Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_09913

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, 700

Length: 1167
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.23


Found at i:538 original size:21 final size:20

Alignment explanation


    Indices: 512--551  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 20

        502 ATGAAAAAGC

                                 
        512 CCAATGCTGCTATTCGAGATG
          1 CCAATGCTGCT-TTCGAGATG

                         *     
        533 CCAATGCTGCTTTGGAGAT
          1 CCAATGCTGCTTTCGAGAT

        552 AAACCCAGAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    7  0.39
  21   11  0.61

ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30


Consensus pattern (20 bp):   
CCAATGCTGCTTTCGAGATG

Found at i:896 original size:24 final size:24

Alignment explanation


    Indices: 862--968  Score: 90
    Period size: 24  Copynumber: 4.5  Consensus size: 24

        852 TAGAAAACCT

                 *                   
        862 GGAGGCATGCCTGGTGGG-TTTCCA
          1 GGAGGAATGCCTGG-GGGTTTTCCA

              *                    *
        886 GGTGGAATGCCTGGGGGTTTTCCT
          1 GGAGGAATGCCTGGGGGTTTTCCA

                 *        *   * *  *
        910 GGAGGTATGCCTGGAGGTATGCCC
          1 GGAGGAATGCCTGGGGGTTTTCCA

                 *        *        *
        934 GGAGGTATGCCTGGAGGTTTTCCT
          1 GGAGGAATGCCTGGGGGTTTTCCA

                 *     
        958 GGAGGCATGCC
          1 GGAGGAATGCC

        969 AGGTGGCATG


Statistics
Matches: 69,  Mismatches: 13, Indels: 2
        0.82            0.15        0.02

Matches are distributed among these distances:
  23    3  0.04
  24   66  0.96

ACGTcount: A:0.13, C:0.20, G:0.41, T:0.26


Consensus pattern (24 bp):   
GGAGGAATGCCTGGGGGTTTTCCA

Found at i:922 original size:12 final size:12

Alignment explanation


    Indices: 892--984  Score: 96
    Period size: 12  Copynumber: 7.8  Consensus size: 12

        882 TCCAGGTGGA

                    *   
        892 ATGCCTGGGGGT
          1 ATGCCTGGAGGT

            * *         
        904 TTTCCTGGAGGT
          1 ATGCCTGGAGGT

                        
        916 ATGCCTGGAGGT
          1 ATGCCTGGAGGT

                 *      
        928 ATGCCCGGAGGT
          1 ATGCCTGGAGGT

                        
        940 ATGCCTGGAGGT
          1 ATGCCTGGAGGT

            * *        *
        952 TTTCCTGGAGGC
          1 ATGCCTGGAGGT

                 *  *  *
        964 ATGCCAGGTGGC
          1 ATGCCTGGAGGT

                     
        976 ATGCCTGGA
          1 ATGCCTGGA

        985 AATGTTGATT


Statistics
Matches: 65,  Mismatches: 16, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  12   65  1.00

ACGTcount: A:0.14, C:0.20, G:0.40, T:0.26


Consensus pattern (12 bp):   
ATGCCTGGAGGT

Found at i:980 original size:48 final size:48

Alignment explanation


    Indices: 859--980  Score: 145
    Period size: 48  Copynumber: 2.5  Consensus size: 48

        849 CAGTAGAAAA

                                ** *     *           *      
        859 CCTGGAGGCATGCCTGGTGGGTTTCCAGGTGGAATGCCTGGGGGTTTT
          1 CCTGGAGGCATGCCTGGTGGCATGCCAGGAGGAATGCCTGGAGGTTTT

                    *        *  *     *     *               
        907 CCTGGAGGTATGCCTGGAGGTATGCCCGGAGGTATGCCTGGAGGTTTT
          1 CCTGGAGGCATGCCTGGTGGCATGCCAGGAGGAATGCCTGGAGGTTTT

                          *           
        955 CCTGGAGGCATGCCAGGTGGCATGCC
          1 CCTGGAGGCATGCCTGGTGGCATGCC

        981 TGGAAATGTT


Statistics
Matches: 61,  Mismatches: 13, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  48   61  1.00

ACGTcount: A:0.13, C:0.21, G:0.40, T:0.25


Consensus pattern (48 bp):   
CCTGGAGGCATGCCTGGTGGCATGCCAGGAGGAATGCCTGGAGGTTTT
Done.