Template:  SRS043701_LANL_scaffold_6522 strand: + 46304-46418 ref: 46304-46418
Variable:  SRS043701_LANL_scaffold_6522 strand: + 46106-46220 alnlen 114 mutations 19 involve-A 19 involve-T 0

46304      GGTGTCCTTTTCAGCGGTAATACGAATAATGGCGATCATGCAGGCTTCGGTTATGCGAATACGAATAACACCCCCTCGAATACGAATGCGAATGTCAGCTCTCAGCTATGATTT 
           :::::::::::: :::::  : ::: : ::::::::: ::: ::::::::::::::: :::::::: :: :::::::: :::::  ::::: :::: :::::: ::: :: :::
46106      GGTGTCCTTTTCGGCGGTGCTGCGATTTATGGCGATCGTGCGGGCTTCGGTTATGCGGATACGAATTACGCCCCCTCGTATACGTTTGCGATTGTCGGCTCTCGGCTTTGTTTT 
Template:  SRS043701_LANL_scaffold_6522 strand: + 46338-46414 ref: 46304-46418
Variable:  SRS043701_LANL_scaffold_6522 strand: + 7643-7719 alnlen 76 mutations 14 involve-A 14 involve-T 0

46338      ATCATGCAGGCTTCGGTTATGCGAATACGAATAACACCCCCTCGAATACGAATGCGAATGTCAGCTCTCAGCTATG 
           ::: ::: :::::::::::::::  ::::  : :: :::::::: :::::: :::: ::::: :::::: ::: ::
7643       ATCGTGCGGGCTTCGGTTATGCGCTTACGTCTTACGCCCCCTCGTATACGAGTGCGTATGTCGGCTCTCGGCTTTG