Markers + reference

Mimusops

2 species · Sapotaceae · Ericales

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Species 2
Genome length 160–160 kb
Candidate markers 274
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 13 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 512 0.0078 1.00 47.1 yes View details
rps16-trnQ-UUG LSC 2035 0.0030 0.97 53.3 yes View details
psbI-trnS-GCU LSC 142 0.0070 1.00 45.0 yes View details
ycf3 LSC 1972 0.0020 1.00 55.6 yes View details
rpl20-rps12 LSC 786 0.0076 1.00 62.2 yes View details
ycf1 IRb 1056 0.0019 1.00 47.3 no View details
ndhF SSC 2247 0.0044 1.00 47.0 yes View details
rpl32-trnL-UAG SSC 904 0.0100 1.00 53.1 yes View details
ycf1 SSC 5655 0.0039 1.00 55.1 yes View details
trnL-UAA LSC 35 0.0286 1.00 68.9 yes View details
rpl22-rps19 LSC 45 0.0222 1.00 65.3 yes View details
trnC-GCA-petN LSC 767 0.0039 1.00 61.0 yes View details
trnK-UUU-rps16 LSC 834 0.0036 1.00 60.9 yes View details
atpH-atpI LSC 1138 0.0035 1.00 60.9 yes View details
psaA-ycf3 LSC 760 0.0013 0.99 60.7 yes View details
atpB-rbcL LSC 798 0.0013 0.99 60.6 yes View details
rpoB-trnC-GCA LSC 1222 0.0025 1.00 60.2 yes View details
trnM-CAU LSC 75 0.0133 1.00 60.2 yes View details
accD-psaI LSC 920 0.0011 0.99 60.0 yes View details
trnM-CAU IRb 75 0.0000 1.00 33.8 no View details
trnM-CAU IRa 75 0.0000 1.00 33.8 no View details
trnM-CAU LSC 73 0.0000 1.00 33.1 no 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 95 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 TCGTATTTCAGGCTGAGCAC 1107–1132 1.000 79.6
trnH-GUG-psbA_p2 trnH-GUG-psbA TTAGTTATGGGCGAACGACG ATTTCAGGCTGAGCACAACA 1103–1128 1.000 79.6
trnH-GUG-psbA_p3 trnH-GUG-psbA TTAGTTATGGGCGAACGACG TTCAGGCTGAGCACAACATT 1101–1126 1.000 79.6
trnH-GUG-psbA_p4 trnH-GUG-psbA TTAGTTATGGGCGAACGACG TTTCAGGCTGAGCACAACAT 1102–1127 1.000 79.6
trnH-GUG-psbA_p5 trnH-GUG-psbA TTAGTTATGGGCGAACGACG CTGATGGTATGCCCCTAGGA 1152–1177 1.000 79.5
trnK-UUU_p1 trnK-UUU GCCCGTGTCAACCAATATCT TCAATGTTTTGATTGCCTCGT 2785–2800 1.000 61.6
trnK-UUU_p2 trnK-UUU TGAATCCAGTGGGTTGCAAA TCAATGTTTTGATTGCCTCGT 2738–2753 1.000 61.3
trnK-UUU_p3 trnK-UUU TGCCCGTGTCAACCAATATC TCAATGTTTTGATTGCCTCGT 2786–2801 1.000 59.9
trnK-UUU_p4 trnK-UUU AATGAATCCAGTGGGTTGCA TCAATGTTTTGATTGCCTCGT 2740–2755 1.000 59.5
trnK-UUU_p5 trnK-UUU ATGAATCCAGTGGGTTGCAA TCAATGTTTTGATTGCCTCGT 2739–2754 1.000 59.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTCCTTGAAAGGGGTGCTC 977–980 1.000 78.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCCTTGAAAGGGGTGCTC 976–979 1.000 78.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTTCCTTGAAAGGGGTGCTC 1062–1065 1.000 78.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTTCCTTGAAAGGGGTGCTC 1061–1064 1.000 78.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TTTCCTTGAAAGGGGTGCTC 992–995 1.000 78.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 2093–2115 1.000 81.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCTGTCTTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 2097–2119 1.000 80.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 2086–2108 1.000 80.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACGGATCCTGTCTTT GAGGTTCGAATCCTTCCGTC 2107–2129 1.000 80.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG AAATTTAAATGGGGCGTGGC 2150–2172 1.000 79.2
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GGGTTCGAATCCCTCTCTTT 189 1.000 64.3
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GGGTTCGAATCCCTCTCTTTC 189 1.000 64.2
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GGTTCGAATCCCTCTCTTTCC 188 1.000 64.2
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA GGGTTCGAATCCCTCTCTTT 189 1.000 62.0
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA GGTTCGAATCCCTCTCTTTCC 188 1.000 61.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1226 1.000 75.9
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT AGGTGAATCTATGGAGGGCC 1198 1.000 75.5
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1282 1.000 75.3
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT AGGTGAATCTATGGAGGGCC 1254 1.000 74.9
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1227 1.000 74.7

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
Mimusops coriacea NC_058625.1 159689 View on NCBI ↗
Mimusops elengi NC_061660.1 159719 View on NCBI ↗