Locus 77

Sequence ID Bcere.0
Location 225,068 – 3,833,676
Length 3608608
Max. P 0.999997
window435 window436 window437 window438 window439 window440 window441 window442

overview

Window 5

Location 3,833,644 – 3,833,676
Length 32
Sequences 3
Columns 32
Reading direction forward
Mean pairwise identity 85.42
Mean single sequence MFE -12.43
Consensus MFE -11.75
Energy contribution -12.53
Covariance contribution 0.78
Combinations/Pair 1.08
Mean z-score -4.16
Structure conservation index 0.95
SVM decision value 2.28
SVM RNA-class probability 0.991621
Prediction RNA
WARNING Sequence 1 too short.
WARNING Sequence 2 too short.
WARNING Sequence 3 too short.

Download alignment: ClustalW | MAF

>Bcere.0 3833644 32 + 5224283
AGAGGUUUUUCUGACGUAGAAAAACCUCUUUC
(((((((((((((...)))))))))))))... ( -14.60)
>Banth.0 3890530 32 + 5227293
AGAGGUUUUUCUGACGUAGAAAAACCUCUUUC
(((((((((((((...)))))))))))))... ( -14.60)
>Bsubt.0 1384971 31 + 4214630
AGAGGUUUU-CUCACAACAAAAAGCCUCUUUC
(((((((((-..........)))))))))... (  -8.10)
>consensus
AGAGGUUUUUCUGACGUAGAAAAACCUCUUUC
((((((((((((.....))))))))))))... (-11.75 = -12.53 +   0.78)

alignment

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secondary structure

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Window 6

Location 3,833,644 – 3,833,676
Length 32
Sequences 3
Columns 32
Reading direction reverse
Mean pairwise identity 85.42
Mean single sequence MFE -12.33
Consensus MFE -10.99
Energy contribution -11.77
Covariance contribution 0.78
Combinations/Pair 1.08
Mean z-score -3.85
Structure conservation index 0.89
SVM decision value 2.19
SVM RNA-class probability 0.989885
Prediction RNA
WARNING Sequence 1 too short.
WARNING Sequence 2 too short.
WARNING Sequence 3 too short.

Download alignment: ClustalW | MAF

>Bcere.0 3833644 32 + 5224283
GAAAGAGGUUUUUCUACGUCAGAAAAACCUCU
...((((((((((((.....)))))))))))) ( -14.70)
>Banth.0 3890530 32 + 5227293
GAAAGAGGUUUUUCUACGUCAGAAAAACCUCU
...((((((((((((.....)))))))))))) ( -14.70)
>Bsubt.0 1384971 31 + 4214630
GAAAGAGGCUUUUUGUUGUGAG-AAAACCUCU
...(((((.(((((......))-))).))))) (  -7.60)
>consensus
GAAAGAGGUUUUUCUACGUCAGAAAAACCUCU
...((((((((((((.....)))))))))))) (-10.99 = -11.77 +   0.78)

alignment

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secondary structure

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Window 7

Location 225,068 – 225,185
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 69.19
Mean single sequence MFE -35.07
Consensus MFE -20.09
Energy contribution -21.32
Covariance contribution 1.23
Combinations/Pair 1.18
Mean z-score -3.63
Structure conservation index 0.57
SVM decision value 6.08
SVM RNA-class probability 0.999996
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 225068 117 + 5224283/0-120
AAAAAAUCCCUCUUUUCAUAUUGAGAAAGAGGGAUUUUUACGUACAA---GUUAUGCACCCGUAUAUAAACGAAGUCCCUCAUUCUAUCUUUCAAGCUAUAAAGCUUGCAGGAAGUGGCA
.(((((((((((((((........))))))))))))))).(((....---..(((((....)))))...)))..(((.((.......((((.((((((....)))))).)))))).))). ( -33.31)
>Banth.0 197002 117 + 5227293/0-120
AAAAAAUCCCUCUUUUCGUAUUGAGAAAGAGGGAUUUUUACGUACAA---GUUAUGCACCCGUAUAUAAACGAAGUCCCUCAUUCUAUCUUUCAAGCUAUAAAGCUUGCAGGAAGUGGCA
.(((((((((((((((........))))))))))))))).(((....---..(((((....)))))...)))..(((.((.......((((.((((((....)))))).)))))).))). ( -33.31)
>Bsubt.0 2024288 118 + 4214630/0-120
AAAAAAUCUCUUUCCGAAGAUGGAAAGAGAUUCAUAUAUAGGCGCGCUCUGUUACAGGCAGACGCCGGUAUAAACCUUGCUUUCCUAUCUUUCAAGCUA--GCGCUUGCUGGAAUUGGCA
....(((((((((((......)))))))))))..(((((.((((...(((((.....))))))))).))))).....((((......(((..(((((..--..)))))..)))...)))) ( -38.60)
>consensus
AAAAAAUCCCUCUUUUCAUAUUGAGAAAGAGGGAUUUUUACGUACAA___GUUAUGCACCCGUAUAUAAACGAAGUCCCUCAUUCUAUCUUUCAAGCUAUAAAGCUUGCAGGAAGUGGCA
.(((((((((((((((........)))))))))))))))..((((................))))......................((((.(((((......))))).))))....... (-20.09 = -21.32 +   1.23)

