Locus 15518

Sequence ID dm3.chrX
Location 19,353,538 – 19,353,744
Length 206
Max. P 0.989256
window21396 window21397 window21398 window21399 window21400 window21401

overview

Window 6

Location 19,353,538 – 19,353,635
Length 97
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 90.07
Shannon entropy 0.13245
G+C content 0.42465
Mean single sequence MFE -23.03
Consensus MFE -18.30
Energy contribution -18.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.19
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.794529
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19353538 97 - 22422827
GCAAGAACACUUUCACACACAUGUGUUUUUGUUUCGCAAAAGUUCUAUUGGUGUUUGCUCUUUCGCCAGC-AAACUUCUG------UGCACUCCUGCCAAAUAC
((((((((((............))))))))))...(((..(((..(((.((.(((((((........)))-)))).)).)------)).)))..)))....... ( -22.80, z-score =  -1.74, R)
>droYak2.chrX 9788906 94 + 21770863
GCAAGAACACUUC--UUCACAUGUGUUUUUGUUUCGC-AAAGUUCUAUUGGUGUUUGCUCUUUCGCCAGC-AAACUUCUG------CGCACUCCUGCCAAAUAU
((((((((((...--.......))))))))))...((-((((((...((((((..........)))))).-.))))).))------)(((....)))....... ( -23.00, z-score =  -2.34, R)
>droEre2.scaffold_4690 9593527 101 - 18748788
GCAAGAACACUUC--UUCACAUGUGUUUUUGUUUCGC-AAAGUUCUAUUGGUGUUUGCUCUUUCGCCAGCAAAACUUCUGCACUUCCGCACUCCUGCCAAAUAU
((((((((((...--.......))))))))))...((-((((((.(.((((((..........)))))).).))))).)))......(((....)))....... ( -23.30, z-score =  -2.49, R)
>consensus
GCAAGAACACUUC__UUCACAUGUGUUUUUGUUUCGC_AAAGUUCUAUUGGUGUUUGCUCUUUCGCCAGC_AAACUUCUG______CGCACUCCUGCCAAAUAU
((((((((((............)))))))))).......(((((...((((((..........))))))...)))))..........(((....)))....... (-18.30 = -18.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,353,561 – 19,353,665
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.96
Shannon entropy 0.15912
G+C content 0.45236
Mean single sequence MFE -32.06
Consensus MFE -26.75
Energy contribution -26.95
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.640400
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19353561 104 + 22422827
-GUUUGCUGGCGAAAGAGCAAACACCAAUAGAACUUUUGCGAAACAAAAACACAUGUGUGUG-----AAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCG----------
-(((((((..(....)))))))).......((((...(((((((((...((((....)))).-----....)))).)))))..)))).((((((....))))))......---------- ( -34.50, z-score =  -2.59, R)
>droSec1.super_8 1637266 109 + 3762037
-GUUUGCUGGCGAAAGAGCAAACACCAAUAGAACUUUUGCGAAACAAAAACACAUGUGUGUGUAAUGGAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCG----------
-(((((((..(....))))))))......(((((.(((.((..(((...(((....))).)))..)).))).))))).....((((..((((((....))))))..))))---------- ( -32.70, z-score =  -1.55, R)
>droSim1.chrX 14970608 109 + 17042790
-GUUUGCUGGCGAAAGAGCAAACACCAAUAGAACUUUUGCGAAACAAAAACACAUGUGUGUGUAAUGGAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCG----------
-(((((((..(....))))))))......(((((.(((.((..(((...(((....))).)))..)).))).))))).....((((..((((((....))))))..))))---------- ( -32.70, z-score =  -1.55, R)
>droYak2.chrX 9788929 101 - 21770863
-GUUUGCUGGCGAAAGAGCAAACACCAAUAGAACUUU-GCGAAACAAAAACACAUGUGAA-------GAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCG----------
-(((((((..(....)))))))).......((((..(-((((((((....((....))..-------....)))).)))))..)))).((((((....))))))......---------- ( -30.50, z-score =  -1.94, R)
