Locus 1580

Sequence ID dm3.chr2L
Location 12,263,069 – 12,263,172
Length 103
Max. P 0.999769
window2160 window2161

overview

Window 0

Location 12,263,069 – 12,263,172
Length 103
Sequences 8
Columns 115
Reading direction forward
Mean pairwise identity 68.36
Shannon entropy 0.62892
G+C content 0.42115
Mean single sequence MFE -19.16
Consensus MFE -11.50
Energy contribution -11.70
Covariance contribution 0.20
Combinations/Pair 1.17
Mean z-score -1.17
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.82
SVM RNA-class probability 0.969505
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12263069 103 + 23011544
-----UGCGAGGA---AAA----GCGUUUCAAAUGCCAGGAUACAAAAUAAAAAAAAAAUGCCGCCAAGUCACGUAAAUAAUUAAACACGUGACAUGCGUCAAGUAGAGCCUGGC
-----.((.....---...----)).........((((((.(((....(......)...((.(((...(((((((............)))))))..))).)).)))...)))))) ( -24.10, z-score =  -2.16, R)
>droSim1.chr2L 12064435 100 + 22036055
-----UGCGAGGA---AAAAAAAGCGUUUCAAAUGCCAGGAUACAAAA-------AAAAUGCCGCCAAGUCACGUAAAUAAUUAAACACGUGACAUGCGUCAAGUAGAGCCUAGC
-----.((.(((.---.......((((.....))))............-------....((.(((...(((((((............)))))))..))).)).......))).)) ( -19.20, z-score =  -0.91, R)
>droSec1.super_16 453261 96 + 1878335
-----UGCGAGGA---AAA----UCGUUUCAAAUGCCCGGAUACAAAA-------AAAAUGCCGCCAAGUCACGUAAAUAAUUAAACACGUGACAUGCGUCAAGUAGAGCCUAGC
-----.((.(((.---...----((((.((.........)).))....-------....((.(((...(((((((............)))))))..))).))....)).))).)) ( -18.60, z-score =  -0.69, R)
>droYak2.chr2L 8692578 107 + 22324452
UUCCAAGCAAGAAUCCAAGAAAAGCGUCGCAAAGGCCAGGAUACAAAA-------AAA-UGCCGCCAAGUCACGUAAAUAAUUAAACACGUGACAUGCGUCAAGUAGAGCCUAGC
......((.((..((...(.....)(.((((..(((..((((......-------..)-).)))))..(((((((............))))))).)))).).....))..)).)) ( -19.70, z-score =  -1.24, R)
>droEre2.scaffold_4929 13486541 106 - 26641161
--CCAAGCAAAAAUCCGAGAAAAGCGUUUCAAAUGCCACGACACAAAA-------AAAAUGCCGCCAAGUCACGUAAAUAAUUAAACACGUGACAUGCGUCAAGUAGAGCCUUGC
--....((((...((........((((.....))))............-------....((.(((...(((((((............)))))))..))).))....))...)))) ( -17.90, z-score =  -0.80, R)
>droAna3.scaffold_12916 3052214 99 - 16180835
--CUUGAAGAAAAAGCCAGGAAGCCAUUCAAAAUAGACAAAUAAGAAA--------AUAUGUCGCCAAGUCACGUAAAUAAUUAAACACGUGACAUGCGUCAAGCAAAG------
--(((((.(((...((......))..)))......((((.((......--------)).))))((...(((((((............)))))))..)).))))).....------ ( -17.90, z-score =  -2.70, R)
>droWil1.scaffold_180708 2611221 102 - 12563649
------CAGAGAAAAAGAAACAAACGUGGGGCCACACACAACACACAA-------AAAAUUUAGCCAAGUCACGUAAAUAAUUAAACACGUGACAUGCGUCGAGGCGUUAUUUUC
------..........((((..((((((....))).............-------....((..((((.(((((((............))))))).)).))..))..)))..)))) ( -17.20, z-score =  -0.62, R)
>droVir3.scaffold_12963 2868054 99 - 20206255
----UGCGGGAGAGCGGGAGAGUGAGUAAAGAGGAGAGCGAGAAAAAA-------GUAACGCAGCCAAGUCACGUAAAUAAUUAAACACGUGACAUGCGUGGGGCGUCAU-----
----.((......)).................................-------...((((.((((.(((((((............))))))).)).))...))))...----- ( -18.70, z-score =  -0.21, R)
>consensus
_____UGCGAGAA___AAAAAAAGCGUUUCAAAUGCCAGGAUACAAAA_______AAAAUGCCGCCAAGUCACGUAAAUAAUUAAACACGUGACAUGCGUCAAGUAGAGCCUAGC
...........................................................((.(((...(((((((............)))))))..))).))............. (-11.50 = -11.70 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,263,069 – 12,263,172
