Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: scaffold9624.1 Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 1000 Length: 4315 ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36 Found at i:2422 original size:34 final size:33 Alignment explanation
Indices: 2350--2449 Score: 164 Period size: 34 Copynumber: 3.0 Consensus size: 33 2340 GTAAACTTCG * * 2350 ATTTAGTTGTCACTGTGTTGACCGAAAAGTTCA 1 ATTTAGTTGTCACTGTGTTGACCAAAAATTTCA 2383 ATTTAGTTGTCACTGTGTTGACCAAAAAATTTCA 1 ATTTAGTTGTCACTGTGTTGACC-AAAAATTTCA 2417 ATTTAGTTGTCACTGTGTTGACCGAAAAATTTC 1 ATTTAGTTGTCACTGTGTTGACC-AAAAATTTC 2450 GTTGGCCGAA Statistics Matches: 63, Mismatches: 3, Indels: 1 0.94 0.04 0.01 Matches are distributed among these distances: 33 23 0.37 34 40 0.63 ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38 Consensus pattern (33 bp): ATTTAGTTGTCACTGTGTTGACCAAAAATTTCA Found at i:2469 original size:16 final size:16 Alignment explanation
Indices: 2432--2476 Score: 54 Period size: 17 Copynumber: 2.8 Consensus size: 16 2422 GTTGTCACTG 2432 TGTTGACCGAAAAATT 1 TGTTGACCGAAAAATT * * 2448 TCGTTGGCCGAAAACTT 1 T-GTTGACCGAAAAATT * 2465 TGTTGCCCGAAA 1 TGTTGACCGAAA 2477 TTTTTATCAC Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 16 11 0.44 17 14 0.56 ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29 Consensus pattern (16 bp): TGTTGACCGAAAAATT Found at i:2567 original size:18 final size:18 Alignment explanation
Indices: 2518--2594 Score: 82 Period size: 18 Copynumber: 4.1 Consensus size: 18 2508 CGTCGAATTA * 2518 GTTGGCACTATGTTGCCC 1 GTTGGCACTATGTCGCCC * * * 2536 GAAATTGGCTCTTTGTTGCCC 1 G---TTGGCACTATGTCGCCC * 2557 GTTGGCACTTTGTCGCCC 1 GTTGGCACTATGTCGCCC 2575 GTTGGCACTATGTCGCCC 1 GTTGGCACTATGTCGCCC 2593 GT 1 GT 2595 AATTTTTGAC Statistics Matches: 51, Mismatches: 5, Indels: 6 0.82 0.08 0.10 Matches are distributed among these distances: 18 35 0.69 21 16 0.31 ACGTcount: A:0.10, C:0.29, G:0.27, T:0.34 Consensus pattern (18 bp): GTTGGCACTATGTCGCCC Done.