Markers + reference

Manilkara

2 species · Sapotaceae · Ericales

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Species 2
Genome length 158–159 kb
Candidate markers 263
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 536 0.0186 0.80 68.3 yes View details
rps16-trnQ-UUG LSC 1222 0.0140 0.88 59.4 yes View details
trnS-GCU-trnS-CGA LSC 725 0.0111 0.99 59.9 yes View details
trnC-GCA-petN LSC 747 0.0127 0.95 62.4 yes View details
petN-psbM LSC 1232 0.0117 0.90 68.8 yes View details
trnT-GGU-psbD LSC 1593 0.0065 0.97 65.3 yes View details
petA-psbJ LSC 1064 0.0232 0.97 74.5 yes View details
infA LSC 234 0.0000 1.00 19.0 yes View details
ndhF-trnL-UAG SSC 2064 0.0100 0.88 60.0 yes View details
ycf1 SSC 5640 0.0060 1.00 44.9 yes View details
rps11-rpl36 LSC 111 0.0541 1.00 81.8 yes View details
psbL-psbF LSC 22 0.0455 1.00 78.6 yes View details
matK LSC 1533 0.0111 1.00 65.5 yes View details
atpH-atpI LSC 1143 0.0054 0.96 65.4 yes View details
clpP LSC 2099 0.0055 0.95 65.2 yes View details
trnM-CAU-atpE LSC 210 0.0147 0.97 63.7 yes View details
ycf15-trnL-CAA IRb 370 0.0162 1.00 63.3 yes View details
trnL-CAA-ycf15 IRa 370 0.0162 1.00 63.3 yes View details
accD-psaI LSC 891 0.0039 0.86 63.2 yes View details
trnL-UAG-ccsA SSC 94 0.0213 1.00 63.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA TTAGTTATGGGCGAACGACG CCCTCTAGACCTTGCTGCTA 559–665 1.000 82.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCCTCTAGACCTTGCTGCTA 504–610 1.000 82.3
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCCTCTAGACCTTGCTGCTA 505–611 1.000 82.1
trnH-GUG-psbA_p4 trnH-GUG-psbA TTAGTTATGGGCGAACGACG CCGTGCTAACCTTGGTATGG 610–716 1.000 81.6
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 555–661 1.000 81.3
trnK-UUU_p1 trnK-UUU ACATATGATTTCGAGATGACA TCAATGTTTTGATTGCCTCGT 2703–2704 1.000 40.9
trnK-UUU_p2 trnK-UUU ACATATGATTTCGAGATGACAA TCAATGTTTTGATTGCCTCGT 2703–2704 1.000 40.9
trnK-UUU_p3 trnK-UUU ACATATGATTTCGAGATGACA TTCAATGTTTTGATTGCCTCGT 2704–2705 1.000 40.9
trnK-UUU_p4 trnK-UUU ACATATGATTTCGAGATGACAA TTCAATGTTTTGATTGCCTCGT 2704–2705 1.000 40.9
trnK-UUU_p5 trnK-UUU ACATATGATTTCGAGATGACA CAATGTTTTGATTGCCTCGT 2702–2703 1.000 40.9
matK_p1 matK AAGCCTTACTACATGCTGCT CCTTGTTTTGACTGAATCGCA 1725–1731 1.000 59.4
matK_p2 matK AAGCCTTACTACATGCTGCT ACCTTGTTTTGACTGAATCGC 1726–1732 1.000 59.3
matK_p3 matK AAGCCTTACTACATGCTGCT TGTTTTGACTGAATCGCACT 1722–1728 1.000 55.6
matK_p4 matK AAGCCTTACTACATGCTGCT CTTGTTTTGACTGAATCGCACT 1724–1730 1.000 54.6
matK_p5 matK AAGCCTTACTACATGCTGCT TTGTTTTGACTGAATCGCACT 1723–1729 1.000 53.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1302–1763 1.000 84.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCTGTCTTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1306–1767 1.000 83.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1295–1756 1.000 83.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACGGATCCTGTCTTT GAGGTTCGAATCCTTCCGTC 1316–1777 1.000 82.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 1303–1764 1.000 81.4
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTTA AGGAATTAAACCGAAAGAACCCT 841–845 1.000 57.0
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTTA AGGGGGTTAATAGAACGAATCAC 809–813 1.000 56.8
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTTA GGGGGTTAATAGAACGAATCACA 808–812 1.000 55.3
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA GCTTTAGTCCACTCAGCCAT AGGAATTAAACCGAAAGAACCCT 827–831 1.000 54.0
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTTA AGGGGGTTAATAGAACGAATCA 809–813 1.000 53.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1197–1231 1.000 78.7
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT AGGTGAATCTATGGAGGGCC 1169–1203 1.000 78.4
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1253–1287 1.000 78.0
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT AGGTGAATCTATGGAGGGCC 1225–1259 1.000 77.7
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1198–1232 1.000 77.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Manilkara kauki PV010369.1 158743 View on NCBI ↗
Manilkara zapota MN295595.1 158386 View on NCBI ↗