Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign26 - back to list
Summary
./analyse_probe_search_results : Mon Sep 5 11:54:51 2005
Connected to host: host, as user: user Database : gene_targeting_production Fetched probe design: ProbeDesign26 assembly : NCBIM33 bias : 5prime chromosome : 3 id : 3 strand : 1 ------------- Design window length: 2001bp All jobs for probe design are successful - total: 41 Fetched conf : Exonerate mouse_NCBI33 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM33/genome/masked_dusted Fetched 405 putative probes to analyse Selection criteria to rank probes: Minimum score ratio : 10 (i.e. self-hit must score at least 10 times higher than the next best hit) Maximum percent repetitive bases: 5 Favour probes to the 5prime end of design window ------------------------ Putative probes without hits : 0 Putative probes with single_self_hit : 405/405 Putative probes exceeding selection criteria: 249/405 PASSED (GREEN) AND FAILED PUTATIVE PROBES IN THE DESIGN WINDOW --------------------------------------------------------------
Image
Unique (yellow), passed (green) and failed putative probes in the design window
Unique putative probes
No probes
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
811 | 1000 | 31.8 | 5000 | - | 0 | 31.8 |
812 | 1000 | 31.8 | 5000 | - | 50 | 31.8 |
832 | 950 | 30.3 | 4750 | - | 0 | 30.3 |
833 | 950 | 30.3 | 4750 | - | 47 | 30.3 |
834 | 950 | 30.3 | 4750 | - | 94 | 30.3 |
813 | 1000 | 29.9 | 5000 | - | 100 | 29.9 |
814 | 1000 | 29.9 | 5000 | - | 150 | 29.9 |
815 | 1000 | 29.9 | 5000 | - | 200 | 29.9 |
816 | 1000 | 29.9 | 5000 | - | 250 | 29.9 |
817 | 1000 | 29.9 | 5000 | - | 300 | 29.9 |
818 | 1000 | 29.9 | 5000 | - | 350 | 29.9 |
819 | 1000 | 29.9 | 5000 | - | 400 | 29.9 |
820 | 1000 | 29.9 | 5000 | - | 450 | 29.9 |
821 | 1000 | 29.9 | 5000 | - | 500 | 29.9 |
822 | 1000 | 29.9 | 5000 | - | 550 | 29.9 |
835 | 950 | 29.3 | 4750 | - | 141 | 29.3 |
855 | 900 | 28.7 | 4500 | - | 0 | 28.7 |
856 | 900 | 28.7 | 4500 | - | 45 | 28.7 |
857 | 900 | 28.7 | 4500 | - | 90 | 28.7 |
858 | 900 | 28.7 | 4500 | - | 135 | 28.7 |
859 | 900 | 28.7 | 4500 | - | 180 | 28.7 |
836 | 950 | 28.4 | 4750 | - | 188 | 28.4 |
837 | 950 | 28.4 | 4750 | - | 235 | 28.4 |
838 | 950 | 28.4 | 4750 | - | 282 | 28.4 |
839 | 950 | 28.4 | 4750 | - | 329 | 28.4 |
840 | 950 | 28.4 | 4750 | - | 376 | 28.4 |
841 | 950 | 28.4 | 4750 | - | 423 | 28.4 |
842 | 950 | 28.4 | 4750 | - | 470 | 28.4 |
