Markers + reference

Dracaena

11 species · Asparagaceae · Asparagales

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Species 11
Genome length 155–157 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 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
trnQ-UUG-psbK LSC 313 0.0494 1.00 72.8 yes View details
trnS-GCU-trnG-UCC LSC 1082 0.0222 0.97 66.7 yes View details
ycf3-trnS-GGA LSC 574 0.0287 1.00 68.6 yes View details
trnT-UGU-trnL-UAA LSC 899 0.0154 0.94 66.9 yes View details
trnW-CCA-trnP-UGG LSC 183 0.0147 1.00 45.7 yes View details
clpP LSC 2021 0.0132 1.00 54.8 yes View details
rps12-trnV-GAC IRb 1857 0.0146 1.00 56.5 yes View details
ycf1 IRb 896 0.0040 0.99 52.2 no View details
rpl32-trnL-UAG SSC 903 0.0161 1.00 65.5 yes View details
ycf1 SSC 5460 0.0120 1.00 50.7 yes View details
trnV-GAC-rps12 IRa 1857 0.0146 1.00 56.5 yes View details
petG-trnW-CCA LSC 115 0.1048 1.00 78.1 yes View details
ccsA-ndhD SSC 223 0.0351 1.00 68.2 yes View details
petN-psbM LSC 897 0.0080 1.00 66.6 yes View details
trnR-ACG-trnN-GUU IRb 596 0.0037 1.00 64.5 yes View details
trnN-GUU-trnR-ACG IRa 596 0.0037 1.00 64.5 yes View details
trnF-GAA-ndhJ LSC 724 0.0080 1.00 63.9 yes View details
psbM-trnD-GUC LSC 720 0.0108 1.00 62.7 yes View details
psaJ-rpl33 LSC 381 0.0126 1.00 62.0 yes View details
accD-psaI LSC 384 0.0149 1.00 61.9 yes View details
trnP-UGG-psaJ LSC 361 0.0092 1.00 61.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnQ-UUG-psbK_p1 trnQ-UUG-psbK AACAAAGAAGGGGTTGGGTC AGCAGCTTGCCAAACAAAAG 659–660 1.000 88.0
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GAACAAAGAAGGGGTTGGGT AGCAGCTTGCCAAACAAAAG 660–661 1.000 88.0
trnQ-UUG-psbK_p3 trnQ-UUG-psbK AACAAAGAAGGGGTTGGGTC CTTACAGCAGCTTGCCAAAC 664–665 1.000 87.9
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GAACAAAGAAGGGGTTGGGT CTTACAGCAGCTTGCCAAAC 665–666 1.000 87.9
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AACAAAGAAGGGGTTGGGTC CTTCACGTCCAGGATTACGG 1209–1241 1.000 86.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC CGAACGAATCACACTTTTACCA 1113–1305 1.000 65.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCTGCCGCTTTAGTCCA CGAACGAATCACACTTTTACCA 1114–1306 1.000 64.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT CGAACGAATCACACTTTTACCA 1105–1297 1.000 63.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC CGAACGAATCACACTTTTACCA 1100–1292 1.000 62.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC TCGAACGAATCACACTTTTACC 1114–1306 1.000 62.9
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 996–1075 1.000 75.2
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 945–1024 1.000 74.4
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 944–1023 1.000 74.4
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTGTTCATTCT 943–1022 1.000 73.9
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 1002–1081 1.000 73.7
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TGCTATACACCTTGCTGGGA 853–868 1.000 63.1
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 827–842 1.000 62.8
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC ACACCTTGCTGGGATTGTAG 847–862 1.000 62.5
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CACCTTGCTGGGATTGTAGT 846–861 1.000 62.5
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC ATGCTATACACCTTGCTGGG 854–869 1.000 61.3
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA ACGGAAAGAGAGGGATTCGA 758–759 1.000 74.3
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA ACGGAAAGAGAGGGATTCGA 759–760 1.000 74.3
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA TTCCAATGCTACGCCTTGAA 707–708 1.000 74.0
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA TTCCAATGCTACGCCTTGAA 708–709 1.000 74.0
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TCTCCTGAAGTTGTCGGAAT ACGGAAAGAGAGGGATTCGA 757–758 1.000 72.5
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA AGAGAAAAAGCCGGCTATCG ACCAATTTCGCCATATCCCC 701–1037 1.000 87.5
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA CGATAGAGAAAAAGCCGGCT ACCAATTTCGCCATATCCCC 705–1041 1.000 87.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA TCGATAGAGAAAAAGCCGGC ACCAATTTCGCCATATCCCC 706–1042 1.000 87.4
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA AGAGAAAAAGCCGGCTATCG TAGCGTCTACCAATTTCGCC 709–1045 1.000 86.9
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA CGATAGAGAAAAAGCCGGCT TAGCGTCTACCAATTTCGCC 713–1049 1.000 86.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Dracaena angustifolia MN200193.1 155332 View on NCBI ↗
Dracaena cambodiana NC_039776.1 156697 View on NCBI ↗
Dracaena cinnabari NC_068653.1 155371 View on NCBI ↗
Dracaena cochinchinensis NC_039943.1 155182 View on NCBI ↗
Dracaena elliptica NC_084216.1 155092 View on NCBI ↗
Dracaena fragrans NC_054234.1 155183 View on NCBI ↗
Dracaena hokouensis MN200197.1 155340 View on NCBI ↗
Dracaena marginata NC_072262.1 154926 View on NCBI ↗
Dracaena sanderiana NC_070393.1 155108 View on NCBI ↗
Dracaena serrulata MT408026.1 155398 View on NCBI ↗
Dracaena terniflora MN200198.1 155347 View on NCBI ↗