Locus 206

Sequence ID pao.2750
Location 5,203,376 – 5,203,667
Length 291
Max. P 0.999993
window803 window804 window805 window806 window807 window808 window809 window810 window811 window812

overview

Window 3

Location 5,203,376 – 5,203,491
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.54
Mean single sequence MFE -42.03
Consensus MFE -36.11
Energy contribution -36.00
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -2.08
Structure conservation index 0.86
SVM decision value 1.31
SVM RNA-class probability 0.941043
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2750 5203376 115 + 6264404
UUCUGUAACCCAC---ACAGGAGU--CCUGCAUUGGACAACAGCCCUAGUCGAUUGCGACAGGUCCAUCCGGCGAGCUAGUCCAGCAGAACCCUCUGCCACUGCCUCGCCGAACAUGGCG
((((((.......---))))))((--((......))))......(((.((((....))))))).((((.(((((((.((((...(((((....))))).)))).)))))))...)))).. ( -42.90)
>pau.2886 5475355 115 + 6537648
UUCUGUAACCCAC---ACAGGAGU--CCUGCAUUGGACAACAGCCCUAGUCGAUUGCGACAGGUCCAUCCGGCGAGCUAGUCCAGCAGAACCCUCUGCCACUGCCUCGCCGAACAUGGCG
((((((.......---))))))((--((......))))......(((.((((....))))))).((((.(((((((.((((...(((((....))))).)))).)))))))...)))).. ( -42.90)
>pel.1792 3328656 119 + 5888780
CUCAAGCAUCCCUUCAACAGGAGUCCCCUGCAUUGGACAGUAGCCCCAGUCGAUUGCGACAGGCCCACACGGCGAGCUAGUCCGGCAGCGUUC-CUGCCACUGUCUCGCCGCACCCGGUA
.................((((.....)))).(((((...((.(((...((((....)))).)))..)).(((((((.((((..(((((.....-))))))))).)))))))...))))). ( -40.30)
>consensus
UUCUGUAACCCAC___ACAGGAGU__CCUGCAUUGGACAACAGCCCUAGUCGAUUGCGACAGGUCCAUCCGGCGAGCUAGUCCAGCAGAACCCUCUGCCACUGCCUCGCCGAACAUGGCG
.........(((.....((((.....))))...)))......(((((.((((....)))).))......(((((((.((((...((((......)))).)))).))))))).....))). (-36.11 = -36.00 +  -0.11) 

alignment

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secondary structure

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dotplot

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Window 4

Location 5,203,376 – 5,203,491
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.54
Mean single sequence MFE -50.60
Consensus MFE -46.65
Energy contribution -45.67
Covariance contribution -0.99
Combinations/Pair 1.18
Mean z-score -1.82
Structure conservation index 0.92
SVM decision value 1.65
SVM RNA-class probability 0.969960
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2750 5203376 115 - 6264404
CGCCAUGUUCGGCGAGGCAGUGGCAGAGGGUUCUGCUGGACUAGCUCGCCGGAUGGACCUGUCGCAAUCGACUAGGGCUGUUGUCCAAUGCAGG--ACUCCUGU---GUGGGUUACAGAA
..(((..(((((((((..((((((((......)))))..)))..)))))))))))).(((((((....)))).))).((((..((((.((((((--...)))))---)))))..)))).. ( -49.10)
>pau.2886 5475355 115 - 6537648
CGCCAUGUUCGGCGAGGCAGUGGCAGAGGGUUCUGCUGGACUAGCUCGCCGGAUGGACCUGUCGCAAUCGACUAGGGCUGUUGUCCAAUGCAGG--ACUCCUGU---GUGGGUUACAGAA
..(((..(((((((((..((((((((......)))))..)))..)))))))))))).(((((((....)))).))).((((..((((.((((((--...)))))---)))))..)))).. ( -49.10)
>pel.1792 3328656 119 - 5888780
UACCGGGUGCGGCGAGACAGUGGCAG-GAACGCUGCCGGACUAGCUCGCCGUGUGGGCCUGUCGCAAUCGACUGGGGCUACUGUCCAAUGCAGGGGACUCCUGUUGAAGGGAUGCUUGAG
...(((((((((((((..((((((((-.....)))))..)))..))))))))((((.(((((((....)))).))).)))).((((...(((((.....))))).....))))))))).. ( -53.60)
>consensus
CGCCAUGUUCGGCGAGGCAGUGGCAGAGGGUUCUGCUGGACUAGCUCGCCGGAUGGACCUGUCGCAAUCGACUAGGGCUGUUGUCCAAUGCAGG__ACUCCUGU___GUGGGUUACAGAA
..(((..(((((((((..((((((((......)))))..)))..)))))))))))).(((((((....)))).))).((((..((((..(((((.....)))))....))))..)))).. (-46.65 = -45.67 +  -0.99) 

