diffseq.txt

emboss的linux版本的源代码

Sequence "AP000504.8" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        8218    8221    1.000   +       .
Sequence "AP000504.9" ; note "Insertion of 4 bases in AP000504" ; replace ""
AP000504        diffseq conflict        9096    9096    1.000   +       .
Sequence "AP000504.10" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        11149   11149   1.000   +       .
Sequence "AP000504.11" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        13718   13718   1.000   +       .
Sequence "AP000504.12" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        14248   14248   1.000   +       .
Sequence "AP000504.13" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        14419   14419   1.000   +       .
Sequence "AP000504.14" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        19643   19643   1.000   +       .
Sequence "AP000504.15" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        20149   20149   1.000   +       .
Sequence "AP000504.16" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        21316   21319   1.000   +       .
Sequence "AP000504.17" ; note "Insertion of 4 bases in AP000504" ; replace ""
AP000504        diffseq conflict        21797   21797   1.000   +       .
Sequence "AP000504.18" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        23288   23288   1.000   +       .
Sequence "AP000504.19" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        23418   23418   1.000   +       .
Sequence "AP000504.20" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        23589   23589   1.000   +       .
Sequence "AP000504.21" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        23606   23606   1.000   +       .
Sequence "AP000504.22" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        24798   24798   1.000   +       .
Sequence "AP000504.23" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        25309   25309   1.000   +       .
Sequence "AP000504.24" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        25861   25861   1.000   +       .
Sequence "AP000504.25" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        28039   28040   1.000   +       .
Sequence "AP000504.26" ; note "Insertion of 2 bases in AP000504" ; replace ""
AP000504        diffseq conflict        30644   30644   1.000   +       .
Sequence "AP000504.27" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        32339   32339   1.000   +       .
Sequence "AP000504.28" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        32497   32497   1.000   +       .
Sequence "AP000504.29" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        33074   33074   1.000   +       .
Sequence "AP000504.30" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        33776   33776   1.000   +       .
Sequence "AP000504.31" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        34767   34767   1.000   +       .
Sequence "AP000504.32" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        35163   35163   1.000   +       .
Sequence "AP000504.33" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        36507   36507   1.000   +       .
Sequence "AP000504.34" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        37760   37762   1.000   +       .
Sequence "AP000504.35" ; note "Insertion of 3 bases in AP000504" ; replace ""
AP000504        diffseq conflict        38680   38683   1.000   +       .
Sequence "AP000504.36" ; note "Insertion of 4 bases in AP000504" ; replace ""
AP000504        diffseq conflict        42347   42347   1.000   +       .
Sequence "AP000504.37" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        42637   42638   1.000   +       .
Sequence "AP000504.38" ; note "Insertion of 2 bases in AP000504" ; replace ""
AP000504        diffseq conflict        44602   44602   1.000   +       .
Sequence "AP000504.39" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        44776   44776   1.000   +       .
Sequence "AP000504.40" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        45253   45253   1.000   +       .
Sequence "AP000504.41" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        46354   46354   1.000   +       .
Sequence "AP000504.42" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        46612   46612   1.000   +       .
Sequence "AP000504.43" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        47562   47562   1.000   +       .
Sequence "AP000504.44" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        47587   47587   1.000   +       .
Sequence "AP000504.45" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        48849   48849   1.000   +       .
Sequence "AP000504.46" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        49343   49343   1.000   +       .
Sequence "AP000504.47" ; note "SNP in AF129756" ; replace "a"


  [Part of this file has been deleted for brevity]

