Markers + reference

Cautleya

2 species · Zingiberaceae · Zingiberales

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Species 2
Genome length 164–164 kb
Candidate markers 269
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 797 0.0246 0.97 71.7 yes View details
psbH LSC 222 0.0045 1.00 41.4 yes View details
petB LSC 1459 0.0172 0.99 63.8 yes View details
rpl16 LSC 1505 0.0198 0.97 60.2 yes View details
ndhB IRb 2233 0.0119 0.98 65.9 yes View details
psaC-ndhE SSC 853 0.0157 0.89 70.8 yes View details
ndhB IRa 2233 0.0000 1.00 38.5 no View details
psbT-psbN LSC 64 0.1250 1.00 87.5 yes View details
trnL-UAG-ccsA SSC 28 0.0357 1.00 73.0 yes View details
trnT-UGU-trnL-UAA LSC 1171 0.0044 0.97 63.7 yes View details
psbE-petL LSC 1285 0.0047 0.99 62.6 yes View details
trnE-UUC-trnT-GGU LSC 861 0.0024 0.98 62.5 yes View details
rps15-ycf1 SSC 442 0.0049 0.93 62.5 yes View details
atpH-atpI LSC 1483 0.0021 0.98 61.9 yes View details
trnC-GCA-petN LSC 880 0.0024 0.95 61.8 yes View details
atpF-atpH LSC 512 0.0078 1.00 61.6 yes View details
rpoB-trnC-GCA LSC 1200 0.0034 0.99 61.6 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CGGAGATACCCCTTCCCTTA 883–907 1.000 80.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CGGAGATACCCCTTCCCTTA 882–906 1.000 80.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGTATCAAGCGGGTCGAGTA CGGAGATACCCCTTCCCTTA 967–991 1.000 80.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GAGCGGAGAAAGAGGGATTC CGGAGATACCCCTTCCCTTA 939–963 1.000 78.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GTCGAGTAATCAGAGCGAGC CGGAGATACCCCTTCCCTTA 955–979 1.000 78.4
atpF-atpH_p1 atpF-atpH AGTGGCCCAAGTAAACGAAA TGGTTGTGGCATTAGCACTT 596 1.000 77.8
atpF-atpH_p2 atpF-atpH CAGTGGCCCAAGTAAACGAA TGGTTGTGGCATTAGCACTT 597 1.000 77.4
atpF-atpH_p3 atpF-atpH TGGCCCAAGTAAACGAAAGA TGGTTGTGGCATTAGCACTT 594 1.000 75.5
atpF-atpH_p4 atpF-atpH GTGGCCCAAGTAAACGAAAG TGGTTGTGGCATTAGCACTT 595 1.000 75.0
atpF-atpH_p5 atpF-atpH TTAAACCCGAAACTTCCGGC TGGTTGTGGCATTAGCACTT 624 1.000 74.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACCTTAGCCGC 1572–1609 1.000 80.7
atpH-atpI_p2 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACCTTAGCCGC 1655–1692 1.000 80.6
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACCTTAGCCGC 1628–1665 1.000 80.1
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATTTTTGCAACCTTAGCCGC 1573–1610 1.000 79.6
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATTTTTGCAACCTTAGCCGC 1632–1669 1.000 79.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTC AAAGGATTTGCAGTCCCCTG 1344–1350 1.000 79.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTC GCGACACCCAGATTTGAACT 1370–1376 1.000 76.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTC CCTTACCACTTGGCCATGTC 1324–1330 1.000 75.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT AAAGGATTTGCAGTCCCCTG 1345–1351 1.000 75.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTTCCGTCAAGCCCTCATTA AAAGGATTTGCAGTCCCCTG 1340–1346 1.000 74.8
trnC-GCA-petN_p1 trnC-GCA-petN ATTTGGATCGGATTTGGCGA AGTCCACTCCTTCCCCATAC 1008–1052 1.000 82.4
trnC-GCA-petN_p2 trnC-GCA-petN ATTTGGATCGGATTTGGCGA GTCCACTCCTTCCCCATACT 1007–1051 1.000 82.4
trnC-GCA-petN_p3 trnC-GCA-petN ATTTGGATCGGATTTGGCGA AAAGTCCACTCCTTCCCCAT 1010–1054 1.000 81.4
trnC-GCA-petN_p4 trnC-GCA-petN ATTTGGATCGGATTTGGCGA CCTCCCTAAAGTCCACTCCT 1017–1061 1.000 81.2
trnC-GCA-petN_p5 trnC-GCA-petN ATTTGGATCGGATTTGGCGA TACCCCTCCCTAAAGTCCAC 1021–1065 1.000 81.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG GAACCGATGACTTACGCCTT 979–1000 1.000 80.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG CCATGGCGTTACTCTACCAC 958–979 1.000 80.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG TGGCGTTACTCTACCACTGA 955–976 1.000 80.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 943–964 1.000 79.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 922–943 1.000 79.7

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
Cautleya gracilis NC_046845.1 164001 View on NCBI ↗
Cautleya spicata PP542019.1 164450 View on NCBI ↗