Markers + reference

Ipomoea

20 species · Convolvulaceae · Solanales

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Species 20
Genome length 161–163 kb
Candidate markers 269
Primer pairs 100

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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 456 0.0290 0.49 56.2 yes View details
trnG-UCC-trnR-UCU LSC 527 0.0316 0.91 76.0 yes View details
petN-psbM LSC 1221 0.0155 0.98 57.1 yes View details
trnS-UGA-lhbA LSC 357 0.0148 0.99 52.4 yes View details
trnI-CAU-ycf2 IRb 228 0.0340 0.98 59.3 yes View details
trnN-GUU-rps15 IRb 6738 0.0042 0.99 62.2 yes View details
ndhH-ndhF SSC 1078 0.0140 0.99 62.0 yes View details
rpl32-trnL-UAG SSC 915 0.0284 0.95 81.9 yes View details
ndhA SSC 2549 0.0136 0.99 69.3 yes View details
rps15-trnN-GUU IRa 6738 0.0044 1.00 60.8 yes View details
ycf2-trnI-CAU IRa 228 0.0321 1.00 59.6 yes View details
trnI-CAU-trnH-GUG IRa 200 0.0664 0.77 71.5 no View details
psaA-ycf3 LSC 774 0.0090 0.99 66.0 yes View details
ndhF-rpl32 SSC 654 0.0124 1.00 65.0 yes View details
psbC-trnS-UGA LSC 246 0.0279 1.00 64.6 yes View details
trnE-UUC-trnT-GGU LSC 756 0.0094 0.99 62.9 yes View details
psbM-trnD-GUC LSC 675 0.0134 0.97 62.6 yes View details
trnC-GCA-petN LSC 910 0.0116 0.99 62.0 yes View details
trnT-UGU-trnL-UAA LSC 875 0.0082 0.99 61.2 yes View details
petA-psbJ LSC 872 0.0057 0.99 61.1 yes View details
trnM-CAU-psbD LSC 1342 0.0047 0.98 60.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CAATCCACCGCCTTAATCCA CCGTGCTAACCTTGGTATGG 349–589 0.750 77.4
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACCGCCTTAATCCAC CCGTGCTAACCTTGGTATGG 348–588 0.750 77.4
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACCGCCTTAATCC CCGTGCTAACCTTGGTATGG 350–590 0.750 77.4
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACCGCCTTAATCCA ACCGTGCTAACCTTGGTATG 350–590 0.750 76.9
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACCGCCTTAATCCAC ACCGTGCTAACCTTGGTATG 349–589 0.750 76.9
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU ACCAAAGTTTCATGCTCGGT ACCTCTACCCTATCCATTAGGC 672–727 1.000 74.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU ACCAAAGTTTCATGCTCGGT CCTCTACCCTATCCATTAGGCA 671–726 1.000 74.2
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG ACCTCTACCCTATCCATTAGGC 602–657 1.000 74.1
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG CCTCTACCCTATCCATTAGGCA 601–656 1.000 74.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG ACCTCTACCCTATCCATTAGGC 605–660 1.000 73.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 972–991 1.000 84.9
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CCACTTCTTCCCCACACTAC 1028–1047 1.000 81.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 971–990 1.000 79.0
trnC-GCA-petN_p4 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC AGCCCAAGCGAGACTTACTA 967–986 1.000 78.9
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 980–999 1.000 78.8
petN-psbM_p1 petN-psbM CGGAAACCCCAAGTCAAGAA GTGGAAGGACGCTTTGATGA 1919–2195 1.000 86.8
petN-psbM_p2 petN-psbM TTCGGAAACCCCAAGTCAAG GTGGAAGGACGCTTTGATGA 1921–2197 1.000 86.8
petN-psbM_p3 petN-psbM CGGAAACCCCAAGTCAAGAA TAATCCAAGGCAAGGTTGGG 1808–2080 0.950 84.4
petN-psbM_p4 petN-psbM CGGAAACCCCAAGTCAAGAA AGTGGAAGGACGCTTTGATG 1920–2196 0.750 76.2
petN-psbM_p5 petN-psbM TTCGGAAACCCCAAGTCAAG AGTGGAAGGACGCTTTGATG 1922–2198 0.750 76.2
psbM-trnD-GUC_p1 psbM-trnD-GUC AAGGAGAAAGGCGGTAGGAA TTCAATTGGTCAGAGCACCG 782–808 1.000 80.0
psbM-trnD-GUC_p2 psbM-trnD-GUC TAAGGAGAAAGGCGGTAGGA TTCAATTGGTCAGAGCACCG 783–809 1.000 78.4
psbM-trnD-GUC_p3 psbM-trnD-GUC AAGGAGAAAGGCGGTAGGAA GTTCAATTGGTCAGAGCACC 783–809 1.000 75.8
psbM-trnD-GUC_p4 psbM-trnD-GUC ATAAGGAGAAAGGCGGTAGGA TTCAATTGGTCAGAGCACCG 784–810 1.000 74.4
psbM-trnD-GUC_p5 psbM-trnD-GUC TAAGGAGAAAGGCGGTAGGA GTTCAATTGGTCAGAGCACC 784–810 1.000 74.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG GAACCGATGACTTACGCCTT 876–897 1.000 86.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG CCATGGCGTTACTCTACCAC 855–876 1.000 86.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG TGGCGTTACTCTACCACTGA 852–873 1.000 86.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CATAGTACCCTACCCCCAGG CCGATGACTTACGCCTTACC 873–894 1.000 85.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 841–862 1.000 84.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (20)

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

Species Accession Length (bp) Link
Ipomoea alba NC_068906.1 161353 View on NCBI ↗
Ipomoea aquatica NC_056300.1 162663 View on NCBI ↗
Ipomoea batatas NC_026703.1 161303 View on NCBI ↗
Ipomoea cordatotriloba NC_041204.1 161242 View on NCBI ↗
Ipomoea cynanchifolia NC_041203.1 161386 View on NCBI ↗
Ipomoea hederacea NC_037911.1 161354 View on NCBI ↗
Ipomoea hederacea var. integriuscula MG973748.1 161714 View on NCBI ↗
Ipomoea imperati LC729552.1 161861 View on NCBI ↗
Ipomoea indica LC729553.1 162077 View on NCBI ↗
Ipomoea lacunosa NC_037912.1 161492 View on NCBI ↗
Ipomoea nil MG973745.1 161747 View on NCBI ↗
Ipomoea pes-caprae LC729555.1 161618 View on NCBI ↗
Ipomoea purpurea NC_009808.1 162046 View on NCBI ↗
Ipomoea ramosissima NC_041205.1 161402 View on NCBI ↗
Ipomoea splendor-sylvae NC_041206.1 161721 View on NCBI ↗
Ipomoea tabascana NC_041207.1 161225 View on NCBI ↗
Ipomoea trifida NC_034670.1 161133 View on NCBI ↗
Ipomoea triloba NC_037913.1 161750 View on NCBI ↗
Ipomoea x leucantha NC_041208.1 161296 View on NCBI ↗
Ipomoea x sloteri LC729557.1 161841 View on NCBI ↗