Markers + reference

Neolitsea

6 species · Lauraceae · Laurales

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Species 6
Genome length 152–153 kb
Candidate markers 261
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 396 0.0084 1.00 46.3 yes View details
trnK-UUU-rps16 LSC 825 0.0025 1.00 66.0 yes View details
psbM-trnD-GUC LSC 975 0.0016 1.00 50.4 yes View details
petA-psbJ LSC 1141 0.0102 1.00 66.2 yes View details
rpl2 LSC 1500 0.0000 1.00 26.6 yes View details
rpl2-trnl-CAU LSC 527 0.0037 1.00 59.2 yes View details
ycf1 IRb 1383 0.0012 1.00 44.1 no View details
ndhF SSC 2229 0.0010 1.00 44.6 yes View details
rpl32-trnL-UAG SSC 1352 0.0017 1.00 60.5 yes View details
ndhD SSC 1506 0.0007 1.00 42.7 yes View details
ycf1 SSC 5568 0.0012 1.00 49.9 yes View details
ndhF-rpl32 SSC 1136 0.0012 1.00 64.6 yes View details
ccsA-ndhD SSC 237 0.0113 1.00 60.7 yes View details
trnG-GCC-trnfM-CAU LSC 164 0.0041 0.97 60.0 yes View details
ycf3-trnS-GGA LSC 815 0.0008 1.00 59.9 yes View details
ycf4-cemA LSC 915 0.0011 1.00 59.9 yes View details
petB LSC 1439 0.0009 1.00 59.7 yes View details
psaJ-rpl33 LSC 428 0.0039 1.00 58.6 yes View details
atpF LSC 1283 0.0005 1.00 54.6 yes View details
rpoC2 LSC 4158 0.0007 1.00 54.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 463–466 1.000 80.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 477–480 1.000 80.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 476–479 1.000 80.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 478–481 1.000 80.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 466–469 1.000 80.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 834–965 1.000 82.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 833–964 1.000 82.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAAGACCATAGCCGCACTT AAAAAGGCGCTCAACCTACA 855–986 1.000 82.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 843–974 1.000 82.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 837–968 1.000 81.2
atpF_p1 atpF ACTAATTTCGTCGGCTCGAA GGGGGCGAAGTGATACAAAA 1444–1452 1.000 74.2
atpF_p2 atpF ACTAATTTCGTCGGCTCGAA CAATCCAAAACAAAGGGGGC 1458–1466 1.000 74.1
atpF_p3 atpF AATTTCGTCGGCTCGAATGG GGGGGCGAAGTGATACAAAA 1441–1449 1.000 71.4
atpF_p4 atpF AATTTCGTCGGCTCGAATGG CAATCCAAAACAAAGGGGGC 1455–1463 1.000 71.2
atpF_p5 atpF ACTAATTTCGTCGGCTCGAA CAAAGGGGGCGAAGTGATAC 1448–1456 1.000 70.6
rpoC2_p1 rpoC2 TGTTACTGCATGAATCGGGA TCCGATTGTTCTCGAATTGGT 292 1.000 61.4
rpoC2_p2 rpoC2 TGTTACTGCATGAATCGGGA CCGATTGTTCTCGAATTGGTC 291 1.000 58.7
rpoC2_p3 rpoC2 ATGTTACTGCATGAATCGGGA TCCGATTGTTCTCGAATTGGT 293 1.000 57.4
rpoC2_p4 rpoC2 TGTTACTGCATGAATCGGGAT TCCGATTGTTCTCGAATTGGT 292 1.000 57.4
rpoC2_p5 rpoC2 TGTTACTGCATGAATCGGGA CCGATTGTTCTCGAATTGGT 291 1.000 57.2
psbM-trnD-GUC_p1 psbM-trnD-GUC TGAACAACGCAGTGGCAATA AGTTCAATCGGTCAGAGCAC 1080–1087 1.000 77.0
psbM-trnD-GUC_p2 psbM-trnD-GUC TGAACAACGCAGTGGCAATA ATGCTGTACACCCCATTTCC 1109–1116 1.000 76.5
psbM-trnD-GUC_p3 psbM-trnD-GUC GAACAACGCAGTGGCAATAA AGTTCAATCGGTCAGAGCAC 1079–1086 1.000 74.6
psbM-trnD-GUC_p4 psbM-trnD-GUC GAACAACGCAGTGGCAATAA ATGCTGTACACCCCATTTCC 1108–1115 1.000 74.1
psbM-trnD-GUC_p5 psbM-trnD-GUC GAACAACGCAGTGGCAATAAA AGTTCAATCGGTCAGAGCAC 1079–1086 1.000 72.1
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AGTGCGGATATGGTCGAATG CTTGAGGTCACGGGTTCAAA 265–272 1.000 81.1
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU AGTGCGGATATGGTCGAATG GGGTAGAGCAGTTTGGTAGC 301–308 1.000 80.9
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU GAAAGTGCGGATATGGTCGA CTTGAGGTCACGGGTTCAAA 268–275 1.000 80.6
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GAAAGTGCGGATATGGTCGA GGGTAGAGCAGTTTGGTAGC 304–311 1.000 80.4
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU AGAAAGTGCGGATATGGTCG GGGTAGAGCAGTTTGGTAGC 305–312 1.000 80.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Neolitsea aciculata MW845678.2 152722 View on NCBI ↗
Neolitsea aurata var. paraciculata OR260548.1 152734 View on NCBI ↗
Neolitsea homilantha MT621638.1 152765 View on NCBI ↗
Neolitsea levinei MT621611.1 152643 View on NCBI ↗
Neolitsea pallens NC_050370.1 152699 View on NCBI ↗
Neolitsea sericea NC_059697.1 152446 View on NCBI ↗