Locus 12548

Sequence ID dm3.chrX
Location 853,626 – 853,752
Length 126
Max. P 0.999412
window17255 window17256 window17257

overview

Window 5

Location 853,626 – 853,729
Length 103
Sequences 7
Columns 118
Reading direction reverse
Mean pairwise identity 60.05
Shannon entropy 0.73203
G+C content 0.34880
Mean single sequence MFE -23.57
Consensus MFE -7.04
Energy contribution -7.03
Covariance contribution -0.02
Combinations/Pair 1.75
Mean z-score -2.04
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.41
SVM RNA-class probability 0.937311
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 853626 103 - 22422827
UAUAAAUUAACAAUUAUUUUGA--GCAGUUCUUCGGAACUCGAAAACCAGAAUGAUUGUCAUUUAUUCCAGCCAAUGGAGCAGUUUCAUUGAAAAAAUACAAAUA-------------
.((((((..((((((((((((.--.((((((....))))).).....)))))))))))).))))))......((((((((...))))))))..............------------- ( -23.00, z-score =  -3.13, R)
>dp4.chrXL_group1a 3811832 92 + 9151740
-----GCAGAAAAGUGCCCCAUUAGAAGGGUUUUAAUGCGCAUCGAGUGGGGGAAGUGUGCUUUCGCCCAGCAAAUGUA-CAUUUCCAAUUGAAAAUC--------------------
-----(((......)))((((((.((.(.((......)).).)).))))))((((((((((.((.((...)).)).)))-)))))))...........-------------------- ( -27.70, z-score =  -2.00, R)
>droEre2.scaffold_4644 828404 103 - 2521924
UAUAAAUGGACAAUUAUUUUGU--GCAGCUUUCUGGAACUCGAAAACCAGAAUGAUUGUCAUUUAUGCCAGCGAAUGUGGCAGUUUCAAUGAAAAAAUAUAUACG-------------
.(((((((.((((((((((((.--(....((((........)))).))))))))))))))))))))((((.......))))........................------------- ( -21.30, z-score =  -1.12, R)
>droYak2.chrX 771413 116 - 21770863
UAUAAAUGGACAAUUAUUGUGU--GCAGCUUUCUGGAACUCGGAAACCAGAGUGAUUGUCAUUUAUCCCAGCCAAUGUUGCAGUUUCAAUGAAAAAAUAUAUACGAGUAUACAUACAU
.....(((.....((((((..(--(((((...((((.(((((....)..))))(((........))))))).....))))))....)))))).....(((((....)))))))).... ( -21.30, z-score =   0.06, R)
>droSec1.super_10 695008 94 - 3036183
UAUAAAUGAACAAUUAUUUUGU--GCAGUUCUUCGGAACUCGGAAACCAGAAUGAUUGCCAUUUAUUCCAGCCAAUGGAGCAGUUUCAUUGAAAUG----------------------
.(((((((..(((((((((((.--(.(((((....))))))(....)))))))))))).)))))))......((((((((...)))))))).....---------------------- ( -26.40, z-score =  -3.29, R)
>droSim1.chrX 688316 103 - 17042790
UAUAAAUGAACAAUUAUUUUGU--GCAGUUCUUCGGAACUCGGAAACCAGAAUGAUUGUCAUUUAUUCCAGCCAAUGGAGCAGUUUCAUUGAAAAAAUACAGAUA-------------
.((((((((.(((((((((((.--(.(((((....))))))(....))))))))))))))))))))......((((((((...))))))))..............------------- ( -29.50, z-score =  -4.14, R)
>droGri2.scaffold_15203 3902192 91 + 11997470
------UAAAAAUACACCAGAUGAGAAUCGCUUUUGCAUU-GUAUAUUUGUAC-AUUAUC--UUAAGGCAGUCAUUUGGUUUCUACCAAUGAAUUGAAAUG-----------------
------.........(((((((((.....(((((.....(-((((....))))-).....--..)))))..))))))))).....................----------------- ( -15.80, z-score =  -0.66, R)
>consensus
UAUAAAUGAACAAUUAUUUUGU__GCAGCUCUUUGGAACUCGGAAACCAGAAUGAUUGUCAUUUAUUCCAGCCAAUGGAGCAGUUUCAAUGAAAAAAUAUA_A_______________
.........((((((((((((.....((.((....)).)).......))))))))))))........................................................... ( -7.04 =  -7.03 +  -0.02)