>droEre2.scaffold_4690 9593556 112 + 18748788
GUUUUGCUGGCGAAAGAGCAAACACCAAUAGAACUUU-GCGAAACAAAAACACAUGUGAA-------GAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCGAGGAAAAGCG
((((((((..(....)))).....((..........(-((((((((....((....))..-------....)))).)))))(((((..((((((....))))))..))))))).))))). ( -29.90, z-score =  -0.69, R)
>consensus
_GUUUGCUGGCGAAAGAGCAAACACCAAUAGAACUUUUGCGAAACAAAAACACAUGUGUGUG_____GAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCG__________
.(((((((..(....)))))))).................((..(((.(((((.................))))).)))..))(((..((((((....))))))..)))........... (-26.75 = -26.95 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,353,561 – 19,353,665
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.96
Shannon entropy 0.15912
G+C content 0.45236
Mean single sequence MFE -30.86
Consensus MFE -29.19
Energy contribution -29.19
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.18
SVM RNA-class probability 0.984891
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19353561 104 - 22422827
----------CGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUU-----CACACACAUGUGUUUUUGUUUCGCAAAAGUUCUAUUGGUGUUUGCUCUUUCGCCAGCAAAC-
----------.(((..((((((....))))))((((.((.((((((((((...-----.........)))))))))).))(((((...((....))..)))))...))))..)))....- ( -30.90, z-score =  -2.23, R)
>droSec1.super_8 1637266 109 - 3762037
----------CGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUCCAUUACACACACAUGUGUUUUUGUUUCGCAAAAGUUCUAUUGGUGUUUGCUCUUUCGCCAGCAAAC-
----------.(((..((((((....))))))((((.((.((((((((((.................)))))))))).))(((((...((....))..)))))...))))..)))....- ( -30.53, z-score =  -2.17, R)
>droSim1.chrX 14970608 109 - 17042790
----------CGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUCCAUUACACACACAUGUGUUUUUGUUUCGCAAAAGUUCUAUUGGUGUUUGCUCUUUCGCCAGCAAAC-
----------.(((..((((((....))))))((((.((.((((((((((.................)))))))))).))(((((...((....))..)))))...))))..)))....- ( -30.53, z-score =  -2.17, R)
>droYak2.chrX 9788929 101 + 21770863
----------CGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUC-------UUCACAUGUGUUUUUGUUUCGC-AAAGUUCUAUUGGUGUUUGCUCUUUCGCCAGCAAAC-
----------.(((..((((((....))))))((((.((.((((((((((...-------.......)))))))))).))((-(((..((....))..)))))...))))..)))....- ( -31.00, z-score =  -2.51, R)
>droEre2.scaffold_4690 9593556 112 - 18748788
CGCUUUUCCUCGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUC-------UUCACAUGUGUUUUUGUUUCGC-AAAGUUCUAUUGGUGUUUGCUCUUUCGCCAGCAAAAC
((((.......(((((((((((....))))))....(((.((((((((((...-------.......)))))))))).))).-)))))......))))((((((........)))))).. ( -31.32, z-score =  -2.13, R)
>consensus
__________CGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUC_____CACACACAUGUGUUUUUGUUUCGCAAAAGUUCUAUUGGUGUUUGCUCUUUCGCCAGCAAAC_
...........((.....))(((..((((.(((...(((.((((((((((.................)))))))))).))).....)))))))..)))((((((........)))))).. (-29.19 = -29.19 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,353,600 – 19,353,705
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.25
Shannon entropy 0.17180
G+C content 0.38299
Mean single sequence MFE -26.55
Consensus MFE -22.44
Energy contribution -22.84
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.97
SVM RNA-class probability 0.864451
