Markers + reference

Mangifera

2 species · Anacardiaceae · Sapindales

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Species 2
Genome length 158–159 kb
Candidate markers 273
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1094 0.0106 0.78 50.7 yes View details
trnE-UUC-trnT-UGU LSC 1195 0.0081 0.72 49.7 yes View details
atpB-rbcL LSC 767 0.0118 1.00 55.6 yes View details
rbcL LSC 1428 0.0063 1.00 59.2 yes View details
ycf4-cemA LSC 648 0.0201 1.00 57.1 yes View details
petA-psbJ LSC 860 0.0103 0.56 53.6 yes View details
psbE-petL LSC 1397 0.0065 0.99 58.8 yes View details
petD LSC 1237 0.0074 0.99 60.0 yes View details
infA LSC 247 0.0000 1.00 18.8 yes View details
ndhF-rpl32 SSC 967 0.0207 1.00 59.2 yes View details
rpl32-trnL-UAG SSC 694 0.0113 0.77 56.8 yes View details
rpl36-infA LSC 117 0.0631 0.95 87.3 yes View details
trnK-UUU LSC 37 0.0270 1.00 65.8 yes View details
rpoA-rps11 LSC 65 0.0308 1.00 65.7 yes View details
trnS-UGA-psbC LSC 244 0.0205 1.00 64.3 yes View details
ndhI-ndhA SSC 81 0.0247 1.00 63.8 yes View details
petN-psbM LSC 791 0.0076 1.00 63.1 yes View details
accD-psaI LSC 709 0.0071 1.00 62.8 yes View details
trnS-GCU-trnG-UCC LSC 745 0.0067 1.00 62.7 yes View details
trnS-GGA-ycf3 LSC 902 0.0055 1.00 62.0 yes View details
rbcL-accD LSC 614 0.0049 1.00 61.6 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TCAGGATCAGTCGTGGTCTT CCGATTGTACCTACAGATTCGA 155 1.000 59.4
trnK-UUU_p2 trnK-UUU TCAGGATCAGTCGTGGTCTT TCCGATTGTACCTACAGATTCG 156 1.000 59.4
trnK-UUU_p3 trnK-UUU TTCAGGATCAGTCGTGGTCT CCGATTGTACCTACAGATTCGA 156 1.000 59.4
trnK-UUU_p4 trnK-UUU TTCAGGATCAGTCGTGGTCT TCCGATTGTACCTACAGATTCG 157 1.000 59.4
trnK-UUU_p5 trnK-UUU ACGACATGCTGGTTTTTCCA CCGATTGTACCTACAGATTCGA 185 1.000 57.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CCCAATGAGCCGTTTATCGA 1215–1452 1.000 83.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT TCCCAATGAGCCGTTTATCG 1216–1453 1.000 83.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT CCCAATGAGCCGTTTATCGA 1216–1453 1.000 83.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT TCCCAATGAGCCGTTTATCG 1217–1454 1.000 83.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAATTTCTTTTGGTCCCCGC CCCAATGAGCCGTTTATCGA 1332–1569 1.000 83.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TGAATGAAACTGAAGGACCCC 855–883 1.000 71.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA ACGAATCGCACTTTTACCACT 810–838 1.000 70.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA ACGAATCGCACTTTTACCAC 810–838 1.000 70.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATGAAACTGAAGGACCCC 913–941 1.000 70.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 868–896 1.000 69.4
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 953–954 1.000 68.0
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 892–893 1.000 66.5
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 953–954 1.000 63.9
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTC 892–893 1.000 62.3
petN-psbM_p5 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTCT 954–955 1.000 62.1
trnE-UUC-trnT-UGU_p1 trnE-UUC-trnT-UGU GCTGCCTCCTTGAAAGAGAG GCGATGCTCTAACCTCTGAG 939–1273 1.000 81.3
trnE-UUC-trnT-UGU_p2 trnE-UUC-trnT-UGU TGTCCTGAACCACTAGACGA GCGATGCTCTAACCTCTGAG 918–1252 1.000 81.2
trnE-UUC-trnT-UGU_p3 trnE-UUC-trnT-UGU AACTTCCTTTCGTGGTACCC GCGATGCTCTAACCTCTGAG 984–1318 1.000 79.0
trnE-UUC-trnT-UGU_p4 trnE-UUC-trnT-UGU CCTGAACCACTAGACGATGG GCGATGCTCTAACCTCTGAG 915–1249 1.000 78.8
trnE-UUC-trnT-UGU_p5 trnE-UUC-trnT-UGU CTGAACCACTAGACGATGGG GCGATGCTCTAACCTCTGAG 914–1248 1.000 78.8
trnS-GGA-ycf3_p1 trnS-GGA-ycf3 CCCTCGGTAAACAAAAGCCT CATTTATCCGCGATCTAGGCA 991–995 1.000 71.4
trnS-GGA-ycf3_p2 trnS-GGA-ycf3 ACGGAAAGAGAGGGATTCGA CATTTATCCGCGATCTAGGCA 1012–1016 1.000 70.9
trnS-GGA-ycf3_p3 trnS-GGA-ycf3 TTCCAATGCTACGCCTTGAA CATTTATCCGCGATCTAGGCA 962–966 1.000 70.6
trnS-GGA-ycf3_p4 trnS-GGA-ycf3 TGGGTGAAGGTACGGAAAGA CATTTATCCGCGATCTAGGCA 1023–1027 1.000 69.9
trnS-GGA-ycf3_p5 trnS-GGA-ycf3 GGGTGAAGGTACGGAAAGAG CATTTATCCGCGATCTAGGCA 1022–1026 1.000 69.1

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
Mangifera odorata NC_066470.1 158889 View on NCBI ↗
Mangifera siamensis NC_066471.1 157604 View on NCBI ↗