Markers + reference

Dactyloctenium

2 species · Poaceae · Poales

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Species 2
Genome length 135–135 kb
Candidate markers 273
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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1267 0.0183 0.95 66.8 yes View details
trnG-GCC-trnfM-CAU LSC 376 0.0324 0.98 64.8 yes View details
trnT-GGU-trnE-UUC LSC 506 0.0238 1.00 56.5 yes View details
petN-trnC-GCA LSC 797 0.0227 0.99 61.7 yes View details
trnT-UGU-trnL-UAA LSC 848 0.0292 0.97 73.4 yes View details
rbcL-psaI LSC 877 0.0183 0.99 57.5 yes View details
psbE-petL LSC 1186 0.0144 1.00 67.4 yes View details
ndhF SSC 2220 0.0149 1.00 54.0 yes View details
rpl32-trnL-UAG SSC 360 0.0279 0.99 57.8 yes View details
C2H24_pgr006-C2H24_pgr005 IRb 227 0.0441 1.00 77.8 yes View details
C2H24_pgr004-C2H24_pgr003 IRa 227 0.0441 1.00 77.8 yes View details
rpl14-rpl16 LSC 111 0.0521 0.86 71.5 yes View details
ndhC-trnV-UAC LSC 935 0.0173 0.99 69.7 yes View details
psbC-trnS-UGA LSC 156 0.0323 0.99 68.3 yes View details
clpP-psbB LSC 512 0.0160 0.98 66.3 yes View details
psaJ-rpl33 LSC 418 0.0148 0.97 66.2 yes View details
atpF-atpA LSC 96 0.0208 1.00 64.5 yes View details
ndhE-ndhG SSC 196 0.0204 1.00 64.2 yes View details
trnY-GUA-trnD-GUC LSC 343 0.0175 1.00 63.5 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 95 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 1291–1341 1.000 83.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CGCATAAAAGAAATGGGGCG 1352–1402 1.000 82.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATCTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1302–1352 1.000 81.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATCTCCTTCAAGTCGCAC CGCATAAAAGAAATGGGGCG 1363–1413 1.000 80.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1295–1345 1.000 78.7
psbC-trnS-UGA_p1 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG GAGAGATGGCTGAGTGGTTG 344–345 1.000 81.2
psbC-trnS-UGA_p2 psbC-trnS-UGA AGCAGGCTTTGAAAAGGGAA GAGAGATGGCTGAGTGGTTG 309–310 1.000 80.7
psbC-trnS-UGA_p3 psbC-trnS-UGA ATTTGTGGCATGCAGGAAGA GAGAGATGGCTGAGTGGTTG 343–344 1.000 80.6
psbC-trnS-UGA_p4 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG ATAGCCCCGGTCTTGAAAAC 324–325 1.000 80.4
psbC-trnS-UGA_p5 psbC-trnS-UGA ATTTGTGGCATGCAGGAAGA ATAGCCCCGGTCTTGAAAAC 323–324 1.000 79.9
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GAAGGTACGGGTTCGATTCC AGTTTTTGGCCCTACAGAGC 498–510 1.000 81.6
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA AGTTTTTGGCCCTACAGAGC 538–550 1.000 81.3
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU GAAGGTACGGGTTCGATTCC CGAGGCTCATAACCTTGAGG 454–466 1.000 80.7
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA CGAGGCTCATAACCTTGAGG 494–506 1.000 80.4
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU TAGCGAGCGTAGTTCAATGG AGTTTTTGGCCCTACAGAGC 540–552 1.000 80.3
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GTGGTAGAGTAATGCCACGG GCATCGACCCAGGAAGAATT 704–705 1.000 81.0
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GACCAAAGTCATCGGTTCGA GCATCGACCCAGGAAGAATT 681–682 1.000 80.9
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGACCAAAGTCATCGGTTCG GCATCGACCCAGGAAGAATT 682–683 1.000 80.9
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GTGGTAGAGTAATGCCACGG TTGAACTACAATCCCTGCGG 1136–1139 1.000 80.2
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC CCCGTTGAAAATTGCTGCAA GCATCGACCCAGGAAGAATT 1288–1338 1.000 80.0
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GCGGTGCTCTAACCAATTGA 468–470 1.000 76.3
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC ACTCTAGTTCGGGACTGACG 520–522 1.000 76.2
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG GCGGTGCTCTAACCAATTGA 435–437 1.000 73.9
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG ACTCTAGTTCGGGACTGACG 487–489 1.000 73.8
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT ACTCTAGTTCGGGACTGACG 486–488 1.000 73.6
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 846–900 1.000 72.4
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 848–902 1.000 71.9
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CAGTTCAAATCTGGGTGCCG 847–901 1.000 69.0
petN-trnC-GCA_p4 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGGGGACTGCAAATCCTTTA 871–925 1.000 68.0
petN-trnC-GCA_p5 petN-trnC-GCA AGCCCAAGCGAGACTTACTA TGCAAATCCTTTATCCCCAGT 864–918 1.000 66.7

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
Dactyloctenium aegyptium NC_036714.1 134889 View on NCBI ↗
Dactyloctenium radulans NC_042838.1 135050 View on NCBI ↗