Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_4532

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: 14492
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32


Found at i:2302 original size:26 final size:26

Alignment explanation


    Indices: 2253--2302  Score: 73
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       2243 GTCTGAAGAC

                        *     *       
       2253 CCTTGAGTTTGATTTGGTTAGAGATT
          1 CCTTGAGTTTGAGTTGGTCAGAGATT

                               *    
       2279 CCTTGAGTTTGAGTTGGTCGGAGA
          1 CCTTGAGTTTGAGTTGGTCAGAGA

       2303 CCATGAAGAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  26   21  1.00

ACGTcount: A:0.18, C:0.10, G:0.32, T:0.40


Consensus pattern (26 bp):   
CCTTGAGTTTGAGTTGGTCAGAGATT

Found at i:3846 original size:86 final size:86

Alignment explanation


    Indices: 3701--3947  Score: 370
    Period size: 86  Copynumber: 2.9  Consensus size: 86

       3691 ATGCATAAGA

                    *              *      *                                  
       3701 TTGAG-TTATTACTCTTAATGAATTCATAGCCCAAAGTTTGGGTGGTCCTATTGAGACGGACTTG
          1 TTGAGTTTCTTACTCTTAATGAACTCATA-TCCAAAGTTTGGGTGGTCCTATTGAGACGGACTTG

                                  
       3765 ATGAATTCACCGACATATGAGG
         65 ATGAATTCACCGACATATGAGG

                                                    *   *                    
       3787 TTGAGTTTCTTACTCTTAATGAACTCATATCCAAAGTTTGAGTGATCCTATTGAGACGGACTTGA
          1 TTGAGTTTCTTACTCTTAATGAACTCATATCCAAAGTTTGGGTGGTCCTATTGAGACGGACTTGA

                     *     *     
       3852 TGAATTCACTGACATGTGAGG
         66 TGAATTCACCGACATATGAGG

              *                   *                        **                
       3873 TTAAGTTTCTTACTCTTAATGAGCTCATATCCTAAAGTTTGGGTGGTTTTATTGAGACGGACTTG
          1 TTGAGTTTCTTACTCTTAATGAACTCATATCC-AAAGTTTGGGTGGTCCTATTGAGACGGACTTG

                      
       3938 ATGAATTCAC
         65 ATGAATTCAC

       3948 TGAATTTTAA


Statistics
Matches: 146,  Mismatches: 13, Indels: 3
        0.90            0.08        0.02

Matches are distributed among these distances:
  86   87  0.60
  87   59  0.40

ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36


Consensus pattern (86 bp):   
TTGAGTTTCTTACTCTTAATGAACTCATATCCAAAGTTTGGGTGGTCCTATTGAGACGGACTTGA
TGAATTCACCGACATATGAGG

Found at i:8152 original size:43 final size:43

Alignment explanation


    Indices: 8091--8176  Score: 136
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       8081 ATCACATGTA

                      *         *                *     
       8091 TCGCATCCATTATGAACTCGGACCACTCAACGAGCTCGGATGC
          1 TCGCATCCATAATGAACTCGAACCACTCAACGAGCTCAGATGC

                                    *                  
       8134 TCGCATCCATAATGAACTCGAACCTCTCAACGAGCTCAGATGC
          1 TCGCATCCATAATGAACTCGAACCACTCAACGAGCTCAGATGC

       8177 CACATATATC


Statistics
Matches: 39,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  43   39  1.00

ACGTcount: A:0.28, C:0.33, G:0.19, T:0.21


Consensus pattern (43 bp):   
TCGCATCCATAATGAACTCGAACCACTCAACGAGCTCAGATGC
Done.