Locus 10023

Sequence ID dm3.chr3R
Location 10,667,981 – 10,668,082
Length 101
Max. P 0.996252
window13774 window13775

overview

Window 4

Location 10,667,981 – 10,668,082
Length 101
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 63.44
Shannon entropy 0.67127
G+C content 0.33168
Mean single sequence MFE -21.73
Consensus MFE -7.16
Energy contribution -9.30
Covariance contribution 2.14
Combinations/Pair 1.22
Mean z-score -2.89
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.87
SVM RNA-class probability 0.996012
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10667981 101 + 27905053
UUGUUCCUUAACAAAUCUAUCAUCG---GGCUACCAAUAAGCUAAAUGUAUUUGAUAGAUUUGUUUAAGUGUUUUCCUAGUCUUCGUAGACAAAUUAUUUUCUG-------
......((((((((((((((((..(---(....)).....((.....))...))))))))))).)))))..........((((....)))).............------- ( -21.90, z-score =  -3.22, R)
>droSim1.chr3R 16720750 101 - 27517382
UCGUUCCUUGGCAAAUCUAUCAUCG---GGCUACCAAUAAGCUAAAUGAAUUUGAUAGAUUUGCUUAAGUGUUUUCCUCGUCUUCAUAGACAAAUUCUUUUCUG-------
......(((((((((((((((((((---((((.......))))...)))...)))))))))))).))))..........((((....)))).............------- ( -24.50, z-score =  -3.46, R)
>droSec1.super_0 9853505 101 - 21120651
UCGUUCCCUGACAAAUCUAUCAUAG---GGCUACCAAUAAGCUCAAUGAAUUUGAUAGAUUUGCUUAAGUGUUUUACUCGUCUUCAUAGACAAAUUCUUUUCUG-------
........((((((((((((((..(---((((.......)))))........))))))))))).)))............((((....)))).............------- ( -19.60, z-score =  -1.77, R)
>droYak2.chr3R 13071609 86 - 28832112
CUGUUCCUUGGAAAAUCUUUCAUCG---GGCUACCAAGAAACUAAAUGAAUCUGAUAGAUUCG--------UUUUUCU----UUUCUA---AAGCUACUUUCUG-------
..((((..(((((....)))))..)---))).....(((((..(((((((((.....))))))--------)))....----))))).---.............------- ( -15.90, z-score =  -1.57, R)
>droEre2.scaffold_4770 10202523 98 + 17746568
CUGUUCCUUUGCAAAUCUAUCAUCG---GGCUACCAAAAAACUAAUUGAAUCUGAUAGAUUUGCA-AAGUGUUUCUUU--UUUGCUUCAACAAAUUCCUUGCUG-------
......((((((((((((((((..(---(....))......(.....)....)))))))))))))-))).((......--((((......))))......))..------- ( -23.00, z-score =  -3.71, R)
>droAna3.scaffold_13340 13669476 109 - 23697760
CAAGUUCAAAACCGAACUAUAAUAAAUUGAUUUUGAAUAAAUCCCUGGGAGC--AUAAAGGUAAUAUCCUCAUUUUUCAAUUAAAUAAAACAUAAUGCUCUUAGGGUUUUG
...((((((((.(((...........))).))))))))(((.((((((((((--((..(((......))).((((.......))))........)))))))))))).))). ( -25.50, z-score =  -3.59, R)
>consensus
CUGUUCCUUGACAAAUCUAUCAUCG___GGCUACCAAUAAACUAAAUGAAUCUGAUAGAUUUGCUUAAGUGUUUUUCU_GUCUUCAUAGACAAAUUCCUUUCUG_______
...........((((((((((((((...((((.......))))...)))...)))))))))))................................................ ( -7.16 =  -9.30 +   2.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 10,667,981 – 10,668,082
Length 101
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 63.44
Shannon entropy 0.67127
G+C content 0.33168
Mean single sequence MFE -22.41
Consensus MFE -9.26
Energy contribution -9.71
Covariance contribution 0.45
Combinations/Pair 1.53
Mean z-score -2.42
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.91
SVM RNA-class probability 0.996252
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10667981 101 - 27905053
-------CAGAAAAUAAUUUGUCUACGAAGACUAGGAAAACACUUAAACAAAUCUAUCAAAUACAUUUAGCUUAUUGGUAGCC---CGAUGAUAGAUUUGUUAAGGAACAA
-------.............((((....))))..........(((.(((((((((((((...............((((....)---)))))))))))))))).)))..... ( -19.96, z-score =  -2.49, R)
>droSim1.chr3R 16720750 101 + 27517382
-------CAGAAAAGAAUUUGUCUAUGAAGACGAGGAAAACACUUAAGCAAAUCUAUCAAAUUCAUUUAGCUUAUUGGUAGCC---CGAUGAUAGAUUUGCCAAGGAACGA
-------..........(((((((....))))))).......(((..((((((((((((...............((((....)---)))))))))))))))..)))..... ( -22.76, z-score =  -2.28, R)
>droSec1.super_0 9853505 101 + 21120651
-------CAGAAAAGAAUUUGUCUAUGAAGACGAGUAAAACACUUAAGCAAAUCUAUCAAAUUCAUUGAGCUUAUUGGUAGCC---CUAUGAUAGAUUUGUCAGGGAACGA
-------.........((((((((....))))))))......(((..((((((((((((.....((..(.....)..))....---...))))))))))))..)))..... ( -22.30, z-score =  -1.70, R)
>droYak2.chr3R 13071609 86 + 28832112
-------CAGAAAGUAGCUU---UAGAAA----AGAAAAA--------CGAAUCUAUCAGAUUCAUUUAGUUUCUUGGUAGCC---CGAUGAAAGAUUUUCCAAGGAACAG
-------.............---......----.......--------.(((((.....))))).....(((((((((.....---(.......).....))))))))).. ( -15.60, z-score =  -0.95, R)
>droEre2.scaffold_4770 10202523 98 - 17746568
-------CAGCAAGGAAUUUGUUGAAGCAAA--AAAGAAACACUU-UGCAAAUCUAUCAGAUUCAAUUAGUUUUUUGGUAGCC---CGAUGAUAGAUUUGCAAAGGAACAG
-------(((((((...))))))).......--.........(((-(((((((((((((......(((((....)))))....---...))))))))))))))))...... ( -26.72, z-score =  -3.56, R)
>droAna3.scaffold_13340 13669476 109 + 23697760
CAAAACCCUAAGAGCAUUAUGUUUUAUUUAAUUGAAAAAUGAGGAUAUUACCUUUAU--GCUCCCAGGGAUUUAUUCAAAAUCAAUUUAUUAUAGUUCGGUUUUGAACUUG
.....((((..((((((...((..(((((.(((....)))..)))))..))....))--))))..)))).....(((((((((((((......)))).))))))))).... ( -27.10, z-score =  -3.54, R)
>consensus
_______CAGAAAAGAAUUUGUCUAAGAAGAC_AGAAAAACACUUAAGCAAAUCUAUCAAAUUCAUUUAGCUUAUUGGUAGCC___CGAUGAUAGAUUUGCCAAGGAACAA
...............................................((((((((((((..........(((.......))).......)))))))))))).......... ( -9.26 =  -9.71 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:15:54 2011