Markers + reference

Incarvillea

2 species · Bignoniaceae · Lamiales

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Species 2
Genome length 159–159 kb
Candidate markers 250
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 250 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-trnQ-UUG LSC 4118 0.1409 0.94 78.7 yes View details
atpH-atpI LSC 1227 0.4712 0.78 78.8 yes View details
rbcL-psaI LSC 2692 0.4198 0.87 79.6 yes View details
ycf1 IRb 1296 0.4387 0.71 76.9 yes View details
ycf1 IRa 2115 0.3044 0.80 78.6 no View details
trnT-UGU-trnL-UAA LSC 775 0.0705 0.95 85.7 yes View details
ycf4-cemA LSC 940 0.1157 0.91 85.5 yes View details
rrn16-rps12 IRa 1917 0.0402 0.93 85.1 yes View details
rpl20-rps12 LSC 1054 0.1724 0.90 84.5 yes View details
atpB-rbcL LSC 834 0.1127 0.91 82.8 yes View details
petA-psbJ LSC 1073 0.0896 0.94 82.5 yes View details
ccsA-psaC SSC 1982 0.1132 0.95 82.4 yes View details
rpl32-trnL-UAG SSC 892 0.0955 0.94 82.2 yes View details
trnS-GGA-trnT-UGU LSC 1240 0.0621 0.99 81.3 yes View details
psbM-trnD-GUC LSC 605 0.0515 0.96 81.0 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnQ-UUG_p1 matK-trnQ-UUG AGACCATCCAGTAGCCTGTT TCTATCCCAATGAGCCGTCT 766 0.500 59.0
matK-trnQ-UUG_p2 matK-trnQ-UUG TCTCGGGGCCTTCTTTTCTA TCTATCCCAATGAGCCGTCT 851 0.500 58.9
matK-trnQ-UUG_p3 matK-trnQ-UUG AGACCATCCAGTAGCCTGTT TCTGGGGTCCCCTGATAATC 393 0.500 58.7
matK-trnQ-UUG_p4 matK-trnQ-UUG AGACCATCCAGTAGCCTGTT AGCCGTCTATCGAATCGTTG 754 0.500 58.7
matK-trnQ-UUG_p5 matK-trnQ-UUG TCTCGGGGCCTTCTTTTCTA TCTGGGGTCCCCTGATAATC 478 0.500 58.6
atpH-atpI_p1 atpH-atpI CAGCAGTCCCTTGACCAATT TGCTTTGGCTTTACTCACGT 1529–1652 1.000 91.0
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA TGCTTTGGCTTTACTCACGT 1465–1588 1.000 90.9
atpH-atpI_p3 atpH-atpI CAGCAGTCCCTTGACCAATT CAAACTATTCCGACTGGGGG 1882 0.500 59.0
atpH-atpI_p4 atpH-atpI CAGCAGTCCCTTGACCAATT GAGAAGAATACGGCCCTTGG 1803 0.500 59.0
atpH-atpI_p5 atpH-atpI CAGCAGTCCCTTGACCAATT GGAGAAGAATACGGCCCTTG 1804 0.500 59.0
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 707–730 1.000 73.9
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAAAGGCGGTAGGAACTAGA TTCAATTGGTCAGAGCACCG 711–734 1.000 73.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AGGCGGTAGGAACTAGAATGA GTTCAATTGGTCAGAGCACC 708–731 1.000 69.7
psbM-trnD-GUC_p4 psbM-trnD-GUC GGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 706–729 1.000 69.6
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGCGGTAGGAACTAGAATG TTCAATTGGTCAGAGCACCG 707–730 1.000 69.5
trnS-GGA-trnT-UGU_p1 trnS-GGA-trnT-UGU GCTTCTTCCCTTAGGCTGTC GTTCTGCACGATTGGCTCTA 2903 0.500 59.7
trnS-GGA-trnT-UGU_p2 trnS-GGA-trnT-UGU AGGTGTAGTGCTTCTTCCCT GTTCTGCACGATTGGCTCTA 2912 0.500 59.7
trnS-GGA-trnT-UGU_p3 trnS-GGA-trnT-UGU ACTTCACCTTCAACAAGCGT GTTCTGCACGATTGGCTCTA 2736 0.500 59.6
trnS-GGA-trnT-UGU_p4 trnS-GGA-trnT-UGU TTCTTCCCTTAGGCTGTCCA GTTCTGCACGATTGGCTCTA 2901 0.500 59.6
trnS-GGA-trnT-UGU_p5 trnS-GGA-trnT-UGU AGGCTTTTGTTTACCGAGGG GGAACCGCTAACCAAAAAGC 2754 0.500 58.8
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 819–836 1.000 85.6
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 851–868 1.000 84.4
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CGTCTACCGATTTCGCCATA 813–830 1.000 84.3
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA AAAATAGGAAAAGGCCGGCT CCGTAGCGTCTACCGATTTC 874–891 1.000 84.2
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG GGTTTCCATACCAAGGCTCA 851–868 1.000 83.2
atpB-rbcL_p1 atpB-rbcL CGACCTTTCACTACCAGAGC AGGTTGAGGAGTGACTCGAA 1098–1166 1.000 91.2
atpB-rbcL_p2 atpB-rbcL GACCTTTCACTACCAGAGCG AGGTTGAGGAGTGACTCGAA 1097–1165 1.000 91.2
atpB-rbcL_p3 atpB-rbcL GACCTTTCACTACCAGAGCG AGAAACGATCTCTCCAACGC 1614–1682 1.000 88.7
atpB-rbcL_p4 atpB-rbcL CGACCTTTCACTACCAGAGC AGAAACGATCTCTCCAACGC 1615–1683 1.000 88.6
atpB-rbcL_p5 atpB-rbcL GACCTTTCACTACCAGAGCG GGGGGCCTTGGAAAGTTTTA 1481 0.500 59.8

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
Incarvillea arguta NC_045915.1 159135 View on NCBI ↗
Incarvillea lutea NC_066656.1 159032 View on NCBI ↗