Locus 4533

Sequence ID 2L_DroMel_CAF1
Location 12,975,023 – 12,975,263
Length 240
Max. P 0.989684
window7139 window7140 window7141 window7142 window7143

overview

Window 9

Location 12,975,023 – 12,975,143
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.92
Mean single sequence MFE -43.15
Consensus MFE -42.17
Energy contribution -42.68
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -4.35
Structure conservation index 0.98
SVM decision value 1.27
SVM RNA-class probability 0.938750
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12975023 120 + 22407834
CAAUGACAGUAGUCUUGUGAUCAACGUCAAAAGCAAUUGUCAAAUAUUCGAACUCGAAUGGAGAGCGAGAGAGCCAGAGCGGAGAGUUGCUCUCCCACUCCACCCUCUCUUGUUUUUCUU
...(((((((.(.(((.((((....)))).)))).)))))))...(((((....)))))((((((((((((((...(((.((((((...))))))..)))....)))))))))))))).. ( -44.30)
>DroSec_CAF1 19657 120 + 1
CAAUGACAGUAGUCUUGUGAUCAACGUCAAAAGCAAUUGUCAAAUAUUCGAACUCGAAUGGAGAGCGAGAGAGCCAGAGCGGAGAGUUGCUCUCCCACUCCACCCUCUCUUGUUUUUCUU
...(((((((.(.(((.((((....)))).)))).)))))))...(((((....)))))((((((((((((((...(((.((((((...))))))..)))....)))))))))))))).. ( -44.30)
>DroSim_CAF1 20820 120 + 1
CAAUGACAGUAGUCUUGUGAUCAACGUCAAAAGCAAUUGUCAAAUAUUCGAACUCGAAUGGAGAGCGAGAGAGCCAGAGCGGAGAGUUGCUCUCCCACUCCACCCUCUCUUGUUUUUCUU
...(((((((.(.(((.((((....)))).)))).)))))))...(((((....)))))((((((((((((((...(((.((((((...))))))..)))....)))))))))))))).. ( -44.30)
>DroYak_CAF1 22647 119 + 1
CAAUGACAGUAGUCUUGUGAUCAACGUCAAAAGCAAUUGUCAAAUAUUCGAACUCGAAUGGAGAGCGAGAGAGCCGUAGCGGAGAGUUACUCUCCCACUCCACUCUCUCUUGUUUUU-UU
...(((((((.(.(((.((((....)))).)))).)))))))..((((((....))))))(((((((((((((..(.((.((((((...))))))..)).)...)))))))))))))-.. ( -39.70)
>consensus
CAAUGACAGUAGUCUUGUGAUCAACGUCAAAAGCAAUUGUCAAAUAUUCGAACUCGAAUGGAGAGCGAGAGAGCCAGAGCGGAGAGUUGCUCUCCCACUCCACCCUCUCUUGUUUUUCUU
...(((((((.(.(((.((((....)))).)))).)))))))...(((((....)))))((((((((((((((...(((.((((((...))))))..)))....)))))))))))))).. (-42.17 = -42.68 +   0.50)

