Locus 4207

Sequence ID X_DroMel_CAF1
Location 11,029,225 – 11,029,418
Length 193
Max. P 0.883215
window6914 window6915

overview

Window 4

Location 11,029,225 – 11,029,345
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.47
Mean single sequence MFE -25.81
Consensus MFE -23.66
Energy contribution -24.06
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.29
Structure conservation index 0.92
SVM decision value 0.28
SVM RNA-class probability 0.666216
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11029225 120 + 22224390
UCUGCUCGCCUCCAUCCGUGGCUACAAAUUUAUGGCGAGCCCUCGGCUCCGUUUGAUUGCGAAUAUUAUCUUAUUUUAUGUCAACUCCUUGCCACUUCCCGCUCCUUUUGAAGGCCAUCA
...(((((((........((....)).......)))))))....(((.....(((((...(((((......)))))...)))))......))).((((...........))))....... ( -25.76)
>DroSec_CAF1 21640 111 + 1
UCUGCU---------CCGUGGCUACAAAUUUAUGGCGAGCCCUCGGCUCCGUUUGAUUGGGAAUAUUAUCUUAUUUUAUGUCAACUCCUUGCCACUUCCCGCCCCUUUUGAAGGCCAUCA
......---------..(((((..........(((((((((...)))))...(((((..((((((......))))))..)))))......))))((((...........))))))))).. ( -26.00)
>DroSim_CAF1 13420 111 + 1
UCUGCU---------CCGUGGCUACAAAUUUAUGGCGAGCCCUCGGCUCCGUUUGAUUGCGAAUAUUAUCUUAUUUUAUGUCAACUCCUUGCCACUUCCCGCCCCUUUUGAAGGCCAUCA
......---------..(((((..........(((((((((...)))))...(((((...(((((......)))))...)))))......))))((((...........))))))))).. ( -25.50)
>DroEre_CAF1 15875 117 + 1
U--GCUUGCC-CCAGCGGUGGCUACAAAUUUAUGGCGAGCCCUCGGCUCCGUUUGAUUGCGAAUAUUAUCUUAUUUUAUGUCAACUCCUUGCCACCUCCCGCUCCUUCUGAAGGCCAUCA
.--(((....-..)))(((((((.........(((((((((...)))))...(((((...(((((......)))))...)))))......))))........((.....)).))))))). ( -29.00)
>DroYak_CAF1 16690 104 + 1
C----------------GUGGCUACAAAUUUAUGGCGAGCCACCGGCUACGUUUGAUUGCGAAUAUUAUCUUAUUUUAUGUCAACUCCUUGCCACUUCCCGCUCCUUUUGAAGGCCAUCA
.----------------(((((..........(((((((....((....)).(((((...(((((......)))))...)))))...)))))))((((...........))))))))).. ( -22.80)
>consensus
UCUGCU_________CCGUGGCUACAAAUUUAUGGCGAGCCCUCGGCUCCGUUUGAUUGCGAAUAUUAUCUUAUUUUAUGUCAACUCCUUGCCACUUCCCGCUCCUUUUGAAGGCCAUCA
.................(((((..........(((((((((...)))))...(((((...(((((......)))))...)))))......))))((((...........))))))))).. (-23.66 = -24.06 +   0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,029,305 – 11,029,418
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.65
Mean single sequence MFE -29.78
Consensus MFE -25.30
Energy contribution -25.50
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.85
SVM decision value 0.93
SVM RNA-class probability 0.883215
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11029305 113 + 22224390
UCAACUCCUUGCCACUUCCCGCUCCUUUUGAAGGCCAUCAAAUGCAAAUGUUUAUGGCGGAACACGCCCCCUUUGCGAACCCACAGU------GC-CAUGCAUUUUGCAUGCCGAUGGCG
..............((((...........))))((((((..((((((((((..(((((......(((.......))).((.....))------))-)))))).)))))))...)))))). ( -29.50)
>DroSec_CAF1 21711 119 + 1
UCAACUCCUUGCCACUUCCCGCCCCUUUUGAAGGCCAUCAAAUGCAAAAGUUUAUGGCGGAACACGCCCCCUUUUCGAACCCACCAUGCAUUUGC-CAUGCAUUUUGCAUGCCGAUGGCG
..............((((...........))))((((((..((((((((......((((.....))))..................(((((....-.)))))))))))))...)))))). ( -31.20)
>DroSim_CAF1 13491 119 + 1
UCAACUCCUUGCCACUUCCCGCCCCUUUUGAAGGCCAUCAAAUGCAAAUGUUUAUGGCGGAACACGCCCCCUUUUCGAAGCCACCAUGCAUUUGC-CAUGCAUUUUGCAUGCCGAUGGCG
..............((((...........))))((((((....((((((((..((((.((....((.........))...)).))))))))))))-(((((.....)))))..)))))). ( -33.50)
>DroEre_CAF1 15952 111 + 1
UCAACUCCUUGCCACCUCCCGCUCCUUCUGAAGGCCAUCAAAUGCAAAUGUUUAUGGCGGAACACGCCCC--UUUUCGACCCACAGU------GC-CAUGCAUUUUGCAUGCCGAUGGCG
(((.......((........))......)))..((((((..((((((((((..(((((((........))--......((.....))------))-)))))).)))))))...)))))). ( -26.82)
>DroYak_CAF1 16754 114 + 1
UCAACUCCUUGCCACUUCCCGCUCCUUUUGAAGGCCAUCAAAUGCAAAUGUUUAUGGCGGAACACGCCCCCUUUUCCGACCCACAGC------GCCCAUGCAUUUUGCAUGCCGAUGGCA
..............((((...........))))((((((..(((((((.(((...(((((((...........))))).))...)))------((....))..)))))))...)))))). ( -27.90)
>consensus
UCAACUCCUUGCCACUUCCCGCUCCUUUUGAAGGCCAUCAAAUGCAAAUGUUUAUGGCGGAACACGCCCCCUUUUCGAACCCACAGU______GC_CAUGCAUUUUGCAUGCCGAUGGCG
((((......((........)).....))))..((((((..(((((((.......((((.....)))).........................((....))..)))))))...)))))). (-25.30 = -25.50 +   0.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:11 2006