843 | 950 | 28.4 | 4750 | - | 517 | 28.4 |
844 | 950 | 28.4 | 4750 | - | 564 | 28.4 |
881 | 850 | 28.3 | 4250 | - | 42 | 28.3 |
845 | 950 | 27.3 | 4750 | - | 611 | 27.3 |
882 | 850 | 27.1 | 4250 | - | 84 | 27.1 |
883 | 850 | 27.1 | 4250 | - | 126 | 27.1 |
884 | 850 | 27.1 | 4250 | - | 168 | 27.1 |
885 | 850 | 27.1 | 4250 | - | 210 | 27.1 |
860 | 900 | 26.9 | 4500 | - | 225 | 26.9 |
861 | 900 | 26.9 | 4500 | - | 270 | 26.9 |
862 | 900 | 26.9 | 4500 | - | 315 | 26.9 |
863 | 900 | 26.9 | 4500 | - | 360 | 26.9 |
864 | 900 | 26.9 | 4500 | - | 405 | 26.9 |
865 | 900 | 26.9 | 4500 | - | 450 | 26.9 |
866 | 900 | 26.9 | 4500 | - | 495 | 26.9 |
867 | 900 | 26.9 | 4500 | - | 540 | 26.9 |
868 | 900 | 26.9 | 4500 | - | 585 | 26.9 |
869 | 900 | 26.9 | 4500 | - | 630 | 26.9 |
911 | 800 | 25.5 | 4000 | - | 120 | 25.5 |
912 | 800 | 25.5 | 4000 | - | 160 | 25.5 |
913 | 800 | 25.5 | 4000 | - | 200 | 25.5 |
914 | 800 | 25.5 | 4000 | - | 240 | 25.5 |
915 | 800 | 25.5 | 4000 | - | 280 | 25.5 |
886 | 850 | 25.4 | 4250 | - | 252 | 25.4 |
887 | 850 | 25.4 | 4250 | - | 294 | 25.4 |
888 | 850 | 25.4 | 4250 | - | 336 | 25.4 |
889 | 850 | 25.4 | 4250 | - | 378 | 25.4 |
890 | 850 | 25.4 | 4250 | - | 420 | 25.4 |
891 | 850 | 25.4 | 4250 | - | 462 | 25.4 |
892 | 850 | 25.4 | 4250 | - | 504 | 25.4 |
893 | 850 | 25.4 | 4250 | - | 546 | 25.4 |
894 | 850 | 25.4 | 4250 | - | 588 | 25.4 |
895 | 850 | 25.4 | 4250 | - | 630 | 25.4 |
896 | 850 | 25.4 | 4250 | - | 672 | 25.4 |
916 | 800 | 24.0 | 4000 | - | 320 | 24.0 |
917 | 800 | 24.0 | 4000 | - | 360 | 24.0 |
918 | 800 | 24.0 | 4000 | - | 400 | 24.0 |
919 | 800 | 24.0 | 4000 | - | 440 | 24.0 |
920 | 800 | 24.0 | 4000 | - | 480 | 24.0 |
921 | 800 | 24.0 | 4000 | - | 520 | 24.0 |
922 | 800 | 24.0 | 4000 | - | 560 | 24.0 |
923 | 800 | 24.0 | 4000 | - | 600 | 24.0 |
924 | 800 | 24.0 | 4000 | - | 640 | 24.0 |
925 | 800 | 24.0 | 4000 | - | 680 | 24.0 |
926 | 800 | 24.0 | 4000 | - | 720 | 24.0 |
943 | 750 | 23.9 | 3750 | - | 148 | 23.9 |
944 | 750 | 23.9 | 3750 | - | 185 | 23.9 |
945 | 750 | 23.9 | 3750 | - | 222 | 23.9 |
946 | 750 | 23.9 | 3750 | - | 259 | 23.9 |
947 | 750 | 23.9 | 3750 | - | 296 | 23.9 |
948 | 750 | 23.9 | 3750 | - | 333 | 23.9 |
927 | 800 | 23.7 | 4000 | - | 760 | 23.7 |
897 | 850 | 22.5 | 4250 | - | 714 | 22.5 |
949 | 750 | 22.5 | 3750 | - | 370 | 22.5 |
950 | 750 | 22.5 | 3750 | - | 407 | 22.5 |
951 | 750 | 22.5 | 3750 | - | 444 | 22.5 |
