Locus 12769

Sequence ID dm3.chrX
Location 2,058,091 – 2,058,221
Length 130
Max. P 0.972679
window17551 window17552 window17553 window17554

overview

Window 1

Location 2,058,091 – 2,058,203
Length 112
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 89.18
Shannon entropy 0.16781
G+C content 0.43978
Mean single sequence MFE -24.60
Consensus MFE -23.96
Energy contribution -23.78
Covariance contribution -0.19
Combinations/Pair 1.09
Mean z-score -0.98
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.727688
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2058091 112 + 22422827
-----ACACACAGACACUACAUCAUAACAAUAAAAAUAAUAGUCAUUUGGCAGAGGCGCACCAUUUGCGUCAACGGCACUUGCCUUCUUGGCAUCUAGUACUCGCAUAGGAAAUGCC-
-----....................................(((....)))...((((((.....))))))...((((..((((.....))))((((((....)).))))...))))- ( -21.80, z-score =  -0.39, R)
>droEre2.scaffold_4644 2021105 105 + 2521924
-------------GCACUACAUUAUAACAAUAAAAAUAAUAGCCAUUUGGCAGAGGCGCACCAUUUGCGUCAACGGCACUUGCCUUCUUGGCAUCUAGUACUCGCAUAGAAAAUGCCA
-------------............................(((....)))...((((((.....))))))...((((..((((.....))))((((((....)).))))...)))). ( -27.10, z-score =  -2.00, R)
>droYak2.chrX 15504349 105 - 21770863
-------------GCACUACAUCAUAACAAUAAAAAUAAUGGCCAUUUGGCAGAGGCGCACCAUUUGCGUCAACGGCACUUGCCUUCUUGGCAUCUAGUACUCGCACAGAAAAUGCCA
-------------............................(((....)))...((((((.....))))))...((((..((((.....))))(((.((......)))))...)))). ( -25.50, z-score =  -0.99, R)
>droSec1.super_10 1841791 117 + 3036183
AGACUCUACGCAGACACUACAUCAUAACAAUAAAAAUAAUAGUCAUUUGGCAGAGGCGCACCAUUUGCGUCAACGGCACUUGCCUUCUUGGCAUCUAGUACUCGCAUAGAAAAUGCC-
....((((.((((((..........................(((....)))(((((((((.....)))))).........((((.....))))))).)).)).)).)))).......- ( -24.00, z-score =  -0.53, R)
>consensus
_____________ACACUACAUCAUAACAAUAAAAAUAAUAGCCAUUUGGCAGAGGCGCACCAUUUGCGUCAACGGCACUUGCCUUCUUGGCAUCUAGUACUCGCAUAGAAAAUGCC_
.........................................(((....)))...((((((.....))))))...((((..((((.....))))((((((....)).))))...)))). (-23.96 = -23.78 +  -0.19) 

alignment

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secondary structure

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dotplot

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Window 2

Location 2,058,091 – 2,058,203
Length 112
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 89.18
Shannon entropy 0.16781
G+C content 0.43978
Mean single sequence MFE -32.61
Consensus MFE -27.94
Energy contribution -27.50
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.42
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.587981
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2058091 112 - 22422827
-GGCAUUUCCUAUGCGAGUACUAGAUGCCAAGAAGGCAAGUGCCGUUGACGCAAAUGGUGCGCCUCUGCCAAAUGACUAUUAUUUUUAUUGUUAUGAUGUAGUGUCUGUGUGU-----
-(((((((..(((....)))..))))))).(((.(((..(..(((((......)))))..)))))))((((...(((.(((((..((((....)))).))))))))..)).))----- ( -30.40, z-score =  -0.90, R)
>droEre2.scaffold_4644 2021105 105 - 2521924
UGGCAUUUUCUAUGCGAGUACUAGAUGCCAAGAAGGCAAGUGCCGUUGACGCAAAUGGUGCGCCUCUGCCAAAUGGCUAUUAUUUUUAUUGUUAUAAUGUAGUGC-------------
((((((((..(((....)))..))))))))(((.(((..(..(((((......)))))..)))))))(((....)))((((((..((((....)))).)))))).------------- ( -31.30, z-score =  -1.40, R)
>droYak2.chrX 15504349 105 + 21770863
UGGCAUUUUCUGUGCGAGUACUAGAUGCCAAGAAGGCAAGUGCCGUUGACGCAAAUGGUGCGCCUCUGCCAAAUGGCCAUUAUUUUUAUUGUUAUGAUGUAGUGC-------------
((((((((...(((....))).))))))))(((.(((..(..(((((......)))))..)))))))(((....)))((((((..((((....)))).)))))).------------- ( -33.50, z-score =  -1.68, R)
>droSec1.super_10 1841791 117 - 3036183
-GGCAUUUUCUAUGCGAGUACUAGAUGCCAAGAAGGCAAGUGCCGUUGACGCAAAUGGUGCGCCUCUGCCAAAUGACUAUUAUUUUUAUUGUUAUGAUGUAGUGUCUGCGUAGAGUCU
-(((....((((((((..(((((.((((..(((.(((..(..(((((......)))))..)))))))))...(((((.............))))).)).)))))..))))))))))). ( -35.22, z-score =  -1.72, R)
>consensus
_GGCAUUUUCUAUGCGAGUACUAGAUGCCAAGAAGGCAAGUGCCGUUGACGCAAAUGGUGCGCCUCUGCCAAAUGACUAUUAUUUUUAUUGUUAUGAUGUAGUGC_____________
.(((((((..(((....)))..)))))))....((((..(..(((((......)))))..)))))((((...(((((...((....))..)))))...))))................ (-27.94 = -27.50 +  -0.44) 

