Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold172

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: 1975206
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.26

Warning! 344189 characters in sequence are not A, C, G, or T


File 11 of 11

Found at i:1969315 original size:20 final size:20

Alignment explanation

Indices: 1969292--1969364 Score: 101 Period size: 20 Copynumber: 3.6 Consensus size: 20 1969282 ACAATTCAAA 1969292 GTATCGATACATGTTGCAAT 1 GTATCGATACATGTTGCAAT **** 1969312 GTATCGATACATGAAAAAGAT 1 GTATCGATACATGTTGCA-AT 1969333 GTATCGATACATGTTGCAAT 1 GTATCGATACATGTTGCAAT 1969353 GTATCGATACAT 1 GTATCGATACAT 1969365 AAAAAAGATG Statistics Matches: 44, Mismatches: 8, Indels: 2 0.81 0.15 0.04 Matches are distributed among these distances: 20 28 0.64 21 16 0.36 ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32 Consensus pattern (20 bp): GTATCGATACATGTTGCAAT Found at i:1969336 original size:21 final size:21 Alignment explanation

Indices: 1969310--1969385 Score: 100 Period size: 21 Copynumber: 3.7 Consensus size: 21 1969300 ACATGTTGCA 1969310 ATGTATCGATACATGAAAAAG 1 ATGTATCGATACATGAAAAAG **** 1969331 ATGTATCGATACATGTTGCA- 1 ATGTATCGATACATGAAAAAG * 1969351 ATGTATCGATACATAAAAAAG 1 ATGTATCGATACATGAAAAAG 1969372 ATGTATCGATACAT 1 ATGTATCGATACAT 1969386 TTCTTGGCAG Statistics Matches: 45, Mismatches: 9, Indels: 2 0.80 0.16 0.04 Matches are distributed among these distances: 20 15 0.33 21 30 0.67 ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29 Consensus pattern (21 bp): ATGTATCGATACATGAAAAAG Found at i:1969343 original size:41 final size:41 Alignment explanation

Indices: 1969292--1969385 Score: 179 Period size: 41 Copynumber: 2.3 Consensus size: 41 1969282 ACAATTCAAA * 1969292 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT 1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT 1969333 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT 1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT 1969374 GTATCGATACAT 1 GTATCGATACAT 1969386 TTCTTGGCAG Statistics Matches: 52, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 41 52 1.00 ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30 Consensus pattern (41 bp): GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT Found at i:1969442 original size:13 final size:13 Alignment explanation

Indices: 1969424--1969449 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 1969414 TACAGCAAGT 1969424 ATGTATCGATACA 1 ATGTATCGATACA 1969437 ATGTATCGATACA 1 ATGTATCGATACA 1969450 CAAAAAATTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): ATGTATCGATACA Found at i:1973532 original size:15 final size:15 Alignment explanation

Indices: 1973512--1973542 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 1973502 TAAAAATGTC * 1973512 CAAAATGAGGAAGCT 1 CAAAATGAAGAAGCT 1973527 CAAAATGAAGAAGCT 1 CAAAATGAAGAAGCT 1973542 C 1 C 1973543 CAAACGAAAT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13 Consensus pattern (15 bp): CAAAATGAAGAAGCT Done.