Locus 11211

Sequence ID dm3.chr3R
Location 19,444,312 – 19,444,455
Length 143
Max. P 0.830606
window15407 window15408

overview

Window 7

Location 19,444,312 – 19,444,402
Length 90
Sequences 7
Columns 106
Reading direction forward
Mean pairwise identity 72.89
Shannon entropy 0.52810
G+C content 0.53135
Mean single sequence MFE -15.26
Consensus MFE -7.69
Energy contribution -8.16
Covariance contribution 0.47
Combinations/Pair 1.08
Mean z-score -1.18
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.555538
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19444312 90 + 27905053
CUUCAACCGCCAAACCCCCACC----CCCCC----AACC------AUUCCAGUGGUCUAAGCCC-GCGAAAAACUUUGUUAUGUAAA-GCGUUGACAGCUCAACGA
.......(((.......((((.----.....----....------......)))).........-))).....(((((.....))))-)((((((....)))))). ( -11.28, z-score =  -0.07, R)
>droPer1.super_7 3032089 87 - 4445127
-----------CCCCCCUACCCCUCACCGUCACCCUUUUGCC--------ACUUGUCUAAAAUCCGCGCAAAAGUUUGUUAUGCAAAAGCGUUGACAACUCAACGA
-----------................(((....((((((((--------...............).))))))).(((((((((....))).))))))....))). ( -12.56, z-score =  -1.66, R)
>droAna3.scaffold_13340 3608050 103 - 23697760
AGUCAGCCCCCCCCCCCAAUCUGCCACCCCCUUUUCGCUGCCC--ACGCCAGUGGUCUAAGCCAAGCGCAAAACUUUGUUAUGCAAA-GCGUUGACAACUCAACGA
.((((((........................((((((((((((--((....)))).....))..)))).))))(((((.....))))-).)))))).......... ( -21.30, z-score =  -1.60, R)
>droEre2.scaffold_4820 1868173 88 - 10470090
CUUCAGCCACCACACCCCCACC----CUCCC------CU------AGUCCGCUGGUCUAAGCCC-GCGAAAAACUUUGUUAUGCAAA-GCGUUGACAGCUCAACGA
......................----.....------..------....(((.(((....))).-))).....(((((.....))))-)((((((....)))))). ( -16.60, z-score =  -1.19, R)
>droYak2.chr3R 20338047 103 + 28832112
CUUCAACCACCAAGGCCCCCUU-CAACCCCCCAUCAUUCCCCCCAAUUCCAGUGGUCUAAGCCC-GCGAAAAACUUUGUUAUGCAAA-GCGUUGACAGCUCAACGA
.(((.......((((...))))-............................((((.......))-)))))...(((((.....))))-)((((((....)))))). ( -15.20, z-score =  -0.58, R)
>droSec1.super_0 19801815 93 + 21120651
CUUCAACCACCAAACCCUCCCC-CCACCCCC----AUCC------AUUCCAGUGGUCUAAGCCC-GCGAAAAACUUUGUUAUGCAAA-GCGUUGACAGCUCAACGA
(((..(((((............-........----....------......)))))..)))...-........(((((.....))))-)((((((....)))))). ( -13.91, z-score =  -1.49, R)
>droSim1.chr3R 19273762 94 + 27517382
CUUCAACCACCAAACCCCUCCCGCCACCCCC----AUCC------AUUCCAGUGGUCUAAGCCC-GCGAAAAACUUUGUUAUGCAAA-GCGUUGACAGCUCAACGA
.....................(((.......----..((------((....)))).........-))).....(((((.....))))-)((((((....)))))). ( -15.97, z-score =  -1.70, R)
>consensus
CUUCAACCACCAAACCCCCCCC_CCACCCCC____AUCC______AUUCCAGUGGUCUAAGCCC_GCGAAAAACUUUGUUAUGCAAA_GCGUUGACAGCUCAACGA
............................................................((...(((((....)))))...)).....((((((....)))))). ( -7.69 =  -8.16 +   0.47)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,444,364 – 19,444,455
Length 91
Sequences 5
Columns 91
Reading direction reverse
Mean pairwise identity 91.21
Shannon entropy 0.15867
G+C content 0.45640
Mean single sequence MFE -28.38
Consensus MFE -21.86
Energy contribution -22.70
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -2.25
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.830606
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19444364 91 - 27905053
UCGUGCAUUUCGCAGCGUUUCUGUUUUUGCGCUGCGGUACGUUGUUGUCAUCGUCGUUGAGCUGUCAACGCUUUACAUAACAAAGUUUUUC
.(((((....((((((((..........)))))))))))))(((((((......((((((....))))))......)))))))........ ( -28.00, z-score =  -2.36, R)
>droAna3.scaffold_13340 3608115 83 + 23697760
------UUUUUGCAACGUUGCUGCUCUUG--CUGCGGUACGCUGUUGUCAACGUCGUUGAGUUGUCAACGCUUUGCAUAACAAAGUUUUGC
------.....(((((((.(((((.....--..))))))))..((((.((((........)))).))))((((((.....)))))).)))) ( -23.10, z-score =  -0.34, R)
>droEre2.scaffold_4820 1868223 91 + 10470090
UCGUGCAUUUCGCAGCGUUUCUGUUUUUGCGCUGCGGUACGUUGUUGUCAUCGUCGUUGAGCUGUCAACGCUUUGCAUAACAAAGUUUUUC
.(((((....((((((((..........)))))))))))))(((((((((..(.((((((....)))))))..)).)))))))........ ( -30.70, z-score =  -2.92, R)
>droSec1.super_0 19801870 91 - 21120651
UCGUGCAUUUCGCAGCGUUUCUGUUUUUGCGCUGCGGUACGUUGUUGUCAUCAUCGUUGAGCUGUCAACGCUUUGCAUAACAAAGUUUUUC
.(((((....((((((((..........)))))))))))))(((((((((....((((((....))))))...)).)))))))........ ( -29.40, z-score =  -2.69, R)
>droSim1.chr3R 19273818 91 - 27517382
UCGUGCAUUUCGCAGCGUUUCUGUUUUUGCGCUGCGGUACGUUGUUGUCAUCGUCGUUGAGCUGUCAACGCUUUGCAUAACAAAGUUUUUC
.(((((....((((((((..........)))))))))))))(((((((((..(.((((((....)))))))..)).)))))))........ ( -30.70, z-score =  -2.92, R)
>consensus
UCGUGCAUUUCGCAGCGUUUCUGUUUUUGCGCUGCGGUACGUUGUUGUCAUCGUCGUUGAGCUGUCAACGCUUUGCAUAACAAAGUUUUUC
.........(((((((((..........))))))))).((.(((((((((....((((((....))))))...)).))))))).))..... (-21.86 = -22.70 +   0.84)

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 00:38:33 2011