Locus 23

Sequence ID sy_ha.0
Location 888,823 – 888,943
Length 120
Max. P 0.995212
window114 window115 window116 window117

overview

Window 4

Location 888,823 – 888,934
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 68.73
Mean single sequence MFE -26.18
Consensus MFE -16.92
Energy contribution -13.50
Covariance contribution -3.42
Combinations/Pair 1.48
Mean z-score -1.12
Structure conservation index 0.65
SVM decision value 0.10
SVM RNA-class probability 0.581632
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 888823 111 + 2685015/160-280
-AUAUAAGU---GUACCUAUA-AUCAAAAGUUAA-AUAUGAG-AGCUUUUGUAGG--GCAAUUUAUUUCUUUGCAGACGAGGAGAAUAGUCAUCGAAAAUAUCGGCGGAUGCUAUUCCGG
-..((((((---...((((..-..((((((((..-.......-))))))))))))--...)))))).((((((....))))))((((((.((((.............))))))))))... ( -24.02)
>sy_au.0 600745 117 - 2809422/160-280
UAAAUAUUU---GUAUUUGAAGAUUAAAGGUUAAUAUAUGAGUGGCCUUUAUAGAGUGCAAUAUAUGUAUUUGUAGACGAGGAGGAUAGUGAUCGAAUAGAUCGGCGGAUGCUAUCCCGG
(((((((((---((((((......(((((((((.........)))))))))..)))))))).....)))))))........(.(((((((((((.....)))).......)))))))).. ( -25.31)
>sy_sa.0 759250 116 + 2516575/160-280
UGAAGAGGUUAUGUGUUUGUA-AUUUAAGGUUUA--UAACAGAAAUCUUAAUAGACACGAUAAUCGAAGUUUGUAGACGAGGAGGGUAGUUAUCGAAC-CAUCGGCGGAUGCUAUCCCGG
......((((((((((((((.-...((((((((.--......)))))))))))))))).))))))............((.(((.((((.(..((((..-..))))..).)))).))))). ( -29.20)
>consensus
UAAAUAAGU___GUAUUUGUA_AUUAAAGGUUAA_AUAUGAG_AGCCUUUAUAGA__GCAAUAUAUAUAUUUGUAGACGAGGAGGAUAGUCAUCGAAAACAUCGGCGGAUGCUAUCCCGG
...............((((.....(((((((((.........)))))))))))))..........................(.(((((((..((((.....)))).....)))))))).. (-16.92 = -13.50 +  -3.42)

alignment

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secondary structure

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dotplot

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Window 5

Location 888,823 – 888,943
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.24
Mean single sequence MFE -31.28
Consensus MFE -29.92
Energy contribution -28.49
Covariance contribution -1.43
Combinations/Pair 1.24
Mean z-score -2.29
Structure conservation index 0.96
SVM decision value 2.50
SVM RNA-class probability 0.994670
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 888823 120 + 2685015/240-360
GGAGAAUAGUCAUCGAAAAUAUCGGCGGAUGCUAUUCCGGAUGAGGCUCAUUCGUUAGCUUAUUAUUUAAAACAUUUAGGUAACUAAAUGCACAAAAAUAAUAAGAAUGCCUAAAAUUUA
((.((((((.((((.............))))))))))((((((.....))))))....((((((((((....(((((((....))))))).....))))))))))....))......... ( -28.82)
>sy_au.0 600745 118 - 2809422/240-360
GGAGGAUAGUGAUCGAAUAGAUCGGCGGAUGCUAUCCCGGAUGUGGCUCAUUCGUUAGCUUAUUAAGUAAAACAUUAGGGUGACUUAAUGGACAAAGUUAAUAAGAUCGCCAGAAAUU--
..........((((.....))))(((((..((((...((((((.....)))))).))))(((((((.(....(((((((....))))))).....).)))))))..))))).......-- ( -35.00)
>sy_sa.0 759250 117 + 2516575/240-360
GGAGGGUAGUUAUCGAAC-CAUCGGCGGAUGCUAUCCCGGAUGUGGCUCAUUCGUUAACUUAUUAAGGAAAACAUUAGGGUAACCUGGUGCACAAAGUUAAUAAGAUAGCCAAAAAUU--
(((.((((.(..((((..-..))))..).)))).))).(((((.....)))))((((.((((((((......(((((((....))))))).......)))))))).))))........-- ( -30.02)
>consensus
GGAGGAUAGUCAUCGAAAACAUCGGCGGAUGCUAUCCCGGAUGUGGCUCAUUCGUUAGCUUAUUAAGUAAAACAUUAGGGUAACUUAAUGCACAAAGUUAAUAAGAUAGCCAAAAAUU__
((.(((((((..((((.....)))).....)))))))((((((.....))))))....((((((((......(((((((....))))))).......))))))))....))......... (-29.92 = -28.49 +  -1.43)

