Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign31 - back to list
Summary
./analyse_probe_search_results : Mon Sep 5 11:24:12 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign31 assembly : NCBIM34 bias : 3prime chromosome : 5 id : 6 strand : 1 ------------- Design window length: 4998bp All jobs for probe design are successful - total: 67 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 1329 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 3prime end of design window ------------------------ Putative probes without hits : 0 Putative probes with single_self_hit : 1329/1329 Putative probes exceeding selection criteria: 261/1329 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 |
---|---|---|---|---|---|---|
4782 | 1000 | 30.1 | 5000 | - | 1800 | 30.1 |
4783 | 1000 | 30.1 | 5000 | - | 1850 | 30.1 |
4784 | 1000 | 30.1 | 5000 | - | 1900 | 30.1 |
4864 | 950 | 28.6 | 4750 | - | 1786 | 28.6 |
4865 | 950 | 28.6 | 4750 | - | 1833 | 28.6 |
4866 | 950 | 28.6 | 4750 | - | 1880 | 28.6 |
4867 | 950 | 28.6 | 4750 | - | 1927 | 28.6 |
4868 | 950 | 28.6 | 4750 | 0.2 | 1974 | 28.2 |
4781 | 1000 | 30.1 | 5000 | 1.3 | 1750 | 27.5 |
4953 | 900 | 27.1 | 4500 | - | 1800 | 27.1 |
4954 | 900 | 27.1 | 4500 | - | 1845 | 27.1 |
4955 | 900 | 27.1 | 4500 | - | 1890 | 27.1 |
4956 | 900 | 27.1 | 4500 | - | 1935 | 27.1 |
4957 | 900 | 27.1 | 4500 | - | 1980 | 27.1 |
4958 | 900 | 27.1 | 4500 | 0.3 | 2025 | 26.4 |
5047 | 850 | 25.6 | 4250 | - | 1764 | 25.6 |
5048 | 850 | 25.6 | 4250 | - | 1806 | 25.6 |
5049 | 850 | 25.6 | 4250 | - | 1848 | 25.6 |
5050 | 850 | 25.6 | 4250 | - | 1890 | 25.6 |
5051 | 850 | 25.6 | 4250 | - | 1932 | 25.6 |
5052 | 850 | 25.6 | 4250 | - | 1974 | 25.6 |
5053 | 850 | 25.6 | 4250 | - | 2016 | 25.6 |
5054 | 850 | 25.6 | 4250 | - | 2058 | 25.6 |
4952 | 900 | 27.1 | 4500 | 0.9 | 1755 | 25.3 |
4863 | 950 | 27.3 | 4750 | 1.6 | 1739 | 24.1 |
5149 | 800 | 24.1 | 4000 | - | 1800 | 24.1 |
5150 | 800 | 24.1 | 4000 | - | 1840 | 24.1 |
5151 | 800 | 24.1 | 4000 | - | 1880 | 24.1 |
5152 | 800 | 24.1 | 4000 | - | 1920 | 24.1 |
5153 | 800 | 24.1 | 4000 | - | 1960 | 24.1 |
5154 | 800 | 24.1 | 4000 | - | 2000 | 24.1 |