alignment

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secondary structure

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Window 8

Location 225,068 – 225,185
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 69.19
Mean single sequence MFE -37.43
Consensus MFE -21.55
Energy contribution -22.23
Covariance contribution 0.68
Combinations/Pair 1.24
Mean z-score -3.79
Structure conservation index 0.58
SVM decision value 6.20
SVM RNA-class probability 0.999997
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 225068 117 + 5224283/0-120
UGCCACUUCCUGCAAGCUUUAUAGCUUGAAAGAUAGAAUGAGGGACUUCGUUUAUAUACGGGUGCAUAAC---UUGUACGUAAAAAUCCCUCUUUCUCAAUAUGAAAAGAGGGAUUUUUU
..((...((...((((((....))))))...))..(((((((....)))))))......))(((((....---.)))))..((((((((((((((.((.....)))))))))))))))). ( -36.40)
>Banth.0 197002 117 + 5227293/0-120
UGCCACUUCCUGCAAGCUUUAUAGCUUGAAAGAUAGAAUGAGGGACUUCGUUUAUAUACGGGUGCAUAAC---UUGUACGUAAAAAUCCCUCUUUCUCAAUACGAAAAGAGGGAUUUUUU
..((...((...((((((....))))))...))..(((((((....)))))))......))(((((....---.)))))..((((((((((((((.((.....)))))))))))))))). ( -36.10)
>Bsubt.0 2024288 118 + 4214630/0-120
UGCCAAUUCCAGCAAGCGC--UAGCUUGAAAGAUAGGAAAGCAAGGUUUAUACCGGCGUCUGCCUGUAACAGAGCGCGCCUAUAUAUGAAUCUCUUUCCAUCUUCGGAAAGAGAUUUUUU
(((...((((..(((((..--..))))).......)))).))).(((....)))(((((..(((((...))).))))))).......((((((((((((......))))))))))))... ( -39.80)
>consensus
UGCCACUUCCUGCAAGCUUUAUAGCUUGAAAGAUAGAAUGAGGGACUUCGUUUAUAUACGGGUGCAUAAC___UUGUACGUAAAAAUCCCUCUUUCUCAAUAUGAAAAGAGGGAUUUUUU
.......((...(((((......)))))...))..(((((((....)))))))........(((((........)))))..((((((((((((((..........)))))))))))))). (-21.55 = -22.23 +   0.68)

