Markers + reference

Thespesia

2 species · Malvaceae · Malvales

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Species 2
Genome length 160–161 kb
Candidate markers 266
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 346 0.0557 0.99 74.8 yes View details
trnK-UUU-rps16 LSC 820 0.0318 1.00 63.9 yes View details
rps16-trnQ-UUG LSC 592 0.0320 0.95 71.2 yes View details
trnR-UCU-atpA LSC 221 0.0814 1.00 78.6 yes View details
rpoB-trnC-GCA LSC 1227 0.0255 0.99 64.7 yes View details
psbZ-trnG-GCC LSC 764 0.0413 0.95 87.1 yes View details
trnT-UGU-trnL-UAA LSC 1318 0.0491 0.96 82.5 yes View details
ndhC-trnV-UAC LSC 1143 0.0239 0.99 66.9 yes View details
accD-psaI LSC 747 0.0321 1.00 72.1 yes View details
petA-psbJ LSC 1107 0.0282 0.99 63.4 yes View details
trnL-UAG-rpl32 SSC 1125 0.0286 1.00 66.1 yes View details
rpl32-ndhF SSC 1240 0.0376 0.99 68.6 yes View details
ndhF-trnN-GUU IRa 563 0.0400 0.89 71.0 yes View details
rps19-rpl2 IRb 77 0.1169 1.00 87.5 yes View details
petG-trnW-CCA LSC 192 0.0632 0.91 78.9 yes View details
rpl2-trnH IRa 81 0.1358 1.00 78.3 no View details
psbH-petB LSC 128 0.0391 1.00 75.0 yes View details
rpl22-rps19 LSC 86 0.0779 0.90 72.6 yes View details
psaJ-rpl33 LSC 508 0.0218 0.99 70.1 yes View details
rpl33-rps18 LSC 351 0.0215 0.93 69.9 yes View details
rps4-trnT-UGU LSC 540 0.0321 0.98 69.4 yes View details
trnI-GAU IRb 42 0.0238 1.00 66.2 yes View details
trnI-GAU IRa 42 0.0238 1.00 66.2 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 416–439 1.000 82.9
trnH-psbA_p2 trnH-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 430–453 1.000 82.7
trnH-psbA_p3 trnH-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 429–452 1.000 82.7
trnH-psbA_p4 trnH-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 431–454 1.000 82.7
trnH-psbA_p5 trnH-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 465–488 1.000 80.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGAGCTCAACCCACAG 1043–1086 1.000 82.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGACAGGCGGATTCATCAAC AAAAGGAGCTCAACCCACAG 1559–1609 1.000 81.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1182–1225 1.000 81.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 1183–1226 1.000 81.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGACAGGCGGATTCATCAAC CCCAATGAGCCGTTTATCGA 1698–1748 1.000 81.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AGTGGTGGGTTTTGACATCC GAGGTTCGAATCCTTCCGTC 683–704 1.000 84.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 662–683 1.000 84.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 660–681 1.000 84.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 644–665 1.000 84.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTGGTGGGTTTTGACATCC CTATGCGGAGGTTCGAATCC 690–711 1.000 83.6
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCACTGAGGAAGCAGAAACG 323 1.000 69.7
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TCACTGAGGAAGCAGAAACG 358 1.000 66.4
trnR-UCU-atpA_p3 trnR-UCU-atpA CGTAATGAAAAGCGTCCATTGT TCACTGAGGAAGCAGAAACG 384 1.000 65.9
trnR-UCU-atpA_p4 trnR-UCU-atpA TCGTAATGAAAAGCGTCCATTG TCACTGAGGAAGCAGAAACG 385 1.000 63.8
trnR-UCU-atpA_p5 trnR-UCU-atpA ATGAAAAGCGTCCATTGTCT TCACTGAGGAAGCAGAAACG 380 1.000 63.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTTCTGTTAAGCCCCGATCC CCGGATTTGAACTGGGGAAT 1390–1393 1.000 81.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTTCCCCATTTTCATCCCCG CCGGATTTGAACTGGGGAAT 1315–1318 1.000 80.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGATCCATGAACCCACAAA CCGGATTTGAACTGGGGAAT 1377–1380 1.000 80.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCATTTTCATCCCCGAGCAT CCGGATTTGAACTGGGGAAT 1310–1313 1.000 79.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTAAGCCCCGATCCATGAAC CCGGATTTGAACTGGGGAAT 1384–1387 1.000 78.6
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 921–939 1.000 82.9
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTT CGTCTTCTCCTTGGCAAAGA 919–937 1.000 82.9
psbZ-trnG-GCC_p3 psbZ-trnG-GCC CTCCTGATGGTTGGTTGAGT CGTCTTCTCCTTGGCAAAGA 915–933 1.000 77.6
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TGCTTCTCCTGATGGTTGGT CGTCTTCTCCTTGGCAAAGA 920–938 1.000 77.0
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TCTCCTGATGGTTGGTTGAG CGTCTTCTCCTTGGCAAAGA 916–934 1.000 75.3

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
Thespesia howii NC_070216.1 160435 View on NCBI ↗
Thespesia lampas NC_070217.1 160947 View on NCBI ↗