Markers + reference

Carissa

2 species · Apocynaceae · Gentianales

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Species 2
Genome length 155–155 kb
Candidate markers 271
Primer pairs 105

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 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 453 0.0066 1.00 59.7 yes View details
rps16 LSC 1112 0.0018 1.00 59.8 yes View details
atpH-atpI LSC 1188 0.0008 1.00 47.6 yes View details
rps2-rpoC2 LSC 214 0.0047 1.00 40.9 yes View details
rpoB-trnC-GCA LSC 1264 0.0016 1.00 59.7 yes View details
ycf3 LSC 2022 0.0015 1.00 54.5 yes View details
psbE LSC 252 0.0040 1.00 45.9 yes View details
rpl20-rps12 LSC 794 0.0025 1.00 60.2 yes View details
ycf2-trnL-CAA IRb 702 0.0057 1.00 62.0 yes View details
ndhB-trnL-CAA IRa 551 0.0000 1.00 34.6 yes View details
trnL-CAA-ycf2 IRa 702 0.0057 1.00 62.0 yes View details
psaA-ycf3 LSC 792 0.0000 0.97 62.1 yes View details
rpl22-rps19 LSC 64 0.0156 1.00 61.5 yes View details
psbM-trnD-GUC LSC 888 0.0023 0.99 60.7 yes View details
trnK-UUU-rps16 LSC 776 0.0000 0.98 60.4 yes View details
rpl32-trnL-UAG SSC 984 0.0010 0.99 59.9 yes View details
ndhK LSC 684 0.0015 1.00 59.6 yes View details
ndhC-trnV-UAC LSC 1295 0.0015 1.00 59.6 yes View details
accD-psaI LSC 663 0.0015 1.00 59.6 yes View details
petA-psbJ LSC 686 0.0015 1.00 59.6 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 522 1.000 79.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 536 1.000 78.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 535 1.000 78.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 537 1.000 78.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 571 1.000 76.8
trnK-UUU_p1 trnK-UUU ACGGATTTCTATACATATAATTTCGA TGGTTCGTCTAAATTCTTTGT 2697 1.000 40.1
trnK-UUU_p2 trnK-UUU ACGGATTTCTATACATATAATTTCGA TGGTTCGTCTAAATTCTTTGTT 2697 1.000 40.1
trnK-UUU_p3 trnK-UUU ACGGATTTCTATACATATAATTTCGA TTGGTTCGTCTAAATTCTTTGT 2698 1.000 40.1
trnK-UUU_p4 trnK-UUU ACGGATTTCTATACATATAATTTCG TGGTTCGTCTAAATTCTTTGT 2697 1.000 40.1
trnK-UUU_p5 trnK-UUU ACGGATTTCTATACATATAATTTCGA TGGTTCGTCTAAATTCTTTGTTT 2697 1.000 40.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC GAAAAGGGGGCTCAACCTAC 954–967 1.000 79.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GAAAAGGGGGCTCAACCTAC 893–906 1.000 78.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GAAAAGGGGGCTCAACCTAC 892–905 1.000 78.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC GAAAAGGGGGCTCAACCTAC 908–921 1.000 77.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GAAAAGGGGGCTCAACCTAC 902–915 1.000 77.6
rps16_p1 rps16 TACGAATAGAGCGGGAAAGG ACGATGTCTACGAACCAATGA 1290–1292 1.000 55.9
rps16_p2 rps16 CGAATAGAGCGGGAAAGGG ACGATGTCTACGAACCAATGA 1288–1290 1.000 54.9
rps16_p3 rps16 TACGAATAGAGCGGGAAAGG CGATGTCTACGAACCAATGAC 1289–1291 1.000 53.4
rps16_p4 rps16 ACGAATAGAGCGGGAAAGGG ACGATGTCTACGAACCAATGA 1289–1291 1.000 52.9
rps16_p5 rps16 TACGAATAGAGCGGGAAAGG CGATGTCTACGAACCAATGACT 1289–1291 1.000 52.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1275–1276 1.000 75.7
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1276–1277 1.000 74.5
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT CCGCGGCTTATATAGGTGAA 1260–1261 1.000 73.9
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGC 1248–1249 1.000 72.9
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA CCGCGGCTTATATAGGTGAA 1261–1262 1.000 72.8
rps2-rpoC2_p1 rps2-rpoC2 CCCTTACGCTTTGCAGAGAT AGAAGTGCGCTCGATTGATT 1051–1054 1.000 79.8
rps2-rpoC2_p2 rps2-rpoC2 CCCTTACGCTTTGCAGAGAT CGAGTTTTAGCAAAGGCAGC 627–630 1.000 79.8
rps2-rpoC2_p3 rps2-rpoC2 AACTCCTGCCTCCATCATCT AGAAGTGCGCTCGATTGATT 983–986 1.000 79.2
rps2-rpoC2_p4 rps2-rpoC2 AACTCCTGCCTCCATCATCT CGAGTTTTAGCAAAGGCAGC 559–562 1.000 79.2
rps2-rpoC2_p5 rps2-rpoC2 CCCTTACGCTTTGCAGAGAT TGGGGATTCTTCATTGGTGC 960–963 1.000 78.7

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
Carissa macrocarpa NC_033354.1 155297 View on NCBI ↗
Carissa spinarum PV364605.1 154654 View on NCBI ↗