alignment

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secondary structure

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Window 5

Location 5,203,411 – 5,203,531
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.22
Mean single sequence MFE -50.33
Consensus MFE -44.35
Energy contribution -43.13
Covariance contribution -1.21
Combinations/Pair 1.15
Mean z-score -2.25
Structure conservation index 0.88
SVM decision value 1.79
SVM RNA-class probability 0.977397
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2750 5203411 120 + 6264404
CAGCCCUAGUCGAUUGCGACAGGUCCAUCCGGCGAGCUAGUCCAGCAGAACCCUCUGCCACUGCCUCGCCGAACAUGGCGGACAGUGGCGAUCCGCAUCCCGUCCGGGAUGACGCAUCCC
..(((((.((((....))))..((((..((((((((.((((...(((((....))))).)))).))))))).....)..)))))).)))(((.((((((((....)))))).)).))).. ( -52.70)
>pau.2886 5475390 120 + 6537648
CAGCCCUAGUCGAUUGCGACAGGUCCAUCCGGCGAGCUAGUCCAGCAGAACCCUCUGCCACUGCCUCGCCGAACAUGGCGGACAGUGGCGAUCCGCAUCCCGUCCGGGAUGACGCAUCCC
..(((((.((((....))))..((((..((((((((.((((...(((((....))))).)))).))))))).....)..)))))).)))(((.((((((((....)))))).)).))).. ( -52.70)
>pel.1792 3328696 118 + 5888780
UAGCCCCAGUCGAUUGCGACAGGCCCACACGGCGAGCUAGUCCGGCAGCGUUC-CUGCCACUGUCUCGCCGCACCCGGUAGACGGUGGUUUCCUCCAGCCCUCCAUGGCUGA-GCACCCC
..(((...((((....)))).)))((((.(((((((.((((..(((((.....-))))))))).)))))))....((.....)))))).......(((((......))))).-....... ( -45.60)
>consensus
CAGCCCUAGUCGAUUGCGACAGGUCCAUCCGGCGAGCUAGUCCAGCAGAACCCUCUGCCACUGCCUCGCCGAACAUGGCGGACAGUGGCGAUCCGCAUCCCGUCCGGGAUGACGCAUCCC
..(((((.((((....))))..(((....(((((((.((((...((((......)))).)))).))))))).....)))....)).)))......((((((....))))))......... (-44.35 = -43.13 +  -1.21) 

