Locus 66

Sequence ID pao_1
Location 4,791,492 – 4,791,772
Length 280
Max. P 0.999999
window206 window207 window208 window209 window210

overview

Window 6

Location 4,791,492 – 4,791,612
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 93.67
Mean single sequence MFE -28.42
Consensus MFE -26.17
Energy contribution -24.12
Covariance contribution -2.05
Combinations/Pair 1.19
Mean z-score -1.01
Structure conservation index 0.92
SVM decision value 0.07
SVM RNA-class probability 0.569769
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 4791492 120 + 1
AUCUCGGUUGAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUGCACCUAUGGAUUCAGUACAAGAUACCUAGGUUAUCCUAGGUGGGUUCCCCCAUUCAG
((((.(..(((.(((......((((((.(((..((....)))))..))))))...((.....))......))).)))...).))))(((((((....)))))))(((....)))...... ( -29.30)
>pel_1 2679 120 + 1
AUCUCGGUUGAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUGCACCUAUGUAUUCAGUACAAGAUACUCAGCUUAUGCUGAGUGGGUUCCCCCAUUCAG
.....((((((..((((...((..((((((.(((..(..((((.....))))..)((.....))..))).))))))))...))))...))))))....(((((((((....))))))))) ( -30.40)
>pfs_1 2678 120 + 1
AUCUCGGUUGAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUAAGCCUAUGUAUUCAGCUUAAGAUAACCAUCUUAUGAUGGCUGGGUUCCCCCAUUCAG
.....(((((...........((((((.(((..((....)))))..))))))......((((((((...........))))))))))))).........((..((((....))))..)). ( -28.70)
>ppk_1 2679 120 + 1
AUCUCGGUUGAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUGCACCUAUGUAUUCAGUACAAGAUAACCAGCUUGUGCUGGCUGGGUUCCCCCAUUCAG
.....(((.............((((((.(((..((....)))))..))))))...((.....))))).......((((((((((........)))))))))).((((....))))..... ( -28.50)
>pss_1 2677 120 + 1
AUCUCGGUUGAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUGCACCUAUGUAUUCAGUACAAGAUAACCAUCUUAUGAUGGCUGGGUUCCCCCAUUCAG
((((.(((.............((((((.(((..((....)))))..))))))...((.....)))))..(((((...)))))))))..(((((....))))).((((....))))..... ( -24.80)
>pst_1 2677 120 + 1
AUCUCGGUUGAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUACACCUAUGUAUUCAGUGUAAGAUAACCAUCUUAUGAUGGCUGGGUUCCCCCAUUCAG
.....(((((...........((((((.(((..((....)))))..))))))......((((((((...........))))))))))))).........((..((((....))))..)). ( -28.80)
>consensus
AUCUCGGUUGAUUUCUUUUCCUCAGGGUACUUAGAUGUUUCAGUUCCCCUGGUUCGCCUCUUGCACCUAUGUAUUCAGUACAAGAUAACCAGCUUAUGAUGGCUGGGUUCCCCCAUUCAG
.....(((.(((..........(((((.(((..((....)))))..)))))))).)))(((((.((...........)).)))))...(((((....))))).((((....))))..... (-26.17 = -24.12 +  -2.05)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,791,492 – 4,791,612
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 93.67
Mean single sequence MFE -36.62
Consensus MFE -39.50
Energy contribution -36.62
Covariance contribution -2.88
Combinations/Pair 1.27
Mean z-score -3.17
Structure conservation index 1.08
SVM decision value 6.85
SVM RNA-class probability 0.999999
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 4791492 120 - 1
CUGAAUGGGGGAACCCACCUAGGAUAACCUAGGUAUCUUGUACUGAAUCCAUAGGUGCAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUCAACCGAGAU
.....(((..((.((((((((((....))))))).(((((((((.........))))))))))).)..((.((((.(((..........))).))))..))........))..))).... ( -37.50)
>pel_1 2679 120 - 1
CUGAAUGGGGGAACCCACUCAGCAUAAGCUGAGUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUCAACCGAGAU
.....(((..((.((((((((((....))))))).(((((((((.........))))))))))).)..((.((((.(((..........))).))))..))........))..))).... ( -37.90)
>pfs_1 2678 120 - 1
CUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUAAGCUGAAUACAUAGGCUUAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUCAACCGAGAU
.....(((..((.((((((((((....))))))).(((((((((.........))))))))))).)..((.((((.(((..........))).))))..))........))..))).... ( -35.50)
>ppk_1 2679 120 - 1
CUGAAUGGGGGAACCCAGCCAGCACAAGCUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUCAACCGAGAU
.....(((..((.((((((((((....))))))).(((((((((.........))))))))))).)..((.((((.(((..........))).))))..))........))..))).... ( -37.60)
>pss_1 2677 120 - 1
CUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUCAACCGAGAU
.....(((..((.((((((((((....))))))).(((((((((.........))))))))))).)..((.((((.(((..........))).))))..))........))..))).... ( -35.60)
>pst_1 2677 120 - 1
CUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUACACUGAAUACAUAGGUGUAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUCAACCGAGAU
.....(((..((.((((((((((....))))))).(((((((((.........))))))))))).)..((.((((.(((..........))).))))..))........))..))).... ( -35.60)
>consensus
CUGAAUGGGGGAACCCAGCCAGCAUAAGAUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUGAAACAUCUAAGUACCCUGAGGAAAAGAAAUCAACCGAGAU
.....(((..((.((((((((((....))))))).(((((((((.........))))))))))).)..((.((((.(((..........))).))))..))........))..))).... (-39.50 = -36.62 +  -2.88)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,791,532 – 4,791,652
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 91.83
Mean single sequence MFE -44.80
Consensus MFE -47.11
Energy contribution -44.12
