Markers + reference

Cyrtanthus

2 species · Amaryllidaceae · Asparagales

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Species 2
Genome length 159–160 kb
Candidate markers 271
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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 1289 0.0234 0.96 64.2 yes View details
petN-psbM LSC 1042 0.0158 0.97 55.4 yes View details
trnT-UGU-trnL-UAA LSC 1064 0.0210 0.94 67.4 yes View details
rbcL-accD LSC 780 0.0144 0.98 66.0 yes View details
rps12-trnV-GAC IRb 1819 0.0066 1.00 55.3 yes View details
rrn4.5-rrn5 IRb 217 0.0415 1.00 74.5 yes View details
rpl32-trnL-UAG SSC 821 0.0159 0.99 68.5 yes View details
rps15-ycf1 SSC 365 0.0220 1.00 55.7 yes View details
ycf1 SSC 5469 0.0073 1.00 48.9 yes View details
trnV-GAC-rps12 IRa 1819 0.0066 1.00 55.3 yes View details
petG-trnW-CCA LSC 115 0.0566 0.92 85.6 yes View details
rrn5-rrn4.5 IRa 217 0.0415 1.00 74.5 yes View details
psbA-trnK-UUU LSC 244 0.0287 1.00 69.0 yes View details
ndhF-rpl32 SSC 949 0.0107 0.99 66.2 yes View details
rpl33-rps18 LSC 189 0.0370 1.00 65.6 yes View details
petD-rpoA LSC 152 0.0199 0.99 64.5 yes View details
trnR-ACG-trnN-GUU IRb 557 0.0072 1.00 62.3 yes View details
trnN-GUU-trnR-ACG IRa 557 0.0072 1.00 62.3 yes View details
ndhA SSC 2225 0.0076 1.00 61.6 yes View details
trnK-UUU-rps16 LSC 615 0.0033 0.97 61.5 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 441–457 1.000 78.9
psbA-trnK-UUU_p2 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT GTTTGGGGAGGGGTCTTTTT 420–436 1.000 78.6
psbA-trnK-UUU_p3 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT GTTTGGGGAGGGGTCTTTTT 370–386 1.000 78.3
psbA-trnK-UUU_p4 psbA-trnK-UUU CACCGAACCATCCGATGTAA GTTTGGGGAGGGGTCTTTTT 437–453 1.000 78.1
psbA-trnK-UUU_p5 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC GTTTGGGGAGGGGTCTTTTT 421–437 1.000 78.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCTGGACGAATTCCTTGC GGTGCTCAACCTACAGGAAC 770–777 1.000 79.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCTGGACGAATTCCTTGCT GGTGCTCAACCTACAGGAAC 769–776 1.000 79.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 714–721 1.000 79.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 713–720 1.000 79.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 700–707 1.000 76.8
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA CGAACGAATCACACTTTTACCA 1366–1622 1.000 62.3
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA TCGAACGAATCACACTTTTACC 1367–1623 1.000 60.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTTTAGTCCACTCAGCCAT CGAACGAATCACACTTTTACCA 1352–1608 1.000 59.3
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGTCCACTCAGCCATCTCTC CGAACGAATCACACTTTTACCA 1347–1603 1.000 58.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GCTTTAGTCCACTCAGCCAT TCGAACGAATCACACTTTTACC 1353–1609 1.000 57.3
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA ACCCAGAGAATACCGGTCAT 1577–1598 1.000 81.0
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA ATGACCCAGAGAATACCGGT 1580–1601 1.000 81.0
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA AAGCAACGCCCCTTTCTTAT 1677–1698 1.000 80.5
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA AGCAACGCCCCTTTCTTATT 1676–1697 1.000 80.5
petN-psbM_p5 petN-psbM GTATGGGGAAGGAGTGGACT ACCCAGAGAATACCGGTCAT 1525–1546 1.000 80.1
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1105–1114 1.000 84.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1113–1122 1.000 83.9
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1137–1146 1.000 83.5
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1145–1154 1.000 83.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 1128–1137 1.000 82.6
rbcL-accD_p1 rbcL-accD GCAAATGGAGCCCTGAACTA CTTCCACCGGTATGTCCAAG 971–985 1.000 80.8
rbcL-accD_p2 rbcL-accD GCAAATGGAGCCCTGAACTA ACATCGAATTGAACCACCGT 889–903 1.000 79.8
rbcL-accD_p3 rbcL-accD CGCTGCTTGTGAAGTATGGA CTTCCACCGGTATGTCCAAG 949–963 1.000 79.7
rbcL-accD_p4 rbcL-accD CGCTGCTTGTGAAGTATGGA ACATCGAATTGAACCACCGT 867–881 1.000 78.7
rbcL-accD_p5 rbcL-accD AAATGGAGCCCTGAACTAGC CTTCCACCGGTATGTCCAAG 969–983 1.000 78.4

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
Cyrtanthus falcatus PP853200.1 159210 View on NCBI ↗
Cyrtanthus mackenii NC_057577.1 159998 View on NCBI ↗