Locus 74

Sequence ID pao_1
Location 5,086,925 – 5,087,089
Length 164
Max. P 0.999449
window253 window254 window255 window256 window257

overview

Window 3

Location 5,086,925 – 5,087,045
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.39
Mean single sequence MFE -39.77
Consensus MFE -39.00
Energy contribution -38.33
Covariance contribution -0.66
Combinations/Pair 1.10
Mean z-score -2.01
Structure conservation index 0.98
SVM decision value 3.61
SVM RNA-class probability 0.999449
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 5086925 120 + 1
AUGGUGGGUCGUGUAGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCGACUGAGCUAACGACCCAAGUAUGAGGUGGUCGGGGUAGAGAGAUUCGAACUCCCGACAU
....(((((((((((((.......)))))......(((((.....)))))..((((........))))..))))))))...........((((((((.(((...)))..)).)))))).. ( -41.30)
>pau_1 1 120 + 1
AUGGUGGGUCGUGUAGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCGACUGAGCUAACGACCCAAGUAUGAGGUGGUCGGGGUAGAGAGAUUCGAACUCCCGACAU
....(((((((((((((.......)))))......(((((.....)))))..((((........))))..))))))))...........((((((((.(((...)))..)).)))))).. ( -41.30)
>pel_1 1 116 + 1
AUGGUGGGUCGUGUAGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCGG----AAAAUGGUCGGGGUGAGGGGAUUCGAACUCCUGACAU
....(((((((((((((.......)))))......(((((.....)))))..((((........))))..)))))))).----......((((((((..((....))..)).)))))).. ( -39.30)
>pfo_1 1 115 + 1
AUGGUGGGUCGUGUGGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCA-----AAAAUGGUCGGGGUAAGGGGAUUCGAACUCCUGACAU
....(((((((((((((.......)))))......(((((.....)))))..((((........))))..))))))))-----......((((((((..((....))..)).)))))).. ( -38.70)
>pfs_1 1 115 + 1
AUGGUGGGUCGUGUGGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCA-----AAUAUGGUCGGGGUAAGGGGAUUCGAACUCCUGACAU
....(((((((((((((.......)))))......(((((.....)))))..((((........))))..))))))))-----......((((((((..((....))..)).)))))).. ( -38.70)
>ppk_1 1 116 + 1
AUGGUGGGUCGUGUAGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCGG----AAAAUGGUCGGGGUGAGGGGAUUCGAACUCCUGACAU
....(((((((((((((.......)))))......(((((.....)))))..((((........))))..)))))))).----......((((((((..((....))..)).)))))).. ( -39.30)
>consensus
AUGGUGGGUCGUGUAGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCA_____AAAAUGGUCGGGGUAAGGGGAUUCGAACUCCUGACAU
....(((((((((((((.......)))))......(((((.....)))))..((((........))))..))))))))...........((((((((............)).)))))).. (-39.00 = -38.33 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,086,925 – 5,087,045
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.39
Mean single sequence MFE -38.60
Consensus MFE -35.26
Energy contribution -35.70
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.46
Structure conservation index 0.91
SVM decision value 3.00
SVM RNA-class probability 0.998066
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 5086925 120 - 1
AUGUCGGGAGUUCGAAUCUCUCUACCCCGACCACCUCAUACUUGGGUCGUUAGCUCAGUCGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCUACACGACCCACCAU
..((((((.((..((.....)).))))))))...........((((((((..............((.(((((((.......))))))).))(((((.......))))))))))))).... ( -41.70)
>pau_1 1 120 - 1
AUGUCGGGAGUUCGAAUCUCUCUACCCCGACCACCUCAUACUUGGGUCGUUAGCUCAGUCGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCUACACGACCCACCAU
..((((((.((..((.....)).))))))))...........((((((((..............((.(((((((.......))))))).))(((((.......))))))))))))).... ( -41.70)
>pel_1 1 116 - 1
AUGUCAGGAGUUCGAAUCCCCUCACCCCGACCAUUUU----CCGGGUCGUUAGCUCAGUUGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCUACACGACCCACCAU
..(((.((.((..((......)))))).)))......----..(((((((..(..(((((((((((((.....)))))..))))))))..)(((((.......))))))))))))..... ( -38.20)
