Locus 13242

Sequence ID dm3.chrX
Location 5,279,861 – 5,280,011
Length 150
Max. P 0.998921
window18217 window18218 window18219 window18220

overview

Window 7

Location 5,279,861 – 5,279,960
Length 99
Sequences 7
Columns 114
Reading direction forward
Mean pairwise identity 68.26
Shannon entropy 0.60029
G+C content 0.38745
Mean single sequence MFE -18.87
Consensus MFE -11.24
Energy contribution -12.63
Covariance contribution 1.39
Combinations/Pair 1.14
Mean z-score -2.37
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.55
SVM RNA-class probability 0.998921
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5279861 99 + 22422827
-------------CCACUAC--UAUAUGUGCCAUAUAAAUAUUCCCCACUUUCAUUUCAUUUUCGACUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGA
-------------.......--((((((...)))))).........................((((..(.((.((((((((((((......)))))))))).)).)).).)))) ( -21.90, z-score =  -3.12, R)
>droEre2.scaffold_4690 2637200 99 + 18748788
-------------CCACUAC--UAUGUACGCCAUAUAAAUAUUCCCCACUUUCAUUUCAUUUUUGCCUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGA
-------------.......--.......((.........................((((((.......))))))((((((((((......)))))))))).......)).... ( -20.30, z-score =  -2.95, R)
>droYak2.chrX 18584015 114 - 21770863
CUACAAUGUCACUUCACUGCCAUAUGUAUGCCAUAUAAAUAUUCCCCACUUUCAUUUCAUUUUCGCCUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGA
.(((((((.((......)).))).)))).((.........................((((((.......))))))((((((((((......)))))))))).......)).... ( -22.60, z-score =  -2.22, R)
>droSec1.super_4 4707386 99 - 6179234
-------------CCACUAC--UAUAUGUGCCAUAUAAAUAUUCCCCACUUUCAUUUCAUUUUCGACUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGA
-------------.......--((((((...)))))).........................((((..(.((.((((((((((((......)))))))))).)).)).).)))) ( -21.90, z-score =  -3.12, R)
>droSim1.chrX_random 1820493 99 + 5698898
-------------CCACUAC--UAUAUGUGCCAUAUAAAUAUUCCCCACUUUCAUUUCAUUUUCGACUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGA
-------------.......--((((((...)))))).........................((((..(.((.((((((((((((......)))))))))).)).)).).)))) ( -21.90, z-score =  -3.12, R)
>droAna3.scaffold_13117 2733354 75 + 5790199
-----------------------------------UCGAUAUUUAUAAAUAUUAUCUA--UUUUGCUAGGGAUGAGUGACAUUUAUCGAUU-GCAUGUCACAUC-UCCGCUCGA
-----------------------------------((((................(((--......)))(((.(((((((((.((.....)-).))))))).))-)))..)))) ( -15.30, z-score =  -0.97, R)
>dp4.chrXL_group1e 10872805 90 + 12523060
-------------CUCCUACCGCAUAUAUGAUAGAUUCUUAAACAUGAUUCAAAUUCC--UUCGAUUUCUUUCGAUUACCAUGUUUUUUUUU---UAUAAUUUUUUCC------
-------------.................(((((.....(((((((...........--.((((......))))....)))))))....))---)))..........------ (  -8.19, z-score =  -1.08, R)
>consensus
_____________CCACUAC__UAUAUAUGCCAUAUAAAUAUUCCCCACUUUCAUUUCAUUUUCGACUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGA
......................................................................((.((((((((((((......)))))))))).)).))....... (-11.24 = -12.63 +   1.39)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,279,861 – 5,279,960
Length 99
Sequences 7
Columns 114
Reading direction reverse
Mean pairwise identity 68.26
Shannon entropy 0.60029
G+C content 0.38745
Mean single sequence MFE -22.54
Consensus MFE -10.70
Energy contribution -11.99
Covariance contribution 1.29
Combinations/Pair 1.21
Mean z-score -1.94
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.04
SVM RNA-class probability 0.980031
