Markers + reference

Rhaphiolepis

8 species · Rosaceae · Rosales

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Species 8
Genome length 159–160 kb
Candidate markers 269
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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1010 0.0085 0.98 63.1 yes View details
petN-psbM LSC 1247 0.0087 1.00 52.1 yes View details
trnE-UUC-trnT-GGU LSC 530 0.0042 1.00 45.6 yes View details
trnT-GGU-psbD LSC 1355 0.0025 0.98 48.3 yes View details
psbZ-trnG-GCC LSC 748 0.0060 0.64 53.1 yes View details
ndhC-trnV-UAC LSC 485 0.0049 1.00 43.5 yes View details
petL-petG LSC 158 0.0000 1.00 30.1 yes View details
petB LSC 1447 0.0013 1.00 37.4 yes View details
ndhF SSC 2256 0.0012 1.00 29.7 yes View details
ndhF-rpl32 SSC 1078 0.0043 1.00 56.1 yes View details
ycf1 SSC 5658 0.0017 1.00 44.6 yes View details
petG-trnW-CCA LSC 124 0.0547 0.95 75.6 yes View details
rpl32-trnL-UAG SSC 1491 0.0030 0.99 56.9 yes View details
atpH-atpI LSC 1174 0.0004 1.00 52.8 yes View details
rps16 LSC 1138 0.0020 1.00 51.1 yes View details
psbE-petL LSC 1239 0.0005 1.00 49.2 yes View details
ndhA SSC 2228 0.0011 1.00 49.1 yes View details
trnC-GCA-petN LSC 980 0.0016 0.98 47.8 yes View details
trnH-GUG-psbA LSC 196 0.0035 1.00 47.3 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
trnH-GUG-psbA_p1 trnH-GUG-psbA ATATTATGGGCGAACGACGG GCGCTAACCTTGGTATGGAA 373–442 1.000 80.7
trnH-GUG-psbA_p2 trnH-GUG-psbA ATATTATGGGCGAACGACGG CCTCTAGACCTAGCTGCTGT 323–392 1.000 80.7
trnH-GUG-psbA_p3 trnH-GUG-psbA ATATTATGGGCGAACGACGG TTCCCTCTAGACCTAGCTGC 326–395 1.000 80.6
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 312–381 1.000 80.6
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 326–395 1.000 80.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGGAACTTCGCCCTAATCAA 1057–1092 1.000 81.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGAACTTCGCCCTAATCAA 1056–1091 1.000 81.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CGGAACTTCGCCCTAATCAA 1066–1101 1.000 80.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1112–1147 1.000 80.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1111–1146 1.000 80.3
rps16_p1 rps16 AGAAACAAAAAGGTTATACAAGGCT ACTGGTTCCAAACTGAAGGA 1219–1223 1.000 40.5
rps16_p2 rps16 ACAAAAAGGTTATACAAGGCT ACTGGTTCCAAACTGAAGGA 1215–1219 1.000 40.5
rps16_p3 rps16 GGAAATAGCAAAGAAACAAAAAGGT ACTGGTTCCAAACTGAAGGA 1230–1234 1.000 40.5
rps16_p4 rps16 AGCAAAGAAACAAAAAGGTT ACTGGTTCCAAACTGAAGGA 1224–1228 1.000 40.5
rps16_p5 rps16 AGAACAAAAGAGGAAATAGCAAAGA ACTGGTTCCAAACTGAAGGA 1241–1245 1.000 40.5
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 1262–1268 1.000 80.1
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1228–1234 1.000 80.1
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCAACCTTAGCTGCG 1292–1298 1.000 79.3
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 1258–1264 1.000 79.2
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1229–1235 1.000 78.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCGAGATTTACT 1017–1037 1.000 81.0
trnC-GCA-petN_p2 trnC-GCA-petN GTATCATTTTGGCGGCATGG CAGCCCAAGCGAGATTTACT 1069–1089 1.000 80.4
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGTCCACTCCTTCCCCATAC 1075–1095 1.000 80.2
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GTCCACTCCTTCCCCATACT 1074–1094 1.000 80.2
trnC-GCA-petN_p5 trnC-GCA-petN GTATCATTTTGGCGGCATGG GTCCACTCCTTCCCCATACT 1126–1146 1.000 79.6
petN-psbM_p1 petN-psbM AGTAAATCTCGCTTGGGCTG AAAACAGTCAGCCAAGGTGA 1347–1356 1.000 78.1
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC AAAACAGTCAGCCAAGGTGA 1290–1299 1.000 77.4
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT AAAACAGTCAGCCAAGGTGA 1289–1298 1.000 77.4
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC AAAACAGTCAGCCAAGGTGA 1288–1297 1.000 77.0
petN-psbM_p5 petN-psbM GGGGAAGGAGTGGACTCTAG AAAACAGTCAGCCAAGGTGA 1285–1294 1.000 76.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Rhaphiolepis brevipetiolata NC_061551.1 159566 View on NCBI ↗
Rhaphiolepis ferruginea NC_045332.1 159515 View on NCBI ↗
Rhaphiolepis impressivena NC_045350.1 159554 View on NCBI ↗
Rhaphiolepis indica NC_045330.1 159466 View on NCBI ↗
Rhaphiolepis lanceolata NC_045333.1 159688 View on NCBI ↗
Rhaphiolepis philippinensis NC_066142.1 159654 View on NCBI ↗
Rhaphiolepis salicifolia NC_045342.1 159552 View on NCBI ↗
Rhaphiolepis umbellata NC_045334.1 159547 View on NCBI ↗