Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1236

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: 7644
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35


Found at i:4189 original size:19 final size:20

Alignment explanation


    Indices: 4164--4237  Score: 73
    Period size: 19  Copynumber: 3.8  Consensus size: 20

       4154 TGTATCTATA

                                
       4164 CATTGTATCGATACA-AGTT
          1 CATTGTATCGATACATAGTT

            *               *   
       4183 TATTGTATCGATACATTGTT
          1 CATTGTATCGATACATAGTT

                     *        **
       4203 CATTGTATCAAT-CAT-GGA
          1 CATTGTATCGATACATAGTT

                             
       4221 CAATTGTATCGATACAT
          1 C-ATTGTATCGATACAT

       4238 GAAACTGGCA


Statistics
Matches: 45,  Mismatches: 7, Indels: 5
        0.79            0.12        0.09

Matches are distributed among these distances:
  18    2  0.04
  19   27  0.60
  20   16  0.36

ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39


Consensus pattern (20 bp):   
CATTGTATCGATACATAGTT

Found at i:5165 original size:31 final size:31

Alignment explanation


    Indices: 5112--5170  Score: 75
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       5102 TTTAAAATTA

                *          *       *       
       5112 TTCTTAAAGAATTCAGTCTCTTTTTATAAAG
          1 TTCTAAAAGAATTCACTCTCTTTATATAAAG

                                         
       5143 TTCTAAAAGAATCTCACT-TCTTTATATA
          1 TTCTAAAAGAAT-TCACTCTCTTTATATA

       5171 TCTTTTATTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  31   20  0.83
  32    4  0.17

ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44


Consensus pattern (31 bp):   
TTCTAAAAGAATTCACTCTCTTTATATAAAG

Found at i:5660 original size:31 final size:31

Alignment explanation


    Indices: 5618--5689  Score: 81
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       5608 TTTAAACTTG

                  *                       *
       5618 TGCTTAAGAGTAATATAACAACCTAAGCTCT
          1 TGCTTAGGAGTAATATAACAACCTAAGCTCA

                        *   *    ** *      
       5649 TGCTTAGGAGTAGTATGACAATTTTAGCTCA
          1 TGCTTAGGAGTAATATAACAACCTAAGCTCA

                      
       5680 TGCTTAGGAG
          1 TGCTTAGGAG

       5690 CATCATTATT


Statistics
Matches: 34,  Mismatches: 7, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  31   34  1.00

ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32


Consensus pattern (31 bp):   
TGCTTAGGAGTAATATAACAACCTAAGCTCA
Done.