Locus 88

Sequence ID sy_ha.0
Location 1,799,678 – 1,799,759
Length 81
Max. P 0.998353
window434 window435 window436 window437

overview

Window 4

Location 1,799,678 – 1,799,759
Length 81
Sequences 5
Columns 81
Reading direction forward
Mean pairwise identity 67.37
Mean single sequence MFE -27.48
Consensus MFE -21.52
Energy contribution -18.80
Covariance contribution -2.72
Combinations/Pair 1.50
Mean z-score -2.98
Structure conservation index 0.78
SVM decision value 3.08
SVM RNA-class probability 0.998353
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799678 81 - 2685015
CUAAUAAGUGAGCCAUAGAGGAUUCGAACCUCUGACCCUCUGAUUAAAAGUCAGAUGCUCUACCAACUGAGCUAAUGGCUC
.........((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) ( -26.50)
>sy_sa.0 1767392 81 - 2516575
CUUAAGAGUGAGCCAUAGUGGGCUCGAACCACUGACCCUCUGAUUAAAAGUCAGAUGCUCUACCAACUGAGCUAAUGGCUC
.........((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) ( -27.60)
>sy_au.0 2227973 80 + 2809422
C-AAGUAGUGAGCCAUAGAGGAUUCGAACCUCUGACCCUCUGAUUAAAAGUCAGAUGCUCUACCAACUGAGCUAAUGGCUC
.-.......((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) ( -26.50)
>sp_ag.0 1366783 80 + 2160267
GGCCACGAUAGUCCGUACGGGAUUCGAACCCGUGUUACCGCCGUGAAAAGGCGG-UGUCUUAACCCCUUGACCAACGGACC
..........(((((((((((.......)))))..(((((((.......)))))-)).................)))))). ( -28.40)
>sp_pn.0 2033110 80 + 2038615
GGAUAAAAUAGUCCGUACGGGAUUCGAACCCGUGUUACCGCCGUGAAAAGGCGG-UGUCUUAACCCCUUGACCAACGGACC
..........(((((((((((.......)))))..(((((((.......)))))-)).................)))))). ( -28.40)
>consensus
CGAAAAAGUGAGCCAUAGAGGAUUCGAACCCCUGACCCUCUGAUUAAAAGUCAGAUGCUCUACCAACUGAGCUAAUGGCUC
.........((((((((((((.......))))).......................((((........))))..))))))) (-21.52 = -18.80 +  -2.72)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,799,678 – 1,799,759
Length 81
Sequences 5
Columns 81
Reading direction reverse
Mean pairwise identity 67.37
Mean single sequence MFE -29.94
Consensus MFE -24.64
Energy contribution -22.64
Covariance contribution -2.00
Combinations/Pair 1.43
Mean z-score -2.92
Structure conservation index 0.82
SVM decision value 2.92
SVM RNA-class probability 0.997749
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799678 81 - 2685015
GAGCCAUUAGCUCAGUUGGUAGAGCAUCUGACUUUUAAUCAGAGGGUCAGAGGUUCGAAUCCUCUAUGGCUCACUUAUUAG
(((((((......((..((..((((.((((((((((.....)))))))))).))))....)).)))))))))......... ( -28.70)
>sy_sa.0 1767392 81 - 2516575
GAGCCAUUAGCUCAGUUGGUAGAGCAUCUGACUUUUAAUCAGAGGGUCAGUGGUUCGAGCCCACUAUGGCUCACUCUUAAG
((((((...((((........))))..(((((((((.....)))))))))))))))(((((......)))))......... ( -31.50)
>sy_au.0 2227973 80 + 2809422
GAGCCAUUAGCUCAGUUGGUAGAGCAUCUGACUUUUAAUCAGAGGGUCAGAGGUUCGAAUCCUCUAUGGCUCACUACUU-G
(((((((......((..((..((((.((((((((((.....)))))))))).))))....)).))))))))).......-. ( -28.70)
>sp_ag.0 1366783 80 + 2160267
GGUCCGUUGGUCAAGGGGUUAAGACA-CCGCCUUUUCACGGCGGUAACACGGGUUCGAAUCCCGUACGGACUAUCGUGGCC
((((((.(((((..((((((..((((-(((((.......)))))).......)))..)))))).....))))).)).)))) ( -32.01)
>sp_pn.0 2033110 80 + 2038615
GGUCCGUUGGUCAAGGGGUUAAGACA-CCGCCUUUUCACGGCGGUAACACGGGUUCGAAUCCCGUACGGACUAUUUUAUCC
(((((((..(((..........)))(-(((((.......))))))...(((((.......))))))))))))......... ( -28.80)
>consensus
GAGCCAUUAGCUCAGUUGGUAGAGCAUCUGACUUUUAAUCAGAGGGUCAGAGGUUCGAAUCCCCUAUGGCUCACUUUUUAG
(((((((..((((........))))....(((((((.....)))))))(((((.......))))))))))))......... (-24.64 = -22.64 +  -2.00) 
