Locus 12668

Sequence ID dm3.chrX
Location 1,542,489 – 1,542,638
Length 149
Max. P 0.959067
window17417 window17418 window17419

overview

Window 7

Location 1,542,489 – 1,542,588
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 69.48
Shannon entropy 0.52931
G+C content 0.66049
Mean single sequence MFE -41.20
Consensus MFE -30.12
Energy contribution -29.64
Covariance contribution -0.48
Combinations/Pair 1.48
Mean z-score -0.97
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.22
SVM RNA-class probability 0.911539
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1542489 99 + 22422827
UGAGCGCAGCAGCAGCGGCGGCCAACAAUAGCGUUAAUGUGGGCGGUGGAUCGGUAGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAG
.(.(((((((((((((.((.(((.....((.((((......)))).))....)))..(((..(((...)))..))).)).))))))))))).))).... ( -44.40, z-score =  -0.48, R)
>droSim1.chrU 14847082 99 - 15797150
UGAGCGCAGCAGCAGCGGCGGCCAACAAUAGCGUUAAUGUAGGCGGUGGAUCGGUAGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAG
.(.(((((((((((((.((.(((.....((.((((......)))).))....)))..(((..(((...)))..))).)).))))))))))).))).... ( -44.30, z-score =  -0.69, R)
>droSec1.super_10 1348260 99 + 3036183
UGAGCGCAGCAGCAGCGGCGGCCAACAAUAGCGUUAAUGUAGGCGGUGGAUCGGUAGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAG
.(.(((((((((((((.((.(((.....((.((((......)))).))....)))..(((..(((...)))..))).)).))))))))))).))).... ( -44.30, z-score =  -0.69, R)
>droWil1.scaffold_181150 4589392 75 + 4952429
---------UUAGUGCUGCUGCUGGUAAUAGUGUUGG--------------CGGC-GGUGGGGCCAAUGGCAAUGCUGUGGCAGCGGCAGCUGCAGCAG
---------...((((((((((((.((.((((((((.--------------((..-((.....))..)).)))))))))).)))))))))).))..... ( -35.70, z-score =  -1.73, R)
>droVir3.scaffold_13042 5029588 81 + 5191987
---UAACCGCUGCGGCGGCGGUUAACAAUAGUGUUG---------------CAGGGGGCGGGGCUGGGGGGAAUGCUGUGGCCGCAGCAGCAGCUGCCG
---.....((((((((.(((((...(..((((.(((---------------(.....)))).))))..).....))))).)))))))).((....)).. ( -37.30, z-score =  -1.27, R)
>consensus
UGAGCGCAGCAGCAGCGGCGGCCAACAAUAGCGUUAAUGU_GGCGGUGGAUCGGUAGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAG
.....((.((.(((((((((((((((......)))......................(((..(((...)))..)))...)))))))))))).)).)).. (-30.12 = -29.64 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,542,489 – 1,542,588
Length 99
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 69.48
Shannon entropy 0.52931
G+C content 0.66049
Mean single sequence MFE -32.08
Consensus MFE -21.48
Energy contribution -21.64
Covariance contribution 0.16
Combinations/Pair 1.45
Mean z-score -1.36
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.66
SVM RNA-class probability 0.959067
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1542489 99 - 22422827
CUGCGGCUGCAGCAGCAGCCACUGCAUUGCCCCCGGCCCCGCCUACCGAUCCACCGCCCACAUUAACGCUAUUGUUGGCCGCCGCUGCUGCUGCGCUCA
....(((.(((((((((((....((.........(((...)))............(((.(((.((....)).))).))).)).)))))))))))))).. ( -36.20, z-score =  -1.30, R)
>droSim1.chrU 14847082 99 + 15797150
CUGCGGCUGCAGCAGCAGCCACUGCAUUGCCCCCGGCCCCGCCUACCGAUCCACCGCCUACAUUAACGCUAUUGUUGGCCGCCGCUGCUGCUGCGCUCA
....(((.(((((((((((....((.........(((...)))............(((.(((.((....)).))).))).)).)))))))))))))).. ( -36.20, z-score =  -1.34, R)
