Locus 123

Sequence ID Bhalo.0
Location 1,699,955 – 1,700,069
Length 114
Max. P 0.999966
window860 window861 window862 window863 window864 window865

overview

Window 0

Location 1,699,955 – 1,700,069
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 70.76
Mean single sequence MFE -38.55
Consensus MFE -31.89
Energy contribution -31.82
Covariance contribution -0.06
Combinations/Pair 1.23
Mean z-score -3.13
Structure conservation index 0.83
SVM decision value 4.98
SVM RNA-class probability 0.999966
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 1699955 114 + 4202352/0-120
AUUCUUAUCCAGAGAGGUGGAGGGAACGGCCCGAAGAAACCUCAGCAACCAGCCACGAUCCUGUGGUCAGGUGCUAAUUCCUGCAAGCAUUAUUUG--CUUGAGAGAUAAGAGGA----A
.(((((((((((.(((((...(((.....)))......)))))((((.((.((((((....))))))..)))))).....)))((((((.....))--))))...))))))))..----. ( -42.00)
>Bclau.0 1983210 103 + 4303871/0-120
GUUCUUAUCAAGAGAAGUGGAGGGAAUGGCCCAAUGAAGCUUCAGCAACCAGCCAA----CCAUGGUCAGGUGCUAAAUCCAGCAG------UUUA--UCUGCAAGAUAAGAG-A----A
.((((((((........(((((((.....)))...........((((.((.((((.----...))))..))))))...))))((((------....--.))))..))))))))-.----. ( -32.00)
>Banth.0 320603 115 + 5227293/0-120
AUUCUUAUCCAGAGAGGUGGAGGGACUGGCCCUACGAUACCUCAGCAACGGGUUUU-----UUUAAUACCGUGCUAACUCCAGCAAGCCAUAUAAAGGCUUGGAAGAUGAGAAGAUGUGA
.((((((((....((((((.((((.....))))....))))))((((.(((.....-----.......)))))))........((((((.......))))))...))))))))....... ( -39.40)
>Bcere.0 361552 115 + 5224283/0-120
AUUCUUAUCCAGAGAGGUGGAGGGACUGGCCCUACGAUACCUCAGCAACGGGUUUU-----UUUAAUACCGUGCUAACUCCAGCAAGCCUAUGAAAGGCUUGGAAGAUGAGAAGAUGUGA
.((((((((....((((((.((((.....))))....))))))((((.(((.....-----.......)))))))........(((((((.....)))))))...))))))))....... ( -40.80)
>consensus
AUUCUUAUCCAGAGAGGUGGAGGGAAUGGCCCUACGAAACCUCAGCAACCAGCCAU_____UUUAAUAACGUGCUAACUCCAGCAAGCCUUAUAAA__CUUGGAAGAUAAGAAGA____A
.((((((((....((((((.((((.....))))....))))))((((.(((((((........)))).)))))))........((((((.......))))))...))))))))....... (-31.89 = -31.82 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 1,699,955 – 1,700,069
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 70.76
Mean single sequence MFE -33.10
Consensus MFE -24.52
Energy contribution -25.52
Covariance contribution 1.00
Combinations/Pair 1.12
Mean z-score -2.41
Structure conservation index 0.74
SVM decision value 3.87
SVM RNA-class probability 0.999671
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 1699955 114 + 4202352/0-120
U----UCCUCUUAUCUCUCAAG--CAAAUAAUGCUUGCAGGAAUUAGCACCUGACCACAGGAUCGUGGCUGGUUGCUGAGGUUUCUUCGGGCCGUUCCCUCCACCUCUCUGGAUAAGAAU
.----...(((((((...((((--((.....))))))((((....((((((.(.((((......))))).)).))))(((((......(((.....)))...)))))))))))))))).. ( -36.70)
>Bclau.0 1983210 103 + 4303871/0-120
U----U-CUCUUAUCUUGCAGA--UAAA------CUGCUGGAUUUAGCACCUGACCAUGG----UUGGCUGGUUGCUGAAGCUUCAUUGGGCCAUUCCCUCCACUUCUCUUGAUAAGAAC
