Locus 14604

Sequence ID dm3.chrX
Location 14,336,034 – 14,336,171
Length 137
Max. P 0.975160
window20109 window20110

overview

Window 9

Location 14,336,034 – 14,336,171
Length 137
Sequences 5
Columns 140
Reading direction forward
Mean pairwise identity 69.05
Shannon entropy 0.55860
G+C content 0.43492
Mean single sequence MFE -31.17
Consensus MFE -14.90
Energy contribution -17.14
Covariance contribution 2.24
Combinations/Pair 1.27
Mean z-score -1.22
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.647502
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 14336034 137 + 22422827
UUUCCUUGCCAAAUCAUUUGGCCUGCCGCCAACACAAUCGGCAACAACGAAAACGUUG--GUAAAUGCAACAAAA-AUGCGCAAUUUGCAAUUGCACAGAGAAAACACAGAGGGAAUAUCUCUAUAUUGUUGGCAGUAAA
.......(((((.....))))).(((.(((((((...((.(((((((((....)))))--((((((((.......-....)).))))))..))))...))........(((((.....)))))....))))))).))).. ( -36.40, z-score =  -1.93, R)
>droSec1.super_20 931245 129 + 1148123
UUUCCUUGCCAAAUCAUUUGGCCUGCCGCCAACACAAUCGGCAACAACGAAAACUAUG--GUAAAUGCAACAAAA-AUGCGCAAUUUGCAAUUGCACA-------CACAGAGGGA-UAUCUCUAUAUUGUUGGCAGUAGA
.......(((((.....)))))((((.(((((((...(((.......)))......((--((((.(((((.....-.........))))).)))).))-------...(((((..-..)))))....))))))).)))). ( -33.24, z-score =  -1.48, R)
>droYak2.chrX 8573232 139 + 21770863
UUUCCUUGCCAAAUCAUUUGGCCUGCCGCCAACACAAUCGGCAACAACGAAAACGAUGCAACAAAUGCAACAAAA-AUGCGCAAUUUGCAAUUGCACAGAGAAAACACAGGGUGAAUAUCCCUAUAUUGUUGGCAGUGAA
.......(((((.....)))))((((((((.........)))...(((((...(..(((((.....(((......-.)))((.....))..)))))..).........((((.......))))...)))))))))).... ( -33.20, z-score =  -0.56, R)
>droEre2.scaffold_4690 6131537 125 - 18748788
UUUCCUUGCCAAAUCAUUUGGCCUGCCGCCAACACAAUCGGCAACAACAAAUCCCAGG--CUGAAUGCAACAAAA-AUGCGCA-CUUGCAA---CACAGUAAGGGUAUAUACAAG---UAUGUAUAGUGUUGGCA-----
.......(((((.....))))).....((((((((....(....).......(((..(--(((...(((......-.)))((.-...))..---..))))..)))..((((((..---..)))))))))))))).----- ( -38.10, z-score =  -2.28, R)
>droAna3.scaffold_13248 2038818 116 + 4840945
GCUUCUUGCCAAAUAACUUGGCCUGCCGCCAGUCC---CUGCCUCACUCCCAGUCCCCAGUCUGUUGCCACAAAGCAUCUGCAAUCUGCAACGAAAU--------UAUAUA-----UAUCUCUCUCUUUAUG--------
((((..((.(((.....(((((.....)))))...---............(((.(....).)))))).))..))))...(((.....))).......--------......-----................-------- ( -14.90, z-score =   0.14, R)
>consensus
UUUCCUUGCCAAAUCAUUUGGCCUGCCGCCAACACAAUCGGCAACAACGAAAACCAUG__GUAAAUGCAACAAAA_AUGCGCAAUUUGCAAUUGCACAG__A___CACAGAGGGA_UAUCUCUAUAUUGUUGGCAGU__A
.......(((((.....))))).....(((((((..........................((((.(((((...............))))).)))).............(((((.....)))))....)))))))...... (-14.90 = -17.14 +   2.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,336,034 – 14,336,171
