Markers + reference

Cratoxylum

3 species · Hypericaceae · Malpighiales

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Species 3
Genome length 157–158 kb
Candidate markers 268
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 518 0.0275 0.73 70.1 yes View details
trnG-GCC-psbZ LSC 698 0.0193 0.94 63.0 yes View details
trnY-GUA-trnD-GUC LSC 479 0.0112 1.00 58.7 yes View details
trnR-UCU-trnG-UCC LSC 709 0.0237 0.95 68.5 yes View details
petA-psbJ LSC 1050 0.0239 0.98 64.2 yes View details
trnP-UGG-psaJ LSC 508 0.0187 0.98 49.6 yes View details
clpP LSC 1604 0.0186 0.99 61.1 yes View details
rpl16 LSC 1615 0.0138 0.98 54.2 yes View details
ycf1 IRb 1182 0.0028 1.00 47.4 no View details
ycf1-ndhF SSC 273 0.0596 0.86 71.4 yes View details
ndhF SSC 2265 0.0121 1.00 50.2 yes View details
rpl32-trnL-UAG SSC 701 0.0358 0.98 68.8 yes View details
ndhG-ndhI SSC 597 0.0260 0.94 65.3 yes View details
ycf1 SSC 5874 0.0130 1.00 47.8 yes View details
trnfM-CAU-trnG-GCC LSC 49 0.0408 1.00 74.7 yes View details
petG-trnW-CCA LSC 113 0.0413 1.00 70.9 yes View details
ndhJ-trnF-GAA LSC 481 0.0169 0.99 68.3 yes View details
trnC-GCA-rpoB LSC 1047 0.0150 1.00 68.0 yes View details
rps11-rpl36 LSC 119 0.0230 0.97 66.5 yes View details
petD-rpoA LSC 184 0.0383 0.95 66.1 yes View details
ndhE-ndhG SSC 253 0.0316 1.00 65.9 yes View details
atpH-atpF LSC 533 0.0232 1.00 65.6 yes View details
rrn4.5-rrn5 IRb 236 0.0452 1.00 64.7 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 448–587 1.000 84.8
trnH-GUG-psbA_p2 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC TTCCCTCTAGACCTAGCTGC 453–592 1.000 80.9
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGTGCTAACCTTGGTATGGA 496–635 1.000 79.7
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGTGCTAACCTTGGTATGG 497–636 1.000 79.7
trnH-GUG-psbA_p5 trnH-GUG-psbA CCTTGATCCACTTGGCTACA TTCCCTCTAGACCTAGCTGC 452–591 1.000 79.5
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA CCGGAAAGTTGGATAGGGTG GGGATAGCTCAGCTGGTAGA 622–629 1.000 82.1
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA CGGAAAGTTGGATAGGGTGG GGGATAGCTCAGCTGGTAGA 621–628 1.000 82.1
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA CCGGAAAGTTGGATAGGGTG CCTCGTGTCACCAGTTCAAA 586–593 1.000 81.9
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA CGGAAAGTTGGATAGGGTGG CCTCGTGTCACCAGTTCAAA 585–592 1.000 81.9
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA CGGAAAGTTGGATAGGGTGG CTGGTAGAGCAGAGGACTGA 609–616 1.000 81.1
trnfM-CAU-trnG-GCC_p1 trnfM-CAU-trnG-GCC CTTGAGGTCACGGGTTCAAA TCTTTGCCAAGGAGAAGACG 127 1.000 80.2
trnfM-CAU-trnG-GCC_p2 trnfM-CAU-trnG-GCC TGAGGTCACGGGTTCAAATC TCTTTGCCAAGGAGAAGACG 125 1.000 79.1
trnfM-CAU-trnG-GCC_p3 trnfM-CAU-trnG-GCC GTAGCTCGCAAGGCTCATAA TCTTTGCCAAGGAGAAGACG 148 1.000 78.5
trnfM-CAU-trnG-GCC_p4 trnfM-CAU-trnG-GCC TAGCTCGCAAGGCTCATAAC TCTTTGCCAAGGAGAAGACG 147 1.000 78.5
trnfM-CAU-trnG-GCC_p5 trnfM-CAU-trnG-GCC GAGGTCACGGGTTCAAATCC TCTTTGCCAAGGAGAAGACG 124 1.000 76.2
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA AGTGGGTATCCTTAATTCTCTCA 734–776 1.000 46.0
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GTCTTTCTAGTGGGTATCCT 742–784 1.000 46.0
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GTCTTTCTAGTGGGTATCCTT 742–784 1.000 46.0
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GGTATCCTTAATTCTCTCATCTCGT 730–772 1.000 46.0
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GTGGGTATCCTTAATTCTCTCA 733–775 1.000 46.0
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC ATGGATTCTTCCTGGGTCGA CGGTGCTCTGACCAATTGAA 606–610 1.000 76.4
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC TGGATTCTTCCTGGGTCGAT CGGTGCTCTGACCAATTGAA 605–609 1.000 76.4
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC TGGCAATATGTCTACGCTGG CGGTGCTCTGACCAATTGAA 549–553 1.000 75.6
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC GGCAATATGTCTACGCTGGT CGGTGCTCTGACCAATTGAA 548–552 1.000 75.6
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC GGATTCTTCCTGGGTCGATG CGGTGCTCTGACCAATTGAA 604–608 1.000 75.4
trnC-GCA-rpoB_p1 trnC-GCA-rpoB GCGTCTTTTGTTGATCAGGC AAGCCCTGATCAATGAACCG 1226–1464 1.000 79.4
trnC-GCA-rpoB_p2 trnC-GCA-rpoB GCGTCTTTTGTTGATCAGGC CCCTGATCAATGAACCGACA 1223–1461 1.000 78.1
trnC-GCA-rpoB_p3 trnC-GCA-rpoB CGTCTTTTGTTGATCAGGCG AAGCCCTGATCAATGAACCG 1225–1463 1.000 77.7
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAAGGATTTGCAGTCCCCC AAGCCCTGATCAATGAACCG 1183–1421 1.000 76.8
trnC-GCA-rpoB_p5 trnC-GCA-rpoB CGTCTTTTGTTGATCAGGCG CCCTGATCAATGAACCGACA 1222–1460 1.000 76.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Cratoxylum arborescens NC_062807.1 157792 View on NCBI ↗
Cratoxylum maingayi NC_062806.1 157358 View on NCBI ↗
Cratoxylum sumatranum NC_062804.1 157089 View on NCBI ↗