Locus 15081

Sequence ID dm3.chrX
Location 17,332,012 – 17,332,197
Length 185
Max. P 0.990912
window20780 window20781 window20782 window20783 window20784 window20785

overview

Window 0

Location 17,332,012 – 17,332,126
Length 114
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 90.83
Shannon entropy 0.14872
G+C content 0.38945
Mean single sequence MFE -25.05
Consensus MFE -21.26
Energy contribution -22.20
Covariance contribution 0.94
Combinations/Pair 1.10
Mean z-score -1.65
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.679687
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17332012 114 + 22422827
UCUUUGGCUAAACUAAACCAAAUUUAUUCGAAAAAGCUGAACAAAAUGUUAGCCCAUUCAAGGGACGAACAAACAUUUCACAUAUUUUCCUGGCCA-CCCGAAAAUAUGUGGCAA
..(((((..........))))).............((.........((((..(((......)))...)))).......(((((((((((..((...-.))))))))))))))).. ( -23.60, z-score =  -1.87, R)
>droYak2.chrX 15951537 115 + 21770863
UCUUUGGCUAAACGAAACCAAAUUUAUGCGUAAAGGCUGAACAAAUUGUUCGCCCAUUCGCAGGCAGAAUAAACAUUCCACAUACUUUCCAGGCCAUCCCAAAAAUAUGUGGCAA
..(((((..........)))))....((((....(((.((((.....)))))))....)))).((.((((....))))((((((.(((...((....))..))).)))))))).. ( -23.90, z-score =  -0.78, R)
>droSec1.super_17 1178283 114 + 1527944
UCUUUGGCUAAACUAAACCAAAUUUAUUCGAAAAAGCUGAACAAAAUGUUUGCCCAUUCAAGGGCCGAGCAAACAUUUCACAUAUUUUCCUGGCCA-CCCGAAAAUAUGUGGCAA
..(((((..........))))).............((.........(((((((((......))).)))))).......(((((((((((..((...-.))))))))))))))).. ( -26.70, z-score =  -1.98, R)
>droSim1.chrX 3460174 114 - 17042790
UCUCUGGCUAAACUAAACCAAAUUUAUUCGAAAAAGCUGAACAAAAUGUUUGCCCAUUCAAGGGCCGAGCAAACAUUUCACAUAUUUUCCUGGCCA-CCCGAAAAUAUGUGGCUA
....((((...........................(((((((.....))))((((......))))..)))........(((((((((((..((...-.))))))))))))))))) ( -26.00, z-score =  -1.97, R)
>consensus
UCUUUGGCUAAACUAAACCAAAUUUAUUCGAAAAAGCUGAACAAAAUGUUUGCCCAUUCAAGGGCCGAACAAACAUUUCACAUAUUUUCCUGGCCA_CCCGAAAAUAUGUGGCAA
..(((((..........))))).............((.........(((((((((......)))).))))).......(((((((((((..((.....))))))))))))))).. (-21.26 = -22.20 +   0.94)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,332,012 – 17,332,126
Length 114
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 90.83
Shannon entropy 0.14872
G+C content 0.38945
Mean single sequence MFE -34.83
Consensus MFE -29.62
Energy contribution -29.50
Covariance contribution -0.12
Combinations/Pair 1.17
Mean z-score -2.50
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.78
SVM RNA-class probability 0.967087
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17332012 114 - 22422827
UUGCCACAUAUUUUCGGG-UGGCCAGGAAAAUAUGUGAAAUGUUUGUUCGUCCCUUGAAUGGGCUAACAUUUUGUUCAGCUUUUUCGAAUAAAUUUGGUUUAGUUUAGCCAAAGA
....(((((((((((.((-...))..))))))))))).....((((((((..((......))((((((.....))).))).....))))))))(((((((......))))))).. ( -30.80, z-score =  -1.97, R)
>droYak2.chrX 15951537 115 - 21770863
UUGCCACAUAUUUUUGGGAUGGCCUGGAAAGUAUGUGGAAUGUUUAUUCUGCCUGCGAAUGGGCGAACAAUUUGUUCAGCCUUUACGCAUAAAUUUGGUUUCGUUUAGCCAAAGA
