#FIG 3.2 Landscape Center Metric A4 100.00 Single -2 1200 2 6 1755 1215 8280 1620 2 1 0 2 -1 -1 0 0 -1 0.000 0 0 7 0 0 2 1785 1575 8235 1575 4 1 -1 0 0 18 12 0.0000 4 180 6465 5010 1380 This module searches for specific PCR-primers in the current sequence. \001 -6 6 720 8280 3105 8460 4 0 0 50 0 16 12 0.0000 4 150 555 2520 8415 $result\001 4 0 0 50 0 16 12 0.0000 4 180 660 720 8415 $design\001 -6 6 2340 4500 5805 5220 4 0 -1 0 0 18 12 0.0000 4 135 840 2340 4635 G+C ratio\001 4 0 -1 0 0 18 12 0.0000 4 180 1095 2340 5085 temperature\001 4 0 0 50 0 16 12 0.0000 4 180 600 3960 4725 $mingc\001 4 0 0 50 0 16 12 0.0000 4 180 780 3960 5175 $mintemp\001 4 0 0 50 0 16 12 0.0000 4 180 645 4950 4725 $maxgc\001 4 0 0 50 0 16 12 0.0000 4 180 825 4950 5175 $maxtemp\001 -6 6 2340 3060 5670 4140 6 4005 3060 5400 3195 4 0 -1 0 0 18 12 0.0000 4 135 360 4005 3195 MIN\001 4 0 -1 0 0 18 12 0.0000 4 135 405 4995 3195 MAX\001 -6 6 2340 3420 5670 4140 4 0 -1 0 0 18 12 0.0000 4 180 1170 2340 3555 primer length\001 4 0 -1 0 0 18 12 0.0000 4 180 1380 2340 4005 primer distance\001 4 0 0 50 0 16 12 0.0000 4 150 675 3960 4095 $mindist\001 4 0 0 50 0 16 12 0.0000 4 150 720 4950 4095 $maxdist\001 4 0 0 50 0 16 12 0.0000 4 150 690 4950 3645 $maxlen\001 4 0 0 50 0 16 12 0.0000 4 150 645 3960 3645 $minlen\001 -6 -6 6 2340 2160 5760 2880 4 0 -1 0 0 18 12 0.0000 4 180 1155 2340 2745 right position\001 4 0 -1 0 0 18 12 0.0000 4 180 1050 2340 2295 left position\001 4 0 0 50 0 16 12 0.0000 4 180 750 3960 2835 $minright\001 4 0 -1 0 0 16 12 0.0000 4 150 630 3960 2385 $minleft\001 4 0 -1 0 0 16 12 0.0000 4 150 675 4950 2385 $maxleft\001 4 0 0 50 0 16 12 0.0000 4 180 795 4950 2835 $maxright\001 -6 6 4005 1800 6840 1935 4 0 -1 0 0 18 12 0.0000 4 135 630 4005 1935 START\001 4 0 -1 0 0 18 12 0.0000 4 135 1845 4995 1935 NUMBER OF BASES\001 -6 6 7020 3060 7470 3600 4 0 0 50 0 16 12 0.0000 4 150 450 7020 3555 $init2\001 4 0 0 50 0 16 12 0.0000 4 150 450 7020 3195 $init1\001 -6 2 2 0 1 -1 -1 0 0 -1 0.000 0 0 0 0 0 5 9135 8685 9135 600 585 600 585 8685 9135 8685 2 1 0 2 -1 -1 0 0 -1 0.000 0 0 7 0 0 2 720 7875 9000 7875 2 1 0 1 0 7 50 0 -1 0.000 0 0 7 0 0 2 720 4260 9000 4260 2 1 0 1 0 7 50 0 -1 0.000 0 0 7 0 0 2 720 5340 9000 5340 2 2 0 1 -1 -1 0 0 -1 0.000 0 0 0 0 0 5 8865 3735 8865 2025 6345 2025 6345 3735 8865 3735 4 0 0 50 0 16 12 0.0000 4 150 555 720 1035 $close\001 4 2 0 50 0 16 12 0.0000 4 180 465 9000 1035 $help\001 4 2 0 50 0 16 10 0.0000 4 150 2355 9045 8595 written by Wolfram Foerster 2001\001 4 0 0 50 0 18 12 0.0000 4 180 870 6345 4005 0 = ignore\001 4 2 -1 0 0 18 12 0.0000 4 180 2940 3780 5715 min. dist to next match of primer\001 4 2 -1 0 0 18 12 0.0000 4 180 1830 3780 6165 expand IUPAC codes\001 4 2 -1 0 0 18 12 0.0000 4 135 2070 3780 6615 max. number of results\001 4 2 -1 0 0 18 12 0.0000 4 135 1110 3780 7065 G+C - factor\001 4 2 -1 0 0 18 12 0.0000 4 180 1695 3780 7515 temperature factor\001 4 0 -1 0 0 18 12 0.0000 4 180 1860 5130 5715 <= 0 : singular match\001 4 0 0 50 0 16 12 0.0000 4 180 1065 3960 7605 $temp_factor\001 4 0 0 50 0 16 12 0.0000 4 165 945 3960 7155 $GC_factor\001 4 0 0 50 0 16 12 0.0000 4 180 945 3960 6705 $max_pairs\001 4 0 0 50 0 16 12 0.0000 4 180 1380 3960 6255 $expand_IUPAC\001 4 0 0 50 0 16 12 0.0000 4 165 1350 3960 5805 $allowed_match\001 4 0 0 50 0 16 35 0.0000 4 210 75 5850 7380 }\001 4 0 -1 0 0 18 12 0.0000 4 135 660 5130 7515 0 .. 100\001 4 0 -1 0 0 18 12 0.0000 4 135 660 5130 7065 0 .. 100\001 4 0 0 50 0 18 12 0.0000 4 180 1830 6030 7290 G+C + temp = 100\001 4 0 0 50 0 16 12 0.0000 4 180 1050 7425 8280 $aprox_mem\001 4 0 0 50 0 18 12 0.0000 4 180 2490 4815 8190 estimated memory needed :\001 4 1 0 50 0 18 12 0.0000 4 135 2055 7605 2565 with reasonable values\001 4 1 0 50 0 18 12 0.0000 4 180 2250 7605 2340 fill positions and distance\001 4 1 0 50 0 18 12 0.0000 4 135 1650 7605 2790 from the current ..\001 4 0 0 50 0 0 12 0.0000 4 195 555 3780 8325 $config\001