5155 | 800 | 24.1 | 4000 | - | 2040 | 24.1 |
5156 | 800 | 24.1 | 4000 | - | 2080 | 24.1 |
5157 | 800 | 24.1 | 4000 | - | 2120 | 24.1 |
5148 | 800 | 24.1 | 4000 | 0.4 | 1760 | 23.3 |
5257 | 750 | 22.6 | 3750 | - | 1776 | 22.6 |
5258 | 750 | 22.6 | 3750 | - | 1813 | 22.6 |
5259 | 750 | 22.6 | 3750 | - | 1850 | 22.6 |
5260 | 750 | 22.6 | 3750 | - | 1887 | 22.6 |
5261 | 750 | 22.6 | 3750 | - | 1924 | 22.6 |
5262 | 750 | 22.6 | 3750 | - | 1961 | 22.6 |
5263 | 750 | 22.6 | 3750 | - | 1998 | 22.6 |
5264 | 750 | 22.6 | 3750 | - | 2035 | 22.6 |
5265 | 750 | 22.6 | 3750 | - | 2072 | 22.6 |
5266 | 750 | 22.6 | 3750 | - | 2109 | 22.6 |
5267 | 750 | 22.6 | 3750 | - | 2146 | 22.6 |
4785 | 1000 | 25.6 | 5000 | 1.8 | 1950 | 22.0 |
4786 | 1000 | 25.6 | 5000 | 1.8 | 2000 | 22.0 |
4787 | 1000 | 25.6 | 5000 | 1.8 | 2050 | 22.0 |
4788 | 1000 | 25.6 | 5000 | 1.8 | 2100 | 22.0 |
5375 | 700 | 21.1 | 3500 | - | 1785 | 21.1 |
5376 | 700 | 21.1 | 3500 | - | 1820 | 21.1 |
5377 | 700 | 21.1 | 3500 | - | 1855 | 21.1 |
5378 | 700 | 21.1 | 3500 | - | 1890 | 21.1 |
5379 | 700 | 21.1 | 3500 | - | 1925 | 21.1 |
5380 | 700 | 21.1 | 3500 | - | 1960 | 21.1 |
5381 | 700 | 21.1 | 3500 | - | 1995 | 21.1 |
5382 | 700 | 21.1 | 3500 | - | 2030 | 21.1 |
5383 | 700 | 21.1 | 3500 | - | 2065 | 21.1 |
5384 | 700 | 21.1 | 3500 | - | 2100 | 21.1 |
5385 | 700 | 21.1 | 3500 | - | 2135 | 21.1 |
5386 | 700 | 21.1 | 3500 | - | 2170 | 21.1 |
5387 | 700 | 21.1 | 3500 | - | 2205 | 21.1 |
4872 | 950 | 24.4 | 4750 | 1.9 | 2162 | 20.6 |
5518 | 650 | 19.9 | 3250 | - | 2272 | 19.9 |
5268 | 750 | 22.6 | 3750 | 1.5 | 2183 | 19.7 |
5503 | 650 | 19.6 | 3250 | - | 1792 | 19.6 |
5504 | 650 | 19.6 | 3250 | - | 1824 | 19.6 |
5505 | 650 | 19.6 | 3250 | - | 1856 | 19.6 |
5506 | 650 | 19.6 | 3250 | - | 1888 | 19.6 |
5507 | 650 | 19.6 | 3250 | - | 1920 | 19.6 |
5508 | 650 | 19.6 | 3250 | - | 1952 | 19.6 |
5509 | 650 | 19.6 | 3250 | - | 1984 | 19.6 |
5510 | 650 | 19.6 | 3250 | - | 2016 | 19.6 |
5511 | 650 | 19.6 | 3250 | - | 2048 | 19.6 |
5512 | 650 | 19.6 | 3250 | - | 2080 | 19.6 |
5513 | 650 | 19.6 | 3250 | - | 2112 | 19.6 |
5514 | 650 | 19.6 | 3250 | - | 2144 | 19.6 |
