Markers + reference

Gossypium

17 species · Malvaceae · Malvales

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Species 17
Genome length 159–160 kb
Candidate markers 265
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 357 0.0346 0.97 68.8 yes View details
rps16-trnQ-UUG LSC 586 0.0216 0.99 64.9 yes View details
psbZ-trnG-GCC LSC 759 0.0248 0.98 75.5 yes View details
psaA-ycf3 LSC 926 0.0145 0.99 62.9 yes View details
rps4-trnT-UGU LSC 605 0.0244 0.85 61.7 yes View details
trnT-UGU-trnL-UAA LSC 1361 0.0181 0.98 66.7 yes View details
psbE-petL LSC 850 0.0219 0.99 60.1 yes View details
ndhD-ccsA SSC 311 0.0319 1.00 52.6 yes View details
trnL-UAG-rpl32 SSC 1128 0.0160 1.00 62.5 yes View details
rpl32-ndhF SSC 1224 0.0168 1.00 55.6 yes View details
ndhF-trnN-GUU IRa 543 0.0378 0.99 70.4 yes View details
ndhC-trnV-UAC LSC 885 0.0127 1.00 65.5 yes View details
trnR-UCU-atpA LSC 46 0.0276 1.00 61.5 yes View details
trnS-GCU-trnG-GCC LSC 893 0.0131 0.98 60.7 yes View details
trnK-UUU-rps16 LSC 832 0.0170 0.98 56.4 yes View details
atpF-atpH LSC 620 0.0112 0.96 56.2 yes View details
trnE-UUC-trnT-GGU LSC 812 0.0125 1.00 55.5 yes View details
petN-psbM LSC 1126 0.0065 1.00 55.1 yes View details
psaJ-rpl33 LSC 495 0.0165 1.00 55.1 yes View details
atpH-atpI LSC 1217 0.0101 1.00 53.9 yes View details
rpl33-rps18 LSC 334 0.0189 0.99 52.8 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 TTCCCTCTAGACCTAGCTGC 424–435 1.000 88.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 438–449 1.000 88.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 437–448 1.000 88.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 439–450 1.000 88.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 473–484 1.000 85.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGAGCTCAACCCACAG 964–1058 1.000 87.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCATTGCTACGACATGCTCT AAAAGGAGCTCAACCCACAG 998–1092 1.000 87.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1103–1197 1.000 87.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 1104–1198 1.000 87.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGACAGGCGGATTCATCAAC AAAAGGAGCTCAACCCACAG 1485–1577 0.941 84.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AGTGGTGGGTTTTGACATCC GAGGTTCGAATCCTTCCGTC 692–707 1.000 89.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 653–668 1.000 88.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGTGGTGGGTTTTGACATCC CTATGCGGAGGTTCGAATCC 699–714 1.000 87.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AACGGAAAGTGGTGGGTTTT GAGGTTCGAATCCTTCCGTC 699–714 1.000 87.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CATAACGGAAAGTGGTGGGT GAGGTTCGAATCCTTCCGTC 702–717 1.000 87.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ATGAATCAAACCGAGGGACC 995–1031 1.000 81.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ATGAATCAAACCGAGGGACC 994–1030 1.000 81.9
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CGCACAACGGATTAGCAATC ATGAATCAAACCGAGGGACC 1010–1046 1.000 81.1
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ATGAATCAAACCGAGGGACC 1049–1085 1.000 80.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TCGCACAACGGATTAGCAAT ATGAATCAAACCGAGGGACC 1011–1047 1.000 79.7
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTCACTGAGGAAGCGGAA 146–151 1.000 71.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCACTGAGGAAGCGGAAAC 144–149 1.000 70.9
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTCACTGAGGAAGCG 149–154 1.000 68.6
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT CATTCACTGAGGAAGCGGAA 181–186 1.000 67.1
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TTCACTGAGGAAGCGGAAAC 179–184 1.000 67.0
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA CTGGTTGTAGCATTGGCACT 678–706 1.000 82.7
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAACGAA TGGTTGTAGCATTGGCACTC 677–705 1.000 82.5
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA GGTTGTAGCATTGGCACTCT 676–704 0.941 82.4
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA ATGGGCTGGTTGTAGCATTG 683–711 1.000 82.2
atpF-atpH_p5 atpF-atpH AGTGACCCAAGGAAACGAAA GGTTGTAGCATTGGCACTCT 675–703 0.941 76.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Gossypium aridum NC_033396.1 160257 View on NCBI ↗
Gossypium armourianum NC_033400.1 160068 View on NCBI ↗
Gossypium australe NC_033401.1 159578 View on NCBI ↗
Gossypium davidsonii NC_033395.1 160072 View on NCBI ↗
Gossypium harknessii NC_033333.1 160129 View on NCBI ↗
Gossypium hirsutum NC_007944.1 160301 View on NCBI ↗
Gossypium hirsutum f. palmeri MK792867.1 160418 View on NCBI ↗
Gossypium hirsutum subsp. latifolium MG800784.1 160347 View on NCBI ↗
Gossypium hirsutum var. marie-galante MK792865.1 160310 View on NCBI ↗
Gossypium hirsutum var. punctatum MK792868.1 160427 View on NCBI ↗
Gossypium lobatum NC_039569.1 160205 View on NCBI ↗
Gossypium morrillii MK792866.1 160322 View on NCBI ↗
Gossypium nandewarense NC_039568.1 159677 View on NCBI ↗
Gossypium populifolium NC_033398.1 159444 View on NCBI ↗
Gossypium raimondii NC_016668.1 160161 View on NCBI ↗
Gossypium schwendimanii NC_039570.1 160199 View on NCBI ↗
Gossypium trilobum NC_033397.1 160109 View on NCBI ↗