Locus 71

Sequence ID sy_sa.0
Location 1,972,254 – 1,972,295
Length 41
Max. P 0.999691
window365 window366

overview

Window 5

Location 1,972,254 – 1,972,295
Length 41
Sequences 3
Columns 41
Reading direction forward
Mean pairwise identity 77.24
Mean single sequence MFE -13.13
Consensus MFE -12.18
Energy contribution -12.40
Covariance contribution 0.22
Combinations/Pair 1.10
Mean z-score -3.94
Structure conservation index 0.93
SVM decision value 3.90
SVM RNA-class probability 0.999691
Prediction RNA
WARNING Sequence 1 too short.
WARNING Sequence 2 too short.
WARNING Sequence 3 too short.

Download alignment: ClustalW | MAF

>sy_sa.0 1972254 41 + 2516575
AAAAAUAAAAAGCCCUCAACCACAAUGGUUGAGAGCUCUAU
..........(((.(((((((.....))))))).))).... ( -14.30)
>sy_ha.0 2133934 41 + 2685015
AAAAAUAAAAAGCCCUCAACCAGAUGGGUUGAGAGCUGUAU
..........(((.(((((((.....))))))).))).... ( -14.50)
>sy_au.0 1933065 41 - 2809422
AAAAUAAAAAAGCCCACAACCACAAAGGCUGUAGGCUACAA
..........((((.(((.((.....)).))).)))).... ( -10.60)
>consensus
AAAAAUAAAAAGCCCUCAACCACAAAGGUUGAGAGCUAUAU
..........(((.(((((((.....))))))).))).... (-12.18 = -12.40 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 1,972,254 – 1,972,295
Length 41
Sequences 3
Columns 41
Reading direction reverse
Mean pairwise identity 77.24
Mean single sequence MFE -18.67
Consensus MFE -19.20
Energy contribution -18.10
Covariance contribution -1.10
Combinations/Pair 1.36
Mean z-score -5.30
Structure conservation index 1.03
SVM decision value 1.90
SVM RNA-class probability 0.981818
Prediction RNA
WARNING Sequence 1 too short.
WARNING Sequence 2 too short.
WARNING Sequence 3 too short.

Download alignment: ClustalW | MAF

>sy_sa.0 1972254 41 + 2516575
AUAGAGCUCUCAACCAUUGUGGUUGAGGGCUUUUUAUUUUU
..(((((((((((((.....)))))))))))))........ ( -20.00)
>sy_ha.0 2133934 41 + 2685015
AUACAGCUCUCAACCCAUCUGGUUGAGGGCUUUUUAUUUUU
....(((((((((((.....))))))))))).......... ( -17.20)
>sy_au.0 1933065 41 - 2809422
UUGUAGCCUACAGCCUUUGUGGUUGUGGGCUUUUUUAUUUU
....(((((((((((.....))))))))))).......... ( -18.80)
>consensus
AUACAGCUCUCAACCAUUGUGGUUGAGGGCUUUUUAUUUUU
....(((((((((((.....))))))))))).......... (-19.20 = -18.10 +  -1.10) 
# Strand winner: reverse (1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:55:40 2006