Locus 37

Sequence ID pao_1
Location 3,173,755 – 3,173,916
Length 161
Max. P 0.999959
window106 window107 window108 window109 window110 window111

overview

Window 6

Location 3,173,755 – 3,173,873
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 96.14
Mean single sequence MFE -42.82
Consensus MFE -42.10
Energy contribution -42.10
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.41
Structure conservation index 0.98
SVM decision value 2.44
SVM RNA-class probability 0.993997
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 3173755 118 + 1
GAAUUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAA--UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCG
......((.(((((((..(((.......)))(((((((((....)))...))))))((((........))))..)))))))..--(((.(((((....))))))))...........)). ( -42.20)
>pst_1 1 120 + 1
GAAUAUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAUAUGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCG
.((((.((.(((((((..(((.......)))(((((((((....)))...))))))((((........))))..)))))))....(((.(((((....))))))))...)).)))).... ( -43.10)
>pel_1 1 114 + 1
-----UGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAA-AUGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCG
-----.((.(((((((..(((.......)))(((((((((....)))...))))))((((........))))..)))))))..-.(((.(((((....))))))))...........)). ( -42.20)
>pf5_1 1 119 + 1
GAAUUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAA-UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCG
......((.(((((((..(((.......)))(((((((((....)))...))))))((((........))))..)))))))...-(((.(((((....))))))))...........)). ( -42.20)
>pfs_1 1 119 + 1
GAAUAUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAA-AUGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCG
.((((.((.(((((((..(((.......)))(((((((((....)))...))))))((((........))))..)))))))..-.(((.(((((....))))))))...)).)))).... ( -43.10)
>ppk_1 1 114 + 1
-----UGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAUU-UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCG
-----.((.(((((((..(((.......)))(((((((((....)))...))))))((((........))))..))))))).((-(((.(((((....)))))))))).........)). ( -44.10)
>consensus
GAAU_UGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAA__UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCG
......((.(((((((..(((.......)))(((((((((....)))...))))))((((........))))..)))))))......(.(((((....))))).)............)). (-42.10 = -42.10 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,173,755 – 3,173,873
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.14
Mean single sequence MFE -47.50
Consensus MFE -47.50
Energy contribution -47.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.22
Structure conservation index 1.00
SVM decision value 2.14
SVM RNA-class probability 0.988917
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 3173755 118 - 1
CGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCA--UUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAAUUC
........(((((....(((((....)))))))).--..(((((((..((((........))))..((((((((....).)))))))(((((.......)))))))))))).))...... ( -47.50)
>pst_1 1 120 - 1
CGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCAUAUUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAUAUUC
........(((((....(((((....)))))))).....(((((((..((((........))))..((((((((....).)))))))(((((.......)))))))))))).))...... ( -47.50)
>pel_1 1 114 - 1
CGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCAU-UUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCA-----
........(((((....(((((....))))))))..-..(((((((..((((........))))..((((((((....).)))))))(((((.......)))))))))))).)).----- ( -47.50)
>pf5_1 1 119 - 1
CGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCA-UUUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAAUUC
........(((((....(((((....)))))))).-...(((((((..((((........))))..((((((((....).)))))))(((((.......)))))))))))).))...... ( -47.50)
>pfs_1 1 119 - 1
CGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCAU-UUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAUAUUC
........(((((....(((((....))))))))..-..(((((((..((((........))))..((((((((....).)))))))(((((.......)))))))))))).))...... ( -47.50)
>ppk_1 1 114 - 1
CGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCA-AAUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCA-----
........(((((....(((((....)))))))).-...(((((((..((((........))))..((((((((....).)))))))(((((.......)))))))))))).)).----- ( -47.50)
>consensus
CGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCA__UUGCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCA_AUUC
........(((((....(((((....)))))))).....(((((((..((((........))))..((((((((....).)))))))(((((.......)))))))))))).))...... (-47.50 = -47.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,173,795 – 3,173,913
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 98.72
Mean single sequence MFE -46.02
Consensus MFE -45.50
Energy contribution -45.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.31
Structure conservation index 0.99
SVM decision value 2.10
SVM RNA-class probability 0.987995
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 3173795 118 + 1
ACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAA--UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGA
.((...((..((....((((........))))....)).))..--.)).(((((....))))).....(((((...((((((.......))))))(((.(((....))))))..))))). ( -46.80)
>pst_1 41 120 + 1
ACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAUAUGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGA
.((...((..((....((((........))))....)).)).....)).(((((....))))).....(((((...((((((.......))))))(((.(((....))))))..))))). ( -45.50)
>pf5_1 41 119 + 1
ACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAA-UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGA
.((...((..((....((((........))))....)).))...-.)).(((((....))))).....(((((...((((((.......))))))(((.(((....))))))..))))). ( -46.10)
>ppk_1 36 119 + 1
ACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAUU-UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGA
......((..((....((((........))))....)).)).((-(((.(((((....))))))))))(((((...((((((.......))))))(((.(((....))))))..))))). ( -46.70)
>psp_1 41 120 + 1
ACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAUAUGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGA
