Locus 6953

Sequence ID dm3.chr3L
Location 11,084,743 – 11,084,806
Length 63
Max. P 0.993104
window9573 window9574

overview

Window 3

Location 11,084,743 – 11,084,806
Length 63
Sequences 7
Columns 68
Reading direction forward
Mean pairwise identity 64.23
Shannon entropy 0.69323
G+C content 0.41575
Mean single sequence MFE -9.67
Consensus MFE -4.50
Energy contribution -4.44
Covariance contribution -0.06
Combinations/Pair 1.33
Mean z-score -1.12
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.23
SVM RNA-class probability 0.913468
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11084743 63 + 24543557
AGAUUCUUCCGUAAAAGAUCCUAUGCCUUUAAUA----AUGCUCUACGUGCUCC-UCACGUAAUCGAU
((..((((......))))..))............----......((((((....-.))))))...... (  -7.30, z-score =  -0.79, R)
>droSim1.chr3L 10480335 58 + 22553184
AGAUUCUUCCGUCAAAGAU-----GCCGUUAAUA----AUGCUCUACGUGCUCC-UCACGUAAUCAAU
.((((..........(((.-----((........----..)))))(((((....-.)))))))))... (  -6.70, z-score =  -0.50, R)
>droSec1.super_0 3310384 58 + 21120651
AGAUUCUUCCGUCAAAGAU-----GCCGUUAAUA----AUGCUCUACGUGCUCC-UCACGUAAUCAAU
.((((..........(((.-----((........----..)))))(((((....-.)))))))))... (  -6.70, z-score =  -0.50, R)
>droYak2.chr3L 11115395 63 + 24197627
AAAUUAUUCCUUCAAAGAUCCCAAGUCUUUUAUA----AUGUCCUACGUUCUCC-UCACGUAGUUAAU
.............((((((.....))))))....----.....((((((.....-..))))))..... (  -7.50, z-score =  -3.56, R)
>droEre2.scaffold_4784 11093511 63 + 25762168
AAAUUCUUCCGUCAAAGAUCCCAAGUCUUUUAUA----AUGAUCUACGUGCUCC-UUACGCAGUUAAU
..........((.((((((.....)))))).)).----.(((.((.((((....-.)))).))))).. (  -5.00, z-score =  -0.30, R)
>droAna3.scaffold_13337 8803695 67 - 23293914
AUUUACUCUUGAAACGGACUCUUUCCGGCUGAUGGGUGAUGUUCUACGUACUUC-UUACGUAGUUGGG
..((((((.(.(..((((.....))))..).).))))))....(((((((....-.)))))))..... ( -17.20, z-score =  -1.82, R)
>droPer1.super_9 2021025 63 + 3637205
--GGACUGCGAUCAGGGAGGG-AUACUGGCGGUGG--UUUUCUCUACGUAUUCCCUUACGUAGGCAAC
--...(((((......(((((-(((((((.((...--...)).))).))).)))))).)))))..... ( -17.30, z-score =  -0.37, R)
>consensus
AGAUUCUUCCGUCAAAGAUCC_AUGCCGUUAAUA____AUGCUCUACGUGCUCC_UCACGUAGUCAAU
............................................((((((......))))))...... ( -4.50 =  -4.44 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,084,743 – 11,084,806
Length 63
Sequences 7
Columns 68
Reading direction reverse
Mean pairwise identity 64.23
Shannon entropy 0.69323
G+C content 0.41575
Mean single sequence MFE -10.99
Consensus MFE -7.57
Energy contribution -7.24
Covariance contribution -0.32
Combinations/Pair 1.43
Mean z-score -1.13
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.59
SVM RNA-class probability 0.993104
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11084743 63 - 24543557
AUCGAUUACGUGA-GGAGCACGUAGAGCAU----UAUUAAAGGCAUAGGAUCUUUUACGGAAGAAUCU
.....(((((((.-....))))))).((..----........))...((((((((....)))).)))) ( -10.60, z-score =  -0.61, R)
>droSim1.chr3L 10480335 58 - 22553184
AUUGAUUACGUGA-GGAGCACGUAGAGCAU----UAUUAACGGC-----AUCUUUGACGGAAGAAUCU
...((((.(((((-(((((.(((.((....----..)).)))))-----.))))).)))....)))). ( -13.10, z-score =  -1.83, R)
>droSec1.super_0 3310384 58 - 21120651
AUUGAUUACGUGA-GGAGCACGUAGAGCAU----UAUUAACGGC-----AUCUUUGACGGAAGAAUCU
...((((.(((((-(((((.(((.((....----..)).)))))-----.))))).)))....)))). ( -13.10, z-score =  -1.83, R)
>droYak2.chr3L 11115395 63 - 24197627
AUUAACUACGUGA-GGAGAACGUAGGACAU----UAUAAAAGACUUGGGAUCUUUGAAGGAAUAAUUU
.....((((((..-.....)))))).....----....((((((....).)))))............. (  -8.90, z-score =  -0.95, R)
>droEre2.scaffold_4784 11093511 63 - 25762168
AUUAACUGCGUAA-GGAGCACGUAGAUCAU----UAUAAAAGACUUGGGAUCUUUGACGGAAGAAUUU
.....((((((..-.....)))))).....----....((((((....).)))))..(....)..... (  -8.80, z-score =  -0.17, R)
>droAna3.scaffold_13337 8803695 67 + 23293914
CCCAACUACGUAA-GAAGUACGUAGAACAUCACCCAUCAGCCGGAAAGAGUCCGUUUCAAGAGUAAAU
.....(((((((.-....)))))))................((((.....)))).............. ( -11.50, z-score =  -2.35, R)
>droPer1.super_9 2021025 63 - 3637205
GUUGCCUACGUAAGGGAAUACGUAGAGAAAA--CCACCGCCAGUAU-CCCUCCCUGAUCGCAGUCC--
.(((((((((((......)))))))......--.......(((...-......)))...))))...-- ( -10.90, z-score =  -0.17, R)
>consensus
AUUGACUACGUGA_GGAGCACGUAGAGCAU____UAUUAACGGCAU_GGAUCUUUGACGGAAGAAUCU
.....(((((((......)))))))........................................... ( -7.57 =  -7.24 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:17:41 2011