Locus 76

Sequence ID Bcere.0
Location 2,730,666 – 3,425,135
Length 694469
Max. P 0.999955
window425 window426 window427 window428 window429 window430 window431 window432 window433 window434

overview

Window 5

Location 3,425,079 – 3,425,135
Length 56
Sequences 3
Columns 56
Reading direction forward
Mean pairwise identity 66.67
Mean single sequence MFE -9.87
Consensus MFE -5.63
Energy contribution -6.97
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 0.57
SVM decision value 4.84
SVM RNA-class probability 0.999955
Prediction RNA
WARNING Sequence 1: Base composition out of range.

Download alignment: ClustalW | MAF

>Bcere.0 3425079 56 + 5224283
UGAUUAAUUUUCUAUAAUUAUGUUCCCAAAAAAUUCAAAACCUUUUUUGGGAUCUA
((((((........))))))...((((((((((.........)))))))))).... ( -10.20)
>Banth.0 3409724 56 + 5227293
UGAUUAAUUCUCUAUAAUUAUACUCCCAAAAAAUUCAAGAUCUUUUUUGGGAUGCC
((((((........))))))...((((((((((.........)))))))))).... ( -10.10)
>Bsubt.0 559647 46 + 4214630
AGAUUUGCUUUUCAUCAUAAUAUUCCGAAAUA----------UCUUUUGGGAUGUA
...................(((((((((((..----------..))))))))))). (  -9.30)
>consensus
UGAUUAAUUUUCUAUAAUUAUAUUCCCAAAAAAUUCAA_A_CUUUUUUGGGAUGUA
.......................((((((((((.........)))))))))).... ( -5.63 =  -6.97 +   1.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,425,079 – 3,425,135
Length 56
Sequences 3
Columns 56
Reading direction reverse
Mean pairwise identity 66.67
Mean single sequence MFE -8.53
Consensus MFE -7.05
Energy contribution -7.83
Covariance contribution 0.78
Combinations/Pair 1.10
Mean z-score -1.61
Structure conservation index 0.83
SVM decision value 4.00
SVM RNA-class probability 0.999750
Prediction RNA
WARNING Sequence 1: Base composition out of range.

Download alignment: ClustalW | MAF

>Bcere.0 3425079 56 + 5224283
UAGAUCCCAAAAAAGGUUUUGAAUUUUUUGGGAACAUAAUUAUAGAAAAUUAAUCA
..(.((((((((((.........)))))))))).)..................... ( -11.10)
>Banth.0 3409724 56 + 5227293
GGCAUCCCAAAAAAGAUCUUGAAUUUUUUGGGAGUAUAAUUAUAGAGAAUUAAUCA
.((.((((((((((.........))))))))))))..................... ( -11.70)
>Bsubt.0 559647 46 + 4214630
UACAUCCCAAAAGA----------UAUUUCGGAAUAUUAUGAUGAAAAGCAAAUCU
..((((......((----------((((....))))))..))))............ (  -2.80)
>consensus
UACAUCCCAAAAAAG_U_UUGAAUUUUUUGGGAAUAUAAUUAUAGAAAAUUAAUCA
....((((((((((.........))))))))))....................... ( -7.05 =  -7.83 +   0.78)