Covariance contribution -2.99
Combinations/Pair 1.28
Mean z-score -3.22
Structure conservation index 1.05
SVM decision value 6.33
SVM RNA-class probability 0.999998
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 4791532 120 - 1
GCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUCUCUGAAUGGGGGAACCCACCUAGGAUAACCUAGGUAUCUUGUACUGAAUCCAUAGGUGCAAGAGGCGAACCAGGGGAACUG
.((((((((((((........)))))...))))))).((((((...(((....)))(((((((....))))))).(((((((((.........))))))))).......))))))..... ( -47.30)
>pel_1 2719 120 - 1
GCUUUGGGGAGUCGGCAAACAGACUGUGAUCCAGAGAUCUCUGAAUGGGGGAACCCACUCAGCAUAAGCUGAGUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUG
.(((((((.((((........))))....))))))).((((((...(((....)))(((((((....))))))).(((((((((.........))))))))).......))))))..... ( -45.80)
>pf5_1 2715 120 - 1
GCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUCUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUG
.((((((((((((........)))))...))))))).((((((...(((....)))(((((((....))))))).(((((((((.........))))))))).......))))))..... ( -45.40)
>pfs_1 2718 120 - 1
GCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUGUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUAAGCUGAAUACAUAGGCUUAAGAGGCGAACCAGGGGAACUG
.((((((((((((........)))))...))))))).((((.....(((....)))(((((((....))))))).(((((((((.........)))))))))))))...(((.....))) ( -42.70)
>ppk_1 2719 120 - 1
GCUUUGGGGAGUCGGCAAACAGACUGUGAUCCAGAGAUCUCUGAAUGGGGGAACCCAGCCAGCACAAGCUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUG
.(((((((.((((........))))....))))))).((((((...(((....)))(((((((....))))))).(((((((((.........))))))))).......))))))..... ( -45.50)
>pst_1 2717 120 - 1
GCUUCGGGGAGUCGGCAAACAGACUGUGAUCCGGAGAUGUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUACACUGAAUACAUAGGUGUAAGAGGCGAACCAGGGGAACUG
.(((((((.((((........))))....))))))).((((.....(((....)))(((((((....))))))).(((((((((.........)))))))))))))...(((.....))) ( -42.10)
>consensus
GCUUCGGGGAGUCGGCAAACAGACUGUGAUCCGGAGAUCUCUGAAUGGGGGAACCCAGCCAGCAUAAGAUGGUUAUCUUGUACUGAAUACAUAGGUGCAAGAGGCGAACCAGGGGAACUG
.(((((((.((((........))))....))))))).((((((...(((....)))(((((((....))))))).(((((((((.........))))))))).......))))))..... (-47.11 = -44.12 +  -2.99)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,791,572 – 4,791,692
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 93.39
Mean single sequence MFE -40.82
Consensus MFE -42.02
Energy contribution -40.13
Covariance contribution -1.88
Combinations/Pair 1.19
Mean z-score -1.76
Structure conservation index 1.03
SVM decision value 4.01
SVM RNA-class probability 0.999756
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 4791572 120 - 1
GGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUCUCUGAAUGGGGGAACCCACCUAGGAUAACCUAGGUAUCUUG
.....(((((((..........((..(....)..)).....((((((((((((........)))))...))))))).)))))))..(((....)))(((((((....)))))))...... ( -43.30)
>pel_1 2759 120 - 1
GGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAUAAGCUUUGGGGAGUCGGCAAACAGACUGUGAUCCAGAGAUCUCUGAAUGGGGGAACCCACUCAGCAUAAGCUGAGUAUCUUG
.....(((((((..........((..(....)..)).....(((((((.((((........))))....))))))).)))))))..(((....)))(((((((....)))))))...... ( -41.80)
>pf5_1 2755 120 - 1
GGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAUAAGCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUCUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUG
(((..(((((((..........((..(....)..)).....((((((((((((........)))))...))))))).))))))).((((....)))))))....((((((....)))))) ( -41.60)
>pfs_1 2758 120 - 1
GGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUUUGAUCCGGAGAUGUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUA
(((..(((((.(..........((..(....)..)).....((((((((((((........)))))...))))))).).))))).((((....)))))))....((((((....)))))) ( -38.70)
>ppk_1 2759 120 - 1
GGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAUAAGCUUUGGGGAGUCGGCAAACAGACUGUGAUCCAGAGAUCUCUGAAUGGGGGAACCCAGCCAGCACAAGCUGGUUAUCUUG
.....(((((((..........((..(....)..)).....(((((((.((((........))))....))))))).)))))))..(((....)))(((((((....)))))))...... ( -41.50)
>pst_1 2757 120 - 1
GGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUGUGAUCCGGAGAUGUCUGAAUGGGGGAACCCAGCCAUCAUAAGAUGGUUAUCUUA
(((..(((((.(..........((..(....)..)).....(((((((.((((........))))....))))))).).))))).((((....)))))))....((((((....)))))) ( -38.00)
>consensus
GGCAGUCAGAGGCGAUGAAAGACGUGGUAGCCUGCGAAAAGCUUCGGGGAGUCGGCAAACAGACUGUGAUCCGGAGAUCUCUGAAUGGGGGAACCCAGCCAGCAUAAGAUGGUUAUCUUG
.....(((((((..........((..(....)..)).....(((((((.((((........))))....))))))).)))))))..(((....)))(((((((....)))))))...... (-42.02 = -40.13 +  -1.88)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,791,652 – 4,791,772
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 98.67
Mean single sequence MFE -25.13
Consensus MFE -24.00
Energy contribution -24.03
Covariance contribution 0.03
Combinations/Pair 1.04
Mean z-score -0.87
Structure conservation index 0.96
SVM decision value 0.29
SVM RNA-class probability 0.669694
Prediction RNA

