Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3152

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: 9170
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31


Found at i:7671 original size:27 final size:26

Alignment explanation


    Indices: 7626--7688  Score: 81
    Period size: 27  Copynumber: 2.3  Consensus size: 26

       7616 TAGATGTGCT

                                   *   
       7626 ATTATACCCCTATGATGCAAAATTACC
          1 ATTATA-CCCTATGATGCAAAATGACC

                          *            
       7653 ATTATACCCTATGTTTGCAAAATGACC
          1 ATTATACCCTATG-ATGCAAAATGACC

            *        
       7680 TTTATACCC
          1 ATTATACCC

       7689 CTAGGGTTAA


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

Matches are distributed among these distances:
  26    7  0.22
  27   25  0.78

ACGTcount: A:0.33, C:0.25, G:0.08, T:0.33


Consensus pattern (26 bp):   
ATTATACCCTATGATGCAAAATGACC

Found at i:7829 original size:27 final size:27

Alignment explanation


    Indices: 7797--7885  Score: 110
    Period size: 28  Copynumber: 3.2  Consensus size: 27

       7787 AGGAAGCGTC

                        *               
       7797 CTGGTGGCTATGACA-AAATTATCTGTT
          1 CTGGTGGC-ATGCCACAAATTATCTGTT

                     *                  
       7824 CTGGTGGCCCTGCCACAAATTATCTGTT
          1 CTGGTGG-CATGCCACAAATTATCTGTT

                                         
       7852 CTGGTGGCACTGCCACAAA-TATCTGTAT
          1 CTGGTGGCA-TGCCACAAATTATCTGT-T

                  
       7880 CTGGTG
          1 CTGGTG

       7886 ACTCTGTCAC


Statistics
Matches: 55,  Mismatches: 3, Indels: 7
        0.85            0.05        0.11

Matches are distributed among these distances:
  27   19  0.35
  28   36  0.65

ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33


Consensus pattern (27 bp):   
CTGGTGGCATGCCACAAATTATCTGTT

Found at i:7847 original size:28 final size:28

Alignment explanation


    Indices: 7812--7885  Score: 123
    Period size: 28  Copynumber: 2.6  Consensus size: 28

       7802 GGCTATGACA

                                *       
       7812 AAATTATCTGTTCTGGTGGCCCTGCCAC
          1 AAATTATCTGTTCTGGTGGCACTGCCAC

                                        
       7840 AAATTATCTGTTCTGGTGGCACTGCCAC
          1 AAATTATCTGTTCTGGTGGCACTGCCAC

                               
       7868 AAA-TATCTGTATCTGGTG
          1 AAATTATCTGT-TCTGGTG

       7886 ACTCTGTCAC


Statistics
Matches: 44,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  27    7  0.16
  28   37  0.84

ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34


Consensus pattern (28 bp):   
AAATTATCTGTTCTGGTGGCACTGCCAC

Found at i:8373 original size:20 final size:20

Alignment explanation


    Indices: 8348--8388  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       8338 CTTTTAATTA

                    *    *      
       8348 TTTTTATGGTTTTGTTTTAC
          1 TTTTTATGATTTTATTTTAC

                   *            
       8368 TTTTTATTATTTTATTTTAC
          1 TTTTTATGATTTTATTTTAC

             
       8388 T
          1 T

       8389 ATGATGAAAA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.15, C:0.05, G:0.07, T:0.73


Consensus pattern (20 bp):   
TTTTTATGATTTTATTTTAC
Done.