Locus 15842

Sequence ID dm3.chrX
Location 21,447,125 – 21,447,251
Length 126
Max. P 0.993361
window21829 window21830 window21831 window21832 window21833

overview

Window 9

Location 21,447,125 – 21,447,215
Length 90
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 79.61
Shannon entropy 0.35595
G+C content 0.51835
Mean single sequence MFE -29.08
Consensus MFE -17.97
Energy contribution -20.29
Covariance contribution 2.32
Combinations/Pair 1.15
Mean z-score -2.03
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.872950
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 21447125 90 + 22422827
UUGUUGUCGAUGUGCGGUUGAAUUGCGGUUCGCUUUUGGCCAACUGAACUGAGUUCAGUUCAGUUGGCCAGGACCAAAAGGCAUUGGCCC-------
.....(((((((((((((...)))))(((((.....(((((((((((((((....)))))))))))))))))))).....))))))))..------- ( -44.90, z-score =  -5.82, R)
>droAna3.scaffold_13117 2798910 69 - 5790199
UUACUGUCGAUGUGCGGUUAAAUUGCGGUUCGUUCUUGGCC--------------CAAUUCGAU-------GGCCAAAAUGUCCUCUUCC-------
...(((((((..((.((((((...(((...)))..))))))--------------))..)))))-------)).................------- ( -15.10, z-score =  -0.62, R)
>droEre2.scaffold_4690 17928266 80 + 18748788
UUGUUGUCGAUGUGCGGUUGAAUUGCGGUUCGCUUUUGGCCAACU----------CAGUUCAGUGGCCCAGGACCAAAAAGCGUUGGCUC-------
.....(((((((((((((...)))))(((((......(((((.((----------......)))))))..))))).....))))))))..------- ( -25.70, z-score =  -0.87, R)
>droYak2.chrX 20585056 87 + 21770863
UUGUUGUCGAUGUGCGGUUGAAUUGCGGUUCGCUUUUGGCCAACU----------CAGUUCACUUGGCCAGGACCGAAAAGCGUUGGCCCUUGGCCC
.....(((((...(.(((..(...((..((((.((((((((((..----------........)))))))))).))))..)).)..))))))))).. ( -29.10, z-score =  -0.61, R)
>droSec1.super_8 3732434 79 + 3762037
UUGUUGUCGAUGUGCGGUUGAAUUGCGGUUCGCUUUUGGCCAACU----------CAGUUCAGUUGGCCAGGACC-AAAAGCAUUGGGCC-------
......((((((((((((...)))))(((((.....(((((((((----------......))))))))))))))-....)))))))...------- ( -28.40, z-score =  -1.78, R)
>droSim1.chrX 16531297 80 + 17042790
UUGUUGUCGAUGUGCGGUUGAAUUGCGGUUCGCUUUUGGCCAACU----------CAGUUCAGUUGGCCAGGACCAAAAGGCAUUGGCCC-------
.....(((((((((((((...)))))(((((.....(((((((((----------......)))))))))))))).....))))))))..------- ( -31.30, z-score =  -2.49, R)
>consensus
UUGUUGUCGAUGUGCGGUUGAAUUGCGGUUCGCUUUUGGCCAACU__________CAGUUCAGUUGGCCAGGACCAAAAAGCAUUGGCCC_______
.....(((((((((((((...)))))(((((.....(((((((((................)))))))))))))).....))))))))......... (-17.97 = -20.29 +   2.32)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,447,142 – 21,447,246
Length 104
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 76.28
Shannon entropy 0.39393
G+C content 0.55454
Mean single sequence MFE -39.18
Consensus MFE -20.07
Energy contribution -19.79
Covariance contribution -0.28
Combinations/Pair 1.22
Mean z-score -2.14
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.815302
