Locus 13087

Sequence ID dm3.chrX
Location 4,260,155 – 4,260,356
Length 201
Max. P 0.896470
window17988 window17989 window17990

overview

Window 8

Location 4,260,155 – 4,260,212
Length 57
Sequences 3
Columns 64
Reading direction reverse
Mean pairwise identity 80.00
Shannon entropy 0.26869
G+C content 0.30038
Mean single sequence MFE -7.36
Consensus MFE -6.07
Energy contribution -6.73
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.19
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.07
SVM RNA-class probability 0.529382
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4260155 57 - 22422827
ACAUCAUGUGUCGUCGCAUCGAGAAGUUAUUACCAAUAUUCAUUCAUUUUUCAUUUU-------
.....(((((....))))).(((((((..................))))))).....------- (  -5.07, z-score =  -0.48, R)
>droSec1.super_4 3714777 52 + 6179234
ACAUCAUGUGUCGUCGCAUCGAUGAAUUAUUAGUAAUAUUCAUUAAUUUUUC------------
.(((((((((....))))).))))............................------------ (  -8.50, z-score =  -1.53, R)
>droSim1.chrX 3275195 64 - 17042790
ACAUCAUGUGUCGUCGCAUCGAUGAAUUAUUAGCAAUAUUCAUUAAUUUUUCAUUUCACUUUUC
.(((((((((....))))).))))........................................ (  -8.50, z-score =  -1.55, R)
>consensus
ACAUCAUGUGUCGUCGCAUCGAUGAAUUAUUAGCAAUAUUCAUUAAUUUUUCAUUU________
.(((((((((....))))).))))........................................ ( -6.07 =  -6.73 +   0.67)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,260,212 – 4,260,356
Length 144
Sequences 5
Columns 147
Reading direction forward
Mean pairwise identity 62.77
Shannon entropy 0.66022
G+C content 0.33622
Mean single sequence MFE -29.68
Consensus MFE -10.70
Energy contribution -11.14
Covariance contribution 0.44
Combinations/Pair 1.63
Mean z-score -1.65
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.830615
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4260212 144 + 22422827
CUUGAUUAGGAUUUUAGAGGAAACUAGUUUUCGUUAUUAAACCAGUUUCCU-GUGAAACCUAAACCAAG--AUAUCAAUUUGGUUUUUUAACACUAGAAGAAUACAGCGCGCGAAAUUAUGCUAUUAAUAUUUACGGAAUUUCCGUU
((((.(((((.(((((.((((((((.((((........)))).))))))))-.))))))))))..))))--........(((.(((((((....)))))))...))).(((.((((((.((.((........)))).))))))))). ( -33.70, z-score =  -2.86, R)
>droEre2.scaffold_4690 1630993 140 + 18748788
UGCAGUGAGUACUUUA-----AGUUCACAUCCAUAUUUGUAAUGAUUCCUCGCUAAAAUUCUAAACAAAGCACAUU-UUUUGGUUCAG-AAUAACAGGCGGCCAAUGCGCGCGAAUUUACGCUACACAUAUUUACCCAAUUUCAUGG
....((((((....((-----(((((..........((((....((((...(((((((..................-)))))))...)-))).))))(((((....)).)))))))))).))).)))........(((......))) ( -21.57, z-score =   1.01, R)
>droYak2.chrX 17593044 143 - 21770863
--AGAUUAGAAUUUUAGGGGUAAAUAGUUUUUGUAAACAAACUUUUUGCUC-UUAAAAUUCUAAGCAAGGCAGAUUAUUUGAGUUCCU-GAUGCUAGACGGCCACUGCGCUUGAAAUUAUGAUAUUUAUAUUUACCCAAUCUCAUGC
--...(((((((((((((((((((.(((((........))))).)))))))-)))))))))))).((((((((........(((....-...))).........)))).))))....(((((.(((...........))).))))). ( -34.43, z-score =  -2.10, R)
>droSec1.super_4 3714829 136 - 6179234
AAUGUUUAAAACCUUAGAGGAAACUAGUUUUCGUAAUCAAACUAGAUUCCU-UUAAAGCC-AAAGCAAG--AGAUCACAUUGGUUUUU-AACAC---AAGGAUACAGCGCGCGGAAUUAUACUAUUAAUAAUUACU---CUUCAAGU
..((((.(((((((((((((((.(((((((........))))))).)))))-)))).((.-...))...--..........)))))).-)))).---.................((((((.......))))))...---........ ( -25.80, z-score =  -1.58, R)
>droSim1.chrX 3275259 136 + 17042790
