Markers + reference

Hirtella

5 species · Chrysobalanaceae · Malpighiales

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Species 5
Genome length 162–163 kb
Candidate markers 268
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 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 426 0.0403 1.00 74.6 yes View details
trnR-UCU-atpA LSC 308 0.0286 1.00 67.2 yes View details
trnE-UUC-trnT-GGU LSC 680 0.0179 1.00 59.6 yes View details
ndhC-trnV-UAC LSC 1151 0.0155 0.99 67.3 yes View details
psbE-petL LSC 1492 0.0102 1.00 66.3 yes View details
rpl33-rps18 LSC 278 0.0302 1.00 70.5 yes View details
rps18 LSC 306 0.0026 1.00 25.0 yes View details
ndhF-rpl32 SSC 1125 0.0149 1.00 65.5 yes View details
rpl32-trnL-UAG SSC 1365 0.0140 1.00 61.5 yes View details
ndhA SSC 2306 0.0062 1.00 50.3 yes View details
trnG-GCC-trnR-UCU LSC 655 0.0073 1.00 65.1 yes View details
rps19-trnH-GUG LSC 40 0.0400 1.00 64.6 no View details
trnC-GCA-petN LSC 1003 0.0062 1.00 62.5 yes View details
atpB-rbcL LSC 796 0.0070 1.00 59.7 yes View details
petN-psbM LSC 1105 0.0049 1.00 57.6 yes View details
trnS-GGA-rps4 LSC 296 0.0172 1.00 57.6 yes View details
rpl20-rps12 LSC 820 0.0034 1.00 56.3 yes View details
trnR-ACG-trnN-GUU IRb 630 0.0057 1.00 56.3 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
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ACCTCCAGTTTGATCAGGGA 848–875 1.000 86.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TCAGTGCTATGCATGGTTCC 874–901 1.000 85.8
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC ACCTCCAGTTTGATCAGGGA 849–876 1.000 85.8
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CAGTGCTATGCATGGTTCCT 873–900 1.000 85.7
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TCAGTGCTATGCATGGTTCC 875–902 1.000 85.6
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 735–811 1.000 68.6
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 738–814 1.000 68.4
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 741–817 1.000 67.9
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 744–820 1.000 67.7
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 739–815 1.000 66.2
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT ATTCGGGAACAGATGGAACG 432–455 1.000 84.5
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT CGGGAACAGATGGAACGTTT 429–452 1.000 80.9
trnR-UCU-atpA_p3 trnR-UCU-atpA TTTGGAATGGAAAAGCGTCC ATTCGGGAACAGATGGAACG 439–462 1.000 77.9
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT GCTATTCGGGAACAGATGGA 435–458 1.000 77.4
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT AGCTATTCGGGAACAGATGG 436–459 1.000 77.4
trnC-GCA-petN_p1 trnC-GCA-petN GGGTGTCGCCTGATTAACAA AGCCCAAGCGAGACTTACTA 1029–1051 1.000 80.5
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1065–1087 1.000 79.0
trnC-GCA-petN_p3 trnC-GCA-petN CTGCAAATCCTTTTTCCCCG AGCCCAAGCGAGACTTACTA 1059–1081 1.000 78.9
trnC-GCA-petN_p4 trnC-GCA-petN GGGTGTCGCCTGATTAACAA AGAGTCCACTTCTTCCCCAT 1090–1112 1.000 78.7
trnC-GCA-petN_p5 trnC-GCA-petN TCCTTTTTCCCCGGTTCAAA AGCCCAAGCGAGACTTACTA 1052–1074 1.000 78.2
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT GCGCTGTTCATTCTTGTTCC 1217–1260 1.000 82.5
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT GCGCTGTTCATTCTTGTTCC 1156–1199 1.000 81.1
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT ATTGCTACTGCGCTGTTCAT 1226–1269 1.000 80.7
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TATTGCTACTGCGCTGTTCA 1227–1270 1.000 79.7
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT ACTGCGCTGTTCATTCTTGT 1220–1263 1.000 79.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CCATTTCGTGGTGGATCAGT GAACCGATGACTTACGCCTT 1037–1076 1.000 84.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CCATTTCGTGGTGGATCAGT TACCGCTGAGTTAAAAGGGC 1002–1041 1.000 83.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGCCACGTTGTAACAGAGAC GAACCGATGACTTACGCCTT 1389–1428 1.000 83.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CCATTTCGTGGTGGATCAGT ACTTTTCTGCGGAAGAAGGG 1596–1641 1.000 82.5
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGCCACGTTGTAACAGAGAC ACTTTTCTGCGGAAGAAGGG 1948–1993 1.000 81.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Hirtella macrosepala NC_030561.1 162920 View on NCBI ↗
Hirtella physophora NC_024066.1 162955 View on NCBI ↗
Hirtella racemosa NC_024060.1 162891 View on NCBI ↗
Hirtella suffulta NC_030562.1 162654 View on NCBI ↗
Hirtella zanzibarica NC_030563.1 162341 View on NCBI ↗