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 21447142 104 + 22422827
UUGAAUUGCGGUUCGCUUUUGGCCAACUGAACUGAGUUCAGUUCAGUUGGCCAGGACCAAAAGGCAUUGGCCCGU----UGGU--GG--CGGGUGG--GUGGUGCCUGUGUUUG
.........(((((.....(((((((((((((((....))))))))))))))))))))...(((((((.((((((----....--.)--))))).)--...))))))....... ( -51.50, z-score =  -4.90, R)
>droEre2.scaffold_4690 17928283 86 + 18748788
UUGAAUUGCGGUUCGCUUUUGGCCAACU----------CAGUUCAGUGGCCCAGGACCAAAAAGCGUUGGCUCGU----CGGAUGGG--UGGGCUGU-GUUUG-----------
.(((((((.((((.((.....)).))))----------)))))))(..(((((...(((....(((......)))----....))).--)))))..)-.....----------- ( -27.50, z-score =  -0.17, R)
>droYak2.chrX 20585073 104 + 21770863
UUGAAUUGCGGUUCGCUUUUGGCCAACU----------CAGUUCACUUGGCCAGGACCGAAAAGCGUUGGCCCUUGGCCCGUGUUGGCUUGGGUGGCUGGGUGUUCUGUGUUUG
.......((((..(((((..(((((.((----------((((..((..(((((((.((((......)))).)).)))))...))..)).))))))))))))))..))))..... ( -39.20, z-score =  -1.22, R)
>droSec1.super_8 3732451 95 + 3762037
UUGAAUUGCGGUUCGCUUUUGGCCAACU----------CAGUUCAGUUGGCCAGGACCAAAA-GCAUUGGGCCGU----CGGU--GG--UGGCCCGUCGUUUGGCCAGUGUUUG
.........(((((.....(((((((((----------......))))))))))))))..((-(((((((.(((.----((..--((--....))..))..)))))))))))). ( -39.70, z-score =  -2.66, R)
>droSim1.chrX 16531314 96 + 17042790
UUGAAUUGCGGUUCGCUUUUGGCCAACU----------CAGUUCAGUUGGCCAGGACCAAAAGGCAUUGGCCCGU----CGGU--GG--UGGGUGGGUGGUUGGCCAGUGUUUG
.........(((((.....(((((((((----------......))))))))))))))...(((((((((((..(----((.(--.(--....).).)))..))))))))))). ( -38.00, z-score =  -1.74, R)
>consensus
UUGAAUUGCGGUUCGCUUUUGGCCAACU__________CAGUUCAGUUGGCCAGGACCAAAAAGCAUUGGCCCGU____CGGU__GG__UGGGUGGU_GUUUGGCCAGUGUUUG
......(((..((.(.((((((((((((................)))))))))))).).))..)))...(((((...............))))).................... (-20.07 = -19.79 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,447,142 – 21,447,246
Length 104
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 76.28
Shannon entropy 0.39393
G+C content 0.55454
Mean single sequence MFE -32.58
Consensus MFE -19.09
Energy contribution -20.29
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.87
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.61
SVM RNA-class probability 0.993361
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 21447142 104 - 22422827
CAAACACAGGCACCAC--CCACCCG--CC--ACCA----ACGGGCCAAUGCCUUUUGGUCCUGGCCAACUGAACUGAACUCAGUUCAGUUGGCCAAAAGCGAACCGCAAUUCAA
........(((.....--......)--))--....----..(((((((......)))))))(((((((((((((((....)))))))))))))))...(((...)))....... ( -44.40, z-score =  -6.38, R)
>droEre2.scaffold_4690 17928283 86 - 18748788
-----------CAAAC-ACAGCCCA--CCCAUCCG----ACGAGCCAACGCUUUUUGGUCCUGGGCCACUGAACUG----------AGUUGGCCAAAAGCGAACCGCAAUUCAA
-----------.....-...(((((--.....(((----(.((((....)))).))))...)))))...((((.((----------.(((.((.....)).)))..)).)))). ( -23.70, z-score =  -1.46, R)
