Locus 1054

Sequence ID 2R_DroMel_CAF1
Location 4,319,349 – 4,319,567
Length 218
Max. P 0.914570
window1861 window1862

overview

Window 1

Location 4,319,349 – 4,319,466
Length 117
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 86.39
Mean single sequence MFE -40.83
Consensus MFE -28.82
Energy contribution -29.49
Covariance contribution 0.67
Combinations/Pair 1.10
Mean z-score -3.15
Structure conservation index 0.71
SVM decision value 1.10
SVM RNA-class probability 0.914570
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4319349 117 - 20766785
UUGGGUGGUUAUAUAUGGGUGGUUGAGUACGGGCUGGGUUGGCGGGAAUUUUUCCGCCAUGAGCAGUGCGAACUUGUUCUCGCAUUUUUGGCCAGUACUCUGUACUCUGCUGCAAUU
....(..((.......(((((...((((((.(((..((.((((((((....)))))))).....(((((((........)))))))))..))).))))))..))))).))..).... ( -44.10)
>DroSec_CAF1 74414 104 - 1
UUGGGUGGUUGUAUAUGGGUGGUUGAGUACGGGCUGGGUUGGCGGGGAAUUC-------------GUGCGAACUUGUGCUCGGAUUUUUGGCCACUACUCUGUACUCUGCUGCAAUU
..................(..((.((((((((..(((..((((.((((((((-------------(.(((......))).))))))))).)))))))..)))))))).))..).... ( -40.20)
>DroSim_CAF1 78008 104 - 1
UUGGGUGGUUGUGUAUGGGUGGUUGAGUACGGGCUGCGUUGGCGGGGAAUUC-------------GUGCGAACUUGUGCUUGGAUUUUUGGCCAGUACUCUGUACUCUGCUGCAAUU
..................(..((.((((((((..(((..((((.((((((((-------------(.(((......))).))))))))).)))))))..)))))))).))..).... ( -38.20)
>consensus
UUGGGUGGUUGUAUAUGGGUGGUUGAGUACGGGCUGGGUUGGCGGGGAAUUC_____________GUGCGAACUUGUGCUCGGAUUUUUGGCCAGUACUCUGUACUCUGCUGCAAUU
..................(..((.((((((((..(((..((((.((((((((.............(((((....)))))..)))))))).)))))))..)))))))).))..).... (-28.82 = -29.49 +   0.67) 

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 4,319,466 – 4,319,567
Length 101
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 84.82
Mean single sequence MFE -33.80
Consensus MFE -22.05
Energy contribution -21.41
Covariance contribution -0.64
Combinations/Pair 1.21
Mean z-score -2.32
Structure conservation index 0.65
SVM decision value 0.64
SVM RNA-class probability 0.809932
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4319466 101 - 20766785
AUUCUGCGCCACUCCUGAAAUUCGA-----CCCACAACCAGAAAGUAUAUUCAACGUUGGUGCUUUCCCAGCGAAUUGGUUGAUUACUUUUUCGGUGGU-------GCGAUGG
....(((((((((...((((.....-----....(((((((((......)))..((((((.......))))))...)))))).......))))))))))-------))).... ( -29.49)
>DroSec_CAF1 74518 106 - 1
AUUCUGCGCCACUCCUGAAAUUCGACCCGACCCACGACCAGAAAGUAUAUUCAACGUUGGGGCUUUCCCAGCGAAUUGGUUGAUUACUUUUUCGGUGGU-------GCGAUGG
....(((((((((...((((.(((...)))....(((((((((......)))..(((((((.....)))))))...)))))).......))))))))))-------))).... ( -33.60)
>DroSim_CAF1 78112 101 - 1
AUUCUGCGCCACUCCUGAAAUUCGA-----CCCACGACCAGAAAGUAUAUUCAACGUUGGGGCUUUCCCAACGAAUUGGUUGAUUACUUUUUCGGUGGU-------GCGAUGG
....(((((((((...((((.((((-----((........(((......)))..(((((((.....)))))))....))))))....))))..))))))-------))).... ( -33.20)
>DroEre_CAF1 73719 98 - 1
AUUCUGCGCCACUCCUGAAAUUCGA-----CCGACAACUGGAAAGU--AUUCAACGUUGGGGCUUCACCAGCGAAUCGGUUGAUUACUUUUUCGGUGGUUGGUGG--------
......((((((..((((((.((((-----((((..(((....)))--......((((((.......))))))..))))))))......))))))..).))))).-------- ( -36.00)
>DroYak_CAF1 75999 106 - 1
AUUCUACGUCACUCCUAAAAUUCGA-----CCUACAACCAGAAAGU--AUUCAACGUUGGGGCUUUCCCAGCGAAUUGGUUGAUUACUUUUUCGGUGGUGGGUGGUGCAGUGA
........(((((.(.......(.(-----(((((.((((((((((--(.(((((((((((.....))))))......))))).)))))))).))).)))))).).).))))) ( -36.70)
>consensus
AUUCUGCGCCACUCCUGAAAUUCGA_____CCCACAACCAGAAAGUAUAUUCAACGUUGGGGCUUUCCCAGCGAAUUGGUUGAUUACUUUUUCGGUGGU_______GCGAUGG
.......(((((..........(((.........(((((((((......)))..(((((((.....)))))))...)))))).........)))))))).............. (-22.05 = -21.41 +  -0.64) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:14 2006