java *.java

$ java Application <data.fasta>

0 CGGGCTGC- 7 8 CGGCCTGCA 16 17 C 17

$ java Application data_sample_approx2.fasta 2

[start: 1, end: 4, total length: 16, motif length:4] [start: 10, end: 13, total length: 8, motif length:4] [start: 5, end: 8, total length: 16, motif length:4] [start: 0, end: 7, total length: 18, motif length:8] [start: 9, end: 12, total length: 10, motif length:4] [start: 2, end: 5, total length: 15, motif length:4] [start: 6, end: 9, total length: 15, motif length:4] [start: 1, end: 8, total length: 17, motif length:8] [start: 2, end: 5, total length: 16, motif length:4] [start: 6, end: 9, total length: 16, motif length:4] [start: 1, end: 8, total length: 18, motif length:8] [start: 10, end: 13, total length: 10, motif length:4] [start: 3, end: 6, total length: 15, motif length:4] [start: 7, end: 10, total length: 15, motif length:4] [start: 0, end: 3, total length: 9, motif length:4] [start: 3, end: 6, total length: 16, motif length:4] [start: 7, end: 10, total length: 16, motif length:4] [start: 4, end: 7, total length: 15, motif length:4] [start: 8, end: 11, total length: 15, motif length:4] [start: 0, end: 3, total length: 16, motif length:4] [start: 1, end: 4, total length: 9, motif length:4] [start: 4, end: 7, total length: 16, motif length:4] [start: 8, end: 11, total length: 10, motif length:4] [start: 5, end: 8, total length: 15, motif length:4] [start: 0, end: 7, total length: 17, motif length:8] [start: 9, end: 12, total length: 15, motif length:4]

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0 CA-CAGG 5 6 CACCGGG 13 14 C 14

$ java Application data_sample_approx4.fasta 2 [start: 2, end: 5, total length: 10, motif length:4] [start: 1, end: 6, total length: 13, motif length:6] [start: 0, end: 5, total length: 14, motif length:6] [start: 1, end: 6, total length: 14, motif length:6] [start: 0, end: 3, total length: 10, motif length:4] [start: 1, end: 4, total length: 10, motif length:4] [start: 0, end: 5, total length: 13, motif length:6]

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Repeat of length 21 with 4 errors. Copy 1: CTC--GAG copy 2: CTCCTGAC copy 3: CTCGTGA

$ javac Application.java $ java Application data_sample_approx1.fasta 4 [start: 5, end: 10, total length: 16, motif length:6] [start: 0, end: 5, total length: 18, motif length:6] [start: 7, end: 12, total length: 16, motif length:6] [start: 0, end: 7, total length: 21, motif length:8] [start: 2, end: 7, total length: 18, motif length:6] [start: 2, end: 9, total length: 21, motif length:8] [start: 4, end: 9, total length: 18, motif length:6] [start: 4, end: 11, total length: 21, motif length:8] [start: 6, end: 11, total length: 16, motif length:6] [start: 1, end: 6, total length: 18, motif length:6] [start: 8, end: 13, total length: 16, motif length:6] [start: 1, end: 8, total length: 21, motif length:8] [start: 3, end: 8, total length: 18, motif length:6] [start: 3, end: 10, total length: 21, motif length:8] [start: 5, end: 10, total length: 18, motif length:6]

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