Length 103
Sequences 8
Columns 115
Reading direction reverse
Mean pairwise identity 68.36
Shannon entropy 0.62892
G+C content 0.42115
Mean single sequence MFE -26.05
Consensus MFE -14.75
Energy contribution -15.00
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.93
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.35
SVM RNA-class probability 0.999769
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 12263069 103 - 23011544
GCCAGGCUCUACUUGACGCAUGUCACGUGUUUAAUUAUUUACGUGACUUGGCGGCAUUUUUUUUUUAUUUUGUAUCCUGGCAUUUGAAACGC----UUU---UCCUCGCA-----
((((((..........(((..((((((((..........))))))))...)))(((..............)))..)))))).........((----...---.....)).----- ( -28.64, z-score =  -3.55, R)
>droSim1.chr2L 12064435 100 - 22036055
GCUAGGCUCUACUUGACGCAUGUCACGUGUUUAAUUAUUUACGUGACUUGGCGGCAUUUU-------UUUUGUAUCCUGGCAUUUGAAACGCUUUUUUU---UCCUCGCA-----
((((((..........(((..((((((((..........))))))))...)))(((....-------...)))..)))))).........((.......---.....)).----- ( -26.20, z-score =  -2.86, R)
>droSec1.super_16 453261 96 - 1878335
GCUAGGCUCUACUUGACGCAUGUCACGUGUUUAAUUAUUUACGUGACUUGGCGGCAUUUU-------UUUUGUAUCCGGGCAUUUGAAACGA----UUU---UCCUCGCA-----
((.((((((.......(((..((((((((..........))))))))...)))(((....-------...)))....))))....((((...----.))---)))).)).----- ( -24.90, z-score =  -1.90, R)
>droYak2.chr2L 8692578 107 - 22324452
GCUAGGCUCUACUUGACGCAUGUCACGUGUUUAAUUAUUUACGUGACUUGGCGGCA-UUU-------UUUUGUAUCCUGGCCUUUGCGACGCUUUUCUUGGAUUCUUGCUUGGAA
((((((..........(((..((((((((..........))))))))...)))(((-...-------...)))..))))))((..((((..((......))....))))..)).. ( -29.90, z-score =  -2.74, R)
>droEre2.scaffold_4929 13486541 106 + 26641161
GCAAGGCUCUACUUGACGCAUGUCACGUGUUUAAUUAUUUACGUGACUUGGCGGCAUUUU-------UUUUGUGUCGUGGCAUUUGAAACGCUUUUCUCGGAUUUUUGCUUGG--
((((((.(((......(((..((((((((..........))))))))...)))((.((((-------....((((....))))..)))).)).......))).))))))....-- ( -29.30, z-score =  -2.27, R)
>droAna3.scaffold_12916 3052214 99 + 16180835
------CUUUGCUUGACGCAUGUCACGUGUUUAAUUAUUUACGUGACUUGGCGACAUAU--------UUUCUUAUUUGUCUAUUUUGAAUGGCUUCCUGGCUUUUUCUUCAAG--
------.....(((((.((..((((((((..........))))))))...))((((.((--------......)).))))......(((.((((....))))..))).)))))-- ( -24.70, z-score =  -4.12, R)
>droWil1.scaffold_180708 2611221 102 + 12563649
GAAAAUAACGCCUCGACGCAUGUCACGUGUUUAAUUAUUUACGUGACUUGGCUAAAUUUU-------UUGUGUGUUGUGUGUGGCCCCACGUUUGUUUCUUUUUCUCUG------
(((((.(((((..((((((((((((((((..........)))))))).............-------..)))))))).))(((....)))....)))...)))))....------ ( -24.46, z-score =  -2.36, R)
>droVir3.scaffold_12963 2868054 99 + 20206255
-----AUGACGCCCCACGCAUGUCACGUGUUUAAUUAUUUACGUGACUUGGCUGCGUUAC-------UUUUUUCUCGCUCUCCUCUUUACUCACUCUCCCGCUCUCCCGCA----
-----.((((((.(((.....((((((((..........)))))))).)))..)))))).-------.................................((......)).---- ( -20.30, z-score =  -3.60, R)
>consensus
GCUAGGCUCUACUUGACGCAUGUCACGUGUUUAAUUAUUUACGUGACUUGGCGGCAUUUU_______UUUUGUAUCCUGGCAUUUGAAACGCUUUUUUU___UCCUCGCA_____
................(((..((((((((..........))))))))...))).............................................................. (-14.75 = -15.00 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:34:41 2011