Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2079

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, 669

Length: 1115
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28


Found at i:51 original size:14 final size:14

Alignment explanation


    Indices: 34--64  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

         24 TAAACCTTAG

                          
         34 CCCCAACCTCTAAA
          1 CCCCAACCTCTAAA

                  *       
         48 CCCCAATCTCTAAA
          1 CCCCAACCTCTAAA

               
         62 CCC
          1 CCC

         65 ATAATCCCTA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16


Consensus pattern (14 bp):   
CCCCAACCTCTAAA

Found at i:150 original size:21 final size:21

Alignment explanation


    Indices: 126--169  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        116 AACCCCTATC

                  *   *           
        126 CCTTAATCTCCAACC-TCTAAA
          1 CCTTAAACTCAAACCAT-TAAA

                                 
        147 CCTTAAACTCAAACCATTAAA
          1 CCTTAAACTCAAACCATTAAA

              
        168 CC
          1 CC

        170 AAGTACCCTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21   19  0.95
  22    1  0.05

ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25


Consensus pattern (21 bp):   
CCTTAAACTCAAACCATTAAA

Found at i:372 original size:21 final size:21

Alignment explanation


    Indices: 348--417  Score: 63
    Period size: 21  Copynumber: 3.3  Consensus size: 21

        338 ATAAACTATA

                *                
        348 AACCCTAAACCCCTAACCCTT
          1 AACCATAAACCCCTAACCCTT

                  *     *         
        369 AACCATTAACCCGTAACACC-T
          1 AACCATAAACCCCTAAC-CCTT

                *                 
        390 ATACAATAAACCCC-AACCCTT
          1 A-ACCATAAACCCCTAACCCTT

                   
        411 AAACCAT
          1 -AACCAT

        418 GGCCTGTAAA


Statistics
Matches: 38,  Mismatches: 7, Indels: 8
        0.72            0.13        0.15

Matches are distributed among these distances:
  20    2  0.05
  21   24  0.63
  22   12  0.32

ACGTcount: A:0.40, C:0.40, G:0.01, T:0.19


Consensus pattern (21 bp):   
AACCATAAACCCCTAACCCTT

Found at i:873 original size:114 final size:114

Alignment explanation


    Indices: 659--1115  Score: 571
    Period size: 114  Copynumber: 4.0  Consensus size: 114

        649 GTTTCGGTTT

                                                  ** *                 *   * 
        659 AAAACGATGCGTTTTGGTTAAGATTTATTTGCGGCGCTCAGTATAATGCGCCGCTAATGATGTAC
          1 AAAACGATGCGTTTTGGTTAAGATTT-TTTGCGGCGCTTTGAATAATGCGCCGCTAATGGTGTGC

                      *                                  *    *
        724 TTTAGCGGC-GTTTTAC-TATAGCGCCACTAATTCTAAAATACCTAAACCA
         65 TTTAGCGGCATTTTTACTTA-AGCGCCACTAATTCTAAAATACCTCAACCC

                   *                                                  *    * 
        773 AAAACGACGCGTTTTGGTTAAG-TTTTCTTGCGGCGCTTTGAATAATGCGCCGCTAATTGTGTTC
          1 AAAACGATGCGTTTTGGTTAAGATTTT-TTGCGGCGCTTTGAATAATGCGCCGCTAATGGTGTGC

                         * *               *                  
        837 TTTAGCGGCATTTATCCTTAAGCGCCACTAAATCTAAAATACCTCAACCC
         65 TTTAGCGGCATTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC

                                                       *    *                
        887 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGAATGATGCACCGCTAATGGTGTGCT
          1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGAATAATGCGCCGCTAATGGTGTGCT

              **    *      * *                       *       
        952 TTTCCGGCGTTTTTAGTCAAGCGCCACTAATTCTAAAATACATCAACCC
         66 TTAGCGGCATTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC

             *                              *       * **                     
       1001 AGAACGATGCGTTTTGGTTAAGATTTTTTGCGTCGCTTTGTACGATGCGCCGCTAATGGTGTGCT
          1 AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGAATAATGCGCCGCTAATGGTGTGCT

                            *          *          *   *       
       1066 TCT-GCGGCATTTTTAGTTAAGCGCCAGTAATTCTAAATTACATCAACCC
         66 T-TAGCGGCATTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC

             
       1115 A
          1 A


Statistics
Matches: 301,  Mismatches: 37, Indels: 10
        0.86            0.11        0.03

Matches are distributed among these distances:
 112    1  0.00
 113   43  0.14
 114  250  0.83
 115    7  0.02

ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33


Consensus pattern (114 bp):   
AAAACGATGCGTTTTGGTTAAGATTTTTTGCGGCGCTTTGAATAATGCGCCGCTAATGGTGTGCT
TTAGCGGCATTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCC

Done.