alignment

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secondary structure

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Window 0

Location 12,975,023 – 12,975,143
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.92
Mean single sequence MFE -37.23
Consensus MFE -36.85
Energy contribution -36.73
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -2.11
Structure conservation index 0.99
SVM decision value 1.05
SVM RNA-class probability 0.906596
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12975023 120 - 22407834
AAGAAAAACAAGAGAGGGUGGAGUGGGAGAGCAACUCUCCGCUCUGGCUCUCUCGCUCUCCAUUCGAGUUCGAAUAUUUGACAAUUGCUUUUGACGUUGAUCACAAGACUACUGUCAUUG
...........((((((((((((((((((.....))).))))))).)))))))).......(((((....)))))...(((((...((((.(((......))).))).)...)))))... ( -37.20)
>DroSec_CAF1 19657 120 - 1
AAGAAAAACAAGAGAGGGUGGAGUGGGAGAGCAACUCUCCGCUCUGGCUCUCUCGCUCUCCAUUCGAGUUCGAAUAUUUGACAAUUGCUUUUGACGUUGAUCACAAGACUACUGUCAUUG
...........((((((((((((((((((.....))).))))))).)))))))).......(((((....)))))...(((((...((((.(((......))).))).)...)))))... ( -37.20)
>DroSim_CAF1 20820 120 - 1
AAGAAAAACAAGAGAGGGUGGAGUGGGAGAGCAACUCUCCGCUCUGGCUCUCUCGCUCUCCAUUCGAGUUCGAAUAUUUGACAAUUGCUUUUGACGUUGAUCACAAGACUACUGUCAUUG
...........((((((((((((((((((.....))).))))))).)))))))).......(((((....)))))...(((((...((((.(((......))).))).)...)))))... ( -37.20)
>DroYak_CAF1 22647 119 - 1
AA-AAAAACAAGAGAGAGUGGAGUGGGAGAGUAACUCUCCGCUACGGCUCUCUCGCUCUCCAUUCGAGUUCGAAUAUUUGACAAUUGCUUUUGACGUUGAUCACAAGACUACUGUCAUUG
..-........((((((((.(((((((((.....))).))))).).)))))))).......(((((....)))))...(((((...((((.(((......))).))).)...)))))... ( -37.30)
>consensus
AAGAAAAACAAGAGAGGGUGGAGUGGGAGAGCAACUCUCCGCUCUGGCUCUCUCGCUCUCCAUUCGAGUUCGAAUAUUUGACAAUUGCUUUUGACGUUGAUCACAAGACUACUGUCAUUG
...........((((((((((((((((((.....))).))))))).)))))))).......(((((....)))))...(((((...((((.(((......))).))).)...)))))... (-36.85 = -36.73 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,975,063 – 12,975,183
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.69
Mean single sequence MFE -34.22
Consensus MFE -31.62
Energy contribution -32.62
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.81
Structure conservation index 0.92
SVM decision value 1.92
SVM RNA-class probability 0.982456
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12975063 120 + 22407834
CAAAUAUUCGAACUCGAAUGGAGAGCGAGAGAGCCAGAGCGGAGAGUUGCUCUCCCACUCCACCCUCUCUUGUUUUUCUUUGCUGAUAAUUAUGAAAACCCGCAUAUUUUGAAAAACAUG
......((((((..((((.((((((((((((((...(((.((((((...))))))..)))....))))))))))))))))))........((((........)))).))))))....... ( -33.80)
>DroSec_CAF1 19697 120 + 1
CAAAUAUUCGAACUCGAAUGGAGAGCGAGAGAGCCAGAGCGGAGAGUUGCUCUCCCACUCCACCCUCUCUUGUUUUUCUUCGCUGAUAAAUAUGAAAACCCGCAUAUUUUGAAAAACAUG
......(((((...((((.((((((((((((((...(((.((((((...))))))..)))....))))))))))))))))))......((((((........)))))))))))....... ( -36.90)
>DroSim_CAF1 20860 120 + 1
CAAAUAUUCGAACUCGAAUGGAGAGCGAGAGAGCCAGAGCGGAGAGUUGCUCUCCCACUCCACCCUCUCUUGUUUUUCUUUGCUGAUAAAUAUGAAAACCCGCAUAUUUUGAAAAACAUG
.....(((((....)))))((((((((((((((...(((.((((((...))))))..)))....)))))))))))))).........(((((((........)))))))........... ( -35.60)
>DroYak_CAF1 22687 118 + 1
CAAAUAUUCGAACUCGAAUGGAGAGCGAGAGAGCCGUAGCGGAGAGUUACUCUCCCACUCCACUCUCUCUUGUUUUU-UUCGCUGAUAAAUAU-AAAACCCGCAUAUUUUAAAAAACAAG
....((((((....))))))(((((.(.(((.((....))((((((...))))))..)))).))))).(((((((((-(........((((((-.........)))))).)))))))))) ( -30.60)
>consensus
CAAAUAUUCGAACUCGAAUGGAGAGCGAGAGAGCCAGAGCGGAGAGUUGCUCUCCCACUCCACCCUCUCUUGUUUUUCUUCGCUGAUAAAUAUGAAAACCCGCAUAUUUUGAAAAACAUG
.....(((((....)))))((((((((((((((...(((.((((((...))))))..)))....)))))))))))))).........(((((((........)))))))........... (-31.62 = -32.62 +   1.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,975,063 – 12,975,183
