Locus 12827

Sequence ID dm3.chrX
Location 2,487,300 – 2,487,433
Length 133
Max. P 0.997559
window17632 window17633 window17634

overview

Window 2

Location 2,487,300 – 2,487,393
Length 93
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 77.78
Shannon entropy 0.36735
G+C content 0.42025
Mean single sequence MFE -29.18
Consensus MFE -20.10
Energy contribution -22.46
Covariance contribution 2.36
Combinations/Pair 1.12
Mean z-score -3.10
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.13
SVM RNA-class probability 0.997559
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2487300 93 - 22422827
CUCUCAUUCGCUCGCUUU-GUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGCAUGCAACGCUCCAGCGAUUGCAGGGCAGUG--------
....((((.((((....(-((..((((((((((((((((......)))))))))).)))))))))((((((((....))).)))))))))))))-------- ( -32.10, z-score =  -3.32, R)
>droSim1.chrX 1763759 89 - 17042790
----CUCUCAUUCGCUUU-GUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGAAUGCAACGCUCCAGCGAUUGCAGGGCAGUG--------
----....((((.(((((-(((..(((((((((((((((......)))))))))).)))))..)))(((((((....))).)))))))))))))-------- ( -32.00, z-score =  -4.08, R)
>droSec1.super_10 2260436 89 - 3036183
----CUCUCAUUCGCUUU-GUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGAAUGCAACGCUCCAGCGAUUGCAGGGCAGUG--------
----....((((.(((((-(((..(((((((((((((((......)))))))))).)))))..)))(((((((....))).)))))))))))))-------- ( -32.00, z-score =  -4.08, R)
>droEre2.scaffold_4644 2439846 93 - 2521924
CUCUCAUUUGCGGGCUUU-GUUUGUUUUCGUUUUUCGCAACUAACUGCGAGAAAACGAAAAUGAAUGCAACGCUCCAACGAUUGCAGGGCAGUG--------
((((((.(((.((((.((-(((..(((((((((((((((......)))))).)))))))))..)..)))).))))...))).)).)))).....-------- ( -30.70, z-score =  -2.81, R)
>droAna3.scaffold_12929 2412637 93 - 3277472
----CUUUUGUUUGUUUUAAUUUUUGCUGUUUUUUUGCUAUU-AUUUUGUGA----GAAAAUGAAUGCAACGCUCGAGCGAUUGCAGUCUACUCUGGCUUUG
----.....................((((((((((..(....-.....)..)----))))))((.((((((((....))).))))).))......))).... ( -19.10, z-score =  -1.21, R)
>consensus
____CUUUCGUUCGCUUU_GUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAUGAAUGCAACGCUCCAGCGAUUGCAGGGCAGUG________
.............(((((.((((((((((((((((((((......)))))))))).))))))))))(((((((....))).)))))))))............ (-20.10 = -22.46 +   2.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,487,332 – 2,487,433
Length 101
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 87.54
Shannon entropy 0.20278
G+C content 0.32327
Mean single sequence MFE -21.80
Consensus MFE -14.72
Energy contribution -15.72
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.563733
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2487332 101 + 22422827
AUUUUCAUUUUCUCGCAGUUAGUUGCGAAAAAAGAAAACAAACAAAGCGAGCGAAUGAGAGGCGCAAUAUAUAGUAUAGUAAAGUGCUAUUGUUUAAUUAA
.(((((.((((.((((((....)))))).))))))))).((((((.(((..(......)...)))......((((((......))))))))))))...... ( -22.10, z-score =  -1.62, R)
>droSim1.chrX 1763791 97 + 17042790
AUUUUCAUUUUCUCGCAGUUAGUUGCGAAAAAAGAAAACAAACAAAGCGA----AUGAGAGGCGCGAUAUAUAGUAUAGUAAAGUGCUAUUGUUUAAAUGA
.(((((.((((.((((((....)))))).))))))))).((((((.(((.----.(....).)))......((((((......))))))))))))...... ( -20.60, z-score =  -1.35, R)
>droSec1.super_10 2260468 97 + 3036183
AUUUUCAUUUUCUCGCAGUUAGUUGCGAAAAAAGAAAACAAACAAAGCGA----AUGAGAGGCGCAAUAUAUAGUAUAGUAAAGUGCUAUUGUUUAAAUGA
.(((((.((((.((((((....)))))).))))))))).((((((.(((.----.(....).)))......((((((......))))))))))))...... ( -20.60, z-score =  -1.66, R)
>droEre2.scaffold_4644 2439878 95 + 2521924
AUUUUCGUUUUCUCGCAGUUAGUUGCGAAAAACGAAAACAAACAAAGCCCGCAAAUGAGAGGCACC-CAUAUAGUAUUAUA-----CUAUUGUUGAAAUUA
.((((((((((.((((((....))))))))))))))))..(((((.((((........).)))...-....(((((...))-----))))))))....... ( -23.90, z-score =  -3.68, R)
>consensus
AUUUUCAUUUUCUCGCAGUUAGUUGCGAAAAAAGAAAACAAACAAAGCGA____AUGAGAGGCGCAAUAUAUAGUAUAGUAAAGUGCUAUUGUUUAAAUGA
.(((((.((((.((((((....)))))))))).))))).((((((.((.............))........((((((......))))))))))))...... (-14.72 = -15.72 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,487,332 – 2,487,433
Length 101
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 87.54
Shannon entropy 0.20278
G+C content 0.32327
Mean single sequence MFE -20.35
Consensus MFE -14.99
Energy contribution -15.74
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -3.15
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.34
SVM RNA-class probability 0.988928
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2487332 101 - 22422827
UUAAUUAAACAAUAGCACUUUACUAUACUAUAUAUUGCGCCUCUCAUUCGCUCGCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAU
.....(((((((.(((.......((((...))))..(((.........)))..))))))))))(((((((((((((((......)))))))))).))))). ( -20.80, z-score =  -3.43, R)
>droSim1.chrX 1763791 97 - 17042790
UCAUUUAAACAAUAGCACUUUACUAUACUAUAUAUCGCGCCUCUCAU----UCGCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAU
.....((((((((((.......))))..........(((........----.)))..))))))(((((((((((((((......)))))))))).))))). ( -18.60, z-score =  -3.22, R)
>droSec1.super_10 2260468 97 - 3036183
UCAUUUAAACAAUAGCACUUUACUAUACUAUAUAUUGCGCCUCUCAU----UCGCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAU
.....(((((((.(((...............................----..))))))))))(((((((((((((((......)))))))))).))))). ( -18.31, z-score =  -3.06, R)
>droEre2.scaffold_4644 2439878 95 - 2521924
UAAUUUCAACAAUAG-----UAUAAUACUAUAUG-GGUGCCUCUCAUUUGCGGGCUUUGUUUGUUUUCGUUUUUCGCAACUAACUGCGAGAAAACGAAAAU
.......((((((((-----((...))))))...-...(((((......).))))..)))).((((((((((((((((......)))))).)))))))))) ( -23.70, z-score =  -2.89, R)
>consensus
UCAUUUAAACAAUAGCACUUUACUAUACUAUAUAUUGCGCCUCUCAU____UCGCUUUGUUUGUUUUCUUUUUUCGCAACUAACUGCGAGAAAAUGAAAAU
.....(((((((.(((.....................................))))))))))(((((((((((((((......)))))))))).))))). (-14.99 = -15.74 +   0.75)

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 01:09:32 2011