952 | 750 | 22.5 | 3750 | - | 481 | 22.5 |
953 | 750 | 22.5 | 3750 | - | 518 | 22.5 |
954 | 750 | 22.5 | 3750 | - | 555 | 22.5 |
955 | 750 | 22.5 | 3750 | - | 592 | 22.5 |
956 | 750 | 22.5 | 3750 | - | 629 | 22.5 |
957 | 750 | 22.5 | 3750 | - | 666 | 22.5 |
958 | 750 | 22.5 | 3750 | - | 703 | 22.5 |
959 | 750 | 22.5 | 3750 | - | 740 | 22.5 |
960 | 750 | 22.5 | 3750 | - | 777 | 22.5 |
979 | 700 | 22.3 | 3500 | - | 210 | 22.3 |
980 | 700 | 22.3 | 3500 | - | 245 | 22.3 |
981 | 700 | 22.3 | 3500 | - | 280 | 22.3 |
982 | 700 | 22.3 | 3500 | - | 315 | 22.3 |
983 | 700 | 22.3 | 3500 | - | 350 | 22.3 |
984 | 700 | 22.3 | 3500 | - | 385 | 22.3 |
985 | 700 | 21.0 | 3500 | - | 420 | 21.0 |
986 | 700 | 21.0 | 3500 | - | 455 | 21.0 |
987 | 700 | 21.0 | 3500 | - | 490 | 21.0 |
988 | 700 | 21.0 | 3500 | - | 525 | 21.0 |
989 | 700 | 21.0 | 3500 | - | 560 | 21.0 |
990 | 700 | 21.0 | 3500 | - | 595 | 21.0 |
991 | 700 | 21.0 | 3500 | - | 630 | 21.0 |
992 | 700 | 21.0 | 3500 | - | 665 | 21.0 |
993 | 700 | 21.0 | 3500 | - | 700 | 21.0 |
994 | 700 | 21.0 | 3500 | - | 735 | 21.0 |
995 | 700 | 21.0 | 3500 | - | 770 | 21.0 |
996 | 700 | 21.0 | 3500 | - | 805 | 21.0 |
997 | 700 | 21.0 | 3500 | - | 840 | 21.0 |
1019 | 650 | 20.7 | 3250 | - | 256 | 20.7 |
1020 | 650 | 20.7 | 3250 | - | 288 | 20.7 |
1021 | 650 | 20.7 | 3250 | - | 320 | 20.7 |
1022 | 650 | 20.7 | 3250 | - | 352 | 20.7 |
1023 | 650 | 20.7 | 3250 | - | 384 | 20.7 |
1024 | 650 | 20.7 | 3250 | - | 416 | 20.7 |
870 | 900 | 19.9 | 4500 | - | 675 | 19.9 |
961 | 750 | 19.8 | 3750 | - | 814 | 19.8 |
1025 | 650 | 19.5 | 3250 | - | 448 | 19.5 |
1026 | 650 | 19.5 | 3250 | - | 480 | 19.5 |
1027 | 650 | 19.5 | 3250 | - | 512 | 19.5 |
1028 | 650 | 19.5 | 3250 | - | 544 | 19.5 |
1029 | 650 | 19.5 | 3250 | - | 576 | 19.5 |
1030 | 650 | 19.5 | 3250 | - | 608 | 19.5 |
1031 | 650 | 19.5 | 3250 | - | 640 | 19.5 |
1032 | 650 | 19.5 | 3250 | - | 672 | 19.5 |
1033 | 650 | 19.5 | 3250 | - | 704 | 19.5 |
1034 | 650 | 19.5 | 3250 | - | 736 | 19.5 |
1035 | 650 | 19.5 | 3250 | - | 768 | 19.5 |
1036 | 650 | 19.5 | 3250 | - | 800 | 19.5 |
1037 | 650 | 19.5 | 3250 | - | 832 | 19.5 |
1038 | 650 | 19.5 | 3250 | - | 864 | 19.5 |
1039 | 650 | 19.5 | 3250 | - | 896 | 19.5 |
1064 | 600 | 19.1 | 3000 | - | 300 | 19.1 |
1065 | 600 | 19.1 | 3000 | - | 330 | 19.1 |
1066 | 600 | 19.1 | 3000 | - | 360 | 19.1 |
1067 | 600 | 19.1 | 3000 | - | 390 | 19.1 |
1068 | 600 | 19.1 | 3000 | - | 420 | 19.1 |
