Markers + reference

Clitoria

2 species · Fabaceae · Fabales

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Species 2
Genome length 152–152 kb
Candidate markers 260
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 516 0.2141 0.69 74.7 yes View details
trnK-UUU-rbcL LSC 1159 0.1345 0.72 76.8 yes View details
ycf3-psaA LSC 961 0.0894 0.86 79.8 yes View details
trnY-GUA-trnD-GUC LSC 481 0.1237 0.82 81.2 yes View details
psbM-petN LSC 1170 0.0899 0.86 79.4 yes View details
petN-trnC-GCA LSC 744 0.1319 0.97 82.5 yes View details
atpA-trnR-UCU LSC 368 0.1261 0.62 67.6 yes View details
cemA-psaI LSC 1376 0.1278 0.91 84.7 yes View details
rps8-rpl14 LSC 519 0.1283 0.95 83.1 yes View details
ndhF-rpl32 SSC 812 0.1084 0.80 79.5 yes View details
atpI-atpH LSC 851 0.0731 0.96 82.2 yes View details
psbJ-petA LSC 995 0.0832 0.95 82.2 yes View details
trnQ-UUG-accD LSC 1291 0.0892 0.94 82.0 yes View details
psbD-trnT-GGU LSC 1470 0.0729 0.93 81.8 yes View details
ndhJ-trnF-GAA LSC 650 0.0883 0.98 81.7 yes View details
trnL-UAA-trnT-UGU LSC 775 0.0701 0.96 81.7 yes View details
trnT-GGU-trnE-UUC LSC 806 0.0877 0.95 81.7 yes View details
rpl36-rps8 LSC 473 0.1032 0.92 81.3 yes View details
trnfM-CAU-trnG-GCC LSC 118 0.1238 0.89 81.1 yes View details
rpl32-trnL-UAG SSC 476 0.0958 0.94 80.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGTATCTGGTTTACCGCGTT 616–756 1.000 90.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GGTATCTGGTTTACCGCGTT 630–770 1.000 90.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GGTATCTGGTTTACCGCGTT 629–769 1.000 90.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GGTATCTGGTTTACCGCGTT 631–771 1.000 90.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCAATTGGTCAGGGAAGCTT 976–1116 1.000 88.9
trnK-UUU_p1 trnK-UUU AGTGTCAACCAATACCAATATCCA GCGATTGGATATACACACCCA 2928 0.500 20.0
trnK-UUU_p2 trnK-UUU AGTGTCAACCAATACCAATATCCA TGCGATTGGATATACACACCC 2929 0.500 20.0
trnK-UUU_p3 trnK-UUU TCCCAAGCACACGAATTTCT TGGATATACACACCCAATTCT 3000 0.500 20.0
trnK-UUU_p4 trnK-UUU ACTAGTGTCAACCAATACCA GCGATTGGATATACACACCCA 2931 0.500 20.0
trnK-UUU_p5 trnK-UUU ACTAGTGTCAACCAATACCA TGCGATTGGATATACACACCC 2932 0.500 20.0
trnK-UUU-rbcL_p1 trnK-UUU-rbcL CCTTTCTGGATCAGTCGTGG AGTCCTGAATTAGCTGCTGC 1087–1361 1.000 91.2
trnK-UUU-rbcL_p2 trnK-UUU-rbcL CCTTTCTGGATCAGTCGTGG AATGAGGGACGTGATCTTGC 1147–1421 1.000 90.9
trnK-UUU-rbcL_p3 trnK-UUU-rbcL CCTTTCTGGATCAGTCGTGG GCCGTAGCTAATCGAGTAGC 1192–1466 1.000 90.6
trnK-UUU-rbcL_p4 trnK-UUU-rbcL CCTTTCTGGATCAGTCGTGG TGCTAGAGAATTGGGCGTTC 1947 0.500 59.7
trnK-UUU-rbcL_p5 trnK-UUU-rbcL TGGACGAACCAATTGCTTCA TGCTAGAGAATTGGGCGTTC 1904 0.500 59.6
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA ACTTTTATGAAATACAAGATGCT CCTCGTGTCACCAGTTCAAA 713–716 1.000 48.1
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA ACTTTTATGAAATACAAGATGCT CTGGTAGAGCAGAGGACTGA 737–740 1.000 47.8
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA ACTTTTATGAAATACAAGATGCT GGGATAGCTCAGCTGGTAGA 749–752 1.000 47.7
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA ACTTTTATGAAATACAAGATGCT AGAATGGTCGGGATAGCTCA 758–761 1.000 47.6
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA ACTTTTATGAAATACAAGATGCT GCTTCAAGAATGGTCGGGAT 764–767 1.000 47.5
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 825–1157 1.000 85.8
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 833–1165 1.000 85.2
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GGAATCGAACCGATGACCAT 857–1189 1.000 84.7
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 865–1197 1.000 84.1
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 839–1171 1.000 83.8
ycf3-psaA_p1 ycf3-psaA TCACAGGGCGTTTTGAATAA ACTTCTGGTTCCGGTGAA 918–1010 1.000 50.1
ycf3-psaA_p2 ycf3-psaA ATCACAGGGCGTTTTGAATA ACTTCTGGTTCCGGTGAA 919–1011 1.000 50.1
ycf3-psaA_p3 ycf3-psaA ATCACAGGGCGTTTTGAATAA ACTTCTGGTTCCGGTGAA 919–1011 1.000 50.1
ycf3-psaA_p4 ycf3-psaA ATCACAGGGCGTTTTGAAT ACTTCTGGTTCCGGTGAA 919–1011 1.000 50.1
ycf3-psaA_p5 ycf3-psaA TCACAGGGCGTTTTGAATA ACTTCTGGTTCCGGTGAA 918–1010 1.000 50.1

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
Clitoria mariana NC_067531.1 152364 View on NCBI ↗
Clitoria ternatea NC_047365.1 151673 View on NCBI ↗