Markers + reference

Cenchrus

12 species · Poaceae · Poales

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Species 12
Genome length 138–139 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-TTG LSC 1123 0.0517 0.70 73.0 yes View details
trnG-GCC-trnfM-CAT LSC 348 0.0214 0.64 52.1 yes View details
trnfM-CAT-trnT-GGT LSC 1928 0.0129 0.92 60.9 yes View details
trnC-GCA-rpoB LSC 1226 0.0178 0.95 64.1 yes View details
trnF-GAA-ndhJ LSC 590 0.0196 0.95 67.3 yes View details
ndhC-trnM-CAT LSC 1692 0.0114 0.91 52.8 yes View details
petA-psbJ LSC 881 0.0179 1.00 77.4 yes View details
rpl32-trnL-TAG SSC 494 0.0222 0.70 51.1 yes View details
psbM-petN LSC 733 0.0128 0.99 67.9 yes View details
psbZ-trnG-GCC LSC 305 0.0213 0.93 65.1 yes View details
petN-trnC-GCA LSC 857 0.0151 0.96 65.1 yes View details
rps3-rpl22 LSC 58 0.0295 1.00 64.1 yes View details
ycf3-trnS-GGA LSC 588 0.0109 0.99 63.8 yes View details
trnY-GTA-trnD-GTC LSC 355 0.0129 0.97 62.6 yes View details
trnD-GTC-psbM LSC 1025 0.0128 0.99 61.8 yes View details
ndhG-ndhI SSC 186 0.0327 0.99 61.8 yes View details
ndhI-ndhA SSC 91 0.0275 0.96 61.5 yes View details
rpl23-psaI LSC 382 0.0208 0.98 61.1 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 AAGTCGCACGTTGCTTTCTA CGAAAACTTACAGCGGCTTG 1203–1784 1.000 88.9
rps16-trnQ-TTG_p2 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGTTACTC 644–1217 1.000 87.1
rps16-trnQ-TTG_p3 rps16-trnQ-TTG TCATGTCCTTCAAGTCGCAC GGGTTTTGGTCCCGTTACTC 655–1228 1.000 86.6
rps16-trnQ-TTG_p4 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA TGACAGGCATAACATCCACG 1387–1729 0.917 85.8
rps16-trnQ-TTG_p5 rps16-trnQ-TTG TCATGTCCTTCAAGTCGCAC TGACAGGCATAACATCCACG 1398–1740 0.917 85.2
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG TCGAACCCGTATCTTCTCCT 443–471 1.000 83.7
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC TCGAACCCGTATCTTCTCCT 441–469 1.000 83.3
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG TTACCACTGAACTACGCTCG 408–436 1.000 82.6
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC TTACCACTGAACTACGCTCG 406–434 1.000 82.2
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CCGTATCTTCTCCTTGGCAA 437–465 1.000 81.7
trnG-GCC-trnfM-CAT_p1 trnG-GCC-trnfM-CAT GGCGTAGTTCAATGTAGCGA CGAGGCTCATAACCTTGAGG 402–542 1.000 84.3
trnG-GCC-trnfM-CAT_p2 trnG-GCC-trnfM-CAT GGCGTAGTTCAATGTAGCGA CAGTTTGGTAGCTCACGAGG 417–557 1.000 83.8
trnG-GCC-trnfM-CAT_p3 trnG-GCC-trnfM-CAT GGCGTAGTTCAATGTAGCGA CTACAGAGCGGAGTAGAGCA 435–575 1.000 83.4
trnG-GCC-trnfM-CAT_p4 trnG-GCC-trnfM-CAT GGCGTAGTTCAATGTAGCGA TACAGAGCGGAGTAGAGCAG 434–574 1.000 83.4
trnG-GCC-trnfM-CAT_p5 trnG-GCC-trnfM-CAT GGCGTAGTTCAATGTAGCGA GAGCGGAGTAGAGCAGTTTG 430–570 1.000 83.1
trnfM-CAT-trnT-GGT_p1 trnfM-CAT-trnT-GGT CCTCAAGGTTATGAGCCTCG ACCACTAAGTGAAAAGCCCT 2061–2748 1.000 74.0
trnfM-CAT-trnT-GGT_p2 trnfM-CAT-trnT-GGT CCTCAAGGTTATGAGCCTCG TGAACCGATGACTTATGCCT 2031–2718 1.000 73.8
trnfM-CAT-trnT-GGT_p3 trnfM-CAT-trnT-GGT CCTCGTGAGCTACCAAACTG ACCACTAAGTGAAAAGCCCT 2046–2733 1.000 73.6
trnfM-CAT-trnT-GGT_p4 trnfM-CAT-trnT-GGT CCTCGTGAGCTACCAAACTG TGAACCGATGACTTATGCCT 2016–2703 1.000 73.4
trnfM-CAT-trnT-GGT_p5 trnfM-CAT-trnT-GGT CCTCAAGGTTATGAGCCTCG CCGATGACTTATGCCTTACCA 2027–2714 1.000 73.0
trnY-GTA-trnD-GTC_p1 trnY-GTA-trnD-GTC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 471–479 1.000 81.1
trnY-GTA-trnD-GTC_p2 trnY-GTA-trnD-GTC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 438–446 1.000 79.0
trnY-GTA-trnD-GTC_p3 trnY-GTA-trnD-GTC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 437–445 1.000 78.8
trnY-GTA-trnD-GTC_p4 trnY-GTA-trnD-GTC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 470–478 1.000 76.9
trnY-GTA-trnD-GTC_p5 trnY-GTA-trnD-GTC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 439–447 1.000 75.6
trnD-GTC-psbM_p1 trnD-GTC-psbM TTCAATTGGTCAGAGCACCG TCATTTTGGCTGGCTGTTTT 1164–1250 1.000 73.5
trnD-GTC-psbM_p2 trnD-GTC-psbM TTCAATTGGTCAGAGCACCG AATCATTTTGGCTGGCTGTT 1166–1252 1.000 71.6
trnD-GTC-psbM_p3 trnD-GTC-psbM TTCAATTGGTCAGAGCACCG ATCATTTTGGCTGGCTGTTT 1165–1251 1.000 71.6
trnD-GTC-psbM_p4 trnD-GTC-psbM TTCAATTGGTCAGAGCACCG TCATTTTGGCTGGCTGTTTTT 1164–1250 1.000 71.4
trnD-GTC-psbM_p5 trnD-GTC-psbM TTCAATTGGTCAGAGCACCG TTTGGCTGGCTGTTTTTACA 1160–1246 1.000 70.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Cenchrus ciliaris NC_041434.1 138737 View on NCBI ↗
Cenchrus clandestinus NC_086737.1 138001 View on NCBI ↗
Cenchrus fungigraminus NC_082919.1 138144 View on NCBI ↗
Cenchrus glaucus NC_086743.1 138119 View on NCBI ↗
Cenchrus longisetus NC_086739.1 138554 View on NCBI ↗
Cenchrus longissimus NC_086735.1 138134 View on NCBI ↗
Cenchrus massaicus NC_086736.1 137929 View on NCBI ↗
Cenchrus orientalis NC_086741.1 138406 View on NCBI ↗
Cenchrus polystachios NC_086742.1 138171 View on NCBI ↗
Cenchrus purpurascens NC_086744.1 138053 View on NCBI ↗
Cenchrus purpureus NC_036384.1 138199 View on NCBI ↗
Cenchrus setaceus NC_086740.1 138037 View on NCBI ↗