Markers + reference

Canna

2 species · Cannaceae · Zingiberales

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Species 2
Genome length 164–164 kb
Candidate markers 267
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 40.0 yes View details
trnS-GCU-trnS-CGA LSC 1590 0.0113 1.00 65.3 yes View details
atpH-atpI LSC 1505 0.0007 1.00 59.1 yes View details
rpl22-rps19 LSC 625 0.0032 1.00 60.6 yes View details
trnH-GUG-psbA LSC 565 0.0000 0.82 59.2 no View details
psaC-ndhE SSC 1094 0.0000 0.95 63.5 yes View details
matK-trnK-UUU LSC 929 0.0000 1.00 40.0 yes View details
trnK-UUU-rps16 LSC 801 0.0000 1.00 40.0 yes View details
rps16 LSC 1098 0.0000 1.00 40.0 yes View details
rps16-trnQ-UUG LSC 1497 0.0000 1.00 40.0 yes View details
atpA LSC 1524 0.0000 1.00 40.0 yes View details
atpF LSC 1342 0.0000 1.00 40.0 yes View details
atpI LSC 744 0.0000 1.00 40.0 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA ACAAGATAGGGGGTATTGCT AATACGTGTGCTTGGGAGTC 1185 1.000 59.8
psbA_p2 psbA AACAAGATAGGGGGTATTGCT AATACGTGTGCTTGGGAGTC 1186 1.000 58.3
psbA_p3 psbA ACAAGATAGGGGGTATTGCT GTGTGCTTGGGAGTCCTTAA 1180 1.000 56.0
psbA_p4 psbA ACAAGATAGGGGGTATTGCTAC AATACGTGTGCTTGGGAGTC 1185 1.000 55.4
psbA_p5 psbA AACAAGATAGGGGGTATTGCT GTGTGCTTGGGAGTCCTTAA 1181 1.000 54.5
matK-trnK-UUU_p1 matK-trnK-UUU TGTTGTTGCCGAGATCCATT GGGTCGTGCAGTGTAATTCA 1093 1.000 76.8
matK-trnK-UUU_p2 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA GGGTCGTGCAGTGTAATTCA 1099 1.000 75.8
matK-trnK-UUU_p3 matK-trnK-UUU AAGTGTTGTTGCCGAGATCC GGGTCGTGCAGTGTAATTCA 1096 1.000 74.6
matK-trnK-UUU_p4 matK-trnK-UUU GTGTTGTTGCCGAGATCCAT GGGTCGTGCAGTGTAATTCA 1094 1.000 74.1
matK-trnK-UUU_p5 matK-trnK-UUU TGTTGTTGCCGAGATCCATT TAATGGGGTCGTGCAGTGTA 1098 1.000 72.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 TGGACGAATTTGGTGCTTCA TCAACCAACAGGAACCGTTT 958 1.000 78.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 TGGACGAATTTGGTGCTTCA CTCAACCAACAGGAACCGTT 959 1.000 77.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTGGACGAATTTGGTGCTT TCAACCAACAGGAACCGTTT 960 1.000 76.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTGGACGAATTTGGTGCTT CTCAACCAACAGGAACCGTT 961 1.000 75.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCTGGACGAATTTGGTGCT TCAACCAACAGGAACCGTTT 961 1.000 75.1
rps16_p1 rps16 TGAATTACACTGCACGACCC TACTGCCCGTTGATCCAATG 1945 1.000 78.1
rps16_p2 rps16 ACTGCACGACCCCATTAAAA TACTGCCCGTTGATCCAATG 1937 1.000 77.5
rps16_p3 rps16 TGAATTACACTGCACGACCC TCGTCCCGAACAATCTGTTG 2125 1.000 76.8
rps16_p4 rps16 ACTGCACGACCCCATTAAAA TCGTCCCGAACAATCTGTTG 2117 1.000 76.1
rps16_p5 rps16 TGAATTACACTGCACGACCC TGATCGTCCCGAACAATCTG 2128 1.000 76.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAACAGAAAAATGGGGCGTG 1629 1.000 78.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTGCCGAACAGAAAAATGGG 1634 1.000 78.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1570 1.000 78.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAACAGAAAAATGGGGCGTG 1640 1.000 77.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTGCCGAACAGAAAAATGGG 1645 1.000 77.8
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA TCAAGTAATCAGAGCGAGCG AACTGAGAGACCCCTTAACT 1764–1771 1.000 56.0
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA CGGAGAGAGAGGGATTCGAA AACTGAGAGACCCCTTAACT 1746–1753 1.000 55.0
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA AGCAATCCGACGCTTTAGTC AACTGAGAGACCCCTTAACT 1695–1702 1.000 54.7
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA TCAAGTAATCAGAGCGAGCG AAACTGAGAGACCCCTTAACT 1765–1772 1.000 54.6
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CTTTAGTCCGCTCAGCCATC AACTGAGAGACCCCTTAACT 1683–1690 1.000 54.2

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
Canna indica NC_083981.1 164479 View on NCBI ↗
Canna x generalis NC_083982.1 164427 View on NCBI ↗