Locus 10424

Sequence ID dm3.chr3R
Location 13,715,792 – 13,715,901
Length 109
Max. P 0.999666
window14336 window14337

overview

Window 6

Location 13,715,792 – 13,715,901
Length 109
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 67.65
Shannon entropy 0.61423
G+C content 0.37542
Mean single sequence MFE -27.35
Consensus MFE -13.08
Energy contribution -14.77
Covariance contribution 1.69
Combinations/Pair 1.38
Mean z-score -2.44
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.09
SVM RNA-class probability 0.997393
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13715792 109 + 27905053
GGCUGAUUCUGGCCUUCACUUUCA-UCCAUUUACCUUAAAUCUUACGAUCUUAAGAUACAAAGCUAUUAGGAAAUUUACGAGAGAGACCUAAGAAAGUGAAGACUAGAUC
.......(((((.((((((((((.-..............((((((......)))))).........(((((...(((.(....))))))))))))))))))).))))).. ( -27.50, z-score =  -2.71, R)
>droAna3.scaffold_13340 11700657 99 - 23697760
AGCUGGAUCCGUCUUUCAGUUCAGGACUAUGUGAGUUUAAU------AU-UAAAACUUUUAAUAUAUUCA-AAGUUUCG---UAAAAUCUGUAAAACUGAAAGUCGGAUC
.....((((((.(((((((((((((..((((.((.(((.((------((-(((.....)))))))....)-)).)).))---))...))))...))))))))).)))))) ( -27.30, z-score =  -4.41, R)
>droEre2.scaffold_4770 9837075 105 - 17746568
GGUCGGUUCUGGCCUUCACUUUCA-UCAAUUCAGCUUAAAUCGUACGAU----AGCUACAAAGCUAUUCGGAUACUUCAGAUUGAGACCUGAGAAAGUGAAGACUAGAGC
.....(((((((.((((((((((.-(((......(((((.((...((((----((((....))))).)))((....)).)))))))...))))))))))))).))))))) ( -35.20, z-score =  -3.66, R)
>droYak2.chr3R_random 1876194 102 + 3277457
GGUCGGUUCUGGCCUUCACUUUCA-ACAAUUUUCCUUA-------CGAUCCUUAAUUUCAAUGCUACAAGGAAAUUCAAGAUUGAGUCCUAUAAAAGUGAAGACUAGAGC
.....(((((((.(((((((((..-......((((((.-------......................))))))(((((....)))))......))))))))).))))))) ( -23.30, z-score =  -1.45, R)
>droSec1.super_12 1684430 109 - 2123299
GGUUGAUUCUGGCCUUCACUUUCA-UCCAUUUACCUUAAAUCUUACGAUCUUAAGAAACAAAGCUAUUAGGAAGUUUUAGAUUGUGAGCUGGGAAAGUCCCCCCCAAAUU
((....(((..((..((((..((.-.........((((((((....))).)))))....((((((.......)))))).))..))))))..)))....)).......... ( -20.30, z-score =   0.35, R)
>droSim1.chr3R 19746765 109 - 27517382
GGUUGAUUCUGGCCUUCACUUUCA-UCCAUUUACCUUAAAUCUCACGAUCUUAAGUUACAAAGCUAUUAGGAAGUUAUAGAUUGUGAGCUGGGAAAGUGAAGACCAAAUC
....((((.(((.((((((((((.-.(((............(((((((((((((.((.(.((....)).).)).))).)))))))))).))))))))))))).))))))) ( -30.52, z-score =  -2.74, R)
>consensus
GGUUGAUUCUGGCCUUCACUUUCA_UCCAUUUACCUUAAAUCUUACGAUCUUAAGAUACAAAGCUAUUAGGAAAUUUAAGAUUGAGACCUGAGAAAGUGAAGACCAGAUC
.......(((((.((((((((((.........................((((((............)))))).....(((........))).)))))))))).))))).. (-13.08 = -14.77 +   1.69)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,715,792 – 13,715,901
