LAV is an alignment format developed by Webb Miller.
#:lav
d {
"blastz.v7 H99/cn-h99_chromosome1.fasta JEC21/cn-jec21_chr1.fasta T=3 C=3
A C G T
91 -114 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91
O = 400, E = 30, K = 3000, L = 3000, M = 0"
}
#:lav
s {
"H99/cn-h99_chromosome1.fasta" 1 2291499 0 1
"JEC21/cn-jec21_chr1.fasta" 1 2300533 0 1
}
h {
">cn-h99_chromosome1"
">cn-jec21_chr1"
}
a {
s 3202
b 11013 4
e 11064 55
l 11013 4 11064 55 86
}
a {
s 3506
b 11157 118
e 11201 162
l 11157 118 11201 162 93
}
Converting this to AXT alignment format you see the two alignment blocks.
0 cn-h99_chromosome1 11013 11064 cn-jec21_chr1 4 55 + 3202
CACCCTCCCACCGTGTACTCTGCCACCTGTCCTGCATATCCTCCCTTTCATC
CGCTCTCCCACCGTGTATTCTCCCACCTATCCTGCATATCCTCTCTTGCATC
1 cn-h99_chromosome1 11157 11201 cn-jec21_chr1 118 162 + 3506
GGAGTAGCCGAGCAAATGCGTCGGGCGTTGAGGGATAGCCGAGTG
GGAGTAGCCGAGCAAATGGGTCGGGCGTCGAGGGATAGCCGAATG
In ClustalW multiple alignment format this would be
cn-h99_chromosome_1 CACCCTCCCACCGTGTACTCTGCCACCTGTCCTGCATATCCTCCCTTTCATC
cn-jec21_chr1 CGCTCTCCCACCGTGTATTCTCCCACCTATCCTGCATATCCTCTCTTGCATC
* * ************* *** ****** ************** *** ****
cn-h99_chromosome_1 GGAGTAGCCGAGCAAATGCGTCGGGCGTTGAGGGATAGCCGAGTG
cn-jec21_chr1 GGAGTAGCCGAGCAAATGGGTCGGGCGTCGAGGGATAGCCGAATG
****************** ********* ************* **'