alignment

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secondary structure

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dotplot

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Window 6

Location 5,203,411 – 5,203,531
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.22
Mean single sequence MFE -57.27
Consensus MFE -48.65
Energy contribution -48.33
Covariance contribution -0.32
Combinations/Pair 1.17
Mean z-score -1.75
Structure conservation index 0.85
SVM decision value 0.81
SVM RNA-class probability 0.857596
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2750 5203411 120 - 6264404
GGGAUGCGUCAUCCCGGACGGGAUGCGGAUCGCCACUGUCCGCCAUGUUCGGCGAGGCAGUGGCAGAGGGUUCUGCUGGACUAGCUCGCCGGAUGGACCUGUCGCAAUCGACUAGGGCUG
(((((.((.((((((....)))))))).)))(((((((((((((......)))).))))))))).((((((((....)))))..))).))....((.(((((((....)))).))).)). ( -58.50)
>pau.2886 5475390 120 - 6537648
GGGAUGCGUCAUCCCGGACGGGAUGCGGAUCGCCACUGUCCGCCAUGUUCGGCGAGGCAGUGGCAGAGGGUUCUGCUGGACUAGCUCGCCGGAUGGACCUGUCGCAAUCGACUAGGGCUG
(((((.((.((((((....)))))))).)))(((((((((((((......)))).))))))))).((((((((....)))))..))).))....((.(((((((....)))).))).)). ( -58.50)
>pel.1792 3328696 118 - 5888780
GGGGUGC-UCAGCCAUGGAGGGCUGGAGGAAACCACCGUCUACCGGGUGCGGCGAGACAGUGGCAG-GAACGCUGCCGGACUAGCUCGCCGUGUGGGCCUGUCGCAAUCGACUGGGGCUA
((..(.(-((((((......)))).))).)..)).(((.....)))(..(((((((..((((((((-.....)))))..)))..)))))))..).(((((((((....))))..))))). ( -54.80)
>consensus
GGGAUGCGUCAUCCCGGACGGGAUGCGGAUCGCCACUGUCCGCCAUGUUCGGCGAGGCAGUGGCAGAGGGUUCUGCUGGACUAGCUCGCCGGAUGGACCUGUCGCAAUCGACUAGGGCUG
(((((.((.((((((....)))))))).))).))...((((.(((..(((((((((..((((((((......)))))..)))..))))))))))))....((((....))))..)))).. (-48.65 = -48.33 +  -0.32) 

alignment

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secondary structure

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Window 7

Location 5,203,451 – 5,203,571
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.50
Mean single sequence MFE -42.97
Consensus MFE -31.41
Energy contribution -31.20
Covariance contribution -0.21
Combinations/Pair 1.24
Mean z-score -2.91
Structure conservation index 0.73
SVM decision value 5.72
SVM RNA-class probability 0.999993
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2750 5203451 120 + 6264404
UCCAGCAGAACCCUCUGCCACUGCCUCGCCGAACAUGGCGGACAGUGGCGAUCCGCAUCCCGUCCGGGAUGACGCAUCCCCAUUUUCCCUUCGUGUCCCUUCCCUCGCGCCAACCGCGCA
....(((((....)))))(((......(((......)))(((.(((((.(((.((((((((....)))))).)).))).))))).)))....)))...........((((.....)))). ( -43.90)
>pau.2886 5475430 120 + 6537648
UCCAGCAGAACCCUCUGCCACUGCCUCGCCGAACAUGGCGGACAGUGGCGAUCCGCAUCCCGUCCGGGAUGACGCAUCCCCAUUUUCCCUUCGUGUCCCUUCCCUCGCGCCAUCCGCGCA
....(((((....)))))(((......(((......)))(((.(((((.(((.((((((((....)))))).)).))).))))).)))....)))...........((((.....)))). ( -43.90)
>pel.1792 3328736 108 + 5888780
UCCGGCAGCGUUC-CUGCCACUGUCUCGCCGCACCCGGUAGACGGUGGUUUCCUCCAGCCCUCCAUGGCUGA-GCACCCCUCUUUUCCAGCAG----CCUUGCCACCCG------GCAUG
...(((.((....-..((((((((((.((((....))))))))))))))......(((((......))))).-................)).)----)).((((....)------))).. ( -41.10)
>consensus
UCCAGCAGAACCCUCUGCCACUGCCUCGCCGAACAUGGCGGACAGUGGCGAUCCGCAUCCCGUCCGGGAUGACGCAUCCCCAUUUUCCCUUCGUGUCCCUUCCCUCGCGCCA_CCGCGCA
....((..........(((((((.((.((((....)))))).)))))))......((((((....))))))..))...............................((((.....)))). (-31.41 = -31.20 +  -0.21) 

