Markers + reference

Zephyranthes

5 species · Amaryllidaceae · Asparagales

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Species 5
Genome length 158–159 kb
Candidate markers 286
Primer pairs 100

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 9 remaining regions by MarkerSeek score (out of 286 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 942 0.0102 1.00 48.0 yes View details
atpA LSC 1524 0.0052 1.00 47.9 yes View details
trnT-UGU-trnL-UAA LSC 950 0.0142 1.00 65.4 yes View details
atpB-rbcL LSC 952 0.0090 0.98 48.3 yes View details
petA-psbJ LSC 1163 0.0184 1.00 53.4 yes View details
psbE-petL LSC 951 0.0102 1.00 54.2 yes View details
psaJ-rpl33 LSC 494 0.0145 1.00 56.2 yes View details
rpl22 LSC 387 0.0052 1.00 37.3 yes View details
ycf1 IRb 984 0.0036 1.00 36.0 no View details
rpl32-trnL-UAG SSC 813 0.0133 1.00 48.6 yes View details
ccsA-ndhD SSC 240 0.0358 1.00 59.0 yes View details
ndhD SSC 1497 0.0040 1.00 42.4 yes View details
ycf1 SSC 5379 0.0065 1.00 44.1 yes View details
rps19-psbA LSC 143 0.0615 0.97 78.7 no View details
rpl22-rps19 IRb 50 0.0600 1.00 75.1 yes View details
ycf1-ndhF SSC 12 0.1444 1.00 65.1 yes View details
trnK-UUU-rps16 LSC 583 0.0070 1.00 62.6 yes View details
atpB LSC 1497 0.0027 1.00 58.8 yes View details
rps15-ycf1 SSC 375 0.0149 1.00 58.8 yes View details
trnE-UUC-trnT-GGU LSC 721 0.0069 1.00 58.3 yes View details
psbA-trnK-UUU LSC 239 0.0151 1.00 58.2 yes View details
petN-psbM LSC 969 0.0091 1.00 57.5 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
psbA-trnK-UUU_p1 psbA-trnK-UUU AAAACACCGAACCATCCGAT GTTTGGGGAGGGGTCTTTTT 436 1.000 79.0
psbA-trnK-UUU_p2 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT GTTTGGGGAGGGGTCTTTTT 415 1.000 78.6
psbA-trnK-UUU_p3 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT GTTTGGGGAGGGGTCTTTTT 365 1.000 78.4
psbA-trnK-UUU_p4 psbA-trnK-UUU CACCGAACCATCCGATGTAA GTTTGGGGAGGGGTCTTTTT 432 1.000 78.1
psbA-trnK-UUU_p5 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC GTTTGGGGAGGGGTCTTTTT 416 1.000 78.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCTGGACGAATTCCTTGC GGTGCTCAACCTACAGGAAC 740–745 1.000 79.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCTGGACGAATTCCTTGCT GGTGCTCAACCTACAGGAAC 739–744 1.000 79.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 684–689 1.000 79.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 683–688 1.000 79.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 670–675 1.000 76.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CGAACGAATCACACTTTTACCA 1019–1281 1.000 60.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TCGAACGAATCACACTTTTACC 1020–1282 1.000 58.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA CGAACGAATCACACTTTTACCA 1067–1329 1.000 58.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT CGAACGAATCACACTTTTACCA 1005–1267 1.000 57.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC CGAACGAATCACACTTTTACCA 1000–1262 1.000 57.1
atpA_p1 atpA AGCTCGGTGGAAACCAAATT AGCCTTACAGGGAGCTCTAG 2376–2382 1.000 80.6
atpA_p2 atpA AGCCTTCCAAGCTAACGATG AGCCTTACAGGGAGCTCTAG 2080–2086 1.000 80.5
atpA_p3 atpA AGCTCGGTGGAAACCAAATT AAAATTGAGCGTGAGAGCCA 2774–2780 1.000 80.2
atpA_p4 atpA AGCTCGGTGGAAACCAAATT AAATTGAGCGTGAGAGCCAA 2773–2779 1.000 80.2
atpA_p5 atpA AGCTCGGTGGAAACCAAATT AATTGAGCGTGAGAGCCAAA 2772–2778 1.000 80.2
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA AAAACAGTCAGCCAAAATGA 1064–1079 1.000 50.7
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT AAAACAGTCAGCCAAAATGA 1012–1027 1.000 50.0
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA TGTAAAAACAGTCAGCCAAAATGA 1068–1083 1.000 49.9
petN-psbM_p4 petN-psbM AGTATGGGGAAGGAGTGGAC AAAACAGTCAGCCAAAATGA 1013–1028 1.000 49.9
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA AAAAACAGTCAGCCAAAATGA 1065–1080 1.000 49.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 860–869 1.000 80.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 822–831 1.000 79.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 801–810 1.000 79.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 857–866 1.000 78.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU ACTAGACGATGGGGGCATAT GAACCGATGACTTACGCCTT 790–799 1.000 78.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Zephyranthes bagnoldii PV849990.1 158144 View on NCBI ↗
Zephyranthes candida NC_057164.1 158209 View on NCBI ↗
Zephyranthes mesochloa NC_057554.1 158768 View on NCBI ↗
Zephyranthes phycelloides NC_059688.1 158107 View on NCBI ↗
Zephyranthes sarae PV890574.1 158192 View on NCBI ↗