Locus 6705

Sequence ID dm3.chr3L
Location 9,067,876 – 9,067,982
Length 106
Max. P 0.879923
window9226 window9227

overview

Window 6

Location 9,067,876 – 9,067,982
Length 106
Sequences 7
Columns 116
Reading direction forward
Mean pairwise identity 63.70
Shannon entropy 0.70891
G+C content 0.38805
Mean single sequence MFE -24.98
Consensus MFE -11.53
Energy contribution -11.89
Covariance contribution 0.36
Combinations/Pair 1.67
Mean z-score -1.00
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.873056
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9067876 106 + 24543557
-----AAAUGAUGGCCAAGUGGCUCCUUGGCCUUUGGCUGGCGAUCCUGCUAGUG---GAUGUUAGUGUAGAAAGUUUAUUAAUAAUUUCAAAUUGUGUUUUU--UAAGGAUAUCA
-----.......(((((((......)))))))....(((((((....))))))).---((((((....(((((((..((...............))..)))))--))..)))))). ( -26.26, z-score =  -0.89, R)
>droSim1.chr3L 8506300 100 + 22553184
-----AAAUGAUG-CCAAGUGGCUCUU--GCCUUUG-CUGCGAUCUCUGCUAGUG---GAUGUUAGUGUAGAAAGUUUAU-AAUAAUUUCAGUU-GUGCUAUU--AAAGGAUAAUA
-----....((.(-((....)))))..--.((((((-..((..(((..(((((..---....)))))..)))........-.(((((....)))-))))...)--)))))...... ( -17.40, z-score =   1.11, R)
>droSec1.super_0 1338270 107 + 21120651
-----AAAUGAUGGCCAAGUGGCUCCUUGGCCUUUGGCUGGCGAUCCUGCUAGUG---GAUGUUAGUGUAGAAAGUUUAUUAAUAAUUUCAGUUUGUGUUUUUG-AAAGGAUAAUA
-----.......(((((((......))))))).((.(((((((....))))))).---))((((((((.........)))))))).((((((.........)))-)))........ ( -26.40, z-score =  -0.95, R)
>droYak2.chr3L 21354835 83 - 24197627
--------ACAUGGCCAAGUGGCUCCUUGGCCUUUGGCUGGCGAUCCUGCUAGUG---GAUGUUAGUGUACAAAAUUUAUUCAUAAUUUAAUCU----------------------
--------(((((((((((......))))))).((.(((((((....))))))).---)).....)))).........................---------------------- ( -23.10, z-score =  -1.32, R)
>droEre2.scaffold_4784 20792520 105 - 25762168
--------AUAUGGCCAAGUGGCUCCUUGGCCUUUGGCUGGCGAUCCUGCUAGUG---GACGUUAGUAUCGAAAGUUUAUUAAUAAUUUCACCUUGCUUUUUUUUGAAGAACAAUA
--------....(((((((......))))))).((.(((((((....))))))).---)).(((((((.(....)..)))))))............((((.....))))....... ( -27.00, z-score =  -1.15, R)
>droAna3.scaffold_13337 19478337 99 + 23293914
--------AUAUGGCCAAGUGGCUCCUGAGCCUCUGGCUGGCGGUUCUGCUGGUG---GAUGUUAGUAUUUU---UGUGUUUGUGACUUUAUUU---GCAUGAAAAAAACAUAAUA
--------.((((.((.((.((((....)))).)).((..(((....)))..)))---).........((((---..(((..(((....)))..---)))..))))...))))... ( -25.30, z-score =  -0.76, R)
>droGri2.scaffold_15110 21832361 100 - 24565398
UAUAGAGUCAAUGAUAUAUAGGGUUUUAUGCCUUGGACUGGCACUCCUUUUUGUGCUGGUCGUGAGUAUUUCAA-UUGAU--AUCAAUUUACUUAGACUGACA-------------
.....((((.........((((((.....))))))(((..((((........))))..))).((((((....((-(((..--..)))))))))))))))....------------- ( -29.40, z-score =  -3.03, R)
>consensus
_____A__AGAUGGCCAAGUGGCUCCUUGGCCUUUGGCUGGCGAUCCUGCUAGUG___GAUGUUAGUGUAGAAAGUUUAUUAAUAAUUUCACUU_GUGUUUUU__AAAGGAUAAUA
............(((((((......)))))))....(((((((....)))))))....((.((((..((((.....))))...)))).)).......................... (-11.53 = -11.89 +   0.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,067,876 – 9,067,982
