Locus 1894

Sequence ID dm3.chr2L
Location 14,586,745 – 14,586,796
Length 51
Max. P 0.731252
window2611 window2612

overview

Window 1

Location 14,586,745 – 14,586,796
Length 51
Sequences 9
Columns 56
Reading direction forward
Mean pairwise identity 86.56
Shannon entropy 0.26635
G+C content 0.50576
Mean single sequence MFE -13.06
Consensus MFE -9.79
Energy contribution -9.69
Covariance contribution -0.10
Combinations/Pair 1.15
Mean z-score -1.58
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.26
SVM RNA-class probability 0.615195
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14586745 51 + 23011544
GUCCUCGUUUGCUGAGACUAAUUUGUGGCUCUCU-----UCUGAGACGCCCACUAU
(((.(((.....)))))).....((.(((((((.-----...)))).))))).... ( -12.70, z-score =  -2.04, R)
>droSim1.chr2L 14337368 51 + 22036055
GUCCUCGUUUGCUGAGACUAAUUUGUGGCUCUCU-----UCUGAGACGCCCACUAU
(((.(((.....)))))).....((.(((((((.-----...)))).))))).... ( -12.70, z-score =  -2.04, R)
>droSec1.super_3 859983 51 + 7220098
GUCCUCGUUUGCUGAGACUAAUUUGUGGCUCUCU-----UCUGAGACGCCCACUAU
(((.(((.....)))))).....((.(((((((.-----...)))).))))).... ( -12.70, z-score =  -2.04, R)
>droYak2.chr2L 14698472 53 + 22324452
GUCCUCGUUUGCUGAGACUAAUUUGUGGCUCUCUACU--UCUGAGACGCCCACAA-
(((.(((.....))))))....(((((((((((....--...)))).).))))))- ( -13.80, z-score =  -2.32, R)
>droEre2.scaffold_4929 6341131 51 + 26641161
GUCCUCGUUUGCUGAGACUAAUUUGUGGCUCUCU-----UCUGAGACGCCCACUAU
(((.(((.....)))))).....((.(((((((.-----...)))).))))).... ( -12.70, z-score =  -2.04, R)
>droAna3.scaffold_12916 14947906 52 - 16180835
GUCCUCGUUUGCUGGGACUAAUUUGUGGCCCUCGA----CUAAAGACGCCCACUAA
(((((.(....).)))))......((((.(.((..----.....)).).))))... ( -12.70, z-score =  -1.29, R)
>dp4.chr4_group1 2022971 56 - 5278887
AUCCUCGUUUGCUGGGACUAAUUUGUGGCUCUCCUCUCGACUGAGACGCCCACAGU
.((((.(....).)))).....(((((((((((.........)))).).)))))). ( -13.40, z-score =  -0.43, R)
>droPer1.super_5 1966660 56 + 6813705
AUCCUCGUUUGCUGGGACUAAUUUGUGGCUCUCCUCUCGACUGAGACGCCCACAGU
.((((.(....).)))).....(((((((((((.........)))).).)))))). ( -13.40, z-score =  -0.43, R)
>droWil1.scaffold_180764 2937008 51 + 3949147
GUCCUCGUUUGCUGAGACUAAUUUGUGGCUCUCA-----ACUGGGACGCCCACUAA
(((((.((....((((((((.....))).)))))-----)).)))))......... ( -13.40, z-score =  -1.63, R)
>consensus
GUCCUCGUUUGCUGAGACUAAUUUGUGGCUCUCU_____UCUGAGACGCCCACUAU
...((((.....))))........(((((((((.........)))).).))))... ( -9.79 =  -9.69 +  -0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 14,586,745 – 14,586,796
Length 51
Sequences 9
Columns 56
Reading direction reverse
Mean pairwise identity 86.56
Shannon entropy 0.26635
G+C content 0.50576
Mean single sequence MFE -12.81
Consensus MFE -11.01
Energy contribution -10.53
Covariance contribution -0.48
Combinations/Pair 1.29
Mean z-score -1.28
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.731252
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14586745 51 - 23011544
AUAGUGGGCGUCUCAGA-----AGAGAGCCACAAAUUAGUCUCAGCAAACGAGGAC
...((((.(.((((...-----.))))))))).......((((.......)))).. ( -12.30, z-score =  -1.69, R)
>droSim1.chr2L 14337368 51 - 22036055
AUAGUGGGCGUCUCAGA-----AGAGAGCCACAAAUUAGUCUCAGCAAACGAGGAC
...((((.(.((((...-----.))))))))).......((((.......)))).. ( -12.30, z-score =  -1.69, R)
>droSec1.super_3 859983 51 - 7220098
AUAGUGGGCGUCUCAGA-----AGAGAGCCACAAAUUAGUCUCAGCAAACGAGGAC
...((((.(.((((...-----.))))))))).......((((.......)))).. ( -12.30, z-score =  -1.69, R)
>droYak2.chr2L 14698472 53 - 22324452
-UUGUGGGCGUCUCAGA--AGUAGAGAGCCACAAAUUAGUCUCAGCAAACGAGGAC
-((((((.(.((((...--....))))))))))).....((((.......)))).. ( -13.40, z-score =  -1.62, R)
>droEre2.scaffold_4929 6341131 51 - 26641161
AUAGUGGGCGUCUCAGA-----AGAGAGCCACAAAUUAGUCUCAGCAAACGAGGAC
...((((.(.((((...-----.))))))))).......((((.......)))).. ( -12.30, z-score =  -1.69, R)
>droAna3.scaffold_12916 14947906 52 + 16180835
UUAGUGGGCGUCUUUAG----UCGAGGGCCACAAAUUAGUCCCAGCAAACGAGGAC
...((((.(.((.....----..)).).))))......((((..(....)..)))) ( -13.90, z-score =  -1.43, R)
>dp4.chr4_group1 2022971 56 + 5278887
ACUGUGGGCGUCUCAGUCGAGAGGAGAGCCACAAAUUAGUCCCAGCAAACGAGGAU
..(((((.(.((((....)))).)....))))).....((((..(....)..)))) ( -13.90, z-score =  -0.48, R)
>droPer1.super_5 1966660 56 - 6813705
ACUGUGGGCGUCUCAGUCGAGAGGAGAGCCACAAAUUAGUCCCAGCAAACGAGGAU
..(((((.(.((((....)))).)....))))).....((((..(....)..)))) ( -13.90, z-score =  -0.48, R)
>droWil1.scaffold_180764 2937008 51 - 3949147
UUAGUGGGCGUCCCAGU-----UGAGAGCCACAAAUUAGUCUCAGCAAACGAGGAC
....((((...))))((-----(((((............))))))).......... ( -11.00, z-score =  -0.73, R)
>consensus
AUAGUGGGCGUCUCAGA_____AGAGAGCCACAAAUUAGUCUCAGCAAACGAGGAC
...((((.(.((((.........)))))))))......((((..(....)..)))) (-11.01 = -10.53 +  -0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:40:55 2011