Markers + reference

Crawfurdia

2 species · Gentianaceae · Gentianales

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Species 2
Genome length 150–151 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 306 0.0131 1.00 60.5 yes View details
trnK-UUU-trnQ-UUG LSC 1267 0.0059 0.93 66.5 yes View details
psbK-psbI LSC 431 0.0117 1.00 62.4 yes View details
trnS-GCU-trnG-UCC LSC 572 0.0122 1.00 65.2 yes View details
rpoB-trnC-GCA LSC 1223 0.0049 1.00 61.7 yes View details
trnT-GGU-psbD LSC 1064 0.0056 1.00 62.0 yes View details
ycf3 LSC 2037 0.0025 1.00 45.0 yes View details
trnF-GAA-ndhJ LSC 604 0.0068 0.98 64.9 yes View details
ndhC-trnV-UAC LSC 450 0.0111 1.00 52.8 yes View details
accD-psaI LSC 653 0.0000 1.00 27.5 yes View details
petA LSC 960 0.0010 1.00 49.6 yes View details
petA-psbJ LSC 288 0.0279 1.00 68.4 yes View details
ndhF-rpl32 SSC 712 0.0154 1.00 67.6 yes View details
rpl14-rpl16 LSC 139 0.0152 0.95 66.0 yes View details
psaC-ndhE SSC 354 0.0090 0.94 63.4 yes View details
petN-psbM LSC 1143 0.0018 0.97 62.7 yes View details
rpl22-rps19 LSC 58 0.0172 1.00 62.4 yes View details
ndhH-rps15 SSC 115 0.0093 0.94 62.3 yes View details
rpl2-trnH-GUG IRa 257 0.0000 1.00 61.9 no View details
trnE-UUC-trnT-GGU LSC 721 0.0000 0.97 61.8 yes View details
atpB-rbcL LSC 720 0.0042 1.00 61.1 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 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 CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 430–431 1.000 77.2
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 431–432 1.000 77.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 431–432 1.000 76.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC ACCGTGCTAACCTTGGTATG 432–433 1.000 76.5
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 423–424 1.000 75.6
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG CGAATCCCTTGCTTCATCCA GAGGTTCGAATCCTTCCGTC 1373–1814 1.000 83.4
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG ACGAATCCCTTGCTTCATCC GAGGTTCGAATCCTTCCGTC 1374–1815 1.000 83.4
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG ATGGACGAATCCCTTGCTTC GAGGTTCGAATCCTTCCGTC 1378–1819 1.000 83.4
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG GGACGAATCCCTTGCTTCAT GAGGTTCGAATCCTTCCGTC 1376–1817 1.000 83.4
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG CGATGGTATGGACGAATCCC GAGGTTCGAATCCTTCCGTC 1385–1826 1.000 83.1
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT TCTTCACGTCCAGGATTACG 573–574 1.000 73.1
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 568–569 1.000 73.1
psbK-psbI_p3 psbK-psbI TGCCCATCATACCTCTGCTA TCTTCACGTCCAGGATTACG 606–607 1.000 72.6
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 565–566 1.000 71.1
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 566–567 1.000 71.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGTCGCTTTAATCCACTCA TCAAACCGAAAGCAAAGATCC 682–686 1.000 65.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCGTCGCTTTAATCCACTCA CAAACCGAAAGCAAAGATCCT 681–685 1.000 65.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCGCTTTAATCCACTCAGCC TCAAACCGAAAGCAAAGATCC 679–683 1.000 65.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCGCTTTAATCCACTCAGCC CAAACCGAAAGCAAAGATCCT 678–682 1.000 65.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGGAAGAGGAAAGAGAGGGA TCAAACCGAAAGCAAAGATCC 745–749 1.000 64.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTCA GCGATTTTTATCAGCCGACG 1441 1.000 78.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTCA TTTTATCAGCCGACGAAGGG 1436 1.000 78.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTCA CCGGATTTGAACTGGGGAAA 1388 1.000 77.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTCA GACGAAGGGATTTCAAGGCT 1425 1.000 77.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTTCCGTCAAACCCTCATCA GCGATTTTTATCAGCCGACG 1438 1.000 76.6
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TCATTCTAGTTCCTACCGCCT 1250–1284 1.000 74.0
petN-psbM_p2 petN-psbM CCCTGTCACTTGTAGTGTGG TCATTCTAGTTCCTACCGCCT 1212–1246 1.000 72.8
petN-psbM_p3 petN-psbM CCTGTCACTTGTAGTGTGGG TCATTCTAGTTCCTACCGCCT 1211–1245 1.000 72.8
petN-psbM_p4 petN-psbM CTGTCACTTGTAGTGTGGGG TCATTCTAGTTCCTACCGCCT 1210–1244 1.000 72.8
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TCATTCTAGTTCCTACCGCCT 1256–1290 1.000 72.5

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
Crawfurdia campanulacea MN199164.1 150088 View on NCBI ↗
Crawfurdia poilanei MN199145.1 150594 View on NCBI ↗