Markers + reference

Washingtonia

2 species · Arecaceae · Arecales

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Species 2
Genome length 158–158 kb
Candidate markers 271
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 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
rpl16 LSC 1546 0.0007 0.99 59.7 yes View details
rps19 IRb 279 0.0000 1.00 24.1 yes View details
rpl2 IRb 1484 0.0000 1.00 38.5 no View details
rps15-ycf1 SSC 388 0.0077 1.00 58.8 yes View details
rpl2 IRa 1484 0.0000 1.00 38.5 yes View details
rps19 IRa 279 0.0000 1.00 24.1 no View details
rps19-trnH-GUG IRb 136 0.0221 1.00 65.2 yes View details
trnH-GUG-rps19 IRa 136 0.0221 1.00 65.2 yes View details
rps12-trnV-GAC IRb 1968 0.0000 0.99 59.0 yes View details
trnV-GAC-rps12 IRa 1968 0.0000 0.99 59.0 yes View details
rpl22-rps19 IRb 140 0.0000 0.99 52.3 yes View details
matK-trnK-UUU LSC 803 0.0000 1.00 40.0 yes View details
trnK-UUU-rps16 LSC 740 0.0000 1.00 40.0 yes View details
rps16 LSC 1145 0.0000 1.00 40.0 yes View details
rps16-trnQ-UUG LSC 1114 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TTGCTCCATTCCTTCAACGA GTGTGCTTGGGAGTTCTTGA 1151 1.000 75.3
psbA_p2 psbA TTGCTCCATTCCTTCAACGA ATACGTGTGCTTGGGAGTTC 1155 1.000 74.8
psbA_p3 psbA TGCTCCATTCCTTCAACGAT GTGTGCTTGGGAGTTCTTGA 1150 1.000 73.4
psbA_p4 psbA TGCTCCATTCCTTCAACGAT ATACGTGTGCTTGGGAGTTC 1154 1.000 72.9
psbA_p5 psbA TGCTCCATTCCTTCAACGATT GTGTGCTTGGGAGTTCTTGA 1150 1.000 71.2
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA AACGGTAGAGTACTCGGCTT 906 1.000 61.8
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA ACGGTAGAGTACTCGGCTTT 905 1.000 61.8
matK-trnK-UUU_p3 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA GTCGTGCAGTGCAATTCAAT 996 1.000 60.4
matK-trnK-UUU_p4 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA GGGTTGCTAACTCAACGGTA 919 1.000 59.4
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTTAAAGAGAAGCGGA TTCGGGTTGCTAACTCAACG 922 1.000 59.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GCTCAACCTACGGGAACTG 911 1.000 70.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GCTCAACCTACGGGAACTG 910 1.000 70.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCTGGACGAATCTGTTGC GTGCTCAACCTACGGGAAC 913 1.000 70.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCTGGACGAATCTGTTGCT GTGCTCAACCTACGGGAAC 912 1.000 70.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCTACGGGAACTG 854 1.000 69.5
rps16_p1 rps16 GCAAGAAAAAGGCAAATTGTGT CCGGTTGAGCCAATGACTAT 1320 1.000 54.3
rps16_p2 rps16 GCAAGAAAAAGGCAAATTGTGT TATACACACACCGGTTGAGC 1330 1.000 54.0
rps16_p3 rps16 ACAGCAAGAAAAAGGCAAATTG CCGGTTGAGCCAATGACTAT 1323 1.000 52.2
rps16_p4 rps16 AGCAAGAAAAAGGCAAATTGTG CCGGTTGAGCCAATGACTAT 1321 1.000 52.2
rps16_p5 rps16 CAGCAAGAAAAAGGCAAATTGT CCGGTTGAGCCAATGACTAT 1322 1.000 52.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1205 1.000 79.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1203 1.000 79.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1211 1.000 79.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1212 1.000 79.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAAATTCGAAATGGGGCGTG 1264 1.000 79.0
trnG-UCC_p1 trnG-UCC TGATTGCGCCTCACTCTTTT TGCATATCCAAATTGATGATGCA 877 1.000 48.8
trnG-UCC_p2 trnG-UCC TTGATTGCGCCTCACTCTTT TGCATATCCAAATTGATGATGCA 878 1.000 48.8
trnG-UCC_p3 trnG-UCC GATTGCGCCTCACTCTTTTG TGCATATCCAAATTGATGATGCA 876 1.000 47.6
trnG-UCC_p4 trnG-UCC ATCTTGATTGCGCCTCACTC TGCATATCCAAATTGATGATGCA 881 1.000 46.9
trnG-UCC_p5 trnG-UCC ATTGCGCCTCACTCTTTTGT TGCATATCCAAATTGATGATGCA 875 1.000 46.5

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
Washingtonia filifera NC_079763.1 157924 View on NCBI ↗
Washingtonia robusta NC_029974.1 157866 View on NCBI ↗