Locus 839

Sequence ID 2R_DroMel_CAF1
Location 3,939,162 – 3,939,393
Length 231
Max. P 0.662897
window1459 window1460

overview

Window 9

Location 3,939,162 – 3,939,282
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.29
Mean single sequence MFE -34.83
Consensus MFE -22.71
Energy contribution -23.27
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -1.49
Structure conservation index 0.65
SVM decision value -0.05
SVM RNA-class probability 0.509893
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3939162 120 - 20766785
AAGUUGGCCAAACUCUCGCCUCAAGUGCCAGCUUCUGAGUGCACUGAAUGCCAUUGCAACAAGUUUGUUGUGAUGCCUAUGGACCACUCCUAUGGAGUGGUGCAGUUUUCUUAAGGGCAG
.((((.....))))...((((..(((((..(((....))))))))(((.(((((..(((((....)))))..)))....((.((((((((...)))))))).)))).)))....)))).. ( -40.60)
>DroSim_CAF1 872 110 - 1
AAGUUGGCCAAAGUGUCGCCUCAAGUGCCAGCUCCUGAGUGCACUGAAGGCCAUUGCAACAAGUUUGUUGUGAUGCCUAUGGAC----------GAAUGGAGCAGUUUCCUUUAAGGCAU
......(((....((((((((..(((((..(((....))))))))..))))(((..(((((....)))))..)))......)))----------)...((((....)))).....))).. ( -36.50)
>DroYak_CAF1 783 100 - 1
AAGUUGGCCAAAGUGUAGCCUUAAGUAGCAGCUCUGGAGUGCAUUGAAGGCCAUUGCAACAAGUUUGUUGUGAUGCCUAUGGAC----------GAAUGGAACAGUUCAC----------
..(((((((..((((((..((..(((....)))..))..))))))...))))((..(((((....)))))..)).......)))----------((((......))))..---------- ( -27.40)
>consensus
AAGUUGGCCAAAGUGUCGCCUCAAGUGCCAGCUCCUGAGUGCACUGAAGGCCAUUGCAACAAGUUUGUUGUGAUGCCUAUGGAC__________GAAUGGAGCAGUUUACUU_A_GGCA_
..((...(((.......((((..(((((..(((....))))))))..))))(((..(((((....)))))..)))......................))).))................. (-22.71 = -23.27 +   0.56) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 3,939,282 – 3,939,393
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.26
Mean single sequence MFE -27.20
Consensus MFE -18.79
Energy contribution -19.13
Covariance contribution 0.34
Combinations/Pair 1.13
Mean z-score -1.60
Structure conservation index 0.69
SVM decision value 0.27
SVM RNA-class probability 0.662897
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3939282 111 + 20766785
CAAAAACUGCUCGUUCUGGGCAAUUAGUCAAGAAAAAGUUGACAACAAGCUUUACA--------GGCAACGCUAACAGGGAGA-AACUCUCUAAUUUUCCUUUUAAUCCUCCACGCAGAC
......((((.....((((((.....(((((.......))))).....(((.....--------)))...)))..)))((((.-....))))......................)))).. ( -21.20)
>DroSim_CAF1 982 120 + 1
CAAAAACUGCUCGUUCUGGGCAAUUAGUCAAGAAAAAGUUGACAACAAGCUUUGCAGGCAUGCAGGCAACGCUAAGAGGGAGAAAACUCUCUAAUUUUCCCUUUAAUCCUCCACGCAGAC
......((((........(((.....(((((.......))))).....((((.(((....)))))))...))).((((((((((..........))))))))))..........)))).. ( -30.80)
>DroYak_CAF1 883 99 + 1
CAGGAACUGCUCGUUCCAGGCAAUUAGUCGAGAAAAAGUUGACAAGUU---------------------GGCUGGGAGGGAGAAAACUCUCUAAUUUUCCUUUUAAUCCUUCACGCAGAC
......((((.....((((.(((((.(((((.......))))).))))---------------------).))))(((((((((((........))))).......))))))..)))).. ( -29.61)
>consensus
CAAAAACUGCUCGUUCUGGGCAAUUAGUCAAGAAAAAGUUGACAACAAGCUUU_CA________GGCAACGCUAAGAGGGAGAAAACUCUCUAAUUUUCCUUUUAAUCCUCCACGCAGAC
......((((........(((.....(((((.......))))).....................(....)))).((((((((((..........))))))))))..........)))).. (-18.79 = -19.13 +   0.34) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:40 2006