Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold810

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: 5984
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33


Found at i:552 original size:3 final size:3

Alignment explanation


    Indices: 546--575  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

        536 ATTATTATTA

                                                   
        546 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
          1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG

        576 ACTCATTTAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67


Consensus pattern (3 bp):   
TTG

Found at i:628 original size:8 final size:8

Alignment explanation


    Indices: 615--642  Score: 56
    Period size: 8  Copynumber: 3.5  Consensus size: 8

        605 TTTGTTATGC

                    
        615 ACATATAT
          1 ACATATAT

                    
        623 ACATATAT
          1 ACATATAT

                    
        631 ACATATAT
          1 ACATATAT

                
        639 ACAT
          1 ACAT

        643 TTTTATATTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   20  1.00

ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36


Consensus pattern (8 bp):   
ACATATAT

Found at i:710 original size:4 final size:4

Alignment explanation


    Indices: 701--737  Score: 65
    Period size: 4  Copynumber: 9.2  Consensus size: 4

        691 TTGCTTGATG

                            *                             
        701 TTTA TTTA TTTA TGTA TTTA TTTA TTTA TTTA TTTA T
          1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T

        738 ATGTCAATTA


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   4   31  1.00

ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73


Consensus pattern (4 bp):   
TTTA

Found at i:4833 original size:3 final size:3

Alignment explanation


    Indices: 4825--4857  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

       4815 TCTGTCAAAA

                                                       
       4825 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG

       4858 GAAAACATTC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:5892 original size:22 final size:20

Alignment explanation


    Indices: 5845--5892  Score: 51
    Period size: 22  Copynumber: 2.3  Consensus size: 20

       5835 TTGTCTAAGC

                              * 
       5845 ATATATAATTAATGATATTA
          1 ATATATAATTAATGATATGA

             *             *      
       5865 AAATATAATTTATATTATATGA
          1 ATATATAA-TTA-ATGATATGA

                  
       5887 ATATAT
          1 ATATAT

       5893 GATAATTAAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  20    7  0.32
  21    3  0.14
  22   12  0.55

ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46


Consensus pattern (20 bp):   
ATATATAATTAATGATATGA
Done.