Markers + reference

Syngonium

2 species · Araceae · Alismatales

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Species 2
Genome length 164–165 kb
Candidate markers 269
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 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
tRNA-GUG-psbA LSC 424 0.0330 1.00 74.1 yes View details
rps16 LSC 1452 0.0069 0.99 50.6 yes View details
tRNA-Ser(GCU)-tRNA-Ser (CGA) LSC 1590 0.0065 0.97 57.8 yes View details
tRNA-Glu(UUC)-tRNA-Thr(GGU) LSC 876 0.0080 1.00 63.3 yes View details
rps4-tRNA-Thr(UGU) LSC 676 0.0398 0.93 73.8 yes View details
ndhC-tRNA-Val(UAC) LSC 1325 0.0061 0.99 62.8 yes View details
petA-psbJ LSC 1082 0.0061 0.91 66.0 yes View details
petD LSC 1229 0.0041 1.00 46.9 yes View details
petD-rpoA LSC 284 0.0500 0.92 77.2 yes View details
rpl16 LSC 1984 0.0047 0.96 56.8 yes View details
rrn4.5-rrn5 IRb 216 0.0278 1.00 68.5 yes View details
rrn5-rrn4.5 IRa 216 0.0278 1.00 68.5 yes View details
psaC-ndhE SSC 868 0.0049 0.94 66.1 yes View details
rps15-ycf1 SSC 968 0.0044 0.95 66.0 yes View details
tRNA-Leu(CAA)-ndhB IRb 1152 0.0019 0.92 63.8 yes View details
ndhB-tRNA-Leu(CAA) IRa 1152 0.0019 0.92 63.8 yes View details
rps19-rpl2 IRb 54 0.0185 1.00 63.1 yes View details
tRNA-Arg(ACG)-tRNA-Asn(GUU) IRb 585 0.0052 0.99 62.4 yes View details
tRNA-Asn(GUU)-tRNA-Arg(ACG) IRa 585 0.0052 0.99 62.4 yes View details
tRNA-Cys(GCA)-petN LSC 881 0.0057 1.00 62.1 yes View details
tRNA-Lys(UUU)-rps16 LSC 790 0.0026 0.98 61.8 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
tRNA-GUG-psbA_p1 tRNA-GUG-psbA ATATAATGGGCGAACGACGG GGCTGATATCATCAACCGGG 618 1.000 79.7
tRNA-GUG-psbA_p2 tRNA-GUG-psbA ATATAATGGGCGAACGACGG GGGCTGATATCATCAACCGG 619 1.000 79.7
tRNA-GUG-psbA_p3 tRNA-GUG-psbA GATCCACTTGGCTACATCCG GGCTGATATCATCAACCGGG 557 1.000 79.5
tRNA-GUG-psbA_p4 tRNA-GUG-psbA GATCCACTTGGCTACATCCG GGGCTGATATCATCAACCGG 558 1.000 79.5
tRNA-GUG-psbA_p5 tRNA-GUG-psbA CAATCCACTGCCTTGATCCA GGCTGATATCATCAACCGGG 571 1.000 79.4
tRNA-Lys(UUU)-rps16_p1 tRNA-Lys(UUU)-rps16 AAAGCCGAGTACTCTACCGT AGCTCAACCCACAAGAACTG 872–883 1.000 79.8
tRNA-Lys(UUU)-rps16_p2 tRNA-Lys(UUU)-rps16 AAGCCGAGTACTCTACCGTT AGCTCAACCCACAAGAACTG 871–882 1.000 79.8
tRNA-Lys(UUU)-rps16_p3 tRNA-Lys(UUU)-rps16 CCGCACTTAAAAGCCGAGTA AGCTCAACCCACAAGAACTG 881–892 1.000 78.9
tRNA-Lys(UUU)-rps16_p4 tRNA-Lys(UUU)-rps16 AAAGCCGAGTACTCTACCGT GAGCTCAACCCACAAGAACT 873–884 1.000 77.9
tRNA-Lys(UUU)-rps16_p5 tRNA-Lys(UUU)-rps16 AAGCCGAGTACTCTACCGTT GAGCTCAACCCACAAGAACT 872–883 1.000 77.9
rps16_p1 rps16 AGGGGTGGGGATAAACAGAT ATCAATTCCATCCCGGTTCG 1910–1927 1.000 78.3
