Markers + reference

Schizachyrium

40 species · Poaceae · Poales

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Species 40
Genome length 138–140 kb
Candidate markers 265
Primer pairs 95

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
rps16 LSC 1101 0.0099 0.99 50.4 yes View details
trnG-GCC-trnfM-CAU LSC 379 0.0229 0.99 64.3 yes View details
trnG-UCC-trnT-GGU LSC 2019 0.0162 0.97 72.0 yes View details
psbM-petN LSC 625 0.0157 0.99 70.0 yes View details
trnC-GCA-rpoB LSC 1242 0.0121 0.98 62.6 yes View details
trnF-GAA-ndhJ LSC 449 0.0137 1.00 58.5 yes View details
petL-petG LSC 167 0.0405 1.00 57.9 yes View details
rpl33-rps18 LSC 278 0.0212 0.98 60.3 yes View details
rpl16 LSC 1493 0.0109 1.00 58.4 yes View details
trnT-UGU-trnL-UAA LSC 759 0.0128 1.00 71.7 yes View details
petA-psbJ LSC 899 0.0131 1.00 70.9 yes View details
rbcL-psaI LSC 820 0.0092 1.00 70.7 yes View details
ndhF-rpl32 SSC 855 0.0099 0.98 69.5 yes View details
rps16-trnQ-UUG LSC 689 0.0123 1.00 66.7 yes View details
rpl14-rpl16 LSC 109 0.0203 1.00 65.8 yes View details
trnS-GCU-psbD LSC 958 0.0077 0.99 65.4 yes View details
trnY-GUA-trnD-GUC LSC 353 0.0148 0.99 64.3 yes View details
matK-trnK-UUU LSC 691 0.0084 1.00 63.6 yes View details
rpl32-trnL-UAG SSC 531 0.0141 0.99 63.0 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU ACGAAGTAGTGTTGACGAGA GAGCGTCCGGTGTAATTTCA 839–860 0.975 68.2
matK-trnK-UUU_p2 matK-trnK-UUU ACGAAGTAGTGTTGACGAGA ATGTTTTGACAGGAGCGTCC 851–872 1.000 68.0
matK-trnK-UUU_p3 matK-trnK-UUU ACGAAGTAGTGTTGACGAGA AGCGTCCGGTGTAATTTCAT 838–859 0.975 67.3
matK-trnK-UUU_p4 matK-trnK-UUU TGAAAGAGAAGTGGGTAGACG GAGCGTCCGGTGTAATTTCA 857–878 0.975 66.4
matK-trnK-UUU_p5 matK-trnK-UUU AGAGAAGTGGGTAGACGAAG GAGCGTCCGGTGTAATTTCA 853–874 0.975 66.0
rps16_p1 rps16 GCAAGAGGAGCAACCCTATC GAGGTTCGAATCCTTCCGTC 2099–2948 1.000 85.2
rps16_p2 rps16 GCAAGAGGAGCAACCCTATC ACCCCGTATCTATGGAGTGG 1797–2646 0.625 69.1
rps16_p3 rps16 TGAGGATCAGTCGTGGTCTT ACCCCGTATCTATGGAGTGG 2192–2982 0.300 55.1
rps16_p4 rps16 GCAAGAGGAGCAACCCTATC GCCCTGCACAACACAAAAAT 2043–2048 0.100 44.2
rps16_p5 rps16 TGAGGATCAGTCGTGGTCTT GCCCTGCACAACACAAAAAT 2439–2443 0.100 43.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 761–1611 1.000 84.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 772–1622 1.000 83.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 765–1615 1.000 83.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 776–1626 1.000 82.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 767–1617 1.000 81.2
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ATAAGCCGGACCATCCTACA 1089–1140 1.000 87.2
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA TAAGCCGGACCATCCTACAA 1088–1139 1.000 86.9
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1085–1136 1.000 86.6
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1072–1123 1.000 86.1
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ATAAGCCGGACCATCCTACA 1075–1126 1.000 84.3
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA CGAGGCTCATAACCTTGAGG 303–478 1.000 86.7
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GTAGCGAGCGTAGTTCAGTG CGAGGCTCATAACCTTGAGG 342–517 1.000 86.4
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU ATGTAGCGAGCGTAGTTCAG CGAGGCTCATAACCTTGAGG 344–519 1.000 86.3
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU AGGAGAAGATACGGGTTCGA CAGTTTGGTAGCTCACGAGG 318–493 1.000 86.3
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GTAGCGAGCGTAGTTCAGTG CAGTTTGGTAGCTCACGAGG 357–532 1.000 86.0
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1390–2132 1.000 52.6
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1386–2128 1.000 51.8
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1387–2129 1.000 51.8
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 1393–2135 1.000 51.8
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1392–2134 1.000 51.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (40)