>pfo_1 1 115 - 1
AUGUCAGGAGUUCGAAUCCCCUUACCCCGACCAUUUU-----UGGGUCGUUAGCUCAGUUGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCCACACGACCCACCAU
..(((.((..((((((((..(......(((((.....-----..)))))...(..(((((((((((((.....)))))..))))))))..))..))))))))..))....)))....... ( -35.90)
>pfs_1 1 115 - 1
AUGUCAGGAGUUCGAAUCCCCUUACCCCGACCAUAUU-----UGGGUCGUUAGCUCAGUUGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCCACACGACCCACCAU
..(((.((..((((((((..(......(((((.....-----..)))))...(..(((((((((((((.....)))))..))))))))..))..))))))))..))....)))....... ( -35.90)
>ppk_1 1 116 - 1
AUGUCAGGAGUUCGAAUCCCCUCACCCCGACCAUUUU----CCGGGUCGUUAGCUCAGUUGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCUACACGACCCACCAU
..(((.((.((..((......)))))).)))......----..(((((((..(..(((((((((((((.....)))))..))))))))..)(((((.......))))))))))))..... ( -38.20)
>consensus
AUGUCAGGAGUUCGAAUCCCCUUACCCCGACCAUUUU_____UGGGUCGUUAGCUCAGUUGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCUACACGACCCACCAU
..(((.((.((..(......)..)))).)))............(((((((..(..(((((((((((((.....)))))..))))))))..)(((((.......))))))))))))..... (-35.26 = -35.70 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 5,086,965 – 5,087,085
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.39
Mean single sequence MFE -36.30
Consensus MFE -34.13
Energy contribution -33.80
Covariance contribution -0.33
Combinations/Pair 1.07
Mean z-score -1.02
Structure conservation index 0.94
SVM decision value 0.29
SVM RNA-class probability 0.670396
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 5086965 120 + 1
UAAAAGCCAACUGCUCUACCGACUGAGCUAACGACCCAAGUAUGAGGUGGUCGGGGUAGAGAGAUUCGAACUCCCGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUAC
.....(((....((((........))))..((.(((((....)).))).)).(((((((.((...(((......)))..)))))).)))......)))((((.........))))..... ( -36.10)
>pau_1 41 120 + 1
UAAAAGCCAACUGCUCUACCGACUGAGCUAACGACCCAAGUAUGAGGUGGUCGGGGUAGAGAGAUUCGAACUCCCGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUAC
.....(((....((((........))))..((.(((((....)).))).)).(((((((.((...(((......)))..)))))).)))......)))((((.........))))..... ( -36.10)
>pel_1 41 116 + 1
UAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCGG----AAAAUGGUCGGGGUGAGGGGAUUCGAACUCCUGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUACAC
......((....((((........))))...(((((...----.....)))))))((.(((((.......))))).))..((((((.....)))))).((((.........))))..... ( -37.60)
>pfo_1 41 115 + 1
UAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCA-----AAAAUGGUCGGGGUAAGGGGAUUCGAACUCCUGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUAC
......((....((((........))))...(((((..-----.....)))))))((.(((((.......))))).))..((((((.....)))))).((((.........))))..... ( -35.20)
>pfs_1 41 115 + 1
UAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCA-----AAUAUGGUCGGGGUAAGGGGAUUCGAACUCCUGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUAC
......((....((((........))))...(((((..-----.....)))))))((.(((((.......))))).))..((((((.....)))))).((((.........))))..... ( -35.20)
>ppk_1 41 116 + 1
UAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCGG----AAAAUGGUCGGGGUGAGGGGAUUCGAACUCCUGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUACAC
......((....((((........))))...(((((...----.....)))))))((.(((((.......))))).))..((((((.....)))))).((((.........))))..... ( -37.60)
>consensus
UAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCA_____AAAAUGGUCGGGGUAAGGGGAUUCGAACUCCUGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUAC
......((....((((........))))...(((((............)))))))((.(((((.......))))).))..((((((.....)))))).((((.........))))..... (-34.13 = -33.80 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 5,087,012 – 5,087,089