>droSec1.super_10 1348260 99 - 3036183
CUGCGGCUGCAGCAGCAGCCACUGCAUUGCCCCCGGCCCCGCCUACCGAUCCACCGCCUACAUUAACGCUAUUGUUGGCCGCCGCUGCUGCUGCGCUCA
....(((.(((((((((((....((.........(((...)))............(((.(((.((....)).))).))).)).)))))))))))))).. ( -36.20, z-score =  -1.34, R)
>droWil1.scaffold_181150 4589392 75 - 4952429
CUGCUGCAGCUGCCGCUGCCACAGCAUUGCCAUUGGCCCCACC-GCCG--------------CCAACACUAUUACCAGCAGCAGCACUAA---------
.((((((.((((..((((...)))).......(((((......-...)--------------)))).........)))).))))))....--------- ( -24.20, z-score =  -1.61, R)
>droVir3.scaffold_13042 5029588 81 - 5191987
CGGCAGCUGCUGCUGCGGCCACAGCAUUCCCCCCAGCCCCGCCCCCUG---------------CAACACUAUUGUUAACCGCCGCCGCAGCGGUUA---
....(((((((((.(((((.....................((.....)---------------)((((....))))....))))).))))))))).--- ( -27.60, z-score =  -1.21, R)
>consensus
CUGCGGCUGCAGCAGCAGCCACUGCAUUGCCCCCGGCCCCGCCUACCGAUCCACCGCC_ACAUUAACGCUAUUGUUGGCCGCCGCUGCUGCUGCGCUCA
........(((((((((((....((........(((.........)))...................((((....)))).)).)))))))))))..... (-21.48 = -21.64 +   0.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,542,544 – 1,542,638
Length 94
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 81.38
Shannon entropy 0.33678
G+C content 0.71683
Mean single sequence MFE -53.34
Consensus MFE -40.26
Energy contribution -41.14
Covariance contribution 0.88
Combinations/Pair 1.25
Mean z-score -1.54
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.75
SVM RNA-class probability 0.807376
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1542544 94 + 22422827
AGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAGCUGCCGCGGCGGCCGAACUGCUUCUCUCUCCGAUCGUUGGCGCCGCUGCC
.(((((.((((((((....((((((((((((((.(((((....))))).)))))))))..)))))....)))))(....)..))).)))))... ( -54.20, z-score =  -1.67, R)
>droSim1.chrU 14847137 94 - 15797150
AGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAGCUGCCGCGGCGGCCGAACUGCUUCUCUCUCCGAUCGUUGGCGCCGCUGCC
.(((((.((((((((....((((((((((((((.(((((....))))).)))))))))..)))))....)))))(....)..))).)))))... ( -54.20, z-score =  -1.67, R)
>droSec1.super_10 1348315 94 + 3036183
AGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAGCUGCCGCGGCGGCCGAACUGCUUCUCUCUCCGAUCGUUGGCGCCGCUGCC
.(((((.((((((((....((((((((((((((.(((((....))))).)))))))))..)))))....)))))(....)..))).)))))... ( -54.20, z-score =  -1.67, R)
>droWil1.scaffold_181150 4589426 91 + 4952429
---UGGGGCCAAUGGCAAUGCUGUGGCAGCGGCAGCUGCAGCAGCUGCUGCCGCCGCUGAGUUAUUGCUCUCACCAAUUGUGGGGGCAGCCGCU
---.(.(((.((((((...((.(((((((((((.((....)).))))))))))).))...))))))((((((((.....)))))))).))).). ( -49.50, z-score =  -1.89, R)
>droVir3.scaffold_13042 5029625 94 + 5191987
GGGCGGGGCUGGGGGGAAUGCUGUGGCCGCAGCAGCAGCUGCCGCUGCGGCCGCUGCUGAGCUGCUCCUCUCGCCAAUUGUGGGCGCCGCAGCC
.((((.(((.(((((((..((((((((((((((.((....)).))))))))))).....)))...)))))))(((.......)))))).).))) ( -54.60, z-score =  -0.81, R)
>consensus
AGGCGGGGCCGGGGGCAAUGCAGUGGCUGCUGCUGCAGCCGCAGCUGCCGCGGCGGCCGAACUGCUUCUCUCUCCGAUCGUUGGCGCCGCUGCC
..((((.((((((((....((((((((((((((.(((((....))))).)))))))))..)))))..)))))..(....)..))).)))).... (-40.26 = -41.14 +   0.88)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:06:36 2011