Locus 5860

Sequence ID	2L_DroMel_CAF1
Location	16,588,473 – 16,588,593
Length	120
Max. P	0.999955

overview

Window 4

Location	16,588,473 – 16,588,578
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	96.72
Mean single sequence MFE	-28.78
Consensus MFE	-27.50
Energy contribution	-27.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.01
Structure conservation index	0.96
SVM decision value	4.84
SVM RNA-class probability	0.999955
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16588473 105 - 22407834
UCAAUUGGGAUAUCAGUAACCCAAUUUAGCCGCCUCUUGAAACCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAUUUGUAAUCGAUUUCCCCCCUGAAUGUAU
(((...((((.(((......................(((((....)))))..((((((((((((((....)))).))))))))))))).))))...)))...... ( -29.30)
>DroSec_CAF1 43823 103 - 1
UCAAUUGGGAUAUCAGUAACCCAAUUUAGCCGCCUCUUGAAACCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAUUUGUAAUCGAUUUCCC--CUCAAUGUAU
......((((.(((......................(((((....)))))..((((((((((((((....)))).))))))))))))).))))--.......... ( -28.00)
>DroSim_CAF1 42632 103 - 1
UCAAUUGGGAUAUCAGUAACCCAAUUUAGCCGCCUCUUGAAACCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAUUUGUAAUCGAUUUCCC--CUCAAUGUAU
......((((.(((......................(((((....)))))..((((((((((((((....)))).))))))))))))).))))--.......... ( -28.00)
>DroEre_CAF1 42219 103 - 1
UAAAUUGGGAUAUCAGUAACCCAAUUUAGCCGCCCCUUGAAGCCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAUUUGUAAUCGAUUUCCC--CUCAAUGCAU
(((((((((.((....)).)))))))))...((...(((((....))))).(((((((((((((((....)))).))))))))))).......--......)).. ( -30.50)
>DroYak_CAF1 42373 103 - 1
UCAAUUGGGAUAUCAGUAACCCAAUUUAGCGGCCCCUUGAAACCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAUUUGUAAUCGAUUUCCC--CUCAAUGUAU
......((((.((((((...((........)).....((((....)))))))((((((((((((((....)))).))))))))))))).))))--.......... ( -28.10)
>consensus
UCAAUUGGGAUAUCAGUAACCCAAUUUAGCCGCCUCUUGAAACCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAUUUGUAAUCGAUUUCCC__CUCAAUGUAU
......((((.(((......................(((((....)))))..((((((((((((((....)))).))))))))))))).))))............ (-27.50 = -27.50 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	16,588,501 – 16,588,593
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	95.40
Mean single sequence MFE	-20.64
Consensus MFE	-18.16
Energy contribution	-18.56
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.23
Structure conservation index	0.88
SVM decision value	0.09
SVM RNA-class probability	0.578731
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16588501 92 - 22407834
AGUUUGCCCCAAAACUCAAUUGGGAUAUCAGUAACCCAAUUUAGCCGCCUCUUGAAACCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAU
..(((((.......((.(((((((.((....)).))))))).))....(..(((((....)))))..)...)))))(((((....))))).. ( -20.50)
>DroSec_CAF1 43849 91 - 1
AGUUUGCCCCA-AACUCAAUUGGGAUAUCAGUAACCCAAUUUAGCCGCCUCUUGAAACCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAU
..(((((....-..((.(((((((.((....)).))))))).))....(..(((((....)))))..)...)))))(((((....))))).. ( -20.50)
>DroSim_CAF1 42658 91 - 1
AGUUUGCCCCA-AACUCAAUUGGGAUAUCAGUAACCCAAUUUAGCCGCCUCUUGAAACCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAU
..(((((....-..((.(((((((.((....)).))))))).))....(..(((((....)))))..)...)))))(((((....))))).. ( -20.50)
>DroEre_CAF1 42245 91 - 1
ACUUUCCCCCA-AACUAAAUUGGGAUAUCAGUAACCCAAUUUAGCCGCCCCUUGAAGCCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAU
...........-...(((((((((.((....)).)))))))))(((((((((((.......((....))...)))).)).))).))...... ( -22.10)
>DroYak_CAF1 42399 91 - 1
AGUUCGCCUUA-AACUCAAUUGGGAUAUCAGUAACCCAAUUUAGCGGCCCCUUGAAACCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAU
...........-.....(((((((.((....)).)))))))..(((..(..(((((....)))))..)..)))...(((((....))))).. ( -19.60)
>consensus
AGUUUGCCCCA_AACUCAAUUGGGAUAUCAGUAACCCAAUUUAGCCGCCUCUUGAAACCCUUCAACUGAUUGCAAGUGGAGCGUGCUCCAAU
..(((((.......((.(((((((.((....)).))))))).))....(..(((((....)))))..)...)))))(((((....))))).. (-18.16 = -18.56 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:54 2006