Length 77
Sequences 6
Columns 77
Reading direction forward
Mean pairwise identity 97.75
Mean single sequence MFE -30.47
Consensus MFE -30.93
Energy contribution -30.52
Covariance contribution -0.42
Combinations/Pair 1.09
Mean z-score -1.55
Structure conservation index 1.02
SVM decision value 3.27
SVM RNA-class probability 0.998901
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 5087012 77 + 1
UGGUCGGGGUAGAGAGAUUCGAACUCCCGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUACCCCG
....((((((((.(((.......))).).....((((((.....)))))).((((.........))))..))))))) ( -27.20)
>pf5_1 1 77 + 1
UGGUCGGGGUAAGGGGAUUCGAACUCCUGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUACCCCG
....((((((((((((.......))))).....((((((.....)))))).((((.........))))..))))))) ( -30.60)
>pfo_1 1 77 + 1
UGGUCGGGGUAGGGGGAUUCGAACUCCCGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUACCCCG
....((((((((((((.......))))).....((((((.....)))))).((((.........))))..))))))) ( -33.20)
>psp_1 1 77 + 1
UGGUCGGGGUAAGGGGAUUCGAACUCCUGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUACCCCG
....((((((((((((.......))))).....((((((.....)))))).((((.........))))..))))))) ( -30.60)
>pss_1 1 77 + 1
UGGUCGGGGUAAGGGGAUUCGAACUCCUGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUACCCCG
....((((((((((((.......))))).....((((((.....)))))).((((.........))))..))))))) ( -30.60)
>pst_1 1 77 + 1
UGGUCGGGGUAAGGGGAUUCGAACUCCUGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUACCCCG
....((((((((((((.......))))).....((((((.....)))))).((((.........))))..))))))) ( -30.60)
>consensus
UGGUCGGGGUAAGGGGAUUCGAACUCCUGACAUCCUGCUCCCAAAGCAGGCGCGCUACCGGACUGCGCUAUACCCCG
....((((((((((((.......))))).....((((((.....)))))).((((.........))))..))))))) (-30.93 = -30.52 +  -0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 5,087,012 – 5,087,089
Length 77
Sequences 6
Columns 77
Reading direction reverse
Mean pairwise identity 97.75
Mean single sequence MFE -30.78
Consensus MFE -29.41
Energy contribution -29.27
Covariance contribution -0.14
Combinations/Pair 1.05
Mean z-score -1.13
Structure conservation index 0.96
SVM decision value 1.07
SVM RNA-class probability 0.910954
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 5087012 77 - 1
CGGGGUAUAGCGCAGUCCGGUAGCGCGCCUGCUUUGGGAGCAGGAUGUCGGGAGUUCGAAUCUCUCUACCCCGACCA
(((((((..((((.........)))).(((((((...))))))).....(((((.......)))))))))))).... ( -32.90)
>pf5_1 1 77 - 1
CGGGGUAUAGCGCAGUCCGGUAGCGCGCCUGCUUUGGGAGCAGGAUGUCAGGAGUUCGAAUCCCCUUACCCCGACCA
(((((((..((((.........)))).(((((((...)))))))......(((.......)))...))))))).... ( -29.70)
>pfo_1 1 77 - 1
CGGGGUAUAGCGCAGUCCGGUAGCGCGCCUGCUUUGGGAGCAGGAUGUCGGGAGUUCGAAUCCCCCUACCCCGACCA
(((((((..((((.........)))).(((((((...))))))).....((((.......))))..))))))).... ( -33.00)
>psp_1 1 77 - 1
CGGGGUAUAGCGCAGUCCGGUAGCGCGCCUGCUUUGGGAGCAGGAUGUCAGGAGUUCGAAUCCCCUUACCCCGACCA
(((((((..((((.........)))).(((((((...)))))))......(((.......)))...))))))).... ( -29.70)
>pss_1 1 77 - 1
CGGGGUAUAGCGCAGUCCGGUAGCGCGCCUGCUUUGGGAGCAGGAUGUCAGGAGUUCGAAUCCCCUUACCCCGACCA
(((((((..((((.........)))).(((((((...)))))))......(((.......)))...))))))).... ( -29.70)
>pst_1 1 77 - 1
CGGGGUAUAGCGCAGUCCGGUAGCGCGCCUGCUUUGGGAGCAGGAUGUCAGGAGUUCGAAUCCCCUUACCCCGACCA
(((((((..((((.........)))).(((((((...)))))))......(((.......)))...))))))).... ( -29.70)
>consensus
CGGGGUAUAGCGCAGUCCGGUAGCGCGCCUGCUUUGGGAGCAGGAUGUCAGGAGUUCGAAUCCCCUUACCCCGACCA
(((((((..((((.........)))).(((((((...)))))))......(((.......)))...))))))).... (-29.41 = -29.27 +  -0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:51:08 2007