Markers + reference

Bombycidendron

2 species · Malvaceae · Malvales

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Species 2
Genome length 162–162 kb
Candidate markers 264
Primer pairs 90

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 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhC-trnV-UAC LSC 1288 0.0143 0.98 56.9 yes View details
atpB-rbcL LSC 1147 0.0101 0.95 64.6 yes View details
accD-psaI LSC 810 0.0213 0.93 65.7 yes View details
petA-psbJ LSC 1085 0.0476 0.95 90.3 yes View details
rpl33-rps18 LSC 473 0.0402 0.84 80.2 yes View details
clpP1 LSC 2166 0.0107 0.99 49.8 yes View details
trnN-GUU-ndhF IRb 1509 0.0074 0.99 63.2 yes View details
ccsA-ndhD SSC 314 0.0353 0.99 63.2 yes View details
rpl2-psbA LSC 651 0.0955 0.24 74.6 no View details
petD-rpoA LSC 250 0.0360 1.00 73.2 yes View details
psbH-petB LSC 117 0.0256 1.00 67.2 yes View details
trnK-UUU-rps16 LSC 952 0.0066 0.95 67.1 yes View details
rps12-clpP1 LSC 187 0.0267 1.00 66.4 yes View details
rpl32-trnL-UAG SSC 1219 0.0092 0.98 65.9 yes View details
rps16-trnQ-UUG LSC 587 0.0053 0.96 65.3 yes View details
rps18-rpl20 LSC 296 0.0274 0.99 64.9 yes View details
ndhF-rpl32 SSC 1184 0.0085 0.99 64.5 yes View details
trnT-GGU-psbD LSC 1501 0.0022 0.89 63.2 yes View details
rpl20-rps12 LSC 754 0.0120 1.00 62.7 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAGGAGCTCAACCCACAG 1035–1080 1.000 82.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGAGCTCAACCCACAG 1034–1079 1.000 82.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC AAAAGGAGCTCAACCCACAG 1021–1066 1.000 80.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGAAGGCGGGGGTTTTTAC 995–1040 1.000 79.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGAAGGCGGGGGTTTTTAC 994–1039 1.000 79.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AGTGGTGGGTTTTGACATCC GAGGTTCGAATCCTTCCGTC 678–699 1.000 82.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 657–678 1.000 82.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 655–676 1.000 82.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 639–660 1.000 81.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTTTGACATCCACAGCCGAT GAGGTTCGAATCCTTCCGTC 669–690 1.000 80.9
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GAAACGGTCCCTACGTAACC 1503–1643 1.000 83.6
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GAAACGGTCCCTACGTAACC 1506–1646 1.000 83.4
trnT-GGU-psbD_p3 trnT-GGU-psbD ACGGCCCTTTTAACTCAGTG GAAACGGTCCCTACGTAACC 1520–1660 1.000 83.3
trnT-GGU-psbD_p4 trnT-GGU-psbD AATTGAATCGAACGGCCCTT GAAACGGTCCCTACGTAACC 1531–1671 1.000 82.8
trnT-GGU-psbD_p5 trnT-GGU-psbD ATTGAATCGAACGGCCCTTT GAAACGGTCCCTACGTAACC 1530–1670 1.000 82.8
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TGCCCAGAAAATATCATATTCGT AGAAGGTCTACGGTTCGAGT 1357–1395 1.000 42.6
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TGCCCAGAAAATATCATATTCGT GAAGGTCTACGGTTCGAGTC 1356–1394 1.000 42.6
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TGCCCAGAAAATATCATATTCGT GTTCGAGTCCGTATAGCCCT 1345–1383 1.000 42.6
ndhC-trnV-UAC_p4 ndhC-trnV-UAC ATGCCCAGAAAATATCATATTCGT AGAAGGTCTACGGTTCGAGT 1358–1396 1.000 42.6
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TGCCCAGAAAATATCATATTCGT AAGGTCTACGGTTCGAGTCC 1355–1393 1.000 42.6
atpB-rbcL_p1 atpB-rbcL TTTCAAGCGTGGAAACTCCA AACACCGGCTTTGAATCCAA 1192–1247 1.000 81.9
atpB-rbcL_p2 atpB-rbcL TTTCAAGCGTGGAAACTCCA TAACACCGGCTTTGAATCCA 1193–1248 1.000 79.8
atpB-rbcL_p3 atpB-rbcL TTTCAAGCGTGGAAACTCCA GGCTTTGAATCCAACACCTG 1186–1241 1.000 78.5
atpB-rbcL_p4 atpB-rbcL TTTCAAGCGTGGAAACTCCA CGGCTTTGAATCCAACACCT 1187–1242 1.000 78.3
atpB-rbcL_p5 atpB-rbcL TTTCAAGCGTGGAAACTCCA ACCGGCTTTGAATCCAACAC 1189–1244 1.000 76.0
accD-psaI_p1 accD-psaI GAGTTAGTTCAGCTCCACGG CCATTGCAATTGCCGGAAAT 899–937 1.000 85.2
accD-psaI_p2 accD-psaI AGTTCAGCTCCACGGTTTTT CCATTGCAATTGCCGGAAAT 894–932 1.000 84.8
accD-psaI_p3 accD-psaI GAGTTAGTTCAGCTCCACGG GAGGGAAAGCTGCTGAAAGT 852–890 1.000 84.7
accD-psaI_p4 accD-psaI GAGTTAGTTCAGCTCCACGG AAGAAGCCATTGCAATTGCC 905–943 1.000 84.5
accD-psaI_p5 accD-psaI AGTTCAGCTCCACGGTTTTT GAGGGAAAGCTGCTGAAAGT 847–885 1.000 84.3

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
Bombycidendron grewiifolium PX694244.1 162159 View on NCBI ↗
Bombycidendron vidalianum PX694238.1 161960 View on NCBI ↗