Locus 66

Sequence ID pao.2545
Location 4,793,805 – 4,794,061
Length 256
Max. P 0.999172
window385 window386 window387 window388 window389

overview

Window 5

Location 4,793,805 – 4,793,921
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.16
Mean single sequence MFE -34.31
Consensus MFE -22.51
Energy contribution -22.90
Covariance contribution 0.39
Combinations/Pair 1.24
Mean z-score -2.48
Structure conservation index 0.66
SVM decision value 0.65
SVM RNA-class probability 0.810986
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2545 4793805 116 - 6264404
AA-GC-CUUGACCAACUGCUCUUUAACAAGUCGAAUCAAGCAAUUCGUGUGGGUGCUUGUGAUGUAAGACUGGUGAUC-GCAAGAUUAUCAGCAACGCAAGUAACACU-CGUGAAUUCGA
..-((-.((((...(((...........)))....))))))((((((.(((..((((((((.((.....(((((((((-....))))))))))).)))))))).))).-..))))))... ( -33.00)
>pau.414 5804636 116 + 6537648
AA-GC-CUUGACCAACUGCUCUUUAACAAGUCGAAUCAAGCAAUUCGUGUGGGUGCUUGUGAUGUAAGACUGGUGAUC-GCAAGAUUAUCAGCAGCGCAAGUAACACU-CGUGAAUUCGA
..-((-.((((...(((...........)))....))))))((((((.(((..((((((((.((.....(((((((((-....))))))))))).)))))))).))).-..))))))... ( -33.00)
>pss.3053 5953248 116 - 6093698
AA-GGUCUUAACCCACCGCUCUUUAACAA-CUGAAUCAAGCAAUUCGUGUGGGUGCUUGUGGUGUCAGACUGA-AGUC-AACAGAUUAUCAGCAACCCAAGUUACUCCGCGAGAAAUCAA
..-(((........)))(((.((((....-.))))...)))..((((((.(((((((((.(((....(.((((-((((-....)))).))))).))))))).)))))))))))....... ( -29.10)
>pel.2704 5003748 120 - 5888780
AACGCUCUUAACCAAUCGCUCUUUAACAAAUUGAAUCAAGCAAUUCGUGUGGGUGCUUGUGAGUACGGGCUGAUAGUCACCAAGAUUAUCAGCAUCACAAGUGGCCAUGCGAGAAAUCAC
.................(((.(((((....)))))...)))..(((((((((.(((((((((......((((((((((.....)))))))))).))))))))).)))))))))....... ( -41.50)
>ppk.338 5484115 120 + 6181863
AAAGCUCUUAACCAAACGCUCUUUAACAAAUCGAAUCAAGCAAUUCGUGUGGGUGCUUGUGAGUACGGACUGAUAGUCAAAAAGAUUAUCAGCAUCACAAGUGGCCAUGCGAGAAAUCAC
.................(((..................)))..(((((((((.(((((((((.....(.(((((((((.....)))))))))).))))))))).)))))))))....... ( -36.97)
>pf5.74 6952142 118 + 7074893
AA-GAUCUUAGCCAACCGCUCUUUAACAA-CUGAAUCAAGCAAUUCGUGUGGGUGCUUGUGGAGUCAGACUGAUAGUCAAAAAGAUUAUCAGCAUCACAAGUUACUCCGCGAGAAAUCAA
..-(((...........(((.((((....-.))))...)))..((((((.(((((((((((..(.....(((((((((.....))))))))))..)))))).)))))))))))..))).. ( -32.30)
>consensus
AA_GCUCUUAACCAACCGCUCUUUAACAA_UCGAAUCAAGCAAUUCGUGUGGGUGCUUGUGAUGUCAGACUGAUAGUC_AAAAGAUUAUCAGCAUCACAAGUAACACUGCGAGAAAUCAA
.................(((..................)))..((((((.((.((((((((......(.(((((((((.....))))))))))..)))))))).)).))))))....... (-22.51 = -22.90 +   0.39)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,793,883 – 4,793,989
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.66
Mean single sequence MFE -28.19
Consensus MFE -16.51
Energy contribution -16.48
Covariance contribution -0.02
Combinations/Pair 1.26
Mean z-score -1.68
Structure conservation index 0.59
SVM decision value 0.25
SVM RNA-class probability 0.652029
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2545 4793883 106 - 6264404
