Markers + reference

Bombax

2 species · Malvaceae · Malvales

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Species 2
Genome length 159–161 kb
Candidate markers 265
Primer pairs 85

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 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU LSC 282 0.0000 1.00 25.6 yes View details
trnK-UUU-rps16 LSC 844 0.0025 0.96 63.8 yes View details
atpF LSC 1377 0.0007 1.00 59.2 yes View details
rpoC1 LSC 2824 0.0004 1.00 56.2 yes View details
petA-psbJ LSC 1081 0.0009 1.00 59.3 yes View details
rpl33-rps18 LSC 374 0.0223 0.84 68.2 yes View details
rpl32-ndhF SSC 1235 0.0461 0.97 88.4 yes View details
rbcL LSC 1482 0.0000 0.96 62.3 yes View details
psaA-ycf3 LSC 916 0.0000 0.97 61.9 yes View details
petD LSC 1258 0.0000 0.97 61.8 yes View details
trnS-GCU-trnG-GCC LSC 914 0.0000 0.86 61.2 yes View details
atpH-atpI LSC 1240 0.0000 0.98 61.1 yes View details
trnE-UUC-trnT-GGU LSC 841 0.0000 0.98 61.1 yes View details
atpF-atpH LSC 631 0.0000 0.81 59.6 yes View details
clpP LSC 2210 0.0000 0.98 59.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU AACACCAAACCATCCGATGT ACTCCATCCGACTAGTTCCG 429 1.000 72.8
psbA-trnK-UUU_p2 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA ACTCCATCCGACTAGTTCCG 405 1.000 72.4
psbA-trnK-UUU_p3 psbA-trnK-UUU AACACCAAACCATCCGATGT ACTAGTTCCGGGTTCGAGTC 419 1.000 71.1
psbA-trnK-UUU_p4 psbA-trnK-UUU AACACCAAACCATCCGATGT GACTAGTTCCGGGTTCGAGT 420 1.000 71.1
psbA-trnK-UUU_p5 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA ACTAGTTCCGGGTTCGAGTC 395 1.000 70.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAGGAGCTCAACCCACAG 972–1005 1.000 81.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGAGCTCAACCCACAG 971–1004 1.000 81.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC AAAAGGAGCTCAACCCACAG 958–991 1.000 79.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGAAGGCGGGGGTTTTTAC 932–965 1.000 78.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGAAGGCGGGGGTTTTTAC 931–964 1.000 78.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ATGAATCAAACCGAGGGACC 905–1029 1.000 80.6
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ATGAATCAAACCGAGGGACC 904–1028 1.000 80.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CGCACAACGGATTAGCAATC ATGAATCAAACCGAGGGACC 920–1044 1.000 79.9
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ATGAATCAAACCGAGGGACC 959–1083 1.000 79.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TCGCACAACGGATTAGCAAT ATGAATCAAACCGAGGGACC 921–1045 1.000 78.5
atpF_p1 atpF CGTCGGCTCTAATAGTTACCA GTCTATCTAAAATAAAATAGGAGATCA 1504 1.000 40.1
atpF_p2 atpF CGTCGGCTCTAATAGTTACCA AGTCTATCTAAAATAAAATAGGAGATC 1505 1.000 40.1
atpF_p3 atpF TCGTCGGCTCTAATAGTTACC GTCTATCTAAAATAAAATAGGAGATCA 1505 1.000 40.1
atpF_p4 atpF TCGTCGGCTCTAATAGTTACCA GTCTATCTAAAATAAAATAGGAGATCA 1505 1.000 40.1
atpF_p5 atpF TCGTCGGCTCTAATAGTTACC AGTCTATCTAAAATAAAATAGGAGATC 1506 1.000 40.1
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGTTGTAGCATTGGCACTT 622–744 1.000 83.0
atpF-atpH_p2 atpF-atpH CCAGTAACCCAAGGAAACGA TGGTTGTAGCATTGGCACTT 595–717 1.000 79.5
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG CTGGTTGTAGCATTGGCACT 623–745 1.000 79.4
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG ATGGGCTGGTTGTAGCATTG 628–750 1.000 78.9
atpF-atpH_p5 atpF-atpH GGCCAGTAACCCAAGGAAAC TGGTTGTAGCATTGGCACTT 597–719 1.000 78.0
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTGCAACTTTAGCTGCGG 1331–1361 1.000 80.5
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1297–1327 1.000 80.5
atpH-atpI_p3 atpH-atpI TACCTTCTACAGCTTGGCCT TTTTGCAACTTTAGCTGCGG 1380–1410 1.000 80.3
atpH-atpI_p4 atpH-atpI AATAGAAGCAAGCCCGACAG CGAATCCATGGAGGGTCATC 1301–1331 1.000 80.2
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1267–1297 1.000 80.2

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
Bombax buonopozense NC_054162.1 160876 View on NCBI ↗
Bombax ceiba NC_037494.1 158997 View on NCBI ↗