Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_35238

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: 3021
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28


Found at i:502 original size:24 final size:24

Alignment explanation


    Indices: 475--600  Score: 137
    Period size: 24  Copynumber: 5.2  Consensus size: 24

        465 TAGCCCGGCT

                    *               
        475 TTTGGTGCGACAAGCACCCCTGCG
          1 TTTGGTGCCACAAGCACCCCTGCG

                 *   *       *  *   
        499 TTTGGCGCCTCAAGCACTCCAG-G
          1 TTTGGTGCCACAAGCACCCCTGCG

                                     
        522 TTTCGGTGCCACAAGCACCCCTGCG
          1 TTT-GGTGCCACAAGCACCCCTGCG

                     *    *     *  *
        547 TTTGGTGCCTCAAGTACCCCCGCA
          1 TTTGGTGCCACAAGCACCCCTGCG

                       *           *
        571 TTTGGTGCCACGAGCACCCCTGCA
          1 TTTGGTGCCACAAGCACCCCTGCG

                  
        595 TTTGGT
          1 TTTGGT

        601 TCAACTGGAA


Statistics
Matches: 83,  Mismatches: 17, Indels: 4
        0.80            0.16        0.04

Matches are distributed among these distances:
  23    4  0.05
  24   75  0.90
  25    4  0.05

ACGTcount: A:0.16, C:0.35, G:0.25, T:0.24


Consensus pattern (24 bp):   
TTTGGTGCCACAAGCACCCCTGCG

Found at i:578 original size:48 final size:47

Alignment explanation


    Indices: 475--600  Score: 162
    Period size: 48  Copynumber: 2.6  Consensus size: 47

        465 TAGCCCGGCT

                    *                    *           *    *
        475 TTTGGTGCGACAAGCACCCCTGCGTTTGGCGCCTCAAGCACTCCAGG
          1 TTTGGTGCCACAAGCACCCCTGCGTTTGGTGCCTCAAGCACCCCAGA

                                                   *     *   
        522 TTTCGGTGCCACAAGCACCCCTGCGTTTGGTGCCTCAAGTACCCCCGCA
          1 TTT-GGTGCCACAAGCACCCCTGCGTTTGGTGCCTCAAGCACCCCAG-A

                       *           *      
        571 TTTGGTGCCACGAGCACCCCTGCATTTGGT
          1 TTTGGTGCCACAAGCACCCCTGCGTTTGGT

        601 TCAACTGGAA


Statistics
Matches: 69,  Mismatches: 8, Indels: 3
        0.86            0.10        0.04

Matches are distributed among these distances:
  47    3  0.04
  48   63  0.91
  49    3  0.04

ACGTcount: A:0.16, C:0.35, G:0.25, T:0.24


Consensus pattern (47 bp):   
TTTGGTGCCACAAGCACCCCTGCGTTTGGTGCCTCAAGCACCCCAGA

Found at i:740 original size:24 final size:23

Alignment explanation


    Indices: 700--782  Score: 57
    Period size: 24  Copynumber: 3.6  Consensus size: 23

        690 ATCAAGCTCA

                 *                   
        700 CCTGCGTTTGGCA-CTTCCGCAACT
          1 CCTGCTTTTGG-AGCTT-CGCAACT

                                 * 
        724 CCTGCTTTTGGAGCTT--CAAGT
          1 CCTGCTTTTGGAGCTTCGCAACT

            *          * *           
        745 TCTGCTTTTGGGGGTTCAAGC-ACT
          1 CCTGCTTTTGGAGCTTC--GCAACT

                          
        769 CCTGCTTTTGGAGC
          1 CCTGCTTTTGGAGC

        783 ATCTTCTACT


Statistics
Matches: 45,  Mismatches: 9, Indels: 10
        0.70            0.14        0.16

Matches are distributed among these distances:
  21   17  0.38
  23    1  0.02
  24   26  0.58
  25    1  0.02

ACGTcount: A:0.12, C:0.28, G:0.25, T:0.35


Consensus pattern (23 bp):   
CCTGCTTTTGGAGCTTCGCAACT

Found at i:751 original size:21 final size:22

Alignment explanation


    Indices: 722--782  Score: 70
    Period size: 21  Copynumber: 2.7  Consensus size: 22

        712 ACTTCCGCAA

                                  
        722 CTCCTGCTTTTGGAGCTTCAAG
          1 CTCCTGCTTTTGGAGCTTCAAG

              *          * *      
        744 -TTCTGCTTTTGGGGGTTCAAG
          1 CTCCTGCTTTTGGAGCTTCAAG

                              
        765 CACTCCTGCTTTTGGAGC
          1 --CTCCTGCTTTTGGAGC

        783 ATCTTCTACT


Statistics
Matches: 30,  Mismatches: 6, Indels: 4
        0.75            0.15        0.10

Matches are distributed among these distances:
  21   18  0.60
  24   12  0.40

ACGTcount: A:0.11, C:0.25, G:0.26, T:0.38


Consensus pattern (22 bp):   
CTCCTGCTTTTGGAGCTTCAAG
Done.