...((((((((((((.((.....)).))))))))))))...............((((...((((((((.....)))).))))...))))....(((((((......))))))).. ( -38.40, z-score =  -3.06, R)
>droSec1.super_17 1178283 114 - 1527944
UUGCCACAUAUUUUCGGG-UGGCCAGGAAAAUAUGUGAAAUGUUUGCUCGGCCCUUGAAUGGGCAAACAUUUUGUUCAGCUUUUUCGAAUAAAUUUGGUUUAGUUUAGCCAAAGA
....(((((((((((.((-...))..)))))))))))(((((((((((((.........)))))))))))))(((((.........)))))..(((((((......))))))).. ( -34.80, z-score =  -2.40, R)
>droSim1.chrX 3460174 114 + 17042790
UAGCCACAUAUUUUCGGG-UGGCCAGGAAAAUAUGUGAAAUGUUUGCUCGGCCCUUGAAUGGGCAAACAUUUUGUUCAGCUUUUUCGAAUAAAUUUGGUUUAGUUUAGCCAGAGA
.((((((((((((((.((-...))..)))))))))))(((((((((((((.........)))))))))))))......)))............(((((((......))))))).. ( -35.30, z-score =  -2.55, R)
>consensus
UUGCCACAUAUUUUCGGG_UGGCCAGGAAAAUAUGUGAAAUGUUUGCUCGGCCCUUGAAUGGGCAAACAUUUUGUUCAGCUUUUUCGAAUAAAUUUGGUUUAGUUUAGCCAAAGA
..(((((((((((((.((....))..)))))))))))(((((((((((((.........)))))))))))))......)).............(((((((......))))))).. (-29.62 = -29.50 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,332,052 – 17,332,155
Length 103
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 86.22
Shannon entropy 0.21927
G+C content 0.43377
Mean single sequence MFE -30.88
Consensus MFE -27.08
Energy contribution -28.08
Covariance contribution 1.00
Combinations/Pair 1.15
Mean z-score -2.60
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.42
SVM RNA-class probability 0.990395
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17332052 103 + 22422827
ACAAAAUGUUAGCCCAUUCAAGGGACGAACAAACAUUUCACAUAUUUUCCUGGCCA-CCCGAAAAUAUGUGGCAACAGAAACAAGU-------UGUUUGGCCAGGACACAC----
......((((..(((......)))...))))................(((((((((-..(((.....(.((....)).)......)-------))..))))))))).....---- ( -30.40, z-score =  -3.40, R)
>droYak2.chrX 15951577 115 + 21770863
ACAAAUUGUUCGCCCAUUCGCAGGCAGAAUAAACAUUCCACAUACUUUCCAGGCCAUCCCAAAAAUAUGUGGCAACUGAAACAAGUAUGUCCUUGUUUGGCCAGGACACAUACAU
......(((((((......)).(((....((((((....((((((((..((((((((...........)))))..)))....))))))))...))))))))).)))))....... ( -26.90, z-score =  -1.51, R)
>droSec1.super_17 1178323 110 + 1527944
ACAAAAUGUUUGCCCAUUCAAGGGCCGAGCAAACAUUUCACAUAUUUUCCUGGCCA-CCCGAAAAUAUGUGGCAAUAGAAACUAGUAUGUCCUUGUUUGGCCAGGACACAC----
......(((((((((......))).))))))................(((((((((-..(((..((((((((.........))).)))))..)))..))))))))).....---- ( -32.80, z-score =  -2.69, R)
>droSim1.chrX 3460214 110 - 17042790
ACAAAAUGUUUGCCCAUUCAAGGGCCGAGCAAACAUUUCACAUAUUUUCCUGGCCA-CCCGAAAAUAUGUGGCUACAGAAACAAGUAUGUCCUUGUUUGGCCAGGACACAC----
......(((((((((......))).))))))................((((((((.-.(((........)))......(((((((......))))))))))))))).....---- ( -33.40, z-score =  -2.79, R)
>consensus
ACAAAAUGUUUGCCCAUUCAAGGGCCGAACAAACAUUUCACAUAUUUUCCUGGCCA_CCCGAAAAUAUGUGGCAACAGAAACAAGUAUGUCCUUGUUUGGCCAGGACACAC____
