Locus 12672

Sequence ID dm3.chrX
Location 1,552,141 – 1,552,282
Length 141
Max. P 0.968119
window17423 window17424 window17425

overview

Window 3

Location 1,552,141 – 1,552,244
Length 103
Sequences 7
Columns 116
Reading direction reverse
Mean pairwise identity 67.87
Shannon entropy 0.56558
G+C content 0.40299
Mean single sequence MFE -25.83
Consensus MFE -11.65
Energy contribution -11.70
Covariance contribution 0.05
Combinations/Pair 1.42
Mean z-score -1.75
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.904955
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1552141 103 - 22422827
-------------AUUUUAUGCUUUCUGAAGAGAACGAACCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAUUUUGUCGAUGGCUUGAUACGUUUGAGCCUAGAUUUUGACG
-------------......(((((((.........(((.(((....))).)))..........)))))))(((((....(((...((((..(.....)..))))..))).))))). ( -32.11, z-score =  -3.14, R)
>droPer1.super_11 1827122 81 + 2846995
------------------AUGAUUCC---AGCUAAGUAAUCGCGAGAGAAUAUAGUACAGAACGGAAACGGUU-------UUGGGGGGUAAUUAAUUUUGAAAC--GUUUU-----
------------------...(((((---.((((.((..((....))..)).)))).(((((((....).)))-------))).)))))...............--.....----- ( -17.80, z-score =  -1.80, R)
>dp4.chrXL_group1a 4714068 81 + 9151740
------------------AUGAUUCC---AGCUAAGUAAUCGCGAGAGAAUAUAGUACAGAACGGAAACGGUU-------UUGGGGGGUAAUUAAUUUUGAAAC--GUUUU-----
------------------...(((((---.((((.((..((....))..)).)))).(((((((....).)))-------))).)))))...............--.....----- ( -17.80, z-score =  -1.80, R)
>droEre2.scaffold_4644 1537345 102 - 2521924
-------------AUUAUAUGCUUUCUUCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAUUUUGUCGUAGGCUUGAUAUGUUUGAACCUCG-UUUUGACG
-------------......((((((((((((....(((..((....))..)))..)))))...)))))))(((((......((.(((.(..(.....)..).)))))-..))))). ( -25.20, z-score =  -0.63, R)
>droYak2.chrX 1405369 116 - 21770863
AAUUUCUGCUUUAAUGCAGAAUAUUCUCCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCUGUUAAUUUUGUCGAUGGCUUGAUAUGUUUGAACCUCGAUUUUGACG
...((((((......))))))..((((....))))(((..((....))..))).........(....)..(((((....(((((.((.(..(.....)..).))))))).))))). ( -29.80, z-score =  -1.40, R)
>droSec1.super_10 1357830 103 - 3036183
-------------AUUUUAUGCUUUCUGCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAUUUUGUCGAUGGCUUGAUACGUUUGAACCUCGAUUUUAACG
-------------......(((((((..(((....(((..((....))..)))..))).....)))))))(((((....(((((.((.(..(.....)..).))))))).))))). ( -27.00, z-score =  -1.22, R)
>droSim1.chrX_random 1021331 103 - 5698898
-------------AUUUUCUGCUUUCUGCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAUUUUGUCGAUGGCUUGAUACGUUUGAACCUCGAUUUUAACG
-------------.((((((((.....))))))))(((..((....))..))).........((....))(((((....(((((.((.(..(.....)..).))))))).))))). ( -31.10, z-score =  -2.28, R)
>consensus
_____________AUUUUAUGCUUUCUGCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAUUUUGUCGAUGGCUUGAUACGUUUGAACCUCGAUUUUGACG
....................((((((......((.(((.(((....))).)))..))......))))))((((.....((((((....))))))......))))............ (-11.65 = -11.70 +   0.05)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,552,181 – 1,552,282
Length 101
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 88.88
Shannon entropy 0.18222
G+C content 0.44488
Mean single sequence MFE -23.22
Consensus MFE -17.18
Energy contribution -17.18
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.72
SVM RNA-class probability 0.796521
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1552181 101 + 22422827
AUUAACCGCUUCCGUUUUCAAUCCGACCCGUUUCCGGUUCGUUCUCUUCAGAA-------------AGCAUAAAAUAAA--ACACGAAGAGCACAACGAACCGGAAACCACGAUCG
.......................(((.(.((((((((((((((((((((....-------------.............--....))))))...))))))))))))))...).))) ( -28.10, z-score =  -4.23, R)
>droEre2.scaffold_4644 1537384 101 + 2521924