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

Species Accession Length (bp) Link
Schizachyrium brevifolium NC_035013.1 138027 View on NCBI ↗
Schizachyrium cirratum NC_040130.1 139692 View on NCBI ↗
Schizachyrium claudopus MH181228.1 139385 View on NCBI ↗
Schizachyrium condensatum NC_087635.1 139282 View on NCBI ↗
Schizachyrium crinizonatum NC_087633.1 139274 View on NCBI ↗
Schizachyrium cubense MH181205.1 139130 View on NCBI ↗
Schizachyrium delavayi NC_059825.1 139855 View on NCBI ↗
Schizachyrium delicatum NC_087632.1 138596 View on NCBI ↗
Schizachyrium djalonicum NC_087634.1 138458 View on NCBI ↗
Schizachyrium exile NC_035029.1 138519 View on NCBI ↗
Schizachyrium fragile NC_087636.1 139277 View on NCBI ↗
Schizachyrium glaziovii NC_073108.1 139239 View on NCBI ↗
Schizachyrium gracile MH181191.1 139288 View on NCBI ↗
Schizachyrium gracilipes NC_087637.1 139081 View on NCBI ↗
Schizachyrium gresicola NC_087638.1 139768 View on NCBI ↗
Schizachyrium hatschbachii NC_087639.1 139249 View on NCBI ↗
Schizachyrium imberbe NC_035045.1 139759 View on NCBI ↗
Schizachyrium lomaense MH181201.1 138660 View on NCBI ↗
Schizachyrium maclaudii NC_087640.1 137958 View on NCBI ↗
Schizachyrium malacostachyum NC_087641.1 138229 View on NCBI ↗
Schizachyrium microstachyum MH181233.1 139249 View on NCBI ↗
Schizachyrium nodulosum NC_087642.1 138402 View on NCBI ↗
Schizachyrium platyphyllum NC_087698.1 138004 View on NCBI ↗
Schizachyrium pseudeulalia NC_087643.1 139268 View on NCBI ↗
Schizachyrium pulchellum NC_087644.1 139743 View on NCBI ↗
Schizachyrium reedii MH181217.1 139743 View on NCBI ↗
Schizachyrium ruderale NC_087645.1 138175 View on NCBI ↗
Schizachyrium rupestre NC_087646.1 139722 View on NCBI ↗
Schizachyrium salzmannii MH181208.1 139775 View on NCBI ↗
Schizachyrium sanguineum NC_035015.1 139272 View on NCBI ↗
Schizachyrium sanguineum var. hirtiflorum OQ518163.1 139337 View on NCBI ↗
Schizachyrium scabriflorum NC_087647.1 139230 View on NCBI ↗
Schizachyrium scoparium NC_035032.1 139274 View on NCBI ↗
Schizachyrium semitectum NC_087648.1 138534 View on NCBI ↗
Schizachyrium spicatum NC_035039.1 139205 View on NCBI ↗
Schizachyrium sulcatum NC_087649.1 139236 View on NCBI ↗
Schizachyrium tenerum NC_035043.1 138555 View on NCBI ↗
Schizachyrium thollonii MH181189.1 140395 View on NCBI ↗
Schizachyrium ursulus MH181183.1 140079 View on NCBI ↗
Schizachyrium yangambiense NC_087650.1 139706 View on NCBI ↗