Markers + reference

Musa

48 species · Musaceae · Zingiberales

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Species 48
Genome length 167–173 kb
Candidate markers 279
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

15 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0023 1.00 28.6 yes View details
rps16-trnQ-UUG LSC 1839 0.0211 0.89 63.2 yes View details
trnT-UGU-trnL-UAA LSC 781 0.0261 0.93 63.0 yes View details
accD LSC 1806 0.0175 0.97 58.4 yes View details
accD-psaI LSC 468 0.0402 0.97 62.3 yes View details
rps19 IRb 279 0.0036 1.00 22.6 no View details
ycf1 IRb 6033 0.0118 0.97 53.2 yes View details
ndhA IRb 553 0.0017 1.00 31.3 no View details
ndhA-ndhF IRb 518 0.0386 0.94 61.5 yes View details
ndhF SSC 2211 0.0166 1.00 52.5 yes View details
rpl32-trnL-UAG SSC 870 0.0297 0.90 68.6 yes View details
psaC-ndhE SSC 570 0.0300 1.00 68.4 yes View details
ndhA SSC 2153 0.0140 1.00 57.2 yes View details
ycf1 IRa 6033 0.0112 0.97 52.7 no View details
rps19 IRa 279 0.0000 1.00 19.3 yes View details
rps19-psbA LSC 334 0.0870 0.86 79.0 no View details
atpH-atpI LSC 1135 0.0150 0.97 72.5 yes View details
trnS-GCU-trnG-UCC LSC 630 0.0213 1.00 68.8 yes View details
petA-psbJ LSC 1017 0.0209 0.99 68.4 yes View details
trnG-UCC-trnR-UCU LSC 191 0.0523 0.95 66.8 yes View details
rpl22-rps19 IRb 145 0.0856 1.00 65.5 yes View details
trnE-UUC-trnT-GGU LSC 797 0.0177 0.99 60.3 yes View details
trnG-GCC-trnfM-CAU LSC 146 0.0296 1.00 59.2 yes View details
rbcL-accD LSC 742 0.0194 1.00 59.2 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
psbA_p1 psbA AACAAAGCAGCAATACCCCA CATAGGGAAAGTCGTGTGCA 1546–1577 0.458 61.5
psbA_p2 psbA AACAAAGCAGCAATACCCCA ACATAGGGAAAGTCGTGTGC 1547–1578 0.458 61.5
psbA_p3 psbA ACAAAGCAGCAATACCCCAT CATAGGGAAAGTCGTGTGCA 1545–1576 0.458 59.7
psbA_p4 psbA AACAAAGCAGCAATACCCCA AATACGTGTGCTTGGGAGTC 1202–1203 0.458 58.2
psbA_p5 psbA ACAAAGCAGCAATACCCCAT AATACGTGTGCTTGGGAGTC 1201–1202 0.458 56.4
tRNA-Lys_p1 tRNA-Lys ACCAATCTCAACAGAACAGACA GGTCGTGCAGTGCAATTTAA 2931–2998 0.854 56.9
tRNA-Lys_p2 tRNA-Lys ACCAATCTCAACAGAACAGACA GGGTCGTGCAGTGCAATTTA 2932–2999 0.854 53.5
tRNA-Lys_p3 tRNA-Lys ACCAATCTCAACAGAACAGACA CAATGTTTTGATGGGGTCGTG 2945–2996 0.771 50.4
tRNA-Lys_p4 tRNA-Lys ACCAATCTCAACAGAACAGACA ATGTTTTGATGGGGTCGTGC 2943–2994 0.771 50.0
tRNA-Lys_p5 tRNA-Lys ACCAATCTCAACAGAACAGACA TCAATGTTTTGATGGGGTCGT 2946–2997 0.771 49.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 904–1913 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 915–1924 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 908–1917 1.000 85.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 916–1925 1.000 85.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 896–1905 1.000 85.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACCGAGAGACCCCTTAACT 394–1382 1.000 89.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACCGAGAGACCCCTTAACTT 393–1381 1.000 89.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA AACCGAGAGACCCCTTAACT 442–1430 1.000 86.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA ACCGAGAGACCCCTTAACTT 441–1429 1.000 86.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACCGAGAGACCCCTTAACTT 379–1367 1.000 86.1
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AAGTGATCAAGCAACGTCGA AGAAGACCTCTGTCCTATCCA 157–343 1.000 74.4
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU AAGTGATCAAGCAACGTCGA AGGTTTAGAAGACCTCTGTCCT 163–349 1.000 73.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU GCAACGTCGACTATAACCCC AGAAGACCTCTGTCCTATCCA 147–333 1.000 72.1
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU GCAACGTCGACTATAACCCC AGGTTTAGAAGACCTCTGTCCT 153–339 1.000 71.4
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU AGCAACGTCGACTATAACCC AGAAGACCTCTGTCCTATCCA 148–334 1.000 71.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACGTTAGCTGCG 1026–1580 1.000 85.6
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 999–1553 1.000 85.3
atpH-atpI_p3 atpH-atpI TACCTTCTACAGCTTGGCCT TTTTTGCAACGTTAGCTGCG 1109–1663 1.000 85.2
atpH-atpI_p4 atpH-atpI TACCTTCTACAGCTTGGCCT TAGGTGAATCCATGGAGGGT 1082–1636 1.000 84.9
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACGTTAGCTGCG 1082–1636 1.000 84.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (48)

