Markers + reference

Callitriche

4 species · Plantaginaceae · Lamiales

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Species 4
Genome length 150–151 kb
Candidate markers 269
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 840 0.0625 0.87 72.0 yes View details
rps16-trnQ-UUG LSC 596 0.0710 1.00 78.4 yes View details
trnS-GCU-trnG-UCC LSC 728 0.0646 0.99 76.9 yes View details
ycf4-cemA LSC 845 0.0665 0.98 72.5 yes View details
ycf1 IRb 1158 0.0135 1.00 43.6 no View details
ndhF SSC 2190 0.0394 1.00 60.4 yes View details
ndhF-rpl32 SSC 765 0.0686 0.99 73.6 yes View details
rpl32-trnL-UAG SSC 1117 0.0763 0.72 75.4 yes View details
rps15-ycf1 SSC 349 0.0969 0.87 66.6 yes View details
ycf1 SSC 5436 0.0509 0.99 73.0 yes View details
psbI-trnS-GCU LSC 134 0.0784 0.95 84.6 yes View details
rps2-rpoC2 LSC 235 0.0511 1.00 77.8 yes View details
rpoC2-rpoC1 LSC 166 0.1747 1.00 75.5 yes View details
ndhE-ndhG SSC 233 0.0607 0.98 74.6 yes View details
accD-psaI LSC 701 0.0499 0.97 73.9 yes View details
matK LSC 1530 0.0418 1.00 72.9 yes View details
psbE-petL LSC 823 0.0494 1.00 72.6 yes View details
ndhD-psaC SSC 96 0.0469 1.00 72.4 yes View details
trnL-UAG-ccsA SSC 103 0.0469 0.99 72.2 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
matK_p1 matK TTCGATATGCCAGTGGGTTG AAGACCACGACTGATCCTGA 2463–2498 1.000 85.8
matK_p2 matK TTCGATATGCCAGTGGGTTG AGACCACGACTGATCCTGAA 2462–2497 1.000 85.8
matK_p3 matK TTCGATATGCCAGTGGGTTG TGAAGACCACGACTGATCCT 2465–2500 1.000 85.8
matK_p4 matK TTCGATATGCCAGTGGGTTG TGGAAAAACGAAAGGGCAGA 1981–1996 0.750 73.3
matK_p5 matK CTACTGGAGGAGCAGCAATG TGGAAAAACGAAAGGGCAGA 2375–2390 0.750 73.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCTATCCCAATGAGCCGTCT 1071–1207 0.750 78.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GCCGTACGAGGAGAAAACTT 1128–1266 0.750 78.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1127–1265 0.750 78.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG ACCCAAGAACAAGGAAACCC 1610 0.500 59.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG ACCCAAGAACAAGGAAACCC 1609 0.500 59.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 669–851 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 673–855 1.000 85.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 699–881 1.000 85.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 661–843 1.000 85.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 668–850 1.000 84.5
psbI-trnS-GCU_p1 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT TGGACTAAAGCGTCGGATTG 242–251 1.000 64.7
psbI-trnS-GCU_p2 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT GTGGACTAAAGCGTCGGATT 243–252 1.000 64.6
psbI-trnS-GCU_p3 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT ATTGGGAGAGATGGCTGAGT 261–270 1.000 63.2
psbI-trnS-GCU_p4 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT GACTAAAGCGTCGGATTGCT 240–249 1.000 61.9
psbI-trnS-GCU_p5 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT CTGAGTGGACTAAAGCGTCG 247–256 1.000 61.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 703–830 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 702–829 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 706–833 1.000 62.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 705–832 1.000 62.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 704–831 1.000 62.6
rps2-rpoC2_p1 rps2-rpoC2 CATTTCCTAGTCCCATGGCC GACCCCTTCAAAACAGCAGA 448–475 1.000 89.2
rps2-rpoC2_p2 rps2-rpoC2 CCGCATCTCTTTTCGGAAGA GACCCCTTCAAAACAGCAGA 783–810 1.000 86.5
rps2-rpoC2_p3 rps2-rpoC2 CATTTCCTAGTCCCATGGCC TATAACCCAGGGGCTTCCAA 1021–1048 1.000 85.2
rps2-rpoC2_p4 rps2-rpoC2 CCATTTCCTAGTCCCATGGC TATAACCCAGGGGCTTCCAA 1022–1049 1.000 85.2
rps2-rpoC2_p5 rps2-rpoC2 CCGCATCTCTTTTCGGAAGA TATAACCCAGGGGCTTCCAA 1356–1383 1.000 84.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Callitriche cophocarpa NC_080351.1 150324 View on NCBI ↗
Callitriche hermaphroditica NC_080352.1 150042 View on NCBI ↗
Callitriche palustris NC_080353.1 150071 View on NCBI ↗
Callitriche stagnalis NC_066447.1 150879 View on NCBI ↗