Markers + reference

Spondias

4 species · Anacardiaceae · Sapindales

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Species 4
Genome length 162–162 kb
Candidate markers 261
Primer pairs 100

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 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 537 0.0332 1.00 80.5 yes View details
rps16-trnQ-UUG LSC 1683 0.0171 0.98 65.6 yes View details
trnS-GCU-trnR-UCU LSC 1920 0.0141 0.97 59.0 yes View details
ycf3-trnS-GGA LSC 876 0.0186 1.00 67.1 yes View details
trnT-UGU-trnL-UAA LSC 1005 0.0217 0.99 67.3 yes View details
ndhC-trnT-GGU LSC 1852 0.0136 0.97 58.4 yes View details
accD-psaI LSC 626 0.0197 1.00 58.9 yes View details
ycf4-cemA LSC 926 0.0150 1.00 55.7 yes View details
petA-psbJ LSC 1083 0.0246 1.00 66.7 yes View details
ycf1 SSC 1518 0.0019 1.00 39.7 no View details
ycf1 SSC 5442 0.0097 1.00 45.4 yes View details
ccsA-ndhD SSC 314 0.0292 1.00 67.4 yes View details
trnK-UUU-rps16 LSC 1087 0.0146 1.00 65.6 yes View details
atpI-rps2 LSC 220 0.0174 1.00 64.3 yes View details
trnR-ACG-trnN-GUU SSC 604 0.0052 1.00 62.4 yes View details
trnN-GUU-trnR-ACG SSC 604 0.0044 1.00 61.8 yes View details
matK-trnK-UUU LSC 750 0.0113 0.97 61.6 yes View details
atpF-atpH LSC 511 0.0101 1.00 60.7 yes View details
rbcL LSC 1428 0.0067 1.00 60.7 yes View details
psbE-petL LSC 1401 0.0098 1.00 60.7 yes View details
ndhF-rpl32 SSC 934 0.0129 1.00 60.2 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 100 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 GCGCTAACCTTGGTATGGAA 647–715 1.000 83.6
trnH-GUG-psbA_p2 trnH-GUG-psbA TTAGTTATGGGCGAACGACG GCGCTAACCTTGGTATGGAA 709–777 1.000 83.5
trnH-GUG-psbA_p3 trnH-GUG-psbA TTAGTTATGGGCGAACGACG TTCCCTCTAGACCTAGCTGC 662–730 1.000 83.5
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 661–729 1.000 83.4
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 660–728 1.000 83.4
matK-trnK-UUU_p1 matK-trnK-UUU GTCGTGTTGCTGAGATCCAT AACGGTAGAGTACTCGGCTT 805–825 1.000 82.0
matK-trnK-UUU_p2 matK-trnK-UUU GTCGTGTTGCTGAGATCCAT ACGGTAGAGTACTCGGCTTT 804–824 1.000 82.0
matK-trnK-UUU_p3 matK-trnK-UUU AAGTCGTGTTGCTGAGATCC AACGGTAGAGTACTCGGCTT 807–827 1.000 81.4
matK-trnK-UUU_p4 matK-trnK-UUU AAGTCGTGTTGCTGAGATCC ACGGTAGAGTACTCGGCTTT 806–826 1.000 81.4
matK-trnK-UUU_p5 matK-trnK-UUU GGAAGTCGTGTTGCTGAGAT ACGGTAGAGTACTCGGCTTT 808–828 1.000 81.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TATTTCAAAGAAGGCGGGGG 1080–1187 1.000 83.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TATTTCAAAGAAGGCGGGGG 1079–1186 1.000 83.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TATTTCAAAGAAGGCGGGGG 1089–1196 1.000 82.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGAAGGCGGGGGTTTTTAC 1073–1180 1.000 81.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGAAGGCGGGGGTTTTTAC 1072–1179 1.000 81.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1616–1756 1.000 84.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1627–1767 1.000 84.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1637–1777 1.000 82.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1638–1778 1.000 82.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 1639–1779 1.000 80.6
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CCGACGCTTTAATCCACTCA TGTCCTATCCATTAGACAATG 1961–1978 1.000 45.5
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU ACGCTTTAATCCACTCAGCC TGTCCTATCCATTAGACAATG 1958–1975 1.000 45.5
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CGCTTTAATCCACTCAGCCA TGTCCTATCCATTAGACAATG 1957–1974 1.000 45.5
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU TCCGACGCTTTAATCCACTC TGTCCTATCCATTAGACAATG 1962–1979 1.000 45.5
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU GCAATCCGACGCTTTAATCC TGTCCTATCCATTAGACAATG 1966–1983 1.000 45.5
atpF-atpH_p1 atpF-atpH CCAGTGAACCAAGGAAACGA CGGAGGGAAAAATACGAGGT 666–710 1.000 75.5
atpF-atpH_p2 atpF-atpH CCAGTGAACCAAGGAAACGA CGAGGCGGAGGGAAAAATAC 671–715 1.000 75.4
atpF-atpH_p3 atpF-atpH CCAGTGAACCAAGGAAACGA GAGGCGGAGGGAAAAATACG 670–714 1.000 75.4
atpF-atpH_p4 atpF-atpH CCAGTGAACCAAGGAAACGA GCGGAGGGAAAAATACGAGG 667–711 1.000 75.4
atpF-atpH_p5 atpF-atpH CCAGTGAACCAAGGAAACGA GGCGGAGGGAAAAATACGAG 668–712 1.000 75.4

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
Spondias bahiensis NC_030526.1 162218 View on NCBI ↗
Spondias dulcis NC_059000.1 162256 View on NCBI ↗
Spondias mombin NC_035973.1 162302 View on NCBI ↗
Spondias tuberosa NC_030527.1 162039 View on NCBI ↗