Locus 5949

Sequence ID 2R_DroMel_CAF1
Location 18,765,185 – 18,765,366
Length 181
Max. P 0.998226
window9543 window9544 window9545 window9546 window9547

overview

Window 3

Location 18,765,185 – 18,765,298
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.49
Mean single sequence MFE -36.32
Consensus MFE -29.11
Energy contribution -29.62
Covariance contribution 0.51
Combinations/Pair 1.10
Mean z-score -3.29
Structure conservation index 0.80
SVM decision value 3.04
SVM RNA-class probability 0.998226
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18765185 113 + 20766785
AAGAGUAUGAAUACCCAAUGAACGCAGUCACCUCUGCCACACGAAAUGCCAAAAAGUGGCAAGUGG-------AAUUUGCAAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCU
.......................((((......))))..(((....(((((.....))))).)))(-------(((((((((..(((((((((.....)))))))))..)))))))))). ( -39.70)
>DroSec_CAF1 127704 113 + 1
AAGCGUAUGAAAACCCAAUGAAUGCAGUCACCUCUGCCACACGAAAUGCAAAAAACUGGCAAGUGG-------AAUUUGCAAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCU
..((((.((......))......((((......))))........)))).....(((....)))((-------(((((((((..(((((((((.....)))))))))..))))))))))) ( -34.60)
>DroSim_CAF1 128560 113 + 1
AGGCGUAUGAAUACCCAAUGAAUGCAGUCACCUCUGCCACACGAAAUGCCAAAAAGUGGCAAGUGG-------AAUUUGCAAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCU
.((.(((....))))).......((((......))))..(((....(((((.....))))).)))(-------(((((((((..(((((((((.....)))))))))..)))))))))). ( -42.30)
>DroEre_CAF1 129836 112 + 1
GAAAGUAUGAAUAGCCAAUGAAUGCAGUCACCUCUGGCCGACGAGAUGCCAAAAAGUGGCAAGUGG--------AAUUGCAAAAAGUGCUGUAAGUGAUGCGGCGCUGAUUGCGAAUUCU
....((((..((.....))..)))).(((((...((((.........))))....)))))....((--------((((((((..(((((((((.....)))))))))..)))).)))))) ( -33.00)
>DroYak_CAF1 130643 108 + 1
AGAAGUGUGAAUAUCCAAUGAAUGCAGUCACCUCUGCCUGACGAAAUGCCAAAAAGUGGCAAGUGGCAAGUGGCAUUUGCAAAAAGUGCU------------GCGCUGAUUGCAGAUUCU
........((((..........((((((((.(..((((..((....(((((.....))))).)))))).(..((((((.....)))))).------------.)).)))))))).)))). ( -32.00)
>consensus
AAGAGUAUGAAUACCCAAUGAAUGCAGUCACCUCUGCCACACGAAAUGCCAAAAAGUGGCAAGUGG_______AAUUUGCAAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCU
..............(((......((((......)))).........(((((.....)))))..)))........((((((((..(((((((((.....)))))))))..))))))))... (-29.11 = -29.62 +   0.51)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,765,185 – 18,765,298
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.49
Mean single sequence MFE -28.64
Consensus MFE -20.17
Energy contribution -21.22
Covariance contribution 1.05
Combinations/Pair 1.00
Mean z-score -1.62
Structure conservation index 0.70
SVM decision value -0.03
SVM RNA-class probability 0.520624
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18765185 113 - 20766785
AGAAUCUGCAAUCAGCGCUGCAUCACUUACAGCACUUUUUGCAAAUU-------CCACUUGCCACUUUUUGGCAUUUCGUGUGGCAGAGGUGACUGCGUUCAUUGGGUAUUCAUACUCUU
.((((.(((((..((.((((.........)))).))..))))).)))-------)....((((((...............))))))(((((((.(((.(.....).))).)))).))).. ( -31.46)
>DroSec_CAF1 127704 113 - 1
AGAAUCUGCAAUCAGCGCUGCAUCACUUACAGCACUUUUUGCAAAUU-------CCACUUGCCAGUUUUUUGCAUUUCGUGUGGCAGAGGUGACUGCAUUCAUUGGGUUUUCAUACGCUU
.(((..((((.(((.(.((((..........((((....((((((..-------..(((....)))..))))))....)))).)))).).))).)))))))...(.((......)).).. ( -25.90)
>DroSim_CAF1 128560 113 - 1
AGAAUCUGCAAUCAGCGCUGCAUCACUUACAGCACUUUUUGCAAAUU-------CCACUUGCCACUUUUUGGCAUUUCGUGUGGCAGAGGUGACUGCAUUCAUUGGGUAUUCAUACGCCU
.((((.(((((..((.((((.........)))).))..))))).)))-------)....(((((.....)))))...((((((((((......))))(((.....)))...))))))... ( -31.00)
>DroEre_CAF1 129836 112 - 1
AGAAUUCGCAAUCAGCGCCGCAUCACUUACAGCACUUUUUGCAAUU--------CCACUUGCCACUUUUUGGCAUCUCGUCGGCCAGAGGUGACUGCAUUCAUUGGCUAUUCAUACUUUC
.((((..((.....))((((.........((((((((((.((....--------.....(((((.....)))))........)).))))))).))).......)))).))))........ ( -25.72)
>DroYak_CAF1 130643 108 - 1
AGAAUCUGCAAUCAGCGC------------AGCACUUUUUGCAAAUGCCACUUGCCACUUGCCACUUUUUGGCAUUUCGUCAGGCAGAGGUGACUGCAUUCAUUGGAUAUUCACACUUCU
.((((.(.((((.((.((------------((((((((..((....))....((((((.(((((.....)))))....))..)))))))))).)))).)).)))).).))))........ ( -29.10)
>consensus
AGAAUCUGCAAUCAGCGCUGCAUCACUUACAGCACUUUUUGCAAAUU_______CCACUUGCCACUUUUUGGCAUUUCGUGUGGCAGAGGUGACUGCAUUCAUUGGGUAUUCAUACUCUU
.((((..((((..((.((((.........)))).))..))))............(((..(((((.....))))).........((((......))))......)))..))))........ (-20.17 = -21.22 +   1.05)

