Hi,

This is somewhat redundant with this post, which has not been fully answered.

I'm using Webb Miller's sim4 aligner, which output (specifying A=1 in the arguments) looks like this:

seq1 = /data/seq1.fa, 1095 bp 
seq2 = /data/seq2.fa (chrA:23544043-25452600), 1908558 bp


      0     .    :    .    :    .    :    .    :    .    :
     96 CTTC ACATC CG TGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCG
        ||||-|||||-||-|||||||||||||||  |||||||||||||||||
1136214 CTTCGACATCGCGGTGTCCCGGCCCGGCCAAGGGGAGCCCCGCTTCATGT

     50     .    :    .    :    .    :    .    :    .    :
    143 CCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCC
        |||||||||||||||||||||||||||||||||| |||||||||||||||
1136264 CCGTGGGCTACGTGGACGACACGCAGTTCGTGCGCTTCGACAGCGACGCC

    100     .    :    .    :    .    :    .    :    .    :
    193 GCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCC
        ||||||| |||| |||||||||||||| ||||||| |||| || ||  |
1136314 GCGAGCCCGAGGGTGGAGCCGCGGGCGGCGTGGATGGAGCGGGTGGACCA

    150     .    :    .    :    .
    243 GGAGTATTGGGACCAGGAGACACGGA
        || ||||||||||| |||||||||||
1136364 GGCGTATTGGGACCGGGAGACACGGA

      0     .    :    .    :    .    :    .    :    .    :
    320 GCTACTACAACCAGAGCGAGGCCG         GTTCTCACACCATCCAG
        ||||||||||||||| ||||||||>>>...>>>| ||||||||| |||||
1136441 GCTACTACAACCAGACCGAGGCCGGTG...CAGGCTCTCACACCTTCCAG

     50     .    :    .    :    .    :    .    :    .    :
    361 ATAATGTATGGCTGCGACGTGGGGTCGGACGGGCGCTTCCTCCGCGGGTA
        |  ||||| |||||||| |||||||||||||||||| |||||||||||||
1136677 AGGATGTACGGCTGCGAAGTGGGGTCGGACGGGCGCCTCCTCCGCGGGTA

    100     .    :    .    :    .    :    .    :    .    :
    411 C CGGCAG GACGCCTACGACGGCAAGGATTACATCGCCCT GAACGAGG
        |-||-|||-| -||||||||||||  |||||||||||||||-|  -||||
1136727 CACG CAGTGG GCCTACGACGGCGCGGATTACATCGCCCTCGCT GAGG

    150     .    :    .    :    .    :    .    :    .    :
    458 ACCTGCGCTCTTGGACCGCGGCGGACATGGCGGCTCAGATCAC CAAGCG
        ||||| |||| |||   ||||||||||  ||||||| ||||||-|-||||
1136774 ACCTGAGCTCCTGGGTGGCGGCGGACACCGCGGCTCTGATCACAC AGCG

    200     .    :    .    :    .    :    .    :    .    :
    507 CAAGTGGGAGGCGGCCCATGAGGCGGAGCAGTTGAGAGCCTACCTGGATG
        |||||||| || ||||   | ||| ||||     || ||||||||||| |
1136823 CAAGTGGGTGGAGGCCGGCGTGGCAGAGCGCCACAGGGCCTACCTGGAGG

    250     .    :    .    :    .    :    .    :    .    :
    557 GCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAG AC
        |||| || |||||||||||||||||| ||||||||||||||||||||-|-
1136873 GCACCTGTGTGGAGTGGCTCCGCAGACACCTGGAGAACGGGAAGGAGCA

    300     .    :
    606 GCTGCAGCGCAC
        ||||||||||||
1136922 GCTGCAGCGCAC

What I want to get out of this is what are the indel positions in the alignment. In this example there are two aligned blocks (they start with the 0 indicator in the alignment consensus part on top of the aligned sequences). The results are (0-based):

for the first block: 4, 10, 13

for the second block: 101, 104, 108, 111, 141, 145, 193, 195, 297, 299

Naturally it would be nice to use some existing tool (preferably an R package) to read in this alignment and to extract it directly from the read-in alignment object but I can't even figure out what format this output is in.

Any help would be highly appreciated.