.----.-.(((((((..((((.--....------))))(((((((((((((.(.(((...----.)))).)).)))))))........(((.....)))))))........))))))).. ( -30.90)
>Banth.0 320603 115 + 5227293/0-120
UCACAUCUUCUCAUCUUCCAAGCCUUUAUAUGGCUUGCUGGAGUUAGCACGGUAUUAAA-----AAAACCCGUUGCUGAGGUAUCGUAGGGCCAGUCCCUCCACCUCUCUGGAUAAGAAU
.....((((.((.(((..((((((.......))))))..)))...(((((((.......-----.....))).))))(((((...(.((((.....)))).))))))....)).)))).. ( -31.80)
>Bcere.0 361552 115 + 5224283/0-120
UCACAUCUUCUCAUCUUCCAAGCCUUUCAUAGGCUUGCUGGAGUUAGCACGGUAUUAAA-----AAAACCCGUUGCUGAGGUAUCGUAGGGCCAGUCCCUCCACCUCUCUGGAUAAGAAU
.....((((.((.(((..(((((((.....)))))))..)))...(((((((.......-----.....))).))))(((((...(.((((.....)))).))))))....)).)))).. ( -33.00)
>consensus
U____UCCUCUCAUCUUCCAAG__UAAAUAAGGCUUGCUGGAGUUAGCACCGGACCAAA_____AAAACCCGUUGCUGAGGUAUCGUAGGGCCAGUCCCUCCACCUCUCUGGAUAAGAAU
........(((((((...((((((.......))))))..(((.((((((((((.(((........))))))).)))))).........(((.....)))))).........))))))).. (-24.52 = -25.52 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 1,699,955 – 1,700,069
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 58.20
Mean single sequence MFE -36.17
Consensus MFE -14.31
Energy contribution -17.62
Covariance contribution 3.31
Combinations/Pair 1.30
Mean z-score -3.88
Structure conservation index 0.40
SVM decision value 1.93
SVM RNA-class probability 0.983061
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 1699955 114 + 4202352/40-160
CUCAGCAACCAGCCACGAUCCUGUGGUCAGGUGCUAAUUCCUGCAAGCAUUAUUUG--CUUGAGAGAUAAGAGGA----AGCGAGUGAGAUCCAACACCUACUUCUUCUUAAUCUUACAU
...((((.((.((((((....))))))..))))))........((((((.....))--)))).((((((((((((----((...(((........)))...))))))))).))))).... ( -36.90)
>Bclau.0 1983210 97 + 4303871/40-160
UUCAGCAACCAGCCAA----CCAUGGUCAGGUGCUAAAUCCAGCAG------UUUA--UCUGCAAGAUAAGAG-A----AGCAUGCACG--UAAGCAACCCCUUCUUCU-AAUCUUG---
...((((.((.((((.----...))))..)))))).......((((------....--.))))(((((.((((-(----((..(((...--...)))....)))).)))-.))))).--- ( -26.30)
>Banth.0 320603 115 + 5227293/40-160
CUCAGCAACGGGUUUU-----UUUAAUACCGUGCUAACUCCAGCAAGCCAUAUAAAGGCUUGGAAGAUGAGAAGAUGUGACCGAGUACAUAUAAGUGCUCUCCUUCUUAUCUUUAUGGUU
...((((.(((.....-----.......)))))))....(((.((((((.......))))))((((((((((((....((..((((((......)))))))))))))))))))).))).. ( -38.90)
>Bcere.0 361552 115 + 5224283/40-160
CUCAGCAACGGGUUUU-----UUUAAUACCGUGCUAACUCCAGCAAGCCUAUGAAAGGCUUGGAAGAUGAGAAGAUGUGAACGAGUACAUAUAAGUGCUCUCCUUCUUAUCUUUAUGGUU
...((((.(((.....-----.......)))))))....(((.(((((((.....)))))))((((((((((((..(....)((((((......))))))..)))))))))))).))).. ( -42.60)
>consensus
CUCAGCAACCAGCCAU_____UUUAAUAACGUGCUAACUCCAGCAAGCCUUAUAAA__CUUGGAAGAUAAGAAGA____AGCGAGUACAUAUAAGCACCCUCCUCCUCAUAAUCAUGGUU
...((((.(((((((........)))).)))))))........((((((.......)))))).....((((((((((.....((((((......)))))).......))))))))))... (-14.31 = -17.62 +   3.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 1,699,955 – 1,700,069
