Markers + reference

Enteropogon

2 species · Poaceae · Poales

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Species 2
Genome length 133–136 kb
Candidate markers 269
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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1261 0.0247 1.00 65.5 yes View details
trnG-UCC-trnT-GGU LSC 1008 0.0305 0.98 66.3 yes View details
trnY-GUA-trnD-GUC LSC 356 0.0554 0.96 78.0 yes View details
trnD-GUC-psbM LSC 1015 0.0353 0.98 73.7 yes View details
psbM-petN LSC 635 0.0355 0.80 76.2 yes View details
trnC-GCA-rpoB LSC 1057 0.0339 0.98 72.2 yes View details
trnT-UGU-trnL-UAA LSC 810 0.0299 0.99 70.6 yes View details
ndhC-trnV-UAC LSC 936 0.0586 0.98 80.3 yes View details
rpl16 LSC 1541 0.0204 0.95 59.8 yes View details
ndhF-rpl32 SSC 874 0.0289 0.95 70.6 yes View details
ccsA SSC 969 0.0144 1.00 53.0 yes View details
psbL-psbF LSC 22 0.0455 1.00 78.6 yes View details
trnF-GAA-ndhJ LSC 501 0.0384 0.99 75.5 yes View details
rpl14-rpl16 LSC 112 0.0714 1.00 75.0 yes View details
trnfM-CAU-trnG-UCC LSC 96 0.0610 0.85 73.8 yes View details
trnE-UUC-trnY-GUA LSC 61 0.0492 1.00 71.9 yes View details
ccsA-ndhD SSC 194 0.0881 0.99 71.9 yes View details
petG-trnW-CCA LSC 124 0.0492 0.98 71.5 yes View details
trnR-UCU-rps14 LSC 394 0.0368 0.96 71.1 yes View details
rpl33-rps18 LSC 285 0.0551 0.89 70.9 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 1334–1347 1.000 80.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CGCATAAAAGAAATGGGGCG 1395–1408 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATCTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1345–1358 1.000 78.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATCTCCTTCAAGTCGCAC CGCATAAAAGAAATGGGGCG 1406–1419 1.000 77.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1338–1351 1.000 75.6
trnfM-CAU-trnG-UCC_p1 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG AGCCTTCCAAGCTAACGATG 173–187 1.000 84.1
trnfM-CAU-trnG-UCC_p2 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCTAGCCTTCCAAGCTAACG 176–190 1.000 83.9
trnfM-CAU-trnG-UCC_p3 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG AGCCTTCCAAGCTAACGATG 158–172 1.000 83.9
trnfM-CAU-trnG-UCC_p4 trnfM-CAU-trnG-UCC CCTCGTGAGCTACCAAACTG CCTAGCCTTCCAAGCTAACG 161–175 1.000 83.6
trnfM-CAU-trnG-UCC_p5 trnfM-CAU-trnG-UCC CCTCAAGGTTATGAGCCTCG CCAACGTCGACTATAACCCC 194–208 1.000 82.4
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1081–1098 1.000 44.8
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1077–1094 1.000 44.1
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCATGGCATTACTCTACCAC 1060–1077 1.000 44.1
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1078–1095 1.000 44.0
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1083–1100 1.000 44.0
trnE-UUC-trnY-GUA_p1 trnE-UUC-trnY-GUA CTCTCTTTCAAGGAGGCAGC CTAGATTTTTGGGCCGAGCT 199 1.000 78.7
trnE-UUC-trnY-GUA_p2 trnE-UUC-trnY-GUA TCGTCTAGTGGTTCAGGACA CTAGATTTTTGGGCCGAGCT 220 1.000 78.5
trnE-UUC-trnY-GUA_p3 trnE-UUC-trnY-GUA ATGCCCCTATCGTCTAGTGG CTAGATTTTTGGGCCGAGCT 229 1.000 77.8
trnE-UUC-trnY-GUA_p4 trnE-UUC-trnY-GUA CTCTCTTTCAAGGAGGCAGC TAGATTTTTGGGCCGAGCTG 198 1.000 77.1
trnE-UUC-trnY-GUA_p5 trnE-UUC-trnY-GUA TCGTCTAGTGGTTCAGGACA TAGATTTTTGGGCCGAGCTG 219 1.000 76.8
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GCGGTGCTCTAACCAATTGA 477–481 1.000 80.6
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG GCGGTGCTCTAACCAATTGA 444–448 1.000 78.5
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT GCGGTGCTCTAACCAATTGA 443–447 1.000 78.3
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGCGGTGCTCTAACCAATT 478–482 1.000 75.9
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC GCGGTGCTCTAACCAATTGA 445–449 1.000 75.1
trnD-GUC-psbM_p1 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC GGCAGTAGGAACTAGAATGAACA 1179–1186 1.000 55.0
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG GGCAGTAGGAACTAGAATGAACA 1212–1219 1.000 54.0
trnD-GUC-psbM_p3 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC AGGCAGTAGGAACTAGAATGAAC 1180–1187 1.000 52.9
trnD-GUC-psbM_p4 trnD-GUC-psbM TAGGTATGCCATACACCCCG AGGCAGTAGGAACTAGAATGAAC 1213–1220 1.000 51.9
trnD-GUC-psbM_p5 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC AGGCAGTAGGAACTAGAATGA 1180–1187 1.000 51.6

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
Enteropogon dolichostachyus NC_068113.1 135541 View on NCBI ↗
Enteropogon ramosus NC_042834.1 132690 View on NCBI ↗