Locus 14820

Sequence ID dm3.chrX
Location 15,697,830 – 15,697,992
Length 162
Max. P 0.891518
window20403 window20404 window20405 window20406 window20407

overview

Window 3

Location 15,697,830 – 15,697,941
Length 111
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 85.53
Shannon entropy 0.19028
G+C content 0.30396
Mean single sequence MFE -21.93
Consensus MFE -17.54
Energy contribution -17.77
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -1.87
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.764906
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15697830 111 + 22422827
UUAUAAACUAAUUUUAUACAUUGCUUAAGCGAUAGUUUGACGUAUAAAACUGAGGAGCUUAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAAGGUCUGUUUAU
..((((((...(((((((((((((....))))).(.....)))))))))....................((((((((.((((........)))).))))))))..)))))) ( -22.40, z-score =  -1.38, R)
>droSim1.chrX_random 4103 96 + 5698898
UUAUAAACUCAUUUGAUACAUUGCUUAAGCGAUAGUUUGGUGU---------------CAAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAGGGACUGUUUAU
..((((((....(((((((...(((........)))...))))---------------))).........(((((((.((((........)))).)))))))...)))))) ( -22.50, z-score =  -2.07, R)
>droSec1.super_37 278448 96 + 454039
UUAUAAACUCAUUUGAUACAUUGCUUAAGCGAUAGUUUGAUGU---------------UUAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAAGGACUGUUUAU
.((((((((((......(((((((....))))).)).))).))---------------))))).......(((((((.((((........)))).)))))))......... ( -20.90, z-score =  -2.17, R)
>consensus
UUAUAAACUCAUUUGAUACAUUGCUUAAGCGAUAGUUUGAUGU_______________UUAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAAGGACUGUUUAU
..((((((.((((....(((((((....))))).))..))))............................(((((((.((((........)))).)))))))...)))))) (-17.54 = -17.77 +   0.23)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,697,830 – 15,697,941
Length 111
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 85.53
Shannon entropy 0.19028
G+C content 0.30396
Mean single sequence MFE -18.10
Consensus MFE -13.97
Energy contribution -13.97
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.847827
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15697830 111 - 22422827
AUAAACAGACCUUUGAAUGCAUUCCACUGUGCAGUCAAAAGUAAUAAAUAUAAGCUCCUCAGUUUUAUACGUCAAACUAUCGCUUAAGCAAUGUAUAAAAUUAGUUUAUAA
........((.(((((.(((((......))))).))))).))......((((((((....(((((((((((.....)....((....))...)))))))))))))))))). ( -23.50, z-score =  -3.57, R)
>droSim1.chrX_random 4103 96 - 5698898
AUAAACAGUCCCUUGAAUGCAUUCCACUGUGCAGUCAAAAGUAAUAAAUAUUG---------------ACACCAAACUAUCGCUUAAGCAAUGUAUCAAAUGAGUUUAUAA
((((((.(((..((((.(((((......))))).)))).((((.....)))))---------------))...........((....))..............)))))).. ( -15.10, z-score =  -1.17, R)
>droSec1.super_37 278448 96 - 454039
AUAAACAGUCCUUUGAAUGCAUUCCACUGUGCAGUCAAAAGUAAUAAAUAUAA---------------ACAUCAAACUAUCGCUUAAGCAAUGUAUCAAAUGAGUUUAUAA
...........(((((.(((((......))))).))))).........(((((---------------((...........((....))......((....))))))))). ( -15.70, z-score =  -1.73, R)
>consensus
AUAAACAGUCCUUUGAAUGCAUUCCACUGUGCAGUCAAAAGUAAUAAAUAUAA_______________ACAUCAAACUAUCGCUUAAGCAAUGUAUCAAAUGAGUUUAUAA
((((((......((((.(((((......))))).))))...........................................((....))..............)))))).. (-13.97 = -13.97 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,697,868 – 15,697,980
Length 112
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 83.80
Shannon entropy 0.21318
G+C content 0.40243
Mean single sequence MFE -24.50
Consensus MFE -23.29
Energy contribution -22.97
Covariance contribution -0.33
Combinations/Pair 1.11
Mean z-score -0.81
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.20
SVM RNA-class probability 0.589914
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15697868 112 + 22422827
GACGUAUAAAACUGAGGAGCUUAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAAGGUCUGUUUAUGUUUUUGUUCCGGUGUGACCGUAUUCCGAACAGGAACAC
...............(((((..((((..((.((((((((.((((........)))).))))))))..))..))))....)))))((.....))((.((((.....)))).)) ( -26.60, z-score =  -0.94, R)
>droSim1.chrX_random 4141 97 + 5698898
