Markers + reference

Schrebera

6 species · Oleaceae · Lamiales

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Species 6
Genome length 156–156 kb
Candidate markers 265
Primer pairs 95

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH(GUG)-psbA LSC 444 0.0178 0.98 46.6 yes View details
trnS(GCU)-trnG(GCC) LSC 711 0.0108 0.97 56.7 yes View details
petN-psbM LSC 1155 0.0124 1.00 48.9 yes View details
atpB LSC 1497 0.0031 1.00 38.7 yes View details
psbE-petL LSC 1165 0.0113 1.00 57.6 yes View details
ycf1 IRb 1164 0.0020 1.00 33.9 no View details
ndhF SSC 2217 0.0091 1.00 50.9 yes View details
ndhF-rpl32 SSC 473 0.0163 1.00 47.7 yes View details
rpl32-trnL(UAG) SSC 913 0.0130 0.96 47.9 yes View details
ycf1 SSC 5637 0.0105 1.00 39.3 yes View details
trnM(CAU)-psbD LSC 1331 0.0074 1.00 61.4 yes View details
petA-psbJ LSC 931 0.0066 0.99 59.4 yes View details
ycf3-trnS(GGA) LSC 802 0.0058 0.99 59.2 yes View details
psaC-ndhE SSC 257 0.0127 1.00 56.4 yes View details
rpl22-rps19 LSC 65 0.0185 1.00 54.3 yes View details
rps12-clpP LSC 133 0.0170 1.00 52.4 yes View details
psbM-trnD(GUC) LSC 647 0.0069 1.00 51.5 yes View details
trnM(CAU)-trnL(UAA) LSC 669 0.0095 1.00 51.2 yes View details
trnG(GCC)-tRNA-fM(CAU) LSC 197 0.0139 1.00 50.2 yes View details
rbcL LSC 1428 0.0055 1.00 49.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH(GUG)-psbA_p1 trnH(GUG)-psbA ACTGCCTTAATCCACTTGGC GAGCTTAGTTTCCGTCTGGG 1131–1142 1.000 82.5
trnH(GUG)-psbA_p2 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT GAGCTTAGTTTCCGTCTGGG 1130–1141 0.667 69.0
trnH(GUG)-psbA_p3 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT GAGTGGGAGCTTAGTTTCCG 1136–1147 0.667 69.0
trnH(GUG)-psbA_p4 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT GGAGCTTAGTTTCCGTCTGG 1131–1142 0.667 69.0
trnH(GUG)-psbA_p5 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT GGGAGCTTAGTTTCCGTCTG 1132–1143 0.667 69.0
trnS(GCU)-trnG(GCC)_p1 trnS(GCU)-trnG(GCC) CAATCCGACGCTTTAGTCCA AGACCGAAAGACCCTTTAACT 798–818 1.000 64.4
trnS(GCU)-trnG(GCC)_p2 trnS(GCU)-trnG(GCC) AATCCGACGCTTTAGTCCAC AGACCGAAAGACCCTTTAACT 797–817 1.000 64.4
trnS(GCU)-trnG(GCC)_p3 trnS(GCU)-trnG(GCC) ATCAACGGAACCGGAAAGAG AGACCGAAAGACCCTTTAACT 862–882 1.000 63.4
trnS(GCU)-trnG(GCC)_p4 trnS(GCU)-trnG(GCC) CATCAACGGAACCGGAAAGA AGACCGAAAGACCCTTTAACT 863–883 1.000 62.6
trnS(GCU)-trnG(GCC)_p5 trnS(GCU)-trnG(GCC) TCATCAACGGAACCGGAAAG AGACCGAAAGACCCTTTAACT 864–884 1.000 62.6
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA AGTTCCTACCGCTTTTCTACT 1244–1255 1.000 61.3
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT AGTTCCTACCGCTTTTCTACT 1242–1253 1.000 61.3
petN-psbM_p3 petN-psbM ACTCGTAGTGTGGGGAAGAA TCATTCTAGTTCCTACCGCT 1251–1262 1.000 61.1
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT TCATTCTAGTTCCTACCGCT 1249–1260 1.000 61.1
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG AGTTCCTACCGCTTTTCTACT 1241–1252 1.000 60.7
psbM-trnD(GUC)_p1 psbM-trnD(GUC) AGTAGAAAAGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 778–781 1.000 56.6
psbM-trnD(GUC)_p2 psbM-trnD(GUC) AGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 770–773 1.000 56.5
psbM-trnD(GUC)_p3 psbM-trnD(GUC) AAGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 771–774 1.000 55.0
psbM-trnD(GUC)_p4 psbM-trnD(GUC) AGCGGTAGGAACTAGAATGAA TTCAATTGGTCAGAGCACCG 770–773 1.000 55.0
psbM-trnD(GUC)_p5 psbM-trnD(GUC) AAGTAGAAAAGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 779–782 1.000 54.4
trnM(CAU)-psbD_p1 trnM(CAU)-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1474–1491 1.000 81.1
trnM(CAU)-psbD_p2 trnM(CAU)-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1477–1494 1.000 80.9
trnM(CAU)-psbD_p3 trnM(CAU)-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1464–1481 1.000 80.1
trnM(CAU)-psbD_p4 trnM(CAU)-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1467–1484 1.000 79.9
trnM(CAU)-psbD_p5 trnM(CAU)-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1451–1468 1.000 79.4
trnG(GCC)-tRNA-fM(CAU)_p1 trnG(GCC)-tRNA-fM(CAU) AGAAGATGCGGGTTCGATTC CTTGAGGTCACGGGTTCAAA 250–266 1.000 85.4
trnG(GCC)-tRNA-fM(CAU)_p2 trnG(GCC)-tRNA-fM(CAU) GAGAAGATGCGGGTTCGATT CTTGAGGTCACGGGTTCAAA 251–267 1.000 85.4
trnG(GCC)-tRNA-fM(CAU)_p3 trnG(GCC)-tRNA-fM(CAU) AGAAGATGCGGGTTCGATTC GGGTAGAGCAGTTTGGTAGC 286–302 1.000 85.2
trnG(GCC)-tRNA-fM(CAU)_p4 trnG(GCC)-tRNA-fM(CAU) GAGAAGATGCGGGTTCGATT GGGTAGAGCAGTTTGGTAGC 287–303 1.000 85.2
trnG(GCC)-tRNA-fM(CAU)_p5 trnG(GCC)-tRNA-fM(CAU) AGAAGATGCGGGTTCGATTC TCACTTCTTCTCTTCAGCGC 307–323 1.000 84.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Schrebera alata NC_042467.1 156087 View on NCBI ↗
Schrebera arborea NC_036986.1 155657 View on NCBI ↗
Schrebera capuronii NC_042388.1 155705 View on NCBI ↗
Schrebera orientalis NC_042266.1 155718 View on NCBI ↗
Schrebera swietenioides NC_042267.1 156068 View on NCBI ↗
Schrebera trichoclada NC_042268.1 155644 View on NCBI ↗