Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3142

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: 20712
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30


Found at i:7185 original size:27 final size:27

Alignment explanation


    Indices: 7154--7331  Score: 196
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       7144 TAAATTGTAC

                            *          
       7154 AGCACTAAGTGTGCGATTTGACTATGT
          1 AGCACTAAGTGTGCGAATTGACTATGT

            *                *   *     
       7181 TGCACTAAGTGTGCGAAATGAATATG-
          1 AGCACTAAGTGTGCGAATTGACTATGT

                                   *   *
       7207 ATGCACTAAGTGTGCGAATTGACCATGC
          1 A-GCACTAAGTGTGCGAATTGACTATGT

            *               *          
       7235 GGCACTAAGTGTGCGAGTTGACTATGT
          1 AGCACTAAGTGTGCGAATTGACTATGT

                             *    *     
       7262 AGCACTAAGTGTGCGAGTTTGATTATGT
          1 AGCACTAAGTGTGCGA-ATTGACTATGT

            *               *    *   * 
       7290 GGCACTAAGTGTGCGAGTTGATTATAT
          1 AGCACTAAGTGTGCGAATTGACTATGT

                  *        
       7317 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

       7332 GACTTAATAT


Statistics
Matches: 128,  Mismatches: 20, Indels: 6
        0.83            0.13        0.04

Matches are distributed among these distances:
  27  104  0.81
  28   24  0.19

ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30


Consensus pattern (27 bp):   
AGCACTAAGTGTGCGAATTGACTATGT

Found at i:7215 original size:54 final size:55

Alignment explanation


    Indices: 7154--7331  Score: 236
    Period size: 54  Copynumber: 3.3  Consensus size: 55

       7144 TAAATTGTAC

                                       *               **          
       7154 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
          1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT

                            *     *   *                     *      
       7209 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T
          1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT

                                  *                          *      
       7262 AGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAGTTGATTAT-AT
          1 AGCACTAAGTGTGCGA-TTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT

                  *        
       7317 AGCACTGAGTGTGCG
          1 AGCACTAAGTGTGCG

       7332 GACTTAATAT


Statistics
Matches: 107,  Mismatches: 13, Indels: 6
        0.85            0.10        0.05

Matches are distributed among these distances:
  53    1  0.01
  54   60  0.56
  55   46  0.43

ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30


Consensus pattern (55 bp):   
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTTGAATATGAT

Found at i:14533 original size:40 final size:40

Alignment explanation


    Indices: 14485--14711  Score: 409
    Period size: 40  Copynumber: 5.7  Consensus size: 40

      14475 GCAAACACAT

                            *      *                
      14485 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                          * *       
      14525 TTGCCTTCGGGTCTTAGCCCGGATATATCATCCCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                         *                          
      14565 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                                    
      14605 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                                    
      14645 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                       
      14685 TTGCCTTCGGGTCTTAGCCCGGATATA
          1 TTGCCTTCGGGTCTTAGCCCGGATATA

      14712 ATCCAATGTT


Statistics
Matches: 179,  Mismatches: 8, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  40  179  1.00

ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30


Consensus pattern (40 bp):   
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

Done.