alignment

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secondary structure

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dotplot

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Window 6

Location 853,653 – 853,752
Length 99
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 76.57
Shannon entropy 0.45130
G+C content 0.40521
Mean single sequence MFE -26.55
Consensus MFE -12.66
Energy contribution -14.08
Covariance contribution 1.42
Combinations/Pair 1.24
Mean z-score -2.91
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.48
SVM RNA-class probability 0.991479
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 853653 99 + 22422827
CCAUUGGCUGGAAUAAAUGACAAUCAUUCUGGUUUUCGAGUUCCGAAGAACUGCUCAAAAUAAUUGUUAAUUUAUAAUUGACGAUUACCAGCCAAGCGG
((.((((((((......(((.((((.....)))).)))(((((....)))))........(((((((((((.....)))))))))))))))))))..)) ( -29.50, z-score =  -4.11, R)
>dp4.chrXL_group1a 3811851 91 - 9151740
ACAUUUGCUGGGCGAAAGCACACUUCCCCCACUCGAUGCGCAUUAAAACCCUUC------UAAUGGGGCACUUUUCUGCAUUGUUU--CUACCAAAUGA
.((((((.(((((....))..............(((((((........((((..------....))))........)))))))...--))).)))))). ( -23.99, z-score =  -2.49, R)
>droEre2.scaffold_4644 828431 99 + 2521924
ACAUUCGCUGGCAUAAAUGACAAUCAUUCUGGUUUUCGAGUUCCAGAAAGCUGCACAAAAUAAUUGUCCAUUUAUAAUUGACGAUUACCAGCCAAGCGA
....((((((((...((((.....)))).((((..(((.((..(((....))).))....(((((((......))))))).)))..))))))).))))) ( -24.60, z-score =  -2.61, R)
>droYak2.chrX 771453 99 + 21770863
ACAUUGGCUGGGAUAAAUGACAAUCACUCUGGUUUCCGAGUUCCAGAAAGCUGCACACAAUAAUUGUCCAUUUAUAAUUGACGAUUACCAGCCAAGCGA
...((((((((................(((((..........))))).............((((((((.((.....)).)))))))))))))))).... ( -25.90, z-score =  -2.25, R)
>droSec1.super_10 695026 99 + 3036183
CCAUUGGCUGGAAUAAAUGGCAAUCAUUCUGGUUUCCGAGUUCCGAAGAACUGCACAAAAUAAUUGUUCAUUUAUAAUUGACGAUUACCAGCCAAGCGG
((.((((((((......(((.((((.....)))).)))(((((....)))))........(((((((.((........)))))))))))))))))..)) ( -28.20, z-score =  -2.91, R)
>droSim1.chrX 688343 99 + 17042790
CCAUUGGCUGGAAUAAAUGACAAUCAUUCUGGUUUCCGAGUUCCGAAGAACUGCACAAAAUAAUUGUUCAUUUAUAAUUGACGAUUACCAGCCAAGCGG
((.((((((((..(((((((((((.(((.((((.....(((((....))))))).)).))).)))).)))))))(((((...)))))))))))))..)) ( -27.10, z-score =  -3.10, R)
>consensus
ACAUUGGCUGGAAUAAAUGACAAUCAUUCUGGUUUCCGAGUUCCAAAAAACUGCACAAAAUAAUUGUUCAUUUAUAAUUGACGAUUACCAGCCAAGCGA
...((((((((...........................(((((....)))))........((((((((...........)))))))))))))))).... (-12.66 = -14.08 +   1.42)

alignment

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secondary structure

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dotplot

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Window 7

Location 853,653 – 853,752
Length 99
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 76.57
Shannon entropy 0.45130
G+C content 0.40521
Mean single sequence MFE -31.74
Consensus MFE -15.72
Energy contribution -17.89
Covariance contribution 2.17
Combinations/Pair 1.24
Mean z-score -3.84
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.86
SVM RNA-class probability 0.999412
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 853653 99 - 22422827
CCGCUUGGCUGGUAAUCGUCAAUUAUAAAUUAACAAUUAUUUUGAGCAGUUCUUCGGAACUCGAAAACCAGAAUGAUUGUCAUUUAUUCCAGCCAAUGG
(((.((((((((............((((((..((((((((((((..((((((....))))).).....)))))))))))).)))))).))))))))))) ( -32.82, z-score =  -5.37, R)
>dp4.chrXL_group1a 3811851 91 + 9151740
UCAUUUGGUAG--AAACAAUGCAGAAAAGUGCCCCAUUA------GAAGGGUUUUAAUGCGCAUCGAGUGGGGGAAGUGUGCUUUCGCCCAGCAAAUGU
....((((..(--(((....(((.(....(.(((((((.------((.(.((......)).).)).))))))).)..).)))))))..))))....... ( -24.60, z-score =  -0.72, R)
>droEre2.scaffold_4644 828431 99 - 2521924
UCGCUUGGCUGGUAAUCGUCAAUUAUAAAUGGACAAUUAUUUUGUGCAGCUUUCUGGAACUCGAAAACCAGAAUGAUUGUCAUUUAUGCCAGCGAAUGU
(((((.(((..((((..(.(((((((...((.((((.....)))).))....(((((..........)))))))))))).)..)))))))))))).... ( -28.10, z-score =  -2.55, R)
>droYak2.chrX 771453 99 - 21770863
UCGCUUGGCUGGUAAUCGUCAAUUAUAAAUGGACAAUUAUUGUGUGCAGCUUUCUGGAACUCGGAAACCAGAGUGAUUGUCAUUUAUCCCAGCCAAUGU
..((((((((((((((.....))))((((((.(((((((((.((.(....((((((.....))))))))).)))))))))))))))..)))))))).)) ( -29.40, z-score =  -2.43, R)
>droSec1.super_10 695026 99 - 3036183
CCGCUUGGCUGGUAAUCGUCAAUUAUAAAUGAACAAUUAUUUUGUGCAGUUCUUCGGAACUCGGAAACCAGAAUGAUUGCCAUUUAUUCCAGCCAAUGG
(((.((((((((............(((((((..(((((((((((.(.(((((....))))))(....)))))))))))).))))))).))))))))))) ( -36.22, z-score =  -5.38, R)
>droSim1.chrX 688343 99 - 17042790
CCGCUUGGCUGGUAAUCGUCAAUUAUAAAUGAACAAUUAUUUUGUGCAGUUCUUCGGAACUCGGAAACCAGAAUGAUUGUCAUUUAUUCCAGCCAAUGG
(((.((((((((............((((((((.(((((((((((.(.(((((....))))))(....)))))))))))))))))))).))))))))))) ( -39.32, z-score =  -6.62, R)
>consensus
CCGCUUGGCUGGUAAUCGUCAAUUAUAAAUGAACAAUUAUUUUGUGCAGUUCUUCGGAACUCGGAAACCAGAAUGAUUGUCAUUUAUUCCAGCCAAUGG
.((.((((((((............(((((((.((((((((((((...((.((....)).)).......))))))))))))))))))).)))))))))). (-15.72 = -17.89 +   2.17)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:04:24 2011