Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold714

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: 8986
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:156 original size:22 final size:22

Alignment explanation


    Indices: 128--170  Score: 77
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        118 CTGCGGCGCT

                            *     
        128 AAAAAGCGCCGCTAAAGGCCTA
          1 AAAAAGCGCCGCTAAAAGCCTA

                                 
        150 AAAAAGCGCCGCTAAAAGCCT
          1 AAAAAGCGCCGCTAAAAGCCT

        171 GTTTTGGTGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09


Consensus pattern (22 bp):   
AAAAAGCGCCGCTAAAAGCCTA

Found at i:5042 original size:40 final size:40

Alignment explanation


    Indices: 4998--5073  Score: 109
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       4988 ATTGCAGTCG

                        *                            
       4998 GAGCATTAGCGGCGCTTTTT-AGAAAACGCCGCTAAAAATA
          1 GAGCATTAGCGGAGCTTTTTGA-AAAACGCCGCTAAAAATA

                   *      *                     
       5038 GAGCATTCGCGGAGGTTTTTGAAAAACGCCGCTAAA
          1 GAGCATTAGCGGAGCTTTTTGAAAAACGCCGCTAAA

       5074 GCCCCGAAGA


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  40   31  0.97
  41    1  0.03

ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22


Consensus pattern (40 bp):   
GAGCATTAGCGGAGCTTTTTGAAAAACGCCGCTAAAAATA

Found at i:7153 original size:26 final size:28

Alignment explanation


    Indices: 7118--7170  Score: 74
    Period size: 26  Copynumber: 2.0  Consensus size: 28

       7108 GGTAATTTTC

                                        
       7118 TTTCATTTGCTTAATCCATGAC-ATGCT
          1 TTTCATTTGCTTAATCCATGACTATGCT

                         * *           
       7145 TTTCA-TTGCTTAGTTCATGACTATGC
          1 TTTCATTTGCTTAATCCATGACTATGC

       7171 AATGATTGTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  26   14  0.61
  27    9  0.39

ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45


Consensus pattern (28 bp):   
TTTCATTTGCTTAATCCATGACTATGCT

Done.