Locus 1054

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

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

secondary structure

dotplot

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

secondary structure

dotplot

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