| Location | STS clone | site | sequence | frequency | P1 clone |
| 1C | Dm2977 | 154 | AACTTCC(T/A)CGATAAA | 1 of 7 | DS07883 |
| 2B | Dm1729 | 317 | GAGAGCT(T/C)CTCGACT | 1 of 7 | DS00149 |
| 2B | Dm1729 | 343 | TAGTGGG(A/G)GAGTGCG | 1 of 7 | DS00149 |
| 4C | Dm3238 | 218 | CCGGGAA(A/T)TTCGCGT | 4 of 8 | DS02326 |
| 6B | Dm2931 | 197 | TGTGTGT(-/GT)GTAAATA | 2 of 7 | DS00771 |
| 8C | Dm0426 | 135 | TGTACTT(G/A)ATGTTGC | 2 of 8 | DS07346 |
| 8C | Dm0426 | 246 | AAACAAC(T/A)TACAACT | 4 of 8 | DS07346 |
| 8D | Dm3169 | 94 | AAGGAGT(C/A)TCAAGCG | 1 of 8 | DS02261 |
| 8D | Dm3169 | 204 | TGCCGGA(C/T)ACGAGAT | 1 of 8 | DS02261 |
| 8D | Dm3169 | 243 | TGCCCGT(G/A)TGCTCCC | 3 of 8 | DS02261 |
| 10F | Dm3746 | 159 | CTCACAC(C/T)AAATTCA | 1 of 8 | DS04503 |
| 10F | Dm3746 | 169 | ATTCACA(T/G)CCGTAAC | 3 of 8 | DS04503 |
| 10F | Dm3746 | 176 | TCCGTAA(C/T)GGGATTG | 1 of 8 | DS04503 |
| 13A | Dm0478 | 167 | ATTGGCA(A/G)TTGGCGA | 2 of 8 | DS06569 |
| 15B | Dm3790 | 117 | TCTGTGC(A/C)CTTAAAA | 3 of 7 | DS05272 |
| 17A | Dm0501 | 275 | CGCAA(C/T)GCA(G/A)CTTCA | 3 of 7 | DS05327 |
| 19E | Dm0505 | 199 | TAGCTGC(A/G)TGGTCTT | 3 of 8 | DS02687 |
| 19E | Dm0505 | 239 | CAAATTG(T/C)CCAGGGG | 3 of 8 | DS02687 |
| 19E | Dm0505 | 285 | GTCGGAG(C/T)ATATGAG | 1 of 8 | DS02687 |
| 21D | Dm0447 | 59 | CTCTCGG(CT/-)(CT/-)CTCTCTC | 4 of 7 | l(2)04723 |
| 21D | Dm0447 | 93 | CGCTCTC(T/C)CTCTTTA | 2 of 7 | l(2)04723 |
| 23E | Dm0605 | 215 | AGAGCAA(G/A)GGAGAGA | 4 of 8 | DS04754 |
| 27C | Dm0342 | 159 | TTTCCTA(T/A)CATGTAA | 2 of 8 | l(2)04841 |
| 27C | Dm0342 | 237 | ACGCAAT(C/T)GATTTAA | 1 of 8 | l(2)04841 |
| 27C | Dm0342 | 263 | AGCATAT(T/A)AGAGAGT | 2 of 8 | l(2)04841 |
| 30A | Dm2818 | 82 | CCAAGCA(T/A)ATGTAAT | 2 of 8 | DS06958 |
| 30A | Dm2818 | 177 | ATCCGAA(T/A)CTGCGAA | 1 of 8 | DS06958 |
| 32A | Dm4048 | 115 | CCCATAC(A/T)TTAGATA | 3 of 7 | DS08116 |
| 32A | Dm4048 | 179 | ATAGAA(C/A)CC(C/G)AAGCAA | 1 of 8 | DS08116 |
| 34B | Dm3982 | 210 | CTCATCC(T/G)TACACCT | 1 of 5 | DS05554 |
| 36D | Dm2390 | 131 | TTGTTTT(T/C)GTATTTA | 2 of 8 | DS06098 |
| 38C | Dm0877 | 201 | AGCCGTG(A/T)AGGGAAA | 2 of 8 | DS08927 |
| 38C | Dm0877 | 232 | ACAGAAC(G/AGAAGA)GAACAGA | 3 of 8 | DS08927 |
| 41C | Dm0976 | 168 | AAGGGTT(C/T)CGCAAAA | 2 of 8 | DS03789 |
| 41C | Dm0976 | 281 | TGACACT(TT/-)GTCATAG | 3 of 8 | DS03789 |
| 44A | Dm0746 | 163 | ATGTATC(TG/GCACGGG)TTCTGT | 2 of 8 | DS08206 |
| 46B | Dm0750 | 293 | TTCGTTT(G/T)GAATTCA | 3 of 8 | DS02873 |
| 48C | Dm0084 | 86 | GCTTATT(C/A)G(A/T)GAGTAAG | 3 of 8 | l(2)01275 |
| 50C | Dm2233 | 262 | TGTCCTT(G/T)CGCGC(G/C)A | 2 of 8 | DS00096 |
| 50C | Dm2233 | 268 | T(G/T)CGCGC(G/C)ACTAAAA | 2 of 8 | DS00096 |
