Markers + reference

Celtis

10 species · Cannabaceae · Rosales

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Species 10
Genome length 159–159 kb
Candidate markers 278
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 278 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 764 0.0081 0.97 59.4 yes View details
trnG-UCC-trnR-UCU LSC 344 0.0148 1.00 59.6 yes View details
trnE-UUC-trnT-GGU LSC 675 0.0113 1.00 56.3 yes View details
trnT-GGU-psbD LSC 1211 0.0101 1.00 57.5 yes View details
psbC LSC 1422 0.0018 1.00 38.4 yes View details
rps4-trnT-UGU LSC 559 0.0087 0.96 60.9 yes View details
ndhF-rpl32 SSC 1179 0.0091 0.99 61.0 yes View details
rpl32-trnL-UAG SSC 943 0.0123 0.99 61.5 yes View details
ycf1 SSC 5757 0.0042 1.00 38.6 yes View details
rpl22-trnH-GUG IRa 226 0.0000 1.00 68.8 no View details
psbZ-trnG-GCC LSC 471 0.0077 0.98 59.1 yes View details
accD-psaI LSC 981 0.0052 1.00 55.7 yes View details
trnH-GUG-psbA LSC 308 0.0121 0.96 55.5 yes View details
ycf3 LSC 2060 0.0030 1.00 53.9 yes View details
clpP LSC 2170 0.0028 1.00 53.0 yes View details
trnC-GCA-petN LSC 990 0.0035 1.00 52.7 yes View details
rps8-rpl14 LSC 209 0.0116 1.00 52.5 yes View details
psaC-ndhE SSC 272 0.0074 1.00 52.4 yes View details
petN-psbM LSC 1253 0.0027 1.00 52.2 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 90 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 TCAACCGTGCTAATCTTGGT 417–430 1.000 77.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAACCGTGCTAATCTTGGT 431–444 1.000 77.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAACCGTGCTAATCTTGGT 430–443 1.000 77.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAACCGTGCTAATCTTGGT 432–445 1.000 77.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAATCTTGGTATGG 414–427 1.000 74.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TCAAAGAAGGCAGGGGTTTT 841–867 1.000 79.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTCAAAGAAGGCAGGGGTTT 842–868 1.000 79.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTTCAAAGAAGGCAGGGGTT 843–869 1.000 79.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA ATTTCAAAGAAGGCAGGGGT 844–870 1.000 77.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC TCAAAGAAGGCAGGGGTTTT 840–866 1.000 75.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 421–442 1.000 68.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 424–445 1.000 67.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 427–448 1.000 67.3
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 430–451 1.000 67.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 496–517 1.000 65.6
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTAGAGTCCACTTCGTCCC 1098–1131 1.000 80.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1034–1067 1.000 80.3
trnC-GCA-petN_p3 trnC-GCA-petN GTATCATTTTGGCGGCATGG TCTAGAGTCCACTTCGTCCC 1150–1183 1.000 79.9
trnC-GCA-petN_p4 trnC-GCA-petN GTATCATTTTGGCGGCATGG AGCCCAAGCGAGACTTACTA 1086–1119 1.000 79.8
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CGTCCCCATACTACGAGTGA 1084–1117 1.000 78.8
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCATTGTTCATTCT 1414–1420 1.000 54.6
petN-psbM_p2 petN-psbM CACTCGTAGTATGGGGACGA TGCTACTGCATTGTTCATTCT 1363–1369 1.000 53.3
petN-psbM_p3 petN-psbM TCACTCGTAGTATGGGGACG TGCTACTGCATTGTTCATTCT 1364–1370 1.000 53.3
petN-psbM_p4 petN-psbM ACTCGTAGTATGGGGACGAA TGCTACTGCATTGTTCATTCT 1362–1368 1.000 52.5
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCATTGTTCATTC 1414–1420 1.000 50.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 750–769 1.000 83.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 748–767 1.000 83.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 729–748 1.000 82.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 727–746 1.000 82.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 804–823 1.000 82.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Celtis australis NC_062418.1 158624 View on NCBI ↗
Celtis biondii NC_039727.1 159001 View on NCBI ↗
Celtis bungeana MT742239.1 159059 View on NCBI ↗
Celtis cerasifera MN640571.1 159063 View on NCBI ↗
Celtis julianae NC_053879.1 159064 View on NCBI ↗
Celtis koraiensis NC_065789.1 159039 View on NCBI ↗
Celtis occidentalis MT742242.1 159017 View on NCBI ↗
Celtis sinensis NC_048498.1 159092 View on NCBI ↗
Celtis tetrandra NC_050249.1 159014 View on NCBI ↗
Celtis vandervoetiana MT742243.1 159067 View on NCBI ↗