alignment

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secondary structure

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Window 5

Location 18,765,225 – 18,765,337
Length 112
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 89.11
Mean single sequence MFE -43.06
Consensus MFE -34.14
Energy contribution -35.45
Covariance contribution 1.31
Combinations/Pair 1.09
Mean z-score -5.44
Structure conservation index 0.79
SVM decision value 3.01
SVM RNA-class probability 0.998102
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18765225 112 + 20766785
ACGAAAUGCCAAAAAGUGGCAAGUGG-------AAUUUGCAAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCUGUUUCUGCCACAGUGGGGCAAUUAGAAGAAUGCGCCAAA
...............((((((((..(-------(((((((((..(((((((((.....)))))))))..))))))))))..))..))))))..(((.(((.((....)).))).))).. ( -47.40)
>DroSec_CAF1 127744 112 + 1
ACGAAAUGCAAAAAACUGGCAAGUGG-------AAUUUGCAAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCUGUUUAUGCCACAGUGGGGCAAUUAGAAGAAUGCGCCAAA
................(((((((..(-------(((((((((..(((((((((.....)))))))))..))))))))))..))..)))))...(((.(((.((....)).))).))).. ( -43.40)
>DroSim_CAF1 128600 112 + 1
ACGAAAUGCCAAAAAGUGGCAAGUGG-------AAUUUGCAAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCUGUUUCUGCCACAGUGGGGCAAUUAGAAGAAUGCGCCAAA
...............((((((((..(-------(((((((((..(((((((((.....)))))))))..))))))))))..))..))))))..(((.(((.((....)).))).))).. ( -47.40)
>DroEre_CAF1 129876 111 + 1
ACGAGAUGCCAAAAAGUGGCAAGUGG--------AAUUGCAAAAAGUGCUGUAAGUGAUGCGGCGCUGAUUGCGAAUUCUGUUUCUGCCACAGUUGGGCAAUUAGAAGAAUGCGCCAAA
......((((.((..((((((((..(--------((((((((..(((((((((.....)))))))))..)))).)))))..))..))))))..)).))))................... ( -40.80)
>DroYak_CAF1 130683 107 + 1
ACGAAAUGCCAAAAAGUGGCAAGUGGCAAGUGGCAUUUGCAAAAAGUGCU------------GCGCUGAUUGCAGAUUCUGUUUCUGCCACAGCCGGGCAAUUAGAAGAAUGCGCCAAA
......(((((.....)))))..((((..(..((((((.....)))))).------------.)((((...(((((.......)))))..))))...(((.((....)).))))))).. ( -36.30)
>consensus
ACGAAAUGCCAAAAAGUGGCAAGUGG_______AAUUUGCAAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCUGUUUCUGCCACAGUGGGGCAAUUAGAAGAAUGCGCCAAA
......(((((.....))))).((((.......(((((((((..(((((((((.....)))))))))..))))))))).........))))..(((.(((.((....)).))).))).. (-34.14 = -35.45 +   1.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,765,225 – 18,765,337
Length 112
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 89.11
Mean single sequence MFE -30.02
Consensus MFE -21.17
Energy contribution -21.82
Covariance contribution 0.65
Combinations/Pair 1.00
Mean z-score -3.05
Structure conservation index 0.71
SVM decision value 1.24
SVM RNA-class probability 0.935366
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18765225 112 - 20766785
UUUGGCGCAUUCUUCUAAUUGCCCCACUGUGGCAGAAACAGAAUCUGCAAUCAGCGCUGCAUCACUUACAGCACUUUUUGCAAAUU-------CCACUUGCCACUUUUUGGCAUUUCGU
...................((((.....(((((((.....((((.(((((..((.((((.........)))).))..))))).)))-------)...))))))).....))))...... ( -31.30)
>DroSec_CAF1 127744 112 - 1
UUUGGCGCAUUCUUCUAAUUGCCCCACUGUGGCAUAAACAGAAUCUGCAAUCAGCGCUGCAUCACUUACAGCACUUUUUGCAAAUU-------CCACUUGCCAGUUUUUUGCAUUUCGU
..(((.(((..........))).)))...(((((......((((.(((((..((.((((.........)))).))..))))).)))-------)....)))))................ ( -27.40)
