Table 3. INDEL markers, genes affected by the INDELs, and primers.
| INDEL | SCHU S4 INDEL position | SCHU S4 locus ID | SCHU S4 gene | Primer | Primer sequences |
| Ftind43 | 1541234..1541239 | FTTt30, FTTt31 | Arg-tRNA, Gly-tRNA | IN | GTTTCACAAATTTGCGGGAA |
| (intergenic) | OUT | AATCCCTTTGGGTGTGCCAT | |||
| CP | TGGAGCGGGAAACGAGGC | ||||
| Ftind44 | 895956..896021 | FTT0886, FTT0887 | recN, FTT0887 | IN | TCGACAAGTAGTTACTCAGCCTA |
| (intergenic) | OUT | TAAATCTAGTTGGCTGAGTAAT | |||
| CP | ACTGTTGTCATTCCCACGTA | ||||
| Ftind18b | 439349..439371 | FTT0425 | asd | IN | AGACCCTCTAAATCACGATCA |
| OUT | AGGTTTCTGGATAGACGCTGCA | ||||
| CP | ACTAACAGTACAATTACTACCGAT | ||||
| Ftind45 | 725227..725228 | FTT0706 | glk2 | IN | ACCTAATATGACCATAGATGGAT |
| (pseudogene) | OUT | TCACCAATAGCTTCCATAACA | |||
| CP | ACTCAGTGAAGCTATGGAATATCT | ||||
| Ftind46 | 1830698..1830699 | FTT1739 | kdpA | IN | AGTTCTGTACTGCAAGAGCGA |
| (pseudogene) | OUT | GTAGCTGTTTCATGCCTTGCT | |||
| CP | AGCACTTAATACAGCAGTTAGT | ||||
| Ftind47 | 271674..271683 | FTT0255 | IN | AGTAATACGCAAAGATTTTCTACA | |
| OUT | TCTTAACTGTATGCTAGTCTATGA | ||||
| CP | TAATAGAGCGGCTCTTCGAAT | ||||
| Ftind48 | 960987..961011 | FTT0948 | IN | ATCCTACTAATATCAATTCCAGT | |
| OUT | CCTTCAGCTTGAGTATTTTGACGT | ||||
| CP | ACTGTTATATTCAGTTATTTGCT | ||||
| Ftind38 b | 95661..95674 | FTT0092 | appC | IN | ACCCAATAAGCTCACCATCA |
| (pseudogene) | OUT | ATCTTTCTCAGGTACAGACTTTA | |||
| CP | AGTACTATTTGCTTATCCAAGTGAA | ||||
| Ftind49 | 834341..834349 | FTT0816 | IN | AAGATTAAGTGGCAATTTAC | |
| OUT | TTCAACCTGGACAACCACTA | ||||
| CP | AGGATCCCAGTTAGGTTTAGTA | ||||
| Ftind33b | 512045..512063 | FTT0492 | lysR | IN | TCTAAATTTAAGCAATGTTTCTAACT |
| OUT | ATCATCGTATAAGAAATCAACTT | ||||
| CP | TCAACCTTACAGAATAAGAATGT | ||||
| Ftind50 | 88484..88576 | FTT0086 | IN | CATCACTGCCACCAAGCATAT | |
| OUT | TGGGCACCATAAATAGCTAGT | ||||
| CP | CGATGCCATGGTCAGATGATCA |