Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2683

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: 12600
ACGTcount: A:0.18, C:0.29, G:0.34, T:0.20


Found at i:11085 original size:64 final size:64

Alignment explanation


    Indices: 10984--11105  Score: 199
    Period size: 64  Copynumber: 1.9  Consensus size: 64

      10974 CACCGATAGC

                                 *                                          
      10984 ACATGCGGAGGCCCAAGCGTGGGCAACGAGTCCCTCCCAACCATCCGGCCCTCCCCCCTCTCTA
          1 ACATGCGGAGGCCCAAGCGTGCGCAACGAGTCCCTCCCAACCATCCGGCCCTCCCCCCTCTCTA

                       *                          * *      *          
      11048 ACATGCGGAGGGCCAAGCGTGCGCAACGAGTCCCTCCCCAGCATCCGTCCCTCCCCCC
          1 ACATGCGGAGGCCCAAGCGTGCGCAACGAGTCCCTCCCAACCATCCGGCCCTCCCCCC

      11106 CAACCAAACG


Statistics
Matches: 53,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  64   53  1.00

ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13


Consensus pattern (64 bp):   
ACATGCGGAGGCCCAAGCGTGCGCAACGAGTCCCTCCCAACCATCCGGCCCTCCCCCCTCTCTA

Found at i:11353 original size:63 final size:62

Alignment explanation


    Indices: 11165--11359  Score: 200
    Period size: 63  Copynumber: 3.1  Consensus size: 62

      11155 CGACAACGGT

                      *             *                                      
      11165 GCGCACCCGGTGCCCCGCGAGGTGTGCGCCCCGACCGCCCCCACCCCAGGGGGCGGGAAGGGC
          1 GCGCA-CCGGCGCCCCGCGAGGTGCGCGCCCCGACCGCCCCCACCCCAGGGGGCGGGAAGGGC

                *      *     *      *  *   *  *      *        *        *     
      11228 GCGCCCCGTGCTCCCGCCCG-GGTCCGTGCCGCGGCCGCCCGCA--CCAGAGGGCGGG-CGAGGC
          1 GCGCACCG-GCGCCC-CGCGAGGTGCGCGCCCCGACCGCCCCCACCCCAGGGGGCGGGAAG-GGC

                                   *                                       
      11289 GCGCACCGGCGCCCCGCGAGGTGGGCGCCCCGACCGCCCCCCACCCCAGGGGGCGGGAAGGGC
          1 GCGCACCGGCGCCCCGCGAGGTGCGCGCCCCGACCG-CCCCCACCCCAGGGGGCGGGAAGGGC

                    
      11352 GCGCACCG
          1 GCGCACCG

      11360 TGCTCCTGGC


Statistics
Matches: 101,  Mismatches: 23, Indels: 16
        0.72            0.16        0.11

Matches are distributed among these distances:
  59    3  0.03
  60   18  0.18
  61   26  0.26
  62    3  0.03
  63   47  0.47
  64    4  0.04

ACGTcount: A:0.10, C:0.46, G:0.41, T:0.04


Consensus pattern (62 bp):   
GCGCACCGGCGCCCCGCGAGGTGCGCGCCCCGACCGCCCCCACCCCAGGGGGCGGGAAGGGC

Found at i:11387 original size:103 final size:101

Alignment explanation


    Indices: 11266--11454  Score: 297
    Period size: 103  Copynumber: 1.9  Consensus size: 101

      11256 CCGCGGCCGC

                                                                             
      11266 CCGCACCAGAGGGCGGGCGAGGCGCGCACCGGCGCCCCGCGAGGTGGGCGCCCCGACCGCCCCCC
          1 CCGCACCAGAGGGCGGGCGAGGCGCGCACCGGCGCCCCGCGAGGTGGGCGCCCCGACCG-CCCCC

               *                                  
      11331 ACCCCAGGGGGCGGGAAGGGCGCGCACCGTGCTCCTGG
         65 ACCAC-GGGGGCGGGAAGGGCGCGCACCGTGCTCCTGG

                   *     *                     *     *    *        *         
      11369 CCGCACCCGAGGGTGGGCGAGGCGCGCACCGGCGCTCCGCGTGGTGTGCGCCCCGGCCGCCCCCA
          1 CCGCACCAGAGGGCGGGCGAGGCGCGCACCGGCGCCCCGCGAGGTGGGCGCCCCGACCGCCCCCA

                                 
      11434 CCACGGGGGCGGGAAGGGCGC
         66 CCACGGGGGCGGGAAGGGCGC

      11455 CCCCGGGCCG


Statistics
Matches: 79,  Mismatches: 7, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
 101   17  0.22
 102    9  0.11
 103   53  0.67

ACGTcount: A:0.11, C:0.42, G:0.43, T:0.05


Consensus pattern (101 bp):   
CCGCACCAGAGGGCGGGCGAGGCGCGCACCGGCGCCCCGCGAGGTGGGCGCCCCGACCGCCCCCA
CCACGGGGGCGGGAAGGGCGCGCACCGTGCTCCTGG
Done.