Length 137
Sequences 5
Columns 140
Reading direction reverse
Mean pairwise identity 69.05
Shannon entropy 0.55860
G+C content 0.43492
Mean single sequence MFE -39.12
Consensus MFE -22.77
Energy contribution -25.14
Covariance contribution 2.37
Combinations/Pair 1.26
Mean z-score -1.63
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.92
SVM RNA-class probability 0.975160
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 14336034 137 - 22422827
UUUACUGCCAACAAUAUAGAGAUAUUCCCUCUGUGUUUUCUCUGUGCAAUUGCAAAUUGCGCAU-UUUUGUUGCAUUUAC--CAACGUUUUCGUUGUUGCCGAUUGUGUUGGCGGCAGGCCAAAUGAUUUGGCAAGGAAA
....(((((((((((((((((.......)))))))))........((((((((((..((((((.-...)).)))).....--(((((....)))))))).)))))))))))))))...(((((.....)))))....... ( -43.40, z-score =  -2.71, R)
>droSec1.super_20 931245 129 - 1148123
UCUACUGCCAACAAUAUAGAGAUA-UCCCUCUGUG-------UGUGCAAUUGCAAAUUGCGCAU-UUUUGUUGCAUUUAC--CAUAGUUUUCGUUGUUGCCGAUUGUGUUGGCGGCAGGCCAAAUGAUUUGGCAAGGAAA
(((.(((((((((((((((((...-...))))))(-------((((((((.....)))))))))-...............--..........))))))((((((...)))))))))))(((((.....)))))..))).. ( -42.00, z-score =  -2.47, R)
>droYak2.chrX 8573232 139 - 21770863
UUCACUGCCAACAAUAUAGGGAUAUUCACCCUGUGUUUUCUCUGUGCAAUUGCAAAUUGCGCAU-UUUUGUUGCAUUUGUUGCAUCGUUUUCGUUGUUGCCGAUUGUGUUGGCGGCAGGCCAAAUGAUUUGGCAAGGAAA
(((..((((((.(((((((((.......))))))))).....((((((((.....)))))))).-......((((.....))))((((((...(((((((((((...)))))))))))...)))))).))))))..))). ( -46.30, z-score =  -2.27, R)
>droEre2.scaffold_4690 6131537 125 + 18748788
-----UGCCAACACUAUACAUA---CUUGUAUAUACCCUUACUGUG---UUGCAAG-UGCGCAU-UUUUGUUGCAUUCAG--CCUGGGAUUUGUUGUUGCCGAUUGUGUUGGCGGCAGGCCAAAUGAUUUGGCAAGGAAA
-----((((((...((((((..---..))))))..(((...(((((---(.(((((-.......-.))))).)))..)))--...)))((((((((((((((((...)))))))))))..)))))...))))))...... ( -37.30, z-score =  -0.41, R)
>droAna3.scaffold_13248 2038818 116 - 4840945
--------CAUAAAGAGAGAGAUA-----UAUAUA--------AUUUCGUUGCAGAUUGCAGAUGCUUUGUGGCAACAGACUGGGGACUGGGAGUGAGGCAG---GGACUGGCGGCAGGCCAAGUUAUUUGGCAAGAAGC
--------..........(((((.-----......--------))))).((((.....))))..(((((.((.(((..((((..((.(((...((.((....---...)).))..))).)).))))..))).)).))))) ( -26.60, z-score =  -0.29, R)
>consensus
U__ACUGCCAACAAUAUAGAGAUA_UCCCUCUGUG___U__CUGUGCAAUUGCAAAUUGCGCAU_UUUUGUUGCAUUUAC__CAUCGUUUUCGUUGUUGCCGAUUGUGUUGGCGGCAGGCCAAAUGAUUUGGCAAGGAAA
........(((((((((((((.......))))))).......(((((((((...)))))))))....))))))....................((((((((((.....))))))))))((((((...))))))....... (-22.77 = -25.14 +   2.37)

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 01:43:19 2011