak2.chr3R 18341680 91 + 28832112
-----------GUGAUGUCGUUUAGCCAUU------AUGUGGCAUGAAUUUGCCACUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGCCAACUC--UGAAUUCCUAGGGAA
-----------((((((.(.....).))))------))((((((......))))))...........((((((.....))))))......(((--((......))))).. ( -25.90, z-score =  -1.38, R)
>droEre2.scaffold_4770 2668205 104 + 17746568
GUUUUGCUCUUCUGAUGUCGUUUAACCAUU------AUGUGGCAUGAGUUUGCCAUUUUCAUUUAAAUGGUUCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUUGCGAU
...((((.......((((((..((.....)------)..))))))(((...(((((((......))))))).)))..(.(((((((....))))))).)......)))). ( -28.30, z-score =  -2.33, R)
>droGri2.scaffold_14830 4714662 109 - 6267026
GUGUGAAUAUUGUCGAUUUAUUUAAUCUUCUUCGCAAUUUAAUAAUAUGUUUGAAUAUGCAUUUAGUUGAGCGUUUUUCCCUCUCUCCAA-UUAUUAUUGCUCUGUUGAC
...........((((((................(((((((((........)))))).)))........(((((.................-.......))))).)))))) ( -13.36, z-score =   0.01, R)
>consensus
GUGUUGCUCUUCUGAUGUCGUUUAACCAUU______AUGUGGCAUGAAUUUGCCAUUUUCAUUUAAAUGCUGCUCUUGGCAGCGAGUCAACUCGUUGGCUUUUUAGCGAA
............((((......................((((((......))))))............(((((.....)))))..))))..((((((......)))))). (-14.34 = -14.52 +   0.18)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,425,412 – 2,425,516
Length 104
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 72.64
Shannon entropy 0.51959
G+C content 0.40256
Mean single sequence MFE -22.82
Consensus MFE -12.51
Energy contribution -12.40
Covariance contribution -0.11
Combinations/Pair 1.43
Mean z-score -1.94
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.93
SVM RNA-class probability 0.975450
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2425412 104 - 27905053
GUCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAU------AAUGGUUAAACGACAUCAGAAGAGCAACAC
((((......(((((..(((....)))(((((.....))))).............(((((......)))))...------..)))))...))))................ ( -25.50, z-score =  -2.34, R)
>droSec1.super_6 2519224 104 - 4358794
UUCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAU------AAUGGUUAAACGGCAUCAGAAGAGCAACAC
...(((.....((((..(((....)))(((((.....))))).............))))...((((((((....------...........)))))..))).)))..... ( -26.46, z-score =  -2.24, R)
>droSim1.chr3R 2455006 104 - 27517382
UUCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAU------AAUGGUUAAACGGCAUCAGAAGAGCAACAC
...(((.....((((..(((....)))(((((.....))))).............))))...((((((((....------...........)))))..))).)))..... ( -26.46, z-score =  -2.24, R)
>droYak2.chr3R 18341680 91 - 28832112
UUCCCUAGGAAUUCA--GAGUUGGCUCGCUGCCAAGAGCAGCAUUUAAAUGAAAGUGGCAAAUUCAUGCCACAU------AAUGGCUAAACGACAUCAC-----------
((((...))))....--...((((((.(((((.....)))))............((((((......))))))..------...))))))..........----------- ( -24.50, z-score =  -1.85, R)
>droEre2.scaffold_4770 2668205 104 - 17746568
AUCGCAAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGAACCAUUUAAAUGAAAAUGGCAAACUCAUGCCACAU------AAUGGUUAAACGACAUCAGAAGAGCAAAAC
...((......(.((.((((....)))).)).).....(((((((...(((....(((((......))))))))------)))))))................))..... ( -20.20, z-score =  -1.71, R)
>droGri2.scaffold_14830 4714662 109 + 6267026
GUCAACAGAGCAAUAAUAA-UUGGAGAGAGGGAAAAACGCUCAACUAAAUGCAUAUUCAAACAUAUUAUUAAAUUGCGAAGAAGAUUAAAUAAAUCGACAAUAUUCACAC
(((......((((((((((-(((....(((.(.....).))).......((......))..)).)))))))..))))......((((.....)))))))........... ( -13.80, z-score =  -1.25, R)
>consensus
UUCGCUAAAAAGCCAACGAGUUGACUCGCUGCCAAGAGCAGCAUUUAAAUGAAAAUGGCAAAUUCAUGCCACAU______AAUGGUUAAACGACAUCAGAAGAGCAACAC
...................((((....(((((.....))))).............(((((......)))))...................))))................ (-12.51 = -12.40 +  -0.11)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:54:00 2011