----------AAAUUUUC--GAAAAUAACGCUUGACGGAACGAGAGGUUGCUGUAGAAUGCGCGGCCUCGGUUGAGACGAAA-GC-CUUGACCAACUGCUCUUUAACAAGUCGAAUCAAG
----------.....(((--((...........(((((.....((((((((.((.....))))))))))(((..((.(....-).-))..)))..))).)).........)))))..... ( -31.75)
>pss.3053 5953326 113 - 6093698
GCUUUG----AAAACUUCUUGAAAUAACCGCUUGACAGAUACAGAGGGUGCUGUAGAAUUCGC-GCCUCGGUUGAGACGAAA-GGUCUUAACCCACCGCUCUUUAACAA-CUGAAUCAAG
......----....................((((((((.((.(((((((((..........))-)))..(((((((((....-.))))))))).....)))).))....-)))..))))) ( -26.90)
>pel.2704 5003828 107 - 5888780
----------AAAACUUC--GAAAAUAACGCUUGACACGAAAUGAGGUUAGCGUAGAAUGCGC-GCCUCGGUUGAGACGAAACGCUCUUAACCAAUCGCUCUUUAACAAAUUGAAUCAAG
----------........--..........(((((..(((...(((((..((((.....))))-)))))((((((((((...)).)))))))).................)))..))))) ( -26.70)
>ppk.338 5484195 117 + 6181863
UUUCUCGCAAAAAACUUC--AAAAUAAACGCUUGACAGGCUCUGAGGAAAGCGUAGAAUGCGC-GCCUCGGUUGAGACGAAAAGCUCUUAACCAAACGCUCUUUAACAAAUCGAAUCAAG
..................--.........(.((((..(((...((((...((((.....))))-.))))(((((((((.....).))))))))....)))..)))))............. ( -26.40)
>pf5.74 6952222 113 + 7074893
ACUUUG----AAAACUUCUUAAAAAAAUCACUUGACAGCAAAUGAGGCUGCUGUAGAAUGCGC-GCCUCGGUUGAGACGAAA-GAUCUUAGCCAACCGCUCUUUAACAA-CUGAAUCAAG
......----....................((((((((.....((((((((........))).-)))))(((((((((....-).))))))))................-)))..))))) ( -30.80)
>psp.2973 5784503 113 - 5928787
ACUUUG----AAAACUUCUUAAAAUAACCGCUUGACAGAUACAAGAGACGCUGUAGAAUGCGC-GCCUCGGUUGAGACGAAA-GCUCUUAACCACCCGCUCUUUAACAA-CUGAAUCAAG
......----....................((((((((......(((.(((.((.....))))-).)))(((((((((....-).))))))))................-)))..))))) ( -26.60)
>consensus
_CUUUG____AAAACUUC__AAAAAAAACGCUUGACAGAAACAGAGGAUGCUGUAGAAUGCGC_GCCUCGGUUGAGACGAAA_GCUCUUAACCAACCGCUCUUUAACAA_CUGAAUCAAG
..............................((((((((.....((((....(((.....)))...))))((((((((........)))))))).................)))..))))) (-16.51 = -16.48 +  -0.02)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,793,921 – 4,794,021
Length 100
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 75.53
Mean single sequence MFE -25.82
Consensus MFE -8.23
Energy contribution -8.85
Covariance contribution 0.61
Combinations/Pair 1.11
Mean z-score -2.30
Structure conservation index 0.32
SVM decision value 0.06
SVM RNA-class probability 0.562105
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2545 4793921 100 + 6264404
UCGUCUCAACCGAGGCCGCGCAUUCUACAGCAACCUCUCGUUCCGUCAAGCGUUAUUUUC--GAAAAUUU-------UCUUUUCUA--CUCAACCGCUUG---CGC--CGACCUUC
..(((......((((..((..........))..))))......((.((((((........--(((((...-------..)))))..--......))))))---)).--.))).... ( -19.89)
>pss.3053 5953364 112 + 6093698
UCGUCUCAACCGAGGC-GCGAAUUCUACAGCACCCUCUGUAUCUGUCAAGCGGUUAUUUCAAGAAGUUUUCAAAGCUUCCUUUGCAACUUCAACCACUUG---CGCUGCGAUCAAC
(((((((....)))((-((((....(((((......)))))....))(((.((((.......((((((..(((((....))))).)))))))))).))))---))).))))..... ( -28.31)
>pel.2704 5003868 101 + 5888780
UCGUCUCAACCGAGGC-GCGCAUUCUACGCUAACCUCAUUUCGUGUCAAGCGUUAUUUUC--GAAGUUUU-------UCGUU--CAACUUCAACCGCUUAACUCGCUGCGAUC---