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5279861 99 - 22422827
UCGAGCGGAGGAUGUGACACGCAAAUCAAUACGUGUCACUCAUCUGAGUCGAAAAUGAAAUGAAAGUGGGGAAUAUUUAUAUGGCACAUAUA--GUAGUGG-------------
((((.((((.((.((((((((..........)))))))))).))))..))))...((..(((.(((((.....))))).)))..))(((...--...))).------------- ( -24.30, z-score =  -1.66, R)
>droEre2.scaffold_4690 2637200 99 - 18748788
UCGAGCGGAGGAUGUGACACGCAAAUCAAUACGUGUCACUCAUCUGAGGCAAAAAUGAAAUGAAAGUGGGGAAUAUUUAUAUGGCGUACAUA--GUAGUGG-------------
..(..((((.((.((((((((..........)))))))))).))))...)....(((..(((.(((((.....))))).)))..))).(((.--...))).------------- ( -21.00, z-score =  -0.67, R)
>droYak2.chrX 18584015 114 + 21770863
UCGAGCGGAGGAUGUGACACGCAAAUCAAUACGUGUCACUCAUCUGAGGCGAAAAUGAAAUGAAAGUGGGGAAUAUUUAUAUGGCAUACAUAUGGCAGUGAAGUGACAUUGUAG
(((..((((.((.((((((((..........)))))))))).))))...))).........................((((((.....))))))((((((......)))))).. ( -29.60, z-score =  -1.98, R)
>droSec1.super_4 4707386 99 + 6179234
UCGAGCGGAGGAUGUGACACGCAAAUCAAUACGUGUCACUCAUCUGAGUCGAAAAUGAAAUGAAAGUGGGGAAUAUUUAUAUGGCACAUAUA--GUAGUGG-------------
((((.((((.((.((((((((..........)))))))))).))))..))))...((..(((.(((((.....))))).)))..))(((...--...))).------------- ( -24.30, z-score =  -1.66, R)
>droSim1.chrX_random 1820493 99 - 5698898
UCGAGCGGAGGAUGUGACACGCAAAUCAAUACGUGUCACUCAUCUGAGUCGAAAAUGAAAUGAAAGUGGGGAAUAUUUAUAUGGCACAUAUA--GUAGUGG-------------
((((.((((.((.((((((((..........)))))))))).))))..))))...((..(((.(((((.....))))).)))..))(((...--...))).------------- ( -24.30, z-score =  -1.66, R)
>droAna3.scaffold_13117 2733354 75 - 5790199
UCGAGCGGA-GAUGUGACAUGC-AAUCGAUAAAUGUCACUCAUCCCUAGCAAAA--UAGAUAAUAUUUAUAAAUAUCGA-----------------------------------
(((((((((-...(((((((..-.........)))))))...)))...)).(((--((.....))))).......))))----------------------------------- ( -16.70, z-score =  -2.17, R)
>dp4.chrXL_group1e 10872805 90 - 12523060
------GGAAAAAAUUAUA---AAAAAAAAACAUGGUAAUCGAAAGAAAUCGAA--GGAAUUUGAAUCAUGUUUAAGAAUCUAUCAUAUAUGCGGUAGGAG-------------
------.............---......(((((((((..((....))..(((((--....)))))))))))))).....((((((........))))))..------------- ( -17.60, z-score =  -3.76, R)
>consensus
UCGAGCGGAGGAUGUGACACGCAAAUCAAUACGUGUCACUCAUCUGAGGCGAAAAUGAAAUGAAAGUGGGGAAUAUUUAUAUGGCACAUAUA__GUAGUGG_____________
.....((((.((.((((((((..........)))))))))).)))).................................................................... (-10.70 = -11.99 +   1.29)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,279,881 – 5,279,998
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 85.75
Shannon entropy 0.27425
G+C content 0.37913
Mean single sequence MFE -21.43
Consensus MFE -17.81
Energy contribution -17.51
Covariance contribution -0.30
Combinations/Pair 1.15
Mean z-score -2.43
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.21
SVM RNA-class probability 0.985651
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5279881 117 + 22422827
UAAAUAUUCCCCACUUUCAUUUCAUUUUCGACUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUCCUUUCCCACGAUUUCAUUACUU
................(((...((...((((..(.((.((((((((((((......)))))))))).)).)).).))))..))....)))........................... ( -22.50, z-score =  -3.13, R)
>droEre2.scaffold_4690 2637220 117 + 18748788
UAAAUAUUCCCCACUUUCAUUUCAUUUUUGCCUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUGCUUUCCCACGAUUUCAUUACUU
...................................(((((((((((((((......)))))))))).......((..((((.......))))..))............))))).... ( -22.30, z-score =  -3.04, R)
>droYak2.chrX 18584050 117 - 21770863
