Locus 50

Sequence ID sy_sa.0
Location 1,558,211 – 1,558,329
Length 118
Max. P 0.986937
window221 window222 window223 window224

overview

Window 1

Location 1,558,211 – 1,558,329
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.55
Mean single sequence MFE -23.80
Consensus MFE -16.51
Energy contribution -16.40
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -1.90
Structure conservation index 0.69
SVM decision value 0.84
SVM RNA-class probability 0.863208
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1558211 118 + 2516575/0-120
GACCUCCUUUUUUGGCAAAUAGAAAAGAGCGGGUAUUAUGCCCACUCUUUCUGCCUGAGUCUAAU--UUUUUAAGCACUAUUAUUAUACCAUAUGUUCAUUUUCUAUACAAAUAACUAUA
..........((((....((((((((((((((((.....))))........(((.((((......--..)))).))).................)))).)))))))).))))........ ( -20.70)
>sy_ha.0 1699301 117 + 2685015/0-120
GGCCUCCUUUUUCGGCAAAUAGAAAAGAGCGGGUAU-AUGCCCACUCUUUCUGCCUGAGUCUAAU--UUUUUACGCAACUUAAGUAUAUCACACUUUAAUUCCUUAAACAAAUGUCUAUA
.(((.........)))..(((((((((((.((((..-..)))).)))))).(((.((((......--..)))).))).....................................))))). ( -22.60)
>sy_au.0 1511527 117 - 2809422/0-120
GGCCUCCCUUUUUGGCAAAUAGAAAAGAGCGGGAAU--CUCCCACUCUU-CUGCCUGAGUUCACUAAUUUUUAAGCAACUUAAUUAUAGCAUAAGUUUAUGCUUGAAACAAAUGACUUCA
.(((.........)))...((((..((((.(((...--..))).)))))-)))...(((.(((.....((((((((((((((.........)))))...)))))))))....))).))). ( -28.10)
>consensus
GGCCUCCUUUUUUGGCAAAUAGAAAAGAGCGGGUAU_AUGCCCACUCUUUCUGCCUGAGUCUAAU__UUUUUAAGCAACUUAAUUAUACCAUAAGUUAAUUCUUUAAACAAAUGACUAUA
.............((((......((((((.((((.....)))).)))))).))))................................................................. (-16.51 = -16.40 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,558,211 – 1,558,329
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.55
Mean single sequence MFE -30.45
Consensus MFE -20.93
Energy contribution -21.27
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.69
SVM decision value 2.01
SVM RNA-class probability 0.985557
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1558211 118 + 2516575/0-120
UAUAGUUAUUUGUAUAGAAAAUGAACAUAUGGUAUAAUAAUAGUGCUUAAAAA--AUUAGACUCAGGCAGAAAGAGUGGGCAUAAUACCCGCUCUUUUCUAUUUGCCAAAAAAGGAGGUC
(((..((((((.......))))))..)))(((((....((((((((((.....--.........)))))(((((((((((.......)))))))))))))))))))))............ ( -25.54)
>sy_ha.0 1699301 117 + 2685015/0-120
UAUAGACAUUUGUUUAAGGAAUUAAAGUGUGAUAUACUUAAGUUGCGUAAAAA--AUUAGACUCAGGCAGAAAGAGUGGGCAU-AUACCCGCUCUUUUCUAUUUGCCGAAAAAGGAGGCC
..(((((....))))).(.((((.((((((...)))))).)))).).......--......(((.(((((((((((((((...-...))))))))))).....)))).......)))... ( -30.60)
>sy_au.0 1511527 117 - 2809422/0-120
UGAAGUCAUUUGUUUCAAGCAUAAACUUAUGCUAUAAUUAAGUUGCUUAAAAAUUAGUGAACUCAGGCAG-AAGAGUGGGAG--AUUCCCGCUCUUUUCUAUUUGCCAAAAAGGGAGGCC
(((..(((((..(((.(((((...(((((.........)))))))))).)))...)))))..)))(((((-(((((((((..--...)))))))))))....((.((.....)).))))) ( -35.20)
>consensus
UAUAGUCAUUUGUUUAAAGAAUAAACAUAUGAUAUAAUUAAGUUGCUUAAAAA__AUUAGACUCAGGCAGAAAGAGUGGGCAU_AUACCCGCUCUUUUCUAUUUGCCAAAAAAGGAGGCC
.............................................................(((.(((((((((((((((.......))))))))).....)))))).......)))... (-20.93 = -21.27 +   0.33) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,558,211 – 1,558,329