AUUGUUUGAAACGUUAGAGGAAACUAGUUUUCGUAAUUAAACUAGCUUCCU-UUAAUGCC-AAAGCAAG--AGAUCACAUUGGUUUUU-AACAC---AAUGAUGCAGCGCGCGGAAUUAUACUAUUAAUAUUUACU---CUUCAAGU
.((((((....(((((((((((.(((((((........))))))).)))))-))))))..-.))))))(--((....(((((((....-.)).)---)))).(((.....))).....................))---)....... ( -32.90, z-score =  -2.73, R)
>consensus
AUUGAUUAGAACUUUAGAGGAAACUAGUUUUCGUAAUUAAACUAGUUUCCU_UUAAAACC_AAAGCAAG__AGAUCACUUUGGUUUUU_AACAC_AGAAGGAUACAGCGCGCGAAAUUAUGCUAUUAAUAUUUACC_AAUUUCAAGU
...........(((((((((((((((((((........))))))))))))).))))))......................................................................................... (-10.70 = -11.14 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,260,212 – 4,260,356
Length 144
Sequences 5
Columns 147
Reading direction reverse
Mean pairwise identity 62.77
Shannon entropy 0.66022
G+C content 0.33622
Mean single sequence MFE -31.22
Consensus MFE -10.08
Energy contribution -10.72
Covariance contribution 0.64
Combinations/Pair 1.68
Mean z-score -2.04
Structure conservation index 0.32
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.13
SVM RNA-class probability 0.896470
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4260212 144 - 22422827
AACGGAAAUUCCGUAAAUAUUAAUAGCAUAAUUUCGCGCGCUGUAUUCUUCUAGUGUUAAAAAACCAAAUUGAUAU--CUUGGUUUAGGUUUCAC-AGGAAACUGGUUUAAUAACGAAAACUAGUUUCCUCUAAAAUCCUAAUCAAG
.((((.....))))..((((((((.((........))((((((........))))))...........))))))))--(((((((..(((((.(.-(((((((((((((........))))))))))))).).)))))..))))))) ( -38.90, z-score =  -5.36, R)
>droEre2.scaffold_4690 1630993 140 - 18748788
CCAUGAAAUUGGGUAAAUAUGUGUAGCGUAAAUUCGCGCGCAUUGGCCGCCUGUUAUU-CUGAACCAAAA-AAUGUGCUUUGUUUAGAAUUUUAGCGAGGAAUCAUUACAAAUAUGGAUGUGAACU-----UAAAGUACUCACUGCA
(((((...((((((....((((((.(((......)))))))))..))).(((((((((-((((((.(((.-.......)))))))))))...)))).)))........))).)))))..((((((.-----....))..)))).... ( -32.10, z-score =  -0.34, R)
>droYak2.chrX 17593044 143 + 21770863
GCAUGAGAUUGGGUAAAUAUAAAUAUCAUAAUUUCAAGCGCAGUGGCCGUCUAGCAUC-AGGAACUCAAAUAAUCUGCCUUGCUUAGAAUUUUAA-GAGCAAAAAGUUUGUUUACAAAAACUAUUUACCCCUAAAAUUCUAAUCU--
((.((((((((((((........)))).)))))))).))((((.(((.(..((.....-...........))..).)))))))(((((((((((.-(.(.(((.(((((........))))).))).).).)))))))))))...-- ( -29.59, z-score =  -1.69, R)
>droSec1.super_4 3714829 136 + 6179234
ACUUGAAG---AGUAAUUAUUAAUAGUAUAAUUCCGCGCGCUGUAUCCUU---GUGUU-AAAAACCAAUGUGAUCU--CUUGCUUU-GGCUUUAA-AGGAAUCUAGUUUGAUUACGAAAACUAGUUUCCUCUAAGGUUUUAAACAUU
.......(---.(.((((((.......)))))).).).............---(((((-.((((((..........--...((...-.)).(((.-(((((.(((((((........))))))).))))).))))))))).))))). ( -26.10, z-score =  -0.89, R)
>droSim1.chrX 3275259 136 - 17042790
ACUUGAAG---AGUAAAUAUUAAUAGUAUAAUUCCGCGCGCUGCAUCAUU---GUGUU-AAAAACCAAUGUGAUCU--CUUGCUUU-GGCAUUAA-AGGAAGCUAGUUUAAUUACGAAAACUAGUUUCCUCUAACGUUUCAAACAAU
..((((((---.((.....................((.((..(((.((((---(.((.-....)))))))......--..)))..)-)))..((.-(((((((((((((........))))))))))))).)))).))))))..... ( -29.40, z-score =  -1.93, R)
>consensus
ACAUGAAAUU_AGUAAAUAUUAAUAGCAUAAUUUCGCGCGCUGUAUCCUUCU_GUGUU_AAAAACCAAAAUGAUCU__CUUGCUUU_GGUUUUAA_AGGAAACUAGUUUAAUUACGAAAACUAGUUUCCUCUAAAGUUCUAAACAAU
.......................................................................................((((((...(((((((((((((........)))))))))))))..))))))......... (-10.08 = -10.72 +   0.64)

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 01:14:24 2011