Locus 15254

Sequence ID dm3.chrX
Location 18,133,962 – 18,134,132
Length 170
Max. P 0.975612
window21014 window21015 window21016 window21017

overview

Window 4

Location 18,133,962 – 18,134,061
Length 99
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 89.13
Shannon entropy 0.19002
G+C content 0.54026
Mean single sequence MFE -34.34
Consensus MFE -26.20
Energy contribution -26.92
Covariance contribution 0.72
Combinations/Pair 1.18
Mean z-score -1.76
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.532034
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18133962 99 + 22422827
ACGAGUGUCCGAAGUGGCGGGCUUAUAGGGC-CAUAAGGCGUAUAUAUGCCCCAUAAUUGCCCGAUAAGCAGCUUCCGAUCGGAAGUGUCGAGAGCUCCC
..((((.(((((........((((((.((((-.....(((((....)))))........)))).)))))).((((((....)))))).))).)))))).. ( -35.12, z-score =  -1.86, R)
>droEre2.scaffold_4690 8464385 99 + 18748788
CCGAGUGUGCCAAGUGCCGGGCUUAUUGGGC-CAUAAGGCGCAAAUAGGCUCAAUAAUUGCCCGAUAAGAAGCUUCCGAUCGGAAGUGUCAAGAGCUCUC
..((((...........((((((((((((((-(..............))))))))))..)))))....((.((((((....)))))).))....)))).. ( -36.34, z-score =  -2.48, R)
>droYak2.chrX 16763668 99 + 21770863
UCAAGUGUCCCAAGUGGCGGACUUAUUGGGC-CAUAAGGCGCAGAUACGCUCAAUAAUUGCCCGAUAAGCAGCUUCCGAUCGGAAGUGCAAAGAGCUCUC
......((((........))))(((((((((-.....((((......))))........)))))))))(((.(((((....))))))))........... ( -30.32, z-score =  -1.09, R)
>droSec1.super_8 446312 99 + 3762037
ACAAGUGUCCCAAGUGGCGGGCUUAUAGGGU-CAUAAGGCGUAGAUACGCCCCAUAAUUGGCCGAUAAGCAGCUUCCGAUCGGAAGUGUCGAGAGCUCCC
......(((......)))((((((((..(((-((...(((((....))))).......))))).))))))((((..(((((....).))))..)))))). ( -34.30, z-score =  -1.72, R)
>droSim1.chrX 13999005 100 + 17042790
ACGAGUGUCCCAAGUGGCGGGCUUAUAGGGCGCAUAAGGCGCAAAAACGCCCCAUAAUUGCCCGAUAAGCAGCUUCCGAUCGGAAGUGUCGAGAGCUCCC
..((((........((((..((((((.(((((.....((((......)))).......))))).)))))).((((((....))))))))))...)))).. ( -35.60, z-score =  -1.65, R)
>consensus
ACGAGUGUCCCAAGUGGCGGGCUUAUAGGGC_CAUAAGGCGCAAAUACGCCCCAUAAUUGCCCGAUAAGCAGCUUCCGAUCGGAAGUGUCGAGAGCUCCC
..((((........((((..((((((.((((......((((......))))........)))).)))))).((((((....))))))))))...)))).. (-26.20 = -26.92 +   0.72)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,133,962 – 18,134,061
Length 99
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 89.13
Shannon entropy 0.19002
G+C content 0.54026
Mean single sequence MFE -34.06
Consensus MFE -29.14
Energy contribution -30.38
Covariance contribution 1.24
Combinations/Pair 1.17
Mean z-score -1.91
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.17
SVM RNA-class probability 0.903559
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18133962 99 - 22422827
GGGAGCUCUCGACACUUCCGAUCGGAAGCUGCUUAUCGGGCAAUUAUGGGGCAUAUAUACGCCUUAUG-GCCCUAUAAGCCCGCCACUUCGGACACUCGU
(((((((..((((......).)))..))))((((((.((((...((((((((........))))))))-)))).))))))(((......)))...))).. ( -35.80, z-score =  -2.43, R)
>droEre2.scaffold_4690 8464385 99 - 18748788
GAGAGCUCUUGACACUUCCGAUCGGAAGCUUCUUAUCGGGCAAUUAUUGAGCCUAUUUGCGCCUUAUG-GCCCAAUAAGCCCGGCACUUGGCACACUCGG
(((.(((...((..(((((....)))))..))...((((((..((((((.((......))(((....)-)).)))))))))))).....)))...))).. ( -30.20, z-score =  -1.52, R)
