Markers + reference

Hesperaloe

2 species · Asparagaceae · Asparagales

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Species 2
Genome length 157–157 kb
Candidate markers 269
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0047 1.00 50.4 yes View details
rps16-trnQ-UUG LSC 1446 0.0035 1.00 49.5 yes View details
rpoB-trnC-GCA LSC 1174 0.0043 0.99 62.0 yes View details
trnE-UUC-trnT-GGU LSC 483 0.0166 1.00 65.8 yes View details
petA-psbJ LSC 1112 0.0072 1.00 63.3 yes View details
rpl16 LSC 1393 0.0029 1.00 49.4 yes View details
rpl22 LSC 381 0.0079 1.00 50.2 yes View details
ndhF SSC 2229 0.0040 1.00 45.4 yes View details
rpl32-trnL-UAG SSC 686 0.0044 0.99 55.9 yes View details
ndhD SSC 1503 0.0047 1.00 47.5 yes View details
ndhG-ndhI SSC 361 0.0083 1.00 51.3 yes View details
ycf1 SSC 5337 0.0034 1.00 54.4 yes View details
trnH-GUG-psbA IRa 299 0.0274 0.98 70.4 no View details
petN-psbM LSC 931 0.0012 0.89 62.5 yes View details
ycf4-cemA LSC 854 0.0000 0.89 61.8 yes View details
trnR-ACG-trnN-GUU IRb 624 0.0048 1.00 61.5 yes View details
trnN-GUU-trnR-ACG IRa 624 0.0048 1.00 61.5 yes View details
psbM-trnD-GUC LSC 1068 0.0047 1.00 61.4 yes View details
trnT-UGU-trnL-UAA LSC 864 0.0046 1.00 61.3 yes View details
atpB-rbcL LSC 801 0.0037 1.00 60.9 yes View details
trnR-UCU LSC 72 0.0139 1.00 60.5 yes View details
ndhJ-ndhK LSC 75 0.0133 1.00 60.2 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TTGGGTATGGCTCCTTCAAC GTGCTTGGGAGTCCTTGAAA 1152 1.000 76.1
psbA_p2 psbA GGTATGGCTCCTTCAACGAT GTGCTTGGGAGTCCTTGAAA 1149 1.000 75.2
psbA_p3 psbA TGGCTCCTTCAACGATTCTT GTGCTTGGGAGTCCTTGAAA 1145 1.000 73.3
psbA_p4 psbA TTGGGTATGGCTCCTTCAAC TAGTACGTGTGCTTGGGAGT 1160 1.000 73.3
psbA_p5 psbA TTGGGTATGGCTCCTTCAAC GTTAGTACGTGTGCTTGGGA 1162 1.000 72.7
trnK-UUU_p1 trnK-UUU TGAAGTGGGTGAAAATCGAA TTTCGATCGTATCTACATATCA 2727–2735 1.000 40.6
trnK-UUU_p2 trnK-UUU TTGAAGTGGGTGAAAATCGA TTTCGATCGTATCTACATATCA 2728–2736 1.000 40.6
trnK-UUU_p3 trnK-UUU TGTCAACCAATCTCAACCAA TTTCGATCGTATCTACATATCA 2794–2802 1.000 40.6
trnK-UUU_p4 trnK-UUU TGAAGTGGGTGAAAATCGAA TTTTCGATCGTATCTACATATCA 2728–2736 1.000 40.6
trnK-UUU_p5 trnK-UUU TTGAAGTGGGTGAAAATCGA TTTTCGATCGTATCTACATATCA 2729–2737 1.000 40.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1518–1519 1.000 78.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCACTCGGAGGTTCGAATC 1526–1527 1.000 78.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1529–1530 1.000 78.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTCACTCGGAGGTTCGAATC 1537–1538 1.000 78.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1522–1523 1.000 77.6
trnR-UCU_p1 trnR-UCU TCCATTCGGATATGCATGCT AGGGTTTCTTGATATCGCCA 224–226 1.000 63.0
trnR-UCU_p2 trnR-UCU TCCATTCGGATATGCATGCT AAGGGTTTCTTGATATCGCCA 225–227 1.000 61.0
trnR-UCU_p3 trnR-UCU TCCATTCGGATATGCATGCTT AGGGTTTCTTGATATCGCCA 224–226 1.000 60.7
trnR-UCU_p4 trnR-UCU TCCATTCGGATATGCATGCT AGGGTTTCTTGATATCGCCAT 224–226 1.000 59.2
trnR-UCU_p5 trnR-UCU TCCATTCGGATATGCATGCTT AAGGGTTTCTTGATATCGCCA 225–227 1.000 58.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TGAAATTCCTCCGACAAGCC TAAAGGATTTGCAGTCCCCC 1322–1325 1.000 75.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TGAAATTCCTCCGACAAGCC TTTGTTGATCAGGCGACACC 1359–1362 1.000 73.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TGAAATTCCTCCGACAAGCC GACACCCGGATTTGAACTGG 1345–1348 1.000 72.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TGAAATTCCTCCGACAAGCC CCGGATTTGAACTGGGGATA 1340–1343 1.000 71.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TGAAATTCCTCCGACAAGCC ATAAAGGATTTGCAGTCCCCC 1323–1326 1.000 71.2
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 984–1086 1.000 72.8
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 933–1035 1.000 71.9
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 932–1034 1.000 71.9
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTGTTCATTCT 931–1033 1.000 71.4
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 990–1092 1.000 71.3

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
Hesperaloe campanulata NC_032702.1 157446 View on NCBI ↗
Hesperaloe parviflora NC_032703.1 157393 View on NCBI ↗