Markers + reference

Acidosasa

3 species · Poaceae · Poales

Back to catalogue

Species 3
Genome length 140–140 kb
Candidate markers 258
Primer pairs 85

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 8 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petN-trnC-GCA LSC 898 0.0015 1.00 47.2 yes View details
atpH-atpF LSC 455 0.0015 1.00 56.9 yes View details
rbcL LSC 1434 0.0005 1.00 41.1 yes View details
rbcL-psaI LSC 1292 0.0036 1.00 52.7 yes View details
rps18 LSC 492 0.0014 1.00 44.9 yes View details
petB LSC 1464 0.0005 1.00 46.5 yes View details
rpl22 LSC 450 0.0000 1.00 23.2 yes View details
rpl32-trnL-UAG SSC 703 0.0047 1.00 61.8 yes View details
rpl22-rps19 IRb 64 0.0417 1.00 66.6 yes View details
atpI LSC 744 0.0009 1.00 46.8 yes View details
ndhC-trnV-UAC LSC 744 0.0009 1.00 46.8 yes View details
atpB-rbcL LSC 780 0.0009 1.00 46.8 yes View details
ccsA SSC 978 0.0007 1.00 46.7 yes View details
rps16 LSC 1087 0.0006 1.00 46.6 yes View details
matK LSC 1536 0.0004 1.00 46.5 yes View details
rps16-trnQ-UUG LSC 1531 0.0004 1.00 46.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK TCAGAAGAACATTTCAGAATGGA ATGCAACACCCTGTTTTGAC 1715 1.000 40.0
matK_p2 matK TCAGAAGAACATTTCAGAATGGA AATGCAACACCCTGTTTTGAC 1716 1.000 40.0
matK_p3 matK TCAGAAGAACATTTCAGAATGGA GCAACACCCTGTTTTGACCA 1713 1.000 40.0
matK_p4 matK TCAGAAGAACATTTCAGAATGGA TGCAACACCCTGTTTTGACC 1714 1.000 40.0
matK_p5 matK TCAGAAGAACATTTCAGAATGGAA ATGCAACACCCTGTTTTGAC 1715 1.000 40.0
rps16_p1 rps16 TGGCACGACATAAATCCAGT TCCCTATACCACTTTGCAATGA 1248 1.000 51.0
rps16_p2 rps16 TGGCACGACATAAATCCAGT TCAATTCCCTATACCACTTTGCA 1253 1.000 48.3
rps16_p3 rps16 TGGCACGACATAAATCCAGT TCCCTATACCACTTTGCAATGAA 1248 1.000 48.3
rps16_p4 rps16 TGGCACGACATAAATCCAGT TTCCCTATACCACTTTGCAATGA 1249 1.000 48.3
rps16_p5 rps16 TGGCACGACATAAATCCAGT CCCTATACCACTTTGCAATGA 1247 1.000 46.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1605 1.000 78.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1616 1.000 77.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAAACCAGAAATGGGGCGT 1665 1.000 76.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TAAAACCAGAAATGGGGCGT 1676 1.000 76.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1609 1.000 73.6
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 947–948 1.000 70.5
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 949–950 1.000 70.1
petN-trnC-GCA_p3 petN-trnC-GCA CCACTCCTCCCCCATACTAC AGTTCAAATCTGGGTGCCG 1003–1004 1.000 69.5
petN-trnC-GCA_p4 petN-trnC-GCA CCACTCCTCCCCCATACTAC CCAGTTCAAATCTGGGTGCC 1005–1006 1.000 69.0
petN-trnC-GCA_p5 petN-trnC-GCA TCCACTCCTCCCCCATACTA AGTTCAAATCTGGGTGCCG 1004–1005 1.000 68.8
atpI_p1 atpI GCTGAGTTGAGAAAGAGATGGT AGTTTTCCAACCAAGCGGAT 900 1.000 63.5
atpI_p2 atpI TGCTGAGTTGAGAAAGAGATGG AGTTTTCCAACCAAGCGGAT 901 1.000 63.5
atpI_p3 atpI ACTTCAAGTTGCTGAGTTGAGA AGTTTTCCAACCAAGCGGAT 910 1.000 62.9
atpI_p4 atpI ACTTCAAGTTGCTGAGTTGAG AGTTTTCCAACCAAGCGGAT 910 1.000 59.3
atpI_p5 atpI GCTGAGTTGAGAAAGAGATGG AGTTTTCCAACCAAGCGGAT 900 1.000 58.8
atpH-atpF_p1 atpH-atpF TGTGGCACTAGCGCTTTTAT GGATGGCCAGTGAGCTAAAA 542–543 1.000 78.4
atpH-atpF_p2 atpH-atpF TTGTGGCACTAGCGCTTTTA GGATGGCCAGTGAGCTAAAA 543–544 1.000 78.3
atpH-atpF_p3 atpH-atpF TGTGGCACTAGCGCTTTTAT ATTAAGCCCGAAACTCCCAG 563–564 1.000 76.1
atpH-atpF_p4 atpH-atpF TTGTGGCACTAGCGCTTTTA ATTAAGCCCGAAACTCCCAG 564–565 1.000 76.0
atpH-atpF_p5 atpH-atpF GTGGCACTAGCGCTTTTATT GGATGGCCAGTGAGCTAAAA 541–542 1.000 69.6

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
Acidosasa glauca PQ576951.1 139667 View on NCBI ↗
Acidosasa purpurea NC_015820.1 139697 View on NCBI ↗
Acidosasa venusta PP681647.1 139677 View on NCBI ↗