PSL alignment format

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PSL format is a simple tabular format produced by BLAT and other UCSC tools.

Here are the columns as taken from the UCSC documentation.

  1. matches - Number of bases that match that aren't repeats
  2. misMatches - Number of bases that don't match
  3. repMatches - Number of bases that match but are part of repeats
  4. nCount - Number of 'N' bases
  5. qNumInsert - Number of inserts in query
  6. qBaseInsert - Number of bases inserted in query
  7. tNumInsert - Number of inserts in target
  8. tBaseInsert - Number of bases inserted in target
  9. strand - '+' or '-' for query strand. In mouse, second '+'or '-' is for genomic strand
  10. qName - Query sequence name
  11. qSize - Query sequence size
  12. qStart - Alignment start position in query
  13. qEnd - Alignment end position in query
  14. tName - Target sequence name
  15. tSize - Target sequence size
  16. tStart - Alignment start position in target
  17. tEnd - Alignment end position in target
  18. blockCount - Number of blocks in the alignment
  19. blockSizes - Comma-separated list of sizes of each block
  20. qStarts - Comma-separated list of starting positions of each block in query
  21. tStarts - Comma-separated list of starting positions of each block in target
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