Markers + reference

Purshia

2 species · Rosaceae · Rosales

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Species 2
Genome length 159–159 kb
Candidate markers 267
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 385 0.0341 0.99 73.5 yes View details
trnT-GGU-psbD LSC 1290 0.0095 0.98 66.1 yes View details
trnS-UGA-psbZ LSC 382 0.0132 0.99 62.8 yes View details
psbZ-trnG-GCC LSC 512 0.0209 0.84 70.3 yes View details
accD-psaI LSC 793 0.0145 0.96 70.9 yes View details
rps12-trnV-GAC IRb 1703 0.0053 1.00 61.7 yes View details
ycf1 SSC 5670 0.0014 1.00 46.9 yes View details
trnV-GAC-rps12 IRa 1703 0.0053 1.00 61.7 yes View details
rpl2-trnH-GUG LSC 361 0.0339 1.00 85.0 no View details
ndhC-trnV-UAC LSC 722 0.0062 0.90 65.7 yes View details
ndhD-psaC SSC 133 0.0156 0.96 65.1 yes View details
trnT-UGU-trnL-UAA LSC 1308 0.0016 0.96 63.4 yes View details
psbK-psbI LSC 257 0.0120 0.97 62.4 yes View details
rbcL-accD LSC 715 0.0000 0.96 62.3 yes View details
petN-psbM LSC 840 0.0048 1.00 61.5 yes View details
rpl32-trnL-UAG SSC 901 0.0023 0.98 61.5 yes View details
psaJ-rpl33 LSC 526 0.0000 0.96 61.3 yes View details
matK LSC 1512 0.0040 1.00 61.0 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 GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 448–451 1.000 81.5
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 498–501 1.000 81.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 512–515 1.000 81.3
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 511–514 1.000 81.3
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 513–516 1.000 81.3
matK_p1 matK TTTCCATTTCCACGGTCACA ACCTTGTTTTGACTGTATCGT 1631 1.000 49.2
matK_p2 matK TTCCATTTCCACGGTCACAT ACCTTGTTTTGACTGTATCGT 1630 1.000 47.4
matK_p3 matK TTCCACGGTCACATAACCAA ACCTTGTTTTGACTGTATCGT 1624 1.000 44.5
matK_p4 matK TTTCCACGGTCACATAACCA ACCTTGTTTTGACTGTATCGT 1625 1.000 44.5
matK_p5 matK TTTCCATTTCCACGGTCACA ACCTTGTTTTGACTGTATCGTACT 1631 1.000 44.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 388–394 1.000 74.3
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 385–391 1.000 72.3
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 386–392 1.000 72.3
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCTTCACGTCCAGGATTACG 387–393 1.000 72.3
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGTCCAGGATTACG 389–395 1.000 72.0
petN-psbM_p1 petN-psbM ACATTTTCCCTTTCGCTCGT AAAACAGTCAGCCAAGGTGA 909 1.000 76.0
petN-psbM_p2 petN-psbM CCCTTTCGCTCGTAGTATGG AAAACAGTCAGCCAAGGTGA 902 1.000 75.8
petN-psbM_p3 petN-psbM CCTTTCGCTCGTAGTATGGG AAAACAGTCAGCCAAGGTGA 901 1.000 75.8
petN-psbM_p4 petN-psbM CTTTCGCTCGTAGTATGGGG AAAACAGTCAGCCAAGGTGA 900 1.000 75.8
petN-psbM_p5 petN-psbM TTCGCTCGTAGTATGGGGAA AAAACAGTCAGCCAAGGTGA 898 1.000 75.0
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGCCAGACCAACCTACAAAA 1454–1465 1.000 81.5
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGCCAGACCAACCTACAAAA 1457–1468 1.000 81.3
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TAGGCCAGACCAACCTACAA 1456–1467 1.000 81.3
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA TAGGCCAGACCAACCTACAA 1459–1470 1.000 81.1
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGCCAGACCAACCTACAAAA 1431–1442 1.000 79.8
trnS-UGA-psbZ_p1 trnS-UGA-psbZ AAGGAGAGAGAGGGATTCGA CAACCCTCAGGAGAAGCAAA 570–574 1.000 70.0
trnS-UGA-psbZ_p2 trnS-UGA-psbZ AGGAGAGAGAGGGATTCGAA CAACCCTCAGGAGAAGCAAA 569–573 1.000 70.0
trnS-UGA-psbZ_p3 trnS-UGA-psbZ AAGGAGAGAGAGGGATTCGA TTTTGTTACCCGACCAACCC 584–588 1.000 69.7
trnS-UGA-psbZ_p4 trnS-UGA-psbZ AGGAGAGAGAGGGATTCGAA TTTTGTTACCCGACCAACCC 583–587 1.000 69.7
trnS-UGA-psbZ_p5 trnS-UGA-psbZ GAGAGAGAGGGATTCGAACC CAACCCTCAGGAGAAGCAAA 567–571 1.000 69.7

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
Purshia glandulosa NC_088511.1 159266 View on NCBI ↗
Purshia tridentata NC_088513.1 159023 View on NCBI ↗