AP000504        diffseq conflict        58685   58685   1.000   +       .
Sequence "AP000504.55" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        60558   60558   1.000   +       .
Sequence "AP000504.56" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        61209   61209   1.000   +       .
Sequence "AP000504.57" ; note "Insertion of 1 bases in AP000504" ; replace ""
AP000504        diffseq conflict        62958   62959   1.000   +       .
Sequence "AP000504.58" ; note "Insertion of 2 bases in AP000504" ; replace ""
AP000504        diffseq conflict        63402   63402   1.000   +       .
Sequence "AP000504.59" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        64139   64140   1.000   +       .
Sequence "AP000504.60" ; note "AF129756" ; replace "at"
AP000504        diffseq conflict        64152   64152   1.000   +       .
Sequence "AP000504.61" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        65317   65317   1.000   +       .
Sequence "AP000504.62" ; note "Insertion of 1 bases in AP000504" ; replace ""
AP000504        diffseq conflict        67523   67523   1.000   +       .
Sequence "AP000504.63" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        67715   67715   1.000   +       .
Sequence "AP000504.64" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        68554   68554   1.000   +       .
Sequence "AP000504.65" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        69285   69285   1.000   +       .
Sequence "AP000504.66" ; note "Insertion of 1 bases in AP000504" ; replace ""
AP000504        diffseq conflict        70419   70419   1.000   +       .
Sequence "AP000504.67" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        70666   70666   1.000   +       .
Sequence "AP000504.68" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        71287   71287   1.000   +       .
Sequence "AP000504.69" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        71553   71553   1.000   +       .
Sequence "AP000504.70" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        72048   72048   1.000   +       .
Sequence "AP000504.71" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        73627   73627   1.000   +       .
Sequence "AP000504.72" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        73998   73998   1.000   +       .
Sequence "AP000504.73" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        74071   74071   1.000   +       .
Sequence "AP000504.74" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        75838   75845   1.000   +       .
Sequence "AP000504.75" ; note "AF129756" ; replace "g"
AP000504        diffseq conflict        76095   76095   1.000   +       .
Sequence "AP000504.76" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        77612   77612   1.000   +       .
Sequence "AP000504.77" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        78253   78253   1.000   +       .
Sequence "AP000504.78" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        80428   80428   1.000   +       .
Sequence "AP000504.79" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        80974   80974   1.000   +       .
Sequence "AP000504.80" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        81564   81564   1.000   +       .
Sequence "AP000504.81" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        81852   81852   1.000   +       .
Sequence "AP000504.82" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        82318   82318   1.000   +       .
Sequence "AP000504.83" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        82594   82594   1.000   +       .
Sequence "AP000504.84" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        82709   82709   1.000   +       .
Sequence "AP000504.85" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        83072   83072   1.000   +       .
Sequence "AP000504.86" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        83692   83692   1.000   +       .
Sequence "AP000504.87" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        86264   86264   1.000   +       .
Sequence "AP000504.88" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        86298   86298   1.000   +       .
Sequence "AP000504.89" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        87932   87932   1.000   +       .
Sequence "AP000504.90" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        88912   88912   1.000   +       .
Sequence "AP000504.91" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        89199   89199   1.000   +       .
Sequence "AP000504.92" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        89762   89764   1.000   +       .
Sequence "AP000504.93" ; note "AF129756" ; replace "ca"
AP000504        diffseq conflict        90710   90710   1.000   +       .
Sequence "AP000504.94" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        91667   91683   1.000   +       .
Sequence "AP000504.95" ; note "AF129756" ; replace "g"
AP000504        diffseq conflict        91797   91797   1.000   +       .
Sequence "AP000504.96" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        92165   92165   1.000   +       .
Sequence "AP000504.97" ; note "SNP in AF129756" ; replace "a"
AP000504        diffseq conflict        93250   93250   1.000   +       .
Sequence "AP000504.98" ; note "SNP in AF129756" ; replace "c"
AP000504        diffseq conflict        93696   93696   1.000   +       .
Sequence "AP000504.99" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        93860   93860   1.000   +       .
Sequence "AP000504.100" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        95451   95451   1.000   +       .
Sequence "AP000504.101" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        96650   96650   1.000   +       .
Sequence "AP000504.102" ; note "SNP in AF129756" ; replace "t"
AP000504        diffseq conflict        97273   97274   1.000   +       .
Sequence "AP000504.103" ; note "Insertion of 2 bases in AP000504" ; replace ""
AP000504        diffseq conflict        97716   97716   1.000   +       .
Sequence "AP000504.104" ; note "SNP in AF129756" ; replace "g"
AP000504        diffseq conflict        97827   97827   1.000   +       .
Sequence "AP000504.105" ; note "SNP in AF129756" ; replace "t"

   The first line is the title giving the names of the sequences used.

   The next two non-blank lines state the positions in each sequence
   where the detected overlap between them starts.

   There then follows a set of reports of the mismatches between the
   sequences.
   Each report consists of 4 or more lines.
     * The first line has the name of the first sequence followed by the
       start and end positions of the mismatched region in that sequence,
       followed by the length of the mismatched region. If the mismatched
       region is of zero length in this sequence, then only the position
       of the last matching base before the mismatch is given.
     * If a feature of the first sequence overlaps with this mismatch
       region, then one or more lines starting with 'Feature:' comes next
       with the type, position and tag field of the feature.
     * Next is a line starting "Sequence:" giving the sequence of the
       mismatch in the first sequence.

   This is followed by the equivalent information for the second
   sequence, but in the reverse order, namely 'Sequence:' line,
   'Feature:' lines and line giving the position of the mismatch in the
   second sequence.

   At the end of the report are two non-blank lines giving the positions
   in each sequence where the detected overlap between them ends.

   The last three lines of the report gives the counts of SNPs (defined
   as a change of one nucleotide to one other nucleotide, no deletions or
   insertions are counted, no multi-base changes are counted).

   If the input sequences are nucleic acid, The counts of transitions
   (Pyrimide to Pyrimidine or Purine to Purine) and transversions
   (Pyrimidine to Purine) are also given.

   It should be noted that not all features are reported.

   The 'source' feature found in all EMBL/Genbank feature table entries
   is not reported as this covers all of the sequence and so overlaps
   with any difference found in that sequence and so is uninformative and
   irritating. It has therefore been removed from the output report.

   The translation information of CDS features is often extremely long
   and does not add useful information to the report. It has therefore
   been removed from the output report.

Data files

   None

Notes

   It should be noted that not all features are reported.

   The 'source' feature found in all EMBL/Genbank feature table entries
   is not reported as this covers all of the sequence and so overlaps
   with any difference found in that sequence and so is uninformative and
   irritating. It has therefore been removed from the output report.

   The translation information of CDS features is often extremely long
   and does not add useful information to the report. It has therefore
   been removed from the output report.

   If you run out of memory, use a larger word size.

   Using a larger word size increases the length between mismatches that
   will be reported as one event. Thus a word size of 50 will report two
   single-base differences that are with 50 bases of each other as one
   mismatch.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name Description

Author(s)

   Gary Williams (gwilliam