alignment

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secondary structure

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Window 7

Location 2,730,666 – 2,730,784
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.45
Mean single sequence MFE -25.80
Consensus MFE -16.10
Energy contribution -17.10
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.84
Structure conservation index 0.62
SVM decision value 1.76
SVM RNA-class probability 0.975822
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 2730666 118 - 5224283/0-120
AUCCCUUUCAUUAA-GGGAGAAUAAAAAAAUCCUCCCAAAUAAAUUUGGCAGGAUUAGUCGUUAAAAUAUUUAUACCCAAAUAAGCUAUUGCGCAACAUAAAUAGCAAUACCGU-UGUAU
.((((((.....))-)))).........((((((.(((((....))))).))))))............................((((((..........))))))........-..... ( -24.50)
>Banth.0 2806177 117 - 5227293/0-120
AUCCCUUUCAUUAA-GGGAGAAUAAAAAA-UCCUCCCAAAUAAAUUUGGCAGGAUUAGUCGUUAAAAUAUUUAUACCCAAAUAAACUAUUGCGCAACAUAAAUAGCAAUACCGU-UGUAU
.((((((.....))-))))........((-((((.(((((....))))).))))))........................((((..((((((............))))))...)-))).. ( -24.40)
>Bsubt.0 605927 114 + 4214630/0-120
AUCCCUCGCUUUAAAGGGAGAAUAAAAAAAUCCUCCCAAAUGUGUU-GGAAGGAUUAGCCGU--GCCUGUGCAUGAUCAAAUAAGCUAUUUUU---UAUAAAUAGCAGUGUCGUAUAUAU
.(((((........)))))((.......((((((.((((.....))-)).))))))...(((--((....))))).))......(((((((..---...))))))).............. ( -28.50)
>consensus
AUCCCUUUCAUUAA_GGGAGAAUAAAAAAAUCCUCCCAAAUAAAUUUGGCAGGAUUAGUCGUUAAAAUAUUUAUACCCAAAUAAGCUAUUGCGCAACAUAAAUAGCAAUACCGU_UGUAU
.((((..........)))).........((((((.(((((....))))).))))))............................((((((..........)))))).............. (-16.10 = -17.10 +   1.00)

alignment

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secondary structure

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Window 8

Location 2,730,666 – 2,730,784
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.45
Mean single sequence MFE -27.30
Consensus MFE -18.74
Energy contribution -18.63
Covariance contribution -0.10
Combinations/Pair 1.14
Mean z-score -2.14
Structure conservation index 0.69
SVM decision value 1.06
SVM RNA-class probability 0.908854
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 2730666 118 - 5224283/0-120
AUACA-ACGGUAUUGCUAUUUAUGUUGCGCAAUAGCUUAUUUGGGUAUAAAUAUUUUAACGACUAAUCCUGCCAAAUUUAUUUGGGAGGAUUUUUUUAUUCUCCC-UUAAUGAAAGGGAU
((((.-..((((..((((((..........)))))).))))...))))................((((((.(((((....))))).)))))).........((((-((.....)))))). ( -26.40)
>Banth.0 2806177 117 - 5227293/0-120
AUACA-ACGGUAUUGCUAUUUAUGUUGCGCAAUAGUUUAUUUGGGUAUAAAUAUUUUAACGACUAAUCCUGCCAAAUUUAUUUGGGAGGA-UUUUUUAUUCUCCC-UUAAUGAAAGGGAU
.....-.((.((((((............))))))((((((......)))))).......))...((((((.(((((....))))).))))-))........((((-((.....)))))). ( -26.30)
>Bsubt.0 605927 114 + 4214630/0-120
AUAUAUACGACACUGCUAUUUAUA---AAAAAUAGCUUAUUUGAUCAUGCACAGGC--ACGGCUAAUCCUUCC-AACACAUUUGGGAGGAUUUUUUUAUUCUCCCUUUAAAGCGAGGGAU
.......((.....(((((((...---..)))))))...........(((....))--)))...(((((((((-((.....))))))))))).........((((((......)))))). ( -29.20)
>consensus
AUACA_ACGGUAUUGCUAUUUAUGUUGCGCAAUAGCUUAUUUGGGUAUAAAUAUUUUAACGACUAAUCCUGCCAAAUUUAUUUGGGAGGAUUUUUUUAUUCUCCC_UUAAUGAAAGGGAU
.......(((....((((((..........))))))....)))......................(((((......((((((.((((((((......))))))))...)))))).))))) (-18.74 = -18.63 +  -0.10)