Length 106
Sequences 7
Columns 116
Reading direction reverse
Mean pairwise identity 63.70
Shannon entropy 0.70891
G+C content 0.38805
Mean single sequence MFE -16.67
Consensus MFE -8.51
Energy contribution -8.96
Covariance contribution 0.45
Combinations/Pair 1.57
Mean z-score -0.78
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.04
SVM RNA-class probability 0.879923
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9067876 106 - 24543557
UGAUAUCCUUA--AAAAACACAAUUUGAAAUUAUUAAUAAACUUUCUACACUAACAUC---CACUAGCAGGAUCGCCAGCCAAAGGCCAAGGAGCCACUUGGCCAUCAUUU-----
((((.......--..........................................(((---(.......))))...........(((((((......)))))))))))...----- ( -17.90, z-score =  -1.39, R)
>droSim1.chr3L 8506300 100 - 22553184
UAUUAUCCUUU--AAUAGCAC-AACUGAAAUUAUU-AUAAACUUUCUACACUAACAUC---CACUAGCAGAGAUCGCAG-CAAAGGC--AAGAGCCACUUGG-CAUCAUUU-----
......(((((--..(.((.(-....)........-........(((...(((.....---...)))...)))..))).-.))))).--..(((((....))-).))....----- ( -10.10, z-score =   0.79, R)
>droSec1.super_0 1338270 107 - 21120651
UAUUAUCCUUU-CAAAAACACAAACUGAAAUUAUUAAUAAACUUUCUACACUAACAUC---CACUAGCAGGAUCGCCAGCCAAAGGCCAAGGAGCCACUUGGCCAUCAUUU-----
(((((...(((-((...........)))))....)))))................(((---(.......))))...........(((((((......))))))).......----- ( -18.00, z-score =  -1.90, R)
>droYak2.chr3L 21354835 83 + 24197627
----------------------AGAUUAAAUUAUGAAUAAAUUUUGUACACUAACAUC---CACUAGCAGGAUCGCCAGCCAAAGGCCAAGGAGCCACUUGGCCAUGU--------
----------------------.........((..((.....))..)).....((((.---.....((.((....)).))....(((((((......)))))))))))-------- ( -17.20, z-score =  -0.73, R)
>droEre2.scaffold_4784 20792520 105 + 25762168
UAUUGUUCUUCAAAAAAAAGCAAGGUGAAAUUAUUAAUAAACUUUCGAUACUAACGUC---CACUAGCAGGAUCGCCAGCCAAAGGCCAAGGAGCCACUUGGCCAUAU--------
..(((((.((.....)).)))))(((((......................(....)((---(.......)))))))).......(((((((......)))))))....-------- ( -22.50, z-score =  -1.24, R)
>droAna3.scaffold_13337 19478337 99 - 23293914
UAUUAUGUUUUUUUCAUGC---AAAUAAAGUCACAAACACA---AAAAUACUAACAUC---CACCAGCAGAACCGCCAGCCAGAGGCUCAGGAGCCACUUGGCCAUAU--------
...((((.....(((.(((---...................---..............---.....))))))......(((((.((((....)))).).)))))))).-------- ( -14.06, z-score =   0.01, R)
>droGri2.scaffold_15110 21832361 100 + 24565398
-------------UGUCAGUCUAAGUAAAUUGAU--AUCAA-UUGAAAUACUCACGACCAGCACAAAAAGGAGUGCCAGUCCAAGGCAUAAAACCCUAUAUAUCAUUGACUCUAUA
-------------.((((((.......(((((..--..)))-))((.(((.....(((..((((........))))..)))..(((........))).))).))))))))...... ( -16.90, z-score =  -1.02, R)
>consensus
UAUUAUCCUUU__AAAAACAC_AAAUGAAAUUAUUAAUAAACUUUCUACACUAACAUC___CACUAGCAGGAUCGCCAGCCAAAGGCCAAGGAGCCACUUGGCCAUCA__U_____
....................................................................................(((((((......)))))))............ ( -8.51 =  -8.96 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:12:53 2011