Markers + reference

Talipariti

2 species · Malvaceae · Malvales

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Species 2
Genome length 162–162 kb
Candidate markers 271
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK_uuu LSC 293 0.0000 1.00 32.2 yes View details
petN-psbM LSC 1163 0.0034 1.00 60.8 yes View details
rps4-trnT_ugu LSC 577 0.0035 0.99 61.5 yes View details
petA-psbJ LSC 1104 0.0174 0.99 62.6 yes View details
clpP LSC 2185 0.0018 1.00 58.4 yes View details
ycf1 IRb 966 0.0000 1.00 38.5 yes View details
ycf1-ndhF SSC 276 0.0145 1.00 60.8 yes View details
rpl32-trnL_uag SSC 1164 0.0017 1.00 50.2 yes View details
ycf1 SSC 5706 0.0007 1.00 51.8 no View details
trnK_uuu-rps16 LSC 910 0.0011 0.96 63.3 yes View details
trnS_gcu-trnG_ucc LSC 854 0.0000 0.92 62.8 yes View details
atpB-rbcL LSC 1126 0.0009 0.98 60.8 yes View details
atpF-atpH LSC 612 0.0016 1.00 60.2 yes View details
rps16-trnQ_uug LSC 567 0.0018 0.99 60.1 yes View details
trnL_uag SSC 80 0.0125 1.00 59.7 yes View details
trnR_acg-trnN_guu IRb 654 0.0015 1.00 59.6 yes View details
trnN_guu-trnR_acg IRa 654 0.0015 1.00 59.6 yes View details
trnT_ugu-trnL_uaa LSC 752 0.0013 1.00 59.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK_uuu_p1 psbA-trnK_uuu TAAAGACGGTTTTCGGTGCT ACTCCATCCGACTAGTTCCG 421 1.000 73.2
psbA-trnK_uuu_p2 psbA-trnK_uuu AACACCAAACCATCCGATGT ACTCCATCCGACTAGTTCCG 440 1.000 72.8
psbA-trnK_uuu_p3 psbA-trnK_uuu GTAAAGACGGTTTTCGGTGC ACTCCATCCGACTAGTTCCG 422 1.000 72.7
psbA-trnK_uuu_p4 psbA-trnK_uuu TAAAGACGGTTTTCGGTGCT ACTAGTTCCGGGTTCGAGTC 411 1.000 71.4
psbA-trnK_uuu_p5 psbA-trnK_uuu TAAAGACGGTTTTCGGTGCT GACTAGTTCCGGGTTCGAGT 412 1.000 71.4
trnK_uuu-rps16_p1 trnK_uuu-rps16 AAAGCCGAGTACTCTACCGT AAAAGGAGCTCAACCCACAG 1001–1038 1.000 81.5
trnK_uuu-rps16_p2 trnK_uuu-rps16 AAGCCGAGTACTCTACCGTT AAAAGGAGCTCAACCCACAG 1000–1037 1.000 81.5
trnK_uuu-rps16_p3 trnK_uuu-rps16 TACCGTTGAGTTAGCAACCC AAAAGGAGCTCAACCCACAG 987–1024 1.000 79.2
trnK_uuu-rps16_p4 trnK_uuu-rps16 AAAGCCGAGTACTCTACCGT AAGAAGGCGGGGGTTTTTAC 961–998 1.000 78.8
trnK_uuu-rps16_p5 trnK_uuu-rps16 AAGCCGAGTACTCTACCGTT AAGAAGGCGGGGGTTTTTAC 960–997 1.000 78.8
rps16-trnQ_uug_p1 rps16-trnQ_uug AGTGGTGGGTTTTGACATCC GAGGTTCGAATCCTTCCGTC 673–679 1.000 80.2
rps16-trnQ_uug_p2 rps16-trnQ_uug CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 652–658 1.000 80.0
rps16-trnQ_uug_p3 rps16-trnQ_uug GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 650–656 1.000 80.0
rps16-trnQ_uug_p4 rps16-trnQ_uug AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 634–640 1.000 79.2
rps16-trnQ_uug_p5 rps16-trnQ_uug TTTTGACATCCACAGCCGAT GAGGTTCGAATCCTTCCGTC 664–670 1.000 78.6
trnS_gcu-trnG_ucc_p1 trnS_gcu-trnG_ucc CAATCCGACGCTTTAGTCCA ATGAATCAAACCGAGGGACC 903–969 1.000 80.6
trnS_gcu-trnG_ucc_p2 trnS_gcu-trnG_ucc AATCCGACGCTTTAGTCCAC ATGAATCAAACCGAGGGACC 902–968 1.000 80.6
trnS_gcu-trnG_ucc_p3 trnS_gcu-trnG_ucc CGCACAACGGATTAGCAATC ATGAATCAAACCGAGGGACC 918–984 1.000 79.9
trnS_gcu-trnG_ucc_p4 trnS_gcu-trnG_ucc ACGGAAAGAGAGGGATTCGA ATGAATCAAACCGAGGGACC 957–1023 1.000 79.4
trnS_gcu-trnG_ucc_p5 trnS_gcu-trnG_ucc TCGCACAACGGATTAGCAAT ATGAATCAAACCGAGGGACC 919–985 1.000 78.5
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA TGGTTGTAGCATTGGCACTT 694–697 1.000 80.1
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAACGAA CTGGTTGTAGCATTGGCACT 695–698 1.000 76.5
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA ATGGGCTGGTTGTAGCATTG 700–703 1.000 76.0
atpF-atpH_p4 atpF-atpH AGTGACCCAAGGAAACGAAA TGGTTGTAGCATTGGCACTT 693–696 1.000 74.6
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAACGAA CCGAGGCAGAGGGAAAAATA 769–772 1.000 74.4
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACAGCGCTGTTTATTCT 1318 1.000 72.0
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACAGCGCTGTTTATTCT 1324 1.000 70.6
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACAGCGCTGTTTATTC 1318 1.000 68.5
petN-psbM_p4 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACAGCGCTGTTTATTC 1324 1.000 67.1
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA CATTTATTGCTACAGCGCTGT 1325 1.000 66.8

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
Talipariti hamabo NC_030195.1 161729 View on NCBI ↗
Talipariti tiliaceum NC_053627.1 161748 View on NCBI ↗