Locus 110

Sequence ID sy_ha.0
Location 970,890 – 970,986
Length 96
Max. P 0.999508
window630 window631 window632 window633

overview

Window 0

Location 970,890 – 970,986
Length 96
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 76.51
Mean single sequence MFE -39.62
Consensus MFE -42.14
Energy contribution -39.33
Covariance contribution -2.81
Combinations/Pair 1.45
Mean z-score -2.31
Structure conservation index 1.06
SVM decision value 3.67
SVM RNA-class probability 0.999508
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 970890 96 + 2685015
GCGGUCGUGGCGGAAUGGCAGACGCGCUAGGUUGAGGGCCUAGUGGGAGAAAUCCCGUGGAGGUUCAAGUCCUCUCGGCCGCACC---AAAUAAACUUU
(((((((.((.(((..(((...((((((((((.....)))))))((((....)))))))...)))....))))).)))))))...---........... ( -41.70)
>sy_au.0 691909 93 - 2809422
GCGGUCGUGGCGGAAUGGCAGACGCGCUAGGUUGAGGGCCUAGUGGGAGAAAUCCCGUGGAGGUUCAAGUCCUCUCGGCCGCAUC---AAA---AUUCU
(((((((.((.(((..(((...((((((((((.....)))))))((((....)))))))...)))....))))).)))))))...---...---..... ( -41.70)
>sy_sa.0 841385 94 + 2516575
GCGGCCGUGGCGGAACGGCAGACGCGCUAGGUUGAGGGCCUAGUGGGAGUAUUCCCGUGGAGGUUCAAAUCCUCUCGGCCGCAUC---AAAU--ACCUU
(((((((.((.(((..(((...((((((((((.....)))))))(((......))))))...)))....))))).)))))))...---....--..... ( -40.10)
>sp_mu.0 1702479 97 - 2030921
GCGGAGAUGGUGGAACGGCAGACACGCAUGCUUCAGGCGCAUGUGCUCGUAUGAGCGUGAGGGUUCAAAUCCCUUUCUCCGCAUUUUUGAAU--GCCUU
(((((((.((.(((..(((...(((((((((.......))))))((((....)))))))...)))....))))).)))))))..........--..... ( -35.00)
>consensus
GCGGUCGUGGCGGAACGGCAGACGCGCUAGGUUGAGGGCCUAGUGGGAGAAAUCCCGUGGAGGUUCAAAUCCUCUCGGCCGCAUC___AAAU__ACCUU
(((((((.((.(((..(((...((((((((((.....)))))))((((....)))))))...)))....))))).)))))))................. (-42.14 = -39.33 +  -2.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 970,890 – 970,986
Length 96
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 76.51
Mean single sequence MFE -29.45
Consensus MFE -29.90
Energy contribution -26.15
Covariance contribution -3.75
Combinations/Pair 1.52
Mean z-score -1.01
Structure conservation index 1.02
SVM decision value 2.36
SVM RNA-class probability 0.992912
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 970890 96 + 2685015
AAAGUUUAUUU---GGUGCGGCCGAGAGGACUUGAACCUCCACGGGAUUUCUCCCACUAGGCCCUCAACCUAGCGCGUCUGCCAUUCCGCCACGACCGC
...........---(((..(((((.((((.......)))))..((((....))))....))))....)))..(((.(((.((......))...)))))) ( -27.90)
>sy_au.0 691909 93 - 2809422
AGAAU---UUU---GAUGCGGCCGAGAGGACUUGAACCUCCACGGGAUUUCUCCCACUAGGCCCUCAACCUAGCGCGUCUGCCAUUCCGCCACGACCGC
.....---.((---((.(.(((((.((((.......)))))..((((....))))....)))))))))....(((.(((.((......))...)))))) ( -27.20)
>sy_sa.0 841385 94 + 2516575
AAGGU--AUUU---GAUGCGGCCGAGAGGAUUUGAACCUCCACGGGAAUACUCCCACUAGGCCCUCAACCUAGCGCGUCUGCCGUUCCGCCACGGCCGC
.((((--...(---((.(.(((((.((((.......)))))..((((....))))....))))))))))))...(((...(((((......)))))))) ( -32.80)
>sp_mu.0 1702479 97 - 2030921
AAGGC--AUUCAAAAAUGCGGAGAAAGGGAUUUGAACCCUCACGCUCAUACGAGCACAUGCGCCUGAAGCAUGCGUGUCUGCCGUUCCACCAUCUCCGC
...((--(((....)))))(((((.((((.......))))(((((((....)))).(((((.......))))).)))...............))))).. ( -29.90)
>consensus
AAAGU__AUUU___GAUGCGGCCGAGAGGACUUGAACCUCCACGGGAAUACUCCCACUAGGCCCUCAACCUAGCGCGUCUGCCAUUCCGCCACGACCGC
.................(((((((.((((.......))))...((((....)))).(((((.......))))).(((..........)))..))))))) (-29.90 = -26.15 +  -3.75) 