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 58.20
Mean single sequence MFE -33.62
Consensus MFE -17.52
Energy contribution -18.78
Covariance contribution 1.25
Combinations/Pair 1.32
Mean z-score -2.68
Structure conservation index 0.52
SVM decision value 2.95
SVM RNA-class probability 0.997869
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 1699955 114 + 4202352/40-160
AUGUAAGAUUAAGAAGAAGUAGGUGUUGGAUCUCACUCGCU----UCCUCUUAUCUCUCAAG--CAAAUAAUGCUUGCAGGAAUUAGCACCUGACCACAGGAUCGUGGCUGGUUGCUGAG
.........(((((.((((..((((........))))..))----)).)))))(((..((((--((.....))))))..))).((((((((.(.((((......))))).)).)))))). ( -39.10)
>Bclau.0 1983210 97 + 4303871/40-160
---CAAGAUU-AGAAGAAGGGGUUGCUUA--CGUGCAUGCU----U-CUCUUAUCUUGCAGA--UAAA------CUGCUGGAUUUAGCACCUGACCAUGG----UUGGCUGGUUGCUGAA
---.......-..((((.((((((((...--...))).)))----)-)))))((((.((((.--....------)))).))))((((((((.(.(((...----.)))).)).)))))). ( -29.40)
>Banth.0 320603 115 + 5227293/40-160
AACCAUAAAGAUAAGAAGGAGAGCACUUAUAUGUACUCGGUCACAUCUUCUCAUCUUCCAAGCCUUUAUAUGGCUUGCUGGAGUUAGCACGGUAUUAAA-----AAAACCCGUUGCUGAG
..(((..(((((.((((((.(((.((......)).)))(....).)))))).))))).((((((.......)))))).)))..(((((((((.......-----.....))).)))))). ( -32.60)
>Bcere.0 361552 115 + 5224283/40-160
AACCAUAAAGAUAAGAAGGAGAGCACUUAUAUGUACUCGUUCACAUCUUCUCAUCUUCCAAGCCUUUCAUAGGCUUGCUGGAGUUAGCACGGUAUUAAA-----AAAACCCGUUGCUGAG
.......(((((..(((.(((.(((......))).))).)))..)))))....(((..(((((((.....)))))))..))).(((((((((.......-----.....))).)))))). ( -33.40)
>consensus
AACCAAAAAGAAAAAAAAGAGAGCACUUAUACGUACUCGCU____UCCUCUCAUCUUCCAAG__UAAAUAAGGCUUGCUGGAGUUAGCACCGGACCAAA_____AAAACCCGUUGCUGAG
....................((((((......))))))...............(((..((((((.......))))))..))).((((((((((.(((........))))))).)))))). (-17.52 = -18.78 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 1,699,955 – 1,700,069
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 59.10
Mean single sequence MFE -38.46
Consensus MFE -24.33
Energy contribution -25.09
Covariance contribution 0.75
Combinations/Pair 1.41
Mean z-score -4.05
Structure conservation index 0.63
SVM decision value 3.29
SVM RNA-class probability 0.998941
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 1699955 114 + 4202352/62-182
GUGGUCAGGUGCUAAUUCCUGCAAGCAUUAUUUG--CUUGAGAGAUAAGAGGA----AGCGAGUGAGAUCCAACACCUACUUCUUCUUAAUCUUACAUGACGAGAAGGUAGGUGUUUUUU
(.((((...((((..(((((.((((((.....))--)))).........))))----)...)))).)))))(((((((((..((((((..((......)).))))))))))))))).... ( -34.10)
>Bclau.0 1983210 95 + 4303871/62-182
AUGGUCAGGUGCUAAAUCCAGCAG------UUUA--UCUGCAAGAUAAGAG-A----AGCAUGCACG--UAAGCAACCCCUUCUUCU-AAUCUUG------GAGAAGG---GUUUUUUGU
...(((.((........)).((((------....--.))))..)))..(((-(----(((.(((...--...)))...((((((((.-......)------)))))))---))))))).. ( -26.50)