alignment

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secondary structure

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Window 9

Location 2,730,666 – 2,730,785
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.94
Mean single sequence MFE -25.73
Consensus MFE -18.99
Energy contribution -18.00
Covariance contribution -0.99
Combinations/Pair 1.23
Mean z-score -1.98
Structure conservation index 0.74
SVM decision value 1.08
SVM RNA-class probability 0.911488
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 2730666 119 - 5224283/40-160
UAAAUUUGGCAGGAUUAGUCGUUAAAAUAUUUAUACCCAAAUAAGCUAUUGCGCAACAUAAAUAGCAAUACCGU-UGUAUGGAAAUUGGGCAGACUAAUCCUAUUUUUUAGAAAUUGAAA
..........((((((((((..(((.....)))..(((((....((((((..........))))))....((((-...))))...)))))..)))))))))).................. ( -26.40)
>Banth.0 2806177 119 - 5227293/40-160
UAAAUUUGGCAGGAUUAGUCGUUAAAAUAUUUAUACCCAAAUAAACUAUUGCGCAACAUAAAUAGCAAUACCGU-UGUAUGGAAAUUGGGCAGACUAAUCCUAUUUUUUAGAAAUUGAAA
..........((((((((((..(((.....)))..(((((......((((((............))))))((((-...))))...)))))..)))))))))).................. ( -25.20)
>Bsubt.0 605927 112 + 4214630/40-160
UGUGUU-GGAAGGAUUAGCCGU--GCCUGUGCAUGAUCAAAUAAGCUAUUUUU---UAUAAAUAGCAGUGUCGUAUAUAUAGAAAAUGGGCAGACUAAUCCUAUUUUUU--GAUUUGAAA
((..(.-((..((.....))..--.)).)..))...((((((..(((((((..---...))))))).............(((((((((((.(......)))))))))))--))))))).. ( -25.60)
>consensus
UAAAUUUGGCAGGAUUAGUCGUUAAAAUAUUUAUACCCAAAUAAGCUAUUGCGCAACAUAAAUAGCAAUACCGU_UGUAUGGAAAUUGGGCAGACUAAUCCUAUUUUUUAGAAAUUGAAA
..........((((((((((....((....))...((((.....((((((..........)))))).((((.....))))......))))..)))))))))).................. (-18.99 = -18.00 +  -0.99)

alignment

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secondary structure

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Window 0

Location 2,730,666 – 2,730,785
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.94
Mean single sequence MFE -25.83
Consensus MFE -19.22
Energy contribution -18.57
Covariance contribution -0.66
Combinations/Pair 1.21
Mean z-score -3.33
Structure conservation index 0.74
SVM decision value 3.18
SVM RNA-class probability 0.998669
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 2730666 119 - 5224283/40-160
UUUCAAUUUCUAAAAAAUAGGAUUAGUCUGCCCAAUUUCCAUACA-ACGGUAUUGCUAUUUAUGUUGCGCAAUAGCUUAUUUGGGUAUAAAUAUUUUAACGACUAAUCCUGCCAAAUUUA
.................((((((((((((((((((.....((((.-...)))).((((((..........))))))....)))))))(((.....)))..)))))))))))......... ( -26.40)
>Banth.0 2806177 119 - 5227293/40-160
UUUCAAUUUCUAAAAAAUAGGAUUAGUCUGCCCAAUUUCCAUACA-ACGGUAUUGCUAUUUAUGUUGCGCAAUAGUUUAUUUGGGUAUAAAUAUUUUAACGACUAAUCCUGCCAAAUUUA
.................((((((((((((((((((...((.....-..))((((((............))))))......)))))))(((.....)))..)))))))))))......... ( -26.10)
>Bsubt.0 605927 112 + 4214630/40-160
UUUCAAAUC--AAAAAAUAGGAUUAGUCUGCCCAUUUUCUAUAUAUACGACACUGCUAUUUAUA---AAAAAUAGCUUAUUUGAUCAUGCACAGGC--ACGGCUAAUCCUUCC-AACACA
.........--.......(((((((((((((((((..((...(((.........(((((((...---..))))))).)))..))..)))....)))--).))))))))))...-...... ( -25.00)
>consensus
UUUCAAUUUCUAAAAAAUAGGAUUAGUCUGCCCAAUUUCCAUACA_ACGGUAUUGCUAUUUAUGUUGCGCAAUAGCUUAUUUGGGUAUAAAUAUUUUAACGACUAAUCCUGCCAAAUUUA
.................(((((((((((((((((.......(((.....)))..((((((..........)))))).....)))))).((....))....)))))))))))......... (-19.22 = -18.57 +  -0.66)

