Locus 2827

Sequence ID dm3.chr2RHet
Location 65,906 – 66,014
Length 108
Max. P 0.950312
window3898 window3899 window3900 window3901

overview

Window 8

Location 65,906 – 66,013
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 66.86
Shannon entropy 0.59036
G+C content 0.43277
Mean single sequence MFE -26.00
Consensus MFE -12.36
Energy contribution -13.72
Covariance contribution 1.36
Combinations/Pair 1.15
Mean z-score -1.58
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.36
SVM RNA-class probability 0.930741
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 65906 107 + 3288761
GGAGUUGGCACUGACGCUAGCAGAAGCAGCGACGGUGCUGGGGGGUAUAAAUACCACCCAAUUUUGUACUUUAAAUUUAGAUUCUAAAUAUCUUCUCGUGAAAACAA
(((((((((((((.((((.((....)))))).)))))))(((.((((....)))).)))....................))))))............((....)).. ( -33.20, z-score =  -3.13, R)
>droSim1.chr3h_random 391462 94 - 1452968
GGAGUUGGCACUGAAGCUAGCAGAAGCAGCGACGGUGCU-------AUAAAUACCACCCAAUUUUGUACUUUAAAUUUAGUUCCGA------UUUUUGUCAAAAUAA
((.((((((((((..(((.((....)))))..)))))))-------)...)).)).....((((((.((...(((((.......))------)))..)))))))).. ( -22.70, z-score =  -1.73, R)
>droSec1.super_134 19166 101 - 53330
UGAGUUGGCACUGACGCUAGCAGAAGCAGCGACGGUGCUGGGGGGUAUAAAUACCACCCAAUUUUGUACUUUAAAUUUAGUUCCGA------UUUUUGUCAAAAUAA
......(((((((.((((.((....)))))).)))))))(((.((((....)))).))).((((((.((...(((((.......))------)))..)))))))).. ( -31.80, z-score =  -2.82, R)
>droEre2.scaffold_4929 760939 99 - 26641161
GGAGUUGGCACCGACGCUGGCAGAGGCAGCGACGGAGCUGGG--GCAUAAAUAUCACCCAAACUUGUAAUUCAGAUUUAUUUCCAA------UUUUUAUGCAAAUAA
((((..(((.(((.(((((.(...).))))).))).)))(((--............))).....................))))..------............... ( -24.50, z-score =  -0.72, R)
>droAna3.scaffold_13417 745187 96 - 6960332
-GACAUCG-AGGGACGCCAGCAGCAGCAGCAACCACGACCGAGAUCGCGGCAGCGAUGGAGCAACGCA---UAGGUGUAAUUAUUAA-----UUAUAAGAAACAUA-
-.(((((.-.((....)).((.((....))..(((((.(((......)))...)).)))......)).---..))))).........-----..............- ( -17.80, z-score =   0.50, R)
>consensus
GGAGUUGGCACUGACGCUAGCAGAAGCAGCGACGGUGCUGGGG_GCAUAAAUACCACCCAAUUUUGUACUUUAAAUUUAGUUCCGA______UUUUUGUCAAAAUAA
