Markers + reference

Psidium

2 species · Myrtaceae · Myrtales

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Species 2
Genome length 159–159 kb
Candidate markers 268
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 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 472 0.0237 0.99 63.5 yes View details
trnS-GCU-trnG-UCC LSC 782 0.0219 0.99 60.2 yes View details
rpoC2 LSC 4134 0.0051 1.00 52.8 yes View details
petN-psbM LSC 959 0.0177 1.00 68.9 yes View details
trnT-GGU-psbD LSC 1366 0.0088 1.00 57.4 yes View details
psbZ-trnG-GCC LSC 863 0.0133 0.96 62.4 yes View details
ndhC-trnV-UAC LSC 454 0.0176 1.00 54.7 yes View details
psbE-petL LSC 1245 0.0212 0.98 72.5 yes View details
clpP-psbB LSC 405 0.0222 1.00 62.0 yes View details
ycf1 SSC 1080 0.0009 0.99 54.9 no View details
rpl32-trnL-UAG SSC 739 0.0178 0.99 61.4 yes View details
ycf1 SSC 5550 0.0065 1.00 53.7 yes View details
rpoC1-rpoB LSC 5 0.2000 1.00 87.5 yes View details
rpl14-rpl16 LSC 131 0.0400 0.95 79.7 yes View details
rps2-rpoC2 LSC 227 0.0441 1.00 77.8 yes View details
ndhK-ndhC LSC 54 0.0370 1.00 67.8 yes View details
trnF-GAA-ndhJ LSC 787 0.0131 0.97 66.5 yes View details
ycf4-cemA LSC 949 0.0084 0.88 66.2 yes View details
trnE-UUC-trnT-GGU LSC 763 0.0093 0.98 65.9 yes View details
psbM-trnD-GUC LSC 1014 0.0070 0.99 64.2 yes View details
rps3 LSC 651 0.0092 1.00 64.0 yes View details
trnC-GCA-petN LSC 890 0.0090 1.00 63.6 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 532–539 1.000 81.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 546–553 1.000 81.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 545–552 1.000 81.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 547–554 1.000 81.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 535–542 1.000 81.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 903–905 1.000 52.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACGAATCACACTTTTACCACT 904–906 1.000 50.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 889–891 1.000 48.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC ACGAATCACACTTTTACCACT 839–841 1.000 48.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AACGGAAAGAGAGGGATTCG ACGAATCACACTTTTACCACT 904–906 1.000 48.2
rps2-rpoC2_p1 rps2-rpoC2 ACCAAAATGAACTCCCGCTT TTCGAGGGGGAAATCAGAGA 407 1.000 79.9
rps2-rpoC2_p2 rps2-rpoC2 AATGAACTCCCGCTTCCATC TTCGAGGGGGAAATCAGAGA 402 1.000 79.7
rps2-rpoC2_p3 rps2-rpoC2 CCCGCTTCCATCATCTCTTC TTCGAGGGGGAAATCAGAGA 394 1.000 79.1
rps2-rpoC2_p4 rps2-rpoC2 CCGCTTCCATCATCTCTTCC TTCGAGGGGGAAATCAGAGA 393 1.000 79.1
rps2-rpoC2_p5 rps2-rpoC2 ACCAAAATGAACTCCCGCTT TCGAGGGGGAAATCAGAGAT 406 1.000 78.1
rpoC2_p1 rpoC2 GTCTGTTTTAAATTTTCAAGTTGCA TCAAGGAACTATTCGCACGT 282 1.000 40.9
rpoC2_p2 rpoC2 AGTCTGTTTTAAATTTTCAAGTTGCA TCAAGGAACTATTCGCACGT 283 1.000 40.8
rpoC2_p3 rpoC2 AGTCTGTTTTAAATTTTCAAGTTGCA TCAAGGAACTATTCGCACGTT 283 1.000 40.8
rpoC2_p4 rpoC2 AAGTCTGTTTTAAATTTTCAAGTTGCA TCAAGGAACTATTCGCACGT 284 1.000 40.8
rpoC2_p5 rpoC2 AGTCTGTTTTAAATTTTCAAGTTGCAA TCAAGGAACTATTCGCACGT 283 1.000 40.8
rpoC1-rpoB_p1 rpoC1-rpoB TGGCCCAAGCACTTATTTGT TTGCTCGTTCGAGAACTACG 192 1.000 80.0
rpoC1-rpoB_p2 rpoC1-rpoB TGGCCCAAGCACTTATTTGT CTTTGGCCCTGGAACTGAAT 170 1.000 79.8
rpoC1-rpoB_p3 rpoC1-rpoB TGGCCCAAGCACTTATTTGT TTTGGCCCTGGAACTGAATC 169 1.000 79.8
rpoC1-rpoB_p4 rpoC1-rpoB TGGCCCAAGCACTTATTTGT GGCCCTGGAACTGAATCATT 166 1.000 79.2
rpoC1-rpoB_p5 rpoC1-rpoB TGGCCCAAGCACTTATTTGT TTCGATTGCTCGTTCGAGAA 197 1.000 77.6
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 953–954 1.000 80.0
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 947–948 1.000 78.5
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 971–972 1.000 77.8
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 1007–1008 1.000 77.2
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCAAGACTTACT 965–966 1.000 76.3

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
Psidium cattleyanum MN095413.1 159088 View on NCBI ↗
Psidium guajava NC_033355.1 158841 View on NCBI ↗