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Table 2 Example of the FONZIE final result table, run on Supercontig 16 of the Leptosphaeria maculans genome.

From: FONZIE: An optimized pipeline for minisatellite marker discovery and primer design from large sequence data sets

MARKER_ID

MOTIFa

REPETITIONb

MARKER_STATUS_ON_GENOMELEPTOV2c

LEFT_PRIMERd

RIGHT_PRIMERe

START_AMPLIF_PRODUCT_ON_SUPERCONTIG_16f

END_AMPLIF_ PRODUCT_ON_SUPERCONTIG_16g

STATUS_AMPLIF_ PRODUCT_ON_GENOMELEPTOV2h

min_supercontig_16_10

ATAAAAGTAAACTACTACTTTA

2.0

MULTIPLE_COPIES

GCATAAAGCTAATCTTCTCTACCCC

GTATAAACTGCCCTTGTGTATACCT

100841

101019

MULTIPLE_COPIES

min_supercontig_16_11

GGATCATCAAGGA

17.3

UNIQUE_COPY

CGTTTTGGCTTTGTTGTTGA

ACTATGAGCCAGGTGAACCG

111896

112241

UNIQUE_COPY

min_supercontig_16_12

CGCTCTCTCTCTCTCTCTTTCTCTCT

4.3

MULTIPLE_COPIES

CGCCAACAAGACTACCCATC

GAAGCGGTGGCAGTTTTTAG

112524

112812

UNIQUE_COPY

min_supercontig_16_13

CCATGT

5.8

UNIQUE_COPY

ACCTCCCGAGGAAAAGTGAC

CTTGTGTGGTCTGGTTGCAG

134392

134595

UNIQUE_COPY

min_supercontig_16_14

GAGAGAGAGAGAGAGAGA

7.4

MULTIPLE_COPIES

TGACTCGGCGTCTACCCTAC

AGCCAGCCAGCCAGTACTAA

136186

136390

UNIQUE_COPY

min_supercontig_16_15

AAGCAGAAGGCTATTGAGTCGCCAGAGACAAGTCCACAGTCC

2.1

UNIQUE_COPY

AAGTGGCTGGACCTAGCAGA

ACATCGGCGACACGTTTAGT

142179

142347

UNIQUE_COPY

min_supercontig_16_16

GTGTGG

11.2

MULTIPLE_COPIES

TGTGGATGATAGGATGGGGT

GTGACAAGCACATGATTCGC

156524

156707

UNIQUE_COPY

  1. Only a few markers generated by FONZIE are displayed in the table.
  2. a consensus sequence of the core motif of the minisatellite (MS)
  3. b number of repeats of the core motif
  4. c results of the first BLAST step on the BLAST database: UNIQUE_COPY, the unique sequence matching the MS (query) is the query sequence; MULTIPLE_COPIES, more than one sequence of the BLAST database match the query sequence and the best hit is obtained for the query sequence (E-value cut-off e-10)
  5. d and e, sequences of the left and right primers, respectively, generated by Primer3 to amplify the minisatellite locus and flanking sequences
  6. f and g, location (in base pairs) of the primers along Super-Contig 16 sequence.
  7. h, results of the second BLAST step, where the amplification product is blasted on the BLAST database: UNIQUE_COPY, the unique sequence matching the PCR product (query) is the query sequence; MULTIPLE_COPIES, more than one sequence of the BLAST database match the query sequence and the best hit is obtained for the query sequence (E value cut-off e-40).