Markers + reference

Mussaenda

2 species · Rubiaceae · Gentianales

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Species 2
Genome length 155–156 kb
Candidate markers 270
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 829 0.0060 1.00 54.2 yes View details
rps16-trnQ-UUG LSC 1444 0.0035 1.00 60.7 yes View details
trnQ-UUG-psbk LSC 329 0.0030 1.00 48.3 yes View details
trnF-GAA-ndhJ LSC 689 0.0104 0.98 67.1 yes View details
accD-psaI LSC 763 0.0697 0.90 92.6 yes View details
rrn16 IRb 1491 0.0000 1.00 29.0 yes View details
rrn16-trnI-GAU IRb 302 0.0373 0.98 76.1 yes View details
ndhF-rpl32 SSC 877 0.0107 0.96 69.2 yes View details
rpl32-trnL-UAG SSC 706 0.1789 0.87 96.4 yes View details
trnI-GAU-rrn16 IRa 302 0.0373 0.98 76.1 yes View details
rrn16 IRa 1491 0.0000 1.00 29.0 no View details
atpB-rbcL LSC 789 0.0039 0.97 63.9 yes View details
petN-psbM LSC 1193 0.0034 0.97 63.3 yes View details
psbA LSC 1100 0.0019 0.97 63.2 yes View details
trnL-CAA-ndhB IRb 585 0.0000 0.96 62.2 yes View details
ndhB-trnL-CAA IRa 585 0.0000 0.96 62.2 yes View details
rps4-trnT-UGU LSC 393 0.0027 0.94 60.6 yes View details
rps15-ycf1 SSC 386 0.0027 0.95 60.6 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.

Primer pairs

Showing the top 30 of 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA AAGGAGCAATAACGCCTTCT ATTTGTGTGCTTGGGAGTCC 1212–1250 1.000 73.3
psbA_p2 psbA AGGAGCAATAACGCCTTCTT ATTTGTGTGCTTGGGAGTCC 1211–1249 1.000 73.3
psbA_p3 psbA AAGGAGCAATAACGCCTTCTT ATTTGTGTGCTTGGGAGTCC 1212–1250 1.000 71.0
psbA_p4 psbA AAGGAGCAATAACGCCTTCT TTTGTGTGCTTGGGAGTCC 1211–1249 1.000 67.4
psbA_p5 psbA AGGAGCAATAACGCCTTCTT TTTGTGTGCTTGGGAGTCC 1210–1248 1.000 67.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTCCTTGAAAGGGGTGCTC 964–966 1.000 79.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCCTTGAAAGGGGTGCTC 963–965 1.000 79.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TTTCCTTGAAAGGGGTGCTC 979–981 1.000 78.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTTCCTTGAAAGGGGTGCTC 973–975 1.000 78.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 950–952 1.000 77.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1517 1.000 78.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1531 1.000 76.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAAAATCGAAATGGGGCGTG 1576 1.000 76.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG AAAAATCGAAATGGGGCGTG 1590 1.000 74.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1521 1.000 73.8
trnQ-UUG-psbk_p1 trnQ-UUG-psbk GATATGCTCTGGGACGGAAG AAAAAGCATAGGCCTCGGG 506 1.000 67.1
trnQ-UUG-psbk_p2 trnQ-UUG-psbk GACCAAAACCCGTTGCCTTA AAAAAGCATAGGCCTCGGG 464 1.000 65.2
trnQ-UUG-psbk_p3 trnQ-UUG-psbk AATGGATATGCTCTGGGACG AAAAAGCATAGGCCTCGGG 510 1.000 63.8
trnQ-UUG-psbk_p4 trnQ-UUG-psbk GAATAGCGGGACCAAAACCC AAAAAGCATAGGCCTCGGG 473 1.000 63.4
trnQ-UUG-psbk_p5 trnQ-UUG-psbk ATATGCTCTGGGACGGAAGG AAAAAGCATAGGCCTCGGG 505 1.000 63.0
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA TCATTCTAGTTCCTACGGCCT 1257–1289 1.000 74.0
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT TCATTCTAGTTCCTACGGCCT 1255–1287 1.000 74.0
petN-psbM_p3 petN-psbM TCGTAGTGTGGGGAAGAAGT TCTAGTTCCTACGGCCTTTCT 1251–1283 1.000 73.5
petN-psbM_p4 petN-psbM ACTCGTAGTGTGGGGAAGAA TCTAGTTCCTACGGCCTTTCT 1253–1285 1.000 73.4
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG TCATTCTAGTTCCTACGGCCT 1254–1286 1.000 73.4
rps4-trnT-UGU_p1 rps4-trnT-UGU CTCCTAGGCGGCGTATTTTT CTCAGAGGTTAGAGCATCGC 483–505 1.000 82.3
rps4-trnT-UGU_p2 rps4-trnT-UGU CTCCTAGGCGGCGTATTTTT ATGGTCATCGGTTCGATTCC 451–473 1.000 81.7
rps4-trnT-UGU_p3 rps4-trnT-UGU CTCCTAGGCGGCGTATTTTT TGGATGTTATATGAGCCCGC 507–529 1.000 79.4
rps4-trnT-UGU_p4 rps4-trnT-UGU CTCCTAGGCGGCGTATTTTT CCGCTTAGCTCAGAGGTTAG 491–513 1.000 79.3
rps4-trnT-UGU_p5 rps4-trnT-UGU CTCCTAGGCGGCGTATTTTT CAGAGGTTAGAGCATCGCAT 481–503 1.000 79.2

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
Mussaenda hirsutula MK203878.1 155503 View on NCBI ↗
Mussaenda shikokiana PQ464577.1 155186 View on NCBI ↗