alignment

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secondary structure

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Window 1

Location 2,730,666 – 2,730,785
Length 119
Sequences 2
Columns 119
Reading direction forward
Mean pairwise identity 98.32
Mean single sequence MFE -25.95
Consensus MFE -25.15
Energy contribution -25.15
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.88
Structure conservation index 0.97
SVM decision value 2.34
SVM RNA-class probability 0.992564
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 2730666 119 - 5224283/80-200
AUAAGCUAUUGCGCAACAUAAAUAGCAAUACCGUUGUAUGGAAAUUGGGCAGACUAAUCCUAUUUUUUAGAAAUUGAAAUGUAUUGAAUUUCAACAUUUAAAAAUAAGAUUAGUUAAUC
....((((((((............))))).((((...))))......))).((((((((.(((((((.(((..(((((((.......)))))))..)))))))))).)))))))).... ( -25.70)
>Banth.0 2806177 119 - 5227293/80-200
AUAAACUAUUGCGCAACAUAAAUAGCAAUACCGUUGUAUGGAAAUUGGGCAGACUAAUCCUAUUUUUUAGAAAUUGAAAUUUAUUGAAUUUCAACAUUUAAAAAUAAGAUUAGUUAAUC
.........(((.(((..((.(((((......))))).))....))).)))((((((((.(((((((.(((..(((((((((...)))))))))..)))))))))).)))))))).... ( -26.20)
>consensus
AUAAACUAUUGCGCAACAUAAAUAGCAAUACCGUUGUAUGGAAAUUGGGCAGACUAAUCCUAUUUUUUAGAAAUUGAAAUGUAUUGAAUUUCAACAUUUAAAAAUAAGAUUAGUUAAUC
.........(((.(((..((.(((((......))))).))....))).)))((((((((.(((((((.(((..(((((((.......)))))))..)))))))))).)))))))).... (-25.15 = -25.15 +   0.00)

alignment

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secondary structure

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Window 2

Location 2,730,666 – 2,730,785
Length 119
Sequences 2
Columns 119
Reading direction reverse
Mean pairwise identity 98.32
Mean single sequence MFE -25.20
Consensus MFE -24.30
Energy contribution -24.55
Covariance contribution 0.25
Combinations/Pair 1.03
Mean z-score -3.14
Structure conservation index 0.96
SVM decision value 2.52
SVM RNA-class probability 0.994862
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 2730666 119 - 5224283/80-200
GAUUAACUAAUCUUAUUUUUAAAUGUUGAAAUUCAAUACAUUUCAAUUUCUAAAAAAUAGGAUUAGUCUGCCCAAUUUCCAUACAACGGUAUUGCUAUUUAUGUUGCGCAAUAGCUUAU
.....(((((((((((((((....((((((((.......)))))))).....)))))))))))))))....................(.((((((............)))))).).... ( -24.90)
>Banth.0 2806177 119 - 5227293/80-200
GAUUAACUAAUCUUAUUUUUAAAUGUUGAAAUUCAAUAAAUUUCAAUUUCUAAAAAAUAGGAUUAGUCUGCCCAAUUUCCAUACAACGGUAUUGCUAUUUAUGUUGCGCAAUAGUUUAU
((((((((((((((((((((....(((((((((.....))))))))).....))))))))))))))).(((.((((....((((((.....))).)))....)))).))).)))))... ( -25.50)
>consensus
GAUUAACUAAUCUUAUUUUUAAAUGUUGAAAUUCAAUAAAUUUCAAUUUCUAAAAAAUAGGAUUAGUCUGCCCAAUUUCCAUACAACGGUAUUGCUAUUUAUGUUGCGCAAUAGCUUAU
.....(((((((((((((((....(((((((((.....))))))))).....)))))))))))))))....................(.((((((............)))))).).... (-24.30 = -24.55 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,730,666 – 2,730,786
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.00
Mean single sequence MFE -24.03
Consensus MFE -19.07
Energy contribution -19.73
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.84
Structure conservation index 0.79
SVM decision value 1.44
SVM RNA-class probability 0.954459
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 2730666 120 - 5224283/120-240
GGAAAUUGGGCAGACUAAUCCUAUUUUUUAGAAAUUGAAAUGUAUUGAAUUUCAACAUUUAAAAAUAAGAUUAGUUAAUCAUCGUCCACCCAUCAUUCCUUUCCGUCGUUAAUAACCAUA
((((..((((..((((((((.(((((((.(((..(((((((.......)))))))..)))))))))).))))))))............))))...))))..................... ( -23.84)
>Banth.0 2806177 120 - 5227293/120-240
GGAAAUUGGGCAGACUAAUCCUAUUUUUUAGAAAUUGAAAUUUAUUGAAUUUCAACAUUUAAAAAUAAGAUUAGUUAAUCAUCGUCCACCCAUCAUUCCUUUCCGUCAUUAAUAACCAUA
((((..((((..((((((((.(((((((.(((..(((((((((...)))))))))..)))))))))).))))))))............))))...))))..................... ( -24.34)
>Bsubt.0 605927 115 + 4214630/120-240
AGAAAAUGGGCAGACUAAUCCUAUUUUUU--GAUUUGAAAU--AUUGA-UUUCAAACGGUAAAAAUAAGAUUAGUUAAUCAUUGUCCACCCAUCAUCCCUUCUUGUUUUGAUUACAAACA
......((((((((((((((.(((((((.--..((((((((--....)-)))))))....))))))).))))))))......))))))..............((((.......))))... ( -23.90)
>consensus
GGAAAUUGGGCAGACUAAUCCUAUUUUUUAGAAAUUGAAAU_UAUUGAAUUUCAACAUUUAAAAAUAAGAUUAGUUAAUCAUCGUCCACCCAUCAUUCCUUUCCGUCAUUAAUAACCAUA
(((...(((...((((((((.(((((((......(((((((.......))))))).....))))))).))))))))..)))...)))................................. (-19.07 = -19.73 +   0.67)

