Markers + reference

Phyllanthus

6 species · Phyllanthaceae · Malpighiales

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Species 6
Genome length 144–157 kb
Candidate markers 264
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 267 0.1001 0.97 76.5 yes View details
trnK-UUU-rps16 LSC 1218 0.0663 0.98 84.0 yes View details
trnS-GCU-trnR-UCU LSC 1864 0.0664 0.98 83.1 yes View details
psbZ-trnG-GCC LSC 734 0.0663 0.96 80.3 yes View details
petA-psbJ LSC 976 0.0694 0.97 83.8 yes View details
rpl22 LSC 426 0.0814 1.00 75.1 yes View details
ycf1 IRb 231 0.0244 1.00 58.4 no View details
ndhF SSC 2232 0.0486 1.00 77.3 yes View details
ndhF-rpl32 SSC 960 0.0919 0.80 78.9 yes View details
ycf1 SSC 5664 0.0608 1.00 76.2 yes View details
trnD-GUC-trnY-GUA LSC 427 0.0575 0.97 85.4 yes View details
trnE-UUC-trnT-GGU LSC 1006 0.0502 1.00 84.4 yes View details
trnW-CCA-trnP-UGG LSC 163 0.0509 0.99 84.3 yes View details
matK-trnK-UUU LSC 746 0.0461 0.97 83.3 yes View details
atpH-atpI LSC 1120 0.0457 0.99 83.0 yes View details
rps16 LSC 1151 0.0578 0.99 82.8 yes View details
trnG-GCC-trnM LSC 179 0.0566 0.98 82.7 yes View details
clpP-psbB LSC 442 0.0523 1.00 82.7 yes View details
psaA-ycf3 LSC 677 0.0446 1.00 82.5 yes View details
rbcL-accD LSC 750 0.0441 1.00 82.5 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 95 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 TCAGTGCTATGCATGGTTCC 714–733 0.667 75.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 713–732 0.667 75.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 728–747 0.667 74.8
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAGTGCTATGCATGGTTCC 727–746 0.667 74.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAGTGCTATGCATGGTTCC 729–748 0.667 74.8
matK-trnK-UUU_p1 matK-trnK-UUU GCTCAAGAAGGACCCGAAAA AACGGTAGAGTACTCGGCTT 1482–1509 1.000 88.2
matK-trnK-UUU_p2 matK-trnK-UUU GCTCAAGAAGGACCCGAAAA ACGGTAGAGTACTCGGCTTT 1481–1508 1.000 88.2
matK-trnK-UUU_p3 matK-trnK-UUU GATTCGCTCAAGAAGGACCC AACGGTAGAGTACTCGGCTT 1487–1514 1.000 86.3
matK-trnK-UUU_p4 matK-trnK-UUU GATTCGCTCAAGAAGGACCC ACGGTAGAGTACTCGGCTTT 1486–1513 1.000 86.3
matK-trnK-UUU_p5 matK-trnK-UUU GCTCAAGAAGGACCCGAAAA TTGGGTTGCTAACTCAACGG 1500–1524 0.833 79.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAGTCGCACTTAAAAGCCGA CCCAATGAGCCGTTTATCGA 1360–1497 1.000 90.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGTCGCACTTAAAAGCCGA TCCCAATGAGCCGTTTATCG 1361–1498 1.000 90.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGTCGCACTTAAAAGCCGA GCCGTACGAGGAGAAAACTT 1421–1559 1.000 90.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 TACACACTCATCTCCCCCTC CCCAATGAGCCGTTTATCGA 1812–1946 0.667 74.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACACACTCATCTCCCCCTC TCCCAATGAGCCGTTTATCG 1813–1947 0.667 74.7
rps16_p1 rps16 AGTCCCGACAAAAAGAATCCA CTGGATTACTATGTACCCGCG 1524–1540 0.333 35.6
rps16_p2 rps16 AGTCCCGACAAAAAGAATCCA TGGATTACTATGTACCCGCG 1523–1539 0.333 35.3
rps16_p3 rps16 GAGAGAGTCCCGACAAAAAGA CTGGATTACTATGTACCCGCG 1529–1545 0.333 34.3
rps16_p4 rps16 AGAGAGAGTCCCGACAAAAAG CTGGATTACTATGTACCCGCG 1530–1546 0.333 34.2
rps16_p5 rps16 GAGAGAGTCCCGACAAAAAGA TGGATTACTATGTACCCGCG 1528–1544 0.333 34.0
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGGAACAGCTGGAACGTTTT 2228–2332 1.000 91.5
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU ATCTAATGATCCGGGGCGTA AGGAACAGCTGGAACGTTTT 2463–2570 1.000 91.0
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU TATCTAATGATCCGGGGCGT AGGAACAGCTGGAACGTTTT 2464–2571 1.000 91.0
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGGAACAGCTGGAACGTTTT 2229–2333 0.833 84.9
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU CCATTCCCAGAAACCGCTTA AGGAACAGCTGGAACGTTTT 2667–2728 0.500 66.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TATGGTCCATGGGTTCCCTT 1603–1635 1.000 91.1
atpH-atpI_p2 atpH-atpI CAGTGACCCAAGGAAACGAA TATGGTCCATGGGTTCCCTT 2233–2364 0.833 83.3
atpH-atpI_p3 atpH-atpI CCTCAAATCAGTCCTTCCCG TATGGTCCATGGGTTCCCTT 1866–1956 0.833 83.2
atpH-atpI_p4 atpH-atpI CAGTGACCCAAGGAAACGAA TCGGTCATTGTAGCTGTTCG 2347–2478 0.833 83.1
atpH-atpI_p5 atpH-atpI CCTCAAATCAGTCCTTCCCG TCGGTCATTGTAGCTGTTCG 1980–2070 0.833 83.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Phyllanthus acidus NC_070169.1 156331 View on NCBI ↗
Phyllanthus fluitans NC_086711.1 152927 View on NCBI ↗
Phyllanthus hirsutus NC_086712.1 157276 View on NCBI ↗
Phyllanthus niruri NC_070171.1 155900 View on NCBI ↗
Phyllanthus niruri subsp. lathyroides OP009348.1 143563 View on NCBI ↗
Phyllanthus pulcher NC_070172.1 155589 View on NCBI ↗