Locus 451

Sequence ID 3R_DroMel_CAF1
Location 1,720,276 – 1,720,396
Length 120
Max. P 0.957557
window729 window730

overview

Window 9

Location 1,720,276 – 1,720,396
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.89
Mean single sequence MFE -32.80
Consensus MFE -21.79
Energy contribution -26.23
Covariance contribution 4.44
Combinations/Pair 1.13
Mean z-score -2.67
Structure conservation index 0.66
SVM decision value 1.48
SVM RNA-class probability 0.957557
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1720276 120 + 27905053
AGAGUUGGAAACCAUUUUUGACCAAAUAUAUUGUCCUGAAAUGGCAAUAUAUUUGCAUUUGGAAUGACCUCAUAUUGCGCAUUCGACUAGUUGAACAGUACUAGUUGAAAGUGAGUCUGC
.(((..(....)((((((....(((((((((((.((......))))))))))))).....))))))..)))......(((.((((((((((........)))))))))).)))....... ( -35.20)
>DroSec_CAF1 29221 120 + 1
AGAGUAGGAAAUCAUUUUUGCCCAAAUAUAUUGUCCUGCAAUGGCAAUAUAUUUGCAUUUGGAAUGACCUCAUAUUGCGCAUUCGACUAGUUGUACAGUAUUAGUUGAAAGUGCGUCUGC
...((((((..(((((((....(((((((((((.((......))))))))))))).....)))))))..)).....((((.((((((((((........)))))))))).))))..)))) ( -38.70)
>DroSim_CAF1 30498 120 + 1
AGAGUAGAAAAUCAUUUUUGCCCAAAUAUAUUGUCCUGCAAUGGCAAUAUAUUUGCAUUUGGAAUGACCUCAUAUUGCGCAUUCGACUAGUUGUACAGUAUUAGUUGAAAGUGCGUCUGC
...(((((...(((((((....(((((((((((.((......))))))))))))).....))))))).........((((.((((((((((........)))))))))).)))).))))) ( -38.80)
>DroEre_CAF1 29444 102 + 1
---GUGGGAAAUCAUGUUUGGCAA-ACAUAUUGCUCUGAAAUGGCAAUACAUUUGCAUUUGGACUGACCUCAAAU--------CGACUAGUUAAACAG------UUAGAAGUGCGUCUGC
---((((....)))).....(((.-((.(((((((.......))))))).....((((((.(((((.........--------............)))------))..)))))))).))) ( -18.50)
>consensus
AGAGUAGGAAAUCAUUUUUGCCCAAAUAUAUUGUCCUGAAAUGGCAAUAUAUUUGCAUUUGGAAUGACCUCAUAUUGCGCAUUCGACUAGUUGAACAGUAUUAGUUGAAAGUGCGUCUGC
...(((((...(((((((....(((((((((((((.......))))))))))))).....))))))).........((((.((((((((((........)))))))))).)))).))))) (-21.79 = -26.23 +   4.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,720,276 – 1,720,396
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.89
Mean single sequence MFE -25.62
Consensus MFE -15.57
Energy contribution -15.88
Covariance contribution 0.31
Combinations/Pair 1.19
Mean z-score -1.85
Structure conservation index 0.61
SVM decision value 0.02
SVM RNA-class probability 0.544683
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1720276 120 - 27905053
GCAGACUCACUUUCAACUAGUACUGUUCAACUAGUCGAAUGCGCAAUAUGAGGUCAUUCCAAAUGCAAAUAUAUUGCCAUUUCAGGACAAUAUAUUUGGUCAAAAAUGGUUUCCAACUCU
(((........(((.((((((........)))))).)))))).......(((..((((.......(((((((((((((......)).)))))))))))......))))..)))....... ( -26.32)
>DroSec_CAF1 29221 120 - 1
GCAGACGCACUUUCAACUAAUACUGUACAACUAGUCGAAUGCGCAAUAUGAGGUCAUUCCAAAUGCAAAUAUAUUGCCAUUGCAGGACAAUAUAUUUGGGCAAAAAUGAUUUCCUACUCU
...(.((((..(((.((((............)))).)))))))).....(((((((((.....(.(((((((((((((......)).))))))))))).)....)))))))))....... ( -27.90)
>DroSim_CAF1 30498 120 - 1
GCAGACGCACUUUCAACUAAUACUGUACAACUAGUCGAAUGCGCAAUAUGAGGUCAUUCCAAAUGCAAAUAUAUUGCCAUUGCAGGACAAUAUAUUUGGGCAAAAAUGAUUUUCUACUCU
...(.((((..(((.((((............)))).))))))))..((.(((((((((.....(.(((((((((((((......)).))))))))))).)....))))))))).)).... ( -25.90)
>DroEre_CAF1 29444 102 - 1
GCAGACGCACUUCUAA------CUGUUUAACUAGUCG--------AUUUGAGGUCAGUCCAAAUGCAAAUGUAUUGCCAUUUCAGAGCAAUAUGU-UUGCCAAACAUGAUUUCCCAC---
...(((..........------...........))).--------....(((((((........((((((((((((((......).)))))))))-))))......)))))))....--- ( -22.34)
>consensus
GCAGACGCACUUUCAACUAAUACUGUACAACUAGUCGAAUGCGCAAUAUGAGGUCAUUCCAAAUGCAAAUAUAUUGCCAUUGCAGGACAAUAUAUUUGGGCAAAAAUGAUUUCCUACUCU
...(((.......((........))........))).............(((((((((.......(((((((((((((......)).)))))))))))......)))))))))....... (-15.57 = -15.88 +   0.31)

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 09:43:29 2006