Locus 218

Sequence ID 3L_DroMel_CAF1
Location 611,724 – 611,829
Length 105
Max. P 0.533208
window321 window322

overview

Window 1

Location 611,724 – 611,829
Length 105
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 76.29
Mean single sequence MFE -32.80
Consensus MFE -19.78
Energy contribution -20.44
Covariance contribution 0.66
Combinations/Pair 1.05
Mean z-score -1.56
Structure conservation index 0.60
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 611724 105 + 23771897
UUCCAAUUCCGAUGCCGAGUACCCCGAUUGUGUGGCGUCAACCAUUACAUGCAAACUCACACCUACAGGCGAUGCCGGCAGAGUCGUCGGCAGAGGCCGCGGCAA
............((((((((........(((((((......))).)))).....)))).........(((..(((((((......)))))))...)))..)))). ( -32.52)
>DroSec_CAF1 23010 83 + 1
----------------------UUCGAUUGUGUGGCGUUAACCAUUACAUGCAAACUCACACCUACAGGCGAUGCCGGCAGAGCCGUCGGCAGAGGCCGCGGCAA
----------------------.....(((((((((((........)).......(((.(.((....)).).(((((((......))))))))))))))).)))) ( -26.90)
>DroSim_CAF1 21420 83 + 1
----------------------UUCGAUUGUGUGGCGUUAACCAUUACAUGCAAACUCACACCUACAGGCGAUGCCGGCAGAGCCGUCGGCAGAGGCCGCGGCAA
----------------------.....(((((((((((........)).......(((.(.((....)).).(((((((......))))))))))))))).)))) ( -26.90)
>DroEre_CAF1 24779 82 + 1
----------AAUGCCGAGUCCCCCGAUUGUGUGGCGUUAACCAUUACAUGCAAACUCACACCUACAG--GAUGCCGACAGGGGCCUCGGCAGA-----------
----------..(((((((.((((....(((.((((((........)).............((....)--)..))))))))))).)))))))..----------- ( -29.10)
>DroYak_CAF1 26130 105 + 1
UGCCGAUGCCGAUGCCGAGUACCCGGAUUGUGUGGCGUUAACCAUUACAUGCAAACUCACACCUACAGGCGAUGCCGACAGAGGCGUCGGCAGAGGCGUCGGCAA
((((((((((..((((......((.....((((((.(((...(((...)))..))))))))).....)).((((((......))))))))))..)))))))))). ( -48.60)
>consensus
___________AUGCCGAGU_CCCCGAUUGUGUGGCGUUAACCAUUACAUGCAAACUCACACCUACAGGCGAUGCCGGCAGAGCCGUCGGCAGAGGCCGCGGCAA
.............................((((((.(((...(((...)))..))))))))).....(((..(((((((......)))))))...)))....... (-19.78 = -20.44 +   0.66) 

alignment

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secondary structure

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dotplot

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Window 2

Location 611,724 – 611,829
Length 105
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 76.29
Mean single sequence MFE -35.50
Consensus MFE -17.96
Energy contribution -18.50
Covariance contribution 0.54
Combinations/Pair 1.05
Mean z-score -1.75
Structure conservation index 0.51
SVM decision value -0.00
SVM RNA-class probability 0.533208
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 611724 105 - 23771897
UUGCCGCGGCCUCUGCCGACGACUCUGCCGGCAUCGCCUGUAGGUGUGAGUUUGCAUGUAAUGGUUGACGCCACACAAUCGGGGUACUCGGCAUCGGAAUUGGAA
...(((...((..((((((..((((((..(((...))).....(((((.(((.((........)).)))..)))))...))))))..))))))..))...))).. ( -34.60)
>DroSec_CAF1 23010 83 - 1
UUGCCGCGGCCUCUGCCGACGGCUCUGCCGGCAUCGCCUGUAGGUGUGAGUUUGCAUGUAAUGGUUAACGCCACACAAUCGAA----------------------
..((((((((....)))).)))).((((.(((...))).))))(((((.(((.((........)).)))..))))).......---------------------- ( -31.20)
>DroSim_CAF1 21420 83 - 1
UUGCCGCGGCCUCUGCCGACGGCUCUGCCGGCAUCGCCUGUAGGUGUGAGUUUGCAUGUAAUGGUUAACGCCACACAAUCGAA----------------------
..((((((((....)))).)))).((((.(((...))).))))(((((.(((.((........)).)))..))))).......---------------------- ( -31.20)
>DroEre_CAF1 24779 82 - 1
-----------UCUGCCGAGGCCCCUGUCGGCAUC--CUGUAGGUGUGAGUUUGCAUGUAAUGGUUAACGCCACACAAUCGGGGGACUCGGCAUU----------
-----------..(((((((.((((((.(((....--)))...(((((.(((.((........)).)))..)))))...)))))).)))))))..---------- ( -33.70)
>DroYak_CAF1 26130 105 - 1
UUGCCGACGCCUCUGCCGACGCCUCUGUCGGCAUCGCCUGUAGGUGUGAGUUUGCAUGUAAUGGUUAACGCCACACAAUCCGGGUACUCGGCAUCGGCAUCGGCA
.((((((.(((..((((((.(((......)))...(((((...(((((.(((.((........)).)))..)))))....)))))..))))))..))).)))))) ( -46.80)
>consensus
UUGCCGCGGCCUCUGCCGACGCCUCUGCCGGCAUCGCCUGUAGGUGUGAGUUUGCAUGUAAUGGUUAACGCCACACAAUCGGGG_ACUCGGCAU___________
.......(((...(((((.((....)).)))))..))).....(((((.(((.((........)).)))..)))))............................. (-17.96 = -18.50 +   0.54) 

alignment

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secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:36 2006