Sorry, sorry, sorry Monks! Here are some verbose explanations and examples, hope these help

Before that, just a lil bit of sequence alignment lingo from biologists dictionary:

substitution: when a letter in one sequence is replaced by a different letter. in another sequence. eg.GGTA is substituted in 2 places to give CCTA , TACGACT substituted in 1 place to give AACGACT etc.

indel: when one letter in one sequence is replaced by nothing in the second sequence. 1st sequence is said to have an insertion (IN) and 2nd sequence has a deletion (DEL). Hence the term INDEL eg. TAGAGGATC and TAGAGATC differ by 1 indel position, so 2nd sequence when aligned would be TAGAG-ATC or TAGA-GATC

case c: the mismatch is not due to substitution of one letter for another, but a gap (shown as '-' here) due to a missing letter when comparing the 2 sequences

 AC-TACGTAC
 ACGTACGTAC

[download]

or

 ACGTACGTAC
 ACGTACGT-C

[download]

case d: the mismatch is due to substitution of one letter for another, and not an insertion or deletion as show in examples above, for case c.

 CTTACGTAC
 CGTACGTAC

[download]

or

 CGTACGTGC
 CGTACGTCC

[download]

case e: same as case d. above, except the matched lengths are 10 letters long, and not 9 letters as for case d.. Mis-match is not due to insertion or deletion, but a substitution, again as for case d.

 ACCTACGTAC
 ACGTACGTAC

[download]

or

 GTACGTACGG
 GTACGTTCGG

[download]

Some examples of what should pass the filters and what should not are shown below

10nt sequences, no indels, no substitutions, perfect matches, passes filter, all OK 

 ATGGACGTAC
 ATGGACGTAC

[download]

9nt sequences, no indels, no substitutions, perfect matches, passes filter, all OK 

 CGTACAGTA
 CGTACAGTA

[download]

10nt sequences, 1 indel position, passes filter, OK 

 AC-TACGTAC
 ACGTACGTAC

[download]

10nt sequences, 2 indel positions in total,1 indel on one sequence and 2nd indel on 2nd sequence, does not passes filter, not OK 

 AC-TACGTAC
 ACGTACG-AC

[download]

10nt sequences, 2 indel positions in total, both indels on same sequence, does not passes filter, not OK 

 AC-TAC-TAC
 ACGTACGTAC

[download]

Bottom line is that when sequences of 10 letters are aligned to each other, there should be at the very minimum 9 letters that are aligned with a maximum of 1 indel or substitution. At the very best, all 10 letters are perfectly matched with no indels and no substitutions. And all other intermediate cases, some with examples of alignments above. I hope things are a little better to understand now, especially for non-biologists. Sorry for the cryptic explanation in my OP!

In reply to Re^2: Filtering matches of near-perfect-matched DNA sequence pairs by onlyIDleft
in thread Filtering matches of near-perfect-matched DNA sequence pairs by onlyIDleft

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