Markers + reference

Osyris

2 species · Santalaceae · Santalales

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Species 2
Genome length 147–148 kb
Candidate markers 238
Primer pairs 55

Genome-wide nucleotide diversity

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

Candidate markers

2 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 238 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
APL01_gp032 Genome 70089 0.0057 1.00 55.9 yes View details
APL01_gp033 Genome 63341 0.0055 1.00 47.8 yes View details
APL01_gp042-APL01_gp041 Genome 22 0.0455 1.00 78.6 yes View details
APL01_gp010-APL01_gt028 Genome 96 0.0521 1.00 75.0 yes View details
APL01_gp020-APL01_gp019 Genome 121 0.0496 1.00 70.6 yes View details
APL01_gp001-APL01_gp032 Genome 184 0.0000 1.00 70.0 no View details
APL01_gp067-APL01_gp066 Genome 1075 0.0094 0.99 64.9 yes View details
APL01_gp013-APL01_gp012 Genome 80 0.0132 0.95 64.8 yes View details
APL01_gt002-APL01_gp072 Genome 789 0.0077 0.99 64.5 yes View details
APL01_gt028-APL01_gp009 Genome 787 0.0191 1.00 64.4 yes View details
APL01_gp069-APL01_gp068 Genome 51 0.0196 1.00 63.8 yes View details
APL01_gt004-APL01_gt005 Genome 560 0.0089 1.00 63.1 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 55 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
APL01_gp032_p1 APL01_gp032 CAATCCACTGCCTTGATCCA GAGGTATTGAAGGTAAAGGAGCA 331–338 1.000 58.2
APL01_gp032_p2 APL01_gp032 AATCCACTGCCTTGATCCAC GAGGTATTGAAGGTAAAGGAGCA 330–337 1.000 58.2
APL01_gp032_p3 APL01_gp032 ACAATCCACTGCCTTGATCC GAGGTATTGAAGGTAAAGGAGCA 332–339 1.000 58.2
APL01_gp032_p4 APL01_gp032 CTTGATCCACTTGGCCACAT GAGGTATTGAAGGTAAAGGAGCA 320–327 1.000 58.2
APL01_gp032_p5 APL01_gp032 TTGATCCACTTGGCCACATC GAGGTATTGAAGGTAAAGGAGCA 319–326 1.000 58.1
APL01_gt002-APL01_gp072_p1 APL01_gt002-APL01_gp072 CGAATCCCTTGCTTCATCCA AAAAAGGCGCTCAACCTACA 947–951 1.000 80.9
APL01_gt002-APL01_gp072_p2 APL01_gt002-APL01_gp072 ACGAATCCCTTGCTTCATCC AAAAAGGCGCTCAACCTACA 948–952 1.000 80.9
APL01_gt002-APL01_gp072_p3 APL01_gt002-APL01_gp072 ATGGACGAATCCCTTGCTTC AAAAAGGCGCTCAACCTACA 952–956 1.000 80.9
APL01_gt002-APL01_gp072_p4 APL01_gt002-APL01_gp072 GGACGAATCCCTTGCTTCAT AAAAAGGCGCTCAACCTACA 950–954 1.000 80.9
APL01_gt002-APL01_gp072_p5 APL01_gt002-APL01_gp072 CGATGGTATGGACGAATCCC AAAAAGGCGCTCAACCTACA 959–963 1.000 80.6
APL01_gt004-APL01_gt005_p1 APL01_gt004-APL01_gt005 CAATCCACCGCTTTAGTCCA ACGAATCGCACTTTTACCACT 629–630 1.000 69.9
APL01_gt004-APL01_gt005_p2 APL01_gt004-APL01_gt005 AATCCACCGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 628–629 1.000 69.9
APL01_gt004-APL01_gt005_p3 APL01_gt004-APL01_gt005 CAATCCACCGCTTTAGTCCA ACGAATCGCACTTTTACCAC 629–630 1.000 69.8
APL01_gt004-APL01_gt005_p4 APL01_gt004-APL01_gt005 AATCCACCGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 628–629 1.000 69.8
APL01_gt004-APL01_gt005_p5 APL01_gt004-APL01_gt005 CTCGTACAGCGGATTAGCAA ACGAATCGCACTTTTACCACT 646–647 1.000 69.1
APL01_gp069-APL01_gp068_p1 APL01_gp069-APL01_gp068 ATGCCATCGCCTACTTGAAG TGTTTGGGGCGATGAAAGAA 199–200 1.000 80.0
APL01_gp069-APL01_gp068_p2 APL01_gp069-APL01_gp068 ATGCCATCGCCTACTTGAAG ACAAGGGGCTTTAGCAACTC 276–277 1.000 79.3
APL01_gp069-APL01_gp068_p3 APL01_gp069-APL01_gp068 ATGCCATCGCCTACTTGAAG GGGGCTTTAGCAACTCTGAA 272–273 1.000 78.4
APL01_gp069-APL01_gp068_p4 APL01_gp069-APL01_gp068 ATGCCATCGCCTACTTGAAG AAGGGGCTTTAGCAACTCTG 274–275 1.000 78.3
APL01_gp069-APL01_gp068_p5 APL01_gp069-APL01_gp068 ATGCCATCGCCTACTTGAAG CAAGGGGCTTTAGCAACTCT 275–276 1.000 78.3
APL01_gp067-APL01_gp066_p1 APL01_gp067-APL01_gp066 TACCTTCTACAGCTTGGCCT GCGAATCTTTGGAGGGTCAT 1216–1242 1.000 80.5
APL01_gp067-APL01_gp066_p2 APL01_gp067-APL01_gp066 CAGTACCTTGACCAACTCCG GCGAATCTTTGGAGGGTCAT 1192–1218 1.000 80.3
APL01_gp067-APL01_gp066_p3 APL01_gp067-APL01_gp066 AACGGAAGCAGCAGAAATCA GCGAATCTTTGGAGGGTCAT 1131–1157 1.000 80.1
APL01_gp067-APL01_gp066_p4 APL01_gp067-APL01_gp066 TACCTTCTACAGCTTGGCCT TTTTGCAACTTTAGCTGCGG 1245–1271 1.000 79.8
APL01_gp067-APL01_gp066_p5 APL01_gp067-APL01_gp066 AGCCAATCCAGCAGCAATAA GCGAATCTTTGGAGGGTCAT 1149–1175 1.000 79.8
APL01_gp042-APL01_gp041_p1 APL01_gp042-APL01_gp041 TTCGGATTTGATTGTGTCGT ACGGACTAGCTGTACCTACC 110 1.000 61.9
APL01_gp042-APL01_gp041_p2 APL01_gp042-APL01_gp041 TTCGGATTTGATTGTGTCGT GGACTAGCTGTACCTACCGT 108 1.000 61.9
APL01_gp042-APL01_gp041_p3 APL01_gp042-APL01_gp041 CATTCGGATTTGATTGTGTCGT ACGGACTAGCTGTACCTACC 112 1.000 61.6
APL01_gp042-APL01_gp041_p4 APL01_gp042-APL01_gp041 CATTCGGATTTGATTGTGTCGT GGACTAGCTGTACCTACCGT 110 1.000 61.6
APL01_gp042-APL01_gp041_p5 APL01_gp042-APL01_gp041 TTCGGATTTGATTGTGTCGT ATGGTTAGCTGTTCACGGAC 124 1.000 61.5

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
Osyris alba NC_027960.1 147253 View on NCBI ↗
Osyris wightiana NC_048952.1 147544 View on NCBI ↗