| Label | Region | Length (bp) | Pi | Alignment reliability | MarkerSeek score | Primer available | Action |
|---|---|---|---|---|---|---|---|
| rps16-trnQ-UUG | LSC | 988 | 0.0056 | 1.00 | 61.6 | yes | View details |
| trnS-GCU-trnG-UCC | LSC | 1287 | 0.0063 | 0.98 | 61.0 | yes | View details |
| trnC-GCA-petN | LSC | 920 | 0.0066 | 1.00 | 53.0 | yes | View details |
| trnE-UUC-trnT-GGU | LSC | 447 | 0.0123 | 1.00 | 56.7 | yes | View details |
| trnT-UGU-trnL-UAA | LSC | 1009 | 0.0061 | 0.99 | 68.2 | yes | View details |
| petA-psbJ | LSC | 1092 | 0.0072 | 1.00 | 68.2 | yes | View details |
| psaJ-rpl33 | LSC | 527 | 0.0044 | 0.97 | 57.9 | yes | View details |
| rpl20-rps12 | LSC | 743 | 0.0070 | 1.00 | 58.1 | yes | View details |
| infA | LSC | 233 | 0.0084 | 1.00 | 42.5 | yes | View details |
| rps3 | LSC | 663 | 0.0041 | 1.00 | 47.8 | yes | View details |
| ndhD | SSC | 1503 | 0.0039 | 1.00 | 44.0 | yes | View details |
| rps15 | SSC | 270 | 0.0038 | 1.00 | 33.1 | yes | View details |
| ccsA-ndhD | SSC | 231 | 0.0267 | 1.00 | 68.8 | yes | View details |
| ycf4-cemA | LSC | 868 | 0.0042 | 0.99 | 64.2 | yes | View details |
| matK-trnK-UUU | LSC | 774 | 0.0043 | 1.00 | 59.7 | yes | View details |
| atpF-atpH | LSC | 511 | 0.0047 | 0.97 | 59.1 | yes | View details |
| petD | LSC | 1243 | 0.0029 | 0.99 | 58.4 | yes | View details |
| rpl33-rps18 | LSC | 212 | 0.0139 | 0.94 | 58.1 | yes | View details |
| rps12-trnV-GAC | IRb | 1880 | 0.0016 | 1.00 | 57.8 | yes | View details |
| rpl32-trnL-UAG | SSC | 928 | 0.0029 | 1.00 | 57.8 | yes | View details |
| trnV-GAC-rps12 | IRa | 1880 | 0.0016 | 1.00 | 57.8 | yes | View details |
| atpB-rbcL | LSC | 785 | 0.0027 | 1.00 | 56.6 | yes | View details |
| Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped. | |||||||
Species
32
Genome length
156–157 kb
Candidate markers
271
Primer pairs
110
Genome-wide nucleotide diversity
Candidate markers
12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).
Primer pairs
Showing the top 30 of 110 primer pairs (ranked by primer score).
| Primer ID | Label | Forward | Reverse | Amplicon (bp) | Cross-species rate | Score |
|---|---|---|---|---|---|---|
| matK-trnK-UUU_p1 | matK-trnK-UUU | TAGGAAGTGTTGTTGCCGAG |
TCTGGGTTGCTAACTCAACG |
865–877 | 1.000 | 81.3 |
| matK-trnK-UUU_p2 | matK-trnK-UUU | TAGGAAGTGTTGTTGCCGAG |
AACGGTAGAGTACTCGGCTT |
849–861 | 1.000 | 81.3 |
| matK-trnK-UUU_p3 | matK-trnK-UUU | TAGGAAGTGTTGTTGCCGAG |
ACGGTAGAGTACTCGGCTTT |
848–860 | 1.000 | 81.3 |
| matK-trnK-UUU_p4 | matK-trnK-UUU | TAGGAAGTGTTGTTGCCGAG |
GGGTTGCTAACTCAACGGTA |
862–874 | 1.000 | 78.9 |
| matK-trnK-UUU_p5 | matK-trnK-UUU | GGAAGTGTTGTTGCCGAGAT |
TCTGGGTTGCTAACTCAACG |
863–875 | 1.000 | 78.8 |
| rps16-trnQ-UUG_p1 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
GAGGTTCGAATCCTTCCGTC |