# Strand winner: forward (1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 970,890 – 970,986
Length 96
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 76.51
Mean single sequence MFE -39.62
Consensus MFE -42.14
Energy contribution -39.33
Covariance contribution -2.81
Combinations/Pair 1.45
Mean z-score -2.31
Structure conservation index 1.06
SVM decision value 3.67
SVM RNA-class probability 0.999508
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 970890 96 + 2685015/0-99
GCGGUCGUGGCGGAAUGGCAGACGCGCUAGGUUGAGGGCCUAGUGGGAGAAAUCCCGUGGAGGUUCAAGUCCUCUCGGCCGCACC---AAAUAAACUUU
(((((((.((.(((..(((...((((((((((.....)))))))((((....)))))))...)))....))))).)))))))...---........... ( -41.70)
>sy_au.0 691909 93 - 2809422/0-99
GCGGUCGUGGCGGAAUGGCAGACGCGCUAGGUUGAGGGCCUAGUGGGAGAAAUCCCGUGGAGGUUCAAGUCCUCUCGGCCGCAUC---AAA---AUUCU
(((((((.((.(((..(((...((((((((((.....)))))))((((....)))))))...)))....))))).)))))))...---...---..... ( -41.70)
>sy_sa.0 841385 94 + 2516575/0-99
GCGGCCGUGGCGGAACGGCAGACGCGCUAGGUUGAGGGCCUAGUGGGAGUAUUCCCGUGGAGGUUCAAAUCCUCUCGGCCGCAUC---AAAU--ACCUU
(((((((.((.(((..(((...((((((((((.....)))))))(((......))))))...)))....))))).)))))))...---....--..... ( -40.10)
>sp_mu.0 1702479 97 - 2030921/0-99
GCGGAGAUGGUGGAACGGCAGACACGCAUGCUUCAGGCGCAUGUGCUCGUAUGAGCGUGAGGGUUCAAAUCCCUUUCUCCGCAUUUUUGAAU--GCCUU
(((((((.((.(((..(((...(((((((((.......))))))((((....)))))))...)))....))))).)))))))..........--..... ( -35.00)
>consensus
GCGGUCGUGGCGGAACGGCAGACGCGCUAGGUUGAGGGCCUAGUGGGAGAAAUCCCGUGGAGGUUCAAAUCCUCUCGGCCGCAUC___AAAU__ACCUU
(((((((.((.(((..(((...((((((((((.....)))))))((((....)))))))...)))....))))).)))))))................. (-42.14 = -39.33 +  -2.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 970,890 – 970,986
Length 96
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 76.51
Mean single sequence MFE -29.45
Consensus MFE -29.90
Energy contribution -26.15
Covariance contribution -3.75
Combinations/Pair 1.52
Mean z-score -1.01
Structure conservation index 1.02
SVM decision value 2.36
SVM RNA-class probability 0.992912
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 970890 96 + 2685015/0-99
AAAGUUUAUUU---GGUGCGGCCGAGAGGACUUGAACCUCCACGGGAUUUCUCCCACUAGGCCCUCAACCUAGCGCGUCUGCCAUUCCGCCACGACCGC
...........---(((..(((((.((((.......)))))..((((....))))....))))....)))..(((.(((.((......))...)))))) ( -27.90)
>sy_au.0 691909 93 - 2809422/0-99
AGAAU---UUU---GAUGCGGCCGAGAGGACUUGAACCUCCACGGGAUUUCUCCCACUAGGCCCUCAACCUAGCGCGUCUGCCAUUCCGCCACGACCGC
.....---.((---((.(.(((((.((((.......)))))..((((....))))....)))))))))....(((.(((.((......))...)))))) ( -27.20)
>sy_sa.0 841385 94 + 2516575/0-99
AAGGU--AUUU---GAUGCGGCCGAGAGGAUUUGAACCUCCACGGGAAUACUCCCACUAGGCCCUCAACCUAGCGCGUCUGCCGUUCCGCCACGGCCGC
.((((--...(---((.(.(((((.((((.......)))))..((((....))))....))))))))))))...(((...(((((......)))))))) ( -32.80)
>sp_mu.0 1702479 97 - 2030921/0-99
AAGGC--AUUCAAAAAUGCGGAGAAAGGGAUUUGAACCCUCACGCUCAUACGAGCACAUGCGCCUGAAGCAUGCGUGUCUGCCGUUCCACCAUCUCCGC
...((--(((....)))))(((((.((((.......))))(((((((....)))).(((((.......))))).)))...............))))).. ( -29.90)
>consensus
AAAGU__AUUU___GAUGCGGCCGAGAGGACUUGAACCUCCACGGGAAUACUCCCACUAGGCCCUCAACCUAGCGCGUCUGCCAUUCCGCCACGACCGC
.................(((((((.((((.......))))...((((....)))).(((((.......))))).(((..........)))..))))))) (-29.90 = -26.15 +  -3.75) 
# Strand winner: forward (1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:59:20 2006