Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1031

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: 3236
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.21

Warning! 884 characters in sequence are not A, C, G, or T


Found at i:937 original size:52 final size:53

Alignment explanation


    Indices: 857--958  Score: 152
    Period size: 52  Copynumber: 1.9  Consensus size: 53

        847 TTAAGAAGTC

                                   *             *    *          
        857 TGACTTAATAACATGCATTGATGTTGTTCAAACTAGAGCATAGTTAATAGGTG
          1 TGACTTAATAACATGCATTGATGATGTTCAAACTAGAACATACTTAATAGGTG

                                         *  *                 
        910 TGACTTAA-AACATGCATTGATGATGTTCGAATTAGAACATACTTAATAG
          1 TGACTTAATAACATGCATTGATGATGTTCAAACTAGAACATACTTAATAG

        959 ACATAAATCA


Statistics
Matches: 44,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  52   36  0.82
  53    8  0.18

ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33


Consensus pattern (53 bp):   
TGACTTAATAACATGCATTGATGATGTTCAAACTAGAACATACTTAATAGGTG

Found at i:3091 original size:10 final size:10

Alignment explanation


    Indices: 3076--3137  Score: 52
    Period size: 10  Copynumber: 5.9  Consensus size: 10

       3066 TTTGAACCAT

                     *
       3076 TACCAATTCG
          1 TACCAATTCA

                     *  
       3086 TACCAAATACCA
          1 TACC-AAT-TCA

                 *    
       3098 TACCATTTCA
          1 TACCAATTCA

                       
       3108 TACCAATTCCA
          1 TACCAATT-CA

                 *   *
       3119 TACCATTTCG
          1 TACCAATTCA

                     
       3129 TACCAATTC
          1 TACCAATTC

       3138 CCAAATACCA


Statistics
Matches: 41,  Mismatches: 8, Indels: 6
        0.75            0.15        0.11

Matches are distributed among these distances:
  10   22  0.54
  11   14  0.34
  12    5  0.12

ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31


Consensus pattern (10 bp):   
TACCAATTCA

Found at i:3121 original size:21 final size:21

Alignment explanation


    Indices: 3076--3138  Score: 90
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       3066 TTTGAACCAT

                 *            *   
       3076 TACCAATTCGTACCAAATACCA
          1 TACCATTTCGTACC-AATTCCA

                     *           
       3098 TACCATTTCATACCAATTCCA
          1 TACCATTTCGTACCAATTCCA

                                
       3119 TACCATTTCGTACCAATTCC
          1 TACCATTTCGTACCAATTCC

       3139 CAAATACCAA


Statistics
Matches: 37,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  21   25  0.68
  22   12  0.32

ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30


Consensus pattern (21 bp):   
TACCATTTCGTACCAATTCCA
Done.