Locus 3913

Sequence ID 3R_DroMel_CAF1
Location 10,658,827 – 10,658,959
Length 132
Max. P 0.983986
window6264 window6265 window6266 window6267

overview

Window 4

Location 10,658,827 – 10,658,922
Length 95
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 86.09
Mean single sequence MFE -34.53
Consensus MFE -26.93
Energy contribution -27.10
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.78
SVM decision value -0.02
SVM RNA-class probability 0.522773
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10658827 95 + 27905053
AGUAUGUGGAUGUGAGUCGA------------------------GUCGCAUGUUGAAGUGCUCGAGUGCUGGUGUAGUAAUAGUUGUAGCUACACGACCAGCACGCCUGCGUUAUGAAU
...(((..(.......((((------------------------(.(((........))))))))(((((((((((((.((....)).)))))...))))))))..)..)))....... ( -31.30)
>DroSec_CAF1 483 107 + 1
AGUAUGUGGAUGUGAGUCGAG------------AAGUGUUCGCAGUCGCAUGUUGAAGUGCUCGAGUGCUGGUGUAGUAAUAGUUGUAGCUACACGACCAGCACGCCUGCGUUAUGAAU
..((((((..((((((.((..------------...))))))))..)))))).......((..(.(((((((((((((.((....)).)))))...)))))))).)..))......... ( -33.30)
>DroSim_CAF1 484 119 + 1
AGUAUGUGGAUGUGAGUCGAGAUGUGGCAAUGGAAGUGUUCGCAGUCGCAUGUUGAAGUGCUCGAGUGCUGGUGUAGUAAUAGUUGUAGCUACACGACCAGCACGCCUGCGUUAUGAAU
.(((.((.((.(((..((((.(((((((..((((....))))..))))))).))))..)))))..(((((((((((((.((....)).)))))...)))))))))).)))......... ( -39.00)
>consensus
AGUAUGUGGAUGUGAGUCGAG____________AAGUGUUCGCAGUCGCAUGUUGAAGUGCUCGAGUGCUGGUGUAGUAAUAGUUGUAGCUACACGACCAGCACGCCUGCGUUAUGAAU
...(((..(.......((((...............((....))....((((......))))))))(((((((((((((.((....)).)))))...))))))))..)..)))....... (-26.93 = -27.10 +   0.17)

alignment

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secondary structure

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Window 5

Location 10,658,827 – 10,658,922
Length 95
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 86.09
Mean single sequence MFE -25.07
Consensus MFE -21.03
Energy contribution -22.37
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.44
Structure conservation index 0.84
SVM decision value 1.10
SVM RNA-class probability 0.915372
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10658827 95 - 27905053
AUUCAUAACGCAGGCGUGCUGGUCGUGUAGCUACAACUAUUACUACACCAGCACUCGAGCACUUCAACAUGCGAC------------------------UCGACUCACAUCCACAUACU
............((.((((((((.((((((.........)))).))))))))))((((((.(........).).)------------------------)))).......))....... ( -22.40)
>DroSec_CAF1 483 107 - 1
AUUCAUAACGCAGGCGUGCUGGUCGUGUAGCUACAACUAUUACUACACCAGCACUCGAGCACUUCAACAUGCGACUGCGAACACUU------------CUCGACUCACAUCCACAUACU
........((((((.((((((((.((((((.........)))).)))))))))).)..(((........)))..))))).......------------..................... ( -26.40)
>DroSim_CAF1 484 119 - 1
AUUCAUAACGCAGGCGUGCUGGUCGUGUAGCUACAACUAUUACUACACCAGCACUCGAGCACUUCAACAUGCGACUGCGAACACUUCCAUUGCCACAUCUCGACUCACAUCCACAUACU
........((((((.((((((((.((((((.........)))).)))))))))).)..(((........)))..)))))........................................ ( -26.40)
>consensus
AUUCAUAACGCAGGCGUGCUGGUCGUGUAGCUACAACUAUUACUACACCAGCACUCGAGCACUUCAACAUGCGACUGCGAACACUU____________CUCGACUCACAUCCACAUACU
........((((((.((((((((.((((((.........)))).)))))))))).)..(((........)))..)))))........................................ (-21.03 = -22.37 +   1.33)

