Markers + reference

Sartidia

3 species · Poaceae · Poales

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Species 3
Genome length 138–139 kb
Candidate markers 265
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-GCC-trnfM-CAU LSC 365 0.0110 1.00 54.3 yes View details
trnT-GGU-trnE-UUC LSC 535 0.0138 0.99 55.3 yes View details
trnT-UGU-trnL-UAA LSC 795 0.0105 1.00 56.5 yes View details
trnL-UAA-trnF-GAA LSC 301 0.0155 1.00 47.5 yes View details
rbcL-psaI LSC 918 0.0122 0.98 55.3 yes View details
rpl16 LSC 1479 0.0077 1.00 50.7 yes View details
rps3 LSC 675 0.0049 1.00 50.0 yes View details
ndhF-rpl32 SSC 722 0.0106 1.00 61.6 yes View details
rpl32-trnL-UAG SSC 489 0.0204 1.00 61.6 yes View details
ndhC-trnV-UAC LSC 908 0.0044 1.00 63.4 yes View details
ycf3-trnS-GGA LSC 576 0.0064 1.00 62.4 yes View details
psbE-petL LSC 1128 0.0053 1.00 62.2 yes View details
atpI-atpH LSC 830 0.0040 1.00 61.9 yes View details
petN-trnC-GCA LSC 938 0.0079 0.99 61.8 yes View details
trnD-GUC-psbM LSC 555 0.0036 1.00 61.1 yes View details
trnP-UGG-psaJ LSC 388 0.0137 1.00 61.0 yes View details
rps12-clpP LSC 140 0.0190 1.00 60.9 yes View details
psbM-petN LSC 510 0.0027 0.98 60.6 yes View details
trnK-UUU-rps16 LSC 578 0.0035 1.00 60.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU GCCAGCCCTAACAATTGGAT TGCCCCCTTTGCAAGTATTT 2927–2949 1.000 78.6
trnK-UUU_p2 trnK-UUU GCCAGCCCTAACAATTGGAT TTGCCCCCTTTGCAAGTATT 2928–2950 1.000 78.6
trnK-UUU_p3 trnK-UUU GACTCCCAAGCACACGTATT CAGTAGCGTCCGGTGTAATT 2807–2829 1.000 77.5
trnK-UUU_p4 trnK-UUU TGCGGTCAATAAGGTAGGGA CAGTAGCGTCCGGTGTAATT 2969–2991 1.000 77.2
trnK-UUU_p5 trnK-UUU ACGGAAGTTGCGGTCAATAA CAGTAGCGTCCGGTGTAATT 2977–2999 1.000 76.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAAGAACT 704–706 1.000 66.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA GGTGCTCAACCTACAAGAACT 705–707 1.000 65.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACT 702–704 1.000 65.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACT 701–703 1.000 65.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCACTTAAAAGCCGAGT GGTGCTCAACCTACAAGAACT 703–705 1.000 64.5
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GTGTAGCGAGCGTAGTTCAA ACCTGTTTTTGGCCCTACAG 531–535 1.000 81.4
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU TGTAGCGAGCGTAGTTCAAC ACCTGTTTTTGGCCCTACAG 530–534 1.000 81.4
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU TGTAGCGAGCGTAGTTCAAC GACCTGTTTTTGGCCCTACA 531–535 1.000 81.4
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GTGTAGCGAGCGTAGTTCAA GACCTGTTTTTGGCCCTACA 532–536 1.000 81.3
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GAAGGTACGGGTTCGATTCC ACCTGTTTTTGGCCCTACAG 486–490 1.000 81.2
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 631–635 1.000 68.9
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 594–598 1.000 68.8
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG TGTCCTGAACCACTAGACGA 599–603 1.000 68.0
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GGTAAGGCATAAGTCATCGGT TGTCCTGAACCACTAGACGA 598–602 1.000 68.0
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC GTGGTAGAGTAATGCCATGGT TGTCCTGAACCACTAGACGA 616–620 1.000 67.2
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TAATCGTTTTGGCTGGCTGT 723–1176 1.000 76.0
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG CGTTTTGGCTGGCTGTTTTT 719–1172 1.000 74.0
trnD-GUC-psbM_p3 trnD-GUC-psbM CCTGCAGGGATTGTAGTTCA TAATCGTTTTGGCTGGCTGT 739–1192 1.000 73.6
trnD-GUC-psbM_p4 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC TAATCGTTTTGGCTGGCTGT 724–1177 1.000 71.9
trnD-GUC-psbM_p5 trnD-GUC-psbM CCTGCAGGGATTGTAGTTCA CGTTTTGGCTGGCTGTTTTT 735–1188 1.000 71.5
psbM-petN_p1 psbM-petN ACAGCCAGCCAAAACGATTA TAGTAAGTCTCGCTTGGGCT 603–614 1.000 79.7
psbM-petN_p2 psbM-petN ACAGCCAGCCAAAACGATTA GTAGTATGGGGGAGGAGTGG 547–558 1.000 78.9
psbM-petN_p3 psbM-petN ACAGCCAGCCAAAACGATTA TAGTATGGGGGAGGAGTGGA 546–557 1.000 78.1
psbM-petN_p4 psbM-petN AAAAACAGCCAGCCAAAACG TAGTAAGTCTCGCTTGGGCT 607–618 1.000 77.7
psbM-petN_p5 psbM-petN ACAGCCAGCCAAAACGATTA CGCTAGTAGTATGGGGGAGG 552–563 1.000 77.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Sartidia dewinteri NC_027147.1 138074 View on NCBI ↗
Sartidia isaloensis NC_036117.1 138607 View on NCBI ↗
Sartidia perrieri NC_027146.1 138471 View on NCBI ↗