rps16_p2 rps16 ATTGCACGATCCCACCAAAA ATCAATTCCATCCCGGTTCG 2161–2165 1.000 78.1
rps16_p3 rps16 AGGGGTGGGGATAAACAGAT GAGGTTCGAATCCTTCCGTC 2590–2605 1.000 77.8
rps16_p4 rps16 AGGGGTGGGGATAAACAGAT ATCCTTCCGTCCCAGATCAA 2581–2596 1.000 77.4
rps16_p5 rps16 AGGGGTGGGGATAAACAGAT TCCTTCCGTCCCAGATCAAT 2580–2595 1.000 77.4
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p1 tRNA-Ser(GCU)-tRNA-Ser (CGA) GAGAAAGCGGAGAAAGAGGG AGGACGAATCACACTTTTACCA 1722–1744 1.000 64.0
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p2 tRNA-Ser(GCU)-tRNA-Ser (CGA) ATTAGCAATCCGCCGCTTTA AGGACGAATCACACTTTTACCA 1667–1689 1.000 63.9
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p3 tRNA-Ser(GCU)-tRNA-Ser (CGA) GAGAAAGCGGAGAAAGAGGG GGACGAATCACACTTTTACCAC 1721–1743 1.000 63.6
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p4 tRNA-Ser(GCU)-tRNA-Ser (CGA) ATTAGCAATCCGCCGCTTTA GGACGAATCACACTTTTACCAC 1666–1688 1.000 63.5
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p5 tRNA-Ser(GCU)-tRNA-Ser (CGA) AGAAAGCGGAGAAAGAGGGA AGGACGAATCACACTTTTACCA 1721–1743 1.000 61.3
tRNA-Cys(GCA)-petN_p1 tRNA-Cys(GCA)-petN TTTTGTTTTGGCGACATGGC AGTCCACTCCTTCCCCATAC 1046–1047 1.000 76.1
tRNA-Cys(GCA)-petN_p2 tRNA-Cys(GCA)-petN TTTTGTTTTGGCGACATGGC GTCCACTCCTTCCCCATACT 1045–1046 1.000 76.1
tRNA-Cys(GCA)-petN_p3 tRNA-Cys(GCA)-petN TTTTGTTTTGGCGACATGGC AGCCCAAGCGAGACTTACTA 987–988 1.000 75.9
tRNA-Cys(GCA)-petN_p4 tRNA-Cys(GCA)-petN AGTTCAAATCTGGGTGTCGC AGTCCACTCCTTCCCCATAC 988–989 1.000 75.7
tRNA-Cys(GCA)-petN_p5 tRNA-Cys(GCA)-petN AGTTCAAATCTGGGTGTCGC GTCCACTCCTTCCCCATACT 987–988 1.000 75.7
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p1 tRNA-Glu(UUC)-tRNA-Thr(GGU) AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 963–1007 1.000 79.4
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p2 tRNA-Glu(UUC)-tRNA-Thr(GGU) AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 961–1005 1.000 79.4
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p3 tRNA-Glu(UUC)-tRNA-Thr(GGU) AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 942–986 1.000 78.9
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p4 tRNA-Glu(UUC)-tRNA-Thr(GGU) AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 940–984 1.000 78.9
tRNA-Glu(UUC)-tRNA-Thr(GGU)_p5 tRNA-Glu(UUC)-tRNA-Thr(GGU) GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 960–1004 1.000 78.8

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
Syngonium angustatum MN046894.1 164929 View on NCBI ↗
Syngonium podophyllum NC_070391.1 163988 View on NCBI ↗