Markers + reference

Celosia

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 153–154 kb
Candidate markers 269
Primer pairs 95

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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 436 0.0171 0.94 69.6 yes View details
atpF LSC 1410 0.0066 0.96 66.3 yes View details
trnC-GCA-petN LSC 497 0.0800 0.80 81.2 yes View details
trnT-GGU-psbD LSC 1296 0.0170 1.00 59.2 yes View details
psbC-trnS-UGA LSC 241 0.0290 1.00 60.3 yes View details
petA-psbJ LSC 901 0.0191 0.99 71.1 yes View details
psbE-petL LSC 1344 0.0112 1.00 53.9 yes View details
psaJ-rpl33 LSC 465 0.0304 0.99 74.4 yes View details
psbH LSC 222 0.0045 1.00 40.3 yes View details
psbT-psbN LSC 59 0.0847 1.00 85.0 yes View details
rps18-rpl20 LSC 251 0.0200 1.00 64.4 yes View details
psbI-trnS-GCU LSC 229 0.0136 0.96 64.1 yes View details
trnK-UUU-rps16 LSC 927 0.0044 0.97 63.7 yes View details
ndhC-trnV-UAC LSC 712 0.0071 0.99 63.5 yes View details
rps3 LSC 657 0.0061 1.00 62.3 yes View details
petN-psbM LSC 826 0.0061 1.00 62.2 yes View details
rps16 LSC 1151 0.0035 1.00 61.2 yes View details
trnS-GCU-trnG-UCC LSC 846 0.0036 0.98 61.1 yes View details
ndhF-rpl32 SSC 1078 0.0037 1.00 61.0 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 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 GATCCACTTGGCTACATCCG GCTATCGAAGCCCCATCTAC 473–487 1.000 81.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 540–554 1.000 81.1
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 554–568 1.000 80.9
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 553–567 1.000 80.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 555–569 1.000 80.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACCCACAGAAACTGT 1018–1042 1.000 78.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCCACAGAAACT 1020–1044 1.000 78.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCCACAGAAACTGT 1017–1041 1.000 78.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGAAACT 1019–1043 1.000 78.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCCACAGAAACTG 1018–1042 1.000 78.4
rps16_p1 rps16 TTGTGTTGGATTGGCGCTAT TCCATAATTGAATCAACCGCA 1297–1302 1.000 54.7
rps16_p2 rps16 TTGTGTTGGATTGGCGCTAT GTTCTGACTGAACCAATGACT 1327–1332 1.000 53.8
rps16_p3 rps16 TTGTGTTGGATTGGCGCTAT AATTGAATCAACCGCATAGC 1292–1297 1.000 53.0
rps16_p4 rps16 TTTGTGTTGGATTGGCGCTA TCCATAATTGAATCAACCGCA 1298–1303 1.000 52.9
rps16_p5 rps16 TTTTTGTGTTGGATTGGCGC TCCATAATTGAATCAACCGCA 1300–1305 1.000 52.6
psbI-trnS-GCU_p1 psbI-trnS-GCU AATCCTGGGCGCGAAGAATA GTCATTCGTACCGAGGGTTC 278–287 1.000 70.5
psbI-trnS-GCU_p2 psbI-trnS-GCU ATCCTGGGCGCGAAGAATAA GTCATTCGTACCGAGGGTTC 277–286 1.000 70.5
psbI-trnS-GCU_p3 psbI-trnS-GCU TAATCCTGGGCGCGAAGAAT GTCATTCGTACCGAGGGTTC 279–288 1.000 70.5
psbI-trnS-GCU_p4 psbI-trnS-GCU ATCCTGGGCGCGAAGAATA GTCATTCGTACCGAGGGTTC 277–286 1.000 67.8
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCCTGGGCGCGAAGAATAA AGTCATTCGTACCGAGGGTT 278–287 1.000 67.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GTATTCAAACCAAACCCGCG 1012–1018 1.000 79.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CGAATGACTCGTACAACGGA GTATTCAAACCAAACCCGCG 982–988 1.000 79.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TGGAAACGGAAAGAGAGGGA GTATTCAAACCAAACCCGCG 1017–1023 1.000 78.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC GTATTCAAACCAAACCCGCG 948–954 1.000 76.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AACGGAAAGAGAGGGATTCG GTATTCAAACCAAACCCGCG 1013–1019 1.000 75.7
atpF_p1 atpF TTTCGTCTGCTCGAATGGTT AGCAAAGAAGTGAAATAATACAACGA 1507–1560 1.000 43.3
atpF_p2 atpF TCGTCTGCTCGAATGGTTAC AGCAAAGAAGTGAAATAATACAACGA 1505–1558 1.000 43.3
atpF_p3 atpF GTCTGCTCGAATGGTTACCA AGCAAAGAAGTGAAATAATACAACGA 1503–1556 1.000 43.3
atpF_p4 atpF TTTCGTCTGCTCGAATGGTT GCAAAGAAGTGAAATAATACAACGA 1506–1559 1.000 43.3
atpF_p5 atpF ATTTCGTCTGCTCGAATGGT AGCAAAGAAGTGAAATAATACAACGA 1508–1561 1.000 43.3

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
Celosia argentea NC_041294.1 153673 View on NCBI ↗
Celosia cristata NC_045887.1 153472 View on NCBI ↗