alignment

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secondary structure

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Window 6

Location 10,658,847 – 10,658,959
Length 112
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 96.01
Mean single sequence MFE -40.87
Consensus MFE -38.43
Energy contribution -38.77
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.20
Structure conservation index 0.94
SVM decision value 1.96
SVM RNA-class probability 0.983986
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10658847 112 + 27905053
-----GUCGCAUGUUGAAGUGCUCGAGUGCUGGUGUAGUAAUAGUUGUAGCUACACGACCAGCACGCCUGCGUUAUGAAUUAAUAAUCAUAAUAAGCCAUUAGGGUGGGCAACACGA
-----...((((......))))(((.(((((((((((((.((....)).)))))...))))))))(((..((((((((........)))))))...((....)))..)))....))) ( -38.80)
>DroSec_CAF1 510 117 + 1
UCGCAGUCGCAUGUUGAAGUGCUCGAGUGCUGGUGUAGUAAUAGUUGUAGCUACACGACCAGCACGCCUGCGUUAUGAAUUAAUAAUCAUAAUAAGCCAUUAGGGUGGGCAGCACGA
..((....))........(((((...(((((((((((((.((....)).)))))...))))))))(((..((((((((........)))))))...((....)))..)))))))).. ( -41.90)
>DroSim_CAF1 523 117 + 1
UCGCAGUCGCAUGUUGAAGUGCUCGAGUGCUGGUGUAGUAAUAGUUGUAGCUACACGACCAGCACGCCUGCGUUAUGAAUUAAUAAUCAUAAUAAGCCAUUAGGGUGGGCAGCACAA
..((....))........(((((...(((((((((((((.((....)).)))))...))))))))(((..((((((((........)))))))...((....)))..)))))))).. ( -41.90)
>consensus
UCGCAGUCGCAUGUUGAAGUGCUCGAGUGCUGGUGUAGUAAUAGUUGUAGCUACACGACCAGCACGCCUGCGUUAUGAAUUAAUAAUCAUAAUAAGCCAUUAGGGUGGGCAGCACGA
..................(((((...(((((((((((((.((....)).)))))...))))))))(((..((((((((........)))))))...((....)))..)))))))).. (-38.43 = -38.77 +   0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,658,847 – 10,658,959
Length 112
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 96.01
Mean single sequence MFE -31.33
Consensus MFE -30.92
Energy contribution -30.70
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.04
Structure conservation index 0.99
SVM decision value 1.17
SVM RNA-class probability 0.925976
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10658847 112 - 27905053
UCGUGUUGCCCACCCUAAUGGCUUAUUAUGAUUAUUAAUUCAUAACGCAGGCGUGCUGGUCGUGUAGCUACAACUAUUACUACACCAGCACUCGAGCACUUCAACAUGCGAC-----
..((((((((...((....))....((((((........))))))....)))((((((((.((((((.........)))).))))))))))...))))).............----- ( -29.20)
>DroSec_CAF1 510 117 - 1
UCGUGCUGCCCACCCUAAUGGCUUAUUAUGAUUAUUAAUUCAUAACGCAGGCGUGCUGGUCGUGUAGCUACAACUAUUACUACACCAGCACUCGAGCACUUCAACAUGCGACUGCGA
..((((((((...((....))....((((((........))))))....)))((((((((.((((((.........)))).))))))))))...))))).......(((....))). ( -32.50)
>DroSim_CAF1 523 117 - 1
UUGUGCUGCCCACCCUAAUGGCUUAUUAUGAUUAUUAAUUCAUAACGCAGGCGUGCUGGUCGUGUAGCUACAACUAUUACUACACCAGCACUCGAGCACUUCAACAUGCGACUGCGA
.......(((.........)))...((((((........))))))((((((.((((((((.((((((.........)))).)))))))))).)..(((........)))..))))). ( -32.30)
>consensus
UCGUGCUGCCCACCCUAAUGGCUUAUUAUGAUUAUUAAUUCAUAACGCAGGCGUGCUGGUCGUGUAGCUACAACUAUUACUACACCAGCACUCGAGCACUUCAACAUGCGACUGCGA
..((((((((...((....))....((((((........))))))....)))((((((((.((((((.........)))).))))))))))...))))).................. (-30.92 = -30.70 +  -0.22)

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 11:13:13 2006