alignment

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secondary structure

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Window 9

Location 225,068 – 225,185
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 67.98
Mean single sequence MFE -30.67
Consensus MFE -16.39
Energy contribution -16.85
Covariance contribution 0.45
Combinations/Pair 1.21
Mean z-score -1.61
Structure conservation index 0.53
SVM decision value 0.39
SVM RNA-class probability 0.718710
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 225068 117 + 5224283/40-160
CGUACAA---GUUAUGCACCCGUAUAUAAACGAAGUCCCUCAUUCUAUCUUUCAAGCUAUAAAGCUUGCAGGAAGUGGCACAGUAUUCAAAAAAUGAACCUGCUGCCGAGGUUUCAAAGG
.......---..(((((....))))).....((((..((((......((((.((((((....)))))).))))...(((((((..((((.....)))).))).))))))))))))..... ( -29.90)
>Banth.0 197002 116 + 5227293/40-160
CGUACAA---GUUAUGCACCCGUAUAUAAACGAAGUCCCUCAUUCUAUCUUUCAAGCUAUAAAGCUUGCAGGAAGUGGCACAGUAUUCAAAAA-UGAACCUGCUGCCGAGGUUUCAAAGG
.......---..(((((....))))).....((((..((((......((((.((((((....)))))).))))...(((((((..((((....-)))).))).))))))))))))..... ( -29.90)
>Bsubt.0 2024288 104 + 4214630/40-160
GGCGCGCUCUGUUACAGGCAGACGCCGGUAUAAACCUUGCUUUCCUAUCUUUCAAGCUA--GCGCUUGCUGGAAUUGGCACAAUAAU--------------GUUGCCGAGGUUUCAUAGG
((((...(((((.....)))))))))..((((((((((.........(((..(((((..--..)))))..)))...((((((....)--------------).))))))))))).))).. ( -32.20)
>consensus
CGUACAA___GUUAUGCACCCGUAUAUAAACGAAGUCCCUCAUUCUAUCUUUCAAGCUAUAAAGCUUGCAGGAAGUGGCACAGUAUUCAAAAA_UGAACCUGCUGCCGAGGUUUCAAAGG
.((((................))))............((((......((((.(((((......))))).))))...(((((((................))).))))))))......... (-16.39 = -16.85 +   0.45)

alignment

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secondary structure

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Window 0

Location 225,068 – 225,185
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 67.98
Mean single sequence MFE -33.70
Consensus MFE -21.43
Energy contribution -22.83
Covariance contribution 1.40
Combinations/Pair 1.19
Mean z-score -2.09
Structure conservation index 0.64
SVM decision value 3.97
SVM RNA-class probability 0.999732
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 225068 117 + 5224283/40-160
CCUUUGAAACCUCGGCAGCAGGUUCAUUUUUUGAAUACUGUGCCACUUCCUGCAAGCUUUAUAGCUUGAAAGAUAGAAUGAGGGACUUCGUUUAUAUACGGGUGCAUAAC---UUGUACG
.........((((((((.((((((((.....))))).))))))).((((...((((((....))))))...)).))...))))....((((......))))(((((....---.))))). ( -35.20)
>Banth.0 197002 116 + 5227293/40-160
CCUUUGAAACCUCGGCAGCAGGUUCA-UUUUUGAAUACUGUGCCACUUCCUGCAAGCUUUAUAGCUUGAAAGAUAGAAUGAGGGACUUCGUUUAUAUACGGGUGCAUAAC---UUGUACG
.........((((((((.((((((((-....))))).))))))).((((...((((((....))))))...)).))...))))....((((......))))(((((....---.))))). ( -35.20)
>Bsubt.0 2024288 104 + 4214630/40-160
CCUAUGAAACCUCGGCAAC--------------AUUAUUGUGCCAAUUCCAGCAAGCGC--UAGCUUGAAAGAUAGGAAAGCAAGGUUUAUACCGGCGUCUGCCUGUAACAGAGCGCGCC
(((((........((((.(--------------(....))))))........(((((..--..)))))....))))).......(((....)))(((((..(((((...))).))))))) ( -30.70)
>consensus
CCUUUGAAACCUCGGCAGCAGGUUCA_UUUUUGAAUACUGUGCCACUUCCUGCAAGCUUUAUAGCUUGAAAGAUAGAAUGAGGGACUUCGUUUAUAUACGGGUGCAUAAC___UUGUACG
....((((.((((((((.((((((((.....))))).)))))))...((...(((((......)))))...))......))))...))))...........(((((........))))). (-21.43 = -22.83 +   1.40)

