Markers + reference

Trachelospermum

2 species · Apocynaceae · Gentianales

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Species 2
Genome length 155–156 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 8 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 299 0.0344 0.97 74.7 yes View details
psbA LSC 1062 0.0028 1.00 49.5 yes View details
rps16 LSC 1100 0.0027 1.00 50.8 yes View details
rpoB LSC 3210 0.0025 1.00 43.2 yes View details
rpoB-trnC-GCA LSC 1238 0.0235 1.00 63.6 yes View details
trnC-GCA-petN LSC 875 0.0114 1.00 58.4 yes View details
trnE-UUC-trnT-GGU LSC 915 0.0034 0.95 56.8 yes View details
psbC LSC 1422 0.0028 1.00 51.7 yes View details
ndhF SSC 2229 0.0050 0.99 60.6 yes View details
ndhF-rpl32 SSC 777 0.0103 1.00 55.1 yes View details
rpl32-trnL-UAG SSC 959 0.0094 0.99 59.3 yes View details
ccsA SSC 969 0.0072 1.00 50.0 yes View details
trnY-GUA-trnE-UUC LSC 50 0.0400 1.00 66.0 yes View details
atpH-atpI LSC 1199 0.0035 0.96 64.8 yes View details
psbC-trnS-UGA LSC 257 0.0195 1.00 63.7 yes View details
atpA-atpF LSC 55 0.0182 1.00 63.0 yes View details
cemA LSC 681 0.0059 1.00 62.1 yes View details
matK LSC 1518 0.0053 1.00 61.7 yes View details
rps14-psaB LSC 133 0.0150 1.00 61.1 yes View details
rpl20-rps12 LSC 795 0.0038 1.00 60.9 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 360–368 1.000 82.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 374–382 1.000 82.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 373–381 1.000 82.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 375–383 1.000 82.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 409–417 1.000 80.0
psbA_p1 psbA TCCTATACACCAAGACCGGG AACAAGTCCGCCATTCTCTC 1171 1.000 77.7
psbA_p2 psbA TCCTATACACCAAGACCGGG TGGGAGTCCCTGACGATTAA 1124 1.000 76.6
psbA_p3 psbA TCCTATACACCAAGACCGGG TTGGGAGTCCCTGACGATTA 1125 1.000 76.6
psbA_p4 psbA TCCTATACACCAAGACCGGG TAGAGAATGTGTGCGCTTGG 1141 1.000 76.3
psbA_p5 psbA TCCTATACACCAAGACCGGG ACAAGTCCGCCATTCTCTCT 1170 1.000 72.6
trnK-UUU_p1 trnK-UUU TGCTAGTGTCAACCAATATCGA TCTTCTATAGTTGGTTTCTTCTT 2689–2690 1.000 40.3
trnK-UUU_p2 trnK-UUU TGCTAGTGTCAACCAATATCGA TCTTCTATAGTTGGTTTCTTCTTT 2689–2690 1.000 40.3
trnK-UUU_p3 trnK-UUU TGCTAGTGTCAACCAATATCGA ATCTTCTATAGTTGGTTTCTTCT 2690–2691 1.000 40.3
trnK-UUU_p4 trnK-UUU TGCTAGTGTCAACCAATATCGA TCTTCTATAGTTGGTTTCTTCTTTTC 2689–2690 1.000 40.3
trnK-UUU_p5 trnK-UUU TGCTAGTGTCAACCAATATCGA ATCTTCTATAGTTGGTTTCTTCTT 2690–2691 1.000 40.3
matK_p1 matK ACAAGCTACTTACATGCTACATCA GCTAACCCCAAAATCGCCTA 1674 1.000 47.8
matK_p2 matK AGCTACTTACATGCTACATCAACA GCTAACCCCAAAATCGCCTA 1671 1.000 47.8
matK_p3 matK GCTACTTACATGCTACATCAACA GCTAACCCCAAAATCGCCTA 1670 1.000 45.6
matK_p4 matK ACAAGCTACTTACATGCTACA GCTAACCCCAAAATCGCCTA 1674 1.000 45.5
matK_p5 matK AGCTACTTACATGCTACATCAACA TGTTTTGACTCTATCGCGCT 1702 1.000 45.3
rps16_p1 rps16 AGTTATATACAAATCACTACCCCC ACGATGTCTACGAGCCAATG 1217–1225 1.000 40.2
rps16_p2 rps16 AGTTATATACAAATCACTACCCCC CGATGTCTACGAGCCAATGA 1216–1224 1.000 40.2
rps16_p3 rps16 AAGTTATATACAAATCACTACCCCC ACGATGTCTACGAGCCAATG 1218–1226 1.000 40.2
rps16_p4 rps16 GTTATATACAAATCACTACCCCC ACGATGTCTACGAGCCAATG 1216–1224 1.000 40.2
rps16_p5 rps16 AAGTTATATACAAATCACTACCCCC CGATGTCTACGAGCCAATGA 1217–1225 1.000 40.2
trnG-UCC_p1 trnG-UCC ATTAGCAATCCGCCGCTTTA ATGGACGCTTTTCATTCCGA 1559–1576 1.000 80.3
trnG-UCC_p2 trnG-UCC ATTAGCAATCCGCCGCTTTA TGGACGCTTTTCATTCCGAT 1558–1575 1.000 80.3
trnG-UCC_p3 trnG-UCC CCAGTTCGACAAAAGGTCCA ATGGACGCTTTTCATTCCGA 948–949 1.000 79.2
trnG-UCC_p4 trnG-UCC CCAGTTCGACAAAAGGTCCA TGGACGCTTTTCATTCCGAT 947–948 1.000 79.2
trnG-UCC_p5 trnG-UCC CCCATTTCCCAGTTCGACAA TGGACGCTTTTCATTCCGAT 955–956 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
Trachelospermum asiaticum PP078667.1 155611 View on NCBI ↗
Trachelospermum axillare PP056253.1 155483 View on NCBI ↗