---------------GGUGUCAAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAGGGACUGUUUAUGUUUUUGUUCCGGUGUGACCAUAUUCCGAACAGGGACAC
---------------.((((((((((..((..(((((((.((((........)))).)))))))...))..)))))(((((((.((.(((....))).)))))))))))))) ( -23.90, z-score =  -0.62, R)
>droSec1.super_37 278486 97 + 454039
---------------GAUGUUUAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAAGGACUGUUUAUGUUUUUGUUCCGGUGUGACCGUAAUCCGAACAGGGACGC
---------------.................(((((((.((((........)))).))))))).........(((((((((((((.....)))......)))))))))).. ( -23.00, z-score =  -0.86, R)
>consensus
_______________GGUGUUUAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAAGGACUGUUUAUGUUUUUGUUCCGGUGUGACCGUAUUCCGAACAGGGACAC
................................(((((((.((((........)))).)))))))........(((((((((((.((.(((....))).))))))))))))). (-23.29 = -22.97 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,697,880 – 15,697,992
Length 112
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 89.63
Shannon entropy 0.13938
G+C content 0.38141
Mean single sequence MFE -28.00
Consensus MFE -25.29
Energy contribution -25.30
Covariance contribution 0.01
Combinations/Pair 1.10
Mean z-score -1.82
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.10
SVM RNA-class probability 0.891518
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15697880 112 + 22422827
UGAGGAGCUUAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAAGGUCUGUUUAUGUUUUUGUUCCGGUGUGACCGUAUUCCGAACAGGAACACAGUCUAAUUUAA
...(((((..((((..((.((((((((.((((........)))).))))))))..))..))))....))))).....(((.((.((((.....)))).)).)))........ ( -30.10, z-score =  -2.10, R)
>droSim1.chrX_random 4146 104 + 5698898
--------CAAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAGGGACUGUUUAUGUUUUUGUUCCGGUGUGACCAUAUUCCGAACAGGGACACAGUCUGAUUUAA
--------..............(((((.((((........)))).)))))(((((((....((((((((((.((.(((....))).)))))))))))))))))))....... ( -26.60, z-score =  -1.56, R)
>droSec1.super_37 278491 104 + 454039
--------UUAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAAGGACUGUUUAUGUUUUUGUUCCGGUGUGACCGUAAUCCGAACAGGGACGCAGUCUGAUUUAA
--------..............(((((.((((........)))).)))))(((((((....(((((((((((((.....)))......)))))))))))))))))....... ( -27.30, z-score =  -1.79, R)
>consensus
________UUAUAUUUAUUACUUUUGACUGCACAGUGGAAUGCAUUCAAAGGACUGUUUAUGUUUUUGUUCCGGUGUGACCGUAUUCCGAACAGGGACACAGUCUGAUUUAA
......................(((((.((((........)))).)))))(((((((....((((((((((.((.(((....))).)))))))))))))))))))....... (-25.29 = -25.30 +   0.01)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,697,880 – 15,697,992
Length 112
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 89.63
Shannon entropy 0.13938
G+C content 0.38141
Mean single sequence MFE -23.53
Consensus MFE -18.36
Energy contribution -18.81
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -2.11
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.731845
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 15697880 112 - 22422827
UUAAAUUAGACUGUGUUCCUGUUCGGAAUACGGUCACACCGGAACAAAAACAUAAACAGACCUUUGAAUGCAUUCCACUGUGCAGUCAAAAGUAAUAAAUAUAAGCUCCUCA
........(((((((((((.....))))))))))).....(((................((.(((((.(((((......))))).))))).)).............)))... ( -28.85, z-score =  -3.58, R)
>droSim1.chrX_random 4146 104 - 5698898
UUAAAUCAGACUGUGUCCCUGUUCGGAAUAUGGUCACACCGGAACAAAAACAUAAACAGUCCCUUGAAUGCAUUCCACUGUGCAGUCAAAAGUAAUAAAUAUUG--------
........((((((.....((((.......(((.....))).......))))...))))))..((((.(((((......))))).))))...............-------- ( -19.94, z-score =  -0.95, R)
>droSec1.super_37 278491 104 - 454039
UUAAAUCAGACUGCGUCCCUGUUCGGAUUACGGUCACACCGGAACAAAAACAUAAACAGUCCUUUGAAUGCAUUCCACUGUGCAGUCAAAAGUAAUAAAUAUAA--------
........(((((.((((......))))..(((.....)))...............))))).(((((.(((((......))))).)))))..............-------- ( -21.80, z-score =  -1.80, R)
>consensus
UUAAAUCAGACUGUGUCCCUGUUCGGAAUACGGUCACACCGGAACAAAAACAUAAACAGUCCUUUGAAUGCAUUCCACUGUGCAGUCAAAAGUAAUAAAUAUAA________
........((((((.....((((.......(((.....))).......))))...))))))..((((.(((((......))))).))))....................... (-18.36 = -18.81 +   0.45)

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 01:47:26 2011