((((.......((((.-(((.......)))...))))....((.((.(((((........--((((((..-------.....--.))))))...))))).)).))..))))..--- ( -21.10)
>pf5.74 6952260 104 - 7074893
UCGUCUCAACCGAGGC-GCGCAUUCUACAGCAGCCUCAUUUGCUGUCAAGUGAUUUUUUUAAGAAGUUUUCAAAGUUUCCUUUUUAACUUCAACCACUUG---CGCUU--------
..(((((....)))))-((((.....(((((((......))))))).(((((.((.....))((((((...((((....))))..))))))...))))))---)))..-------- ( -29.30)
>psp.2973 5784541 112 + 5928787
UCGUCUCAACCGAGGC-GCGCAUUCUACAGCGUCUCUUGUAUCUGUCAAGCGGUUAUUUUAAGAAGUUUUCAAAGUUUCCUUUGCAACUUCAACCACUUG---CGCUUCGAUCAAC
..........((((((-(((((...(((((......)))))..))).(((.((((.......((((((..(((((....))))).)))))))))).))))---)))))))...... ( -29.11)
>pst.3250 6219330 112 + 6397126
UCAUCUCAACCGAGGC-GCGCAUUCUACAGCGUCUCUUGUAUCUGUCAAGCGGUUAUUUUCAGAAGCUUUCAAAGUUUCCUUUGCAACUUCAACCACUUG---CGCUUCGAUCAAC
..........((((((-(((((...(((((......)))))..))).(((.((((.......((((.((.(((((....))))).)))))))))).))))---)))))))...... ( -27.21)
>consensus
UCGUCUCAACCGAGGC_GCGCAUUCUACAGCAACCUCUGUAUCUGUCAAGCGGUUAUUUCAAGAAGUUUUCAAAGUUUCCUUUGCAACUUCAACCACUUG___CGCUUCGAUCAAC
..(((((....))))).(((......((((............))))................((((((.................))))))............))).......... ( -8.23 =  -8.85 +   0.61)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,793,921 – 4,794,021
Length 100
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 75.53
Mean single sequence MFE -36.69
Consensus MFE -17.55
Energy contribution -18.71
Covariance contribution 1.16
Combinations/Pair 1.28
Mean z-score -3.86
Structure conservation index 0.48
SVM decision value 3.20
SVM RNA-class probability 0.998711
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2545 4793921 100 - 6264404
GAAGGUCG--GCG---CAAGCGGUUGAG--UAGAAAAGA-------AAAUUUUC--GAAAAUAACGCUUGACGGAACGAGAGGUUGCUGUAGAAUGCGCGGCCUCGGUUGAGACGA
....(((.--.((---((((((......--..(((((..-------...)))))--........)))))).)).(((..((((((((.((.....)))))))))).)))..))).. ( -32.29)
>pss.3053 5953364 112 - 6093698
GUUGAUCGCAGCG---CAAGUGGUUGAAGUUGCAAAGGAAGCUUUGAAAACUUCUUGAAAUAACCGCUUGACAGAUACAGAGGGUGCUGUAGAAUUCGC-GCCUCGGUUGAGACGA
.(..((((..(((---(((((((((((((((.(((((....)))))..)))))).......))))))))((....(((((......)))))....))))-))..))))..)..... ( -37.31)
>pel.2704 5003868 101 - 5888780
---GAUCGCAGCGAGUUAAGCGGUUGAAGUUG--AACGA-------AAAACUUC--GAAAAUAACGCUUGACACGAAAUGAGGUUAGCGUAGAAUGCGC-GCCUCGGUUGAGACGA
---..((.((((..((((((((.((((((((.--.....-------..))))))--))......))))))))......((((((..((((.....))))-)))))))))).))... ( -36.30)
>pf5.74 6952260 104 + 7074893
--------AAGCG---CAAGUGGUUGAAGUUAAAAAGGAAACUUUGAAAACUUCUUAAAAAAAUCACUUGACAGCAAAUGAGGCUGCUGUAGAAUGCGC-GCCUCGGUUGAGACGA
--------..((.---(((((((((((((((..((((....))))...)))))).......)))))))))...))...(((((((((........))).-)))))).......... ( -35.21)
>psp.2973 5784541 112 - 5928787
GUUGAUCGAAGCG---CAAGUGGUUGAAGUUGCAAAGGAAACUUUGAAAACUUCUUAAAAUAACCGCUUGACAGAUACAAGAGACGCUGUAGAAUGCGC-GCCUCGGUUGAGACGA
.(..(((((.(((---(((((((((((((((.(((((....)))))..)))))).......))))))))(.((..((((........))))...)))))-)).)))))..)..... ( -39.51)