>droYak2.chrX 16763668 99 - 21770863
GAGAGCUCUUUGCACUUCCGAUCGGAAGCUGCUUAUCGGGCAAUUAUUGAGCGUAUCUGCGCCUUAUG-GCCCAAUAAGUCCGCCACUUGGGACACUUGA
(((.((((...((((((((....))))).))).....))))..((((((.(((....)))(((....)-)).))))))((((........)))).))).. ( -30.60, z-score =  -1.10, R)
>droSec1.super_8 446312 99 - 3762037
GGGAGCUCUCGACACUUCCGAUCGGAAGCUGCUUAUCGGCCAAUUAUGGGGCGUAUCUACGCCUUAUG-ACCCUAUAAGCCCGCCACUUGGGACACUUGU
((.((((..((((......).)))..))))((((((.((....(((((((((((....))))))))))-).)).)))))))).((....))......... ( -32.60, z-score =  -1.61, R)
>droSim1.chrX 13999005 100 - 17042790
GGGAGCUCUCGACACUUCCGAUCGGAAGCUGCUUAUCGGGCAAUUAUGGGGCGUUUUUGCGCCUUAUGCGCCCUAUAAGCCCGCCACUUGGGACACUCGU
(((.(.((((((..(((((....)))))..((((((.((((...((((((((((....)))))))))).)))).)))))).......))))))).))).. ( -41.10, z-score =  -2.87, R)
>consensus
GGGAGCUCUCGACACUUCCGAUCGGAAGCUGCUUAUCGGGCAAUUAUGGGGCGUAUCUGCGCCUUAUG_GCCCUAUAAGCCCGCCACUUGGGACACUCGU
(((.(.((((((..(((((....)))))..((((((.((((...((((((((((....)))))))))).)))).)))))).......))))))).))).. (-29.14 = -30.38 +   1.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,134,025 – 18,134,132
Length 107
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 70.23
Shannon entropy 0.56776
G+C content 0.49435
Mean single sequence MFE -35.49
Consensus MFE -18.20
Energy contribution -18.27
Covariance contribution 0.06
Combinations/Pair 1.48
Mean z-score -1.86
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.93
SVM RNA-class probability 0.975612
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18134025 107 + 22422827
AUAAGCAGCUUCCGAUCGGAAGUGUCGA---GAGCUCCCAUCGAACCGAUCGGCUGGGCUAUCAGUUCGCUAUCGUCGAUGGUGGAC---ACAAGCCUCAACUGACUGAUUAU---
...(((((...((((((((.....((((---.........)))).)))))))).((((((....((((((((((...))))))))))---...)))).)).))).))......--- ( -36.00, z-score =  -1.36, R)
>droAna3.scaffold_13248 3732951 106 - 4840945
AUAAGCGUGUUCCGAUCGGAAGUUGGAAACAGAAACGUUUCGAAAACGUUUAGUCAAGUGGGCCAUAAA-UAUUGCCAGAGAUAGGGCUAAUAAGCC--AACUUCCGAU-------
..............((((((((((((......(((((((.....)))))))((((.....(((.((...-.)).)))........))))......))--))))))))))------- ( -30.52, z-score =  -2.70, R)
>droEre2.scaffold_4690 8464448 110 + 18748788
AUAAGAAGCUUCCGAUCGGAAGUGUCAA---GAGCUCUCGUCGAACCGAUCGGCUGGGCUAACAGUUCGCUAUCGGCGAUGGUGGCA---ACAAGCCCCAACCCUUUGAAUUUUCC
....((.((((((....)))))).))..---.(((((..(((((.....))))).)))))......((((.....))))(((.(((.---....))))))................ ( -34.50, z-score =  -1.03, R)
>droYak2.chrX 16763731 110 + 21770863
AUAAGCAGCUUCCGAUCGGAAGUGCAAA---GAGCUCUCAGCGAACCGAUCGACUGCGUUAUCAGUUCGCUAUCGUCGAUGGUGGAA---ACAAGCCUCAACUGCUAAAGAAUUAU
....(((.(((((....))))))))...---.(((....(((((((.(((.(((...)))))).)))))))...((.((.((((...---.)..))))).)).))).......... ( -31.20, z-score =  -1.00, R)
>droSec1.super_8 446375 110 + 3762037
AUAAGCAGCUUCCGAUCGGAAGUGUCGA---GAGCUCCCAUCGAACCGAUCGGCUGGGCUAUCAGUUUGCUAUCGUCGAUGGUGGACCCAAUCAGUCUCAACUGACUGAUUAU---
......(((((((((((((.....((((---.........)))).))))))))..)))))....(((..(((((...)))))..)))..((((((((......))))))))..--- ( -40.50, z-score =  -2.63, R)
>droSim1.chrX 13999069 110 + 17042790