alignment

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secondary structure

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Window 4

Location 2,730,666 – 2,730,786
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.00
Mean single sequence MFE -33.03
Consensus MFE -29.92
Energy contribution -29.37
Covariance contribution -0.55
Combinations/Pair 1.09
Mean z-score -4.21
Structure conservation index 0.91
SVM decision value 2.14
SVM RNA-class probability 0.988943
Prediction RNA

Download alignment: ClustalW | MAF

>Bcere.0 2730666 120 - 5224283/120-240
UAUGGUUAUUAACGACGGAAAGGAAUGAUGGGUGGACGAUGAUUAACUAAUCUUAUUUUUAAAUGUUGAAAUUCAAUACAUUUCAAUUUCUAAAAAAUAGGAUUAGUCUGCCCAAUUUCC
....(((......))).....((((...((((..((((........)(((((((((((((....((((((((.......)))))))).....))))))))))))))))..))))..)))) ( -31.00)
>Banth.0 2806177 120 - 5227293/120-240
UAUGGUUAUUAAUGACGGAAAGGAAUGAUGGGUGGACGAUGAUUAACUAAUCUUAUUUUUAAAUGUUGAAAUUCAAUAAAUUUCAAUUUCUAAAAAAUAGGAUUAGUCUGCCCAAUUUCC
....((((....)))).....((((...((((..((((........)(((((((((((((....(((((((((.....))))))))).....))))))))))))))))..))))..)))) ( -33.10)
>Bsubt.0 605927 115 + 4214630/120-240
UGUUUGUAAUCAAAACAAGAAGGGAUGAUGGGUGGACAAUGAUUAACUAAUCUUAUUUUUACCGUUUGAAA-UCAAU--AUUUCAAAUC--AAAAAAUAGGAUUAGUCUGCCCAUUUUCU
(((((.......))))).....(((.((((((..(((..........(((((((((((((...((((((((-(....--))))))))).--.))))))))))))))))..)))))).))) ( -35.00)
>consensus
UAUGGUUAUUAAAGACGGAAAGGAAUGAUGGGUGGACGAUGAUUAACUAAUCUUAUUUUUAAAUGUUGAAAUUCAAUA_AUUUCAAUUUCUAAAAAAUAGGAUUAGUCUGCCCAAUUUCC
.....................((((...((((..(((..........(((((((((((((....((((((((.......)))))))).....))))))))))))))))..))))..)))) (-29.92 = -29.37 +  -0.55)

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 17:21:16 2006