Locus 10055

Sequence ID dm3.chr3R
Location 10,894,199 – 10,894,332
Length 133
Max. P 0.765972
window13821 window13822 window13823

overview

Window 1

Location 10,894,199 – 10,894,304
Length 105
Sequences 8
Columns 117
Reading direction reverse
Mean pairwise identity 78.36
Shannon entropy 0.39416
G+C content 0.49636
Mean single sequence MFE -32.10
Consensus MFE -17.50
Energy contribution -18.04
Covariance contribution 0.53
Combinations/Pair 1.08
Mean z-score -1.90
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.765972
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10894199 105 - 27905053
------CCGGAGCCAAAGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAGC------GGGCUAAAGCUGAUGCUCAGCUAAUAGUUUGG
------(((((((....))(((((((.((....((.....))..))...)))))))..)))))..(((((.(((((...------.))))).(((((.....)))))....))))). ( -33.40, z-score =  -1.55, R)
>droPer1.super_3 3620187 83 - 7375914
-----------------------------GAGGAAGAUGAUGAAGGAUAUGCGACUUAUCUGGUUGUAACAUGGCCAAC-----GGGGCCAAAGCUGAUGCUCAGCUAAUAGUUUGG
-----------------------------....................(((((((.....)))))))...(((((...-----..))))).(((((.....))))).......... ( -21.50, z-score =  -1.04, R)
>dp4.chr2 20866932 83 - 30794189
-----------------------------GAGGAAGAUGAUGAAGGAUAUGCGACUUAUCUGGUUGUAACAUGGCCAAC-----GGGGCCAAAGCUGAUGCUCAGCUAAUAGUUUGG
-----------------------------....................(((((((.....)))))))...(((((...-----..))))).(((((.....))))).......... ( -21.50, z-score =  -1.04, R)
>droAna3.scaffold_13340 5971269 110 - 23697760
-------AAGAGCUUGCGCCACCGAACCAGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGCUUCUAACAUGGCCAACGGGCAGGAGCUGAAGCUGAAGCAGAGCUAAUAGUUUUG
-------...(((((((.((........((((((((((((((((.....))))..))))))))))))......(((....))).)).))..)))))....((((((.....)))))) ( -34.80, z-score =  -1.75, R)
>droEre2.scaffold_4770 10427586 111 - 17746568
AAGGAGCCGGAGCCAAAGCAGUUGAAGCUGGGGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAGC------GGGCCAAUGCUGAUGCUCAGCUAAUAGUUUGG
.....(((((((((..(((.......)))..)))......((((.....)))).....)))))).(((((.(((((...------.)))))..((((.....)))).....))))). ( -37.40, z-score =  -1.59, R)
>droYak2.chr3R 13304689 93 + 28832112
------------------CAGUUGAAGCUGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAGC------GGGCCAAAGCUGAUGCUCAGCUAAUAGUUUGG
------------------((((....)))).(.(((((((((((.....))))..))))))).).(((((.(((((...------.))))).(((((.....)))))....))))). ( -31.10, z-score =  -2.42, R)
>droSec1.super_0 10073693 105 + 21120651
------CCGGAGCCAGAGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAGC------GGGCUAAAGCUGAUGCUCAGCUAAUAGUUUGG
------.....((((((..(((((((.((....((.....))..))...)))))))..)))))).(((((.(((((...------.))))).(((((.....)))))....))))). ( -37.40, z-score =  -2.61, R)
>droSim1.chr3R 16952606 105 + 27517382
------CCGGAGCCAGAGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAGC------GGGCCAAAGCUGAUGCUCAGCUAAUAGUUUGG
------.....((((((..(((((((.((....((.....))..))...)))))))..)))))).(((((.(((((...------.))))).(((((.....)))))....))))). ( -39.70, z-score =  -3.22, R)
>consensus
_______CGGAGCCA_AGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAGC______GGGCCAAAGCUGAUGCUCAGCUAAUAGUUUGG
.................................(((((((((((.....))))..))))))).....(((.(((((..........))))).(((((.....)))))....)))... (-17.50 = -18.04 +   0.53)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,894,232 – 10,894,331
Length 99
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 71.93
Shannon entropy 0.50792
G+C content 0.53216
Mean single sequence MFE -28.85
Consensus MFE -12.69
Energy contribution -12.50
Covariance contribution -0.19
Combinations/Pair 1.20
Mean z-score -1.75
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.52
SVM RNA-class probability 0.727639
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10894232 99 - 27905053
UCUGAGGGGGCAC----GGCGAGGGCGAA-----AGCCGGAGCCAAAGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAG
........(((.(----(((...(((...-----.)))...((....)).......)))).(.(((((((((((.....))))..))))))).).........))).. ( -30.40, z-score =  -1.05, R)
>droAna3.scaffold_13340 5971308 81 - 23697760