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19353600 105 + 22422827
GAAACAAAAACACAUGUGUGUG-----AAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCGA----------CGAAAAGCUAAUAUGUGUAUAAAAAUGUUUUCCUUUGGU
((((((...((((((((.((..-----(........)..))(((((..((((((....))))))..)))))----------..........)))))))).......))))))........ ( -26.00, z-score =  -1.68, R)
>droSec1.super_8 1637305 108 + 3762037
GAAACAAAAACACAUGUGUGUGUAAUGGAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCGA----------CGAAAAGCUAAUAUGUGUAUAAAAAUGUUUUCCUUUG--
((((((...((((((((..((....((.(((....))).))(((((..((((((....))))))..)))))----------......))..)))))))).......))))))......-- ( -27.80, z-score =  -2.14, R)
>droSim1.chrX 14970647 108 + 17042790
GAAACAAAAACACAUGUGUGUGUAAUGGAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCGA----------CGAAAAGCUAAUAUGUGUAUAAAAAUGUUUUCCUUUG--
((((((...((((((((..((....((.(((....))).))(((((..((((((....))))))..)))))----------......))..)))))))).......))))))......-- ( -27.80, z-score =  -2.14, R)
>droYak2.chrX 9788967 102 - 21770863
GAAACAAAAACACAUGUGAA-------GAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCGA----------CGAAAAGCUAAUAUGUAUAUAAAAAUGUUUUUCUUUGU-
....(((.(((((.......-------...))))).)))..(((((..((((((....))))))..)))))----------.(((((((..................))))))).....- ( -24.87, z-score =  -2.01, R)
>droEre2.scaffold_4690 9593595 112 + 18748788
GAAACAAAAACACAUGUGAA-------GAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCGAGGAAAAGCGACGAAAAGCUAAUAUGUAUAUAAAAAUGUUUUCCUUUGU-
....(((.(((((.......-------...))))).)))..(((((..((((((....))))))..)))))((((((((........))).((((..........))))))))).....- ( -26.30, z-score =  -1.53, R)
>consensus
GAAACAAAAACACAUGUGUGUG_____GAAGUGUUCUUGCAUCGUUCGUCGCCAUCAGUGGCGAAAAGCGA__________CGAAAAGCUAAUAUGUGUAUAAAAAUGUUUUCCUUUG__
((((((...((((((((..............(((....)))(((((..((((((....))))))..)))))....................)))))))).......))))))........ (-22.44 = -22.84 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,353,600 – 19,353,705
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.25
Shannon entropy 0.17180
G+C content 0.38299
Mean single sequence MFE -25.26
Consensus MFE -21.08
Energy contribution -20.92
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -2.94
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.36
SVM RNA-class probability 0.989256
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19353600 105 - 22422827
ACCAAAGGAAAACAUUUUUAUACACAUAUUAGCUUUUCG----------UCGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUU-----CACACACAUGUGUUUUUGUUUC
...................................((((----------(((((..(((....))).))))))))).((.((((((((((...-----.........)))))))))).)) ( -25.20, z-score =  -3.00, R)
>droSec1.super_8 1637305 108 - 3762037
--CAAAGGAAAACAUUUUUAUACACAUAUUAGCUUUUCG----------UCGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUCCAUUACACACACAUGUGUUUUUGUUUC
--.................................((((----------(((((..(((....))).))))))))).((.((((((((((.................)))))))))).)) ( -24.83, z-score =  -2.89, R)
>droSim1.chrX 14970647 108 - 17042790
--CAAAGGAAAACAUUUUUAUACACAUAUUAGCUUUUCG----------UCGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUCCAUUACACACACAUGUGUUUUUGUUUC
--.................................((((----------(((((..(((....))).))))))))).((.((((((((((.................)))))))))).)) ( -24.83, z-score =  -2.89, R)