>pst.3250 6219330 112 - 6397126
GUUGAUCGAAGCG---CAAGUGGUUGAAGUUGCAAAGGAAACUUUGAAAGCUUCUGAAAAUAACCGCUUGACAGAUACAAGAGACGCUGUAGAAUGCGC-GCCUCGGUUGAGAUGA
.(..(((((.(((---(((((((((((((((.(((((....)))))..)))))).......))))))))(.((..((((........))))...)))))-)).)))))..)..... ( -39.51)
>consensus
GUUGAUCGAAGCG___CAAGUGGUUGAAGUUGCAAAGGAAACUUUGAAAACUUCUUAAAAAAACCGCUUGACAGAAACAGAGGAUGCUGUAGAAUGCGC_GCCUCGGUUGAGACGA
..........(((...(((((((((((((((..((((....))))...)))))).......)))))))))((((............))))......)))...(((....))).... (-17.55 = -18.71 +   1.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,793,961 – 4,794,061
Length 100
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 72.47
Mean single sequence MFE -35.09
Consensus MFE -16.71
Energy contribution -18.29
Covariance contribution 1.57
Combinations/Pair 1.26
Mean z-score -3.38
Structure conservation index 0.48
SVM decision value 3.41
SVM RNA-class probability 0.999172
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2545 4793961 100 - 6264404
ACGCUGUAGAAUGCGCCUCCCGCUGAUCGGAAGAUGGUUUGAAGGUCG--GCG---CAAGCGGUUGAG--UAGAAAAGA-------AAAUUUUC--GAAAAUAACGCUUGACGGAA
...((((.....(((((..(((((.(((....)))))).....))..)--)))---)(((((......--..(((((..-------...)))))--........))))).)))).. ( -29.79)
>pss.3053 5953403 113 - 6093698
ACGCUGUAGAAUUCGCCUCCCGCUGAUGAGCAACUCAAGAGUUGAUCGCAGCG---CAAGUGGUUGAAGUUGCAAAGGAAGCUUUGAAAACUUCUUGAAAUAACCGCUUGACAGAU
...((((.............(((((.(((.(((((....))))).))))))))---(((((((((((((((.(((((....)))))..)))))).......))))))))))))).. ( -39.61)
>pel.2704 5003907 92 - 5888780
ACGCUGUAUGAUUCGCCUCCCGCU-ACGAGA------------GAUCGCAGCGAGUUAAGCGGUUGAAGUUG--AACGA-------AAAACUUC--GAAAAUAACGCUUGACACGA
.((((((..(((.(..(((.....-..))).------------)))))))))).((((((((.((((((((.--.....-------..))))))--))......)))))))).... ( -30.80)
>pf5.74 6952299 102 + 7074893
ACGCUGUAGAAUUCGCCUCCCGCUAACGAGAGAUCGG-----------AAGCG---CAAGUGGUUGAAGUUAAAAAGGAAACUUUGAAAACUUCUUAAAAAAAUCACUUGACAGCA
..(((((.............((((..(((....))).-----------.))))---(((((((((((((((..((((....))))...)))))).......)))))))))))))). ( -35.61)
>psp.2973 5784580 113 - 5928787
ACGCUGUAUAAUUCGCCUCCCGCUGAUGAGCAACUGAAGAGUUGAUCGAAGCG---CAAGUGGUUGAAGUUGCAAAGGAAACUUUGAAAACUUCUUAAAAUAACCGCUUGACAGAU
...((((.............((((..(((.(((((....))))).))).))))---(((((((((((((((.(((((....)))))..)))))).......))))))))))))).. ( -38.31)
>pst.3250 6219369 112 - 6397126
ACGCUGUAGAAUUCGCCUCCCGCUGAUGAGCAACCCA-GCGUUGAUCGAAGCG---CAAGUGGUUGAAGUUGCAAAGGAAACUUUGAAAGCUUCUGAAAAUAACCGCUUGACAGAU
...((((.............((((..(((.((((...-..)))).))).))))---(((((((((((((((.(((((....)))))..)))))).......))))))))))))).. ( -36.41)
>consensus
ACGCUGUAGAAUUCGCCUCCCGCUGAUGAGAAACUGA_G_GUUGAUCGAAGCG___CAAGUGGUUGAAGUUGCAAAGGAAACUUUGAAAACUUCUUAAAAAAACCGCUUGACAGAA
...((((.............((((.........................))))...(((((((((((((((..((((....))))...)))))).......))))))))))))).. (-16.71 = -18.29 +   1.57)

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 21:10:24 2007