alignment

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secondary structure

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dotplot

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Window 8

Location 5,203,451 – 5,203,571
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 72.50
Mean single sequence MFE -49.80
Consensus MFE -35.33
Energy contribution -37.90
Covariance contribution 2.57
Combinations/Pair 1.19
Mean z-score -1.81
Structure conservation index 0.71
SVM decision value 2.51
SVM RNA-class probability 0.994729
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2750 5203451 120 - 6264404
UGCGCGGUUGGCGCGAGGGAAGGGACACGAAGGGAAAAUGGGGAUGCGUCAUCCCGGACGGGAUGCGGAUCGCCACUGUCCGCCAUGUUCGGCGAGGCAGUGGCAGAGGGUUCUGCUGGA
.((((.....)))).......(((((................(((.((.((((((....)))))))).)))(((((((((((((......)))).))))))))).....)))))...... ( -54.30)
>pau.2886 5475430 120 - 6537648
UGCGCGGAUGGCGCGAGGGAAGGGACACGAAGGGAAAAUGGGGAUGCGUCAUCCCGGACGGGAUGCGGAUCGCCACUGUCCGCCAUGUUCGGCGAGGCAGUGGCAGAGGGUUCUGCUGGA
.((((.....)))).......(((((................(((.((.((((((....)))))))).)))(((((((((((((......)))).))))))))).....)))))...... ( -54.30)
>pel.1792 3328736 108 - 5888780
CAUGC------CGGGUGGCAAGG----CUGCUGGAAAAGAGGGGUGC-UCAGCCAUGGAGGGCUGGAGGAAACCACCGUCUACCGGGUGCGGCGAGACAGUGGCAG-GAACGCUGCCGGA
....(------((.(..((....----(((((........(((((.(-((((((......)))).)))...))).))((((.(((....)))..))))...)))))-....))..)))). ( -40.80)
>consensus
UGCGCGG_UGGCGCGAGGGAAGGGACACGAAGGGAAAAUGGGGAUGCGUCAUCCCGGACGGGAUGCGGAUCGCCACUGUCCGCCAUGUUCGGCGAGGCAGUGGCAGAGGGUUCUGCUGGA
(((((.....))))).((...(((((.(..............(((.((.((((((....)))))))).)))(((((((((((((......)))).)))))))))...).))))).))... (-35.33 = -37.90 +   2.57) 

alignment

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secondary structure

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dotplot

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Window 9

Location 5,203,491 – 5,203,611
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 70.28
Mean single sequence MFE -39.97
Consensus MFE -24.38
Energy contribution -25.03
Covariance contribution 0.65
Combinations/Pair 1.26
Mean z-score -2.04
Structure conservation index 0.61
SVM decision value 2.83
SVM RNA-class probability 0.997277
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2750 5203491 120 + 6264404
GACAGUGGCGAUCCGCAUCCCGUCCGGGAUGACGCAUCCCCAUUUUCCCUUCGUGUCCCUUCCCUCGCGCCAACCGCGCAGCGGGAAGCCGCGGUCCUGCGCAAUCCAUCGUCCCUUAUC
((((((((.(((.((((((((....)))))).)).))).)))))......(((((...((((((.(((((.....)))).).)))))).)))))................)))....... ( -43.10)
>pau.2886 5475470 120 + 6537648
GACAGUGGCGAUCCGCAUCCCGUCCGGGAUGACGCAUCCCCAUUUUCCCUUCGUGUCCCUUCCCUCGCGCCAUCCGCGCAGCGGGAAGCCGCGGUCCUGCGCAAUCCAUCUUCCUUUAUC
((((((((.(((.((((((((....)))))).)).))).))))).......((((...((((((.(((((.....)))).).)))))).)))))))........................ ( -42.40)
>pel.1792 3328775 101 + 5888780
GACGGUGGUUUCCUCCAGCCCUCCAUGGCUGA-GCACCCCUCUUUUCCAGCAG----CCUUGCCACCCG------GCAUGGCG------CGUGGUCCUGCGCAUUCC-UCG-CUUUCAAU
((.((.(((...(((.((((......))))))-).)))))))......(((.(----((.((((....)------))).)))(------(((......)))).....-..)-))...... ( -34.40)
>consensus
GACAGUGGCGAUCCGCAUCCCGUCCGGGAUGACGCAUCCCCAUUUUCCCUUCGUGUCCCUUCCCUCGCGCCA_CCGCGCAGCGGGAAGCCGCGGUCCUGCGCAAUCCAUCGUCCUUUAUC
((.(((((.(((.((((((((....)))))).)).))).))))).))............................(((((((((....)))).....))))).................. (-24.38 = -25.03 +   0.65) 

