Markers + reference

Schnabelia

5 species · Lamiaceae · Lamiales

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Species 5
Genome length 156–157 kb
Candidate markers 280
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 280 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 317 0.0419 0.96 75.6 yes View details
trnK-UUU-rps16 LSC 950 0.0203 1.00 65.0 yes View details
petN-psbM LSC 967 0.0209 1.00 62.4 yes View details
trnE-UUC-trnT-GGU LSC 557 0.0240 1.00 61.5 yes View details
trnT-UGU-trnL-UAA LSC 739 0.0242 0.99 66.4 yes View details
petB LSC 1394 0.0118 1.00 55.0 yes View details
ndhF-rpl32 SSC 518 0.0414 1.00 75.7 yes View details
ndhD SSC 1311 0.0139 1.00 38.4 yes View details
ndhG-ndhI SSC 326 0.0282 1.00 47.5 yes View details
ndhA SSC 2106 0.0116 1.00 58.9 yes View details
ccsA-ndhD SSC 217 0.0747 1.00 80.9 yes View details
atpA-atpF LSC 98 0.0520 0.96 69.5 yes View details
rps12-clpP LSC 131 0.0310 1.00 67.5 yes View details
trnT-GGU-psbD LSC 1326 0.0189 0.99 67.4 yes View details
trnG-GCC-trnfM-CAU LSC 148 0.0351 0.99 67.0 yes View details
rpl2-trnH-GUG IRa 137 0.0122 1.00 64.0 no View details
rbcL-accD LSC 675 0.0160 1.00 60.7 yes View details
psbT-psbN LSC 60 0.0500 1.00 59.9 yes View details
psbE-petL LSC 914 0.0175 1.00 59.7 yes View details
petA-psbJ LSC 952 0.0134 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 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 GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 376–386 1.000 87.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 390–400 1.000 87.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 389–399 1.000 87.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 391–401 1.000 87.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 428–438 1.000 86.0
trnK-UUU_p1 trnK-UUU GGACTCCCAAGCACACAAAT TCCCCGTGTTGAAGTTTTGT 2844–2890 0.800 70.9
trnK-UUU_p2 trnK-UUU TTTTCGGTGCTGGTTATCCA TCCCCGTGTTGAAGTTTTGT 2950–2996 0.800 69.3
trnK-UUU_p3 trnK-UUU GGACTCCCAAGCACACAAAT ACATCCCCGTGTTGAAGTTT 2847–2893 0.800 69.1
trnK-UUU_p4 trnK-UUU TGTTCGTGTCAACCAATCCT TCCCCGTGTTGAAGTTTTGT 2758–2804 0.800 69.0
trnK-UUU_p5 trnK-UUU ATCCAGTTACAGAAGCGACC TCCCCGTGTTGAAGTTTTGT 2935–2981 0.800 68.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGAACTTCCGCCTAATGAA 1010–1024 1.000 71.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTTCCGCCTAATGAA 1009–1023 1.000 71.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AGGAACTTCCGCCTAATGAA 1024–1038 1.000 71.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGGAACTTCCGCCTAATGAA 1019–1033 1.000 71.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTTCCGCCTAATGAAA 1009–1023 1.000 70.0
atpA-atpF_p1 atpA-atpF ATACGAGCAATACCATCGCC AGCCATTCAACAGCTGGAAA 552–572 1.000 84.6
atpA-atpF_p2 atpA-atpF AACGCCGGGAAATAATACCC AGCCATTCAACAGCTGGAAA 851–871 1.000 83.3
atpA-atpF_p3 atpA-atpF AACGCCGGGAAATAATACCC GTTTGGTTCGGGAAGGGATT 985–1005 1.000 82.3
atpA-atpF_p4 atpA-atpF ACTGCTGTTTTACCGGTCTG AGCCATTCAACAGCTGGAAA 963–983 1.000 82.2
atpA-atpF_p5 atpA-atpF CTGCTGTTTTACCGGTCTGT AGCCATTCAACAGCTGGAAA 962–982 1.000 82.2
petN-psbM_p1 petN-psbM TCGTAGTGTGGGGAAGAAGT TCCAAACGAGTCAAAGGGTG 1414–1585 1.000 86.4
petN-psbM_p2 petN-psbM ATCCTCGTTCGCATCTAGGA TCCAAACGAGTCAAAGGGTG 2049–2226 1.000 86.2
petN-psbM_p3 petN-psbM TCCTCGTTCGCATCTAGGAT TCCAAACGAGTCAAAGGGTG 2048–2225 1.000 86.2
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT GGTGTCGAGTGGCATACTTT 1398–1569 1.000 86.0
petN-psbM_p5 petN-psbM TCGTAGTGTGGGGAAGAAGT TCCCTTAATTTCCCCGGGAT 1534–1704 1.000 85.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 695–703 1.000 83.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 674–682 1.000 83.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 671–679 1.000 83.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 657–665 1.000 83.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 692–700 1.000 82.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Schnabelia aureoglandulosa NC_088034.1 156866 View on NCBI ↗
Schnabelia nepetifolia NC_088035.1 155733 View on NCBI ↗
Schnabelia oligophylla NC_088036.1 156944 View on NCBI ↗
Schnabelia terniflora NC_065394.1 156672 View on NCBI ↗
Schnabelia tetrodonta NC_067499.1 156931 View on NCBI ↗