Markers + reference

Ripogonum

6 species · Ripogonaceae · Liliales

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Species 6
Genome length 160–161 kb
Candidate markers 273
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-trnC_GCA LSC 980 0.0055 1.00 51.5 yes View details
petN-psbM LSC 860 0.0063 0.99 58.0 yes View details
psbM-trnD_GUC LSC 1069 0.0044 1.00 51.4 yes View details
psbC LSC 1422 0.0005 1.00 33.2 yes View details
trnT_UGU-trnL_UAA LSC 961 0.0051 0.98 59.9 yes View details
ndhK LSC 702 0.0017 1.00 30.4 yes View details
rbcL LSC 1443 0.0037 1.00 49.1 yes View details
psbE-petL LSC 1342 0.0061 1.00 53.7 yes View details
petD LSC 1284 0.0020 1.00 38.0 yes View details
rpl16 LSC 1483 0.0027 0.99 35.1 yes View details
rps15-ycf1 SSC 397 0.0160 1.00 46.4 yes View details
petA-psbJ LSC 1172 0.0026 0.99 62.1 yes View details
clpP LSC 2100 0.0008 0.99 59.7 yes View details
atpF-atpH LSC 514 0.0047 0.98 59.0 yes View details
ndhK-ndhC LSC 56 0.0845 1.00 59.0 yes View details
trnC_GCA-petN LSC 1132 0.0023 1.00 55.7 yes View details
rpl20-rps12 LSC 766 0.0013 0.99 55.4 yes View details
trnS_GCU-trnG_UCC LSC 1072 0.0036 0.98 54.4 yes View details
ndhA SSC 2162 0.0020 1.00 52.7 yes View details
ndhF SSC 2238 0.0022 1.00 52.6 yes View details
trnE_UUC-trnT_GGU LSC 765 0.0039 0.97 52.5 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
trnS_GCU-trnG_UCC_p1 trnS_GCU-trnG_UCC GATGGGGGATAACGGAGAGA ACGAATCACACTTTTACCACT 1185–1213 1.000 53.8
trnS_GCU-trnG_UCC_p2 trnS_GCU-trnG_UCC ATGGGGGATAACGGAGAGAG ACGAATCACACTTTTACCACT 1184–1212 1.000 53.7
trnS_GCU-trnG_UCC_p3 trnS_GCU-trnG_UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 1123–1151 1.000 53.7
trnS_GCU-trnG_UCC_p4 trnS_GCU-trnG_UCC CAAGTGATGGGGGATAACGG ACGAATCACACTTTTACCACT 1190–1218 1.000 53.6
trnS_GCU-trnG_UCC_p5 trnS_GCU-trnG_UCC AAGTCTCAAGTGATGGGGGA ACGAATCACACTTTTACCACT 1196–1224 1.000 53.5
atpF-atpH_p1 atpF-atpH TTAAACCCGAAACTCCCTGC AATTTACGGACTGGTCGTGG 626–638 1.000 80.6
atpF-atpH_p2 atpF-atpH CCAATAGCCCAAGGAAACGA AATTTACGGACTGGTCGTGG 600–612 1.000 80.5
atpF-atpH_p3 atpF-atpH TTAAACCCGAAACTCCCTGC GCGGAGGGTAAAATACGAGG 685–697 1.000 80.1
atpF-atpH_p4 atpF-atpH CCAATAGCCCAAGGAAACGA GCGGAGGGTAAAATACGAGG 659–671 1.000 80.0
atpF-atpH_p5 atpF-atpH TTAAACCCGAAACTCCCTGC TCGTGGCATTAGCGCTTTTA 612–624 1.000 79.2
rpoB-trnC_GCA_p1 rpoB-trnC_GCA GTGGACATCCCCTCATTTCC CCCAATTTGTTGATCAGGCG 1094–1098 1.000 78.7
rpoB-trnC_GCA_p2 rpoB-trnC_GCA GTGGACATCCCCTCATTTCC GCGACACCCAGATTTGAACT 1077–1081 1.000 77.2
rpoB-trnC_GCA_p3 rpoB-trnC_GCA GTGGACATCCCCTCATTTCC TAAAGGATTTGCAGTCCCCC 1052–1056 1.000 76.8
rpoB-trnC_GCA_p4 rpoB-trnC_GCA CATCCCCTCATTTCCCTTCC CCCAATTTGTTGATCAGGCG 1089–1093 1.000 76.2
rpoB-trnC_GCA_p5 rpoB-trnC_GCA GTGGACATCCCCTCATTTCC TTTGTTGATCAGGCGACACC 1089–1093 1.000 74.9
trnC_GCA-petN_p1 trnC_GCA-petN AGTTCAAATCTGGGTGTCGC AGTCCACTCCTTCCCCATAC 1124–1241 1.000 79.6
trnC_GCA-petN_p2 trnC_GCA-petN AGTTCAAATCTGGGTGTCGC GTCCACTCCTTCCCCATACT 1123–1240 1.000 79.6
trnC_GCA-petN_p3 trnC_GCA-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 1065–1182 1.000 79.4
trnC_GCA-petN_p4 trnC_GCA-petN GGGGGACTGCAAATCCTTTA AGTCCACTCCTTCCCCATAC 1149–1266 1.000 79.2
trnC_GCA-petN_p5 trnC_GCA-petN GGGGGACTGCAAATCCTTTA GTCCACTCCTTCCCCATACT 1148–1265 1.000 79.2
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TCATTCTAGTTCCTACCGCCT 950–1042 1.000 72.4
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TCATTCTAGTTCCTACCGCCT 949–1041 1.000 72.4
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TCATTCTAGTTCCTACCGCCT 1008–1100 1.000 72.1
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC TCATTCTAGTTCCTACCGCCT 948–1040 1.000 72.0
petN-psbM_p5 petN-psbM GGGGAAGGAGTGGACTCTAG TCATTCTAGTTCCTACCGCCT 945–1037 1.000 71.7
psbM-trnD_GUC_p1 psbM-trnD_GUC AGGCGGTAGGAACTAGAATGA CCTCGCTGGGATTGTAGTTC 1205–1216 1.000 72.4
psbM-trnD_GUC_p2 psbM-trnD_GUC AGGCGGTAGGAACTAGAATGA AGTTCAATCGGTCAGAGCAC 1190–1201 1.000 72.2
psbM-trnD_GUC_p3 psbM-trnD_GUC AGGCGGTAGGAACTAGAATGA TACACCTCGCTGGGATTGTA 1209–1220 1.000 71.7
psbM-trnD_GUC_p4 psbM-trnD_GUC AGGCGGTAGGAACTAGAATGA CATACACCTCGCTGGGATTG 1211–1222 1.000 69.6
psbM-trnD_GUC_p5 psbM-trnD_GUC AGGCGGTAGGAACTAGAATGA GTATGCCATACACCTCGCTG 1217–1228 1.000 68.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Ripogonum album NC_081469.1 160751 View on NCBI ↗
Ripogonum brevifolium NC_081470.1 160768 View on NCBI ↗
Ripogonum discolor NC_081471.1 160327 View on NCBI ↗
Ripogonum elseyanum NC_081472.1 160292 View on NCBI ↗
Ripogonum fawcettianum NC_081473.1 160643 View on NCBI ↗
Ripogonum scandens NC_049021.1 160287 View on NCBI ↗