Locus 6234

Sequence ID	3R_DroMel_CAF1
Location	16,289,381 – 16,289,541
Length	160
Max. P	0.868836

overview

Window 8

Location	16,289,381 – 16,289,501
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.89
Mean single sequence MFE	-40.23
Consensus MFE	-40.27
Energy contribution	-40.60
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	1.00
SVM decision value	0.86
SVM RNA-class probability	0.868836
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16289381 120 - 27905053
AGGUGGGCAAAUCACCAGAAAGCCAGAAAGUGGCCAAGCCAAGUGGUCACUGCCGAGUGGCGCCUUUGUUCACCUGCUCCUUGUGGAGCACACAGCACUUUAUUUGCAUAUAAAACGUGU
(((((((((((..........((((.....))))...((((..((((....))))..))))...)))))))))))(((((....))))).....(((((((((......)))))..)))) ( -42.50)
>DroSec_CAF1 10009 120 - 1
AGGUGGGCAAAUCACCAGAAAGCCAGAAAGUGGCCAAGCCAAGUGGUCACUGCCGAGUGGCGCCUUUGUUCACCUGCUCCUUGUGGAGCACGCAGCACUUUAUUUGCAUAUAAAACGUGU
(((((((((((..........((((.....))))...((((..((((....))))..))))...)))))))))))(((((....))))).....(((((((((......)))))..)))) ( -42.50)
>DroSim_CAF1 2136 120 - 1
AGGUGGGCAAAUCACCAGAAAGCCAGAAAGUGGCCAAGCCAAGUGGUCACUGCCGAGUGGCGCCUUUGUUCACCUGCUCCUUGUGAAGCACACAGCACUUUAUUUGCAUAUAAAACGUGU
(((((((((((..........((((.....))))...((((..((((....))))..))))...)))))))))))(((.(....).))).....(((((((((......)))))..)))) ( -35.70)
>consensus
AGGUGGGCAAAUCACCAGAAAGCCAGAAAGUGGCCAAGCCAAGUGGUCACUGCCGAGUGGCGCCUUUGUUCACCUGCUCCUUGUGGAGCACACAGCACUUUAUUUGCAUAUAAAACGUGU
(((((((((((..........((((.....))))...((((..((((....))))..))))...)))))))))))(((((....))))).....(((((((((......)))))..)))) (-40.27 = -40.60 +   0.33)

alignment

secondary structure

dotplot

Window 9

Location	16,289,421 – 16,289,541
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-43.10
Consensus MFE	-43.10
Energy contribution	-43.10
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.40
Structure conservation index	1.00
SVM decision value	0.09
SVM RNA-class probability	0.580851
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16289421 120 - 27905053
CCACCCACAGCCUUUGGAGUCGCGUGAGCAAUCAGAGCACAGGUGGGCAAAUCACCAGAAAGCCAGAAAGUGGCCAAGCCAAGUGGUCACUGCCGAGUGGCGCCUUUGUUCACCUGCUCC
...............(((((.(.((((((((..((.((...(((((.....))))).....((((...((((((((.......))))))))......))))))))))))))))).))))) ( -43.10)
>DroSec_CAF1 10049 120 - 1
CCACCCACAGCCUUUGGAGUCGCGUGAGCAAUCAGAGCACAGGUGGGCAAAUCACCAGAAAGCCAGAAAGUGGCCAAGCCAAGUGGUCACUGCCGAGUGGCGCCUUUGUUCACCUGCUCC
...............(((((.(.((((((((..((.((...(((((.....))))).....((((...((((((((.......))))))))......))))))))))))))))).))))) ( -43.10)
>DroSim_CAF1 2176 120 - 1
CCACCCACAGCCCUUGGAGUCGCGUGAGCAAUCAGAGCACAGGUGGGCAAAUCACCAGAAAGCCAGAAAGUGGCCAAGCCAAGUGGUCACUGCCGAGUGGCGCCUUUGUUCACCUGCUCC
...............(((((.(.((((((((..((.((...(((((.....))))).....((((...((((((((.......))))))))......))))))))))))))))).))))) ( -43.10)
>consensus
CCACCCACAGCCUUUGGAGUCGCGUGAGCAAUCAGAGCACAGGUGGGCAAAUCACCAGAAAGCCAGAAAGUGGCCAAGCCAAGUGGUCACUGCCGAGUGGCGCCUUUGUUCACCUGCUCC
...............(((((.(.((((((((..((.((...(((((.....))))).....((((...((((((((.......))))))))......))))))))))))))))).))))) (-43.10 = -43.10 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:17 2006