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
Image
Unique putative probes (0)
Putative probes (247)
Redundant probes (2)

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