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

Species Accession Length (bp) Link
Musa acuminata subsp. burmannica NC_058951.1 169795 View on NCBI ↗
Musa acuminata subsp. halabanensis NC_058945.1 169658 View on NCBI ↗
Musa acuminata subsp. microcarpa NC_058940.1 170081 View on NCBI ↗
Musa acuminata subsp. truncata NC_058928.1 170137 View on NCBI ↗
Musa acuminata var. zebrina NC_058925.1 169873 View on NCBI ↗
Musa aurantiaca NC_058957.1 170058 View on NCBI ↗
Musa balbisiana NC_028439.1 169503 View on NCBI ↗
Musa balbisiana var. balbisiana NC_039815.1 169458 View on NCBI ↗
Musa banksii NC_058956.1 169808 View on NCBI ↗
Musa barioensis NC_058955.1 168559 View on NCBI ↗
Musa basjoo NC_058954.1 171853 View on NCBI ↗
Musa beccarii NC_058953.1 168209 View on NCBI ↗
Musa borneensis NC_058952.1 168703 View on NCBI ↗
Musa cheesmanii NC_058950.1 170714 View on NCBI ↗
Musa chunii NC_058949.1 169309 View on NCBI ↗
Musa coccinea NC_058948.1 166826 View on NCBI ↗
Musa exotica PX411857.1 167691 View on NCBI ↗
Musa gracilis NC_058946.1 166756 View on NCBI ↗
Musa indandamanensis OP278172.1 170207 View on NCBI ↗
Musa ingens NC_056826.1 168471 View on NCBI ↗
Musa itinerans NC_035723.1 168985 View on NCBI ↗
Musa itinerans var. formosana LC609773.1 171478 View on NCBI ↗
Musa jackeyi NC_056827.1 167975 View on NCBI ↗
Musa johnsii NC_058944.1 167331 View on NCBI ↗
Musa laterita NC_056828.1 170565 View on NCBI ↗
Musa lokok NC_058942.1 166902 View on NCBI ↗
Musa lolodensis NC_056829.1 168542 View on NCBI ↗
Musa maclayi subsp. maclayi NC_058941.1 167586 View on NCBI ↗
Musa mannii NC_056830.1 170699 View on NCBI ↗
Musa ornata NC_042874.1 169989 View on NCBI ↗
Musa paracoccinea NC_058939.1 167601 View on NCBI ↗
Musa peekelii subsp. angustigemma NC_058958.1 167660 View on NCBI ↗
Musa puspanjaliae NC_058938.1 171298 View on NCBI ↗
Musa rosea NC_058937.1 168495 View on NCBI ↗
Musa rubinea NC_056832.1 172653 View on NCBI ↗
Musa rubra NC_058936.1 169309 View on NCBI ↗
Musa ruiliensis NC_058935.1 167806 View on NCBI ↗
Musa salaccensis NC_058934.1 167018 View on NCBI ↗
Musa sanguinea NC_058933.1 170501 View on NCBI ↗
Musa schizocarpa NC_058932.1 169821 View on NCBI ↗
Musa siamensis NC_058931.1 170101 View on NCBI ↗
Musa tonkinensis NC_058929.1 170100 View on NCBI ↗
Musa troglodytarum NC_056833.1 168121 View on NCBI ↗
Musa velutina NC_058927.1 169791 View on NCBI ↗
Musa x chiliocarpa LC609625.1 170959 View on NCBI ↗
Musa x formobisiana LC609772.1 171982 View on NCBI ↗
Musa x paradisiaca LC792614.1 170346 View on NCBI ↗
Musa yunnanensis NC_056834.1 169816 View on NCBI ↗