5515 | 650 | 19.6 | 3250 | - | 2176 | 19.6 |
5516 | 650 | 19.6 | 3250 | - | 2208 | 19.6 |
5517 | 650 | 19.6 | 3250 | - | 2240 | 19.6 |
5415 | 700 | 21.6 | 3500 | 1.1 | 3185 | 19.3 |
5502 | 650 | 19.6 | 3250 | 0.5 | 1760 | 18.7 |
5658 | 600 | 18.4 | 3000 | - | 2250 | 18.4 |
5659 | 600 | 18.4 | 3000 | - | 2280 | 18.4 |
5660 | 600 | 18.4 | 3000 | - | 2310 | 18.4 |
5046 | 850 | 24.0 | 4250 | 2.8 | 1722 | 18.4 |
5295 | 750 | 23.1 | 3750 | 2.4 | 3182 | 18.3 |
5547 | 650 | 20.7 | 3250 | 1.2 | 3200 | 18.2 |
5642 | 600 | 18.1 | 3000 | - | 1770 | 18.1 |
5643 | 600 | 18.1 | 3000 | - | 1800 | 18.1 |
5644 | 600 | 18.1 | 3000 | - | 1830 | 18.1 |
5645 | 600 | 18.1 | 3000 | - | 1860 | 18.1 |
5646 | 600 | 18.1 | 3000 | - | 1890 | 18.1 |
5647 | 600 | 18.1 | 3000 | - | 1920 | 18.1 |
5648 | 600 | 18.1 | 3000 | - | 1950 | 18.1 |
5649 | 600 | 18.1 | 3000 | - | 1980 | 18.1 |
5650 | 600 | 18.1 | 3000 | - | 2010 | 18.1 |
5651 | 600 | 18.1 | 3000 | - | 2040 | 18.1 |
5652 | 600 | 18.1 | 3000 | - | 2070 | 18.1 |
5653 | 600 | 18.1 | 3000 | - | 2100 | 18.1 |
5654 | 600 | 18.1 | 3000 | - | 2130 | 18.1 |
5655 | 600 | 18.1 | 3000 | - | 2160 | 18.1 |
5656 | 600 | 18.1 | 3000 | - | 2190 | 18.1 |
5657 | 600 | 18.1 | 3000 | - | 2220 | 18.1 |
5296 | 750 | 23.1 | 3750 | 2.7 | 3219 | 17.8 |
5548 | 650 | 20.1 | 3250 | 1.2 | 3232 | 17.6 |
5256 | 750 | 21.6 | 3750 | 2.0 | 1739 | 17.6 |
5374 | 700 | 21.1 | 3500 | 1.9 | 1750 | 17.4 |
5059 | 850 | 21.8 | 4250 | 2.4 | 2268 | 17.1 |
5814 | 550 | 16.9 | 2750 | - | 2268 | 16.9 |
5815 | 550 | 16.9 | 2750 | - | 2295 | 16.9 |
5816 | 550 | 16.9 | 2750 | - | 2322 | 16.9 |
5817 | 550 | 16.9 | 2750 | - | 2349 | 16.9 |
5796 | 550 | 16.6 | 2750 | - | 1782 | 16.6 |
5797 | 550 | 16.6 | 2750 | - | 1809 | 16.6 |
5798 | 550 | 16.6 | 2750 | - | 1836 | 16.6 |
5799 | 550 | 16.6 | 2750 | - | 1863 | 16.6 |
5800 | 550 | 16.6 | 2750 | - | 1890 | 16.6 |
5801 | 550 | 16.6 | 2750 | - | 1917 | 16.6 |
5802 | 550 | 16.6 | 2750 | - | 1944 | 16.6 |
5803 | 550 | 16.6 | 2750 | - | 1971 | 16.6 |
5804 | 550 | 16.6 | 2750 | - | 1998 | 16.6 |
5805 | 550 | 16.6 | 2750 | - | 2025 | 16.6 |
5806 | 550 | 16.6 | 2750 | - | 2052 | 16.6 |