1059–1075 | 1.000 | 82.1 |
| rps16-trnQ-UUG_p2 | rps16-trnQ-UUG | TCATGTCCTTCAAGTCGCAC |
GAGGTTCGAATCCTTCCGTC |
1070–1086 | 1.000 | 81.5 |
| rps16-trnQ-UUG_p3 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
TTCGGAGGTTCGAATCCTTC |
1063–1079 | 1.000 | 77.4 |
| rps16-trnQ-UUG_p4 | rps16-trnQ-UUG | AAGTCGCACGTTGCTTTCTA |
TAAGGCAACGGGTTTTGGTC |
1089–1105 | 1.000 | 77.2 |
| rps16-trnQ-UUG_p5 | rps16-trnQ-UUG | ATCATGTCCTTCAAGTCGCA |
GAGGTTCGAATCCTTCCGTC |
1071–1087 | 1.000 | 77.0 |
| trnS-GCU-trnG-UCC_p1 | trnS-GCU-trnG-UCC | GATCAGAGGGAACGGAGAGA |
ACGAATCGCACTTTTACCACT |
1377–1435 | 1.000 | 77.0 |
| trnS-GCU-trnG-UCC_p2 | trnS-GCU-trnG-UCC | AAGTGATCAGAGGGAACGGA |
ACGAATCGCACTTTTACCACT |
1381–1439 | 1.000 | 77.0 |
| trnS-GCU-trnG-UCC_p3 | trnS-GCU-trnG-UCC | ATCAGAGGGAACGGAGAGAG |
ACGAATCGCACTTTTACCACT |
1376–1434 | 1.000 | 77.0 |
| trnS-GCU-trnG-UCC_p4 | trnS-GCU-trnG-UCC | GATCAGAGGGAACGGAGAGA |
ACGAATCGCACTTTTACCAC |
1377–1435 | 1.000 | 77.0 |
| trnS-GCU-trnG-UCC_p5 | trnS-GCU-trnG-UCC | GATCAGAGGGAACGGAGAGA |
CGAACGAATCGCACTTTTACC |
1380–1438 | 1.000 | 77.0 |
| atpF-atpH_p1 | atpF-atpH | ATTAAACCCGAAACTCCCGG |
AATTTACGGACTGGTCGTGG |
613–635 | 1.000 | 85.2 |
| atpF-atpH_p2 | atpF-atpH | CAGTGGCCTAAGGAAACGAA |
AATTTACGGACTGGTCGTGG |
585–607 | 1.000 | 85.0 |
| atpF-atpH_p3 | atpF-atpH | ATTAAACCCGAAACTCCCGG |
TCGTGGCATTAGCGCTTTTA |
599–621 | 1.000 | 83.7 |
| atpF-atpH_p4 | atpF-atpH | CAGTGGCCTAAGGAAACGAA |
TCGTGGCATTAGCGCTTTTA |
571–593 | 1.000 | 83.6 |
| atpF-atpH_p5 | atpF-atpH | ATTAAACCCGAAACTCCCGG |
CGTGGCATTAGCGCTTTTAT |
598–620 | 1.000 | 79.9 |
| trnC-GCA-petN_p1 | trnC-GCA-petN | GGGGGACTGCAAATCCTTTA |
TTAAAGCAGCCCAAGCAAGA |
998–1003 | 1.000 | 80.1 |
| trnC-GCA-petN_p2 | trnC-GCA-petN | GGGGGACTGCAAATCCTTTA |
AGCAATTAGTAGTGCCCAGC |
1075–1080 | 1.000 | 79.6 |
| trnC-GCA-petN_p3 | trnC-GCA-petN | GGGGGACTGCAAATCCTTTA |
AGTCCACTCCTTCCCCATAC |
1050–1055 | 1.000 | 79.1 |
| trnC-GCA-petN_p4 | trnC-GCA-petN | GGGGGACTGCAAATCCTTTA |
GTCCACTCCTTCCCCATACT |
1049–1054 | 1.000 | 79.1 |
| trnC-GCA-petN_p5 | trnC-GCA-petN | GGGGGACTGCAAATCCTTTA |
GAGTCCACTCCTTCCCCATA |
1051–1056 | 1.000 | 78.6 |
| trnE-UUC-trnT-GGU_p1 | trnE-UUC-trnT-GGU | CGTTGCCTCCTTGAAAGAGA |
GAACCGATGACTTACGCCTT |
544–552 | 1.000 | 82.7 |
| trnE-UUC-trnT-GGU_p2 | trnE-UUC-trnT-GGU | CGTTGCCTCCTTGAAAGAGA |
CCATGGCGTTACTCTACCAC |
523–531 | 1.000 | 82.2 |
| trnE-UUC-trnT-GGU_p3 | trnE-UUC-trnT-GGU | CGTTGCCTCCTTGAAAGAGA |
TGGCGTTACTCTACCACTGA |
520–528 | 1.000 | 82.1 |
| trnE-UUC-trnT-GGU_p4 | trnE-UUC-trnT-GGU | CGTTGCCTCCTTGAAAGAGA |
CCGATGACTTACGCCTTACC |
541–549 | 1.000 | 81.5 |
| trnE-UUC-trnT-GGU_p5 | trnE-UUC-trnT-GGU | CGTTGCCTCCTTGAAAGAGA |
TTGAACCGATGACTTACGCC |
546–554 | 1.000 | 80.4 |
Result downloads
Reference species (32)
One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.
