Locus 41

Sequence ID sy_ha.0
Location 1,337,670 – 1,337,789
Length 119
Max. P 0.999967
window196 window197 window198 window199

overview

Window 6

Location 1,337,670 – 1,337,789
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 71.39
Mean single sequence MFE -21.90
Consensus MFE -18.97
Energy contribution -16.43
Covariance contribution -2.53
Combinations/Pair 1.55
Mean z-score -0.84
Structure conservation index 0.87
SVM decision value 1.37
SVM RNA-class probability 0.947128
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1337670 119 + 2685015/0-120
GAAAAUACUUAAAAUAAUCUUAAGUUCGCAUGAAGAUGAGUAGGCAAUUAUUACUUAUAUAGAGAUGUACUGGUUGGUGAAAAGUGCAAUGUAUAUUGUUGAACGCUACUUCAUGU-CAU
......((((((.......))))))..((((((((.(((((((.......)))))))((((.(..((((((...........)))))).).)))).............))))))))-... ( -22.50)
>sy_au.0 1107241 120 - 2809422/0-120
AAAUGUAACUAAAAUAGAAUUAAAUUCGUAUAAAGAUGAGUAGUUAAUGAUUUGUUUAUCAGAGAUGUACUGGUUGGUGAAAAGUACAACAAACAUUAGUGAACGCUACUUUAUGCACAA
...(((..........((((...))))((((((((...(((...(((((.(((((..........((((((...........))))))))))))))))(....)))).))))))))))). ( -19.80)
>sy_sa.0 1191327 119 + 2516575/0-120
GAAAAUAAAUACAAUAUAAUUAACUUCACAUAAAGAUGAGUAAAUUAU-ACUGAGCGAAAAGAGAUGUACUGGUUGGUGAAAAGUACAGUCGGUAUAGUUGAAUGCUACUUUGUGUCAGC
...........................((((((((...((((((((((-(((((.(.....)...((((((...........)))))).)))))))))))...)))).)))))))).... ( -23.40)
>consensus
GAAAAUAAAUAAAAUAAAAUUAAAUUCGCAUAAAGAUGAGUAGAUAAU_AUUAAUUAAAAAGAGAUGUACUGGUUGGUGAAAAGUACAAUAAAUAUUGUUGAACGCUACUUUAUGU_CAA
...........................((((((((...(((.((((((.((((((..........((((((...........))))))))))))))))))....))).)))))))).... (-18.97 = -16.43 +  -2.53)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,337,670 – 1,337,766
Length 96
Sequences 2
Columns 120
Reading direction forward
Mean pairwise identity 56.67
Mean single sequence MFE -26.41
Consensus MFE -17.10
Energy contribution -16.60
Covariance contribution -0.50
Combinations/Pair 1.13
Mean z-score -1.47
Structure conservation index 0.65
SVM decision value 0.74
SVM RNA-class probability 0.838545
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1337670 96 + 2685015/160-280
--------UCUAUCAAGCGAU------AAUUUUUGCAGCUUAAAGAUAGAU----------UGUUUAUAACUAGGGUGGUACCGCGAAAACGUUCGUCCCUUUUUUUGAGGAUGAACGUU
--------((((((((((...------..........))))...)))))).----------..............(((....)))...((((((((((((.......).))))))))))) ( -25.32)
>sy_sa.0 1191327 117 + 2516575/160-280
AAUUAAAGUCAGUCGUUUGAUCUGUGUGAUACUUACAAUUAAGAUUGAAUUAAUUUGUUAACACUUAUAACUAGGGUGGUACCGCGA-AACGUUCGUCCCUUUAU--GAGGAUGGGCGUU
............(((((..((((.(((((...)))))....))))..).............(((((.......))))).....))))-((((((((((((.....--).))))))))))) ( -27.50)
>consensus
________UCAAUCAAGCGAU______AAUACUUACAACUAAAAGAGAAAU__________CACUUAUAACUAGGGUGGUACCGCGA_AACGUUCGUCCCUUUAU__GAGGAUGAACGUU
...........................................................................(((....)))...((((((((((((.......).))))))))))) (-17.10 = -16.60 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,337,670 – 1,337,775
Length 105
Sequences 2
Columns 118
Reading direction forward
Mean pairwise identity 64.41
Mean single sequence MFE -27.25
Consensus MFE -21.95
Energy contribution -21.70
Covariance contribution -0.25
Combinations/Pair 1.22
Mean z-score -2.62
Structure conservation index 0.81
SVM decision value 4.99
SVM RNA-class probability 0.999967
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1337670 105 + 2685015/184-304
---AAUUUUUGCAGCUUAAAGAUAGAU----------UGUUUAUAACUAGGGUGGUACCGCGAAAACGUUCGUCCCUUUUUUUGAGGAUGAACGUUUUUUUGUUUUUAGUUAAAAUAU
---.(((((((.....)))))))....----------(((((.(((((((((((....)))(((((((((((((((.......).)))))))))))))).....))))))))))))). ( -28.30)
>sy_sa.0 1191327 115 + 2516575/184-304
UGUGAUACUUACAAUUAAGAUUGAAUUAAUUUGUUAACACUUAUAACUAGGGUGGUACCGCGA-AACGUUCGUCCCUUUAU--GAGGAUGGGCGUUUUUUAUUUUCUUUUUUAAUUAU
............((((((((..(((............(((((.......))))).......((-((((((((((((.....--).))))))))))))).....)))..)))))))).. ( -26.20)
>consensus
___AAUACUUACAACUAAAAGAGAAAU__________CACUUAUAACUAGGGUGGUACCGCGA_AACGUUCGUCCCUUUAU__GAGGAUGAACGUUUUUUAGUUUCUAGUUAAAAUAU
................(((((((((..........................(((....)))(((((((((((((((.......).))))))))))))))))))))))).......... (-21.95 = -21.70 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,337,670 – 1,337,775
Length 105
Sequences 2
Columns 118
Reading direction reverse
Mean pairwise identity 64.41
Mean single sequence MFE -16.57
Consensus MFE -11.15
Energy contribution -11.65
Covariance contribution 0.50
Combinations/Pair 1.11
Mean z-score -1.76
Structure conservation index 0.67
SVM decision value 1.30
SVM RNA-class probability 0.939664
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1337670 105 + 2685015/184-304
AUAUUUUAACUAAAAACAAAAAAACGUUCAUCCUCAAAAAAAGGGACGAACGUUUUCGCGGUACCACCCUAGUUAUAAACA----------AUCUAUCUUUAAGCUGCAAAAAUU---
....................(((((((((.((((........)))).))))))))).(((((.......(((.........----------..))).......))))).......--- ( -19.44)
>sy_sa.0 1191327 115 + 2516575/184-304
AUAAUUAAAAAAGAAAAUAAAAAACGCCCAUCCUC--AUAAAGGGACGAACGUU-UCGCGGUACCACCCUAGUUAUAAGUGUUAACAAAUUAAUUCAAUCUUAAUUGUAAGUAUCACA
(((((((..............(((((..(.((((.--.....)))).)..))))-)...((.....)).)))))))..(((.((...((((((.......)))))).....)).))). ( -13.70)
>consensus
AUAAUUAAAAAAAAAAAAAAAAAACGCCCAUCCUC__AAAAAGGGACGAACGUU_UCGCGGUACCACCCUAGUUAUAAACA__________AACUAAAUCUAAACUGCAAAAAUC___
..........((((......(((((((((.((((........)))).)))))))))...((.....))..............................))))................ (-11.15 = -11.65 +   0.50) 
# Strand winner: forward (1.00)

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 18:53:21 2006