alignment

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secondary structure

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dotplot

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Window 0

Location 5,203,531 – 5,203,651
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 71.39
Mean single sequence MFE -47.74
Consensus MFE -26.25
Energy contribution -26.23
Covariance contribution -0.02
Combinations/Pair 1.25
Mean z-score -2.35
Structure conservation index 0.55
SVM decision value 2.43
SVM RNA-class probability 0.993889
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2750 5203531 120 + 6264404
CAUUUUCCCUUCGUGUCCCUUCCCUCGCGCCAACCGCGCAGCGGGAAGCCGCGGUCCUGCGCAAUCCAUCGUCCCUUAUCCGCGCGGACCGUCGGCCCGCGCCAGCUCCGGCCGUCGGCC
...................(((((.(((((.....)))).).)))))((((((((((.((((...................)))))))))))(((((.((....))...)))))..))). ( -47.01)
>pau.2886 5475510 120 + 6537648
CAUUUUCCCUUCGUGUCCCUUCCCUCGCGCCAUCCGCGCAGCGGGAAGCCGCGGUCCUGCGCAAUCCAUCUUCCUUUAUCCGCGCGGACCGACGGCCCGCGCCAGCUCCGGCCGUCGGCC
.......((...(((...((((((.(((((.....)))).).)))))).)))(((((.((((...................)))))))))(((((((.((....))...))))))))).. ( -50.41)
>pel.1792 3328814 101 + 5888780
UCUUUUCCAGCAG----CCUUGCCACCCG------GCAUGGCG------CGUGGUCCUGCGCAUUCC-UCG-CUUUCAAUCGCGCCG-UCUUCGGCCGGCGCUGCCGCGGGCCAUCGCCC
............(----((.((((....)------))).)))(------(((((.(((((((.....-..)-)........((((((-.(....).))))))....)))))))).))).. ( -45.80)
>consensus
CAUUUUCCCUUCGUGUCCCUUCCCUCGCGCCA_CCGCGCAGCGGGAAGCCGCGGUCCUGCGCAAUCCAUCGUCCUUUAUCCGCGCGGACCGUCGGCCCGCGCCAGCUCCGGCCGUCGGCC
.....................((..((.(((....(((((((((....)))).....)))))...................((((((.((...)).)))))).......)))))..)).. (-26.25 = -26.23 +  -0.02) 