......(((((((.((((.((....)))))).))))))).................................................................... (-12.36 = -13.72 +   1.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 65,906 – 66,013
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 66.86
Shannon entropy 0.59036
G+C content 0.43277
Mean single sequence MFE -24.44
Consensus MFE -9.78
Energy contribution -10.38
Covariance contribution 0.60
Combinations/Pair 1.27
Mean z-score -1.65
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.69
SVM RNA-class probability 0.787897
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 65906 107 - 3288761
UUGUUUUCACGAGAAGAUAUUUAGAAUCUAAAUUUAAAGUACAAAAUUGGGUGGUAUUUAUACCCCCCAGCACCGUCGCUGCUUCUGCUAGCGUCAGUGCCAACUCC
.(((((((....)))))))..................(((.......((((.((((....)))).))))((((.(.((((((....)).)))).).))))..))).. ( -29.10, z-score =  -3.07, R)
>droSim1.chr3h_random 391462 94 + 1452968
UUAUUUUGACAAAAA------UCGGAACUAAAUUUAAAGUACAAAAUUGGGUGGUAUUUAU-------AGCACCGUCGCUGCUUCUGCUAGCUUCAGUGCCAACUCC
...((((((......------))))))...........((((.......((((.((....)-------).))))(..(((((....)).)))..).))))....... ( -17.00, z-score =  -0.03, R)
>droSec1.super_134 19166 101 + 53330
UUAUUUUGACAAAAA------UCGGAACUAAAUUUAAAGUACAAAAUUGGGUGGUAUUUAUACCCCCCAGCACCGUCGCUGCUUCUGCUAGCGUCAGUGCCAACUCA
...((((((......------))))))..........(((.......((((.((((....)))).))))((((.(.((((((....)).)))).).))))..))).. ( -26.80, z-score =  -2.61, R)
>droEre2.scaffold_4929 760939 99 + 26641161
UUAUUUGCAUAAAAA------UUGGAAAUAAAUCUGAAUUACAAGUUUGGGUGAUAUUUAUGC--CCCAGCUCCGUCGCUGCCUCUGCCAGCGUCGGUGCCAACUCC
......(((((((..------(..((......))..)(((((........))))).)))))))--....((.(((.(((((.......))))).))).))....... ( -25.70, z-score =  -1.69, R)
>droAna3.scaffold_13417 745187 96 + 6960332
-UAUGUUUCUUAUAA-----UUAAUAAUUACACCUA---UGCGUUGCUCCAUCGCUGCCGCGAUCUCGGUCGUGGUUGCUGCUGCUGCUGGCGUCCCU-CGAUGUC-
-..............-----................---...((.((..((..((.((((((((....)))))))).))))..)).)).((((((...-.))))))- ( -23.60, z-score =  -0.83, R)
>consensus
UUAUUUUCACAAAAA______UAGGAACUAAAUUUAAAGUACAAAAUUGGGUGGUAUUUAUAC_CCCCAGCACCGUCGCUGCUUCUGCUAGCGUCAGUGCCAACUCC
.....................................................................((((.(.((((((....)).)))).).))))....... ( -9.78 = -10.38 +   0.60)