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 69.12
Mean single sequence MFE -21.67
Consensus MFE -13.21
Energy contribution -12.77
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -1.76
Structure conservation index 0.61
SVM decision value 2.06
SVM RNA-class probability 0.986937
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1558211 118 + 2516575/25-145
AGAGCGGGUAUUAUGCCCACUCUUUCUGCCUGAGUCUAAU--UUUUUAAGCACUAUUAUUAUACCAUAUGUUCAUUUUCUAUACAAAUAACUAUAUUUGUUAAACGGCACAAUGACAACU
((((.((((.....)))).))))...((((...(..(((.--...)))..)...............................(((((((....))))))).....))))........... ( -20.20)
>sy_ha.0 1699301 113 + 2685015/25-145
AGAGCGGGUAU-AUGCCCACUCUUUCUGCCUGAGUCUAAU--UUUUUACGCAACUUAAGUAUAUCACACUUUAAUUCCUUAAACAAAUGUCUAUAUCU----UGCGUCACAGAGACUACU
((((.((((..-..)))).)))).........(((((...--.....((((((..((((.((((.....(((((....)))))...)))))).))..)----))))).....)))))... ( -21.62)
>sy_au.0 1511527 111 - 2809422/25-145
AGAGCGGGAAU--CUCCCACUCUU-CUGCCUGAGUUCACUAAUUUUUAAGCAACUUAAUUAUAGCAUAAGUUUAUGCUUGAAACAAAUGACUUCACU------AUUAAUCAGAGAUUCUU
.(((.(((...--..))).)))((-(((..((((.(((.....((((((((((((((.........)))))...)))))))))....))).))))..------......)))))...... ( -23.20)
>consensus
AGAGCGGGUAU_AUGCCCACUCUUUCUGCCUGAGUCUAAU__UUUUUAAGCAACUUAAUUAUACCAUAAGUUAAUUCUUUAAACAAAUGACUAUAUUU_____ACGACACAGAGACUACU
((((.((((.....)))).))))...(((.((((..........)))).))).................................................................... (-13.21 = -12.77 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,558,211 – 1,558,329
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 69.12
Mean single sequence MFE -28.47
Consensus MFE -13.19
Energy contribution -13.52
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.42
Structure conservation index 0.46
SVM decision value 1.13
SVM RNA-class probability 0.919221
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 1558211 118 + 2516575/25-145
AGUUGUCAUUGUGCCGUUUAACAAAUAUAGUUAUUUGUAUAGAAAAUGAACAUAUGGUAUAAUAAUAGUGCUUAAAAA--AUUAGACUCAGGCAGAAAGAGUGGGCAUAAUACCCGCUCU
..(((((((((((((((((((((((((....)))))))........)))))....))))))))...(((.((......--...)))))..)))))..((((((((.......)))))))) ( -27.60)
>sy_ha.0 1699301 113 + 2685015/25-145
AGUAGUCUCUGUGACGCA----AGAUAUAGACAUUUGUUUAAGGAAUUAAAGUGUGAUAUACUUAAGUUGCGUAAAAA--AUUAGACUCAGGCAGAAAGAGUGGGCAU-AUACCCGCUCU
.(.((((((((((.(...----.).))))))......((((.(.((((.((((((...)))))).)))).).))))..--....)))))........((((((((...-...)))))))) ( -29.20)
>sy_au.0 1511527 111 - 2809422/25-145
AAGAAUCUCUGAUUAAU------AGUGAAGUCAUUUGUUUCAAGCAUAAACUUAUGCUAUAAUUAAGUUGCUUAAAAAUUAGUGAACUCAGGCAG-AAGAGUGGGAG--AUUCCCGCUCU
.......((((......------..(((..(((((..(((.(((((...(((((.........)))))))))).)))...)))))..)))..)))-)((((((((..--...)))))))) ( -28.60)
>consensus
AGUAGUCUCUGUGACGU_____AAAUAUAGUCAUUUGUUUAAAGAAUAAACAUAUGAUAUAAUUAAGUUGCUUAAAAA__AUUAGACUCAGGCAGAAAGAGUGGGCAU_AUACCCGCUCU
....................................................................(((((................)))))...((((((((.......)))))))) (-13.19 = -13.52 +   0.33) 
# Strand winner: reverse (0.76)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:53:41 2006