>DroSim_CAF1 128600 112 - 1
UUUGGCGCAUUCUUCUAAUUGCCCCACUGUGGCAGAAACAGAAUCUGCAAUCAGCGCUGCAUCACUUACAGCACUUUUUGCAAAUU-------CCACUUGCCACUUUUUGGCAUUUCGU
...................((((.....(((((((.....((((.(((((..((.((((.........)))).))..))))).)))-------)...))))))).....))))...... ( -31.30)
>DroEre_CAF1 129876 111 - 1
UUUGGCGCAUUCUUCUAAUUGCCCAACUGUGGCAGAAACAGAAUUCGCAAUCAGCGCCGCAUCACUUACAGCACUUUUUGCAAUU--------CCACUUGCCACUUUUUGGCAUCUCGU
...................((((.((..(((((((.....(((((.((((..((.((.(.........).)).))..))))))))--------)...)))))))..)).))))...... ( -26.20)
>DroYak_CAF1 130683 107 - 1
UUUGGCGCAUUCUUCUAAUUGCCCGGCUGUGGCAGAAACAGAAUCUGCAAUCAGCGC------------AGCACUUUUUGCAAAUGCCACUUGCCACUUGCCACUUUUUGGCAUUUCGU
...((.(((..........)))))(((.((((((....(((((.((((.......))------------))....)))))....))))))..)))...(((((.....)))))...... ( -33.90)
>consensus
UUUGGCGCAUUCUUCUAAUUGCCCCACUGUGGCAGAAACAGAAUCUGCAAUCAGCGCUGCAUCACUUACAGCACUUUUUGCAAAUU_______CCACUUGCCACUUUUUGGCAUUUCGU
..((((..(((((.....((((((....).)))))....)))))..((((..((.((((.........)))).))..))))..................))))................ (-21.17 = -21.82 +   0.65)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,765,258 – 18,765,366
Length 108
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 84.72
Mean single sequence MFE -35.46
Consensus MFE -28.93
Energy contribution -30.12
Covariance contribution 1.19
Combinations/Pair 1.10
Mean z-score -1.81
Structure conservation index 0.82
SVM decision value 0.68
SVM RNA-class probability 0.820865
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18765258 108 + 20766785
AAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCUGUUUCUGCCACAGUGGGGCAAUUAGAAGAAUGCGCCAAAUGGGCUCCAAAGCCCGGUUGAGCGCGGCC
....(((((((((.....)))))))))....((..(((((.....((((.......))))......)))))(((((((.((((((....)))))).))).)))).)). ( -41.40)
>DroSec_CAF1 127777 108 + 1
AAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCUGUUUAUGCCACAGUGGGGCAAUUAGAAGAAUGCGCCAAAUGGGCUCCAAAGCUCGACUGAGCCCGGCC
....(((((((((.....)))))))))....(((..(((((....((((.......))))..)))))...)))(((....((((((............))))))))). ( -37.80)
>DroSim_CAF1 128633 108 + 1
AAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCUGUUUCUGCCACAGUGGGGCAAUUAGAAGAAUGCGCCAAAUGGGCUCCGAAGCUCGGCUGAGCACGGCC
....(((((((((.....)))))))))....(((((.......))))).....(((.(((.((....)).))).)))...(((((....)))))(((((....))))) ( -37.30)
>DroEre_CAF1 129908 95 + 1
AAAAAGUGCUGUAAGUGAUGCGGCGCUGAUUGCGAAUUCUGUUUCUGCCACAGUUGGGCAAUUAGAAGAAUGCGCCAAAUGGG-------------UUGAGAUCGGCC
....(((((((((.....)))))))))....(((.(((((.....((((.(....)))))......))))).)))......((-------------(((....))))) ( -28.90)
>DroYak_CAF1 130723 96 + 1
AAAAAGUGCU------------GCGCUGAUUGCAGAUUCUGUUUCUGCCACAGCCGGGCAAUUAGAAGAAUGCGCCAAAUGGGCUCCGUAACUCGGUGGAGCUCGGCC
........((------------(.((((...(((((.......)))))..)))))))(((.((....)).)))(((....((((((((........))))))))))). ( -31.90)
>consensus
AAAAAGUGCUGUAAGUGAUGCAGCGCUGAUUGCAGAUUCUGUUUCUGCCACAGUGGGGCAAUUAGAAGAAUGCGCCAAAUGGGCUCCAAAGCUCGGUUGAGCUCGGCC
....(((((((((.....)))))))))....(((..(((((....((((.......))))..)))))...)))(((....((((((............))))))))). (-28.93 = -30.12 +   1.19)

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 Mon Dec 4 11:58:51 2006