Template:  SRS056259_LANL_scaffold_17268 strand: + 13771-13944 ref: 13771-13943
Variable:  SRS056259_LANL_scaffold_17268 strand: + 12377-12550 alnlen 173 mutations 24 involve-A 24 involve-T 0

13771      CCCCGCTTCGGGGTATCGCAACAACAATAACGGGCAGTTGAACAACGTGGGCAACAACGGCAACTATTGGTCGGGCTCGCCGAACGGTACGAACGGGTATAACCTGAACTTCAACAATGGTAACGTGAACCCGGCGAACAACAACAACCGCTCGAACGGCTTCTCCGTGAGGT 
           :::::::::::::: :::: ::  ::::: ::::::::::  : :::::::: :: ::::: ::::::::::::::::::::: ::::::::::::::::: ::::  :::::::  ::::::::::: ::::::: :: :::::  :::::::  :::::::::::::::::
12377      CCCCGCTTCGGGGTGTCGCTACGCCAATAGCGGGCAGTTGCTCTACGTGGGCTACTACGGCTACTATTGGTCGGGCTCGCCGATCGGTACGAACGGGTATAGCCTGTCCTTCAACGGTGGTAACGTGAGCCCGGCGTACTACAACGCCCGCTCGTTCGGCTTCTCCGTGAGGT 
Template:  SRS056259_LANL_scaffold_17268 strand: + 13771-13891 ref: 13771-13943
Variable:  SRS056259_LANL_scaffold_17268 strand: + 9350-9470 alnlen 120 mutations 29 involve-A 15 involve-T 4

13771      CCCCGCTTCGGGGTATCGCAACAACAATAACGGGCAGTTGAACAACGTGGGCAACAACGGCAACTATTGGTCGGGCTCGCCGAACGGTACGAACGGGTATAACCTGAACTTCAACAATGG 
           ::: ::: ::::::: ::::   ::   :: ::::::::: ::::::::::: :: ::::: ::::::::::::: :: :: ::: :::  : ::::::   : :: :::::  :: :::
9350       CCCGGCTGCGGGGTACCGCACTTACGGCAATGGGCAGTTGTACAACGTGGGCTACTACGGCTACTATTGGTCGGGGTCTCCTAACAGTATAAGCGGGTACTCCTTGTACTTCCTCAGTGG