| 54A | Dm2192 | 261 | TTAAATG(T/G)TGGTTCT | 4 of 8 | DS00062 |
| 54A | Dm2192 | 293 | GCATTTC(G/C)GGAATTG | 4 of 8 | DS00062 |
| 56B | Dm0800 | 173 | TAGGTTAAAATATGA | 2 of 6 | DS03261 |
| 56B | Dm0800 | 198 | ATATAGT(G/A)GCAACCC | 3 of 6 | DS03261 |
| 58C | Dm0932 | 247 | TGAGACA(G/A)TTGCACA | 2 of 7 | DS02641 |
| 58C | Dm0932 | 292 | AAGGCGC(A/C)TACGTTT | 3 of 7 | DS02641 |
| 60B | Dm0891 | 196 | GCTACGA(C/G)CAC(G/A)CCG | 3 of 6 | DS04170 |
| 60B | Dm0891 | 200 | CGA(C/G)CAC(G/A)CCGTGCT | 2 of 6 | DS04170 |
| 61D | Dm0688 | 186 | CAAGAAT(C/G)TGGAATT | 3 of 7 | l(3)04322 |
| 63D | Dm2349 | 140 | TATCCGG(G/A)ATAATAG | 3 of 7 | DS01105 |
| 63D | Dm2349 | 154 | GTTCATT(T/A)TGAAAGC | 3 of 7 | DS01105 |
| 63D | Dm2349 | 180 | ATGGGAA(A/-)TCCAGCA | 1 of 7 | DS01105 |
| 66A | Dm0925 | 234 | AACACA(CA/--)ATATACA | 3 of 7 | DS05040 |
| 66A | Dm0925 | 277 | AAACGTT(A/G/C)CAATATT | 3 of 7 | DS05040 |
| 66A | Dm0925 | 348 | CAATTAA(AA/--)TCGAAT | 1 of 7 | DS05040 |
| 67F | Dm3873 | 138 | CAAAAGA(T/C)ATATATA | 3 of 8 | DS08623 |
| 67F | Dm3873 | 149 | ATATATA(CTATATA/-)TATACTT | 2 of 8 | DS08623 |
| 67F | Dm3873 | 267 | CAGTTGC(G/A)GACCCGG | 3 of 8 | DS08623 |
| 70A | Dm3681 | 120 | TAAGGTT(G/A)GCTGCTG | 1 of 7 | DS08890 |
| 70A | Dm3681 | 165 | CCAAAAA(A/-)GTGGCAA | 1 of 7 | DS08890 |
| 70A | Dm3681 | 209 | GTTGGCA(G/A)GCAGAGG | 1 of 7 | DS08890 |
| 74A | Dm2140 | 85 | CAATTTA(A/C)TGAATAG | 3 of 8 | DS00720 |
| 74A | Dm2140 | 195 | AAAAGGT(A/G)AACTATT | 2 of 8 | DS00720 |
| 76B | Dm0970 | 226 | GCATTTG(C/A)ATAAAAT | 4 of 8 | DS02828 |
| 77B | Dm0184 | 237 | ATAATCG(T/C)TGCAGTG | 1 of 8 | l(3)00103 |
| 77E | Dm0980 | 271 | ATGTAAA(C/A)TTTTTAT | 3 of 8 | DS00718 |
| 80B | Dm2723 | 119 | ACGAACT(T/A)AAGTGGT | 1 of 8 | DS04193 |
| 83C | Dm2182 | 116 | GTGAGTT(C/T)CACTGTC | 2 of 8 | DS05418 |
| 86C | Dm2758 | 197 | TGTGTGC(A/G)TGGTCTT | 2 of 8 | DS00759 |
| 86C | Dm2758 | 248 | GCTGCAC(A/G)CGTCGCT | 1 of 8 | DS00759 |
| 88B | Dm0038 | 152 | TGTTTCT(T/A/G)TTTTTAT | 2 of 8 | DS08489 |
| 88B | Dm0038 | 187 | GGCTGGG(A/G)AAGTTAA | 2 of 8 | DS08489 |
| 90A | Dm2494 | 147 | GTACT(GTTGTT/AG----)GAATGAA | 2 of 6 | DS02270 |
| 92B | Dm3710 | 171 | TTGTGTG(T/C)CGGCGTG | 2 of 6 | DS06321 |
| 92B | Dm3710 | 212 | CTTTTTT(T/C)GCCATTT | 3 of 6 | DS06321 |
| 94C | Dm2730 | 192 | GNTTCTG(T/C)TCCTGCA | 4 of 8 | DS03019 |
| 94C | Dm2730 | 213 | GAGCCAA(A/G)TAGTTGT | 2 of 8 | DS03019 |
| 94C | Dm2730 | 246 | ANTGCAT(G/A)GATGTGA | 4 of 8 | DS03019 |
| 96B | Dm1624 | 92 | CCGTGAT(T/A)AAGAAAG | 2 of 5 | DS02495 |
| 96B | Dm1624 | 155 | TACACAA(G/A)ATGGCAC | 1 of 5 | DS02495 |
| 98A | Dm2759 | 114 | TATTTTA(A/G)TTATGTC | 3 of 8 | DS00282 |
| 100B | Dm2288 | 155 | TTTTGGC(A/G)TTTGGTG | 3 of 6 | DS06092 |