>droYak2.chrX 20585073 104 - 21770863
CAAACACAGAACACCCAGCCACCCAAGCCAACACGGGCCAAGGGCCAACGCUUUUCGGUCCUGGCCAAGUGAACUG----------AGUUGGCCAAAAGCGAACCGCAAUUCAA
........(((...............((((((...(((((.(((((..........)))))))))).((....)).----------.)))))).....(((...)))..))).. ( -31.20, z-score =  -1.36, R)
>droSec1.super_8 3732451 95 - 3762037
CAAACACUGGCCAAACGACGGGCCA--CC--ACCG----ACGGCCCAAUGC-UUUUGGUCCUGGCCAACUGAACUG----------AGUUGGCCAAAAGCGAACCGCAAUUCAA
........(((((((.(..(((((.--..--....----..)))))....)-.))))))).(((((((((......----------)))))))))...(((...)))....... ( -34.50, z-score =  -3.03, R)
>droSim1.chrX 16531314 96 - 17042790
CAAACACUGGCCAACCACCCACCCA--CC--ACCG----ACGGGCCAAUGCCUUUUGGUCCUGGCCAACUGAACUG----------AGUUGGCCAAAAGCGAACCGCAAUUCAA
.......((((((((((..((.(((--..--((((----(.((((....)))).)))))..))).....))...))----------.))))))))...(((...)))....... ( -29.10, z-score =  -2.12, R)
>consensus
CAAACACAGGCCAAAC_ACCACCCA__CC__ACCG____ACGGGCCAAUGCCUUUUGGUCCUGGCCAACUGAACUG__________AGUUGGCCAAAAGCGAACCGCAAUUCAA
.........................................(((((((......)))))))(((((((((................)))))))))...(((...)))....... (-19.09 = -20.29 +   1.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,447,148 – 21,447,251
Length 103
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 77.94
Shannon entropy 0.36298
G+C content 0.59175
Mean single sequence MFE -41.50
Consensus MFE -21.87
Energy contribution -22.15
Covariance contribution 0.28
Combinations/Pair 1.09
Mean z-score -1.92
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.581540
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 21447148 103 + 22422827
UGCGGUUCGCUUUUGGCCAACUGAACUGAGUUCAGUUCAGUUGGCCAGGACCAAAAGGCAUUGGCCCGUUGGUGGCG--------GGUGGGUGGU--GCCUGUGUUUGCGCAC
((((...(((((((((((((((((((((....)))))))))))))))))).....(((((((.((((((.....)))--------))).)...))--)))))))....)))). ( -54.60, z-score =  -4.82, R)
>droEre2.scaffold_4690 17928289 85 + 18748788
UGCGGUUCGCUUUUGGCCAACU----------CAGUUCAGUGGCCCAGGACCAAAAAGCGUUGGCUCGUCGG--AUG--------GGUGGG--------CUGUGUUUGCGCAC
((((((((......(((((.((----------......)))))))..))))).....(((.((((((..(..--...--------)..)))--------)))....)))))). ( -27.90, z-score =   0.52, R)
>droYak2.chrX 20585079 103 + 21770863
UGCGGUUCGCUUUUGGCCAACU----------CAGUUCACUUGGCCAGGACCGAAAAGCGUUGGCCCUUGGCCCGUGUUGGCUUGGGUGGCUGGGUGUUCUGUGUUUGCGCAC
(((((....))....((.(((.----------(((..((((..((((...((((..((((..((((...))))..))))...)))).))))..))))..))).))).))))). ( -41.50, z-score =  -0.82, R)
>droSec1.super_8 3732457 94 + 3762037
UGCGGUUCGCUUUUGGCCAACU----------CAGUUCAGUUGGCCAGGACCAAAAG-CAUUGGGCCGUCGGUGGUG--------GCCCGUCGUUUGGCCAGUGUUUGCGCAC
((((((((.....(((((((((----------......))))))))))))))..(((-((((((.(((.((..((..--------..))..))..))))))))))))..))). ( -42.60, z-score =  -2.68, R)
