Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1089

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: 18179
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32


Found at i:5170 original size:29 final size:29

Alignment explanation


    Indices: 5128--5228  Score: 150
    Period size: 29  Copynumber: 3.5  Consensus size: 29

       5118 CATGAAATTG

                                         
       5128 GCACTAAGTGTGCGGGTTCAAATTGTATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

                                 *       
       5157 GCACTAAGTGTGCGGGTTCAAGTTGTATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

                          *     *   *    
       5186 GCACTAAGTGTGCGAGTTC-GATTATATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

            *              
       5214 ACACTAAGTGTGCGG
          1 GCACTAAGTGTGCGG

       5229 ACTTACTATA


Statistics
Matches: 65,  Mismatches: 7, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  28   19  0.29
  29   46  0.71

ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30


Consensus pattern (29 bp):   
GCACTAAGTGTGCGGGTTCAAATTGTATA

Found at i:12954 original size:29 final size:29

Alignment explanation


    Indices: 12912--13012  Score: 150
    Period size: 29  Copynumber: 3.5  Consensus size: 29

      12902 CATGAAATTG

                                         
      12912 GCACTAAGTGTGCGGGTTCAAATTGTATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

                                 *       
      12941 GCACTAAGTGTGCGGGTTCAAGTTGTATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

                          *     *   *    
      12970 GCACTAAGTGTGCGAGTTC-GATTATATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

            *              
      12998 ACACTAAGTGTGCGG
          1 GCACTAAGTGTGCGG

      13013 ACTTACTATA


Statistics
Matches: 65,  Mismatches: 7, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  28   19  0.29
  29   46  0.71

ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30


Consensus pattern (29 bp):   
GCACTAAGTGTGCGGGTTCAAATTGTATA

Found at i:15410 original size:15 final size:15

Alignment explanation


    Indices: 15390--15466  Score: 54
    Period size: 15  Copynumber: 5.2  Consensus size: 15

      15380 CATAGTATCG

                  *        
      15390 TATCTTGGGTTTCTT
          1 TATCTTAGGTTTCTT

                       *    
      15405 TATCTT-GGATCTCTT
          1 TATCTTAGG-TTTCTT

                     *      
      15420 TAT-TCTAGATTTCTT
          1 TATCT-TAGGTTTCTT

                           *
      15435 TAT-TCTAGGTTTCTC
          1 TATCT-TAGGTTTCTT

                     *     
      15450 TATCTT-GGATTCTT
          1 TATCTTAGGTTTCTT

               
      15464 TAT
          1 TAT

      15467 TCGGTTTTCT


Statistics
Matches: 51,  Mismatches: 7, Indels: 9
        0.76            0.10        0.13

Matches are distributed among these distances:
  14   12  0.24
  15   37  0.73
  16    2  0.04

ACGTcount: A:0.14, C:0.16, G:0.13, T:0.57


Consensus pattern (15 bp):   
TATCTTAGGTTTCTT

Found at i:17977 original size:93 final size:92

Alignment explanation


    Indices: 17819--17989  Score: 227
    Period size: 93  Copynumber: 1.8  Consensus size: 92

      17809 TAGGATATTT

                         *                      * *     *  *   **     *      
      17819 GGCATCCGAACTCGTTGAGTTGAGTCGAGTTCACTTGTGGATGCGAATGTCTGAACTCGTTGAGT
          1 GGCATCCGAACTCATTGAGTTGAGTCGAGTTCACTTATAGATGCAAACGTCCCAACTCATTGAGT

                                       
      17884 TGAGTCCGAGTTCGAGAGATGTAACTG
         66 TGAGTCCGAGTTCGAGAGATGTAACTG

                     *                                                       
      17911 GGCATCCGAGCTCATTGAGTTGAGTCTGAGTTCACTTATAGATGCAAACG-CCCAAGCTCATTGA
          1 GGCATCCGAACTCATTGAGTTGAGTC-GAGTTCACTTATAGATGCAAACGTCCCAA-CTCATTGA

                    *      
      17975 GTTGAGTCTGAGTTC
         64 GTTGAGTCCGAGTTC

      17990 ACTTATGGGC


Statistics
Matches: 67,  Mismatches: 10, Indels: 3
        0.84            0.12        0.04

Matches are distributed among these distances:
  92   27  0.40
  93   40  0.60

ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29


Consensus pattern (92 bp):   
GGCATCCGAACTCATTGAGTTGAGTCGAGTTCACTTATAGATGCAAACGTCCCAACTCATTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTG
Done.