Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2309

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: 51500
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:34 original size:15 final size:16

Alignment explanation

Indices: 14--44 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 4 ATCTCCATCG 14 TTAGT-AACATGTACC 1 TTAGTAAACATGTACC 29 TTAGTAAACATGTACC 1 TTAGTAAACATGTACC 45 AATATGTTGG Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 5 0.33 16 10 0.67 ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32 Consensus pattern (16 bp): TTAGTAAACATGTACC Found at i:3027 original size:31 final size:31 Alignment explanation

Indices: 2992--3050 Score: 82 Period size: 31 Copynumber: 1.9 Consensus size: 31 2982 CAAAATAATC * * * 2992 ATTAAATTATTCAAATGTTTTCATTTAATTT 1 ATTAAACTATTAAAAAGTTTTCATTTAATTT * 3023 ATTAAACTATTAAAAAGTTTTTATTTAA 1 ATTAAACTATTAAAAAGTTTTCATTTAA 3051 ACCACTGGCT Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 31 24 1.00 ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51 Consensus pattern (31 bp): ATTAAACTATTAAAAAGTTTTCATTTAATTT Found at i:3954 original size:18 final size:19 Alignment explanation

Indices: 3931--3972 Score: 59 Period size: 19 Copynumber: 2.3 Consensus size: 19 3921 TTTGGGTATC * 3931 TAAAATTGAT-TTCATTAT 1 TAAAATTAATATTCATTAT * 3949 TAAAATTAATATTGATTAT 1 TAAAATTAATATTCATTAT 3968 TAAAA 1 TAAAA 3973 AGAATTACAG Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 18 9 0.43 19 12 0.57 ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45 Consensus pattern (19 bp): TAAAATTAATATTCATTAT Found at i:4137 original size:6 final size:6 Alignment explanation

Indices: 4126--4167 Score: 84 Period size: 6 Copynumber: 7.0 Consensus size: 6 4116 ACGGGAGGGA 4126 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG 1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG 4168 AACGAAGCTG Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 36 1.00 ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00 Consensus pattern (6 bp): GAGAGG Found at i:8984 original size:29 final size:29 Alignment explanation

Indices: 8942--8999 Score: 116 Period size: 29 Copynumber: 2.0 Consensus size: 29 8932 TTTTCCTCCC 8942 TTTTTGTGGCCATCAAAGCTCATAGTTTG 1 TTTTTGTGGCCATCAAAGCTCATAGTTTG 8971 TTTTTGTGGCCATCAAAGCTCATAGTTTG 1 TTTTTGTGGCCATCAAAGCTCATAGTTTG 9000 GTAGACTTTA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 29 29 1.00 ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41 Consensus pattern (29 bp): TTTTTGTGGCCATCAAAGCTCATAGTTTG Found at i:10026 original size:31 final size:31 Alignment explanation

Indices: 9988--10051 Score: 119 Period size: 31 Copynumber: 2.1 Consensus size: 31 9978 AGCCTTCCTT * 9988 TGTCATACCTCTATGCCTTCGCTCATCATAG 1 TGTCATACCTCTATGCCTTAGCTCATCATAG 10019 TGTCATACCTCTATGCCTTAGCTCATCATAG 1 TGTCATACCTCTATGCCTTAGCTCATCATAG 10050 TG 1 TG 10052 AGTAAACGTG Statistics Matches: 32, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 32 1.00 ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36 Consensus pattern (31 bp): TGTCATACCTCTATGCCTTAGCTCATCATAG Found at i:10252 original size:25 final size:25 Alignment explanation

Indices: 10224--10274 Score: 102 Period size: 25 Copynumber: 2.0 Consensus size: 25 10214 CAAGTGAGTC 10224 GATCAGGACTTCCATCAAGCATTGG 1 GATCAGGACTTCCATCAAGCATTGG 10249 GATCAGGACTTCCATCAAGCATTGG 1 GATCAGGACTTCCATCAAGCATTGG 10274 G 1 G 10275 GGCATTAAAC Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24 Consensus pattern (25 bp): GATCAGGACTTCCATCAAGCATTGG Found at i:17229 original size:2 final size:2 Alignment explanation

Indices: 17210--17245 Score: 54 Period size: 2 Copynumber: 18.0 Consensus size: 2 17200 AAAGAGAAAC * * 17210 AG AG AT AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 17246 GTGCTTCATT Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.44, T:0.06 Consensus pattern (2 bp): AG Done.