Locus 1088

Sequence ID dm3.chr2L
Location 8,155,637 – 8,155,739
Length 102
Max. P 0.999950
window1489 window1490

overview

Window 9

Location 8,155,637 – 8,155,739
Length 102
Sequences 7
Columns 112
Reading direction forward
Mean pairwise identity 56.38
Shannon entropy 0.84051
G+C content 0.31010
Mean single sequence MFE -20.88
Consensus MFE -10.36
Energy contribution -12.01
Covariance contribution 1.65
Combinations/Pair 1.48
Mean z-score -2.88
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 5.14
SVM RNA-class probability 0.999950
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8155637 102 + 23011544
CGAUUUUAAAUGGUGACUGUUAAUGGUCAUAA------GCUAAUUAGCCAAGCAGCUAUCU----UACAAACAUUAAAAUGCAACUUAGCCAUUUAAAAUCGAAUAUUUUGC
((((((((((((((((((......))))))..------(((((.((((......))))...----......(((....)))....))))))))))))))))).......... ( -24.90, z-score =  -3.13, R)
>droSim1.chr2L 7937776 99 + 22036055
CGAUUUUAAAUGGUGACUGUUAAUGGUCAUAA------GCUAAUUAGCCAAGCUGAUUUC-------AAAACAAUUUAAUGCAACUCAGCCAUUUAAAAUCGAAUAUUUUGC
((((((((((((((((((......))))....------((.(((((((...)))))))..-------.............))......)))))))))))))).......... ( -25.49, z-score =  -3.57, R)
>droSec1.super_3 3652869 102 + 7220098
CGAUUUUAAAUGGUGACCGUUAAUGGUCAUAA------GCUAAUUAGCCGAGCAGCUGAUU----CCAAAACAAUUUAAUGCAACUCAGCCAUUUAAAAUCGAAUAUUUUGC
(((((((((((((((((((....)))))....------...(((((((......)))))))----.......................)))))))))))))).......... ( -28.60, z-score =  -4.09, R)
>droYak2.chr2L 10787237 77 + 22324452
CGAUUUUAAAUGGUGACUGUUAAUGGUCAUUA------GCUAAUUACCCAAGC---UUUC--------------------------UAUCCAUUUAAAAUCGAAUAUUUUUC
((((((((((((((((((......)))))..(------(((.........)))---)...--------------------------...))))))))))))).......... ( -21.30, z-score =  -5.18, R)
>droEre2.scaffold_4929 17061681 88 + 26641161
CGAUUUUAAAUGCAGACUGUUAGUGGUCAAAA------AAAGCUGUAUUACAAAAAUGCA------------------AUACAACUUAGCAAUUUAAAAUCGAAUAUUUUCC
(((((((((((((.((((......))))....------.(((.((((((.((....)).)------------------))))).))).)).))))))))))).......... ( -22.50, z-score =  -4.41, R)
>droGri2.scaffold_15126 6042109 93 + 8399593
------UAAAUGUUAAGCUUUAAUGGUCUAAAAUAAAAAACAACGUUUAAAAAAGACACAC------------ACACAACCAAUUCUAGCUAAUCACAA-CAAAUAUUUCUC
------.........((((..(((.((((....((((........))))....))))....------------.........)))..))))........-............ (  -4.94, z-score =   0.22, R)
>triCas2.ChLG8 279110 112 + 15773733
CAGUUCUAAAGGGCGAAUUCAAGAAUGCAAUAAAAAUAGGUGAUUACCCUUACAAAUUUCAAAGUUGGCGCCAAUUACUCGUAGUUCAGCCAUCUUGAAAAUAAUUUUUUGU
..((((....))))...(((((((.........((((..((((......))))..))))......((((...(((((....)))))..)))))))))))............. ( -18.40, z-score =  -0.00, R)
>consensus
CGAUUUUAAAUGGUGACUGUUAAUGGUCAUAA______GCUAAUUAGCCAAGCAGAUUUC___________CAAUU_AAUGCAACUUAGCCAUUUAAAAUCGAAUAUUUUGC
((((((((((((((((((......))))..........(((....)))........................................)))))))))))))).......... (-10.36 = -12.01 +   1.65)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,155,637 – 8,155,739
