Markers + reference

Otatea

2 species · Poaceae · Poales

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Species 2
Genome length 136–136 kb
Candidate markers 263
Primer pairs 85

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 11 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 399 0.0175 1.00 57.0 yes View details
psbZ-trnfM-CAU LSC 786 0.0179 1.00 69.4 yes View details
rps2 LSC 711 0.0098 1.00 64.4 yes View details
psaA-ycf3 LSC 614 0.0147 1.00 67.2 yes View details
trnT-UGU-trnL-UAA LSC 758 0.0053 1.00 62.0 yes View details
trnL-UAA-trnF-GAA LSC 355 0.0056 1.00 57.2 yes View details
ndhC-trnV-UAC LSC 885 0.0090 1.00 63.9 yes View details
ndhH IRb 222 0.0180 1.00 48.5 yes View details
ndhH SSC 1182 0.0025 1.00 55.0 no View details
trnT-GGU LSC 67 0.0299 1.00 69.7 yes View details
atpF-atpA LSC 92 0.0217 1.00 65.0 yes View details
psbM-petN LSC 767 0.0014 0.96 63.4 yes View details
rps19-psbA LSC 126 0.0161 0.98 63.3 no View details
trnfM-CAU LSC 57 0.0175 1.00 62.6 yes View details
matK LSC 1536 0.0039 1.00 60.9 yes View details
rps16 LSC 1127 0.0000 0.98 60.7 yes View details
rbcL-psaI LSC 1291 0.0031 1.00 60.6 yes View details
petA-psbJ LSC 988 0.0030 1.00 60.6 yes View details
psbE-petL LSC 1242 0.0000 0.98 60.5 yes View details
trnfM-CAU LSC 74 0.0000 1.00 30.7 no 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 TCAGAATGGAAAACGTGAAAGT CAACACCCTGTTCTGACCAT 1699 1.000 50.0
matK_p2 matK TCAGAATGGAAAACGTGAAAGT AATGCAACACCCTGTTCTGA 1703 1.000 49.3
matK_p3 matK TCAGAATGGAAAACGTGAAAGT ATGCAACACCCTGTTCTGAC 1702 1.000 49.1
matK_p4 matK ACATTTCAGAATGGAAAACGTGA CAACACCCTGTTCTGACCAT 1704 1.000 47.9
matK_p5 matK AGGGAACATTTCAGAATGGA CAACACCCTGTTCTGACCAT 1709 1.000 47.6
rps16_p1 rps16 ACAGCGAGGGATACTAGTGA TCCCTATACCACTTTGCAATGA 1201–1224 1.000 52.8
rps16_p2 rps16 AGACAGCGAGGGATACTAGT TCCCTATACCACTTTGCAATGA 1203–1226 1.000 50.4
rps16_p3 rps16 ACAGCGAGGGATACTAGTGA TCAATTCCCTATACCACTTTGCA 1206–1229 1.000 50.2
rps16_p4 rps16 ACAGCGAGGGATACTAGTGA TCCCTATACCACTTTGCAATGAA 1201–1224 1.000 50.2
rps16_p5 rps16 ACAGCGAGGGATACTAGTGA TTCCCTATACCACTTTGCAATGA 1202–1225 1.000 50.2
psbK-psbI_p1 psbK-psbI CGTGGATGTTATGCCTGTCA GGATTACGTCCTGGGTCATT 573–579 1.000 72.8
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGTCCTGGGTCATT 524–530 1.000 72.6
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGATTACGTCCTGGGTCATT 521–527 1.000 70.6
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT GGATTACGTCCTGGGTCATT 522–528 1.000 70.6
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT GGATTACGTCCTGGGTCATT 523–529 1.000 70.6
psbZ-trnfM-CAU_p1 psbZ-trnfM-CAU TTGCTTCTCCTGATGGTTGG CGAGGCTCATAACCTTGAGG 943–948 1.000 77.9
psbZ-trnfM-CAU_p2 psbZ-trnfM-CAU GCTTCTCCTGATGGTTGGTC CGAGGCTCATAACCTTGAGG 941–946 1.000 77.5
psbZ-trnfM-CAU_p3 psbZ-trnfM-CAU TTGCTTCTCCTGATGGTTGG CAGTTTGGTAGCTCACGAGG 958–963 1.000 77.5
psbZ-trnfM-CAU_p4 psbZ-trnfM-CAU GCTTCTCCTGATGGTTGGTC CAGTTTGGTAGCTCACGAGG 956–961 1.000 77.1
psbZ-trnfM-CAU_p5 psbZ-trnfM-CAU TTGCTTCTCCTGATGGTTGG GAGCGGAGTAGAGCAGTTTG 971–976 1.000 76.8
trnT-GGU_p1 trnT-GGU AGCCCTTTTAACTCAGTGGT ACCAAAAATGCATGCATCCC 247 1.000 66.6
trnT-GGU_p2 trnT-GGU AGGCATAAGTCATCGGTTCA ACCAAAAATGCATGCATCCC 210 1.000 66.5
trnT-GGU_p3 trnT-GGU AGCCCTTTTAACTCAGTGGT GCATCCCGCACTAAGTCATA 234 1.000 65.7
trnT-GGU_p4 trnT-GGU TGGTAAGGCATAAGTCATCGG ACCAAAAATGCATGCATCCC 215 1.000 65.7
trnT-GGU_p5 trnT-GGU GGTAAGGCATAAGTCATCGGT ACCAAAAATGCATGCATCCC 214 1.000 65.7
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 898–929 1.000 70.3
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT GTAGTATGGGGGAGGAGTGG 842–873 1.000 69.5
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTCT TAGTATGGGGGAGGAGTGGA 841–872 1.000 68.8
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTC TAGTAAGTCTCGCTTGGGCT 898–929 1.000 66.2
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT AGTAGTATGGGGGAGGAGTG 843–874 1.000 65.5

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
Otatea acuminata NC_026971.1 136351 View on NCBI ↗
Otatea glauca NC_028631.1 136377 View on NCBI ↗