# Strand winner: reverse (0.98)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,799,678 – 1,799,759
Length 81
Sequences 5
Columns 81
Reading direction forward
Mean pairwise identity 67.37
Mean single sequence MFE -27.48
Consensus MFE -21.52
Energy contribution -18.80
Covariance contribution -2.72
Combinations/Pair 1.50
Mean z-score -2.98
Structure conservation index 0.78
SVM decision value 3.08
SVM RNA-class probability 0.998353
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799678 81 - 2685015/0-81
CUAAUAAGUGAGCCAUAGAGGAUUCGAACCUCUGACCCUCUGAUUAAAAGUCAGAUGCUCUACCAACUGAGCUAAUGGCUC
.........((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) ( -26.50)
>sy_sa.0 1767392 81 - 2516575/0-81
CUUAAGAGUGAGCCAUAGUGGGCUCGAACCACUGACCCUCUGAUUAAAAGUCAGAUGCUCUACCAACUGAGCUAAUGGCUC
.........((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) ( -27.60)
>sy_au.0 2227973 80 + 2809422/0-81
C-AAGUAGUGAGCCAUAGAGGAUUCGAACCUCUGACCCUCUGAUUAAAAGUCAGAUGCUCUACCAACUGAGCUAAUGGCUC
.-.......((((((((((((.......))))).....((((((.....)))))).((((........))))..))))))) ( -26.50)
>sp_ag.0 1366783 80 + 2160267/0-81
GGCCACGAUAGUCCGUACGGGAUUCGAACCCGUGUUACCGCCGUGAAAAGGCGG-UGUCUUAACCCCUUGACCAACGGACC
..........(((((((((((.......)))))..(((((((.......)))))-)).................)))))). ( -28.40)
>sp_pn.0 2033110 80 + 2038615/0-81
GGAUAAAAUAGUCCGUACGGGAUUCGAACCCGUGUUACCGCCGUGAAAAGGCGG-UGUCUUAACCCCUUGACCAACGGACC
..........(((((((((((.......)))))..(((((((.......)))))-)).................)))))). ( -28.40)
>consensus
CGAAAAAGUGAGCCAUAGAGGAUUCGAACCCCUGACCCUCUGAUUAAAAGUCAGAUGCUCUACCAACUGAGCUAAUGGCUC
.........((((((((((((.......))))).......................((((........))))..))))))) (-21.52 = -18.80 +  -2.72)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,799,678 – 1,799,759
Length 81
Sequences 5
Columns 81
Reading direction reverse
Mean pairwise identity 67.37
Mean single sequence MFE -29.94
Consensus MFE -24.64
Energy contribution -22.64
Covariance contribution -2.00
Combinations/Pair 1.43
Mean z-score -2.92
Structure conservation index 0.82
SVM decision value 2.92
SVM RNA-class probability 0.997749
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799678 81 - 2685015/0-81
GAGCCAUUAGCUCAGUUGGUAGAGCAUCUGACUUUUAAUCAGAGGGUCAGAGGUUCGAAUCCUCUAUGGCUCACUUAUUAG
(((((((......((..((..((((.((((((((((.....)))))))))).))))....)).)))))))))......... ( -28.70)
>sy_sa.0 1767392 81 - 2516575/0-81
GAGCCAUUAGCUCAGUUGGUAGAGCAUCUGACUUUUAAUCAGAGGGUCAGUGGUUCGAGCCCACUAUGGCUCACUCUUAAG
((((((...((((........))))..(((((((((.....)))))))))))))))(((((......)))))......... ( -31.50)
>sy_au.0 2227973 80 + 2809422/0-81
GAGCCAUUAGCUCAGUUGGUAGAGCAUCUGACUUUUAAUCAGAGGGUCAGAGGUUCGAAUCCUCUAUGGCUCACUACUU-G
(((((((......((..((..((((.((((((((((.....)))))))))).))))....)).))))))))).......-. ( -28.70)
>sp_ag.0 1366783 80 + 2160267/0-81
GGUCCGUUGGUCAAGGGGUUAAGACA-CCGCCUUUUCACGGCGGUAACACGGGUUCGAAUCCCGUACGGACUAUCGUGGCC
((((((.(((((..((((((..((((-(((((.......)))))).......)))..)))))).....))))).)).)))) ( -32.01)
>sp_pn.0 2033110 80 + 2038615/0-81
GGUCCGUUGGUCAAGGGGUUAAGACA-CCGCCUUUUCACGGCGGUAACACGGGUUCGAAUCCCGUACGGACUAUUUUAUCC
(((((((..(((..........)))(-(((((.......))))))...(((((.......))))))))))))......... ( -28.80)
>consensus
GAGCCAUUAGCUCAGUUGGUAGAGCAUCUGACUUUUAAUCAGAGGGUCAGAGGUUCGAAUCCCCUAUGGCUCACUUUUUAG
(((((((..((((........))))....(((((((.....)))))))(((((.......))))))))))))......... (-24.64 = -22.64 +  -2.00) 
# Strand winner: reverse (0.98)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:56:38 2006