Markers + reference

Heritiera

4 species · Malvaceae · Malvales

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Species 4
Genome length 161–169 kb
Candidate markers 270
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbZ-trnG-UCC LSC 832 0.0222 1.00 66.1 yes View details
psaJ-rpl33 LSC 517 0.0164 1.00 54.9 yes View details
clpP LSC 2197 0.0121 1.00 61.6 yes View details
ycf1 IRb 5652 0.0030 1.00 46.8 yes View details
ndhA IRb 567 0.0000 1.00 36.0 no View details
ndhF-rpl32 SSC 1057 0.0117 1.00 57.2 yes View details
rpl32-trnL-UAG SSC 1089 0.0124 1.00 55.2 yes View details
ccsA-ndhD SSC 279 0.0394 1.00 67.4 yes View details
ndhD SSC 1404 0.0043 1.00 49.0 yes View details
ndhG-ndhI SSC 420 0.0155 1.00 52.8 yes View details
ndhA IRa 2230 0.0063 1.00 48.7 yes View details
ycf1 IRa 5652 0.0032 1.00 51.7 no View details
trnK-UUU-rps16 LSC 897 0.0077 0.99 67.3 yes View details
trnT-UGU-trnL-UAA LSC 1089 0.0098 0.97 66.0 yes View details
atpB-rbcL LSC 896 0.0084 1.00 65.7 yes View details
atpF-atpH LSC 628 0.0064 0.99 64.2 yes View details
rps16 LSC 1159 0.0061 0.99 61.9 yes View details
rps4-trnT-UGU LSC 473 0.0074 1.00 61.5 yes View details
rpl36-rps8 LSC 478 0.0119 1.00 61.0 yes View details
rpl2-trnH-GUG IRa 59 0.0311 1.00 60.7 no View details
psaI-ycf4 LSC 410 0.0126 1.00 60.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAGGAGCTCAACCCACAG 1006–1025 1.000 81.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGAGCTCAACCCACAG 1005–1024 1.000 81.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC AAAAGGAGCTCAACCCACAG 992–1011 1.000 79.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGGAAGGCGGGTGTTTTTA 966–985 1.000 79.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TAAGGAAGGCGGGTGTTTTT 967–986 1.000 79.1
rps16_p1 rps16 TGAGTCATCCACACCCTCTT TGTATCGACTGAACCAATGACT 1252–1260 1.000 58.8
rps16_p2 rps16 ATGAGTCATCCACACCCTCT TGTATCGACTGAACCAATGACT 1253–1261 1.000 57.0
rps16_p3 rps16 TGAGTCATCCACACCCTCTT TGTATCGACTGAACCAATGAC 1252–1260 1.000 55.1
rps16_p4 rps16 TGAGTCATCCACACCCTCTT ATGTATCGACTGAACCAATGACT 1253–1261 1.000 54.5
rps16_p5 rps16 TGAGTCATCCACACCCTCTT TCGACTGAACCAATGACTATTCA 1248–1256 1.000 54.0
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGTTGTAGCATTGGCACTT 736–742 1.000 80.5
atpF-atpH_p2 atpF-atpH CCAGTAACCCAAGGAAACGA TGGTTGTAGCATTGGCACTT 709–715 1.000 77.1
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG CTGGTTGTAGCATTGGCACT 737–743 1.000 76.9
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG ATGGGCTGGTTGTAGCATTG 742–748 1.000 76.4
atpF-atpH_p5 atpF-atpH GGCCAGTAACCCAAGGAAAC TGGTTGTAGCATTGGCACTT 711–717 1.000 75.6
psbZ-trnG-UCC_p1 psbZ-trnG-UCC GGTATCCTTAATTCTCTTATTTCTTGA TACCATTCGACCATATCCGC 831–886 1.000 47.2
psbZ-trnG-UCC_p2 psbZ-trnG-UCC GGTATCCTTAATTCTCTTATTTCTTG TACCATTCGACCATATCCGC 831–886 1.000 47.2
psbZ-trnG-UCC_p3 psbZ-trnG-UCC GGTATCCTTAATTCTCTTATTTCTTGA CGTCTTCTCCTTGGCAAAGA 858–913 1.000 47.1
psbZ-trnG-UCC_p4 psbZ-trnG-UCC GGTATCCTTAATTCTCTTATTTCTTG CGTCTTCTCCTTGGCAAAGA 858–913 1.000 47.1
psbZ-trnG-UCC_p5 psbZ-trnG-UCC GGTATCCTTAATTCTCTTATTTCTT CGTCTTCTCCTTGGCAAAGA 858–913 1.000 47.1
rps4-trnT-UGU_p1 rps4-trnT-UGU TAAGATCGCTTCCGGCTCTA CTCAGAGGTTAGAGCATCGC 633–704 1.000 79.7
rps4-trnT-UGU_p2 rps4-trnT-UGU TTTCTAAGATCGCTTCCGGC CTCAGAGGTTAGAGCATCGC 637–708 1.000 79.4
rps4-trnT-UGU_p3 rps4-trnT-UGU TAAGATCGCTTCCGGCTCTA ATGGTCATCGGTTCGATTCC 601–672 1.000 78.9
rps4-trnT-UGU_p4 rps4-trnT-UGU TTTCTAAGATCGCTTCCGGC ATGGTCATCGGTTCGATTCC 605–676 1.000 78.6
rps4-trnT-UGU_p5 rps4-trnT-UGU TAAGATCGCTTCCGGCTCTA CCGCTTAGCTCAGAGGTTAG 641–712 1.000 76.8
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1108–1140 1.000 83.3
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1116–1148 1.000 82.8
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1140–1172 1.000 82.3
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCAAGGCTCAATCCAATCCA 1146–1178 1.000 82.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAAGGCTCAATCCAATCC 1147–1179 1.000 82.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Heritiera angustata NC_037784.1 168953 View on NCBI ↗
Heritiera fomes NC_043924.1 168904 View on NCBI ↗
Heritiera javanica NC_057264.1 161419 View on NCBI ↗
Heritiera littoralis NC_043923.1 168778 View on NCBI ↗