1069 | 600 | 19.1 | 3000 | - | 450 | 19.1 |
1070 | 600 | 19.1 | 3000 | - | 480 | 19.1 |
1071 | 600 | 18.0 | 3000 | - | 510 | 18.0 |
1072 | 600 | 18.0 | 3000 | - | 540 | 18.0 |
1073 | 600 | 18.0 | 3000 | - | 570 | 18.0 |
1074 | 600 | 18.0 | 3000 | - | 600 | 18.0 |
1075 | 600 | 18.0 | 3000 | - | 630 | 18.0 |
1076 | 600 | 18.0 | 3000 | - | 660 | 18.0 |
1077 | 600 | 18.0 | 3000 | - | 690 | 18.0 |
1078 | 600 | 18.0 | 3000 | - | 720 | 18.0 |
1079 | 600 | 18.0 | 3000 | - | 750 | 18.0 |
1080 | 600 | 18.0 | 3000 | - | 780 | 18.0 |
1081 | 600 | 18.0 | 3000 | - | 810 | 18.0 |
1082 | 600 | 18.0 | 3000 | - | 840 | 18.0 |
1083 | 600 | 18.0 | 3000 | - | 870 | 18.0 |
1084 | 600 | 18.0 | 3000 | - | 900 | 18.0 |
1085 | 600 | 18.0 | 3000 | - | 930 | 18.0 |
1086 | 600 | 17.8 | 3000 | - | 960 | 17.8 |
1138 | 550 | 17.7 | 2750 | - | 999 | 17.7 |
1114 | 550 | 17.5 | 2750 | - | 351 | 17.5 |
1115 | 550 | 17.5 | 2750 | - | 378 | 17.5 |
1116 | 550 | 17.5 | 2750 | - | 405 | 17.5 |
1117 | 550 | 17.5 | 2750 | - | 432 | 17.5 |
1118 | 550 | 17.5 | 2750 | - | 459 | 17.5 |
1119 | 550 | 17.5 | 2750 | - | 486 | 17.5 |
1120 | 550 | 17.5 | 2750 | - | 513 | 17.5 |
1121 | 550 | 17.5 | 2750 | - | 540 | 17.5 |
1122 | 550 | 16.5 | 2750 | - | 567 | 16.5 |
1123 | 550 | 16.5 | 2750 | - | 594 | 16.5 |
1124 | 550 | 16.5 | 2750 | - | 621 | 16.5 |
1125 | 550 | 16.5 | 2750 | - | 648 | 16.5 |
1126 | 550 | 16.5 | 2750 | - | 675 | 16.5 |
1127 | 550 | 16.5 | 2750 | - | 702 | 16.5 |
1128 | 550 | 16.5 | 2750 | - | 729 | 16.5 |
1129 | 550 | 16.5 | 2750 | - | 756 | 16.5 |
1130 | 550 | 16.5 | 2750 | - | 783 | 16.5 |
1131 | 550 | 16.5 | 2750 | - | 810 | 16.5 |
1132 | 550 | 16.5 | 2750 | - | 837 | 16.5 |
1133 | 550 | 16.5 | 2750 | - | 864 | 16.5 |
1134 | 550 | 16.5 | 2750 | - | 891 | 16.5 |
1135 | 550 | 16.5 | 2750 | - | 918 | 16.5 |
1136 | 550 | 16.5 | 2750 | - | 945 | 16.5 |
1137 | 550 | 16.5 | 2750 | - | 972 | 16.5 |
823 | 1000 | 16.1 | 5000 | - | 600 | 16.1 |
1195 | 500 | 16.1 | 2500 | - | 1000 | 16.1 |
1171 | 500 | 15.9 | 2500 | - | 400 | 15.9 |
1172 | 500 | 15.9 | 2500 | - | 425 | 15.9 |
1173 | 500 | 15.9 | 2500 | - | 450 | 15.9 |
1174 | 500 | 15.9 | 2500 | - | 475 | 15.9 |
1175 | 500 | 15.9 | 2500 | - | 500 | 15.9 |
1176 | 500 | 15.9 | 2500 | - | 525 | 15.9 |
1177 | 500 | 15.9 | 2500 | - | 550 | 15.9 |
1178 | 500 | 15.9 | 2500 | - | 575 | 15.9 |
998 | 700 | 15.5 | 3500 | - | 875 | 15.5 |
1179 | 500 | 15.0 | 2500 | - | 600 | 15.0 |
1180 | 500 | 15.0 | 2500 | - | 625 | 15.0 |