5807 | 550 | 16.6 | 2750 | - | 2079 | 16.6 |
5808 | 550 | 16.6 | 2750 | - | 2106 | 16.6 |
5809 | 550 | 16.6 | 2750 | - | 2133 | 16.6 |
5810 | 550 | 16.6 | 2750 | - | 2160 | 16.6 |
5811 | 550 | 16.6 | 2750 | - | 2187 | 16.6 |
5812 | 550 | 16.6 | 2750 | - | 2214 | 16.6 |
5813 | 550 | 16.6 | 2750 | - | 2241 | 16.6 |
5416 | 700 | 21.6 | 3500 | 2.6 | 3220 | 16.5 |
5417 | 700 | 21.6 | 3500 | 2.6 | 3255 | 16.5 |
5689 | 600 | 19.1 | 3000 | 1.3 | 3180 | 16.4 |
5690 | 600 | 19.1 | 3000 | 1.3 | 3210 | 16.4 |
5691 | 600 | 19.1 | 3000 | 1.3 | 3240 | 16.4 |
5692 | 600 | 19.1 | 3000 | 1.3 | 3270 | 16.4 |
5183 | 800 | 24.7 | 4000 | 4.1 | 3160 | 16.4 |
4780 | 1000 | 25.6 | 5000 | 4.6 | 1700 | 16.4 |
4951 | 900 | 24.3 | 4500 | 4.0 | 1710 | 16.3 |
5147 | 800 | 22.6 | 4000 | 3.2 | 1720 | 16.1 |
5546 | 650 | 20.7 | 3250 | 2.3 | 3168 | 16.1 |
5693 | 600 | 18.5 | 3000 | 1.3 | 3300 | 15.9 |
5966 | 500 | 15.6 | 2500 | - | 1775 | 15.6 |
5967 | 500 | 15.6 | 2500 | - | 1800 | 15.6 |
5818 | 550 | 16.9 | 2750 | 0.7 | 2376 | 15.4 |
5985 | 500 | 15.3 | 2500 | - | 2250 | 15.3 |
5986 | 500 | 15.3 | 2500 | - | 2275 | 15.3 |
5987 | 500 | 15.3 | 2500 | - | 2300 | 15.3 |
5988 | 500 | 15.3 | 2500 | - | 2325 | 15.3 |
5989 | 500 | 15.3 | 2500 | - | 2350 | 15.3 |
5990 | 500 | 15.3 | 2500 | - | 2375 | 15.3 |
5991 | 500 | 15.3 | 2500 | - | 2400 | 15.3 |
5848 | 550 | 18.1 | 2750 | 1.5 | 3186 | 15.2 |
5849 | 550 | 18.1 | 2750 | 1.5 | 3213 | 15.2 |
5968 | 500 | 15.1 | 2500 | - | 1825 | 15.1 |
5969 | 500 | 15.1 | 2500 | - | 1850 | 15.1 |
5970 | 500 | 15.1 | 2500 | - | 1875 | 15.1 |
5971 | 500 | 15.1 | 2500 | - | 1900 | 15.1 |
5972 | 500 | 15.1 | 2500 | - | 1925 | 15.1 |
5973 | 500 | 15.1 | 2500 | - | 1950 | 15.1 |
5974 | 500 | 15.1 | 2500 | - | 1975 | 15.1 |
5975 | 500 | 15.1 | 2500 | - | 2000 | 15.1 |
5976 | 500 | 15.1 | 2500 | - | 2025 | 15.1 |
5977 | 500 | 15.1 | 2500 | - | 2050 | 15.1 |
5978 | 500 | 15.1 | 2500 | - | 2075 | 15.1 |
5979 | 500 | 15.1 | 2500 | - | 2100 | 15.1 |
5980 | 500 | 15.1 | 2500 | - | 2125 | 15.1 |
5981 | 500 | 15.1 | 2500 | - | 2150 | 15.1 |
5982 | 500 | 15.1 | 2500 | - | 2175 | 15.1 |
5983 | 500 | 15.1 | 2500 | - | 2200 | 15.1 |
