Markers + reference

Crinum

3 species · Amaryllidaceae · Asparagales

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Species 3
Genome length 159–159 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

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 614 0.0055 1.00 54.5 yes View details
rps16-trnQ-UUG LSC 1498 0.0040 1.00 63.2 yes View details
trnS-GCU-trnG-GCC LSC 1155 0.0032 1.00 62.0 yes View details
ndhC-trnV-UAC LSC 1731 0.0035 1.00 61.9 yes View details
rbcL LSC 1440 0.0032 1.00 48.3 yes View details
petA-psbJ LSC 1145 0.0093 1.00 60.2 yes View details
clpP LSC 2067 0.0027 1.00 59.4 yes View details
rpl32-trnL-UAG SSC 924 0.0084 0.90 66.0 yes View details
ndhD SSC 1502 0.0009 1.00 34.3 yes View details
rps15 SSC 270 0.0000 1.00 19.7 yes View details
rps15-ycf1 SSC 383 0.0122 1.00 62.5 yes View details
atpF LSC 1433 0.0009 1.00 63.6 yes View details
psaC-ndhE SSC 499 0.0060 1.00 62.9 yes View details
psbE-petL LSC 1007 0.0013 1.00 62.3 yes View details
trnF-GAA-ndhJ LSC 715 0.0009 1.00 62.2 yes View details
trnT-UGU-trnL-UAA LSC 802 0.0000 1.00 60.7 yes View details
ycf4-cemA LSC 900 0.0015 1.00 60.6 yes View details
petA LSC 963 0.0028 1.00 60.5 yes View details
ccsA-ndhD SSC 258 0.0092 0.98 60.4 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-rps16_p1 trnK-UUU-rps16 AGTCTGGACGAATTCCTTGC AGGTGCTCAATCTACAGGAAC 773–777 1.000 67.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCTGGACGAATTCCTTGC GGTGCTCAATCTACAGGAACT 772–776 1.000 67.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 GTCTGGACGAATTCCTTGCT AGGTGCTCAATCTACAGGAAC 772–776 1.000 67.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCTGGACGAATTCCTTGCT GGTGCTCAATCTACAGGAACT 771–775 1.000 67.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAATCTACAGGAACT 715–719 1.000 66.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCGAATCATGTCC GAGGTTCGAATCCTTCCGTC 1566–1594 1.000 81.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATCCACAGCGAATCATGTCC CTCGGAGGTTCGAATCCTTC 1570–1598 1.000 80.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCGAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1564–1592 1.000 79.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1538–1566 1.000 79.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCGAATCATGTCCTT CTCGGAGGTTCGAATCCTTC 1568–1596 1.000 78.7
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGTCGCTTTAGTCCA CGGACGAATCACACTTTTACC 1216–1239 1.000 67.4
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGTCGCTTTAGTCCAC CGGACGAATCACACTTTTACC 1215–1238 1.000 67.4
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC AGCAATCCGTCGCTTTAGTC CGGACGAATCACACTTTTACC 1218–1241 1.000 64.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CGTCGCTTTAGTCCACTCAG CGGACGAATCACACTTTTACC 1211–1234 1.000 64.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GCTTTAGTCCACTCAGCCAT CGGACGAATCACACTTTTACC 1207–1230 1.000 64.2
trnG-GCC_p1 trnG-GCC CGGAGTGTCAACGCTAGAAT CGCATTCTCCCCCTTTCTTT 989–997 1.000 77.8
trnG-GCC_p2 trnG-GCC CGGAGTGTCAACGCTAGAAT CTTTCGCATTCTCCCCCTTT 993–1001 1.000 77.8
trnG-GCC_p3 trnG-GCC CGGAGTGTCAACGCTAGAAT TTTCGCATTCTCCCCCTTTC 992–1000 1.000 77.7
trnG-GCC_p4 trnG-GCC ACGGAGTGTCAACGCTAGAA CGCATTCTCCCCCTTTCTTT 990–998 1.000 71.7
trnG-GCC_p5 trnG-GCC ACGGAGTGTCAACGCTAGAA CTTTCGCATTCTCCCCCTTT 994–1002 1.000 71.7
atpF_p1 atpF ACTAATTTCGTCAGCTCGAA GGCGAGCCAAGTGATACAAA 1570–1605 1.000 53.3
atpF_p2 atpF ACTAATTTCGTCAGCTCGAA ATCGATCAAAAAGGGCGAGC 1583–1618 1.000 49.8
atpF_p3 atpF ACTAATTTCGTCAGCTCGAA ATCAAAAAGGGCGAGCCAA 1579–1614 1.000 49.3
atpF_p4 atpF ACTAATTTCGTCAGCTCGAA ATCAAAAAGGGCGAGCCAAG 1579–1614 1.000 48.8
atpF_p5 atpF ACTAATTTCGTCAGCTCGAA GATCAAAAAGGGCGAGCCAA 1580–1615 1.000 48.8
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA AAAGCCAGCTATCGGAATCG ACCAATTTCGCCATATCCCC 897–928 1.000 80.2
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 852–883 1.000 80.2
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 860–891 1.000 79.7
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA AAAGCCAGCTATCGGAATCG TAGCGTCTACCAATTTCGCC 905–936 1.000 79.6
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 884–915 1.000 79.3

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
Crinum asiaticum PP853198.1 158727 View on NCBI ↗
Crinum asiaticum var. pedunculatum MT348448.1 158683 View on NCBI ↗
Crinum brachynema PQ278975.1 158570 View on NCBI ↗