Markers + reference

Crotalaria

4 species · Fabaceae · Fabales

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Species 4
Genome length 152–153 kb
Candidate markers 262
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL LSC 934 0.0510 0.94 83.5 yes View details
trnV-UAC-ndhC LSC 526 0.0444 0.84 71.7 yes View details
ycf1 SSC 5313 0.0439 0.99 70.3 yes View details
rpl32-ndhF SSC 661 0.0415 0.98 75.5 yes View details
psbI-psbK LSC 489 0.0362 0.99 82.0 yes View details
rpl2-trnH-GUG IRa 120 0.0618 0.99 79.7 no View details
atpH-atpI LSC 1069 0.0332 0.98 78.2 yes View details
atpA-atpF LSC 85 0.0667 1.00 76.5 yes View details
trnG-UCC-trnR-UCU LSC 308 0.0455 0.99 76.3 yes View details
rps3-rps19 LSC 325 0.0497 0.93 74.2 yes View details
trnH-GUG-psbA LSC 275 0.0586 0.86 74.0 yes View details
rps11-rpl36 LSC 289 0.0456 0.98 72.9 yes View details
ndhG-ndhE SSC 216 0.0440 1.00 72.4 yes View details
trnS-GGA-psbI LSC 192 0.0362 0.97 72.1 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 65 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 476–520 1.000 87.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GGTATCTGGTTTACCGCGTT 490–534 1.000 87.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GGTATCTGGTTTACCGCGTT 489–533 1.000 87.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GGTATCTGGTTTACCGCGTT 491–535 1.000 87.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCAATTGGTCAGGGAAGCTT 836–876 0.750 75.4
trnK-UUU-rbcL_p1 trnK-UUU-rbcL AGCCGAGTACTCTACCATTGA TTTGAATTCCCAGCAATGGA 956–996 1.000 62.0
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AGCCGAGTACTCTACCATTGA TGAATTCCCAGCAATGGATACT 954–994 1.000 61.9
trnK-UUU-rbcL_p3 trnK-UUU-rbcL AGCCGAGTACTCTACCATTGA TTGAATTCCCAGCAATGGAT 955–995 1.000 60.1
trnK-UUU-rbcL_p4 trnK-UUU-rbcL GCCGAGTACTCTACCATTGAG TTTGAATTCCCAGCAATGGA 955–995 1.000 59.3
trnK-UUU-rbcL_p5 trnK-UUU-rbcL GCCGAGTACTCTACCATTGAG TGAATTCCCAGCAATGGATACT 953–993 1.000 59.2
trnV-UAC-ndhC_p1 trnV-UAC-ndhC CCGAGAAAGTCTACGGTTCG AGAGAAGCGGCCATAAACTG 1022–1099 1.000 86.6
trnV-UAC-ndhC_p2 trnV-UAC-ndhC CCGAGAAAGTCTACGGTTCG TTCATAGTTACTGTGCCCGC 1158–1235 1.000 86.4
trnV-UAC-ndhC_p3 trnV-UAC-ndhC AGCCTGACAAAAGGTGGTTT AGAGAAGCGGCCATAAACTG 1499–1576 1.000 85.9
trnV-UAC-ndhC_p4 trnV-UAC-ndhC AGCCTGACAAAAGGTGGTTT TTCATAGTTACTGTGCCCGC 1635–1712 1.000 85.8
trnV-UAC-ndhC_p5 trnV-UAC-ndhC CCGAGAAAGTCTACGGTTCG TTTGGGTTGTTCGGTCAAGT 950–1027 0.750 75.3
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 377–404 1.000 70.1
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 380–407 1.000 69.9
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 383–410 1.000 69.4
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 386–413 1.000 69.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 381–408 1.000 67.6
atpA-atpF_p1 atpA-atpF CCGAGATTCCGAAGCTGAAA AGTCGAAACGGAAGCAGATC 759–763 1.000 82.2
atpA-atpF_p2 atpA-atpF CTGACCACGCCCTATAGGTA CGGTTTCGAGTGAATGGCTA 848–852 1.000 82.1
atpA-atpF_p3 atpA-atpF CTGACCACGCCCTATAGGTA AGTCGAAACGGAAGCAGATC 867–871 1.000 82.0
atpA-atpF_p4 atpA-atpF CCGAGATTCCGAAGCTGAAA ATACCGTGCGAAATCAACGA 1207–1210 0.500 61.2
atpA-atpF_p5 atpA-atpF CTGACCACGCCCTATAGGTA ATACCGTGCGAAATCAACGA 1315–1318 0.500 61.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CCGCGGCTTATATAGGTGAA 1120–1142 1.000 80.8
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT ACAAGCGGTATTCAAGCTCT 1157–1179 1.000 80.3
atpH-atpI_p3 atpH-atpI GTCCAATAGAAGCAAGCCCA CCGCGGCTTATATAGGTGAA 1158–1180 1.000 79.9
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA CCGCGGCTTATATAGGTGAA 1121–1143 1.000 79.6
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCA ACAAGCGGTATTCAAGCTCT 1195–1217 1.000 79.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Crotalaria albida NC_061361.1 152743 View on NCBI ↗
Crotalaria cytisoides PV870833.1 152401 View on NCBI ↗
Crotalaria juncea PP998656.1 152635 View on NCBI ↗
Crotalaria pallida NC_053562.1 152658 View on NCBI ↗