Markers + reference

Callisia

3 species · Commelinaceae · Commelinales

Back to catalogue

Species 3
Genome length 162–164 kb
Candidate markers 275
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 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 2403 0.0886 0.86 78.6 yes View details
rpoB-trnC-GCA LSC 1602 0.0616 0.99 83.1 yes View details
trnE-UUC-trnT-GGU LSC 1195 0.1132 0.88 85.9 yes View details
ndhC-trnV-UAC LSC 1861 0.0765 0.50 66.2 yes View details
accD-psaI LSC 1107 0.1523 0.83 76.6 yes View details
clpP1 LSC 2758 0.0514 0.94 75.3 yes View details
rps3-rpl22 LSC 570 0.1761 0.96 81.1 yes View details
ycf1 SSC 5466 0.0632 0.99 77.3 yes View details
rrn4.5-rrn5 IRb 224 0.0685 1.00 86.5 yes View details
rrn5-rrn4.5 IRa 224 0.0685 1.00 86.5 yes View details
rps4-trnT-UGU LSC 563 0.0740 1.00 85.9 yes View details
petA-psbJ LSC 632 0.0810 1.00 85.5 yes View details
rpl32-trnL-UAG SSC 858 0.0795 0.99 85.4 yes View details
petN-psbM LSC 646 0.0872 1.00 84.8 yes View details
trnM-CAU-atpE LSC 337 0.1240 0.89 84.8 yes View details
trnF-GAA-ndhJ LSC 447 0.0544 1.00 84.5 yes View details
trnS-GCU-trnG-UCC LSC 643 0.0684 0.98 84.3 yes View details
psbM-trnD-GUC LSC 1049 0.0479 0.99 83.9 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1550–2468 1.000 85.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTTAAACAGTGATGGGGCGT 1610–2528 1.000 83.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTAAACAGTGATGGGGCGTG 1609–2527 1.000 81.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 1554–2472 1.000 80.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TAAGGCAACGGGTTTTGGTC 1580–2498 1.000 80.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCGCACTTTTACCACT 662–750 1.000 77.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCGCACTTTTACCAC 662–750 1.000 77.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC ACGAATCGCACTTTTACCACT 657–745 1.000 76.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC ACGAATCGCACTTTTACCAC 657–745 1.000 76.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AACGAATCGCACTTTTACCAC 663–751 1.000 75.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGGATCCCCACTTACACAAG TTACCACTTGGCTATGTCGC 2337–2440 1.000 88.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGGATCCCCACTTACACAAG TGTTTGTTGATCAGGCGACA 2399–2502 1.000 88.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TGAAATTCTTCCCCCAAGCC TACCCCTAGAGTCCACTCCT 2314–2792 0.667 74.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGGATCCCCACTTACACAAG TACCCCTAGAGTCCACTCCT 2918 0.333 53.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGGATCCCCACTTACACAAG AAAAAGCTTGGCAAAACGCT 2995 0.333 53.0
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TCTACGTAAAAACAGTCAGTCA 608–1144 1.000 51.1
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TCTACGTAAAAACAGTCAGTCA 607–1143 1.000 51.1
petN-psbM_p3 petN-psbM TATGGGGAAGGAGTGGACTC TCTACGTAAAAACAGTCAGTCA 606–1142 1.000 51.1
petN-psbM_p4 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTTATTT 655–1191 1.000 50.7
petN-psbM_p5 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTTATTT 654–1190 1.000 50.7
psbM-trnD-GUC_p1 psbM-trnD-GUC TGACTGACTGTTTTTACGTAGA TTCAATTGGTCAGAGCACCG 1145–1212 1.000 48.6
psbM-trnD-GUC_p2 psbM-trnD-GUC TTGACTGACTGTTTTTACGT TTCAATTGGTCAGAGCACCG 1146–1213 1.000 48.6
psbM-trnD-GUC_p3 psbM-trnD-GUC TGACTGACTGTTTTTACGTAGATG TTCAATTGGTCAGAGCACCG 1145–1212 1.000 48.6
psbM-trnD-GUC_p4 psbM-trnD-GUC TTTGACTGACTGTTTTTACGT TTCAATTGGTCAGAGCACCG 1147–1214 1.000 48.6
psbM-trnD-GUC_p5 psbM-trnD-GUC TCATTTTGACTGACTGTTTTTACGT TTCAATTGGTCAGAGCACCG 1151–1218 1.000 48.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CTTCTTTTCGTGGTACCCCC TACCGCTGAGTTAAAAGGGC 1115–1301 1.000 89.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TACCGCTGAGTTAAAAGGGC 1077–1263 1.000 89.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA TACCGCTGAGTTAAAAGGGC 1056–1242 1.000 88.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CTTCTTTTCGTGGTACCCCC ACGACTTACGCCTTACCATG 1144–1330 1.000 88.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG ACGACTTACGCCTTACCATG 1106–1292 1.000 87.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Callisia fragrans PQ834833.1 163887 View on NCBI ↗
Callisia insignis NC_071224.1 162850 View on NCBI ↗
Callisia repens MW617982.1 161854 View on NCBI ↗