Locus 4576

Sequence ID X_DroMel_CAF1
Location 12,009,901 – 12,010,101
Length 200
Max. P 0.986919
window7523 window7524 window7525 window7526 window7527

overview

Window 3

Location 12,009,901 – 12,010,021
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.66
Mean single sequence MFE -41.67
Consensus MFE -39.17
Energy contribution -39.83
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -4.32
Structure conservation index 0.94
SVM decision value 2.02
SVM RNA-class probability 0.985885
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12009901 120 + 22224390
UUGCUGGCAUAACCCAUUUGUCACACUCCCUUAACCCUGGGGUCAUAUCAAGUGGGAAACAAGUGGGGAACACGGUAUUCGAGUUUCCCAACUGUGUACCAAAACAAGAAAAAAAAACAA
....(((.....((((((((....((.(((........))))).....))))))))..(((..((((((((.((.....)).))))))))..)))...)))................... ( -34.80)
>DroSec_CAF1 43341 108 + 1
UUGCUGGCAUAACCCAUUUGUCACACUCCCUUAACCCUGGGGUCAUAUCAAGUGGGGAACAAGUGGGGAACACGGCGUUCGAGUUUCCCCACUGUGUGCCAGAA--------AAAA----
...((((((((.((((((((....((.(((........))))).....)))))))).....((((((((((.((.....)).).))))))))).))))))))..--------....---- ( -46.00)
>DroSim_CAF1 42601 108 + 1
UUGCUGGCAUAACCCAUUUGUCACACUCCCUUAACCCUGGGGUCAUAUCAAGUGGGAAACAAGUGGGGAACACGGUGUUCGAGUUUCCCAACUGUGUGCCAGAA--------AAAA----
...(((((((..((((((((....((.(((........))))).....))))))))..(((..((((((((.((.....)).))))))))..))))))))))..--------....---- ( -44.20)
>consensus
UUGCUGGCAUAACCCAUUUGUCACACUCCCUUAACCCUGGGGUCAUAUCAAGUGGGAAACAAGUGGGGAACACGGUGUUCGAGUUUCCCAACUGUGUGCCAGAA________AAAA____
...((((((((.((((((((....((.(((........))))).....)))))))).....((((((((((.((.....)).))))))).))).)))))))).................. (-39.17 = -39.83 +   0.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,009,901 – 12,010,021
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.66
Mean single sequence MFE -35.80
Consensus MFE -33.41
Energy contribution -33.30
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.94
Structure conservation index 0.93
SVM decision value 0.97
SVM RNA-class probability 0.892299
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12009901 120 - 22224390
UUGUUUUUUUUUCUUGUUUUGGUACACAGUUGGGAAACUCGAAUACCGUGUUCCCCACUUGUUUCCCACUUGAUAUGACCCCAGGGUUAAGGGAGUGUGACAAAUGGGUUAUGCCAGCAA
..............(((..(((((.((((.((((.(((.((.....)).))).)))).))))..((((.(((.((((..(((........)))..)))).))).))))...)))))))). ( -31.90)
>DroSec_CAF1 43341 108 - 1
----UUUU--------UUCUGGCACACAGUGGGGAAACUCGAACGCCGUGUUCCCCACUUGUUCCCCACUUGAUAUGACCCCAGGGUUAAGGGAGUGUGACAAAUGGGUUAUGCCAGCAA
----....--------..((((((((.(((((((((...((.....))..))))))))))))..((((.(((.((((..(((........)))..)))).))).))))....)))))... ( -40.30)
>DroSim_CAF1 42601 108 - 1
----UUUU--------UUCUGGCACACAGUUGGGAAACUCGAACACCGUGUUCCCCACUUGUUUCCCACUUGAUAUGACCCCAGGGUUAAGGGAGUGUGACAAAUGGGUUAUGCCAGCAA
----....--------..((((((.((((.((((.(((.((.....)).))).)))).))))..((((.(((.((((..(((........)))..)))).))).))))...))))))... ( -35.20)
>consensus
____UUUU________UUCUGGCACACAGUUGGGAAACUCGAACACCGUGUUCCCCACUUGUUUCCCACUUGAUAUGACCCCAGGGUUAAGGGAGUGUGACAAAUGGGUUAUGCCAGCAA
..................((((((.((((.((((.(((.((.....)).))).)))).))))..((((.(((.((((..(((........)))..)))).))).))))...))))))... (-33.41 = -33.30 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,009,941 – 12,010,061
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.85
Mean single sequence MFE -26.90
Consensus MFE -24.11
Energy contribution -23.45
Covariance contribution -0.66
Combinations/Pair 1.11
Mean z-score -2.07
Structure conservation index 0.90
SVM decision value 1.59
SVM RNA-class probability 0.965939
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12009941 120 + 22224390
GGUCAUAUCAAGUGGGAAACAAGUGGGGAACACGGUAUUCGAGUUUCCCAACUGUGUACCAAAACAAGAAAAAAAAACAAAACAAAAAAAACUUUAAAAUACGCUUUCCACUCCACAUGC
...(((....(((((((((((..((((((((.((.....)).))))))))..)))((......)).......................................))))))))....))). ( -23.80)
>DroSec_CAF1 43381 104 + 1
