Picky computation complexity level ==> Use the better nonlinear salt effect equation Picky parameter settings for this computation: selection_left_begin = 0 selection_right_end = 0 maximum_oligo_size = 35 minimum_oligo_size = 25 maximum_match_len = 15 minimum_match_len = 9 maximum_gc_content = 70 minimum_gc_content = 30 candidates_per_gene = 20 probes_per_gene = 5 minimum_similarity = 75 minimum_temp_separation = 10 DNA_concentration = 1 Salt_concentration = 500 single_strand_only = 1 prefer_unique_oligos = 1 Job started on Tue 13 Oct 2009 09:54:57 AM CDT Step 1 of 6: Constructing the suffix array... 23215 target sequences. 23215 total sequences. 30640552 total DNA bases and sequence markers. 16380 is the longest target sequence length. 51 is the shortest target sequence length. Step 2 of 6: Computing invert and LCP arrays... 16380 is the longest common overlap region length among sequences. 272.12 is the average common overlap region length among sequences. Step 3 of 6: Generating unique probe candidates... 4 CPU(s) used in this computation; step 3 is slower, be patient.... 0 sequences have no available user defined region to select probes. 0 sequences have no unique probe due to short overlaps with others. 2213 sequences have no unique probe due to long overlaps with others. 191 sequences have no good probe candidates due to temperature limit. 306653 initial unique probe candidates detected. Step 4 of 6: Identifying long common overlap regions... 16860 potentially sharable long common overlap regions identified. 6410 sequences hosting long common overlap regions identified. Step 5 of 6: Generating shared probe candidates... 4 CPU(s) used in this computation; step 5 is also slow, be patient... 0 host sequences had no members with qualified user defined region. 122 host sequences were not useful due to short overlaps with others. 603 host sequences were already covered by some other host sequences. 235 host sequences produced no valid probes due to temperature limit. 65527 additional sharable probe candidates detected. Step 6 of 6: Determining the optimal oligo set... 2889 sequences/regions without probe at 68.27 C, 1892 below, 997 above. 2837 sequences/regions without probe at 68.07 C, 1779 below, 1058 above. 2795 sequences/regions without probe at 67.89 C, 1687 below, 1108 above. 2781 sequences/regions without probe at 67.75 C, 1626 below, 1155 above. 2731 sequences/regions without probe at 67.38 C, 1457 below, 1274 above. 2716 sequences/regions without probe at 67.18 C, 1382 below, 1334 above. 2713 sequences/regions without probe at 66.93 C, 1284 below, 1429 above. 2716 sequences/regions without probe at 67.18 C, 1382 below, 1334 above. 2713 sequences/regions without probe at 10.00 C separation temperature. 91062 unique oligo probes designed for 20124 sequences. 9449 shared oligo probes designed for 2921 additional sequences. 10 maximum number of sequences sharing the same oligo probe. 2.30 average number of sequences sharing the same oligo probe. 61.93 C is the maximum estimated probe-nontarget temperature. 71.93 C is the minimum estimated probe-target temperature. 66.93 C is the optimal estimated experiment temperature. 100511 total oligo probes designed for 23045 sequences. Job completed on Tue 13 Oct 2009 01:19:48 PM CDT Total time elapsed 03h:24m:51s.