alignment

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secondary structure

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dotplot

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Window 1

Location 5,203,547 – 5,203,667
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 67.88
Mean single sequence MFE -53.34
Consensus MFE -29.27
Energy contribution -31.03
Covariance contribution 1.76
Combinations/Pair 1.18
Mean z-score -2.44
Structure conservation index 0.55
SVM decision value 3.63
SVM RNA-class probability 0.999467
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2750 5203547 120 + 6264404
CCCUUCCCUCGCGCCAACCGCGCAGCGGGAAGCCGCGGUCCUGCGCAAUCCAUCGUCCCUUAUCCGCGCGGACCGUCGGCCCGCGCCAGCUCCGGCCGUCGGCCGGCAACGAGGUGAAAC
...(((((((((((.....)))).((((....))))(((((.((((...................)))))))))(((((((.(((((......)).))).)))))))...)))).))).. ( -58.91)
>pau.2886 5475526 118 + 6537648
CCCUUCCCUCGCGCCAUCCGCGCAGCGGGAAGCCGCGGUCCUGCGCAAUCCAUCUUCCUUUAUCCGCGCGGACCGACGGCCCGCGCCAGCUCCGGCCGUCGGCCGGCAACGAGGUGAA--
....(((((((.(((.(((((((.((((....))))((...........))..............)))))))(((((((((.((....))...)))))))))..)))..))))).)).-- ( -58.80)
>pel.1792 3328827 89 + 5888780
-CCUUGCCACCCG------GCAUGGCG------CGUGGUCCUGCGCAUUCC-UCG-CUUUCAAUCGCGCCG-UCUUCGGCCGGCGCUGCCGCGGGCCAUCGCCCG---------------
-...((((....)------))).((((------.((((.(((((((.....-..)-)........((((((-.(....).))))))....)))))))))))))..--------------- ( -42.30)
>consensus
CCCUUCCCUCGCGCCA_CCGCGCAGCGGGAAGCCGCGGUCCUGCGCAAUCCAUCGUCCUUUAUCCGCGCGGACCGUCGGCCCGCGCCAGCUCCGGCCGUCGGCCGGCAACGAGGUGAA__
......(((((........(((((((((....)))).....)))))...................((((((.((...)).)))))).....((((((...))))))...)))))...... (-29.27 = -31.03 +   1.76) 

alignment

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secondary structure

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dotplot

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Window 2

Location 5,203,547 – 5,203,667
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 67.88
Mean single sequence MFE -57.17
Consensus MFE -33.21
Energy contribution -34.33
Covariance contribution 1.12
Combinations/Pair 1.21
Mean z-score -1.47
Structure conservation index 0.58
SVM decision value 0.71
SVM RNA-class probability 0.828872
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2750 5203547 120 - 6264404
GUUUCACCUCGUUGCCGGCCGACGGCCGGAGCUGGCGCGGGCCGACGGUCCGCGCGGAUAAGGGACGAUGGAUUGCGCAGGACCGCGGCUUCCCGCUGCGCGGUUGGCGCGAGGGAAGGG
.((((.((((((.((((((((.((((((....))))((((((((.((((((((((((.((........))..)))))).))))))))))...))))..)))))))))))))))))))).. ( -67.80)
>pau.2886 5475526 118 - 6537648
--UUCACCUCGUUGCCGGCCGACGGCCGGAGCUGGCGCGGGCCGUCGGUCCGCGCGGAUAAAGGAAGAUGGAUUGCGCAGGACCGCGGCUUCCCGCUGCGCGGAUGGCGCGAGGGAAGGG
--(((.((((((.((((((((((((((.(.(....).).))))))))))((((((((.....(((((.....(((((......))))))))))..)))))))).)))))))))))))... ( -65.20)
>pel.1792 3328827 89 - 5888780
---------------CGGGCGAUGGCCCGCGGCAGCGCCGGCCGAAGA-CGGCGCGAUUGAAAG-CGA-GGAAUGCGCAGGACCACG------CGCCAUGC------CGGGUGGCAAGG-
---------------(((((....))))).(((.((((((........-))))))........(-((.-((...........)).))------)))).(((------(....))))...- ( -38.50)
>consensus
__UUCACCUCGUUGCCGGCCGACGGCCGGAGCUGGCGCGGGCCGACGGUCCGCGCGGAUAAAGGACGAUGGAUUGCGCAGGACCGCGGCUUCCCGCUGCGCGG_UGGCGCGAGGGAAGGG
..............((((((...))))))..((.(((((((((...))))))))).................((((((.....((((((.....))))))......)))))).))..... (-33.21 = -34.33 +   1.12) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:17:56 2007