Locus 3355

Sequence ID dm3.chr2R
Location 4,602,916 – 4,603,033
Length 117
Max. P 0.955166
window4614 window4615

overview

Window 4

Location 4,602,916 – 4,603,033
Length 117
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 89.75
Shannon entropy 0.18124
G+C content 0.28181
Mean single sequence MFE -22.49
Consensus MFE -13.22
Energy contribution -14.10
Covariance contribution 0.88
Combinations/Pair 1.11
Mean z-score -2.66
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.678528
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 4602916 117 + 21146708
AUUGAUCCAUAUCAGCCACUUAUAAUACCUACUCAUAAUUUUUAAAACACUUAUAAAUAAGUAAGGAAAAAAUCAAAUCAAUUCCGAUAAGAGGGGUAAAA-UGGCUGAAUAUAAUUU
...........(((((((.((....(((((.(((..............(((((....)))))..((((.............)))).....)))))))))).-)))))))......... ( -22.72, z-score =  -2.88, R)
>droEre2.scaffold_4929 8602445 118 - 26641161
UUUGAUCCAUAUCAGCCACUUAUAAUACCUAUUCACCAUUUUUAAAACACUUAUAAAUAAGUGCUGAAAAGAUCAAAUCAAUUCCGAUAAGAAGUGUAAAAAUGGCUCAAAAUAAUUU
(((((.((((.(((((.((((((.................................))))))))))).....((..(((......)))..)).........)))).)))))....... ( -17.71, z-score =  -2.19, R)
>droYak2.chr2L 17266263 118 + 22324452
UUUGAUUCAUAUCAAGCACUUAUAACACCUACUCAUUAUUUUUAAGGCACUUAUAAAUAACUGCUGAAAGGAGCAAAUCAGUUCCGAUAAGAGGGGUAAAAAUGGCUGAAAAUAAUUU
..((((....))))(((.........((((.(((.(((((.....((((.(((....))).))))....(((((......))))))))))))))))).......)))........... ( -21.79, z-score =  -1.19, R)
>droSec1.super_1 2247311 118 + 14215200
AUUGAUCCAUAUCAGCCACUUAUAAUCCGUACUCAUAAUUUUUAAAACACUUAUAAGUAAGUACGGAAAAAAUCAAAUCAAUUCCGAUAAGAGGGGUAAAAAUGGCUGAAUAUAAUUU
...........(((((((.......((((((((....((((.(((.....))).)))).)))))))).............(((((.......))))).....)))))))......... ( -25.50, z-score =  -3.43, R)
>droSim1.chr2R 3284916 118 + 19596830
AUUGAUCCAUAUCAGCCACUUAUUAUACCUACUCAUAAUUUUUAAAACACUUAUAAAUAAGUACGGAAAAAAUCAAAUCAAUUCCGAUAAGAGGGGUAAAAAUGGCUGAAUAUAAUUU
...........(((((((.((....(((((.(((..............(((((....))))).(((((.............)))))....)))))))).)).)))))))......... ( -24.72, z-score =  -3.63, R)
>consensus
AUUGAUCCAUAUCAGCCACUUAUAAUACCUACUCAUAAUUUUUAAAACACUUAUAAAUAAGUACGGAAAAAAUCAAAUCAAUUCCGAUAAGAGGGGUAAAAAUGGCUGAAUAUAAUUU
...........(((((((.......(((((.(((....(((((.....(((((....)))))....))))).....(((......)))..))))))))....)))))))......... (-13.22 = -14.10 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,602,916 – 4,603,033
Length 117
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 89.75
Shannon entropy 0.18124
G+C content 0.28181
Mean single sequence MFE -27.20
Consensus MFE -19.74
Energy contribution -21.26
Covariance contribution 1.52
Combinations/Pair 1.20
Mean z-score -2.79
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.61
SVM RNA-class probability 0.955166
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 4602916 117 - 21146708
AAAUUAUAUUCAGCCA-UUUUACCCCUCUUAUCGGAAUUGAUUUGAUUUUUUCCUUACUUAUUUAUAAGUGUUUUAAAAAUUAUGAGUAGGUAUUAUAAGUGGCUGAUAUGGAUCAAU
...((((((.((((((-(((.............((((..(((...)))..)))).(((((((((((((............)))))))))))))....)))))))))))))))...... ( -28.60, z-score =  -3.33, R)
>droEre2.scaffold_4929 8602445 118 + 26641161
AAAUUAUUUUGAGCCAUUUUUACACUUCUUAUCGGAAUUGAUUUGAUCUUUUCAGCACUUAUUUAUAAGUGUUUUAAAAAUGGUGAAUAGGUAUUAUAAGUGGCUGAUAUGGAUCAAA
...((((..(.((((((((.(((.((..(((((((((..(((...)))..)))((((((((....)))))))).......))))))..)))))....)))))))).).))))...... ( -25.80, z-score =  -2.12, R)
>droYak2.chr2L 17266263 118 - 22324452
AAAUUAUUUUCAGCCAUUUUUACCCCUCUUAUCGGAACUGAUUUGCUCCUUUCAGCAGUUAUUUAUAAGUGCCUUAAAAAUAAUGAGUAGGUGUUAUAAGUGCUUGAUAUGAAUCAAA
...((((..((((.(((((..((.((((((((.(((.(......).))).....(((.(((....))).)))..........))))).))).))...))))).)))).))))...... ( -21.00, z-score =  -0.80, R)
>droSec1.super_1 2247311 118 - 14215200
AAAUUAUAUUCAGCCAUUUUUACCCCUCUUAUCGGAAUUGAUUUGAUUUUUUCCGUACUUACUUAUAAGUGUUUUAAAAAUUAUGAGUACGGAUUAUAAGUGGCUGAUAUGGAUCAAU
...((((((.(((((((((.((..((......(((((..(((...)))..)))))....(((((((((............))))))))).))..)).)))))))))))))))...... ( -29.50, z-score =  -3.60, R)
>droSim1.chr2R 3284916 118 - 19596830
AAAUUAUAUUCAGCCAUUUUUACCCCUCUUAUCGGAAUUGAUUUGAUUUUUUCCGUACUUAUUUAUAAGUGUUUUAAAAAUUAUGAGUAGGUAUAAUAAGUGGCUGAUAUGGAUCAAU
...((((((.((((((((((((..(((((((((((((..(((...)))..)))))((((((....))))))...........))))).)))..))).)))))))))))))))...... ( -31.10, z-score =  -4.09, R)
>consensus
AAAUUAUAUUCAGCCAUUUUUACCCCUCUUAUCGGAAUUGAUUUGAUUUUUUCCGUACUUAUUUAUAAGUGUUUUAAAAAUUAUGAGUAGGUAUUAUAAGUGGCUGAUAUGGAUCAAU
...((((((.(((((((((..............((((..((.....))..))))((((((((((((((............))))))))))))))...)))))))))))))))...... (-19.74 = -21.26 +   1.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:08:38 2011