Length 102
Sequences 7
Columns 112
Reading direction reverse
Mean pairwise identity 56.38
Shannon entropy 0.84051
G+C content 0.31010
Mean single sequence MFE -22.47
Consensus MFE -6.93
Energy contribution -8.16
Covariance contribution 1.23
Combinations/Pair 1.47
Mean z-score -2.86
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.66
SVM RNA-class probability 0.999127
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8155637 102 - 23011544
GCAAAAUAUUCGAUUUUAAAUGGCUAAGUUGCAUUUUAAUGUUUGUA----AGAUAGCUGCUUGGCUAAUUAGC------UUAUGACCAUUAACAGUCACCAUUUAAAAUCG
..........(((((((((((((((((((.((((((((.......))----)))).)).)))))))........------...((((........)))).)))))))))))) ( -27.80, z-score =  -3.73, R)
>droSim1.chr2L 7937776 99 - 22036055
GCAAAAUAUUCGAUUUUAAAUGGCUGAGUUGCAUUAAAUUGUUUU-------GAAAUCAGCUUGGCUAAUUAGC------UUAUGACCAUUAACAGUCACCAUUUAAAAUCG
..........((((((((((((((..(((((..(((((....)))-------))...)))))..))........------...((((........)))).)))))))))))) ( -26.40, z-score =  -3.87, R)
>droSec1.super_3 3652869 102 - 7220098
GCAAAAUAUUCGAUUUUAAAUGGCUGAGUUGCAUUAAAUUGUUUUGG----AAUCAGCUGCUCGGCUAAUUAGC------UUAUGACCAUUAACGGUCACCAUUUAAAAUCG
..........(((((((((((((((((((.((...............----.....)).)))))))........------...(((((......))))).)))))))))))) ( -30.05, z-score =  -4.11, R)
>droYak2.chr2L 10787237 77 - 22324452
GAAAAAUAUUCGAUUUUAAAUGGAUA--------------------------GAAA---GCUUGGGUAAUUAGC------UAAUGACCAUUAACAGUCACCAUUUAAAAUCG
..........(((((((((((((...--------------------------...(---(((.........)))------)..((((........))))))))))))))))) ( -20.20, z-score =  -4.66, R)
>droEre2.scaffold_4929 17061681 88 - 26641161
GGAAAAUAUUCGAUUUUAAAUUGCUAAGUUGUAU------------------UGCAUUUUUGUAAUACAGCUUU------UUUUGACCACUAACAGUCUGCAUUUAAAAUCG
..........(((((((((((.((.(((((((((------------------((((....))))))))))))).------....(((........))).))))))))))))) ( -27.00, z-score =  -5.87, R)
>droGri2.scaffold_15126 6042109 93 - 8399593
GAGAAAUAUUUG-UUGUGAUUAGCUAGAAUUGGUUGUGU------------GUGUGUCUUUUUUAAACGUUGUUUUUUAUUUUAGACCAUUAAAGCUUAACAUUUA------
......((..((-(((.....(((((....)))))((..------------(((.((((....((((........))))....)))))))....)).)))))..))------ (  -9.40, z-score =   1.66, R)
>triCas2.ChLG8 279110 112 - 15773733
ACAAAAAAUUAUUUUCAAGAUGGCUGAACUACGAGUAAUUGGCGCCAACUUUGAAAUUUGUAAGGGUAAUCACCUAUUUUUAUUGCAUUCUUGAAUUCGCCCUUUAGAACUG
.............(((((((((((.(.....(((....))).)))))...........(((((((((....)))).......))))).)))))))(((........)))... ( -16.41, z-score =   0.56, R)
>consensus
GCAAAAUAUUCGAUUUUAAAUGGCUAAGUUGCAUU_AAUUG___________GAAAUCUGCUUGGCUAAUUAGC______UUAUGACCAUUAACAGUCACCAUUUAAAAUCG
..........(((((((((((((.........................................(((....)))..........(((........))).))))))))))))) ( -6.93 =  -8.16 +   1.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:25:24 2011