GGUCAUAUCAAGUGGGGAACAAGUGGGGAACACGGCGUUCGAGUUUCCCCACUGUGUGCCAGAA--------AAAA--------AUAAAAACUUUAAUACACGCUUUCCACUCCACAUGC
...........((((((....((((((((((.((.....)).).)))))))))(((((....((--------(...--------........)))....)))))......)))))).... ( -29.40)
>DroSim_CAF1 42641 102 + 1
GGUCAUAUCAAGUGGGAAACAAGUGGGGAACACGGUGUUCGAGUUUCCCAACUGUGUGCCAGAA--------AAAA--------ACA--AACUUUGAAAUACGCUUUCCACUUCACAUGC
...(((.(.(((((((((.(.((((((((((.((.....)).))))))).)))((((..((((.--------....--------...--...))))..))))).))))))))).).))). ( -27.50)
>consensus
GGUCAUAUCAAGUGGGAAACAAGUGGGGAACACGGUGUUCGAGUUUCCCAACUGUGUGCCAGAA________AAAA________AAAAAAACUUUAAAAUACGCUUUCCACUCCACAUGC
...(((....((((((((...((((((((((.((.....)).))))))).)))(((((.........................................)))))))))))))....))). (-24.11 = -23.45 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,009,941 – 12,010,061
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.85
Mean single sequence MFE -33.03
Consensus MFE -27.94
Energy contribution -27.83
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -2.81
Structure conservation index 0.85
SVM decision value 2.06
SVM RNA-class probability 0.986919
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12009941 120 - 22224390
GCAUGUGGAGUGGAAAGCGUAUUUUAAAGUUUUUUUUGUUUUGUUUUUUUUUCUUGUUUUGGUACACAGUUGGGAAACUCGAAUACCGUGUUCCCCACUUGUUUCCCACUUGAUAUGACC
.(((((.((((((.(((((((((...(((.......................))).....)))))..(((.(((((...((.....))..))))).))).)))).)))))).)))))... ( -30.00)
>DroSec_CAF1 43381 104 - 1
GCAUGUGGAGUGGAAAGCGUGUAUUAAAGUUUUUAU--------UUUU--------UUCUGGCACACAGUGGGGAAACUCGAACGCCGUGUUCCCCACUUGUUCCCCACUUGAUAUGACC
.(((((.((((((..(((((((...((((.......--------.)))--------)....))))..(((((((((...((.....))..))))))))).)))..)))))).)))))... ( -38.10)
>DroSim_CAF1 42641 102 - 1
GCAUGUGAAGUGGAAAGCGUAUUUCAAAGUU--UGU--------UUUU--------UUCUGGCACACAGUUGGGAAACUCGAACACCGUGUUCCCCACUUGUUUCCCACUUGAUAUGACC
.(((((.((((((.(((((.........(((--((.--------..((--------(((..((.....))..)))))..)))))...(((.....))).))))).)))))).)))))... ( -31.00)
>consensus
GCAUGUGGAGUGGAAAGCGUAUUUUAAAGUUUUUAU________UUUU________UUCUGGCACACAGUUGGGAAACUCGAACACCGUGUUCCCCACUUGUUUCCCACUUGAUAUGACC
.(((((.((((((.(((((.......................................(((.....)))..(((.(((.((.....)).))).)))...))))).)))))).)))))... (-27.94 = -27.83 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,009,981 – 12,010,101
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.85
Mean single sequence MFE -14.76
Consensus MFE -13.18
Energy contribution -12.85
Covariance contribution -0.33
Combinations/Pair 1.13
Mean z-score -1.05
Structure conservation index 0.89
SVM decision value 0.22
SVM RNA-class probability 0.639450
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12009981 120 + 22224390
GAGUUUCCCAACUGUGUACCAAAACAAGAAAAAAAAACAAAACAAAAAAAACUUUAAAAUACGCUUUCCACUCCACAUGCAAAUCACUCGCCAUUCCAAAAAGUAUGGCAACAAAUUUGU
((((........(((........)))....................................((..............)).....))))(((((.(......).)))))........... ( -11.14)
>DroSec_CAF1 43421 104 + 1
GAGUUUCCCCACUGUGUGCCAGAA--------AAAA--------AUAAAAACUUUAAUACACGCUUUCCACUCCACAUGCAAAUCACUUGCCAUCCGAAAAAGUAUGGCAACAAAUUUGU
((((.........(((((....((--------(...--------........)))....))))).....)))).....((((((...(((((((.(......).)))))))...)))))) ( -17.04)
>DroSim_CAF1 42681 102 + 1
GAGUUUCCCAACUGUGUGCCAGAA--------AAAA--------ACA--AACUUUGAAAUACGCUUUCCACUUCACAUGCAAAUCACUUGCCAUCCGAAAAAGUAUGGCAACAAAUUUGU
.((((....))))((((..((((.--------....--------...--...))))..))))................((((((...(((((((.(......).)))))))...)))))) ( -16.10)
>consensus
GAGUUUCCCAACUGUGUGCCAGAA________AAAA________AAAAAAACUUUAAAAUACGCUUUCCACUCCACAUGCAAAUCACUUGCCAUCCGAAAAAGUAUGGCAACAAAUUUGU
((((.........(((((.........................................))))).....)))).....((((((...(((((((.(......).)))))))...)))))) (-13.18 = -12.85 +  -0.33)

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 11:28:35 2006