Dear Alan,
Thank you for using the UCSC Genome Browser and your question about the lengths of alignments and the length of the given positions in the axt alignment files having non-equal values.
It isn't clear about the 5296 and 5290 values referenced, but I have included an example below from the panTro4.hg19.net.axt that might help illustrate differences.
- Alignment number -- The alignment numbering starts with 0 and increments by 1, i.e. the first alignment in a file is numbered 0, the next 1, etc.
- Chromosome (primary organism)
- Alignment start (primary organism) -- The first base is numbered 1
- Alignment end (primary organism) -- The end base is included.
- Chromosome (aligning organism)
- Alignment start (aligning organism)
- Alignment end (aligning organism)
- Strand (aligning organism) -- If the strand value is "-", the values of the aligning organism's start and end fields are relative to the reverse-complemented coordinates of its chromosome.
- Blastz score -- Different blastz scoring matrices are used for different organisms.See the README.txt file in the alignments directory for scoring information specific to a pair of alignments.
- Sequence lines primary assembly (line 2) and aligning assembly (line 3).
Here is an abbreviated version of the first line from the panTro4.hg19.net.axt file, you can find the full value further below.
0 chr1 77637 78679 chr1 87772 88869 + 91752
CCAGCCCTCTTGGCC-TGTGGC-AATTTTTTCTTTT-T ....t---------------------------------------------------ct....CCTCTGA
CCAGCCCTCTTG... ... ... CCTCTGA
Here is the full top line of panTro4.hg19.net.axt:
0 chr1 77637 78679 chr1 87772 88869 + 91752
CCAGCCCTCTTGGCC-TGTGGC-AATTTTTTCTTTT-TAGCCTCATAAAATCACATTATTTGAGTGCCCATGGCTCCAAAACAAGCAGGGATGCCCATGGACCCTGATTATCCATTGTCACCCTTCCCTCCAAACAGCCACCTCTCCCCTGGAGACAGCCCCATACTCCACTCAGACCTGTGTACTTCCTGGTATCCTTGTCACCTGCTTTTTATGCCTCATTTTACAAACACCAAATTGGAAGACAGCAGGAGCTGCCCCATAATACCAGTAAAGTGAGAAGCAGAGATAAATTAGTCCTAGACAACCGACTCATGTTGGGGGCAGCCCACTCACAGTGGCCCTGACCCAACTCTGACTAGAGGCCACTTGctctcaacaccagggtgctcaatggcccgtcctggtactctgctcttctctctccaccttcgctttcctgcaatctatgcagcctgtgactccatccatgggctagagacccccagaccttttcctgggaccacaggcctgtgtctctatctgctgctcaacacctccccttgaacatccatggctaaaactgagctcctgacactctctccatacccgtttctctgtggattccccacctccacgaaggacagcttcatcttttcagctactcaggccagaagactgaagtcatctccttctccaggaaatcgtattgggggagctacaaatatccaaaatccgatcgcttctcctccactacacccgaggcccgccacccatttttgcctgaattgctgcagcagcctcctaaccaatctctgctttcacgtgggcacctcagttttttccagaacaacaaccagagagatctactcacacccaagtcagaccaggttactcctctgctctcatagcatttggaggaaaacccagagtgct---------------------------------------------------cttgccctcagcacccagagtgctcgtgacggccagcaaagcccggccccatctcctctgaacttccacctctcgccctctgcacc-agAGTGCTCGTGACGGCCAGCAGAGCCGGCCCCCATCTCCTCTGA
CCAGCCCTCTTGGCCCTGTGGCCAATTTTTTCTTCAATAGCCTCATAAAATCACATTATTTGAGTGCCCATGGCTCCAAAACAAGCAGGGATGCCCATGGACCCTGATTATCCATTGTCACCCTTCCCTCCAAACAGCCACCTCTCCCCTGGAGACAGCCCCATACTCCACTCAGACCTGTGCACTTTCTGGTATCCTTGTCACCTGCTTTTTATGTCTCATTTTACAAACACCAAATTGGAAGACAGCAGGAGCTGCCCCATAATACCAGTAAAGTGAGAAGCAGAGATAAACTAGTCCTAGACAGCCGACTCATGTTGGGGGCAGCCCACTCACAGTGGCCCTGACCCAACTCTGACTAGAGGCCACTTGctctcaacaccagggtgctcaatggcccgtcctggtactctgctcttctctctccaccttcgctttcctgcaatctatgcagcctgtgactccatccatgggctagtgacccccagaccttctcctgggaccacaggcctgtgtctctatctgctgctcaatacctcccctcgaacatccatggctaaaactgagctcctgatactctctccctacccgcttctctgtggattccccacctccgcgaaggacagcttcatcctttcagctactcaggccagaagattgaagtcatctccttctccaggaaatcgtattgagggagctacaaatatccaaaatccgatcgcttctcctccactacacccgaggcccgccacccatttttgcctgaattgctgcagcagcctcctaaccgatctctgctttcacgtgggcacctcagttttttccagaacaacaaccagagagatctgctcacacccaagtcagaccaggttactcctctgctctcatagcatttggaggaaaacccagagtgctcgtgttggccggcagagccggcccccatctcctctgacctcctccccacctcttgccctcagcacccagagtgctcgtgacggccagcagagccagcctccatctcctctgacctcccacctctcgccctcagcaccCAGAGTGCTCGTGTTGGCCAGCAAAGCCGGCCCCCATCTCCTCTGA