Markers + reference

Pseudogalium

3 species · Rubiaceae · Gentianales

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Species 3
Genome length 153–153 kb
Candidate markers 263
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 9 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1407 0.0118 1.00 57.5 yes View details
trnS-GCU-trnG-UCC LSC 590 0.0113 1.00 44.2 yes View details
ycf15-trnC-GCA LSC 1035 0.0161 1.00 57.8 yes View details
trnE-UUC-trnT-GGU LSC 808 0.0083 1.00 51.5 yes View details
trnT-UGU-trnL-UAA LSC 942 0.0085 1.00 64.3 yes View details
petD LSC 1090 0.0024 1.00 35.7 yes View details
ndhF-rpl32 SSC 738 0.0199 1.00 50.7 yes View details
rpl32-trnL-UAG SSC 657 0.0101 1.00 51.1 yes View details
ycf1 SSC 5580 0.0055 1.00 29.5 yes View details
ycf4-cemA LSC 837 0.0024 1.00 60.7 yes View details
ndhA SSC 2258 0.0041 1.00 60.1 yes View details
ycf3-trnS-GGA LSC 301 0.0089 1.00 58.5 yes View details
rps2-rpoC2 LSC 240 0.0000 1.00 56.8 yes View details
rbcL-accD LSC 638 0.0094 1.00 54.8 yes View details
trnH-GUG-psbA LSC 226 0.0177 1.00 51.8 yes View details
rps12-clpP LSC 121 0.0110 1.00 51.0 yes View details
trnC-GCA-petN LSC 708 0.0028 1.00 50.9 yes View details
trnT-GGU-psbD LSC 1399 0.0038 1.00 50.1 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 CGTGCGAATCTTGGTATGGA 342–343 1.000 80.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CGTGCGAATCTTGGTATGGA 356–357 1.000 80.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CGTGCGAATCTTGGTATGGA 355–356 1.000 80.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CGTGCGAATCTTGGTATGGA 357–358 1.000 80.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTAACCGTGCGAATCTTGGT 347–348 1.000 79.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1470–1507 1.000 80.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1474–1511 1.000 76.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1500–1537 1.000 76.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1462–1499 1.000 75.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 1469–1506 1.000 75.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AAACCGAAAGCAAAGACCCT 702–706 1.000 80.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGCAAAGACCCTT 701–705 1.000 80.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACCGAAAGCAAAGACCCTTT 700–704 1.000 80.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGCAAAGACCCTT 700–704 1.000 80.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACCGAAAGCAAAGACCCTTT 699–703 1.000 80.7
rps2-rpoC2_p1 rps2-rpoC2 CCGCCTCCATCATTTCTTCT TTCGAGAGGGAGATGAGAGA 393–400 1.000 67.8
rps2-rpoC2_p2 rps2-rpoC2 CCGCCTCCATCATTTCTTCT TCGAGAGGGAGATGAGAGATC 392–399 1.000 67.8
rps2-rpoC2_p3 rps2-rpoC2 CCGCCTCCATCATTTCTTCT CGAGAGGGAGATGAGAGATCT 391–398 1.000 67.7
rps2-rpoC2_p4 rps2-rpoC2 CCGCCTCCATCATTTCTTCT TCGAGAGGGAGATGAGAGAT 392–399 1.000 66.0
rps2-rpoC2_p5 rps2-rpoC2 CCCGCCTCCATCATTTCTTC TTCGAGAGGGAGATGAGAGA 394–401 1.000 65.1
ycf15-trnC-GCA_p1 ycf15-trnC-GCA TGTTCTTGCATATCCCTGCC CCGGATTTGAACTGGGGAAA 1367–1387 1.000 81.9
ycf15-trnC-GCA_p2 ycf15-trnC-GCA CCGGGGCTTTGCAATATTTG CCGGATTTGAACTGGGGAAA 1469–1489 1.000 81.7
ycf15-trnC-GCA_p3 ycf15-trnC-GCA TACCGGATCTCCACCTACAC CCGGATTTGAACTGGGGAAA 1791–1811 1.000 81.1
ycf15-trnC-GCA_p4 ycf15-trnC-GCA TTCCCTCATTTCCATCCCCT CCGGATTTGAACTGGGGAAA 1122 0.667 66.1
ycf15-trnC-GCA_p5 ycf15-trnC-GCA TTCCCTCATTTCCATCCCCT GCCAAGAGAATCCCGAAGTT 1330 0.667 65.8
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 739–764 1.000 81.1
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCCACTTCTTCCCCACACTA 796–821 1.000 78.8
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 757–782 1.000 78.8
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAC 800–825 1.000 76.9
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TCCACTTCTTCCCCACACTA 814–839 1.000 76.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Pseudogalium paradoxum OK236360.1 153093 View on NCBI ↗
Pseudogalium paradoxum subsp. duthiei PP836142.1 153302 View on NCBI ↗
Pseudogalium paradoxum subsp. paradoxum PP836144.1 153106 View on NCBI ↗