| Species | Accession | Length (bp) | Link |
|---|---|---|---|
| Aspidistra australis | NC_086925.1 | 156517 | View on NCBI ↗ |
| Aspidistra caespitosa | NC_086929.1 | 156369 | View on NCBI ↗ |
| Aspidistra cavicola | NC_070127.1 | 156385 | View on NCBI ↗ |
| Aspidistra chishuiensis | NC_086940.1 | 156361 | View on NCBI ↗ |
| Aspidistra crassifila | NC_086529.1 | 156373 | View on NCBI ↗ |
| Aspidistra dolichanthera | NC_086530.1 | 156367 | View on NCBI ↗ |
| Aspidistra elatior | NC_066799.1 | 156363 | View on NCBI ↗ |
| Aspidistra erecta | NC_086540.1 | 156388 | View on NCBI ↗ |
| Aspidistra fenghuangensis | NC_086942.1 | 156313 | View on NCBI ↗ |
| Aspidistra fimbriata | NC_080508.1 | 156400 | View on NCBI ↗ |
| Aspidistra fungilliformis | NC_086932.1 | 156307 | View on NCBI ↗ |
| Aspidistra guizhouensis | NC_086930.1 | 156455 | View on NCBI ↗ |
| Aspidistra liboensis | NC_086933.1 | 156410 | View on NCBI ↗ |
| Aspidistra longgangensis | NC_086542.1 | 156335 | View on NCBI ↗ |
| Aspidistra longipetala | NC_086937.1 | 156384 | View on NCBI ↗ |
| Aspidistra luodianensis | NC_086927.1 | 156301 | View on NCBI ↗ |
| Aspidistra maguanensis | NC_086934.1 | 156454 | View on NCBI ↗ |
| Aspidistra marginella | NC_086939.1 | 156439 | View on NCBI ↗ |
| Aspidistra minutiflora | NC_086532.1 | 156389 | View on NCBI ↗ |
| Aspidistra nankunshanensis | NC_086541.1 | 156475 | View on NCBI ↗ |
| Aspidistra oblanceifolia | NC_086938.1 | 156422 | View on NCBI ↗ |
| Aspidistra obliquipeltata | NC_070123.1 | 156415 | View on NCBI ↗ |
| Aspidistra omeiensis | NC_086935.1 | 156382 | View on NCBI ↗ |
| Aspidistra pingfaensis | NC_086926.1 | 156450 | View on NCBI ↗ |
| Aspidistra pingtangensis | NC_086936.1 | 156468 | View on NCBI ↗ |
| Aspidistra retusa | NC_086531.1 | 156348 | View on NCBI ↗ |
| Aspidistra sichuanensis | NC_082963.1 | 156513 | View on NCBI ↗ |
| Aspidistra subrotata | PQ873013.1 | 156189 | View on NCBI ↗ |
| Aspidistra tonkinensis | NC_086941.1 | 156375 | View on NCBI ↗ |
| Aspidistra yingjiangensis | NC_070121.1 | 156413 | View on NCBI ↗ |
| Aspidistra yunwuensis | NC_086931.1 | 156307 | View on NCBI ↗ |
| Aspidistra zhenganensis | NC_086928.1 | 156488 | View on NCBI ↗ |