alignment

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secondary structure

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dotplot

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Window 3

Location 2,058,124 – 2,058,221
Length 97
Sequences 4
Columns 121
Reading direction forward
Mean pairwise identity 84.78
Shannon entropy 0.22500
G+C content 0.45509
Mean single sequence MFE -25.60
Consensus MFE -24.81
Energy contribution -24.62
Covariance contribution -0.19
Combinations/Pair 1.09
Mean z-score -0.98
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.795434
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2058124 97 + 22422827
AUAGUCAUUUGGCAGAGGCGCACCAUUUGCGUCAACGGCACUUGCCUUCUUGGCAUCUAGUACUCGCAUAGGAAAUGCCAUAUACCAUAUAU-CCAUG-----------------------
...(..((.(((((..((((((.....))))))...(((....)))((((((((...........)).)))))).))))).))..)......-.....----------------------- ( -23.90, z-score =  -0.67, R)
>droEre2.scaffold_4644 2021130 106 + 2521924
AUAGCCAUUUGGCAGAGGCGCACCAUUUGCGUCAACGGCACUUGCCUUCUUGGCAUCUAGUACUCGCAUAGAAAAUGCCAUGUACCAUAUAUACCAUAUAUCCAUG---------------
...(((....)))...((((((.....))))))...((((..((((.....))))((((((....)).))))...))))...........................--------------- ( -27.10, z-score =  -1.22, R)
>droYak2.chrX 15504374 120 - 21770863
AUGGCCAUUUGGCAGAGGCGCACCAUUUGCGUCAACGGCACUUGCCUUCUUGGCAUCUAGUACUCGCACAGAAAAUGCCAUAUACCAUAUAUACCAUACA-CCAUAUACCAUAUAUCCAUG
((((..((.(((....((((((.....))))))...((((..((((.....))))(((.((......)))))...)))).....................-.......))).))..)))). ( -27.00, z-score =  -0.81, R)
>droSec1.super_10 1841829 97 + 3036183
AUAGUCAUUUGGCAGAGGCGCACCAUUUGCGUCAACGGCACUUGCCUUCUUGGCAUCUAGUACUCGCAUAGAAAAUGCCAUAUACCAUAUAU-CCAUG-----------------------
...(((....)))...((((((.....))))))...((((..((((.....))))((((((....)).))))...)))).............-.....----------------------- ( -24.40, z-score =  -1.21, R)
>consensus
AUAGCCAUUUGGCAGAGGCGCACCAUUUGCGUCAACGGCACUUGCCUUCUUGGCAUCUAGUACUCGCAUAGAAAAUGCCAUAUACCAUAUAU_CCAUA_______________________
...(((....)))...((((((.....))))))...((((..((((.....))))((((((....)).))))...)))).......................................... (-24.81 = -24.62 +  -0.19) 

alignment

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secondary structure

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dotplot

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Window 4

Location 2,058,124 – 2,058,221
Length 97
Sequences 4
Columns 121
Reading direction reverse
Mean pairwise identity 84.78
Shannon entropy 0.22500
G+C content 0.45509
Mean single sequence MFE -36.02
Consensus MFE -31.20
Energy contribution -31.33
Covariance contribution 0.12
Combinations/Pair 1.06
Mean z-score -2.21
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.87
SVM RNA-class probability 0.972679
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2058124 97 - 22422827
-----------------------CAUGG-AUAUAUGGUAUAUGGCAUUUCCUAUGCGAGUACUAGAUGCCAAGAAGGCAAGUGCCGUUGACGCAAAUGGUGCGCCUCUGCCAAAUGACUAU
-----------------------.((((-.(((.((((...((((((((..(((....)))..))))))))(((.(((..(..(((((......)))))..))))))))))).))).)))) ( -32.30, z-score =  -2.23, R)
>droEre2.scaffold_4644 2021130 106 - 2521924
---------------CAUGGAUAUAUGGUAUAUAUGGUACAUGGCAUUUUCUAUGCGAGUACUAGAUGCCAAGAAGGCAAGUGCCGUUGACGCAAAUGGUGCGCCUCUGCCAAAUGGCUAU
---------------..........((((((...((((((.(.((((.....)))).))))))).))))))(((.(((..(..(((((......)))))..)))))))(((....)))... ( -37.80, z-score =  -2.52, R)
>droYak2.chrX 15504374 120 + 21770863
CAUGGAUAUAUGGUAUAUGG-UGUAUGGUAUAUAUGGUAUAUGGCAUUUUCUGUGCGAGUACUAGAUGCCAAGAAGGCAAGUGCCGUUGACGCAAAUGGUGCGCCUCUGCCAAAUGGCCAU
.........(((((...(((-(...((((((...((((((.(.((((.....)))).))))))).))))))(((.(((..(..(((((......)))))..)))))))))))....))))) ( -41.10, z-score =  -1.56, R)
>droSec1.super_10 1841829 97 - 3036183
-----------------------CAUGG-AUAUAUGGUAUAUGGCAUUUUCUAUGCGAGUACUAGAUGCCAAGAAGGCAAGUGCCGUUGACGCAAAUGGUGCGCCUCUGCCAAAUGACUAU
-----------------------.((((-.(((.((((...((((((((..(((....)))..))))))))(((.(((..(..(((((......)))))..))))))))))).))).)))) ( -32.90, z-score =  -2.54, R)
>consensus
_______________________CAUGG_AUAUAUGGUAUAUGGCAUUUUCUAUGCGAGUACUAGAUGCCAAGAAGGCAAGUGCCGUUGACGCAAAUGGUGCGCCUCUGCCAAAUGACUAU
........................(((((.(((.((((...((((((((..(((....)))..))))))))(((.(((..(..(((((......)))))..))))))))))).)))))))) (-31.20 = -31.33 +   0.12) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:08:26 2011