Length 109
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 67.65
Shannon entropy 0.61423
G+C content 0.37542
Mean single sequence MFE -30.53
Consensus MFE -13.48
Energy contribution -14.45
Covariance contribution 0.97
Combinations/Pair 1.48
Mean z-score -3.40
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.16
SVM RNA-class probability 0.999666
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13715792 109 - 27905053
GAUCUAGUCUUCACUUUCUUAGGUCUCUCUCGUAAAUUUCCUAAUAGCUUUGUAUCUUAAGAUCGUAAGAUUUAAGGUAAAUGGA-UGAAAGUGAAGGCCAGAAUCAGCC
(((((.(((((((((((((((((................)))))...((...(((((((.((((....)))))))))))...)).-.)))))))))))).)).))).... ( -34.19, z-score =  -4.16, R)
>droAna3.scaffold_13340 11700657 99 + 23697760
GAUCCGACUUUCAGUUUUACAGAUUUUA---CGAAACUU-UGAAUAUAUUAAAAGUUUUA-AU------AUUAAACUCACAUAGUCCUGAACUGAAAGACGGAUCCAGCU
((((((.(((((((((...(((......---.(((((((-(..........)))))))).-..------.....(((.....))).)))))))))))).))))))..... ( -25.70, z-score =  -4.89, R)
>droEre2.scaffold_4770 9837075 105 + 17746568
GCUCUAGUCUUCACUUUCUCAGGUCUCAAUCUGAAGUAUCCGAAUAGCUUUGUAGCU----AUCGUACGAUUUAAGCUGAAUUGA-UGAAAGUGAAGGCCAGAACCGACC
..(((.((((((((((((((((((....))))))......(((.(((((....))))----))))..((((((.....)))))).-.)))))))))))).)))....... ( -34.10, z-score =  -3.61, R)
>droYak2.chr3R_random 1876194 102 - 3277457
GCUCUAGUCUUCACUUUUAUAGGACUCAAUCUUGAAUUUCCUUGUAGCAUUGAAAUUAAGGAUCG-------UAAGGAAAAUUGU-UGAAAGUGAAGGCCAGAACCGACC
..(((.((((((((((((((((((.....)))))..((((((((..(..((.......))..)..-------)))))))).....-))))))))))))).)))....... ( -27.60, z-score =  -2.34, R)
>droSec1.super_12 1684430 109 + 2123299
AAUUUGGGGGGGACUUUCCCAGCUCACAAUCUAAAACUUCCUAAUAGCUUUGUUUCUUAAGAUCGUAAGAUUUAAGGUAAAUGGA-UGAAAGUGAAGGCCAGAAUCAACC
..(((((..(((.....)))...((((..((.......(((.....((((((..(((((......)))))..))))))....)))-.))..))))...)))))....... ( -23.40, z-score =   0.24, R)
>droSim1.chr3R 19746765 109 + 27517382
GAUUUGGUCUUCACUUUCCCAGCUCACAAUCUAUAACUUCCUAAUAGCUUUGUAACUUAAGAUCGUGAGAUUUAAGGUAAAUGGA-UGAAAGUGAAGGCCAGAAUCAACC
(((((((((((((((((((((....((((.((((.........))))..)))).((((.(((((....))))).))))...))).-.))))))))))))))).))).... ( -38.20, z-score =  -5.61, R)
>consensus
GAUCUAGUCUUCACUUUCACAGGUCUCAAUCUAAAACUUCCUAAUAGCUUUGUAACUUAAGAUCGUAAGAUUUAAGGUAAAUGGA_UGAAAGUGAAGGCCAGAACCAACC
..(((.((((((((((((...(....)...........................((((((.(((....)))))))))..........)))))))))))).)))....... (-13.48 = -14.45 +   0.97)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:23:42 2011