Markers + reference

Gyrinops

7 species · Thymelaeaceae · Malvales

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Species 7
Genome length 175–175 kb
Candidate markers 287
Primer pairs 100

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 287 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 700 0.0150 1.00 55.2 yes View details
trnS-GCU-trnS-CGA LSC 828 0.0101 0.99 61.9 yes View details
petN-psbM LSC 1101 0.0077 1.00 62.9 yes View details
psaA-ycf3 LSC 975 0.0080 1.00 51.5 yes View details
trnF-GAA-ndhJ LSC 512 0.0199 0.99 69.9 yes View details
ndhC-trnV-UAC LSC 505 0.0149 1.00 59.1 yes View details
psbJ-petA LSC 777 0.0115 1.00 62.7 yes View details
cemA-ycf4 LSC 951 0.0092 1.00 55.6 yes View details
ndhF-rpl32 SSC 805 0.0207 1.00 64.1 yes View details
rpl32-trnL-UAG IRa 1198 0.0092 1.00 54.8 yes View details
rpl2-rpl23 IRb 18 0.1376 1.00 73.6 yes View details
rpl23-rpl2 IRa 18 0.1376 1.00 73.6 yes View details
atpF-atpH LSC 534 0.0089 1.00 65.7 yes View details
trnN-GUU-ycf1 IRb 398 0.0062 1.00 61.4 yes View details
ycf1-trnN-GUU IRa 399 0.0062 1.00 61.4 yes View details
rps2-rpoC2 LSC 328 0.0071 1.00 61.1 yes View details
atpF LSC 1418 0.0029 1.00 61.0 yes View details
rps16-trnQ-UUG LSC 1205 0.0071 1.00 59.0 yes View details
atpH-atpI LSC 1219 0.0061 1.00 58.2 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.

Primer pairs

Showing the top 30 of 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AATTTGGTCCCTAGGGCTCT TCGAGACGTACGAGGAGAAA 1242–1248 1.000 81.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TCGAGACGTACGAGGAGAAA 1076–1082 1.000 80.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TCGAGACGTACGAGGAGAAA 1075–1081 1.000 80.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGAGACGTACGAGGAGAAA 1014–1020 1.000 80.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AATTTGGTCCCTAGGGCTCT GCGGGGTTTTACGGAACTTA 982–987 0.857 74.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATCAAAATGGGGCGTGG 1334–1485 1.000 81.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTTGGTCCCGCTATTCGAAG 1293–1444 1.000 81.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAAATCAAAATGGGGCGTGG 1345–1496 1.000 81.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TTTGGTCCCGCTATTCGAAG 1304–1455 1.000 81.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTTTGGTCCCGCTATTCGA 1295–1446 1.000 79.8
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA CCCTTAACTACTGAGGGGGT 924–939 1.000 80.9
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC CCCTTAACTACTGAGGGGGT 923–938 1.000 80.9
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA CGCACAACGGATTAGCAATC CCCTTAACTACTGAGGGGGT 939–954 1.000 80.2
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA TCGCACAACGGATTAGCAAT CCCTTAACTACTGAGGGGGT 940–955 1.000 78.8
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA AGCAATCCGACGCTTTAGTC CCCTTAACTACTGAGGGGGT 926–941 1.000 78.1
atpF_p1 atpF TCGTCAGCTCTAAGGGGTAC ACAAAAAGGGACAGAGTTCT 1573–1578 1.000 49.8
atpF_p2 atpF TTTCGTCAGCTCTAAGGGGT ACAAAAAGGGACAGAGTTCT 1575–1580 1.000 48.8
atpF_p3 atpF TCGTCAGCTCTAAGGGGTAC ACAAAAAGGGACAGAGTTCTT 1573–1578 1.000 48.7
atpF_p4 atpF TTTCGTCAGCTCTAAGGGGT ACAAAAAGGGACAGAGTTCTT 1575–1580 1.000 47.7
atpF_p5 atpF TTCGTCAGCTCTAAGGGGTA ACAAAAAGGGACAGAGTTCT 1574–1579 1.000 47.5
atpF-atpH_p1 atpF-atpH ATTTAACCCGAAACTCCCGG TGGTCTGGTTGTAGCATTGG 649–655 1.000 79.8
atpF-atpH_p2 atpF-atpH GGCCAGTGACCTAAGGAAAC TGGTCTGGTTGTAGCATTGG 624–630 1.000 79.4
atpF-atpH_p3 atpF-atpH ATGGCCAGTGACCTAAGGAA TGGTCTGGTTGTAGCATTGG 626–632 1.000 78.2
atpF-atpH_p4 atpF-atpH TGGCCAGTGACCTAAGGAAA TGGTCTGGTTGTAGCATTGG 625–631 1.000 76.3
atpF-atpH_p5 atpF-atpH GCCAGTGACCTAAGGAAACG TGGTCTGGTTGTAGCATTGG 623–629 1.000 76.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1306–1308 1.000 79.9
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCTGCGG 1298–1300 1.000 79.7
atpH-atpI_p3 atpH-atpI GAAGCAAGTCCGACAGCTAA TTTTGCAACTTTAGCTGCGG 1336–1338 1.000 79.5
atpH-atpI_p4 atpH-atpI AAGCGGCAGAAATCAATGGA TTTTGCAACTTTAGCTGCGG 1299–1301 1.000 78.9
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1307–1309 1.000 78.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Gyrinops caudata NC_065043.1 174798 View on NCBI ↗
Gyrinops ledermannii NC_065044.1 174819 View on NCBI ↗
Gyrinops moluccana NC_065045.1 174768 View on NCBI ↗
Gyrinops salicifolia NC_065046.1 174892 View on NCBI ↗
Gyrinops versteegii NC_065047.1 174814 View on NCBI ↗
Gyrinops vidalii NC_065048.1 175180 View on NCBI ↗
Gyrinops walla MW557323.1 175130 View on NCBI ↗