5984 | 500 | 15.1 | 2500 | - | 2225 | 15.1 |
5162 | 800 | 20.5 | 4000 | 2.8 | 2320 | 15.0 |
5850 | 550 | 17.5 | 2750 | 1.5 | 3240 | 14.6 |
5851 | 550 | 17.5 | 2750 | 1.5 | 3267 | 14.6 |
5852 | 550 | 17.5 | 2750 | 1.5 | 3294 | 14.6 |
5853 | 550 | 17.5 | 2750 | 1.5 | 3321 | 14.6 |
5549 | 650 | 20.1 | 3250 | 2.8 | 3264 | 14.5 |
5550 | 650 | 20.1 | 3250 | 2.8 | 3296 | 14.5 |
5795 | 550 | 17.2 | 2750 | 1.5 | 1755 | 14.3 |
5992 | 500 | 15.3 | 2500 | 0.6 | 2425 | 14.1 |
5854 | 550 | 17.0 | 2750 | 1.5 | 3348 | 14.1 |
6022 | 500 | 16.6 | 2500 | 1.6 | 3175 | 13.4 |
6023 | 500 | 16.6 | 2500 | 1.6 | 3200 | 13.4 |
6024 | 500 | 16.6 | 2500 | 1.6 | 3225 | 13.4 |
6025 | 500 | 16.4 | 2500 | 1.6 | 3250 | 13.2 |
5501 | 650 | 18.7 | 3250 | 2.8 | 1728 | 13.1 |
5414 | 700 | 22.3 | 3500 | 4.7 | 3150 | 12.9 |
6026 | 500 | 15.9 | 2500 | 1.6 | 3275 | 12.7 |
6027 | 500 | 15.9 | 2500 | 1.6 | 3300 | 12.7 |
6028 | 500 | 15.9 | 2500 | 1.6 | 3325 | 12.7 |
6029 | 500 | 15.9 | 2500 | 1.6 | 3350 | 12.7 |
6030 | 500 | 15.9 | 2500 | 1.6 | 3375 | 12.7 |
5694 | 600 | 18.5 | 3000 | 3.0 | 3330 | 12.5 |
5695 | 600 | 18.5 | 3000 | 3.0 | 3360 | 12.5 |
5641 | 600 | 17.2 | 3000 | 2.5 | 1740 | 12.2 |
6031 | 500 | 15.4 | 2500 | 1.6 | 3400 | 12.2 |
5373 | 700 | 19.4 | 3500 | 4.4 | 1715 | 10.6 |
5855 | 550 | 17.0 | 2750 | 3.3 | 3375 | 10.4 |
5856 | 550 | 17.0 | 2750 | 3.3 | 3402 | 10.4 |
5551 | 650 | 19.2 | 3250 | 4.5 | 3328 | 10.3 |
5965 | 500 | 15.4 | 2500 | 2.6 | 1750 | 10.2 |
5847 | 550 | 18.2 | 2750 | 4.4 | 3159 | 9.5 |
5794 | 550 | 15.8 | 2750 | 3.3 | 1728 | 9.3 |
6032 | 500 | 15.4 | 2500 | 3.6 | 3425 | 8.2 |
6033 | 500 | 15.4 | 2500 | 3.6 | 3450 | 8.2 |
5964 | 500 | 14.3 | 2500 | 4.2 | 1725 | 5.9 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
4869 | 950 | 24.4 | 4750 | 1.9 | 2021 | 20.6 |
4870 | 950 | 24.4 | 4750 | 1.9 | 2068 | 20.6 |
4871 | 950 | 24.4 | 4750 | 1.9 | 2115 | 20.6 |
4959 | 900 | 23.1 | 4500 | 2.0 | 2070 | 19.1 |
4960 | 900 | 23.1 | 4500 | 2.0 | 2115 | 19.1 |
4961 | 900 | 23.1 | 4500 | 2.0 | 2160 | 19.1 |
4962 | 900 | 23.1 | 4500 | 2.0 | 2205 | 19.1 |
5055 | 850 | 21.8 | 4250 | 2.1 | 2100 | 17.6 |