......(((((((((......)))).)))))................((((((((...(((........)))......(((((((......)))))))))))))))......... (-27.08 = -28.08 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,332,052 – 17,332,155
Length 103
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 86.22
Shannon entropy 0.21927
G+C content 0.43377
Mean single sequence MFE -37.53
Consensus MFE -30.84
Energy contribution -31.90
Covariance contribution 1.06
Combinations/Pair 1.15
Mean z-score -2.86
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.45
SVM RNA-class probability 0.990912
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17332052 103 - 22422827
----GUGUGUCCUGGCCAAACA-------ACUUGUUUCUGUUGCCACAUAUUUUCGGG-UGGCCAGGAAAAUAUGUGAAAUGUUUGUUCGUCCCUUGAAUGGGCUAACAUUUUGU
----((((.(((((((((..((-------((........))))((..........)).-)))))))))..))))(..(((((((.((((((.......)))))).)))))))..) ( -31.80, z-score =  -2.34, R)
>droYak2.chrX 15951577 115 - 21770863
AUGUAUGUGUCCUGGCCAAACAAGGACAUACUUGUUUCAGUUGCCACAUAUUUUUGGGAUGGCCUGGAAAGUAUGUGGAAUGUUUAUUCUGCCUGCGAAUGGGCGAACAAUUUGU
.....(((((((((......).)))))))).((((((..(((.((((((((((((.((.....)).)))))))))))))))((((((((.......))))))))))))))..... ( -36.10, z-score =  -1.88, R)
>droSec1.super_17 1178323 110 - 1527944
----GUGUGUCCUGGCCAAACAAGGACAUACUAGUUUCUAUUGCCACAUAUUUUCGGG-UGGCCAGGAAAAUAUGUGAAAUGUUUGCUCGGCCCUUGAAUGGGCAAACAUUUUGU
----((((((((((......).))))))))).............(((((((((((.((-...))..)))))))))))(((((((((((((.........)))))))))))))... ( -40.40, z-score =  -3.53, R)
>droSim1.chrX 3460214 110 + 17042790
----GUGUGUCCUGGCCAAACAAGGACAUACUUGUUUCUGUAGCCACAUAUUUUCGGG-UGGCCAGGAAAAUAUGUGAAAUGUUUGCUCGGCCCUUGAAUGGGCAAACAUUUUGU
----((((.((((((((..(((..((((....))))..))).(((.(........)))-)))))))))..))))(..(((((((((((((.........)))))))))))))..) ( -41.80, z-score =  -3.70, R)
>consensus
____GUGUGUCCUGGCCAAACAAGGACAUACUUGUUUCUGUUGCCACAUAUUUUCGGG_UGGCCAGGAAAAUAUGUGAAAUGUUUGCUCGGCCCUUGAAUGGGCAAACAUUUUGU
....((...(((((((((((((((......)))))))......((..........))...))))))))..))..(..(((((((((((((.........)))))))))))))..) (-30.84 = -31.90 +   1.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,332,092 – 17,332,194
Length 102
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 84.82
Shannon entropy 0.23772
G+C content 0.51564
Mean single sequence MFE -35.95
Consensus MFE -25.05
Energy contribution -25.93
Covariance contribution 0.88
Combinations/Pair 1.08
Mean z-score -2.30
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.872403
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17332092 102 - 22422827
GCCAU-GCCCUCCGCCCACCAACCGGAUUAUUCCGAGA----GUGUGUGUCCUGGCCAAACA-------ACUUGUUUCUGUUGCCACAUAUUUUCGGG-UGGCCAGGAAAAUAUG
.....-..(((((((((.......(((....)))((((----(((((((.(..(((.((((.-------....))))..)))).))))))))))))))-)))..)))........ ( -31.50, z-score =  -1.91, R)
>droYak2.chrX 15951617 115 - 21770863
GCCACAACCGCCCUGCUAACAACCGCAUAAUUCCGAGAGUAUGUAUGUGUCCUGGCCAAACAAGGACAUACUUGUUUCAGUUGCCACAUAUUUUUGGGAUGGCCUGGAAAGUAUG
.......(((((.(((........)))..(((((((((((((((.(((((((((......).))))))))...((.......)).))))))))))))))))))..))........ ( -31.70, z-score =  -1.12, R)
