Locus 12495

Sequence ID dm3.chrX
Location 580,329 – 580,508
Length 179
Max. P 0.973892
window17183 window17184 window17185

overview

Window 3

Location 580,329 – 580,428
Length 99
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 88.31
Shannon entropy 0.19730
G+C content 0.34751
Mean single sequence MFE -23.70
Consensus MFE -21.66
Energy contribution -21.26
Covariance contribution -0.40
Combinations/Pair 1.16
Mean z-score -2.13
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.90
SVM RNA-class probability 0.973892
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 580329 99 - 22422827
UCUGAGUGCCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGAAAAAGAAAGCGCACUAAUUGUGUUUUGUAUUACGAUGAAA-------UAAUACUCAAACCCAAAAA
..(((((((((..(((.......)))..))))...((((.((.(.((((((((.....)))))))).).)).))))....-------....))))).......... ( -21.10, z-score =  -2.29, R)
>droSim1.chrX 465641 99 - 17042790
UCUGAGUGGCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGGAAAAGAAAGCGCGCUAAUUGUGUUUUGCAUUACGAUGAAA-------UAAUACUUAAAACCGAAAA
..((((((...(((((((((((......))))..)))))))....((((((((.....))))))))..............-------...)))))).......... ( -21.20, z-score =  -0.77, R)
>droSec1.super_10 427681 106 - 3036183
UCUGAGUGGCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGGAAAAGAAAGCGCGCUAAUUGUGUUUUGUAUUACGAUGAAAUAUAAUAUAAUACUUAAAACCAAAAA
..((((((((.(((((((((((......))))..)))))))...(....)))....(((((((((..(......)..)))))))))....)))))).......... ( -22.70, z-score =  -1.60, R)
>droYak2.chrX 505583 98 - 21770863
UUUGAGUGGCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGGAAAAGAAAGCGCACUAAUUGUGUUUUGUAUUACAAUAAAA-------UAACACUCAAAACUAAAA-
((((((((...(((((((((((......))))..)))))))..(.((((((((.....)))))))).)............-------...)))))))).......- ( -28.40, z-score =  -3.95, R)
>droEre2.scaffold_4644 543693 99 - 2521924
UUUGAGUGGCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGGAAAUGAAAGCCCACUAAUUGUGUUUUGUAUUACAAUUAAA-------UAAUGCUCAAAACUGUGGA
((((((((((.(((((((((((......))))..))))))).......)))...((((((((........))))))))..-------....)))))))........ ( -25.10, z-score =  -2.05, R)
>consensus
UCUGAGUGGCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGGAAAAGAAAGCGCACUAAUUGUGUUUUGUAUUACGAUGAAA_______UAAUACUCAAAACCAAAAA
..((((((...(((((((((((......))))..)))))))....((((((((.....))))))))........................)))))).......... (-21.66 = -21.26 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 580,361 – 580,468
Length 107
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 78.14
Shannon entropy 0.42045
G+C content 0.43994
Mean single sequence MFE -30.63
Consensus MFE -17.85
Energy contribution -19.75
Covariance contribution 1.90
Combinations/Pair 1.30
Mean z-score -1.61
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.736894
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 580361 107 - 22422827
ACUCGAAAUGGCCAACUUCACUCAACUUUGAGCGGGCUAUUCUGAGUGCCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGAAAAAGA--AAGCGCACUAAUUGUGUUUUG
(((((.(((((((..((.((........))))..))))))).)))))((((..(((.......)))..)))).............(--(((((((.....)))))))). ( -30.10, z-score =  -1.89, R)
>droSim1.chrX 465673 107 - 17042790
ACUCGAAAUGGCCAACUUCACUCAACUUUGAGCGGGCUAUUCUGAGUGGCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGGAAAAGA--AAGCGCGCUAAUUGUGUUUUG
(((((.(((((((..((.((........))))..))))))).)))))....(((((((((((......))))..)))))))....(--(((((((.....)))))))). ( -33.70, z-score =  -2.15, R)
>droSec1.super_10 427720 107 - 3036183
ACUCAAAAUGGCCAACUUCACUCAACUUUGAGCGGGCUAUUCUGAGUGGCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGGAAAAGA--AAGCGCGCUAAUUGUGUUUUG
(((((.(((((((..((.((........))))..))))))).)))))....(((((((((((......))))..)))))))....(--(((((((.....)))))))). ( -34.40, z-score =  -2.50, R)
>droYak2.chrX 505614 107 - 21770863
ACUCGAAAUGGGCAACUUCACUCAACUUUGAGCAGGCUAUUUUGAGUGGCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGGAAAAGA--AAGCGCACUAAUUGUGUUUUG
(((((((((((.(...((((........))))..).)))))))))))....(((((((((((......))))..)))))))....(--(((((((.....)))))))). ( -32.30, z-score =  -2.07, R)
>droEre2.scaffold_4644 543725 107 - 2521924
ACUCAAAACGGCCAACUUCACUCAACUUUGAGCAGGCUAUUUUGAGUGGCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGGAAAUGA--AAGCCCACUAAUUGUGUUUUG
((((((((..(((...((((........))))..)))..))))))))(((.(((((((((((......))))..))))))).....--..)))(((.....)))..... ( -30.30, z-score =  -1.91, R)
>droVir3.scaffold_12970 10476957 104 + 11907090
GAUGCUGUCUGCUCAGUGCAUUUAACUCAGAAU--GCCACUCAAAGUAAC-UUCACUCGCGGA--AAGCGCUCAAGUCAGCCGCGGUUAAAUUCAAAAGGUGUGCUAGG
((((((.(((((..(((((((((......))))--).))))...(((...-...))).)))))--.)))).)).....((((((..((.......))..))).)))... ( -23.00, z-score =   0.88, R)
>consensus
ACUCGAAAUGGCCAACUUCACUCAACUUUGAGCGGGCUAUUCUGAGUGGCAUCCAAUUGCCGUUUGAUUGGCUAAGUUGGAAAAGA__AAGCGCACUAAUUGUGUUUUG
(((((.(((((((.......((((....))))..))))))).)))))....((((((.((((......))))...)))))).......(((((((.....))))))).. (-17.85 = -19.75 +   1.90)

