Markers + reference

Alloteropsis

3 species · Poaceae · Poales

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Species 3
Genome length 139–141 kb
Candidate markers 244
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 244 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 387 0.0423 0.98 73.0 yes View details
trnfM-CAT-trnT-GGT LSC 2762 0.0345 0.99 70.6 yes View details
trnD-GTC-psbM LSC 1068 0.0301 0.98 69.3 yes View details
ycf3-trnS-GGA LSC 569 0.0379 0.99 75.1 yes View details
trnT-TGT-trnF-GAA LSC 1717 0.0263 0.99 66.8 yes View details
trnF-GAA-ndhJ LSC 583 0.0369 0.96 75.3 yes View details
rbcL-psaI LSC 916 0.0277 1.00 63.8 yes View details
ndhF-rpl32 SSC 926 0.0391 0.91 71.1 yes View details
ccsA-ndhD SSC 206 0.0829 1.00 73.5 yes View details
ndhD SSC 1503 0.0142 1.00 54.4 yes View details
psbT-psbN LSC 56 0.0705 0.93 86.3 yes View details
petG-trnW-CCA LSC 119 0.0672 1.00 74.1 yes View details
trnR-TCT-trnfM-CAT LSC 75 0.0516 0.95 73.7 yes View details
rps16-trnQ-TTG LSC 1138 0.0280 0.98 72.4 yes View details
rpl14-rpl16 LSC 108 0.0556 1.00 72.3 yes View details
rpl22-psbA LSC 126 0.0421 0.75 71.5 no View details
rpoA-rps11 LSC 64 0.0521 1.00 70.6 yes View details
atpI-atpH LSC 843 0.0283 0.89 68.8 yes View details
psbE-petL LSC 1148 0.0213 0.99 68.7 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-TTG_p1 rps16-trnQ-TTG TATGTCCTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 1221–1444 1.000 83.4
rps16-trnQ-TTG_p2 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1211–1434 1.000 82.3
rps16-trnQ-TTG_p3 rps16-trnQ-TTG TATGTCCTTCAAGTCGCACG CTCGGAGGTTCGAATCCTTC 1225–1448 1.000 82.3
rps16-trnQ-TTG_p4 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1215–1438 1.000 81.3
rps16-trnQ-TTG_p5 rps16-trnQ-TTG TATGTCCTTCAAGTCGCACG TACTCGGAGGTTCGAATCCT 1227–1450 1.000 80.5
psbK-psbI_p1 psbK-psbI TTAGCGTTTGTTTGGCAAGC ATTTTACTCCTCACGCCCAG 531–540 1.000 80.5
psbK-psbI_p2 psbK-psbI TTAGCGTTTGTTTGGCAAGC AATTTTACTCCTCACGCCCA 532–541 1.000 76.7
psbK-psbI_p3 psbK-psbI TTAGCGTTTGTTTGGCAAGC GGATTACGTCCTGGGTCATT 512–521 1.000 75.9
psbK-psbI_p4 psbK-psbI TTAGCGTTTGTTTGGCAAGC AATTTTACTCCTCACGCCCAG 532–541 1.000 73.4
psbK-psbI_p5 psbK-psbI TTAGCGTTTGTTTGGCAAGC AAATTTTACTCCTCACGCCCA 542 0.333 42.9
trnfM-CAT-trnT-GGT_p1 trnfM-CAT-trnT-GGT CCTCAAGGTTATGAGCCTCG TGAACCGATGACTTATGCCT 2851–2924 1.000 73.0
trnfM-CAT-trnT-GGT_p2 trnfM-CAT-trnT-GGT CCTCGTGAGCTACCAAACTG TGAACCGATGACTTATGCCT 2836–2909 1.000 72.6
trnfM-CAT-trnT-GGT_p3 trnfM-CAT-trnT-GGT CCTCAAGGTTATGAGCCTCG CCGATGACTTATGCCTTACCA 2847–2920 1.000 72.2
trnfM-CAT-trnT-GGT_p4 trnfM-CAT-trnT-GGT CCTCAAGGTTATGAGCCTCG ACCGATGACTTATGCCTTACC 2848–2921 1.000 72.2
trnfM-CAT-trnT-GGT_p5 trnfM-CAT-trnT-GGT CCTCGTGAGCTACCAAACTG CCGATGACTTATGCCTTACCA 2832–2905 1.000 71.8
trnD-GTC-psbM_p1 trnD-GTC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 1127–1153 1.000 53.2
trnD-GTC-psbM_p2 trnD-GTC-psbM TTCAATTGGTCAGAGCACCG GGAACTAGAATGAACAATGCAGT 1159–1185 1.000 50.2
trnD-GTC-psbM_p3 trnD-GTC-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 1128–1154 1.000 50.2
trnD-GTC-psbM_p4 trnD-GTC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 1127–1153 1.000 50.2
trnD-GTC-psbM_p5 trnD-GTC-psbM TTCAATTGGTCAGAGCACCG AGAATGAACAATGCAGTAGC 1153–1179 1.000 49.1
atpI-atpH_p1 atpI-atpH TAGCCGCAGCCTATATAGGT AAGCAGCAGCAATTAGTGGA 823–912 1.000 81.1
atpI-atpH_p2 atpI-atpH TAGCCGCAGCCTATATAGGT GCCAATCCAGCAGCAATAAC 845–934 1.000 81.0
atpI-atpH_p3 atpI-atpH TAGCCGCAGCCTATATAGGT ATAACGGAAGCAGCAGCAAT 830–919 1.000 80.8
atpI-atpH_p4 atpI-atpH TAGCCGCAGCCTATATAGGT TCCAGCAGCAATAACGGAAG 840–929 1.000 80.6
atpI-atpH_p5 atpI-atpH ATTTTTGCAACGTTAGCCGC AAGCAGCAGCAATTAGTGGA 836–925 1.000 80.6
trnR-TCT-trnfM-CAT_p1 trnR-TCT-trnfM-CAT AGAAGACCTCTGTCCTATCCA ACTACCCGCTCCATATTC 122–129 1.000 47.2
trnR-TCT-trnfM-CAT_p2 trnR-TCT-trnfM-CAT AGAAGACCTCTGTCCTATCCAT ACTACCCGCTCCATATTC 122–129 1.000 47.2
trnR-TCT-trnfM-CAT_p3 trnR-TCT-trnfM-CAT GGTTTAGAAGACCTCTGTCCT ACTACCCGCTCCATATTC 127–134 1.000 47.1
trnR-TCT-trnfM-CAT_p4 trnR-TCT-trnfM-CAT AGGTTTAGAAGACCTCTGTCCT ACTACCCGCTCCATATTC 128–135 1.000 47.0
trnR-TCT-trnfM-CAT_p5 trnR-TCT-trnfM-CAT AGGTTTAGAAGACCTCTGTCC ACTACCCGCTCCATATTC 128–135 1.000 47.0

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
Alloteropsis angusta NC_027951.1 140709 View on NCBI ↗
Alloteropsis cimicina NC_027952.1 139317 View on NCBI ↗
Alloteropsis paniculata NC_032078.1 139586 View on NCBI ↗