>droSec1.super_17 1178363 109 - 1527944
GCCAC-GCCCUCCGGCCGCCAGCCGGAUUAUUCCGAGA----GUGUGUGUCCUGGCCAAACAAGGACAUACUAGUUUCUAUUGCCACAUAUUUUCGGG-UGGCCAGGAAAAUAUG
(((((-....((((((.....)))))).....((((((----((((((((((((......).)))))......((.......)).)))))))))))))-))))............ ( -40.70, z-score =  -3.12, R)
>droSim1.chrX 3460254 109 + 17042790
GCCAC-GCCCUCCGCCCGCCAGCCGGAUUAUUCCGAGA----GUGUGUGUCCUGGCCAAACAAGGACAUACUUGUUUCUGUAGCCACAUAUUUUCGGG-UGGCCAGGAAAAUAUG
..(((-((.(((.((......))((((....)))).))----).)))))((((((((..(((..((((....))))..))).(((.(........)))-)))))))))....... ( -39.90, z-score =  -3.03, R)
>consensus
GCCAC_GCCCUCCGCCCACCAACCGGAUUAUUCCGAGA____GUGUGUGUCCUGGCCAAACAAGGACAUACUUGUUUCUGUUGCCACAUAUUUUCGGG_UGGCCAGGAAAAUAUG
.......................((((....)))).......((((...(((((((((((((((......)))))))......((..........))...))))))))..)))). (-25.05 = -25.93 +   0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,332,095 – 17,332,197
Length 102
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 84.38
Shannon entropy 0.24478
G+C content 0.52268
Mean single sequence MFE -36.27
Consensus MFE -22.90
Energy contribution -24.53
Covariance contribution 1.63
Combinations/Pair 1.07
Mean z-score -2.10
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.17
SVM RNA-class probability 0.575128
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 17332095 102 - 22422827
CGAGCCAU-GCCCUCCGCCCACCAACCGGAUUAUUCCGAGA----GUGUGUGUCCUGGCCAAACA-------ACUUGUUUCUGUUGCCACAUAUUUUCGGG-UGGCCAGGAAAAU
........-..(((((((((.......(((....)))((((----(((((((.(..(((.((((.-------....))))..)))).))))))))))))))-)))..)))..... ( -31.50, z-score =  -1.50, R)
>droYak2.chrX 15951620 115 - 21770863
AGAGCCACAACCGCCCUGCUAACAACCGCAUAAUUCCGAGAGUAUGUAUGUGUCCUGGCCAAACAAGGACAUACUUGUUUCAGUUGCCACAUAUUUUUGGGAUGGCCUGGAAAGU
((.(((..........(((........)))..(((((((((((((((.(((((((((......).))))))))...((.......)).))))))))))))))))))))....... ( -32.30, z-score =  -1.15, R)
>droSec1.super_17 1178366 109 - 1527944
CGAGCCAC-GCCCUCCGGCCGCCAGCCGGAUUAUUCCGAGA----GUGUGUGUCCUGGCCAAACAAGGACAUACUAGUUUCUAUUGCCACAUAUUUUCGGG-UGGCCAGGAAAAU
.(.(((((-....((((((.....)))))).....((((((----((((((((((((......).)))))......((.......)).)))))))))))))-)))))........ ( -41.40, z-score =  -3.03, R)
>droSim1.chrX 3460257 109 + 17042790
CGAGCCAC-GCCCUCCGCCCGCCAGCCGGAUUAUUCCGAGA----GUGUGUGUCCUGGCCAAACAAGGACAUACUUGUUUCUGUAGCCACAUAUUUUCGGG-UGGCCAGGAAAAU
.....(((-((.(((.((......))((((....)))).))----).)))))((((((((..(((..((((....))))..))).(((.(........)))-))))))))).... ( -39.90, z-score =  -2.71, R)
>consensus
CGAGCCAC_GCCCUCCGCCCACCAACCGGAUUAUUCCGAGA____GUGUGUGUCCUGGCCAAACAAGGACAUACUUGUUUCUGUUGCCACAUAUUUUCGGG_UGGCCAGGAAAAU
...............(((.(((...(((((....)))).).....))).)))(((((((((((((((......)))))))......((..........))...)))))))).... (-22.90 = -24.53 +   1.63)

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 01:52:41 2011