UAAAUAUUCCCCACUUUCAUUUCAUUUUCGCCUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUGCUUUCCCACGAUUUCAUUACUU
...................................(((((((((((((((......)))))))))).......((..((((.......))))..))............))))).... ( -22.30, z-score =  -2.93, R)
>droSec1.super_4 4707406 117 - 6179234
UAAAUAUUCCCCACUUUCAUUUCAUUUUCGACUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUGCUUUCCCACGAUUUCAUUACUU
......................((...((((..(.((.((((((((((((......)))))))))).)).)).).))))..))....(((..(((........)))..)))...... ( -23.40, z-score =  -3.00, R)
>droSim1.chrX_random 1820513 117 + 5698898
UAAAUAUUCCCCACUUUCAUUUCAUUUUCGACUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUGCUUUCCCACGAUUUCAUUACUU
......................((...((((..(.((.((((((((((((......)))))))))).)).)).).))))..))....(((..(((........)))..)))...... ( -23.40, z-score =  -3.00, R)
>droAna3.scaffold_13117 2733364 102 + 5790199
----------UAAAUAUUAUCUA--UUUUGCUAGGGAUGAGUGACAUUUAUCGAUU-GCAUGUCACAUC-UCCGCUCGAUUUAUUUUUGAUUUCCGUUUCCGUUUCCAUUCUGAUU-
----------.............--........((((((.(((((((.((.....)-).)))))))...-.....((((.......))))................))))))....- ( -14.70, z-score =   0.50, R)
>consensus
UAAAUAUUCCCCACUUUCAUUUCAUUUUCGACUCAGAUGAGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUGCUUUCCCACGAUUUCAUUACUU
................(((........(((.....((.((((((((((((......)))))))))).)).))....)))........)))........................... (-17.81 = -17.51 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,279,920 – 5,280,011
Length 91
Sequences 5
Columns 91
Reading direction forward
Mean pairwise identity 99.56
Shannon entropy 0.00793
G+C content 0.39560
Mean single sequence MFE -21.30
Consensus MFE -21.20
Energy contribution -21.40
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.42
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.13
SVM RNA-class probability 0.997560
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5279920 91 + 22422827
AGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUCCUUUCCCACGAUUUCAUUACUUGGCAUUAUUUUUG
.((((((((((......)))))))))).......((.(((...((...(((...((.........))..)))..))))))).......... ( -18.90, z-score =  -2.91, R)
>droEre2.scaffold_4690 2637259 91 + 18748788
AGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUGCUUUCCCACGAUUUCAUUACUUGGCAUUAUUUUUG
.((((((((((......)))))))))).......((.(((...((...(((..(((........)))..)))..))))))).......... ( -21.90, z-score =  -3.54, R)
>droYak2.chrX 18584089 91 - 21770863
AGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUGCUUUCCCACGAUUUCAUUACUUGGCAUUAUUUUUG
.((((((((((......)))))))))).......((.(((...((...(((..(((........)))..)))..))))))).......... ( -21.90, z-score =  -3.54, R)
>droSec1.super_4 4707445 91 - 6179234
AGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUGCUUUCCCACGAUUUCAUUACUUGGCAUUAUUUUUG
.((((((((((......)))))))))).......((.(((...((...(((..(((........)))..)))..))))))).......... ( -21.90, z-score =  -3.54, R)
>droSim1.chrX_random 1820552 91 + 5698898
AGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUGCUUUCCCACGAUUUCAUUACUUGGCAUUAUUUUUG
.((((((((((......)))))))))).......((.(((...((...(((..(((........)))..)))..))))))).......... ( -21.90, z-score =  -3.54, R)
>consensus
AGUGACACGUAUUGAUUUGCGUGUCACAUCCUCCGCUCGAUUUGUUUCUGAUUUUGCUUUCCCACGAUUUCAUUACUUGGCAUUAUUUUUG
.((((((((((......)))))))))).......((.(((...((...(((..(((........)))..)))..))))))).......... (-21.20 = -21.40 +   0.20)

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 01:17:31 2011