Locus 3667

Sequence ID 3L_DroMel_CAF1
Location 10,725,700 – 10,725,860
Length 160
Max. P 0.965560
window5728 window5729 window5730

overview

Window 8

Location 10,725,700 – 10,725,820
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.08
Mean single sequence MFE -27.70
Consensus MFE -15.59
Energy contribution -16.15
Covariance contribution 0.56
Combinations/Pair 1.17
Mean z-score -3.10
Structure conservation index 0.56
SVM decision value 1.50
SVM RNA-class probability 0.959567
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10725700 120 - 23771897
GCAAAUGAUUAUUUCAUUUCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUCAGCCUUCCUCAGGAGCUUUCAUUUGCCCAUUGGCA
((((((((.............((..((((((((...(((((((....)))))))....))))))))..))...............(((((......)).))).))))))))......... ( -28.30)
>DroSec_CAF1 59541 120 - 1
GCAAAUGAUUAUUUCAUUGCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUUUGCCUGCCUCAGGAGCUUUCAUUUGGCCAUUGGCA
...(((((.....)))))(((((..((((((((...(((((((....)))))))....)))))))).........(((((.......((((...)))).......)))))....))))). ( -31.94)
>DroSim_CAF1 61725 120 - 1
GCAAAUGAUUAUUUCAUUGCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUUUGCCUGCCUCAGGAGCUUUCAUUUGGCCAUUGGCA
...(((((.....)))))(((((..((((((((...(((((((....)))))))....)))))))).........(((((.......((((...)))).......)))))....))))). ( -31.94)
>DroYak_CAF1 74159 100 - 1
GCAAAUG------------AUUAUUUCAAGUUAUUAAAUUCCUUCUACGGUAUACACUUAGUUUGAAAUUCUUUACAAAUUAUGUAGCAUUCGCCAGGAGCUUUAA--------UGGCCA
.....((------------(.....))).((((((((((((((....(((..((((..(((((((.((....)).)))))))))))....)))..))))).)))))--------)))).. ( -18.60)
>consensus
GCAAAUGAUUAUUUCAUUGCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUUAGCCUGCCUCAGGAGCUUUCAUUUGGCCAUUGGCA
..................(((((..((((((((...(((((((....)))))))....))))))))..((((.......................))))...............))))). (-15.59 = -16.15 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,725,740 – 10,725,860
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -30.27
Consensus MFE -24.83
Energy contribution -24.83
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.13
Structure conservation index 0.82
SVM decision value 0.78
SVM RNA-class probability 0.848047
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10725740 120 + 23771897
AUUUGUAAAGGAUUUCAAACUAAAUGAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGAAAUGAAAUAAUCAUUUGCGAGCAUGAAAGAAAGACUUAUUGCAAUUGUAAUGAGCACG
..............((((.(((..(((((((((....))))))))).))).))))(((((.((((((.....)))))).)))))..........(.((((((((....)))))))))... ( -34.40)
>DroSec_CAF1 59581 120 + 1
AUUUGUAAAGGAUUUCAAACUAAAUGAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGCAAUGAAAUAAUCAUUUGCGAGCAUGCAAGAAAGACUUCUUGAAAUUGGAAUGAGUAGG
..((((...(((((.(((.(((..(((((((((....))))))))).))).)))))))).))))........((((((.(((.....((((((....))))))...)))))))))..... ( -29.30)
>DroSim_CAF1 61765 120 + 1
AUUUGUAAAGGAUUUCAAACUAAAUGAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGCAAUGAAAUAAUCAUUUGCGAGCAUGAAAGAAAGACUUAUUGAAACUGGAAUGAGUAGG
..............((((.(((..(((((((((....))))))))).))).))))(((((.((((((.....))).))))))))...........(((((((........)))))))... ( -27.10)
>consensus
AUUUGUAAAGGAUUUCAAACUAAAUGAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGCAAUGAAAUAAUCAUUUGCGAGCAUGAAAGAAAGACUUAUUGAAAUUGGAAUGAGUAGG
.......(((..((((........(((((((((....))))))))).........(((((..(((((.....)))))..)))))......))))..)))..................... (-24.83 = -24.83 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,725,740 – 10,725,860
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -24.17
Consensus MFE -21.53
Energy contribution -21.53
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.59
Structure conservation index 0.89
SVM decision value 1.58
SVM RNA-class probability 0.965560
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10725740 120 - 23771897
CGUGCUCAUUACAAUUGCAAUAAGUCUUUCUUUCAUGCUCGCAAAUGAUUAUUUCAUUUCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAU
.(((............(((..(((.....)))...)))(((.((((((.....)))))).)))..((((((((...(((((((....)))))))....)))))))).......))).... ( -26.20)
>DroSec_CAF1 59581 120 - 1
CCUACUCAUUCCAAUUUCAAGAAGUCUUUCUUGCAUGCUCGCAAAUGAUUAUUUCAUUGCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAU
.................((((((....)))))).....(((..(((((.....)))))..)))..((((((((...(((((((....)))))))....)))))))).............. ( -24.70)
>DroSim_CAF1 61765 120 - 1
CCUACUCAUUCCAGUUUCAAUAAGUCUUUCUUUCAUGCUCGCAAAUGAUUAUUUCAUUGCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAU
......................................(((..(((((.....)))))..)))..((((((((...(((((((....)))))))....)))))))).............. ( -21.60)
>consensus
CCUACUCAUUCCAAUUUCAAUAAGUCUUUCUUUCAUGCUCGCAAAUGAUUAUUUCAUUGCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAU
......................................(((..(((((.....)))))..)))..((((((((...(((((((....)))))))....)))))))).............. (-21.53 = -21.53 +   0.00)

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 11:03:49 2006