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4 0 -1 0 0 18 13 0.0000 4 210 1500 5655 4230 $considbound\001 4 0 -1 0 0 18 12 0.0000 4 225 735 5655 7710 $upper\001 4 0 -1 0 0 18 12 0.0000 4 210 675 5655 8235 $lower\001 4 0 -1 0 0 18 13 0.0000 4 210 2445 3105 1170 What to Do with Gaps ?\001 4 0 -1 0 0 18 13 0.0000 4 225 1185 5655 1620 $gapbound\001 4 2 -1 0 0 16 9 0.0000 4 120 225 4950 5445 0%\001 4 2 -1 0 0 16 9 0.0000 4 120 315 4950 4725 50%\001 4 2 -1 0 0 16 9 0.0000 4 120 405 4950 4005 100%\001 4 2 -1 0 0 16 9 0.0000 4 120 315 5355 2340 50%\001 4 2 -1 0 0 16 9 0.0000 4 120 225 5355 2790 0%\001 4 2 -1 0 0 16 9 0.0000 4 120 405 5355 1890 100%\001 4 0 0 50 0 16 10 0.0000 4 120 720 7380 5580 characters\001 4 0 0 50 0 16 10 0.0000 4 120 555 5760 9360 columns\001 4 0 0 50 0 16 10 0.0000 4 120 555 7155 2880 columns\001 4 1 -1 0 0 16 9 0.0000 4 150 900 4050 1980 Count gaps?\001 4 0 -1 0 0 18 13 0.0000 4 225 1410 6073 6113 $showgroups\001 4 1 -1 0 0 16 9 0.0000 4 120 405 5805 5580 group\001 4 2 -1 0 0 16 9 0.0000 4 90 600 4182 5880 use max:\001 4 2 -1 0 0 16 9 0.0000 4 120 225 3645 9225 0%\001 4 2 0 50 0 16 9 0.0000 4 120 405 3645 7425 100%\001 4 2 0 50 0 16 9 0.0000 4 120 315 3645 8325 50%\001 4 0 -1 0 0 18 13 0.0000 4 225 1230 3465 2370 $countgaps\001 4 0 -1 0 0 18 13 0.0000 4 165 3375 3105 7020 Show as UPPER or lower Case ?\001 4 0 -1 0 0 18 13 0.0000 4 210 2385 3105 3780 Simplify Using IUPAC?\001 4 0 -1 0 0 16 10 0.0000 4 120 465 3240 9873 Result:\001 4 1 -1 0 0 16 10 0.0000 4 120 105 5175 9855 A\001 4 1 -1 0 0 16 10 0.0000 4 90 75 4635 9855 a\001 4 1 -1 0 0 16 10 0.0000 4 15 45 4095 9810 .\001 4 1 -1 0 0 16 10 0.0000 4 90 75 4095 8730 a\001 4 1 -1 0 0 16 10 0.0000 4 90 75 4635 8730 a\001 4 1 -1 0 0 16 10 0.0000 4 90 75 5175 8730 a\001 4 1 -1 0 0 16 10 0.0000 4 120 105 4363 5890 A\001 4 1 -1 0 0 16 10 0.0000 4 15 90 5850 2565 _\001 4 1 -1 0 0 16 10 0.0000 4 15 90 6300 2565 _\001 4 1 -1 0 0 16 10 0.0000 4 120 105 5853 5903 R\001 4 1 -1 0 0 16 10 0.0000 4 15 90 6312 3209 _\001 4 1 -1 0 0 16 10 0.0000 4 45 75 3292 3266 =\001 4 0 -1 0 0 18 13 0.0000 4 225 750 3060 4185 $group\001 4 0 -1 0 0 18 13 0.0000 4 225 1860 525 1650 $which_alignment\001 4 0 -1 0 0 18 13 0.0000 4 210 675 525 9750 $name\001 4 0 -1 0 0 18 13 0.0000 4 165 1320 525 9300 Write to SAI:\001 4 0 -1 0 0 18 13 0.0000 4 225 1635 525 3675 $which_species\001 4 0 -1 0 0 18 13 0.0000 4 210 825 525 3300 Species\001 4 0 -1 0 0 18 13 0.0000 4 210 1050 525 1215 Alignment\001