Markers + reference

Heteroblemma

2 species · Melastomataceae · Myrtales

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Species 2
Genome length 156–156 kb
Candidate markers 265
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnR-UCU LSC 1808 0.0189 1.00 67.1 yes View details
atpH-atpI LSC 936 0.0272 0.98 73.5 yes View details
trnE-UUC-trnT-GGU LSC 982 0.0359 0.79 66.8 yes View details
rps4-trnT-UGU LSC 414 0.0413 0.93 73.3 yes View details
trnT-UGU-trnL-UAA LSC 834 0.0209 0.97 64.1 yes View details
accD-psaI LSC 867 0.0282 0.94 65.2 yes View details
petA-psbJ LSC 903 0.0485 0.98 78.6 yes View details
rps12-clpP1 LSC 176 0.0710 0.96 75.0 yes View details
rpl16 LSC 1418 0.0227 0.99 58.8 yes View details
ycf1 IRb 1899 0.0016 1.00 45.0 no View details
ndhF-rpl32 SSC 890 0.0407 0.99 72.5 yes View details
ccsA-ndhD SSC 316 0.0447 0.99 64.5 yes View details
ycf1 SSC 5502 0.0141 1.00 53.5 yes View details
psbT-pbf1 LSC 72 0.1528 1.00 84.1 yes View details
trnH-GUG-psbA LSC 224 0.0452 0.99 79.7 yes View details
psbH-petB LSC 137 0.0438 1.00 77.7 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0678 1.00 77.1 yes View details
psbL-psbF LSC 22 0.0455 1.00 73.7 yes View details
rpl33-rps18 LSC 220 0.0556 0.98 72.9 yes View details
ndhC-trnV-UAC LSC 718 0.0226 0.99 69.9 yes View details
psbM-trnD-GUC LSC 735 0.0286 1.00 69.4 yes View details
trnC-GCA-petN LSC 845 0.0178 1.00 68.0 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 GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 291–292 1.000 82.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 341–342 1.000 81.8
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 355–356 1.000 81.6
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 354–355 1.000 81.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 356–357 1.000 81.6
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAACTTGCGTCCAATAGGA 1921–1945 1.000 70.2
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAACTTGCGTCCAATAGGA 1920–1944 1.000 70.2
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA ACATAGAAGAACTTGCGTCCA 1928–1952 1.000 68.3
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC ACATAGAAGAACTTGCGTCCA 1927–1951 1.000 68.3
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AAGAACTTGCGTCCAATAGGA 1922–1946 1.000 68.2
atpH-atpI_p1 atpH-atpI GAAGCAAGTCCGACAGCTAA TAGCCGCCGCTTATATAGGA 1042–1048 1.000 81.4
atpH-atpI_p2 atpH-atpI GAAGCAAGTCCGACAGCTAA TTTTTGCAACTTTAGCCGCC 1054–1060 1.000 81.3
atpH-atpI_p3 atpH-atpI AACAGAAGCGGCAGAAATCA TAGCCGCCGCTTATATAGGA 1010–1016 1.000 81.3
atpH-atpI_p4 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTTGCAACTTTAGCCGCC 1022–1028 1.000 81.2
atpH-atpI_p5 atpH-atpI CAGCAGCAATAACAGAAGCG TAGCCGCCGCTTATATAGGA 1020–1026 1.000 80.8
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 918–919 1.000 80.7
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTTAAAGTCCACTTCGCCCC 975–976 1.000 79.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 912–913 1.000 79.2
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGACGACCATTAAAGCAGCC 927–928 1.000 78.6
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 936–937 1.000 78.5
psbM-trnD-GUC_p1 psbM-trnD-GUC TCACTTTGACTCACGGTTTT TCAATTGGTTAGAGCACCGC 899–904 1.000 57.2
psbM-trnD-GUC_p2 psbM-trnD-GUC TCACTTTGACTCACGGTTTTT TCAATTGGTTAGAGCACCGC 899–904 1.000 55.6
psbM-trnD-GUC_p3 psbM-trnD-GUC AATCACTTTGACTCACGGTT TCAATTGGTTAGAGCACCGC 901–906 1.000 55.3
psbM-trnD-GUC_p4 psbM-trnD-GUC ATCACTTTGACTCACGGTTT TCAATTGGTTAGAGCACCGC 900–905 1.000 55.3
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAAGAGTGCAGTAGC TCAATTGGTTAGAGCACCGC 845–850 1.000 55.2
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC CGGATCAGGGAATTCTTGGG AAGTATGCCCCCATCGTCTA 238–260 1.000 80.3
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC CGGATCAGGGAATTCTTGGG TAATATGATGGCGGTTGGGC 258–280 1.000 80.2
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC TCATTTCATGGCGGATCAGG AAGTATGCCCCCATCGTCTA 249–271 1.000 80.2
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC TCATTTCATGGCGGATCAGG TAATATGATGGCGGTTGGGC 269–291 1.000 80.1
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC CGGATCAGGGAATTCTTGGG TCGTCTAGTGGTTCAGGACA 225–247 1.000 78.9

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
Heteroblemma bisetosum NC_068162.1 156124 View on NCBI ↗
Heteroblemma serpens MK994886.1 156047 View on NCBI ↗