alignment

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secondary structure

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dotplot

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Window 0

Location 65,908 – 66,014
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 66.44
Shannon entropy 0.59662
G+C content 0.42091
Mean single sequence MFE -25.27
Consensus MFE -12.30
Energy contribution -13.38
Covariance contribution 1.08
Combinations/Pair 1.23
Mean z-score -1.61
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.56
SVM RNA-class probability 0.950312
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 65908 106 + 3288761
AGUUGGCACUGACGCUAGCAGAAGCAGCGACGGUGCUGGGGGGUAUAAAUACCACCCAAUUUUGUACUUUAAAUUUAGAUUCUAAAUAUCUUCUCGUGAAAACAAA
....(((((((.((((.((....)))))).)))))))(((.((((....)))).)))...(((((..((((.....((((.......)))).....)))).))))) ( -31.50, z-score =  -2.92, R)
>droSim1.chr3h_random 391464 93 - 1452968
AGUUGGCACUGAAGCUAGCAGAAGCAGCGACGGUGCU-------AUAAAUACCACCCAAUUUUGUACUUUAAAUUUAGUUCCGA------UUUUUGUCAAAAUAAA
...((((((((..(((.((....)))))..)))))))-------).............((((((.((...(((((.......))------)))..))))))))... ( -21.90, z-score =  -1.97, R)
>droSec1.super_134 19168 100 - 53330
AGUUGGCACUGACGCUAGCAGAAGCAGCGACGGUGCUGGGGGGUAUAAAUACCACCCAAUUUUGUACUUUAAAUUUAGUUCCGA------UUUUUGUCAAAAUAAA
....(((((((.((((.((....)))))).)))))))(((.((((....)))).))).((((((.((...(((((.......))------)))..))))))))... ( -31.80, z-score =  -3.00, R)
>droEre2.scaffold_4929 760941 98 - 26641161
AGUUGGCACCGACGCUGGCAGAGGCAGCGACGGAGCUGGG--GCAUAAAUAUCACCCAAACUUGUAAUUCAGAUUUAUUUCCAA------UUUUUAUGCAAAUAAA
..(..((.(((.(((((.(...).))))).))).))..).--(((((((........(((.(((.....))).)))........------..)))))))....... ( -23.57, z-score =  -0.74, R)
>droAna3.scaffold_13417 745189 95 - 6960332
CAUCGAGG--GACGCCAGCAGCAGCAGCAACCACGACCGAGAUCGCGGCAGCGAUGGAGCAACGCA---UAGGUGUAAUUAUUAA-----UUAUAAGAAACAUAA-
.....((.--.(((((.((....)).((..(((((.(((......)))...)).))).))......---..)))))..)).....-----...............- ( -17.60, z-score =   0.56, R)
>consensus
AGUUGGCACUGACGCUAGCAGAAGCAGCGACGGUGCUGGGG_GCAUAAAUACCACCCAAUUUUGUACUUUAAAUUUAGUUCCGA______UUUUUGUCAAAAUAAA
....(((((((.((((.((....)))))).)))))))..................................................................... (-12.30 = -13.38 +   1.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 65,908 – 66,014
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 66.44
Shannon entropy 0.59662
G+C content 0.42091
Mean single sequence MFE -24.22
Consensus MFE -9.90
Energy contribution -10.38
Covariance contribution 0.48
Combinations/Pair 1.27
Mean z-score -1.62
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.80
SVM RNA-class probability 0.820003
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 65908 106 - 3288761
UUUGUUUUCACGAGAAGAUAUUUAGAAUCUAAAUUUAAAGUACAAAAUUGGGUGGUAUUUAUACCCCCCAGCACCGUCGCUGCUUCUGCUAGCGUCAGUGCCAACU
..(((((((....)))))))............................((((.((((....)))).))))((((.(.((((((....)).)))).).))))..... ( -29.00, z-score =  -2.99, R)
>droSim1.chr3h_random 391464 93 + 1452968
UUUAUUUUGACAAAAA------UCGGAACUAAAUUUAAAGUACAAAAUUGGGUGGUAUUUAU-------AGCACCGUCGCUGCUUCUGCUAGCUUCAGUGCCAACU
((((((((((......------)))))).))))......((((.......((((.((....)-------).))))(..(((((....)).)))..).))))..... ( -17.20, z-score =  -0.14, R)
>droSec1.super_134 19168 100 + 53330
UUUAUUUUGACAAAAA------UCGGAACUAAAUUUAAAGUACAAAAUUGGGUGGUAUUUAUACCCCCCAGCACCGUCGCUGCUUCUGCUAGCGUCAGUGCCAACU
((((((((((......------)))))).))))...............((((.((((....)))).))))((((.(.((((((....)).)))).).))))..... ( -26.90, z-score =  -2.69, R)
>droEre2.scaffold_4929 760941 98 + 26641161
UUUAUUUGCAUAAAAA------UUGGAAAUAAAUCUGAAUUACAAGUUUGGGUGAUAUUUAUGC--CCCAGCUCCGUCGCUGCCUCUGCCAGCGUCGGUGCCAACU
.......(((((((..------(..((......))..)(((((........))))).)))))))--....((.(((.(((((.......))))).))).))..... ( -25.70, z-score =  -1.67, R)
>droAna3.scaffold_13417 745189 95 + 6960332
-UUAUGUUUCUUAUAA-----UUAAUAAUUACACCUA---UGCGUUGCUCCAUCGCUGCCGCGAUCUCGGUCGUGGUUGCUGCUGCUGCUGGCGUC--CCUCGAUG
-...............-----................---.(((((((..((.(((.((((((((....)))))))).)).).))..)).))))).--........ ( -22.30, z-score =  -0.60, R)
>consensus
UUUAUUUUCACAAAAA______UAGGAACUAAAUUUAAAGUACAAAAUUGGGUGGUAUUUAUAC_CCCCAGCACCGUCGCUGCUUCUGCUAGCGUCAGUGCCAACU
......................................................................((((.(.((((((....)).)))).).))))..... ( -9.90 = -10.38 +   0.48)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:58:49 2011