alignment

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secondary structure

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dotplot

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Window 6

Location 888,823 – 888,943
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.24
Mean single sequence MFE -24.24
Consensus MFE -20.11
Energy contribution -19.57
Covariance contribution -0.55
Combinations/Pair 1.19
Mean z-score -1.63
Structure conservation index 0.83
SVM decision value 0.35
SVM RNA-class probability 0.699599
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 888823 120 + 2685015/240-360
UAAAUUUUAGGCAUUCUUAUUAUUUUUGUGCAUUUAGUUACCUAAAUGUUUUAAAUAAUAAGCUAACGAAUGAGCCUCAUCCGGAAUAGCAUCCGCCGAUAUUUUCGAUGACUAUUCUCC
........((((...((((((((((....((((((((....))))))))...))))))))))(....).....)))).....(((((((((((....((.....)))))).))))))).. ( -28.90)
>sy_au.0 600745 118 - 2809422/240-360
--AAUUUCUGGCGAUCUUAUUAACUUUGUCCAUUAAGUCACCCUAAUGUUUUACUUAAUAAGCUAACGAAUGAGCCACAUCCGGGAUAGCAUCCGCCGAUCUAUUCGAUCACUAUCCUCC
--.......((((...(((((((....(..(((((........)))))..)...)))))))((((.((.(((.....))).))...))))...))))((((.....)))).......... ( -21.60)
>sy_sa.0 759250 117 + 2516575/240-360
--AAUUUUUGGCUAUCUUAUUAACUUUGUGCACCAGGUUACCCUAAUGUUUUCCUUAAUAAGUUAACGAAUGAGCCACAUCCGGGAUAGCAUCCGCCGAUG-GUUCGAUAACUACCCUCC
--......(((((...(..(((((((...(((..(((....)))..)))..........)))))))..)...))))).....(((.(((.(((.(((...)-))..)))..))))))... ( -22.22)
>consensus
__AAUUUUUGGCAAUCUUAUUAACUUUGUGCAUUAAGUUACCCUAAUGUUUUACUUAAUAAGCUAACGAAUGAGCCACAUCCGGGAUAGCAUCCGCCGAUAUAUUCGAUAACUAUCCUCC
........((((...((((((((......((((((((....)))))))).....))))))))(....).....)))).....(((((((.......(((.....)))....))))))).. (-20.11 = -19.57 +  -0.55) 
# Strand winner: forward (1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 888,823 – 888,943
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 81.74
Mean single sequence MFE -27.62
Consensus MFE -25.64
Energy contribution -24.65
Covariance contribution -0.99
Combinations/Pair 1.25
Mean z-score -2.42
Structure conservation index 0.93
SVM decision value 2.55
SVM RNA-class probability 0.995212
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 888823 120 + 2685015/253-373
CGAAAAUAUCGGCGGAUGCUAUUCCGGAUGAGGCUCAUUCGUUAGCUUAUUAUUUAAAACAUUUAGGUAACUAAAUGCACAAAAAUAAUAAGAAUGCCUAAAAUUUAUAAAAUCUUAGAA
..........((((...((((...((((((.....)))))).))))(((((((((....(((((((....))))))).....)))))))))...))))...................... ( -26.20)
>sy_au.0 600745 116 - 2809422/253-373
CGAAUAGAUCGGCGGAUGCUAUCCCGGAUGUGGCUCAUUCGUUAGCUUAUUAAGUAAAACAUUAGGGUGACUUAAUGGACAAAGUUAAUAAGAUCGCCAGAAAUU----GAAUAUAAAAA
..........(((((..((((...((((((.....)))))).))))(((((((.(....(((((((....))))))).....).)))))))..))))).......----........... ( -30.80)
>sy_sa.0 759250 115 + 2516575/253-373
CGAAC-CAUCGGCGGAUGCUAUCCCGGAUGUGGCUCAUUCGUUAACUUAUUAAGGAAAACAUUAGGGUAACCUGGUGCACAAAGUUAAUAAGAUAGCCAAAAAUU----AAAUAUAAAAA
.....-((((.(.((((...))))).))))(((((..((..(((((((...........(((((((....)))))))....)))))))..))..)))))......----........... ( -25.86)
>consensus
CGAAAACAUCGGCGGAUGCUAUCCCGGAUGUGGCUCAUUCGUUAGCUUAUUAAGUAAAACAUUAGGGUAACUUAAUGCACAAAGUUAAUAAGAUAGCCAAAAAUU____AAAUAUAAAAA
..........(((((((...))))((((((.....))))))....((((((((......(((((((....))))))).......))))))))...)))...................... (-25.64 = -24.65 +  -0.99)

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 18:52:09 2006