Download alignment: ClustalW | MAF

>pao_1 4791652 120 + 1
UUUUCGCAGGCUACCACGUCUUUCAUCGCCUCUGACUGCCAAGGCAUCCACCGUAUGCGCUUCUUCACUUGACCAUAUAACCCCAAGCAAUCUGGUUAUACUGUGAAGACGACAUUCGCC
........(((................((((.((.....)))))).......(.(((((..(((((((.((((((.((...........)).))))))....))))))))).))).)))) ( -25.20)
>pel_1 2839 120 + 1
UUAUCGCAGGCUACCACGUCUUUCAUCGCCUCUGACUGCCAAGGCAUCCACCGUAUGCGCUUCUUCACUUGACCAUAUAACCCCAAGCAAUCUGGUUAUACUGUGAAGACGACAUUCGCC
........(((................((((.((.....)))))).......(.(((((..(((((((.((((((.((...........)).))))))....))))))))).))).)))) ( -25.20)
>pf5_1 2835 120 + 1
UUAUCGCAGGCUACCACGUCUUUCAUCGCCUCUGACUGCCAAGGCAUCCACCGUAUGCGCUUCUUCACUUGACCAUAUAACCCCAAGCAAUCUGGUUAUACUAUGAAGACGACAUUCGCC
........(((.....((((((.(((.((((.((.....)))))).......(((((.(((......((((............))))......)))))))).)))))))))......))) ( -22.30)
>pfs_1 2838 120 + 1
UUUUCGCAGGCUACCACGUCUUUCAUCGCCUCUGACUGCCAAGGCAUCCACCGUAUGCGCUUCUUCACUUGACCAUAUAACCCCAAGCAAUCUGGUUAUACUGUGAAGACAACAUUCGCC
....(((((((......))).......((((.((.....))))))..........))))..(((((((.((((((.((...........)).))))))....)))))))........... ( -24.60)
>ppk_1 2839 120 + 1
UUAUCGCAGGCUACCACGUCUUUCAUCGCCUCUGACUGCCAAGGCAUCCACCGUAUGCGCUUCUUCACUUGACCAUAUAACCCCAAGCAAUCUGGUUAUACUGUGAAGACGACAUUCGCC
........(((................((((.((.....)))))).......(.(((((..(((((((.((((((.((...........)).))))))....))))))))).))).)))) ( -25.20)
>pst_1 2837 120 + 1
UUUUCGCAGGCUACCACGUCUUUCAUCGCCUCUGACUGCCGAGGCAUCCACCGUAUGCGCUUCUUCACUUGACCAUAUAACCCCAAGCAAUCUGGUUAUACUGUGAAGACGACAUUCGCC
........(((................(((((........))))).......(.(((((..(((((((.((((((.((...........)).))))))....))))))))).))).)))) ( -28.30)
>consensus
UUAUCGCAGGCUACCACGUCUUUCAUCGCCUCUGACUGCCAAGGCAUCCACCGUAUGCGCUUCUUCACUUGACCAUAUAACCCCAAGCAAUCUGGUUAUACUGUGAAGACGACAUUCGCC
....(((((((......))).......((((.((.....))))))..........))))..(((((((.((((((.((...........)).))))))....)))))))........... (-24.00 = -24.03 +   0.03)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:50:06 2007