Markers + reference

Calystegia

3 species · Convolvulaceae · Solanales

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Species 3
Genome length 152–152 kb
Candidate markers 258
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petN-psbM LSC 1225 0.0038 1.00 45.8 yes View details
psbC LSC 1422 0.0000 1.00 36.5 yes View details
psbC-trnS-UGA LSC 240 0.0278 1.00 57.7 yes View details
trnG-GCC-trnfM-CAU LSC 267 0.0075 1.00 44.3 yes View details
psaA-ycf3 LSC 757 0.0053 1.00 51.3 yes View details
rbcL-psaI LSC 3514 0.0025 1.00 30.5 yes View details
rpl23-trnI-CAU IRb 294 0.0159 1.00 43.4 yes View details
ycf2 IRb 6168 0.0002 1.00 28.4 yes View details
rpl32-trnL-UAG SSC 963 0.0035 1.00 47.3 yes View details
ycf1 SSC 6012 0.0024 1.00 51.9 yes View details
ycf2 IRa 6168 0.0002 1.00 28.4 no View details
psbM-trnD-GUC LSC 665 0.0020 1.00 60.0 yes View details
trnN-GUU-ndhF IRb 1083 0.0018 1.00 59.9 yes View details
trnT-UGU-trnL-UAA LSC 893 0.0037 1.00 56.5 yes View details
ndhA SSC 2560 0.0018 1.00 56.0 yes View details
psaC-ndhE SSC 264 0.0051 1.00 55.7 yes View details
atpF-atpH LSC 361 0.0018 1.00 55.3 yes View details
rps16 LSC 1061 0.0025 1.00 54.8 yes View details
ycf2-trnL-CAA IRb 127 0.0210 1.00 53.4 yes View details
trnL-CAA-ycf2 IRa 127 0.0210 1.00 53.4 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
rps16_p1 rps16 TTTTTCCTTAATTGAATTTGGC TCAAGTCCATACCGGTTCCA 1123–1124 1.000 40.4
rps16_p2 rps16 TTTTTCCTTAATTGAATTTGGC TGCCTACACATCAACCGAAC 1184–1185 1.000 40.3
rps16_p3 rps16 TTTTTCCTTAATTGAATTTGGC CCTACACATCAACCGAACCC 1182–1183 1.000 40.3
rps16_p4 rps16 TTTTTCCTTAATTGAATTTGGC GATGCCTACACATCAACCGA 1186–1187 1.000 40.3
rps16_p5 rps16 TTTTTCCTTAATTGAATTTGGC CTACACATCAACCGAACCCA 1181–1182 1.000 40.3
atpF-atpH_p1 atpF-atpH TTAAACCCGAAACTCCCAGC TGGTTGTGGCATTAGCACTT 472–473 1.000 79.5
atpF-atpH_p2 atpF-atpH TTAAACCCGAAACTCCCAGC TTGGTTGTGGCATTAGCACT 473–474 1.000 79.5
atpF-atpH_p3 atpF-atpH CAGTGGCCCAAAGAAAGGAA TGGTTGTGGCATTAGCACTT 445–446 1.000 77.9
atpF-atpH_p4 atpF-atpH CAGTGGCCCAAAGAAAGGAA TTGGTTGTGGCATTAGCACT 446–447 1.000 77.9
atpF-atpH_p5 atpF-atpH AGTGGCCCAAAGAAAGGAAA TGGTTGTGGCATTAGCACTT 444–445 1.000 76.6
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TTCCTACCGCCTTTCTCCTT 1364 1.000 76.4
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TCCTACCGCCTTTCTCCTTA 1363 1.000 74.9
petN-psbM_p3 petN-psbM TAGTGTGGGGAAGAAGTGGA TTCCTACCGCCTTTCTCCTT 1307 1.000 74.4
petN-psbM_p4 petN-psbM GTAGTGTGGGGAAGAAGTGG TTCCTACCGCCTTTCTCCTT 1308 1.000 73.9
petN-psbM_p5 petN-psbM TAGTGTGGGGAAGAAGTGGA TCCTACCGCCTTTCTCCTTA 1306 1.000 72.9
psbM-trnD-GUC_p1 psbM-trnD-GUC AAGGAGAAAGGCGGTAGGAA TTCAATTGGTCAGAGCACCG 798–799 1.000 73.6
psbM-trnD-GUC_p2 psbM-trnD-GUC TAAGGAGAAAGGCGGTAGGA TTCAATTGGTCAGAGCACCG 799–800 1.000 72.1
psbM-trnD-GUC_p3 psbM-trnD-GUC AAGGAGAAAGGCGGTAGGAA GTTCAATTGGTCAGAGCACC 799–800 1.000 69.4
psbM-trnD-GUC_p4 psbM-trnD-GUC ATAAGGAGAAAGGCGGTAGGA TTCAATTGGTCAGAGCACCG 800–801 1.000 68.0
psbM-trnD-GUC_p5 psbM-trnD-GUC TAAGGAGAAAGGCGGTAGGA GTTCAATTGGTCAGAGCACC 800–801 1.000 67.9
psbC_p1 psbC GCAGCGGAAGATCCTGAATT GCATTGGATCTCTCGTCTCA 1538 1.000 70.4
psbC_p2 psbC AGGTATTCGTGCTTGGATGG GCATTGGATCTCTCGTCTCA 1482 1.000 70.3
psbC_p3 psbC GCAGCGGAAGATCCTGAATT AGCGATTCCTACTTCAAGCA 1555 1.000 68.9
psbC_p4 psbC AGGTATTCGTGCTTGGATGG AGCGATTCCTACTTCAAGCA 1499 1.000 68.9
psbC_p5 psbC TCTCAAGAAATTCGGGCAGC GCATTGGATCTCTCGTCTCA 1553 1.000 68.6
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GAGAGATGGCTGAGTGGTTG 359 1.000 80.8
psbC-trnS-UGA_p2 psbC-trnS-UGA TCGTAGGTCATTTGTGGCAC GAGAGATGGCTGAGTGGTTG 439 1.000 80.1
psbC-trnS-UGA_p3 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC ATAGCCCCGGTCTTGAAAAC 339 1.000 80.1
psbC-trnS-UGA_p4 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC TCTTTCGGAGAGATGGCTGA 366 1.000 79.7
psbC-trnS-UGA_p5 psbC-trnS-UGA GCAGCCGGATTTGAAAAAGG GAGAGATGGCTGAGTGGTTG 398 1.000 79.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Calystegia hederacea NC_085534.1 152057 View on NCBI ↗
Calystegia pubescens PV938954.1 152079 View on NCBI ↗
Calystegia sepium PP103300.1 152092 View on NCBI ↗