>droSim1.chrX 16531320 95 + 17042790
UGCGGUUCGCUUUUGGCCAACU----------CAGUUCAGUUGGCCAGGACCAAAAGGCAUUGGCCCGUCGGUGGUG--------GGUGGGUGGUUGGCCAGUGUUUGCGCAC
((((((((.....(((((((((----------......))))))))))))))...(((((((((((..(((.(.(..--------..).).)))..)))))))))))..))). ( -40.90, z-score =  -1.78, R)
>consensus
UGCGGUUCGCUUUUGGCCAACU__________CAGUUCAGUUGGCCAGGACCAAAAGGCAUUGGCCCGUCGGUGGUG________GGUGGGUGGUUGGCCUGUGUUUGCGCAC
((((...(((...(((((((((................)))))))))((.((((......)))).))..................................)))....)))). (-21.87 = -22.15 +   0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,447,148 – 21,447,251
Length 103
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 77.94
Shannon entropy 0.36298
G+C content 0.59175
Mean single sequence MFE -34.82
Consensus MFE -22.59
Energy contribution -23.79
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.66
SVM RNA-class probability 0.958855
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chrX 21447148 103 - 22422827
GUGCGCAAACACAGGC--ACCACCCACC--------CGCCACCAACGGGCCAAUGCCUUUUGGUCCUGGCCAACUGAACUGAACUCAGUUCAGUUGGCCAAAAGCGAACCGCA
((((((.......(((--..........--------.)))......(((((((......)))))))(((((((((((((((....)))))))))))))))...)))...))). ( -47.50, z-score =  -5.83, R)
>droEre2.scaffold_4690 17928289 85 - 18748788
GUGCGCAAACACAG--------CCCACC--------CAU--CCGACGAGCCAACGCUUUUUGGUCCUGGGCCACUGAACUG----------AGUUGGCCAAAAGCGAACCGCA
.((((........(--------((((..--------...--((((.((((....)))).))))...)))))..........----------.(((.((.....)).))))))) ( -23.80, z-score =  -0.23, R)
>droYak2.chrX 20585079 103 - 21770863
GUGCGCAAACACAGAACACCCAGCCACCCAAGCCAACACGGGCCAAGGGCCAACGCUUUUCGGUCCUGGCCAAGUGAACUG----------AGUUGGCCAAAAGCGAACCGCA
(((.((................)))))....((((((...(((((.(((((..........)))))))))).((....)).----------.)))))).....(((...))). ( -32.79, z-score =  -0.51, R)
>droSec1.super_8 3732457 94 - 3762037
GUGCGCAAACACUGGCCAAACGACGGGC--------CACCACCGACGGCCCAAUG-CUUUUGGUCCUGGCCAACUGAACUG----------AGUUGGCCAAAAGCGAACCGCA
((((((.......(((((((.(..((((--------(.........)))))....-).))))))).(((((((((......----------)))))))))...)))...))). ( -38.00, z-score =  -2.89, R)
>droSim1.chrX 16531320 95 - 17042790
GUGCGCAAACACUGGCCAACCACCCACC--------CACCACCGACGGGCCAAUGCCUUUUGGUCCUGGCCAACUGAACUG----------AGUUGGCCAAAAGCGAACCGCA
((((((......(((....)))......--------..........(((((((......)))))))(((((((((......----------)))))))))...)))...))). ( -32.00, z-score =  -1.78, R)
>consensus
GUGCGCAAACACAGGCCAACCACCCACC________CACCACCGACGGGCCAAUGCCUUUUGGUCCUGGCCAACUGAACUG__________AGUUGGCCAAAAGCGAACCGCA
((((((........................................(((((((......)))))))(((((((((................)))))))))...)))...))). (-22.59 = -23.79 +   1.20)

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 02:06:56 2011