Markers + reference

Commelina

3 species · Commelinaceae · Commelinales

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Species 3
Genome length 160–161 kb
Candidate markers 274
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 544 0.0233 1.00 62.3 yes View details
trnS-GCU-trnG-UCC LSC 1530 0.0196 0.98 67.5 yes View details
trnE-UUC-trnT-GGU LSC 628 0.0311 0.96 71.8 yes View details
accD-psaI LSC 561 0.0354 0.99 71.5 yes View details
clpP1 LSC 2817 0.0151 0.99 55.2 yes View details
rpl16 LSC 1523 0.0151 1.00 56.2 yes View details
ycf1 IRb 1077 0.0037 1.00 46.4 no View details
rpl32-trnL-UAG SSC 755 0.0339 0.99 71.9 yes View details
psaC-ndhE SSC 555 0.0337 1.00 68.9 yes View details
ycf1 SSC 5358 0.0134 1.00 51.2 yes View details
rpl14-rpl16 LSC 122 0.0410 1.00 68.4 yes View details
atpF-atpH LSC 508 0.0132 0.99 66.0 yes View details
rpl33-rps18 LSC 153 0.0218 1.00 65.4 yes View details
ndhC-trnV-UAC LSC 1543 0.0179 0.97 64.5 yes View details
trnC-GCA-petN LSC 993 0.0108 1.00 64.0 yes View details
pafI-trnS-GGA LSC 591 0.0141 1.00 63.8 yes View details
trnT-UGU-trnL-UAA LSC 1195 0.0155 0.99 63.7 yes View details
rpl20-rps12 LSC 756 0.0071 1.00 63.4 yes View details
ndhK LSC 729 0.0046 1.00 61.7 yes View details
rps8-rpl14 LSC 195 0.0246 0.97 61.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGTAAATGAAGTGAAGTTAAAAA TCACATACTTTAGTTATCAGTTATCG 2988–2999 0.667 28.3
trnK-UUU_p2 trnK-UUU TTGTAAATGAAGTGAAGTTAAAA TCACATACTTTAGTTATCAGTTATCG 2989–3000 0.667 28.3
trnK-UUU_p3 trnK-UUU TTGTAAATGAAGTGAAGTTAAAAA TCACATACTTTAGTTATCAGTTATCG 2989–3000 0.667 28.3
trnK-UUU_p4 trnK-UUU CTTTTGTAAATGAAGTGAAGT CATACTTTAGTTATCAGTTATCG 2989–3000 0.667 28.3
trnK-UUU_p5 trnK-UUU CTTTTGTAAATGAAGTGAAGTT CATACTTTAGTTATCAGTTATCG 2989–3000 0.667 28.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGTGGTCTTATAGACTCCGC AGAAGGCAGAAATTTTTAAAGA 700–710 1.000 42.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 TGGTCTTATAGACTCCGCCA AGAAGGCAGAAATTTTTAAAGA 698–708 1.000 42.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGTGGTCTTATAGACTCCGC AAGAAGGCAGAAATTTTTAAAGA 701–711 1.000 42.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGTGGTCTTATAGACTCCGC AGAAGGCAGAAATTTTTAAAGAA 700–710 1.000 42.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 TGGTCTTATAGACTCCGCCA AGAAGGCAGAAATTTTTAAAGAA 698–708 1.000 42.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1604–1808 1.000 56.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 1607–1811 1.000 55.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 1606–1810 1.000 55.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTAAGCGGAGAGAAAGGGA ACGAATCACACTTTTACCACT 1658–1862 1.000 54.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 1605–1809 1.000 54.6
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG ACAATTTACGGGTTGGTCGT 634–641 1.000 79.2
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG AATTTACGGGTTGGTCGTGG 632–639 1.000 77.5
atpF-atpH_p3 atpF-atpH CAGTGGCCCAAGGAAATGAA ACAATTTACGGGTTGGTCGT 606–613 1.000 77.3
atpF-atpH_p4 atpF-atpH AGTGGCCCAAGGAAATGAAA ACAATTTACGGGTTGGTCGT 605–612 1.000 77.1
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CAATTTACGGGTTGGTCGTG 633–640 1.000 76.5
trnC-GCA-petN_p1 trnC-GCA-petN GACATAGCCAAGCGGTAAGG TACCCCTAGAGTCCACTCCT 1153–1156 1.000 78.7
trnC-GCA-petN_p2 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC TACCCCTAGAGTCCACTCCT 1107–1110 1.000 78.3
trnC-GCA-petN_p3 trnC-GCA-petN GACATAGCCAAGCGGTAAGG AGTCCACTCCTTCCCCATAC 1144–1147 1.000 77.8
trnC-GCA-petN_p4 trnC-GCA-petN GACATAGCCAAGCGGTAAGG GTCCACTCCTTCCCCATACT 1143–1146 1.000 77.8
trnC-GCA-petN_p5 trnC-GCA-petN GACATAGCCAAGCGGTAAGG AGCCCAAGCGAGACTTACTA 1085–1088 1.000 77.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA ACGACTTACGCCTTACCATG 680–727 1.000 83.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CTTCTTTTCGTGGTACCCCC ACGACTTACGCCTTACCATG 717–764 1.000 82.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TCCGCTTCTTTTCGTGGTAC ACGACTTACGCCTTACCATG 721–768 1.000 82.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA ACGACTTACGCCTTACCATG 658–705 1.000 82.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TCCACGATCCGCTTCTTTTC ACGACTTACGCCTTACCATG 728–775 1.000 82.0

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
Commelina calandrinioides BK062833.1 160483 View on NCBI ↗
Commelina caroliniana NC_085602.1 160857 View on NCBI ↗
Commelina communis MW617984.1 160116 View on NCBI ↗