Markers + reference

Cryptocoryne

2 species · Araceae · Alismatales

Back to catalogue

Species 2
Genome length 173–173 kb
Candidate markers 255
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 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 2568 0.0354 0.55 54.6 yes View details
trnS-GCU-trnG-UCC LSC 2898 0.0365 0.40 54.2 yes View details
atpH-atpI LSC 1522 0.0532 0.87 79.8 yes View details
trnT-UGU-trnL-UAA LSC 1608 0.0641 0.60 74.4 yes View details
trnF-GAA-ndhJ LSC 1758 0.0939 0.77 85.1 yes View details
accD-psaI LSC 1564 0.0728 0.83 78.3 yes View details
petA-psbJ LSC 1752 0.0942 0.88 79.7 yes View details
ycf1-rps15 SSC 1234 0.0525 0.74 85.1 yes View details
rpl32-ycf1 SSC 1832 0.1862 0.98 86.0 yes View details
psbA-trnK-UUU LSC 390 0.0886 0.90 84.0 yes View details
petN-psbM LSC 1540 0.0431 0.93 82.0 yes View details
psbC-trnS-UGA LSC 137 0.0949 1.00 81.8 yes View details
trnG-UCC-trnR-UCU LSC 151 0.0822 0.97 78.5 yes View details
psbZ-trnG-GCC LSC 841 0.0683 0.84 75.1 yes View details
atpF-atpH LSC 542 0.0481 0.96 74.8 yes View details
trnH-GUG-psbA LSC 714 0.0757 0.72 73.0 yes View details
rpl33-rps18 LSC 308 0.0412 0.79 71.9 yes View details
trnE-UUC-trnT-GGU LSC 993 0.0300 0.97 69.8 yes View details
rpoB-trnC-GCA LSC 1411 0.0297 0.84 69.7 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 GGGTAGAGCCGGATCTAAGT TAGTTGACAGTCAGGGTCGT 1183 0.500 59.9
trnH-GUG-psbA_p2 trnH-GUG-psbA TGGGTAGAGCCGGATCTAAG TAGTTGACAGTCAGGGTCGT 1184 0.500 59.9
trnH-GUG-psbA_p3 trnH-GUG-psbA GGGTAGAGCCGGATCTAAGT GCTGCTGTTGAAATTCCGTC 1070 0.500 59.7
trnH-GUG-psbA_p4 trnH-GUG-psbA TGGGTAGAGCCGGATCTAAG GCTGCTGTTGAAATTCCGTC 1071 0.500 59.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GGGTAGAGCCGGATCTAAGT CATCGTAGCTGCTCATGGTT 1359 0.500 59.5
psbA-trnK-UUU_p1 psbA-trnK-UUU AAGACGGTTTTCGGTGCTAG CAACTAGTTCCGGGTTCGAG 471–510 1.000 87.3
psbA-trnK-UUU_p2 psbA-trnK-UUU AAAGACGGTTTTCGGTGCTA CAACTAGTTCCGGGTTCGAG 472–511 1.000 87.0
psbA-trnK-UUU_p3 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT CAACTAGTTCCGGGTTCGAG 473–512 1.000 87.0
psbA-trnK-UUU_p4 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC CAACTAGTTCCGGGTTCGAG 474–513 1.000 86.5
psbA-trnK-UUU_p5 psbA-trnK-UUU GACGGTTTTCGGTGCTAGTA CAACTAGTTCCGGGTTCGAG 469–508 1.000 86.2
rps16_p1 rps16 ACTTGTGTTGGATTGGCACA ATGACCGAGTTCTATGCCCA 2263–2973 1.000 79.9
rps16_p2 rps16 ACTTGTGTTGGATTGGCACA TGACCGAGTTCTATGCCCAT 2262–2972 1.000 79.9
rps16_p3 rps16 ACTTGTGTTGGATTGGCACA AATGACCGAGTTCTATGCCC 2264–2974 1.000 79.0
rps16_p4 rps16 AGACTTGTGTTGGATTGGCA ATGACCGAGTTCTATGCCCA 2265–2975 1.000 78.8
rps16_p5 rps16 AGACTTGTGTTGGATTGGCA TGACCGAGTTCTATGCCCAT 2264–2974 1.000 78.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGTCGCTTTAGTCCA GGACGAATCACACTTTTACCAC 1238–2969 1.000 66.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGTCGCTTTAGTCCAC GGACGAATCACACTTTTACCAC 1237–2968 1.000 66.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGCAATCCGTCGCTTTAGTC GGACGAATCACACTTTTACCAC 1240–2971 1.000 63.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGTCGCTTTAGTCCACTCAG GGACGAATCACACTTTTACCAC 1233–2964 1.000 63.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGTCGCTTTAGTCCA GGACGAATCACACTTTTACCA 1238–2969 1.000 63.1
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 226–231 1.000 69.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 229–234 1.000 69.0
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 232–237 1.000 68.5
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 235–240 1.000 68.2
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 230–235 1.000 66.8
atpF-atpH_p1 atpF-atpH AAATGGCCAGAGGTTCAAGG TGGTTGTGGCATTAGCACTT 620–634 1.000 85.6
atpF-atpH_p2 atpF-atpH AAATGGCCAGAGGTTCAAGG GGTATTGCAAGACAGCCAGA 711–725 1.000 84.1
atpF-atpH_p3 atpF-atpH TACACAACTCGCACACACTC TGGTTGTGGCATTAGCACTT 731–745 1.000 84.0
atpF-atpH_p4 atpF-atpH AAATGGCCAGAGGTTCAAGG TGATTTCTGCCGCTTCTGTT 812–826 1.000 83.5
atpF-atpH_p5 atpF-atpH TTGTGCCTGGACTTCAAACA TGGTTGTGGCATTAGCACTT 976–990 1.000 83.0

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
Cryptocoryne nurii OM950936.1 173186 View on NCBI ↗
Cryptocoryne striolata OM912764.1 172836 View on NCBI ↗