.((...((..((....((((........))))....)).)).....)).(((((....))))).....(((((...((((((.......))))))(((.(((....))))))..))))). ( -45.50)
>pss_1 41 120 + 1
ACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAUAUGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGA
.((...((..((....((((........))))....)).)).....)).(((((....))))).....(((((...((((((.......))))))(((.(((....))))))..))))). ( -45.50)
>consensus
ACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAU_UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGA
.((...((..((....((((........))))....)).)).....)).(((((....))))).....(((((...((((((.......))))))(((.(((....))))))..))))). (-45.50 = -45.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,173,796 – 3,173,914
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 98.72
Mean single sequence MFE -46.02
Consensus MFE -45.50
Energy contribution -45.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.14
Structure conservation index 0.99
SVM decision value 1.60
SVM RNA-class probability 0.967020
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 3173796 118 + 1
CCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAA--UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGAC
((...((..((....((((........))))....)).))..--.)).((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..))))))) ( -46.80)
>pst_1 42 120 + 1
CCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAUAUGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGAC
((...((..((....((((........))))....)).)).....)).((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..))))))) ( -45.50)
>pf5_1 42 119 + 1
CCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAA-UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGAC
((...((..((....((((........))))....)).))...-.)).((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..))))))) ( -46.10)
>ppk_1 37 119 + 1
CCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAUU-UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGAC
.....((..((....((((........))))....)).)).((-(((.(((((....))))))))))(((((...((((((.......))))))(((.(((....))))))..))))).. ( -46.70)
>psp_1 42 120 + 1
CCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAUAUGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGAC
((...((..((....((((........))))....)).)).....)).((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..))))))) ( -45.50)
>pss_1 42 120 + 1
CCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAUAUGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGAC
((...((..((....((((........))))....)).)).....)).((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..))))))) ( -45.50)
>consensus
CCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGCAAU_UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGAC
((...((..((....((((........))))....)).)).....)).((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..))))))) (-45.50 = -45.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,173,838 – 3,173,916
Length 78
Sequences 6
Columns 78
Reading direction forward
Mean pairwise identity 98.88
Mean single sequence MFE -38.48
Consensus MFE -37.25
Energy contribution -37.42
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -3.01
Structure conservation index 0.97
SVM decision value 4.89
SVM RNA-class probability 0.999959
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 3173838 78 + 1
UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGACGC
..((((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..))))))))) ( -41.00)
>pau_1 1 77 + 1
UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGACG-
...(((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..))))))))- ( -37.80)
>pel_1 1 77 + 1
UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGACG-
...(((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..))))))))- ( -37.80)
>pfs_1 1 76 + 1
UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGAC--
....((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..)))))))-- ( -35.50)
>ppk_1 1 77 + 1
UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGACG-
...(((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..))))))))- ( -37.80)
>pss_1 1 78 + 1
UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGACGC
..((((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..))))))))) ( -41.00)
>consensus
UGGCGUCCCCUAGGGGACUCGAACCCCUGUUACCGCCGUGAAAGGGCGGUGUCCUAGGCCACUAGACGAAGGGGACG_
...(((((((((((((.......)))))...((((((.......))))))(((.(((....))))))..)))))))). (-37.25 = -37.42 +   0.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,173,838 – 3,173,916
Length 78
Sequences 6
Columns 78
Reading direction reverse
Mean pairwise identity 98.88
Mean single sequence MFE -37.18
Consensus MFE -35.45
Energy contribution -35.62
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -3.04
Structure conservation index 0.95
SVM decision value 4.64
SVM RNA-class probability 0.999932
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 3173838 78 - 1
GCGUCCCCUUCGUCUAGUGGCCUAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCA
(((((((((..((((((....))).)))((((((.......))))))...(((((.......)))))))))))))).. ( -39.90)
>pau_1 1 77 - 1
-CGUCCCCUUCGUCUAGUGGCCUAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCA
-((((((((..((((((....))).)))((((((.......))))))...(((((.......)))))))))))))... ( -36.10)
>pel_1 1 77 - 1
-CGUCCCCUUCGUCUAGUGGCCUAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCA
-((((((((..((((((....))).)))((((((.......))))))...(((((.......)))))))))))))... ( -36.10)
>pfs_1 1 76 - 1
--GUCCCCUUCGUCUAGUGGCCUAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCA
--(((((((..((((((....))).)))((((((.......))))))...(((((.......)))))))))))).... ( -35.00)
>ppk_1 1 77 - 1
-CGUCCCCUUCGUCUAGUGGCCUAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCA
-((((((((..((((((....))).)))((((((.......))))))...(((((.......)))))))))))))... ( -36.10)
>pss_1 1 78 - 1
GCGUCCCCUUCGUCUAGUGGCCUAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCA
(((((((((..((((((....))).)))((((((.......))))))...(((((.......)))))))))))))).. ( -39.90)
>consensus
_CGUCCCCUUCGUCUAGUGGCCUAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAGUCCCCUAGGGGACGCCA
.((((((((..((((((....))).)))((((((.......))))))...(((((.......)))))))))))))... (-35.45 = -35.62 +   0.17)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:47:54 2007