Markers + reference

Firmiana

6 species · Malvaceae · Malvales

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Species 6
Genome length 160–161 kb
Candidate markers 275
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpA LSC 1524 0.0020 1.00 31.2 yes View details
psbZ-trnG-GCC LSC 815 0.0202 1.00 65.4 yes View details
ycf3-trnS-GGA LSC 997 0.0074 1.00 52.5 yes View details
rpl33-rps18 LSC 419 0.0124 1.00 43.8 yes View details
clpP LSC 2181 0.0062 1.00 45.8 yes View details
petD LSC 1221 0.0033 1.00 35.4 yes View details
petD-rpoA LSC 252 0.0193 0.99 57.6 yes View details
rpl2 IRb 1523 0.0009 1.00 31.3 no View details
ndhF SSC 2211 0.0034 1.00 39.7 yes View details
ndhF-rpl32 SSC 860 0.0117 1.00 52.9 yes View details
ccsA-ndhD SSC 283 0.0205 1.00 52.2 yes View details
rpl2 IRa 1523 0.0009 1.00 31.3 yes View details
rps19-rpl2 IRb 135 0.0333 0.87 66.5 yes View details
trnE-UUC-trnT-GGU LSC 826 0.0040 1.00 64.0 yes View details
rpl32-trnL-UAG SSC 1111 0.0054 1.00 62.7 yes View details
rpl2-trnH-GUG IRa 143 0.0315 0.87 61.4 no View details
trnR-ACG-trnN-GUU IRb 652 0.0029 1.00 57.7 yes View details
trnN-GUU-trnR-ACG IRa 652 0.0029 1.00 57.7 yes View details
psaJ-rpl33 LSC 521 0.0061 0.99 56.8 yes View details
trnT-UGU-trnL-UAA LSC 1658 0.0043 1.00 56.1 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
trnG-UCC_p1 trnG-UCC CCAATTCCCCTGTTCGACAA TGCATCATTGAATTATCATTGA 951 0.333 13.3
trnG-UCC_p2 trnG-UCC ATTCCCCTGTTCGACAAAGG TGCATCATTGAATTATCATTGA 948 0.333 13.3
trnG-UCC_p3 trnG-UCC CCAATTCCCCTGTTCGACAA TGCATCATTGAATTATCATTGAA 951 0.333 13.3
trnG-UCC_p4 trnG-UCC TTGATTACGCCCAATTCCCC TGCATCATTGAATTATCATTGA 961 0.333 13.3
trnG-UCC_p5 trnG-UCC CTGTTCGACAAAGGTCCCTT TGCATCATTGAATTATCATTGA 942 0.333 13.3
atpA_p1 atpA AGCCTTCCAAGCTAACGATG ATTGGCTTGTTTGGGGTGAT 2111–2224 1.000 84.7
atpA_p2 atpA CCTAGCCTTCCAAGCTAACG ATTGGCTTGTTTGGGGTGAT 2114–2227 1.000 84.4
atpA_p3 atpA AGCCTTCCAAGCTAACGATG AATGGAGGCGGATCAGTTTC 2361–2474 1.000 84.1
atpA_p4 atpA AGCCTTCCAAGCTAACGATG GAAATGGAGGCGGATCAGTT 2363–2476 1.000 84.1
atpA_p5 atpA CCTAGCCTTCCAAGCTAACG AATGGAGGCGGATCAGTTTC 2364–2477 1.000 83.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 899–913 1.000 80.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 897–911 1.000 80.9
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 953–967 1.000 80.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 878–892 1.000 80.5
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 876–890 1.000 80.5
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CAACCACTCAGCCATCTCTC TTTGGTTTCGTTTCATCGCG 1576–1733 1.000 86.1
psbZ-trnG-GCC_p2 psbZ-trnG-GCC CAACCACTCAGCCATCTCTC CATATATGGAAGAGGGGCGC 1620–1777 1.000 86.0
psbZ-trnG-GCC_p3 psbZ-trnG-GCC CAACCACTCAGCCATCTCTC GATGATCATAGAGGGCCCCT 1675–1832 1.000 85.9
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GAGCTATCAACCACTCAGCC TTTGGTTTCGTTTCATCGCG 1583–1740 1.000 85.8
psbZ-trnG-GCC_p5 psbZ-trnG-GCC GGAGCTATCAACCACTCAGC TTTGGTTTCGTTTCATCGCG 1584–1741 1.000 85.8
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TCTCCTGAGGTTGTCGGAAT TTCCAATGCTACGCCTTGAA 1118–1138 1.000 80.5
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TCTCCTGAGGTTGTCGGAAT GTGCGGAAAGAGAGGGATTC 1170–1190 1.000 79.2
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTCTCCTGAGGTTGTCGGAA TTCCAATGCTACGCCTTGAA 1119–1139 1.000 78.7
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTCTCCTGAGGTTGTCGGA TTCCAATGCTACGCCTTGAA 1120–1140 1.000 78.7
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TCTCCTGAGGTTGTCGGAAT AGTTCCAATGCTACGCCTTG 1120–1140 1.000 77.7
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1304–1708 1.000 83.8
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1312–1716 1.000 83.3
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1336–1740 1.000 82.9
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1344–1748 1.000 82.4
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA CAAATAGGGAAAGCCGGCTA ACCAATTTCGCCATATCCCC 1358–1762 1.000 82.1

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
Firmiana calcarea NC_061661.1 161263 View on NCBI ↗
Firmiana danxiaensis NC_057288.1 161205 View on NCBI ↗
Firmiana daweishanensis NC_083141.1 161194 View on NCBI ↗
Firmiana hainanensis NC_065869.1 161031 View on NCBI ↗
Firmiana pulcherrima NC_036395.1 159556 View on NCBI ↗
Firmiana simplex NC_041438.1 161268 View on NCBI ↗