alignment

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secondary structure

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Window 1

Location 225,068 – 225,183
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.23
Mean single sequence MFE -31.73
Consensus MFE -24.33
Energy contribution -24.56
Covariance contribution 0.22
Combinations/Pair 1.04
Mean z-score -2.52
Structure conservation index 0.77
SVM decision value 2.10
SVM RNA-class probability 0.987949
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 225068 115 + 5224283/79-199
UCAUUCUAUCUUUCAAGCUAUAAAGCUUGCAGGAAGUGGCACAGUAUUCAAAAAAUGAACCUGCUGCCGAGGUUUCAAAGGGCCAGUCCCUCCACCUCUCUUGAUACAA-----UGAGUA
(((((.((((...((((((....)))))).((((...(((((((..((((.....)))).))).))))(((((.....((((.....))))..))))))))))))).))-----)))... ( -33.80)
>Banth.0 197002 114 + 5227293/79-199
UCAUUCUAUCUUUCAAGCUAUAAAGCUUGCAGGAAGUGGCACAGUAUUCAAAAA-UGAACCUGCUGCCGAGGUUUCAAAGGGCCAGUCCCUCCACCUCUCUUGAUACAA-----UGAGUA
(((((.((((...((((((....)))))).((((...(((((((..((((....-)))).))).))))(((((.....((((.....))))..))))))))))))).))-----)))... ( -33.80)
>Bsubt.0 2024288 104 + 4214630/79-199
CUUUCCUAUCUUUCAAGCUA--GCGCUUGCUGGAAUUGGCACAAUAAU--------------GUUGCCGAGGUUUCAUAGGGCCAGUCCCUCCACCUCUCUGGAUAGAAAAUAUUGAGUA
((.(((..(((..(((((..--..)))))..)))...((((((....)--------------).))))(((((.....((((.....))))..)))))...))).))............. ( -27.60)
>consensus
UCAUUCUAUCUUUCAAGCUAUAAAGCUUGCAGGAAGUGGCACAGUAUUCAAAAA_UGAACCUGCUGCCGAGGUUUCAAAGGGCCAGUCCCUCCACCUCUCUUGAUACAA_____UGAGUA
.............(((((......)))))(((((...(((((((................))).))))(((((.....((((.....))))..))))))))))................. (-24.33 = -24.56 +   0.22)

alignment

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secondary structure

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Window 2

Location 225,068 – 225,183
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.23
Mean single sequence MFE -40.23
Consensus MFE -28.69
Energy contribution -30.63
Covariance contribution 1.95
Combinations/Pair 1.03
Mean z-score -3.97
Structure conservation index 0.71
SVM decision value 3.30
SVM RNA-class probability 0.998952
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 225068 115 + 5224283/79-199
UACUCA-----UUGUAUCAAGAGAGGUGGAGGGACUGGCCCUUUGAAACCUCGGCAGCAGGUUCAUUUUUUGAAUACUGUGCCACUUCCUGCAAGCUUUAUAGCUUGAAAGAUAGAAUGA
...(((-----((.(((((((.(((((.(((((.....)))))....)))))((((.((((((((.....))))).))))))).)))....((((((....))))))...)))).))))) ( -43.00)
>Banth.0 197002 114 + 5227293/79-199
UACUCA-----UUGUAUCAAGAGAGGUGGAGGGACUGGCCCUUUGAAACCUCGGCAGCAGGUUCA-UUUUUGAAUACUGUGCCACUUCCUGCAAGCUUUAUAGCUUGAAAGAUAGAAUGA
...(((-----((.(((((((.(((((.(((((.....)))))....)))))((((.((((((((-....))))).))))))).)))....((((((....))))))...)))).))))) ( -43.00)
>Bsubt.0 2024288 104 + 4214630/79-199
UACUCAAUAUUUUCUAUCCAGAGAGGUGGAGGGACUGGCCCUAUGAAACCUCGGCAAC--------------AUUAUUGUGCCAAUUCCAGCAAGCGC--UAGCUUGAAAGAUAGGAAAG
.........(((((((((....(((((..((((.....)))).....)))))((((.(--------------(....))))))........(((((..--..)))))...))))))))). ( -34.70)
>consensus
UACUCA_____UUGUAUCAAGAGAGGUGGAGGGACUGGCCCUUUGAAACCUCGGCAGCAGGUUCA_UUUUUGAAUACUGUGCCACUUCCUGCAAGCUUUAUAGCUUGAAAGAUAGAAUGA
...........((.((((....(((((.(((((.....)))))....)))))((((.((((((((.....))))).)))))))........(((((......)))))...)))).))... (-28.69 = -30.63 +   1.95)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 17:21:22 2006