1181 | 500 | 15.0 | 2500 | - | 650 | 15.0 |
1182 | 500 | 15.0 | 2500 | - | 675 | 15.0 |
1183 | 500 | 15.0 | 2500 | - | 700 | 15.0 |
1184 | 500 | 15.0 | 2500 | - | 725 | 15.0 |
1185 | 500 | 15.0 | 2500 | - | 750 | 15.0 |
1186 | 500 | 15.0 | 2500 | - | 775 | 15.0 |
1187 | 500 | 15.0 | 2500 | - | 800 | 15.0 |
1188 | 500 | 15.0 | 2500 | - | 825 | 15.0 |
1189 | 500 | 15.0 | 2500 | - | 850 | 15.0 |
1190 | 500 | 15.0 | 2500 | - | 875 | 15.0 |
1191 | 500 | 15.0 | 2500 | - | 900 | 15.0 |
1192 | 500 | 15.0 | 2500 | - | 925 | 15.0 |
1193 | 500 | 15.0 | 2500 | - | 950 | 15.0 |
1194 | 500 | 15.0 | 2500 | - | 975 | 15.0 |
846 | 950 | 14.9 | 4750 | - | 658 | 14.9 |
824 | 1000 | 13.5 | 5000 | - | 650 | 13.5 |
825 | 1000 | 13.5 | 5000 | - | 700 | 13.5 |
826 | 1000 | 13.5 | 5000 | - | 750 | 13.5 |
1040 | 650 | 13.5 | 3250 | - | 928 | 13.5 |
898 | 850 | 13.4 | 4250 | - | 756 | 13.4 |
928 | 800 | 12.9 | 4000 | - | 800 | 12.9 |
847 | 950 | 12.8 | 4750 | - | 705 | 12.8 |
848 | 950 | 12.8 | 4750 | - | 752 | 12.8 |
849 | 950 | 12.8 | 4750 | - | 799 | 12.8 |
871 | 900 | 12.5 | 4500 | - | 720 | 12.5 |
872 | 900 | 12.2 | 4500 | - | 765 | 12.2 |
873 | 900 | 12.2 | 4500 | - | 810 | 12.2 |
874 | 900 | 12.2 | 4500 | - | 855 | 12.2 |
962 | 750 | 12.1 | 3750 | - | 851 | 12.1 |
1139 | 550 | 11.9 | 2750 | - | 1026 | 11.9 |
850 | 950 | 12.8 | 4750 | 0.6 | 846 | 11.6 |
827 | 1000 | 13.5 | 5000 | 1.0 | 800 | 11.5 |
899 | 850 | 11.5 | 4250 | - | 798 | 11.5 |
900 | 850 | 11.5 | 4250 | - | 840 | 11.5 |
901 | 850 | 11.5 | 4250 | - | 882 | 11.5 |
902 | 850 | 11.5 | 4250 | - | 924 | 11.5 |
1198 | 500 | 11.1 | 2500 | - | 1075 | 11.1 |
999 | 700 | 10.9 | 3500 | - | 910 | 10.9 |
929 | 800 | 10.8 | 4000 | - | 840 | 10.8 |
930 | 800 | 10.8 | 4000 | - | 880 | 10.8 |
931 | 800 | 10.8 | 4000 | - | 920 | 10.8 |
932 | 800 | 10.8 | 4000 | - | 960 | 10.8 |
1087 | 600 | 10.6 | 3000 | - | 990 | 10.6 |
1041 | 650 | 10.2 | 3250 | - | 960 | 10.2 |
963 | 750 | 10.1 | 3750 | - | 888 | 10.1 |
964 | 750 | 10.1 | 3750 | - | 925 | 10.1 |
965 | 750 | 10.1 | 3750 | - | 962 | 10.1 |
966 | 750 | 10.1 | 3750 | - | 999 | 10.1 |
967 | 750 | 10.1 | 3750 | - | 1036 | 10.1 |
903 | 850 | 11.5 | 4250 | 3.1 | 966 | 5.4 |
968 | 750 | 10.1 | 3750 | 4.4 | 1073 | 1.3 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
875 | 900 | 12.2 | 4500 | 1.1 | 900 | 9.9 |
933 | 800 | 10.8 | 4000 | 1.2 | 1000 | 8.3 |
Overall score = score_ratio - 2 * repetitive DNA content