>droYak2.chrX 9788967 102 + 21770863
-ACAAAGAAAAACAUUUUUAUAUACAUAUUAGCUUUUCG----------UCGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUC-------UUCACAUGUGUUUUUGUUUC
-..................................((((----------(((((..(((....))).))))))))).((.((((((((((...-------.......)))))))))).)) ( -25.40, z-score =  -3.24, R)
>droEre2.scaffold_4690 9593595 112 - 18748788
-ACAAAGGAAAACAUUUUUAUAUACAUAUUAGCUUUUCGUCGCUUUUCCUCGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUC-------UUCACAUGUGUUUUUGUUUC
-..................................(((((((((.......((.....)).......))))))))).((.((((((((((...-------.......)))))))))).)) ( -26.04, z-score =  -2.68, R)
>consensus
__CAAAGGAAAACAUUUUUAUACACAUAUUAGCUUUUCG__________UCGCUUUUCGCCACUGAUGGCGACGAACGAUGCAAGAACACUUC_____CACACACAUGUGUUUUUGUUUC
......(((((.(..................).)))))...........(((.((.((((((....)))))).)).))).((((((((((.................))))))))))... (-21.08 = -20.92 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,353,635 – 19,353,744
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.38
Shannon entropy 0.17761
G+C content 0.43666
Mean single sequence MFE -27.45
Consensus MFE -21.62
Energy contribution -21.62
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.23
SVM RNA-class probability 0.602277
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19353635 109 + 22422827
AUCGUUCGUCGCCAUCAGUGGCGAAAAGCGA----------CGAAAAGCUAAUAUGUGUAUAAAAAUGUUUUCCUUUGGUCCCCCCUUUUAGCGGCAA-GCAACGAGCACAUGCUUUUAU
.(((((..((((((....))))))..)))))----------..((((((....((((((.......(((((.((.((((.........)))).)).))-)))....)))))))))))).. ( -28.90, z-score =  -1.73, R)
>droSec1.super_8 1637345 104 + 3762037
AUCGUUCGUCGCCAUCAGUGGCGAAAAGCGA----------CGAAAAGCUAAUAUGUGUAUAAAAAUGUUUUCCUUUG-UCCCCUU-UUA-GCGCCAAAGCACCGAGC---UGCUUUUAU
.(((((..((((((....))))))..)))))----------..((((((......((((.(((((..(..(......)-..)..))-)))-))))...(((.....))---))))))).. ( -24.70, z-score =  -1.53, R)
>droSim1.chrX 14970687 107 + 17042790
AUCGUUCGUCGCCAUCAGUGGCGAAAAGCGA----------CGAAAAGCUAAUAUGUGUAUAAAAAUGUUUUCCUUUG-UCCCCUU-UUA-GCGCCAAAGCACCGAGCACAUGCUUUUAU
.(((((..((((((....))))))..)))))----------..((((((....((((((.(((((..(..(......)-..)..))-)))-((......)).....)))))))))))).. ( -26.70, z-score =  -2.12, R)
>droYak2.chrX 9789000 109 - 21770863
AUCGUUCGUCGCCAUCAGUGGCGAAAAGCGA----------CGAAAAGCUAAUAUGUAUAUAAAAAUGUUUUUCUUUG-UCCCCCCCUUUAGCGCCAAAGCAGCGAGCACAUGCUUUUAU
.(((((..((((((....))))))..)))))----------.(((((((..................)))))))....-............((((....)).))((((....)))).... ( -25.87, z-score =  -1.84, R)
>droEre2.scaffold_4690 9593628 118 + 18748788
AUCGUUCGUCGCCAUCAGUGGCGAAAAGCGAGGAAAAGCGACGAAAAGCUAAUAUGUAUAUAAAAAUGUUUUCCUUUG-UCCCCCU-UCAAGCGCCAAAGCACCGGGCACAUGCUUUUAU
.(((((..((((((....))))))..)))))..((((((((((((.....(((((..........)))))....))))-)).(((.-....((......))...))).....)))))).. ( -31.10, z-score =  -1.55, R)
>consensus
AUCGUUCGUCGCCAUCAGUGGCGAAAAGCGA__________CGAAAAGCUAAUAUGUGUAUAAAAAUGUUUUCCUUUG_UCCCCCU_UUAAGCGCCAAAGCACCGAGCACAUGCUUUUAU
.(((((..((((((....))))))..)))))............((((((.(((((..........))))).....................((......))...........)))))).. (-21.62 = -21.62 +  -0.00)

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 02:01:01 2011