Locus 322

Sequence ID	X_DroMel_CAF1
Location	1,011,066 – 1,011,261
Length	195
Max. P	0.892975

overview

Window 9

Location	1,011,066 – 1,011,157
Length	91
Sequences	3
Columns	91
Reading direction	forward
Mean pairwise identity	91.67
Mean single sequence MFE	-29.00
Consensus MFE	-26.12
Energy contribution	-25.90
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.98
Structure conservation index	0.90
SVM decision value	0.56
SVM RNA-class probability	0.782603
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1011066 91 + 22224390
AGGCGCCAGGUGCCAGGUGCCAGGGGCCCGGGUCAAGGGUCAAGAAGGCUUAGUACAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAAUU
.((((((.(....).))))))...(((((.......)))))......((...(((((...((((....))))...)))))..))....... ( -30.20)
>DroSec_CAF1 96542 82 + 1
AG-------GUGCCAGGUGCCAGGGACCCGGGUCAAGGGUCAAGAAGGCUUAG--CAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACU
..-------((((.((((((....(((((.......)))))....((((((..--..((....)))))))).....))))))))))..... ( -28.40)
>DroSim_CAF1 73740 82 + 1
AG-------GUGCCAGGUGCCAGGGACCCGGGUCAAGGGUCAAGAAGGCUUAG--CAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACU
..-------((((.((((((....(((((.......)))))....((((((..--..((....)))))))).....))))))))))..... ( -28.40)
>consensus
AG_______GUGCCAGGUGCCAGGGACCCGGGUCAAGGGUCAAGAAGGCUUAG__CAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACU
.........((((.((((((....(((((.......)))))(((...(((((........)))))...))).....))))))))))..... (-26.12 = -25.90 +  -0.22)

alignment

secondary structure

dotplot

Window 0

Location	1,011,089 – 1,011,197
Length	108
Sequences	3
Columns	108
Reading direction	forward
Mean pairwise identity	96.27
Mean single sequence MFE	-30.30
Consensus MFE	-30.59
Energy contribution	-29.93
Covariance contribution	-0.66
Combinations/Pair	1.11
Mean z-score	-1.37
Structure conservation index	1.01
SVM decision value	0.14
SVM RNA-class probability	0.603925
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1011089 108 + 22224390
GGGCCCGGGUCAAGGGUCAAGAAGGCUUAGUACAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAAUUUCAAAUACGAACACAAGAGCACAGACACGCAGUGUUUGUG
.(((((.......)))))......((...(((((...((((....))))...)))))..))..........................(((((((((...))))))))) ( -27.50)
>DroSec_CAF1 96558 106 + 1
GGACCCGGGUCAAGGGUCAAGAAGGCUUAG--CAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACUUCAAAUACGAACACAAGAGCACAGACACGCAGUGUCUGUG
.(((((.......)))))..(((((((...--.)))(((((...((.......))..)).)))...)))).................(((((((((...))))))))) ( -31.70)
>DroSim_CAF1 73756 106 + 1
GGACCCGGGUCAAGGGUCAAGAAGGCUUAG--CAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACUUCAAAUACGAACACGAGAGCACAGACACGCAGUGUCUGUG
.(((((.......)))))..(((((((...--.)))(((((...((.......))..)).)))...)))).................(((((((((...))))))))) ( -31.70)
>consensus
GGACCCGGGUCAAGGGUCAAGAAGGCUUAG__CAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACUUCAAAUACGAACACAAGAGCACAGACACGCAGUGUCUGUG
.(((((.......)))))..(((((((......)))(((((...((.......))..)).)))...)))).................(((((((((...))))))))) (-30.59 = -29.93 +  -0.66)

alignment

secondary structure

dotplot

Window 1

Location	1,011,117 – 1,011,227
Length	110
Sequences	3
Columns	110
Reading direction	forward
Mean pairwise identity	96.33
Mean single sequence MFE	-31.73
Consensus MFE	-25.94
Energy contribution	-25.50
Covariance contribution	-0.44
Combinations/Pair	1.08
Mean z-score	-3.03
Structure conservation index	0.82
SVM decision value	0.63
SVM RNA-class probability	0.805023
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1011117 110 + 22224390
AGUACAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAAUUUCAAAUACGAACACAAGAGCACAGACACGCAGUGUUUGUGUGGCCAAAAGGGCCCAAAGUCGAAGAUAUA
(((...((....))..))).....(((((((..((.......................((((((((((...))))))))))((((.....))))....))...))))))) ( -28.40)
>DroSec_CAF1 96586 107 + 1
AG--CAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACUUCAAAUACGAACACAAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGC-CAAAGUCGAAGAUAUA
((--(.((....))..))).....(((((((..((.......................((((((((((...))))))))))((((.....)))-)...))...))))))) ( -33.00)
>DroSim_CAF1 73784 107 + 1
AG--CAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACUUCAAAUACGAACACGAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGC-CAAAGUCGAAGAUAUA
((--(.((....))..))).....(((((((........(((......)))..(((..((((((((((...))))))))))((((.....)))-)....))).))))))) ( -33.80)
>consensus
AG__CAGCGUGAGUAGGCUUAAAAUGUAUCUGCACAAACUUCAAAUACGAACACAAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGC_CAAAGUCGAAGAUAUA
........(((((...((.......))..)).)))...((((................((((((((((...))))))))))((((.....))).)......))))..... (-25.94 = -25.50 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	1,011,157 – 1,011,261
Length	104
Sequences	3
Columns	104
Reading direction	forward
Mean pairwise identity	98.07
Mean single sequence MFE	-32.25
Consensus MFE	-28.97
Energy contribution	-28.75
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-2.60
Structure conservation index	0.90
SVM decision value	0.97
SVM RNA-class probability	0.892975
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1011157 104 + 22224390
UCAAAUACGAACACAAGAGCACAGACACGCAGUGUUUGUGUGGCCAAAAGGGCCCAAAGUCGAAGAUAUAGCCGCACUUUGCAAAUCGUGACUGGGCAAAGGCA
.......(((........((((((((((...))))))))))((((.....)))).....)))...........((.((((((.............)))))))). ( -29.92)
>DroSec_CAF1 96624 103 + 1
UCAAAUACGAACACAAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGC-CAAAGUCGAAGAUAUAGCCGCACUUUGCAAAUCGUGACUGGGCAAAGGCA
.......(((........((((((((((...))))))))))((((.....)))-)....)))...........((.((((((.............)))))))). ( -33.42)
>DroSim_CAF1 73822 103 + 1
UCAAAUACGAACACGAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGC-CAAAGUCGAAGAUAUAGCCGCACUUUGCAAAUCGUGACUGGGCAAAGGCA
.............(((..((((((((((...))))))))))((((.....)))-)....)))...........((.((((((.............)))))))). ( -33.42)
>consensus
UCAAAUACGAACACAAGAGCACAGACACGCAGUGUCUGUGUGGCCAAAAGGGC_CAAAGUCGAAGAUAUAGCCGCACUUUGCAAAUCGUGACUGGGCAAAGGCA
.......(((........((((((((((...))))))))))((((.....))).)....)))...........((.((((((.............)))))))). (-28.97 = -28.75 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:44 2006