Markers + reference

Sporobolus

9 species · Poaceae · Poales

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Species 9
Genome length 135–136 kb
Candidate markers 272
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 904 0.0307 0.99 75.9 yes View details
trnG-UCC-trnT-GGU LSC 589 0.0327 1.00 75.3 yes View details
trnT-GGU-trnE-UUC LSC 556 0.0307 0.98 73.2 yes View details
trnD-GUC-psbM LSC 989 0.0300 0.99 72.3 yes View details
petN-trnC-GCA LSC 822 0.0291 1.00 71.8 yes View details
trnC-GCA-rpoB LSC 1165 0.0301 0.99 69.4 yes View details
trnR-UCU-rps14 LSC 349 0.0507 0.99 76.6 yes View details
ycf3-trnS-GGA LSC 603 0.0326 0.98 70.0 yes View details
trnT-UGU-trnL-UAA LSC 785 0.0361 0.99 82.3 yes View details
trnL-UAA-trnF-GAA LSC 352 0.0351 0.96 73.7 yes View details
rbcL-psaI LSC 884 0.0315 0.99 73.3 yes View details
ndhF-rpl32 SSC 933 0.0417 0.98 82.8 yes View details
rpl32-trnL-UAG SSC 506 0.0405 0.97 78.5 yes View details
trnF-GAA-ndhJ LSC 531 0.0360 1.00 75.0 yes View details
atpH-atpF LSC 459 0.0379 0.98 74.7 yes View details
ccsA-ndhD SSC 192 0.0657 1.00 73.6 yes View details
ndhC-trnV-UAC LSC 868 0.0328 0.99 73.0 yes View details
rpl33-rps18 LSC 277 0.0348 1.00 71.8 yes View details
psbC-trnS-UGA LSC 154 0.0382 0.98 71.6 yes View details
trnK-UUU-rps16 LSC 561 0.0286 0.99 70.6 yes View details
rpl14-rpl16 LSC 105 0.0495 1.00 70.3 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCCCCGTATTAGGCAC TCGAGCCGTATGAGGAGAAA 1076–1199 1.000 86.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCCCCGTATTAGGCAC TTTCTCGAGCCGTATGAGGA 1080–1203 1.000 86.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT TCGAGCCGTATGAGGAGAAA 866–975 1.000 86.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT TTTCTCGAGCCGTATGAGGA 870–979 1.000 86.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCCCCGTATTAGGCAC GCTCAACCCACAAGAACTGT 865–987 1.000 85.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 977–1353 1.000 84.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TATCTCCTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 987–1363 1.000 81.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 981–1357 1.000 79.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 969–1345 1.000 79.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 976–1352 1.000 78.8
psbC-trnS-UGA_p1 psbC-trnS-UGA AGCAGGCTTTGAAAAGGGAA GAGAGATGGCTGAGTGGTTG 301–311 1.000 86.5
psbC-trnS-UGA_p2 psbC-trnS-UGA CATTTGTGGCATGCAGGAAG GAGAGATGGCTGAGTGGTTG 336–346 1.000 86.4
psbC-trnS-UGA_p3 psbC-trnS-UGA ATTTGTGGCATGCAGGAAGA GAGAGATGGCTGAGTGGTTG 335–345 1.000 85.9
psbC-trnS-UGA_p4 psbC-trnS-UGA TTCAACCTTGGCAAGAACGA GAGAGATGGCTGAGTGGTTG 506–516 1.000 84.6
psbC-trnS-UGA_p5 psbC-trnS-UGA CAGCGTCTTGGAGCTAATGT GAGAGATGGCTGAGTGGTTG 693–703 1.000 84.2
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 679–1109 1.000 45.7
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 675–1105 1.000 44.9
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 676–1106 1.000 44.9
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 682–1112 1.000 44.9
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 681–1111 1.000 44.9
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GCCACTAGCGTATGAACCAA GCATCGACCCAGGAAGAATT 1191–1611 1.000 86.8
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GCCACTAGCGTATGAACCAA CTAGATTTTTGGGCCGAGCT 1274–1694 1.000 86.5
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC GTCAAGGGTAGCCATTCGAG GCATCGACCCAGGAAGAATT 1328–1748 1.000 86.4
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GCCACTAGCGTATGAACCAA TTGAACTACAATCCCTGCGG 1628–2051 1.000 86.3
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC GTCAAGGGTAGCCATTCGAG CTAGATTTTTGGGCCGAGCT 1411–1831 1.000 86.1
trnD-GUC-psbM_p1 trnD-GUC-psbM AGCTCGGCCCAAAAATCTAG GGGAGAAGTGGACTCTAGGG 1927–2349 1.000 87.6
trnD-GUC-psbM_p2 trnD-GUC-psbM AGCTCGGCCCAAAAATCTAG GGGGAGAAGTGGACTCTAGG 1928–2350 1.000 87.6
trnD-GUC-psbM_p3 trnD-GUC-psbM AGCTCGGCCCAAAAATCTAG GGGGGAGAAGTGGACTCTAG 1929–2351 1.000 87.6
trnD-GUC-psbM_p4 trnD-GUC-psbM AATTCTTCCTGGGTCGATGC GGGAGAAGTGGACTCTAGGG 2010–2432 1.000 87.4
trnD-GUC-psbM_p5 trnD-GUC-psbM AATTCTTCCTGGGTCGATGC GGGGAGAAGTGGACTCTAGG 2011–2433 1.000 87.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Sporobolus aculeatus NC_068109.1 134822 View on NCBI ↗
Sporobolus alterniflorus MT311317.1 135560 View on NCBI ↗
Sporobolus diandrus NC_068124.1 135381 View on NCBI ↗
Sporobolus fertilis NC_068125.1 135025 View on NCBI ↗
Sporobolus helvolus NC_042237.1 135410 View on NCBI ↗
Sporobolus heterolepis NC_029417.1 135097 View on NCBI ↗
Sporobolus maritimus NC_027650.1 135592 View on NCBI ↗
Sporobolus michauxianus NC_029416.1 135617 View on NCBI ↗
Sporobolus virginicus NC_068126.1 135871 View on NCBI ↗