Markers + reference

Abelmoschus

4 species · Malvaceae · Malvales

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Species 4
Genome length 163–163 kb
Candidate markers 270
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 890 0.0064 1.00 64.0 yes View details
rpoB-trnC-GCA LSC 1295 0.0072 0.98 66.3 yes View details
ndhC-trnV-UAC LSC 1230 0.0115 0.97 71.4 yes View details
atpB-rbcL LSC 1169 0.0119 0.98 68.3 yes View details
clpP LSC 2215 0.0063 1.00 53.9 yes View details
trnN-GUU-ndhF IRb 1280 0.0008 1.00 30.3 yes View details
ndhF-rpl32 SSC 969 0.0069 0.97 55.2 yes View details
rps3-psbA LSC 879 0.0118 0.98 68.7 no View details
atpF-atpH LSC 614 0.0035 1.00 64.8 yes View details
rps4-trnT-UGU LSC 604 0.0037 0.97 63.6 yes View details
atpH-atpI LSC 1205 0.0030 0.97 63.5 yes View details
psaJ-rpl33 LSC 484 0.0052 0.98 61.8 yes View details
petA-psbJ LSC 1184 0.0009 0.98 61.5 yes View details
rpl32-trnL-UAG SSC 1091 0.0035 1.00 61.4 yes View details
psaA-ycf3 LSC 955 0.0026 0.99 61.2 yes View details
petN-psbM LSC 1184 0.0017 1.00 61.1 yes View details
ndhA SSC 2211 0.0008 1.00 57.8 yes View details
trnT-GGU-psbD LSC 1522 0.0028 0.99 56.8 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 AGTCGCACTTAAAAGCCGAG AAAAGGAGCTCAACCCACAG 1029–1077 1.000 76.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA AAAAGGAGCTCAACCCACAG 1030–1078 1.000 75.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA AAAAGGAGCTCAACCCACAG 1027–1075 1.000 75.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC AAAAGGAGCTCAACCCACAG 1026–1074 1.000 75.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 GCTAGTCGCACTTAAAAGCC AAAAGGAGCTCAACCCACAG 1032–1080 1.000 74.8
trnG-UCC_p1 trnG-UCC ATTCCCCTGTTCGACAAAGG GCATCGTTGAATTGAATTAATAA 975–983 1.000 42.5
trnG-UCC_p2 trnG-UCC CCAATTCCCCTGTTCGACAA GCATCGTTGAATTGAATTAATAA 978–986 1.000 42.4
trnG-UCC_p3 trnG-UCC CCAATTCCCCTGTTCGACAA GCATCGTTGAATTGAATTAATAAA 978–986 1.000 42.4
trnG-UCC_p4 trnG-UCC GCGGCAAGGCTCTAATTTTC GCATCGTTGAATTGAATTAATAA 1042–1050 1.000 42.3
trnG-UCC_p5 trnG-UCC GCGGCAAGGCTCTAATTTTC GCATCGTTGAATTGAATTAATAAA 1042–1050 1.000 42.3
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA TGGTTGTAGCATTGGCACTT 698–706 1.000 82.3
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAACGAA TTGGTTGTAGCATTGGCACT 699–707 1.000 82.3
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA GTTGGTTGTAGCATTGGCAC 700–708 1.000 81.8
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA TGGGTTGGTTGTAGCATTGG 703–711 1.000 79.3
atpF-atpH_p5 atpF-atpH AGTGACCCAAGGAAACGAAA TGGTTGTAGCATTGGCACTT 697–705 1.000 76.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1228–1263 1.000 82.3
atpH-atpI_p2 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 1262–1297 1.000 82.2
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT GCGAATCCATGGAAGGTCAT 1284–1319 1.000 81.5
atpH-atpI_p4 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTGCAACTTTAGCTGCGG 1291–1326 1.000 81.3
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1257–1292 1.000 81.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCATTTTCATCTCCGAGCA CCGGATTTGAACTGGGGAAT 1354–1379 1.000 81.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTTCTGTTAAGCCCCGATCC CCGGATTTGAACTGGGGAAT 1433–1458 1.000 81.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGATCCATGAACCCACAAA CCGGATTTGAACTGGGGAAT 1420–1445 1.000 80.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTAAGCCCCGATCCATGAA CCGGATTTGAACTGGGGAAT 1428–1453 1.000 79.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTAAGCCCCGATCCATGAAC CCGGATTTGAACTGGGGAAT 1427–1452 1.000 79.1
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA ATTGCTACAGCGCTGTTCAT 1335–1341 1.000 78.9
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA TATTGCTACAGCGCTGTTCA 1336–1342 1.000 77.9
petN-psbM_p3 petN-psbM AGTAAGTCTTGCTTGGGCTG ATTGCTACAGCGCTGTTCAT 1341–1347 1.000 77.4
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TTGCTACAGCGCTGTTCATT 1334–1340 1.000 77.2
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TATTGCTACAGCGCTGTTCA 1342–1348 1.000 76.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Abelmoschus esculentus NC_035234.1 163121 View on NCBI ↗
Abelmoschus manihot NC_053353.1 163428 View on NCBI ↗
Abelmoschus moschatus NC_053355.1 163430 View on NCBI ↗
Abelmoschus sagittifolius NC_053354.1 163453 View on NCBI ↗