Markers + reference

Cicer

4 species · Fabaceae · Fabales

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Species 4
Genome length 125–126 kb
Candidate markers 224
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 224 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 Genome 5235 0.0322 0.98 63.1 yes View details
trnN-GUU-trnR-ACG Genome 610 0.0533 1.00 86.3 yes View details
ycf2 Genome 5904 0.0355 0.96 65.7 yes View details
accD-trnQ-UUG Genome 1343 0.0386 0.98 73.1 yes View details
trnQ-UUG-psbK Genome 637 0.0409 1.00 76.8 yes View details
trnT-UGU-trnL-UAA Genome 994 0.0374 0.99 73.8 yes View details
trnR-UCU-atpA Genome 191 0.0515 0.95 82.9 yes View details
rpl2-rps19 Genome 203 0.0771 0.92 78.0 yes View details
rbcL-trnK-UUU Genome 664 0.0307 1.00 77.7 yes View details
psbA-trnH-GUG Genome 342 0.0500 0.99 76.9 yes View details
atpH-atpI Genome 1258 0.0302 0.98 76.0 yes View details
trnY-GUA-trnE-UUC Genome 60 0.0722 1.00 75.9 yes View details
rpl20-rps18 Genome 270 0.0431 0.98 75.5 yes View details
trnI-GAU-rrn16 Genome 298 0.0360 0.99 74.7 yes View details
psbZ-trnfM-CAU Genome 779 0.0323 0.93 74.3 yes View details
atpF-atpH Genome 520 0.0344 0.97 73.8 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rbcL-trnK-UUU_p1 rbcL-trnK-UUU AGTCCTGAATTAGCTGCTGC TGGAGTCGCACTTAAAAGCC 783–818 1.000 80.0
rbcL-trnK-UUU_p2 rbcL-trnK-UUU AGTCCTGAATTAGCTGCTGC AACCCTACCGATGGTATGGA 836–871 1.000 79.7
rbcL-trnK-UUU_p3 rbcL-trnK-UUU AGTCCTGAATTAGCTGCTGC AGTCGCACTTAAAAGCCGAG 780–815 1.000 79.3
rbcL-trnK-UUU_p4 rbcL-trnK-UUU AGTCCTGAATTAGCTGCTGC AGTCGTGGTCTTACAAACCC 851–886 1.000 79.2
rbcL-trnK-UUU_p5 rbcL-trnK-UUU AGTCCTGAATTAGCTGCTGC GTCGTGGTCTTACAAACCCT 850–885 1.000 79.2
psbA-trnH-GUG_p1 psbA-trnH-GUG GGTATCTGGTTTACCGCGTT CAATCCACTGCCTTGATCCA 581–600 1.000 86.6
psbA-trnH-GUG_p2 psbA-trnH-GUG GGTATCTGGTTTACCGCGTT AATCCACTGCCTTGATCCAC 580–599 1.000 86.6
psbA-trnH-GUG_p3 psbA-trnH-GUG GGTATCTGGTTTACCGCGTT ACAATCCACTGCCTTGATCC 582–601 1.000 86.6
psbA-trnH-GUG_p4 psbA-trnH-GUG GTTATACAATGGCGGTCCGT CAATCCACTGCCTTGATCCA 1110–1129 1.000 82.8
psbA-trnH-GUG_p5 psbA-trnH-GUG GTTATACAATGGCGGTCCGT AATCCACTGCCTTGATCCAC 1109–1128 1.000 82.8
ycf1_p1 ycf1 CTCGGGAGAAATCTGGTTCG AACAAGTTCCTCGATGGTCA 216–282 1.000 81.7
ycf1_p2 ycf1 CTCGGGAGAAATCTGGTTCG ACGTTTTCGAGGACAAATCCA 602–668 1.000 81.1
ycf1_p3 ycf1 TGTCTTCAGCCTCGTCTTTG ACGTTTTCGAGGACAAATCCA 860–926 1.000 80.1
ycf1_p4 ycf1 TGTGCCAAGGTTTCAGAACA ACGTTTTCGAGGACAAATCCA 1175–1241 1.000 79.2
ycf1_p5 ycf1 TGCTTTCCCAGGATTCTTCG ACGTTTTCGAGGACAAATCCA 953 0.250 39.8
trnN-GUU-trnR-ACG_p1 trnN-GUU-trnR-ACG CCGTTGTTCCTCAGTAGCTC CAGAGGATTAGAGCACGTGG 750–768 1.000 85.4
trnN-GUU-trnR-ACG_p2 trnN-GUU-trnR-ACG ATTTGCCGTTGTTCCTCAGT CAGAGGATTAGAGCACGTGG 755–773 1.000 85.2
trnN-GUU-trnR-ACG_p3 trnN-GUU-trnR-ACG TTGCCGTTGTTCCTCAGTAG CAGAGGATTAGAGCACGTGG 753–771 1.000 84.0
trnN-GUU-trnR-ACG_p4 trnN-GUU-trnR-ACG TTCCTCAGTAGCTCAGTGGT CAGAGGATTAGAGCACGTGG 744–762 1.000 82.9
trnN-GUU-trnR-ACG_p5 trnN-GUU-trnR-ACG CCGATTGGTCGTAGGTTCAA CAGAGGATTAGAGCACGTGG 706–724 1.000 82.8
trnI-GAU-rrn16_p1 trnI-GAU-rrn16 GGCACAACGACGCAATTATC CAAGGTAGCCGTACTGGAAG 390–392 1.000 80.4
trnI-GAU-rrn16_p2 trnI-GAU-rrn16 GGCACAACGACGCAATTATC AGTGACTGGAGTGAAGTCGT 412–414 1.000 80.1
trnI-GAU-rrn16_p3 trnI-GAU-rrn16 GGCACAACGACGCAATTATC AACAAGGTAGCCGTACTGGA 392–394 1.000 79.9
trnI-GAU-rrn16_p4 trnI-GAU-rrn16 GGCACAACGACGCAATTATC ACAAGGTAGCCGTACTGGAA 391–393 1.000 79.9
trnI-GAU-rrn16_p5 trnI-GAU-rrn16 GGCACAACGACGCAATTATC AAGTCGTAACAAGGTAGCCG 399–401 1.000 79.8
ycf2_p1 ycf2 CATGGTTCGATCCTGCAAGA CCGACAGAAAGTCCGTTTGA 363–375 0.750 79.2
ycf2_p2 ycf2 CATGGTTCGATCCTGCAAGA TTTTGAGTTGTTCTGCCGGA 518–530 0.750 78.7
ycf2_p3 ycf2 GGTTCGATCCTGCAAGAACT TTTTGAGTTGTTCTGCCGGA 515–527 0.750 78.2
ycf2_p4 ycf2 GGCTTATTCGAAAAACGCCC TTTTGAGTTGTTCTGCCGGA 573–585 0.750 77.8
ycf2_p5 ycf2 CCCGAAATGACCTTTCCCAA TTTTGAGTTGTTCTGCCGGA 456 0.500 61.8

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
Cicer chorassanicum PZ172408.1 125542 View on NCBI ↗
Cicer judaicum PX659842.1 124578 View on NCBI ↗
Cicer pinnatifidum PZ188367.1 124891 View on NCBI ↗
Cicer yamashitae PZ172410.1 125748 View on NCBI ↗