Locus 11997

Sequence ID dm3.chr3R
Location 25,003,963 – 25,004,069
Length 106
Max. P 0.699193
window16487 window16488

overview

Window 7

Location 25,003,963 – 25,004,069
Length 106
Sequences 6
Columns 121
Reading direction forward
Mean pairwise identity 75.50
Shannon entropy 0.42787
G+C content 0.46786
Mean single sequence MFE -30.52
Consensus MFE -15.59
Energy contribution -16.62
Covariance contribution 1.03
Combinations/Pair 1.14
Mean z-score -1.70
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.24
SVM RNA-class probability 0.607612
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25003963 106 + 27905053
-----------UUCUGGCUUCUGACAGACUUGAUGAUGGCUGUCAGCCACGU-UGAUGAUCAAUGGCCGG-GAGAUAUUUGGCCGGGAAUUAC-GAUUGAGUCACGCCCAUAAAAAUAGA-
-----------(((((((..(((((((.((.......)))))))))...(((-((.....))))))))))-))..(((((....(((....((-......))....)))....)))))..- ( -30.70, z-score =  -1.09, R)
>droSim1.chr3R 24676257 106 + 27517382
-----------UUCUGGCUUCUGACAGACUUGAUGAUGGCUGUCAGCCACGU-UGAUGAUCAAUGGCCGG-GAGAUAUUCGGCCGGGAAUUAC-GAUUGAGUCACGCCCAUAGAAAUAGA-
-----------(((((((..(((((((.((.......)))))))))...(((-((.....))))))))((-(....(((((..((.......)-)..)))))....)))..)))).....- ( -31.70, z-score =  -0.91, R)
>droSec1.super_4 3868488 107 + 6179234
-----------UUCUGGCUUCUGACAGACUCGAUGAUGUCUGUCAGCCACGU-UGAUGAUCAAUGGCCGG-GAGAUAUUCGGCCCGGAAUUAUUGAUUGAGUCACGCCCAUAGAAAUAGA-
-----------(((((((..(((((((((........)))))))))....((-.(((((((((((.((((-(.(.....)..)))))...))))))))..))))))))...)))).....- ( -38.60, z-score =  -2.92, R)
>droYak2.chr3R 7338118 114 - 28832112
UGACUUCUGACUUCUGAGUUCUGACAGACU---UGAUGGCUGUCAGCCACGU-UGAUGAUCAAUGGCCGG-GAGAUAUUUGGCCUGGAAUUAC-GCUUGAGUCACGCCCAUAAAAAUAGA-
.......((((((..((((.(((((((.((---....)))))))))(((.((-((.....))))((((((-(.....))))))))))......-))))))))))................- ( -29.40, z-score =  -0.48, R)
>droEre2.scaffold_4887 1026 96 - 1626
------------------UUCUGACAGACC---UGAUGGCUGUCAGCCACGU-UGAUGAUCAAUGGCCGG-GAGAUAUUUGGCCGGGAACUAC-GAUUGAGUCACGGCCAUAAAAAUAGA-
------------------..(((((((.((---....)))))))))((.(((-((.....)))))....)-).......((((((.((.((..-.....)))).))))))..........- ( -30.60, z-score =  -2.04, R)
>droAna3.scaffold_13340 9459701 87 - 23697760
---------------------------------UGUCAAUCUGACGGAACAUACGAUGAUCAAUGGCCGAAGAAACACUUGGCCAAGAAUCAC-AGUUGAGUCAGAGCCAUAAAAAUAGAA
---------------------------------......((((((....((.((..((((...(((((((........)))))))...)))).-.)))).))))))............... ( -22.10, z-score =  -2.74, R)
>consensus
___________UUCUGGCUUCUGACAGACU___UGAUGGCUGUCAGCCACGU_UGAUGAUCAAUGGCCGG_GAGAUAUUUGGCCGGGAAUUAC_GAUUGAGUCACGCCCAUAAAAAUAGA_
....................(((((((.(........).)))))))..........((((((((((((((........))))))...........))))).)))................. (-15.59 = -16.62 +   1.03)