>Banth.0 320603 120 + 5227293/62-182
UUAAUACCGUGCUAACUCCAGCAAGCCAUAUAAAGGCUUGGAAGAUGAGAAGAUGUGACCGAGUACAUAUAAGUGCUCUCCUUCUUAUCUUUAUGGUUGAUAAGAAGGAGAGCACUUUUU
........(((((...((((.((((((.......)))))).............)).))...)))))....(((((((((((((((((((.........)))))))))))))))))))... ( -45.04)
>Bcere.0 361552 120 + 5224283/62-182
UUAAUACCGUGCUAACUCCAGCAAGCCUAUGAAAGGCUUGGAAGAUGAGAAGAUGUGAACGAGUACAUAUAAGUGCUCUCCUUCUUAUCUUUAUGGUUGAUAAGAAGGAGAGCACUUUUU
........(((((..(((...(((((((.....)))))))......)))....((....)))))))....(((((((((((((((((((.........)))))))))))))))))))... ( -48.20)
>consensus
UUAAUAACGUGCUAACUCCAGCAAGCCUUAUAAA__CUUGGAAGAUAAGAAGA____AGCGAGUACAUAUAAGCACCCUCCUCCUCAUAAUCAUGGUUGAUAAGAAGGAGAGCACUUUUU
........(((((...((...((((((.......))))))...))................)))))....(((((((((((((((((((.........)))))))))))))))))))... (-24.33 = -25.09 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 1,699,955 – 1,700,069
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 59.10
Mean single sequence MFE -36.83
Consensus MFE -23.96
Energy contribution -25.77
Covariance contribution 1.81
Combinations/Pair 1.32
Mean z-score -5.10
Structure conservation index 0.65
SVM decision value 2.33
SVM RNA-class probability 0.992452
Prediction RNA

Download alignment: ClustalW | MAF

>Bhalo.0 1699955 114 + 4202352/62-182
AAAAAACACCUACCUUCUCGUCAUGUAAGAUUAAGAAGAAGUAGGUGUUGGAUCUCACUCGCU----UCCUCUUAUCUCUCAAG--CAAAUAAUGCUUGCAGGAAUUAGCACCUGACCAC
....((((((((((((((.(((......)))..)))))..)))))))))((............----.............((((--((.....))))))((((........)))).)).. ( -29.50)
>Bclau.0 1983210 95 + 4303871/62-182
ACAAAAAAC---CCUUCUC------CAAGAUU-AGAAGAAGGGGUUGCUUA--CGUGCAUGCU----U-CUCUUAUCUUGCAGA--UAAA------CUGCUGGAUUUAGCACCUGACCAU
.........---((((((.------(......-.).))))))((((((...--...)).((((----.-.....((((.((((.--....------)))).))))..))))...)))).. ( -24.10)
>Banth.0 320603 120 + 5227293/62-182
AAAAAGUGCUCUCCUUCUUAUCAACCAUAAAGAUAAGAAGGAGAGCACUUAUAUGUACUCGGUCACAUCUUCUCAUCUUCCAAGCCUUUAUAUGGCUUGCUGGAGUUAGCACGGUAUUAA
...(((((((((((((((((((.........)))))))))))))))))))....((((.((..............(((..((((((.......))))))..)))(....).))))))... ( -46.10)
>Bcere.0 361552 120 + 5224283/62-182
AAAAAGUGCUCUCCUUCUUAUCAACCAUAAAGAUAAGAAGGAGAGCACUUAUAUGUACUCGUUCACAUCUUCUCAUCUUCCAAGCCUUUCAUAGGCUUGCUGGAGUUAGCACGGUAUUAA
...(((((((((((((((((((.........)))))))))))))))))))....((((.(((.............(((..(((((((.....)))))))..)))(....))))))))... ( -47.60)
>consensus
AAAAAAUACUCUCCUUCUCAUCAACCAAAAAGAAAAAAAAGAGAGCACUUAUACGUACUCGCU____UCCUCUCAUCUUCCAAG__UAAAUAAGGCUUGCUGGAGUUAGCACCGGACCAA
...(((((((((((((((((((.........))))))))))))))))))).........................(((..((((((.......))))))..)))................ (-23.96 = -25.77 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 17:26:54 2006