Table 2. Summary of all analyzed probes in this study.
| A | B | C | D | |||||||
| probe (distance to STR marker) | mean GC% | distance of hits in kb with matching 3′end 1 | HSE results 3 | ΔΔG (M-MM) | simulation with Viusal Omp | Match (Target-Probe) | Mismatch (Target-Probe) | |||
| success in % | best tested length | best length | HSE fits with simulation | |||||||
| P30 (18 kb) | FG | 36 | no | 76 | 21* | −1,15 | 21, 22 | r | C-G | T-G |
| FG-1 | 35 | no | 82 | 21 | −1,80 | 21 | r | C-G | T-G | |
| FA | 33 | no | 83 | 20* | −0,40 | 21 | r | T-A | C-A | |
| FA-1 | 30 | no | 95 | 22 | −1,01 | 22 | r | T-A | C-A | |
| RC | 27 | no | 92 | 24* | −0,49 | 24 | r | G-C | A-C | |
| RC-1 | 30 | 2, 24 | 70 | 23 | −2,18 | 23, 27 | r | G-C | A-C | |
| P38 (17 kb) | FA | 77 | no2 | 89 | 21 | −0,60 | 11 | w | T-A | A-G |
| FA-1 | 71 | no2 | 86 | 20 | −1,04 | 12 | w | T-A | A-G | |
| FC | 83 | 2, 9, 10, 13+ | 72 | 15 | −1,19 | 10 | w | G-C | T-C | |
| FC-1 | 79 | 7, 10+ | 49 | n.s. | −1,83 | 12 | w | G-C | T-C | |
| P224 (13 kb) | FC | 40 | no | 90 | 19* | −0,37 | 18 | r | G-C | A-C |
| FT | 34 | no | 86 | 19*, 20* | −0,70 | 19 | r | A-T | G-T | |
| RG | 60 | no | 93 | 17 | −1,31 | 14 | r | C-G | T-G | |
| RA | 53 | no | 86 | 17 | −0,48 | 15, 16 | r | T-A | C-A | |
| P240 (14 kb) | FC | 37 | no | 82 | 22* | −0,48 | 22 | r | G-C | A-C |
| FC-1 | 40 | no | 83 | 20* | −2,43 | 20, 21 | r | G-C | A-C | |
| FT | 32 | no | 84 | 22 | −0,60 | 22 | r | A-T | T-C | |
| FT-1 | 35 | no | 94 | 20 | −1,52 | 20, 21 | r | A-T | T-C | |
| RG | 42 | no | 79 | 18* | −1,14 | 19 | r | C-G | T-G | |
| RG-1 | 40 | no | 73 | 20 | −1,21 | 20 | r | C-G | T-G | |
| RA | 39 | no | 88 | 18 | −0,87 | 18, 20 | r | T-A | C-A | |
| P244 (35 kb) | FG | 66 | 49 | 73 | 13* | −0,95 | 15 | r | C-G | T-G |
| FG-1 | 65 | no | 78 | 15 | −2,11 | 14 | r | C-G | T-G | |
| FA | 57 | 116+ | 54 | n.s. | 0,05 | no | r | T-A | C-A | |
| FA-1 | 59 | 0,6+ | 76 | 15 | −1,04 | 15 | r | T-A | C-A | |
| RC | 68 | 20, 29+ | 68 | 14* | −0,66 | 13 | r | G-C | A-C | |
| RC-1 | 71 | 20+ | 71 | 14 | −2,16 | 14 | r | G-C | A-C | |
| RT | 60 | 2, 9, 13+ | 62 | 13 | −0,69 | 13 | r | A-T | G-T | |
| RT-1 | 64 | 9, 13+ | 66 | 14 | −1,01 | 14 | r | A-T | G-T | |
| Tat (15 kb) | FT | 33 | no | 84 | 20 | −0,57 | 20 | r | T-A | G-T |
| FC | 38 | no | 87 | 18 | −0,52 | 20 | r | G-C | A-C | |
| FG | 40 | no | 75 | 19 | −1,39 | 20 | r | C-G | T-G | |
| FG-1 | 43 | no | 81 | 18 | −2,77 | 19, 20 | r | C-G | T-G | |
| rs13304202 (37 kb) | FA | 34 | no | 77 | 19 | 0,42 | no | w | T-A | C-A |
| FA-1 | 38 | no | 76 | 22 | −1,55 | 20, 22 | r | T-A | C-A | |
| RC | 39 | no | 70 | 21 | −1,17 | 22 | r | G-C | A-C | |
| RC-1 | 43 | no | 81 | 21* | −3,00 | 21, 24 | r | G-C | A-C | |
| Seq.E 2071 (0.3 kb) | RG | 35 | no | 78 | 20 | −1,19 | 19 | r | C-G | T-G |
| RA | 30 | no | 91 | 20 | −0,13 | 20 | r | T-A | C-A | |
| Seq.F 4204 (0,15 kb) | FG | 53 | 0.3 kb with matched 3′ end | 67 | 17 | −0,71 | 18 | r | C-G | G-G |
| FC | 53 | 0.3 kb but no matched 3′ end | 98 | 17 | −0,83 | 14 | r | C-G | C-C | |
(A) and (B) Comparison of HSE results for all probe sets with distance to the STR marker, G/C content, hit frequency, and free energy differences of match and mismatch in kcal/mol.
The number is the distance in kb of strong hits to the extraction locus, + indicates the presence of further hits but greater distance (>30 kb).
Best simulated probes P38FA (11 nucleotides long) and P38FA-1 (12 nucleotides long) show many hits (4, 12, 16 kb+ and 4, 10 16 kb+).
HSE results show the best experimentally evaluated probe length with enrichment of one contributor. Low separation in HSE could be due to a higher hit frequency close to the extraction locus and great distance from the STR marker. Asterix indicate the best probe length. (C) The best probe length was evaluated after simulation and chosen after highest Δcon, and comparison of the prediction for best probe length after Δcon and best probe in HSE: (r) right prediction, (w) wrong prediction. (D) Listing of all analyzed match and mismatch constellations in this study. List of complete data is available in Data S3.