AUAAGCAGCUUCCGAUCGGAAGUGUCGA---GAGCUCCCAUCGAACCGAUCGGCUGGGCUAUCAGUUCGCUAUCGUCGAUGGCGGACUGUAUCACUCUUAACUGACUGAUUAU---
......(((((((((((((.....((((---.........)))).))))))))..)))))..((((((((((((...)))))))))))).((((.((......)).))))...--- ( -40.20, z-score =  -2.45, R)
>consensus
AUAAGCAGCUUCCGAUCGGAAGUGUCAA___GAGCUCCCAUCGAACCGAUCGGCUGGGCUAUCAGUUCGCUAUCGUCGAUGGUGGAC___ACAAGCCUCAACUGACUGAUUAU___
.......((((((....))))))...........((.(((((((..((((.(((.(((((...))))))))))))))))))).))............................... (-18.20 = -18.27 +   0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,134,025 – 18,134,132
Length 107
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 70.23
Shannon entropy 0.56776
G+C content 0.49435
Mean single sequence MFE -34.42
Consensus MFE -12.48
Energy contribution -13.15
Covariance contribution 0.67
Combinations/Pair 1.39
Mean z-score -1.70
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.555863
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18134025 107 - 22422827
---AUAAUCAGUCAGUUGAGGCUUGU---GUCCACCAUCGACGAUAGCGAACUGAUAGCCCAGCCGAUCGGUUCGAUGGGAGCUC---UCGACACUUCCGAUCGGAAGCUGCUUAU
---((((.(((...((((((((((..---.....((((((.(....))((((((((.((...))..))))))))))))))))).)---))))).(((((....)))))))).)))) ( -34.91, z-score =  -1.11, R)
>droAna3.scaffold_13248 3732951 106 + 4840945
-------AUCGGAAGUU--GGCUUAUUAGCCCUAUCUCUGGCAAUA-UUUAUGGCCCACUUGACUAAACGUUUUCGAAACGUUUCUGUUUCCAACUUCCGAUCGGAACACGCUUAU
-------((((((((((--((.......(((........)))....-..............(((.(((((((.....)))))))..))).)))))))))))).............. ( -27.80, z-score =  -2.76, R)
>droEre2.scaffold_4690 8464448 110 - 18748788
GGAAAAUUCAAAGGGUUGGGGCUUGU---UGCCACCAUCGCCGAUAGCGAACUGUUAGCCCAGCCGAUCGGUUCGACGAGAGCUC---UUGACACUUCCGAUCGGAAGCUUCUUAU
((((..(((...((((((((((....---.))).)).((((.....))))......)))))...(((((((.....((((....)---)))......))))))))))..))))... ( -37.70, z-score =  -1.53, R)
>droYak2.chrX 16763731 110 - 21770863
AUAAUUCUUUAGCAGUUGAGGCUUGU---UUCCACCAUCGACGAUAGCGAACUGAUAACGCAGUCGAUCGGUUCGCUGAGAGCUC---UUUGCACUUCCGAUCGGAAGCUGCUUAU
..........(((.(((((((.....---.....)).)))))..((((((((((((..........))))))))))))...))).---...((((((((....))))).))).... ( -34.30, z-score =  -1.61, R)
>droSec1.super_8 446375 110 - 3762037
---AUAAUCAGUCAGUUGAGACUGAUUGGGUCCACCAUCGACGAUAGCAAACUGAUAGCCCAGCCGAUCGGUUCGAUGGGAGCUC---UCGACACUUCCGAUCGGAAGCUGCUUAU
---..((((((((......))))))))(((..(.(((((((((((......(((......)))...))))..))))))))..)))---..(.(((((((....))))).))).... ( -35.80, z-score =  -1.47, R)
>droSim1.chrX 13999069 110 - 17042790
---AUAAUCAGUCAGUUAAGAGUGAUACAGUCCGCCAUCGACGAUAGCGAACUGAUAGCCCAGCCGAUCGGUUCGAUGGGAGCUC---UCGACACUUCCGAUCGGAAGCUGCUUAU
---((((.(((...((..(((((....((((.(((.(((...))).))).))))....((((..(((.....))).)))).))))---)..)).(((((....)))))))).)))) ( -36.00, z-score =  -1.73, R)
>consensus
___AUAAUCAGUCAGUUGAGGCUUAU___GUCCACCAUCGACGAUAGCGAACUGAUAGCCCAGCCGAUCGGUUCGAUGAGAGCUC___UCGACACUUCCGAUCGGAAGCUGCUUAU
................((((..............(((((((((((......(((......)))...))))..)))))))...............(((((....)))))...)))). (-12.48 = -13.15 +   0.67)

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 01:55:53 2011