AUUAACCGCUUCCGUUUUCAAUCCGACCCGUUUCCGAUUCGUUCUCUGAAGAA-------------AGCAUAUAAUAAA--GAAAUAAGAGCACAACGAACCGGAAACCACGAUCG
.......................(((.(.(((((((.((((((((((......-------------.............--......))))...)))))).)))))))...).))) ( -17.91, z-score =  -1.06, R)
>droYak2.chrX 1405409 116 + 21770863
AUUAACAGCUUCCGUUUUCAAUCCGACCCGUUUCCGAUUCGUUCUCUGGAGAAUAUUCUGCAUUAAAGCAGAAAUUAAAUAGAAAGAAGAGCACAACGAACCGGAAACCACGGUCG
.......................(((((.(((((((.((((((((((......((((((((......)))))......)))......))))...)))))).)))))))...))))) ( -31.80, z-score =  -3.41, R)
>droSec1.super_10 1357870 101 + 3036183
AUUAACCGCUUCCGUUUUCAAUCCGACCCGUUUCCGAUUCGUUCUCUGCAGAA-------------AGCAUAAAAUAAA--ACACGAAGAGCACAACGAACCGGAAACCACGAUCG
.......................(((.(.(((((((.((((((((((......-------------.............--......))))...)))))).)))))))...).))) ( -17.91, z-score =  -0.96, R)
>droSim1.chrX_random 1021371 101 + 5698898
AUUAACCGCUUCCGUUUUCAAUCCGACCCGUUUCCGAUUCGUUCUCUGCAGAA-------------AGCAGAAAAUAAA--ACACGAAGAGCACAACGAACCGGAAACCACGAUCG
.......................(((.(.(((((((.((((((.(((((....-------------.))))).......--....(.....)..)))))).)))))))...).))) ( -20.40, z-score =  -1.43, R)
>consensus
AUUAACCGCUUCCGUUUUCAAUCCGACCCGUUUCCGAUUCGUUCUCUGCAGAA_____________AGCAUAAAAUAAA__ACACGAAGAGCACAACGAACCGGAAACCACGAUCG
.......................(((.(.(((((((.((((((((((........................................))))...)))))).)))))))...).))) (-17.18 = -17.18 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,552,181 – 1,552,282
Length 101
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 88.88
Shannon entropy 0.18222
G+C content 0.44488
Mean single sequence MFE -33.96
Consensus MFE -28.70
Energy contribution -28.38
Covariance contribution -0.32
Combinations/Pair 1.07
Mean z-score -2.39
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.79
SVM RNA-class probability 0.968119
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1552181 101 - 22422827
CGAUCGUGGUUUCCGGUUCGUUGUGCUCUUCGUGU--UUUAUUUUAUGCU-------------UUCUGAAGAGAACGAACCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAU
(((((...((((((((((((((...(((((((.((--..........)).-------------...))))))))))))))))))))).))))).(((((...((....)).))))) ( -36.50, z-score =  -3.12, R)
>droEre2.scaffold_4644 1537384 101 - 2521924
CGAUCGUGGUUUCCGGUUCGUUGUGCUCUUAUUUC--UUUAUUAUAUGCU-------------UUCUUCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAU
(((((...((((((((((((((...((((......--.............-------------......)))))))))))))))))).))))).(((((...((....)).))))) ( -28.31, z-score =  -1.26, R)
>droYak2.chrX 1405409 116 - 21770863
CGACCGUGGUUUCCGGUUCGUUGUGCUCUUCUUUCUAUUUAAUUUCUGCUUUAAUGCAGAAUAUUCUCCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCUGUUAAU
(((((...((((((((((((((.....................((((((......))))))..(((....))))))))))))))))).))))).(((((...(....)...))))) ( -38.40, z-score =  -3.34, R)
>droSec1.super_10 1357870 101 - 3036183
CGAUCGUGGUUUCCGGUUCGUUGUGCUCUUCGUGU--UUUAUUUUAUGCU-------------UUCUGCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAU
(((((...((((((((((((((.(((.....((((--........)))).-------------....)))...)))))))))))))).))))).(((((...((....)).))))) ( -31.20, z-score =  -1.57, R)
>droSim1.chrX_random 1021371 101 - 5698898
CGAUCGUGGUUUCCGGUUCGUUGUGCUCUUCGUGU--UUUAUUUUCUGCU-------------UUCUGCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAU
(((((...(((((((((((((((..(.....)..)--......((((((.-------------....)))))))))))))))))))).))))).(((((...((....)).))))) ( -35.40, z-score =  -2.67, R)
>consensus
CGAUCGUGGUUUCCGGUUCGUUGUGCUCUUCGUGU__UUUAUUUUAUGCU_____________UUCUGCAGAGAACGAAUCGGAAACGGGUCGGAUUGAAAACGGAAGCGGUUAAU
(((((...((((((((((((((...((((........................................)))))))))))))))))).))))).(((((...(....)...))))) (-28.70 = -28.38 +  -0.32)

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 01:06:40 2011