---------------------------AGGGUGGAAGAAGAGCUUGCGCCACCGAACCAGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGCUUCUAACAUGGCCAA
---------------------------..((((.(((.....))).)))).(((....((((((((((((((((.....))))..))))))))))))....))).... ( -27.30, z-score =  -2.62, R)
>droEre2.scaffold_4770 10427619 108 - 17746568
UCUGAAGGAAGGCAAAAGGCGAAGCCGGAGAAGGAGCCGGAGCCAAAGCAGUUGAAGCUGGGGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAG
..........(((....(((....((((........)))).)))....((((....)))).(.(((((((((((.....))))..))))))).).........))).. ( -28.70, z-score =  -0.61, R)
>droYak2.chr3R 13304722 78 + 28832112
------------------------------UCUGAGGGAAGGCAAAAGCAGUUGAAGCUGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAG
------------------------------..........(((.....((((....)))).(.(((((((((((.....))))..))))))).).........))).. ( -16.90, z-score =  -0.31, R)
>droSec1.super_0 10073726 99 + 21120651
UCGGAAGGGGCAC----GGCAAGGGCGAA-----AGCCGGAGCCAGAGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAG
((....)).....----(((...(((...-----.))).(.((((((..(((((((.((....((.....))..))...)))))))..)))))).).......))).. ( -34.90, z-score =  -2.96, R)
>droSim1.chr3R 16952639 99 + 27517382
UCGGAAGGGGCAC----GGCAAGGGCGAA-----AGCCGGAGCCAGAGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAG
((....)).....----(((...(((...-----.))).(.((((((..(((((((.((....((.....))..))...)))))))..)))))).).......))).. ( -34.90, z-score =  -2.96, R)
>consensus
UC_GAAGGGGCAC____GGC_AGGGCGAA_____AGCCGGAGCCAAAGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCAG
.........................................((((..((.......))((.(.(((((((((((.....))))..))))))).).))....))))... (-12.69 = -12.50 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,894,233 – 10,894,332
Length 99
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 71.58
Shannon entropy 0.51541
G+C content 0.53318
Mean single sequence MFE -29.88
Consensus MFE -12.69
Energy contribution -12.50
Covariance contribution -0.19
Combinations/Pair 1.20
Mean z-score -1.74
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.37
SVM RNA-class probability 0.663809
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10894233 99 - 27905053
CUCUGAGGGGGCAC----GGCGAGGGCGAA-----AGCCGGAGCCAAAGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCA
.........(((.(----(((...(((...-----.)))...((....)).......)))).(.(((((((((((.....))))..))))))).).........))). ( -30.40, z-score =  -0.72, R)
>droAna3.scaffold_13340 5971309 80 - 23697760
----------------------------AGGGUGGAAGAAGAGCUUGCGCCACCGAACCAGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGCUUCUAACAUGGCCA
----------------------------..((((.(((.....))).)))).(((....((((((((((((((((.....))))..))))))))))))....)))... ( -27.30, z-score =  -2.55, R)
>droEre2.scaffold_4770 10427620 108 - 17746568
CUCUGAAGGAAGGCAAAAGGCGAAGCCGGAGAAGGAGCCGGAGCCAAAGCAGUUGAAGCUGGGGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCA
...........(((....(((....((((........)))).)))....((((....)))).(.(((((((((((.....))))..))))))).).........))). ( -28.70, z-score =  -0.17, R)
>droYak2.chr3R 13304723 78 + 28832112
------------------------------CUCUGAGGGAAGGCAAAAGCAGUUGAAGCUGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCA
------------------------------...........(((.....((((....)))).(.(((((((((((.....))))..))))))).).........))). ( -16.90, z-score =   0.03, R)
>droSec1.super_0 10073727 99 + 21120651
CUCGGAAGGGGCAC----GGCAAGGGCGAA-----AGCCGGAGCCAGAGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCA
(((....)))....----(((...(((...-----.))).(.((((((..(((((((.((....((.....))..))...)))))))..)))))).).......))). ( -38.00, z-score =  -3.52, R)
>droSim1.chr3R 16952640 99 + 27517382
CUCGGAAGGGGCAC----GGCAAGGGCGAA-----AGCCGGAGCCAGAGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCA
(((....)))....----(((...(((...-----.))).(.((((((..(((((((.((....((.....))..))...)))))))..)))))).).......))). ( -38.00, z-score =  -3.52, R)
>consensus
CUC_GAAGGGGCAC____GGC_AGGGCGAA_____AGCCGGAGCCAAAGCAGUUGAAGCCGGAGCAGAUGAUGAAGGAUAUUCGACUUAUCUGGUACGAACAUGGCCA
..........................................((((..((.......))((.(.(((((((((((.....))))..))))))).).))....)))).. (-12.69 = -12.50 +  -0.19)

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 00:16:33 2011