Sputnik DNA microsatellite repeat search utility Chris Abajian http://rast.abajian.com/sputnik/ sputnik query Sequence File (fasta or multifasta format) perl " $query" 1 8 seqfile perl 1 show Show all (even when there is no repeat) (-a) perl (defined $value)?" -a":"" 1 bother Do not bother finding the canonical repeat unit (-x) perl (defined $value)?" -x":"" 1 max_unit Max unit length (-u) perl (defined $value)?" -u $max_unit":"" 2 2 min_unit Min unit length (-v) perl (defined $value)?" -v $min_unit":"" 2 match Points for a match (-m) perl (defined $value)?" -m $match":"" 3 mismatch Points for a mis-match (-n) perl (defined $value)?" -n $mismatch":"" 3 score Minimum score (-s) perl (defined $value)?" -s $score":"" 3 adjust Adjust scores for the first unit cell (-j) perl (defined $value)?" -j":"" 4 error Errors per 100 bases (-e) perl (defined $value)? " -e $value":"" 4 report Report score as percent perfection (-p) perl (defined $value)?" -p":"" 4 fail_score fail score (-f) perl (defined $value)? " -f $value":"" 5 degrade Max degrade and still continue, in bases (-d) perl (defined $value)? " -d $value":"" 5 recursion Max recursion [0, 100] (0 ==> perfect only) (-r) perl (defined $value)? " -r $value":"" 6 Enter a value between 0 and 100 perl $recursion < 0 || $recursion > 100 flanking output this many bases flanking the repeat [0, 1000] (-F) perl (defined $value)? " -F $value":"" 6 Enter a value between 0 and 1000 perl $flanking < 0 || $flanking > 1000 ssr_report Min length of SSR to report (-L) perl (defined $value)? " -L $value":"" 20 7 output_line Max characters on an output line (-l) perl (defined $value)?" -l":"" -1 0 7 collapse Do not collapse unit cell to canonical strand (-z) perl (defined $value)?" -z":"" 7 res perl " > report.out" 9 outfile report.out