Locus 66

Sequence ID sy_sa.0
Location 1,857,412 – 1,857,531
Length 119
Max. P 0.992351
window306 window307

overview

Window 6

Location 1,857,412 – 1,857,531
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -29.77
Consensus MFE -30.28
Energy contribution -29.73
Covariance contribution -0.55
Combinations/Pair 1.13
Mean z-score -2.64
Structure conservation index 1.02
SVM decision value 2.32
SVM RNA-class probability 0.992351
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1857412 119 + 2516575/0-120
UUAAAAGAGAGCAUAAAAAA-CGCCGUGUCUGAUUACACGGCGCUAAACAAAGGGGAUGGGAGAAAUUUUUCACUUCAAACAAAGGGGUAUGUUUGUUAUGUGAUUAAUUUCAUGUUUAU
........((((((......-((((((((......))))))))...................((((((..((((..((((((........))))))....))))..)))))))))))).. ( -32.80)
>sy_ha.0 2004448 120 + 2685015/0-120
UUAAAAAAGAGUAUAAAAAAACGCCGUGUCUGAUUACACGACGCUAAACAAAGGGGAUGGGAGAAAUUUUUCACUUCAAACAAAGGGGUAUGUUUGUUAUGUGAUUAAUUUCAUGUUCAU
........((((((.......((.(((((......))))).))...................((((((..((((..((((((........))))))....))))..)))))))))))).. ( -23.30)
>sy_au.0 1794319 120 - 2809422/0-120
UUAAAAAAGAACAUAAAAAAACGUCGUGUCUGAAUACACGACGCUAAACAAAGGGGAUGGGAGAAAUUUUUCACUUCAAACAAAGGGGUAUGUUUGUUAUGUGAUUAAUUUCAUGUUCAU
........((((((.......((((((((......))))))))...................((((((..((((..((((((........))))))....))))..)))))))))))).. ( -33.20)
>consensus
UUAAAAAAGAGCAUAAAAAAACGCCGUGUCUGAUUACACGACGCUAAACAAAGGGGAUGGGAGAAAUUUUUCACUUCAAACAAAGGGGUAUGUUUGUUAUGUGAUUAAUUUCAUGUUCAU
........((((((.......((((((((......))))))))...................((((((..((((..((((((........))))))....))))..)))))))))))).. (-30.28 = -29.73 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 1,857,412 – 1,857,531
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -29.25
Consensus MFE -27.15
Energy contribution -26.82
Covariance contribution -0.33
Combinations/Pair 1.10
Mean z-score -4.54
Structure conservation index 0.93
SVM decision value 1.62
SVM RNA-class probability 0.967761
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1857412 119 + 2516575/0-120
AUAAACAUGAAAUUAAUCACAUAACAAACAUACCCCUUUGUUUGAAGUGAAAAAUUUCUCCCAUCCCCUUUGUUUAGCGCCGUGUAAUCAGACACGGCG-UUUUUUAUGCUCUCUUUUAA
.((((((.((((((..((((....((((((........))))))..))))..))))))............))))))(((((((((......))))))))-)................... ( -29.32)
>sy_ha.0 2004448 120 + 2685015/0-120
AUGAACAUGAAAUUAAUCACAUAACAAACAUACCCCUUUGUUUGAAGUGAAAAAUUUCUCCCAUCCCCUUUGUUUAGCGUCGUGUAAUCAGACACGGCGUUUUUUUAUACUCUUUUUUAA
.((((((.((((((..((((....((((((........))))))..))))..))))))............))))))(((((((((......))))))))).................... ( -26.72)
>sy_au.0 1794319 120 - 2809422/0-120
AUGAACAUGAAAUUAAUCACAUAACAAACAUACCCCUUUGUUUGAAGUGAAAAAUUUCUCCCAUCCCCUUUGUUUAGCGUCGUGUAUUCAGACACGACGUUUUUUUAUGUUCUUUUUUAA
..((((((((((....((((....((((((........))))))..)))).........................((((((((((......)))))))))).))))))))))........ ( -31.70)
>consensus
AUGAACAUGAAAUUAAUCACAUAACAAACAUACCCCUUUGUUUGAAGUGAAAAAUUUCUCCCAUCCCCUUUGUUUAGCGUCGUGUAAUCAGACACGGCGUUUUUUUAUGCUCUUUUUUAA
.((((((.((((((..((((....((((((........))))))..))))..))))))............))))))(((((((((......))))))))).................... (-27.15 = -26.82 +  -0.33) 
# Strand winner: forward (0.98)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:54:50 2006