Markers + reference

Stenotaphrum

2 species · Poaceae · Poales

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Species 2
Genome length 139–139 kb
Candidate markers 273
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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1259 0.0280 0.93 71.8 yes View details
psbK-psbI LSC 401 0.0274 1.00 59.4 yes View details
trnS-UGA-psbZ LSC 345 0.0348 1.00 67.8 yes View details
trnG-UCC-trnM-CAU LSC 1941 0.0216 1.00 62.9 yes View details
trnD-GUC-psbM LSC 1051 0.0203 0.99 59.1 yes View details
psbM-petN LSC 740 0.0235 0.98 63.9 yes View details
petN-trnC-GCA LSC 942 0.0206 0.98 64.7 yes View details
trnC-GCA-rpoB LSC 1184 0.0192 0.97 66.6 yes View details
trnF-GAA-ndhJ LSC 590 0.0374 0.95 77.8 yes View details
rbcL-psaI LSC 881 0.0183 0.99 56.3 yes View details
psbE-petL LSC 1238 0.0180 0.99 56.8 yes View details
psbT-psbN LSC 74 0.0405 1.00 75.8 yes View details
rpl36-infA LSC 100 0.0600 1.00 72.7 yes View details
rpl14-rpl16 LSC 109 0.0826 1.00 72.1 yes View details
trnV-UAC-trnM-CAU LSC 206 0.0291 1.00 69.2 yes View details
infA-rps8 LSC 81 0.0494 1.00 67.4 yes View details
atpB-rbcL LSC 730 0.0152 0.99 67.1 yes View details
trnL-UAA-trnF-GAA LSC 278 0.0328 0.99 65.7 yes View details
psaA-ycf3 LSC 638 0.0113 0.97 64.6 yes View details
trnG-GCC-trnfM-CAU LSC 362 0.0232 0.95 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1281–1333 1.000 84.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1292–1344 1.000 83.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1285–1337 1.000 83.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1296–1348 1.000 82.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1287–1339 1.000 81.4
psbK-psbI_p1 psbK-psbI CAAGCCGCTGTAAGTTTTCG TTTTTACTCCTCACGCCCAG 539–544 1.000 79.8
psbK-psbI_p2 psbK-psbI AGCCGCTGTAAGTTTTCGAT TTTTTACTCCTCACGCCCAG 537–542 1.000 79.4
psbK-psbI_p3 psbK-psbI AAGCCGCTGTAAGTTTTCGA TTTTTACTCCTCACGCCCAG 538–543 1.000 79.2
psbK-psbI_p4 psbK-psbI TTAGCGTTTGTTTGGCAAGC TTTTTACTCCTCACGCCCAG 554–559 1.000 78.9
psbK-psbI_p5 psbK-psbI GCCGCTGTAAGTTTTCGATG TTTTTACTCCTCACGCCCAG 536–541 1.000 78.9
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC CCAACCATCAGGAGAAGCAA 465–466 1.000 80.3
trnS-UGA-psbZ_p2 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC GACCAACCATCAGGAGAAGC 467–468 1.000 79.8
trnS-UGA-psbZ_p3 trnS-UGA-psbZ GTTTTCAAGACCGGGGCTAT CCAACCATCAGGAGAAGCAA 485–486 1.000 79.3
trnS-UGA-psbZ_p4 trnS-UGA-psbZ GTTTTCAAGACCGGGGCTAT GACCAACCATCAGGAGAAGC 487–488 1.000 78.9
trnS-UGA-psbZ_p5 trnS-UGA-psbZ GCTATCAACCACTCAGCCAT CCAACCATCAGGAGAAGCAA 470–471 1.000 77.7
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GGCGTAGTTCAATGTAGCGA CGAGGCTCATAACCTTGAGG 492–496 1.000 81.5
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GGCGTAGTTCAATGTAGCGA CAGTTTGGTAGCTCACGAGG 507–511 1.000 81.0
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU GGCGTAGTTCAATGTAGCGA CTGTTTTCGGCCCTACAGAG 537–541 1.000 80.9
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GGCGTAGTTCAATGTAGCGA CTACAGAGCGGAGTAGAGCA 525–529 1.000 80.5
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GGCGTAGTTCAATGTAGCGA TACAGAGCGGAGTAGAGCAG 524–528 1.000 80.5
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ATTCGAACCGATGACTTCCG 2095–2106 1.000 52.7
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CCGATGACTTCCGTCTTACC 2088–2099 1.000 51.7
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU AGAACGAATCACACTTTTACCAC ATTCGAACCGATGACTTCCG 2098–2109 1.000 51.7
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT ATTCGAACCGATGACTTCCG 2097–2108 1.000 51.7
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU AACGAATCACACTTTTACCACT ATTCGAACCGATGACTTCCG 2096–2107 1.000 50.8
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 1126–1136 1.000 50.5
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TGCGAGAATATTGACTTCCA 1158–1168 1.000 49.0
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 1127–1137 1.000 47.4
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 1126–1136 1.000 47.4
trnD-GUC-psbM_p5 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC TGCGAGAATATTGACTTCCA 1127–1137 1.000 46.3

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
Stenotaphrum secundatum NC_036704.1 138907 View on NCBI ↗
Stenotaphrum subulatum NC_046568.1 139282 View on NCBI ↗