Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2518

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: 7761
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34


Found at i:5687 original size:25 final size:25

Alignment explanation


    Indices: 5653--5701  Score: 98
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       5643 GAGAGGTTTT

                                     
       5653 GTTTCATGAAATTTGAAATTCCCAC
          1 GTTTCATGAAATTTGAAATTCCCAC

                                    
       5678 GTTTCATGAAATTTGAAATTCCCA
          1 GTTTCATGAAATTTGAAATTCCCA

       5702 TTTTGAAGAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37


Consensus pattern (25 bp):   
GTTTCATGAAATTTGAAATTCCCAC

Found at i:5836 original size:18 final size:17

Alignment explanation


    Indices: 5798--5836  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       5788 AGATATTACC

                            *
       5798 TTAATTTTTTAAAAATT
          1 TTAATTTTTTAAAAATA

                         *    
       5815 TTAATTTTATTAATAATA
          1 TTAATTTT-TTAAAAATA

                
       5833 TTAA
          1 TTAA

       5837 GGAAAATCTG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  17    8  0.42
  18   11  0.58

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (17 bp):   
TTAATTTTTTAAAAATA

Found at i:6266 original size:151 final size:152

Alignment explanation


    Indices: 6078--6426  Score: 353
    Period size: 153  Copynumber: 2.3  Consensus size: 152

       6068 CAGTGATTAT

                *             *      **  *  *                    * *         
       6078 CTAAGACTCAATTTTAGAGAAATTATTAACATACCCTTAAGGTATATCTTCGATATGAAAATATC
          1 CTAAAACTCAATTTTA-AAAAATTACCAAAATGCCCTTAAGGTATATCTTCGACACGAAAATATC

                                    *  * *   **       *                *   * 
       6143 CCAATAACCTTAAAAGACA-AAAAGATCATAAATGGATAAACTTATCCTAAATGCACACTTTTGA
         65 CCAATAACCTTAAAAGACACAAAAAATAAGAAAACGATAAACCTATCCTAAATGCACACCTTTAA

                                   
       6207 CATAAAAAAGACCCAATAACTAC
        130 CATAAAAAAGACCCAATAACTAC

            *                                                 *         *    
       6230 TTAAAACTCAATTTTAAAAAATTACCAAAATGCCCTTACA-GTATATCTTTGACACGAAAGTATC
          1 CTAAAACTCAATTTTAAAAAATTACCAAAATGCCCTTA-AGGTATATCTTCGACACGAAAATATC

              *                                    *       *                 
       6294 CCGATAACCTTAAAAGACACCAAAAAATAAGAAAACGATGAACCTATTCTAAATGCACACCTTTA
         65 CCAATAACCTTAAAAGACA-CAAAAAATAAGAAAACGATAAACCTATCCTAAATGCACACCTTTA

             *      **   *  * *     
       6359 ATATAAAAGCGACTCAGTGACTAC
        129 ACATAAAAAAGACCCAATAACTAC

                * *  *   *                               
       6383 CTAAGATTCGATTCTAATAAAATTACCAAAATGCCCTT-AGGTAT
          1 CTAAAACTCAATTTTAA-AAAATTACCAAAATGCCCTTAAGGTAT

       6427 GCTTTCGATG


Statistics
Matches: 159,  Mismatches: 33, Indels: 9
        0.79            0.16        0.04

Matches are distributed among these distances:
 151   55  0.35
 152   16  0.10
 153   68  0.43
 154   20  0.13

ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27


Consensus pattern (152 bp):   
CTAAAACTCAATTTTAAAAAATTACCAAAATGCCCTTAAGGTATATCTTCGACACGAAAATATCC
CAATAACCTTAAAAGACACAAAAAATAAGAAAACGATAAACCTATCCTAAATGCACACCTTTAAC
ATAAAAAAGACCCAATAACTAC

Done.