Markers + reference

Galium

7 species · Rubiaceae · Gentianales

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Species 7
Genome length 153–155 kb
Candidate markers 273
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-C5T07_pgp085 LSC 824 0.0543 0.96 84.3 yes View details
C5T07_pgp085 LSC 1254 0.0564 0.98 84.9 yes View details
C5T07_pgp085-trnQ-UUG LSC 1155 0.0912 0.97 86.5 yes View details
trnS-GCU-trnG-GCC LSC 585 0.0546 0.98 87.3 yes View details
trnE-UUC-trnT-GGU LSC 884 0.0759 0.98 86.4 yes View details
trnT-GGU-psbD LSC 1430 0.0503 0.97 85.0 yes View details
ycf3 LSC 2105 0.0241 0.99 66.6 yes View details
trnT-UGU-trnL-UAA LSC 1005 0.0764 0.97 82.6 yes View details
infa-rps8 LSC 287 0.0893 0.95 75.4 yes View details
rpl32-trnL-UAG SSC 638 0.0568 1.00 86.8 yes View details
ndhF-rpl32 SSC 741 0.0495 0.98 84.7 yes View details
petN-psbM LSC 710 0.0416 0.99 81.2 yes View details
psaJ-rpl33 LSC 479 0.0459 1.00 81.0 yes View details
trnL-UAA-trnF-GAA LSC 346 0.0441 1.00 80.7 yes View details
trnH-GUG-psbA LSC 234 0.0734 1.00 80.3 yes View details
trnC-GCA-petN LSC 682 0.0341 0.99 80.0 yes View details
psbM-trnD-GUC LSC 575 0.0381 0.99 77.9 yes View details
ccsA-ndhD SSC 255 0.0527 0.98 77.7 yes View details
trnG-GCC-trnR-UCU LSC 176 0.0433 0.99 77.6 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGCTGCTATAGATGCTCCATC 281–307 1.000 75.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTGCTATAGATGCTCCATC 295–321 1.000 75.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCTATAGATGCTCCATC 294–320 1.000 75.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCTATAGATGCTCCATC 296–322 1.000 75.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGCTGCTATAGATGCTCCAT 281–307 1.000 73.8
trnK-UUU-C5T07_pgp085_p1 trnK-UUU-C5T07_pgp085 GTCGTGGTCTTCCAAACCTT CTTGAAAGGGGTGCTCAACT 1006–1061 1.000 91.6
trnK-UUU-C5T07_pgp085_p2 trnK-UUU-C5T07_pgp085 GTCGTGGTCTTCCAAACCTT TCTTGAAAGGGGTGCTCAAC 1007–1062 1.000 91.6
trnK-UUU-C5T07_pgp085_p3 trnK-UUU-C5T07_pgp085 GTCGTGGTCTTCCAAACCTT GCAGAGACAAACGAAAAGGC 1482–1544 1.000 91.4
trnK-UUU-C5T07_pgp085_p4 trnK-UUU-C5T07_pgp085 GTCGTGGTCTTCCAAACCTT GAAGGGGTATGTTGCTACCG 1629–1691 1.000 91.3
trnK-UUU-C5T07_pgp085_p5 trnK-UUU-C5T07_pgp085 GTCGTGGTCTTCCAAACCTT TTGAAAGGGGTGCTCAACTC 1005–1038 0.429 62.7
C5T07_pgp085_p1 C5T07_pgp085 ACACAAAGCAGAAATGCGTG GCCGTAAGTGTATGTAGCCG 2235–2410 0.286 57.1
C5T07_pgp085_p2 C5T07_pgp085 CACACAAAGCAGAAATGCGT GCCGTAAGTGTATGTAGCCG 2236–2411 0.286 57.1
C5T07_pgp085_p3 C5T07_pgp085 CTACCCCCTCCCCCTTTTTA GCCGTAAGTGTATGTAGCCG 1999 0.143 41.5
C5T07_pgp085_p4 C5T07_pgp085 GGTGCAAAAAGAATCCACCG GCCGTAAGTGTATGTAGCCG 2378 0.143 41.1
C5T07_pgp085_p5 C5T07_pgp085 ATAAACAGCGATAAGGGGCG GCCGTAAGTGTATGTAGCCG 2073 0.143 40.6
C5T07_pgp085-trnQ-UUG_p1 C5T07_pgp085-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1020–1477 1.000 90.3
C5T07_pgp085-trnQ-UUG_p2 C5T07_pgp085-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1024–1481 1.000 85.5
C5T07_pgp085-trnQ-UUG_p3 C5T07_pgp085-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1050–1507 1.000 85.4
C5T07_pgp085-trnQ-UUG_p4 C5T07_pgp085-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1012–1469 1.000 85.1
C5T07_pgp085-trnQ-UUG_p5 C5T07_pgp085-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 1019–1476 1.000 84.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 654–857 1.000 63.6
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 653–856 1.000 63.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AACGAATCACACTTTTACCACT 655–858 1.000 61.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC AACGAATCACACTTTTACCACT 654–857 1.000 61.7
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AGCAATCCGACGCTTTAGTC ACGAATCACACTTTTACCACT 656–859 1.000 60.7
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 255–294 1.000 70.4
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 258–297 1.000 70.1
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 261–300 1.000 69.6
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 264–303 1.000 69.3
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 259–298 1.000 67.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Galium aparine NC_036969.1 152712 View on NCBI ↗
Galium mollugo NC_036970.1 153677 View on NCBI ↗
Galium odoratum NC_082335.1 152624 View on NCBI ↗
Galium palustre NC_082336.1 154770 View on NCBI ↗
Galium spurium NC_065832.1 153481 View on NCBI ↗
Galium trifidum NC_082337.1 154611 View on NCBI ↗
Galium verum NC_082338.1 153524 View on NCBI ↗