alignment

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secondary structure

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dotplot

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Window 5

Location 580,399 – 580,508
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.50
Shannon entropy 0.44597
G+C content 0.48803
Mean single sequence MFE -29.97
Consensus MFE -16.04
Energy contribution -17.74
Covariance contribution 1.70
Combinations/Pair 1.26
Mean z-score -1.78
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.84
SVM RNA-class probability 0.831386
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 580399 109 - 22422827
GCCUCACUGUGCAGUUUCCUCUCACAACCAGCGCACAAUCACUCGAAAUGGCCAACUUCACUCAACUUUGAGCGGGCUAUUCUGAGUGCCAUCCAAUUGC------CGUUUGAUU-----
((((...((((.((......))))))...)).)).....((((((.(((((((..((.((........))))..))))))).))))))............------.........----- ( -25.40, z-score =  -0.93, R)
>droSim1.chrX 465711 109 - 17042790
GCCUCACUGUGCAGUUUCCUCUCACAACCAGCGCACAGUCACUCGAAAUGGCCAACUUCACUCAACUUUGAGCGGGCUAUUCUGAGUGGCAUCCAAUUGC------CGUUUGAUU-----
.....(((((((.(((.............)))))))))).(((((.(((((((..((.((........))))..))))))).)))))((((......)))------)........----- ( -32.02, z-score =  -2.09, R)
>droSec1.super_10 427758 109 - 3036183
GCCUCACUGUGCAGUUUCCUCUCACAAUCAGCGCACAGUCACUCAAAAUGGCCAACUUCACUCAACUUUGAGCGGGCUAUUCUGAGUGGCAUCCAAUUGC------CGUUUGAUU-----
.....(((((((.(((.............)))))))))).(((((.(((((((..((.((........))))..))))))).)))))((((......)))------)........----- ( -32.72, z-score =  -2.77, R)
>droYak2.chrX 505652 109 - 21770863
GCACCACUGUGCAGUUUCCUCUCAAAUCCAGCGCAAAGUCACUCGAAAUGGGCAACUUCACUCAACUUUGAGCAGGCUAUUUUGAGUGGCAUCCAAUUGC------CGUUUGAUU-----
((((....))))............((((.(((((((.((((((((((((((.(...((((........))))..).))))))))))))))......))).------)))).))))----- ( -30.70, z-score =  -1.69, R)
>droEre2.scaffold_4644 543763 109 - 2521924
GCCUCACUGUGCGAUUUCCUCUCGAAGCCAGCGCACAGUCACUCAAAACGGCCAACUUCACUCAACUUUGAGCAGGCUAUUUUGAGUGGCAUCCAAUUGC------CGUUUGAUU-----
.....((((((((.((((.....))))....)))))))).((((((((..(((...((((........))))..)))..))))))))((((......)))------)........----- ( -35.20, z-score =  -3.16, R)
>droVir3.scaffold_12970 10476984 117 + 11907090
GUAUCACAGACAACAAUUCUCAUACCACUGUCGCGCAACAGAUGCUGUCUGCUCAGUGCAUUUAACUCAGAAU--GCCACUCAAAGUAAC-UUCACUCGCGGAAAGCGCUCAAGUCAGCC
........(((................((((......))))..(((.(((((..(((((((((......))))--).))))...(((...-...))).))))).)))......))).... ( -23.80, z-score =  -0.05, R)
>consensus
GCCUCACUGUGCAGUUUCCUCUCACAACCAGCGCACAGUCACUCGAAAUGGCCAACUUCACUCAACUUUGAGCGGGCUAUUCUGAGUGGCAUCCAAUUGC______CGUUUGAUU_____
........((((..................))))...((((((((.(((((((.......((((....))))..))))))).)))))))).............................. (-16.04 = -17.74 +   1.70)

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 01:03:24 2011