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.69
Mean single sequence MFE -38.23
Consensus MFE -36.65
Energy contribution -36.52
Covariance contribution -0.13
Combinations/Pair 1.08
Mean z-score -2.76
Structure conservation index 0.96
SVM decision value 2.18
SVM RNA-class probability 0.989684
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12975063 120 - 22407834
CAUGUUUUUCAAAAUAUGCGGGUUUUCAUAAUUAUCAGCAAAGAAAAACAAGAGAGGGUGGAGUGGGAGAGCAACUCUCCGCUCUGGCUCUCUCGCUCUCCAUUCGAGUUCGAAUAUUUG
..((((((((......(((.(((..........))).)))..)))))))).((((((((((((((((((.....))).))))))).)))))))).......(((((....)))))..... ( -38.20)
>DroSec_CAF1 19697 120 - 1
CAUGUUUUUCAAAAUAUGCGGGUUUUCAUAUUUAUCAGCGAAGAAAAACAAGAGAGGGUGGAGUGGGAGAGCAACUCUCCGCUCUGGCUCUCUCGCUCUCCAUUCGAGUUCGAAUAUUUG
..((((((((.(((((((........))))))).((...)).)))))))).((((((((((((((((((.....))).))))))).)))))))).......(((((....)))))..... ( -38.30)
>DroSim_CAF1 20860 120 - 1
CAUGUUUUUCAAAAUAUGCGGGUUUUCAUAUUUAUCAGCAAAGAAAAACAAGAGAGGGUGGAGUGGGAGAGCAACUCUCCGCUCUGGCUCUCUCGCUCUCCAUUCGAGUUCGAAUAUUUG
..((((((((......(((.(((..........))).)))..)))))))).((((((((((((((((((.....))).))))))).)))))))).......(((((....)))))..... ( -38.20)
>DroYak_CAF1 22687 118 - 1
CUUGUUUUUUAAAAUAUGCGGGUUUU-AUAUUUAUCAGCGAA-AAAAACAAGAGAGAGUGGAGUGGGAGAGUAACUCUCCGCUACGGCUCUCUCGCUCUCCAUUCGAGUUCGAAUAUUUG
((((((((((......(((.(((...-......))).))).)-))))))))).((((((((((..((((((...))))))((....)).))).))))))).(((((....)))))..... ( -38.20)
>consensus
CAUGUUUUUCAAAAUAUGCGGGUUUUCAUAUUUAUCAGCAAAGAAAAACAAGAGAGGGUGGAGUGGGAGAGCAACUCUCCGCUCUGGCUCUCUCGCUCUCCAUUCGAGUUCGAAUAUUUG
..((((((((......(((.(((..........))).)))..)))))))).((((((((((((((((((.....))).))))))).)))))))).......(((((....)))))..... (-36.65 = -36.52 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,975,143 – 12,975,263
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.50
Mean single sequence MFE -23.75
Consensus MFE -19.36
Energy contribution -19.68
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -1.82
Structure conservation index 0.82
SVM decision value 0.45
SVM RNA-class probability 0.740282
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12975143 120 - 22407834
AAUCGCUAAAUAAAUAAAAUAAGAGCUGUGAAAAAACAACCACAGGUUGACAAAUUCAACGGAGGAAUGUAACUGAAAUGCAUGUUUUUCAAAAUAUGCGGGUUUUCAUAAUUAUCAGCA
........................((((((((((..(..((.(..(((((.....))))).).))..............((((((((....)))))))))..)))))).......)))). ( -23.21)
>DroSec_CAF1 19777 120 - 1
AAUCGCUAAAUAAAUAAAAUAAUAGCUGUGAAAACACACGCACAGGUUAACAAAUUCAACGGAGGAAUGUAACUGAAAUGCAUGUUUUUCAAAAUAUGCGGGUUUUCAUAUUUAUCAGCG
...((((..(((((((........((((((....)))).))...(((((....((((.......)))).)))))(((((((((((((....)))))))))...)))).))))))).)))) ( -24.90)
>DroSim_CAF1 20940 120 - 1
AAUCGCUAAAUAAAUAAAAUAAUAGCUGUGAAAACACACGCACAGGUUAACAAAUUCAACGGAGGAAUGUAACUGAAAUGCAUGUUUUUCAAAAUAUGCGGGUUUUCAUAUUUAUCAGCA
....(((..(((((((........((((((....)))).))...(((((....((((.......)))).)))))(((((((((((((....)))))))))...)))).))))))).))). ( -24.40)
>DroYak_CAF1 22766 119 - 1
AAUCGCAAAAUAAAUAAAAUAAUUACUGUGAAAAUGCACACACAGGUUGACAAAUUCAACGUAGGAAUGUAACUGAAACGCUUGUUUUUUAAAAUAUGCGGGUUUU-AUAUUUAUCAGCG
...(((...................(((((..........)))))(((((.....)))))(...((((((((..((..(((.(((((....))))).)))..))))-))))))..).))) ( -22.50)
>consensus
AAUCGCUAAAUAAAUAAAAUAAUAGCUGUGAAAACACACGCACAGGUUAACAAAUUCAACGGAGGAAUGUAACUGAAAUGCAUGUUUUUCAAAAUAUGCGGGUUUUCAUAUUUAUCAGCA
....(((..(((((((.........(((((..........)))))((((....((((.......)))).)))).((..(((((((((....)))))))))..))....))))))).))). (-19.36 = -19.68 +   0.31)

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 11:20:22 2006