5056 | 850 | 21.8 | 4250 | 2.1 | 2142 | 17.6 |
5057 | 850 | 21.8 | 4250 | 2.1 | 2184 | 17.6 |
5058 | 850 | 21.8 | 4250 | 2.1 | 2226 | 17.6 |
5158 | 800 | 20.5 | 4000 | 2.2 | 2160 | 16.0 |
5159 | 800 | 20.5 | 4000 | 2.2 | 2200 | 16.0 |
5160 | 800 | 20.5 | 4000 | 2.2 | 2240 | 16.0 |
5161 | 800 | 20.5 | 4000 | 2.2 | 2280 | 16.0 |
5269 | 750 | 19.2 | 3750 | 2.4 | 2220 | 14.4 |
5270 | 750 | 19.2 | 3750 | 2.4 | 2257 | 14.4 |
5271 | 750 | 19.2 | 3750 | 2.4 | 2294 | 14.4 |
5272 | 750 | 19.2 | 3750 | 2.4 | 2331 | 14.4 |
5273 | 750 | 19.2 | 3750 | 2.7 | 2368 | 13.9 |
5388 | 700 | 18.0 | 3500 | 2.6 | 2240 | 12.9 |
5389 | 700 | 17.9 | 3500 | 2.6 | 2275 | 12.8 |
5390 | 700 | 17.9 | 3500 | 2.6 | 2310 | 12.8 |
5391 | 700 | 17.9 | 3500 | 2.6 | 2345 | 12.8 |
5392 | 700 | 17.9 | 3500 | 2.6 | 2380 | 12.8 |
5393 | 700 | 17.9 | 3500 | 2.6 | 2415 | 12.8 |
5519 | 650 | 16.7 | 3250 | 2.8 | 2304 | 11.1 |
5520 | 650 | 16.7 | 3250 | 2.8 | 2336 | 11.1 |
5521 | 650 | 16.7 | 3250 | 2.8 | 2368 | 11.1 |
5522 | 650 | 16.7 | 3250 | 2.8 | 2400 | 11.1 |
5523 | 650 | 16.7 | 3250 | 2.8 | 2432 | 11.1 |
5524 | 650 | 16.7 | 3250 | 2.8 | 2464 | 11.1 |
5661 | 600 | 15.5 | 3000 | 3.0 | 2340 | 9.5 |
5662 | 600 | 15.4 | 3000 | 3.0 | 2370 | 9.4 |
5663 | 600 | 15.4 | 3000 | 3.0 | 2400 | 9.4 |
5664 | 600 | 15.4 | 3000 | 3.0 | 2430 | 9.4 |
5665 | 600 | 15.4 | 3000 | 3.0 | 2460 | 9.4 |
5666 | 600 | 15.4 | 3000 | 3.0 | 2490 | 9.4 |
5667 | 600 | 15.4 | 3000 | 3.7 | 2520 | 8.1 |
5819 | 550 | 14.1 | 2750 | 3.3 | 2403 | 7.6 |
5820 | 550 | 14.1 | 2750 | 3.3 | 2430 | 7.6 |
5821 | 550 | 14.1 | 2750 | 3.3 | 2457 | 7.6 |
5822 | 550 | 14.1 | 2750 | 3.3 | 2484 | 7.6 |
5823 | 550 | 14.1 | 2750 | 3.3 | 2511 | 7.6 |
5824 | 550 | 14.1 | 2750 | 3.3 | 2538 | 7.6 |
5825 | 550 | 14.1 | 2750 | 3.3 | 2565 | 7.6 |
5993 | 500 | 12.8 | 2500 | 3.6 | 2450 | 5.6 |
5994 | 500 | 12.8 | 2500 | 3.6 | 2475 | 5.6 |
5995 | 500 | 12.8 | 2500 | 3.6 | 2500 | 5.6 |
5996 | 500 | 12.8 | 2500 | 3.6 | 2525 | 5.6 |
5997 | 500 | 12.8 | 2500 | 3.6 | 2550 | 5.6 |
5998 | 500 | 12.8 | 2500 | 3.6 | 2575 | 5.6 |
5999 | 500 | 12.8 | 2500 | 3.6 | 2600 | 5.6 |
Overall score = score_ratio - 2 * repetitive DNA content