Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3208

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: 9737
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31


Found at i:573 original size:39 final size:39

Alignment explanation


    Indices: 489--599  Score: 116
    Period size: 40  Copynumber: 2.8  Consensus size: 39

        479 AGATACTAAT

                                      **      *     
        489 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
          1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA

                                       *         ** 
        529 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
          1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA

                  *  *                      
        569 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
          1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG

        600 GAGCTATATC


Statistics
Matches: 60,  Mismatches: 9, Indels: 4
        0.82            0.12        0.05

Matches are distributed among these distances:
  39   25  0.42
  40   35  0.58

ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24


Consensus pattern (39 bp):   
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA

Found at i:5987 original size:12 final size:12

Alignment explanation


    Indices: 5956--5990  Score: 61
    Period size: 12  Copynumber: 2.9  Consensus size: 12

       5946 CTGGGTTTTT

                   *    
       5956 AGACACGAGCGA
          1 AGACACGGGCGA

                        
       5968 AGACACGGGCGA
          1 AGACACGGGCGA

                       
       5980 AGACACGGGCG
          1 AGACACGGGCG

       5991 TGTCTAGGCA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  12   22  1.00

ACGTcount: A:0.34, C:0.26, G:0.40, T:0.00


Consensus pattern (12 bp):   
AGACACGGGCGA

Found at i:6020 original size:28 final size:29

Alignment explanation


    Indices: 5980--6035  Score: 87
    Period size: 28  Copynumber: 2.0  Consensus size: 29

       5970 ACACGGGCGA

                   *                     
       5980 AGACACGGGCGTGT-CTAGGCAGTGTGAG
          1 AGACACGAGCGTGTGCTAGGCAGTGTGAG

                             *          
       6008 AGACACGAGCGTGTGCTTGGCAGTGTGA
          1 AGACACGAGCGTGTGCTAGGCAGTGTGA

       6036 AAACCCCTAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  28   13  0.52
  29   12  0.48

ACGTcount: A:0.21, C:0.18, G:0.41, T:0.20


Consensus pattern (29 bp):   
AGACACGAGCGTGTGCTAGGCAGTGTGAG
Done.