Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold938

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: 4073
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.23

Warning! 701 characters in sequence are not A, C, G, or T


Found at i:102 original size:21 final size:21

Alignment explanation


    Indices: 78--220  Score: 80
    Period size: 21  Copynumber: 6.9  Consensus size: 21

         68 AGGGTTTTCC

                     *           
         78 GGTTTTCAATGTGGTTTTTGT
          1 GGTTTTCAACGTGGTTTTTGT

                  *   *      **  
         99 GGTTTTAAACCTGGTTTCAGT
          1 GGTTTTCAACGTGGTTTTTGT

                 **             **
        120 GGTTTAAAACAG-GG-TTTTCC
          1 GGTTTTCAAC-GTGGTTTTTGT

                                 
        140 GGTTTTCAACGTGGTTTTTGT
          1 GGTTTTCAACGTGGTTTTTGT

                  *   *      **  
        161 GGTTTTAAACCTGGTTTCAGT
          1 GGTTTTCAACGTGGTTTTTGT

                                 **
        182 GG-TTTCAAACAG-GG-TTTTCC
          1 GGTTTTC-AAC-GTGGTTTTTGT

                     *         
        202 GGTTTTCAATGTGGTTTTT
          1 GGTTTTCAACGTGGTTTTT

        221 CTCGTTTTGA


Statistics
Matches: 88,  Mismatches: 26, Indels: 16
        0.68            0.20        0.12

Matches are distributed among these distances:
  19    2  0.02
  20   23  0.26
  21   63  0.72

ACGTcount: A:0.16, C:0.12, G:0.26, T:0.46


Consensus pattern (21 bp):   
GGTTTTCAACGTGGTTTTTGT

Found at i:206 original size:41 final size:41

Alignment explanation


    Indices: 31--207  Score: 94
    Period size: 41  Copynumber: 4.3  Consensus size: 41

         21 CCAGGTTGGT

                *                       **            
         31 TTTTGCGGTTTTAAACCTGGTTTCAGT-AATTCGAAACAGGG
          1 TTTTCCGGTTTTAAACCTGGTTTCAGTGGTTTC-AAACAGGG

                        *  **      **       *    **  
         72 TTTTCCGGTTTTCAATGTGGTTTTTGTGGTTTTAAACCTGG
          1 TTTTCCGGTTTTAAACCTGGTTTCAGTGGTTTCAAACAGGG

                   *     *    **       *   *             
        113 -TTTCAGTGGTTTAAAACAGGGTTTTCCG-GTTTTC-AAC-GTGG
          1 TTTTC--CGGTTTTAAACCTGG-TTTCAGTGGTTTCAAACAG-GG

                 **                                   
        154 TTTTTGTGGTTTTAAACCTGGTTTCAGTGGTTTCAAACAGGG
          1 -TTTTCCGGTTTTAAACCTGGTTTCAGTGGTTTCAAACAGGG

                        
        196 TTTTCCGGTTTT
          1 TTTTCCGGTTTT

        208 CAATGTGGTT


Statistics
Matches: 96,  Mismatches: 30, Indels: 20
        0.66            0.21        0.14

Matches are distributed among these distances:
  40    9  0.09
  41   59  0.61
  42   20  0.21
  43    8  0.08

ACGTcount: A:0.18, C:0.14, G:0.25, T:0.44


Consensus pattern (41 bp):   
TTTTCCGGTTTTAAACCTGGTTTCAGTGGTTTCAAACAGGG

Found at i:228 original size:62 final size:62

Alignment explanation


    Indices: 27--220  Score: 327
    Period size: 62  Copynumber: 3.1  Consensus size: 62

         17 GTTCCCAGGT

                     *                      **                             
         27 TGGTTTTTGCGGTTTTAAACCTGGTTTCAGT-AATTCGAAACAGGGTTTTCCGGTTTTCAATG
          1 TGGTTTTTGTGGTTTTAAACCTGGTTTCAGTGGTTTC-AAACAGGGTTTTCCGGTTTTCAATG

                                                *                       * 
         89 TGGTTTTTGTGGTTTTAAACCTGGTTTCAGTGGTTTAAAACAGGGTTTTCCGGTTTTCAACG
          1 TGGTTTTTGTGGTTTTAAACCTGGTTTCAGTGGTTTCAAACAGGGTTTTCCGGTTTTCAATG

                                                                          
        151 TGGTTTTTGTGGTTTTAAACCTGGTTTCAGTGGTTTCAAACAGGGTTTTCCGGTTTTCAATG
          1 TGGTTTTTGTGGTTTTAAACCTGGTTTCAGTGGTTTCAAACAGGGTTTTCCGGTTTTCAATG

                    
        213 TGGTTTTT
          1 TGGTTTTT

        221 CTCGTTTTGA


Statistics
Matches: 124,  Mismatches: 7, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  62  122  0.98
  63    2  0.02

ACGTcount: A:0.17, C:0.13, G:0.25, T:0.45


Consensus pattern (62 bp):   
TGGTTTTTGTGGTTTTAAACCTGGTTTCAGTGGTTTCAAACAGGGTTTTCCGGTTTTCAATG
Done.