Locus 17

Sequence ID sy_ha.0
Location 114,506 – 114,557
Length 51
Max. P 0.995902
window95 window96 window97 window98

overview

Window 5

Location 114,506 – 114,557
Length 51
Sequences 3
Columns 51
Reading direction forward
Mean pairwise identity 83.66
Mean single sequence MFE -13.39
Consensus MFE -12.91
Energy contribution -12.47
Covariance contribution -0.44
Combinations/Pair 1.23
Mean z-score -2.39
Structure conservation index 0.96
SVM decision value 2.63
SVM RNA-class probability 0.995902
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 114506 51 - 2685015
UAGGGAGUGGGACAGAAAUAAUAUUUUCUCAAAAUUUAUUUCGUUGUCCUA
.......((((((((((((((.((((.....)))))))))))..))))))) ( -11.70)
>sy_au.0 808585 51 + 2809422
UGGGGAGUGGGACAGAAAUGAUAUUUUCGCAAAAUUUAUUUCGUCGUCCCA
.......((((((.(((((((.((((.....)))))))))))...)))))) ( -13.70)
>sy_sa.0 622187 50 + 2516575
UAGGGAGUGGGACAGAAAUCAAAUUUUC-UAAUAGAGAUUUCGUGGUCCCA
.......((((((.((((((........-.......))))))...)))))) ( -14.76)
>consensus
UAGGGAGUGGGACAGAAAUAAUAUUUUC_CAAAAUUUAUUUCGUCGUCCCA
.......((((((.(((((((..............)))))))...)))))) (-12.91 = -12.47 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 114,506 – 114,557
Length 51
Sequences 3
Columns 51
Reading direction reverse
Mean pairwise identity 83.66
Mean single sequence MFE -11.83
Consensus MFE -9.90
Energy contribution -10.90
Covariance contribution 1.00
Combinations/Pair 1.12
Mean z-score -3.25
Structure conservation index 0.84
SVM decision value 2.18
SVM RNA-class probability 0.989700
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 114506 51 - 2685015
UAGGACAACGAAAUAAAUUUUGAGAAAAUAUUAUUUCUGUCCCACUCCCUA
..(((((..(((((((..(((....)))..))))))))))))......... ( -10.10)
>sy_au.0 808585 51 + 2809422
UGGGACGACGAAAUAAAUUUUGCGAAAAUAUCAUUUCUGUCCCACUCCCCA
(((((((.(((((....))))))((((......)))).))))))....... ( -11.80)
>sy_sa.0 622187 50 + 2516575
UGGGACCACGAAAUCUCUAUUA-GAAAAUUUGAUUUCUGUCCCACUCCCUA
((((((...((((((...(((.-...)))..)))))).))))))....... ( -13.60)
>consensus
UGGGACAACGAAAUAAAUUUUG_GAAAAUAUCAUUUCUGUCCCACUCCCUA
(((((((..((((((...(((....)))...)))))))))))))....... ( -9.90 = -10.90 +   1.00) 
# Strand winner: forward (1.00)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 114,506 – 114,557
Length 51
Sequences 3
Columns 51
Reading direction forward
Mean pairwise identity 83.66
Mean single sequence MFE -13.39
Consensus MFE -12.91
Energy contribution -12.47
Covariance contribution -0.44
Combinations/Pair 1.23
Mean z-score -2.39
Structure conservation index 0.96
SVM decision value 2.63
SVM RNA-class probability 0.995902
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 114506 51 - 2685015/0-51
UAGGGAGUGGGACAGAAAUAAUAUUUUCUCAAAAUUUAUUUCGUUGUCCUA
.......((((((((((((((.((((.....)))))))))))..))))))) ( -11.70)
>sy_au.0 808585 51 + 2809422/0-51
UGGGGAGUGGGACAGAAAUGAUAUUUUCGCAAAAUUUAUUUCGUCGUCCCA
.......((((((.(((((((.((((.....)))))))))))...)))))) ( -13.70)
>sy_sa.0 622187 50 + 2516575/0-51
UAGGGAGUGGGACAGAAAUCAAAUUUUC-UAAUAGAGAUUUCGUGGUCCCA
.......((((((.((((((........-.......))))))...)))))) ( -14.76)
>consensus
UAGGGAGUGGGACAGAAAUAAUAUUUUC_CAAAAUUUAUUUCGUCGUCCCA
.......((((((.(((((((..............)))))))...)))))) (-12.91 = -12.47 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 114,506 – 114,557
Length 51
Sequences 3
Columns 51
Reading direction reverse
Mean pairwise identity 83.66
Mean single sequence MFE -11.83
Consensus MFE -9.90
Energy contribution -10.90
Covariance contribution 1.00
Combinations/Pair 1.12
Mean z-score -3.25
Structure conservation index 0.84
SVM decision value 2.18
SVM RNA-class probability 0.989700
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 114506 51 - 2685015/0-51
UAGGACAACGAAAUAAAUUUUGAGAAAAUAUUAUUUCUGUCCCACUCCCUA
..(((((..(((((((..(((....)))..))))))))))))......... ( -10.10)
>sy_au.0 808585 51 + 2809422/0-51
UGGGACGACGAAAUAAAUUUUGCGAAAAUAUCAUUUCUGUCCCACUCCCCA
(((((((.(((((....))))))((((......)))).))))))....... ( -11.80)
>sy_sa.0 622187 50 + 2516575/0-51
UGGGACCACGAAAUCUCUAUUA-GAAAAUUUGAUUUCUGUCCCACUCCCUA
((((((...((((((...(((.-...)))..)))))).))))))....... ( -13.60)
>consensus
UGGGACAACGAAAUAAAUUUUG_GAAAAUAUCAUUUCUGUCCCACUCCCUA
(((((((..((((((...(((....)))...)))))))))))))....... ( -9.90 = -10.90 +   1.00) 
# 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 18:51:48 2006