alignment

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secondary structure

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dotplot

Postscript

Window 8

Location 25,003,963 – 25,004,069
Length 106
Sequences 6
Columns 121
Reading direction reverse
Mean pairwise identity 75.50
Shannon entropy 0.42787
G+C content 0.46786
Mean single sequence MFE -27.82
Consensus MFE -15.59
Energy contribution -17.45
Covariance contribution 1.86
Combinations/Pair 1.08
Mean z-score -1.60
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.45
SVM RNA-class probability 0.699193
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25003963 106 - 27905053
-UCUAUUUUUAUGGGCGUGACUCAAUC-GUAAUUCCCGGCCAAAUAUCUC-CCGGCCAUUGAUCAUCA-ACGUGGCUGACAGCCAUCAUCAAGUCUGUCAGAAGCCAGAA-----------
-(((........(((.((.((......-)).)).)))((((.........-..))))...........-..((..(((((((.(........).)))))))..)).))).----------- ( -24.70, z-score =  -0.47, R)
>droSim1.chr3R 24676257 106 - 27517382
-UCUAUUUCUAUGGGCGUGACUCAAUC-GUAAUUCCCGGCCGAAUAUCUC-CCGGCCAUUGAUCAUCA-ACGUGGCUGACAGCCAUCAUCAAGUCUGUCAGAAGCCAGAA-----------
-.....((((..(((.((.((......-)).)).)))(((((........-.)))))...........-..((..(((((((.(........).)))))))..)).))))----------- ( -27.60, z-score =  -0.92, R)
>droSec1.super_4 3868488 107 - 6179234
-UCUAUUUCUAUGGGCGUGACUCAAUCAAUAAUUCCGGGCCGAAUAUCUC-CCGGCCAUUGAUCAUCA-ACGUGGCUGACAGACAUCAUCGAGUCUGUCAGAAGCCAGAA-----------
-..........(((((((......((((((....(((((..(.....).)-))))..)))))).....-))))..(((((((((........)))))))))...)))...----------- ( -32.50, z-score =  -1.89, R)
>droYak2.chr3R 7338118 114 + 28832112
-UCUAUUUUUAUGGGCGUGACUCAAGC-GUAAUUCCAGGCCAAAUAUCUC-CCGGCCAUUGAUCAUCA-ACGUGGCUGACAGCCAUCA---AGUCUGUCAGAACUCAGAAGUCAGAAGUCA
-............(((.((((((..((-((.......((((.........-..))))..((.....))-))))..(((((((.(....---.).)))))))......).)))))...))). ( -27.30, z-score =  -0.56, R)
>droEre2.scaffold_4887 1026 96 + 1626
-UCUAUUUUUAUGGCCGUGACUCAAUC-GUAGUUCCCGGCCAAAUAUCUC-CCGGCCAUUGAUCAUCA-ACGUGGCUGACAGCCAUCA---GGUCUGUCAGAA------------------
-..........((((((.(((((....-).))))..))))))....(((.-..((((((((.....))-..))))))(((((((....---)).)))))))).------------------ ( -29.50, z-score =  -2.63, R)
>droAna3.scaffold_13340 9459701 87 + 23697760
UUCUAUUUUUAUGGCUCUGACUCAACU-GUGAUUCUUGGCCAAGUGUUUCUUCGGCCAUUGAUCAUCGUAUGUUCCGUCAGAUUGACA---------------------------------
...............((((((.((((.-((((((..((((((((.....))).)))))..)))))).)).))....))))))......--------------------------------- ( -25.30, z-score =  -3.17, R)
>consensus
_UCUAUUUUUAUGGGCGUGACUCAAUC_GUAAUUCCCGGCCAAAUAUCUC_CCGGCCAUUGAUCAUCA_ACGUGGCUGACAGCCAUCA___AGUCUGUCAGAAGCCAGAA___________
........(((((...((((.(((((...........((((............)))))))))))))....)))))(((((((.(........).))))))).................... (-15.59 = -17.45 +   1.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:53:41 2011