Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_4091

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: 16025
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32


Found at i:8758 original size:40 final size:40

Alignment explanation


    Indices: 8713--8971  Score: 384
    Period size: 40  Copynumber: 6.5  Consensus size: 40

       8703 ACTACTTGCT

                      *              *              
       8713 CAAATGCCTTTGGGACTTAGCCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                          *                         
       8753 CAAATGCCTTCGGGTCTTAGCCCGGATATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                      *   *                         
       8793 CAAATGCCTTTGGGTCTTAG-CCGGATATAGTAACTCG-A
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                                   *                
       8831 CAAATGCCTTCGGGACTTAGCCCTG-TATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                                                    
       8870 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

                                    *         *   *   
       8910 CAAATGCCTTC-GGAGCTTAGCCCAGA-ATTAGTCACTAGCA
          1 CAAATGCCTTCGGGA-CTTAGCCCGGATA-TAGTAACTCGCA

                                  
       8950 CAAATGCCTTCGGGACTTAGCC
          1 CAAATGCCTTCGGGACTTAGCC

       8972 TGGTTATCAT


Statistics
Matches: 202,  Mismatches: 11, Indels: 12
        0.90            0.05        0.05

Matches are distributed among these distances:
  38   31  0.15
  39   49  0.24
  40  119  0.59
  41    3  0.01

ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA

Found at i:8929 original size:117 final size:120

Alignment explanation


    Indices: 8713--8978  Score: 407
    Period size: 117  Copynumber: 2.2  Consensus size: 120

       8703 ACTACTTGCT

                      *                                           *          
       8713 CAAATGCCTTTGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGTCTTAGCCCGG
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG

                                     *              *           *   
       8778 ATATAGTAACTCGCACAAATGCCTTTGGGTCTTAG-CC-GGATATAGTAACTCG-A
         66 ATATAGTAACTCGCACAAATGCCTTCGGGTCTTAGCCCAGAAT-TAGTAACTAGCA

                                   *                                         
       8831 CAAATGCCTTCGGGACTTAGCCCTG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
          1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG

                                                            *       
       8895 ATATAGTAACTCGCACAAATGCCTTCGGAG-CTTAGCCCAGAATTAGTCACTAGCA
         66 ATATAGTAACTCGCACAAATGCCTTCGG-GTCTTAGCCCAGAATTAGTAACTAGCA

                                  *      
       8950 CAAATGCCTTCGGGACTTAGCCTGGTTAT
          1 CAAATGCCTTCGGGACTTAGCCCGGTTAT

       8979 CATCCAAATA


Statistics
Matches: 134,  Mismatches: 9, Indels: 8
        0.89            0.06        0.05

Matches are distributed among these distances:
 117   70  0.52
 118   34  0.25
 119   27  0.20
 120    3  0.02

ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26


Consensus pattern (120 bp):   
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATATAGTAACTCGCACAAATGCCTTCGGGTCTTAGCCCAGAATTAGTAACTAGCA

Found at i:13371 original size:12 final size:12

Alignment explanation


    Indices: 13354--13385  Score: 55
    Period size: 12  Copynumber: 2.6  Consensus size: 12

      13344 ACTTAATCTT

                        
      13354 TTTAATATTAAA
          1 TTTAATATTAAA

                        
      13366 TTTAATATTAAA
          1 TTTAATATTAAA

                    
      13378 TCTTAATA
          1 T-TTAATA

      13386 AAATAATAGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12   13  0.68
  13    6  0.32

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (12 bp):   
TTTAATATTAAA
Done.