Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold9949.1

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: 4117
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31


Found at i:2872 original size:40 final size:40

Alignment explanation


    Indices: 2828--3037  Score: 271
    Period size: 40  Copynumber: 5.2  Consensus size: 40

       2818 TCTTCGAGGT

                 *         *                *       
       2828 TTAGCACGGATATATTACTAGCACGAATGCTCTTCGGAAC
          1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGAAC

                        *                        *  
       2868 TTAGCCCGGATACATCACTAGCACGAATGCTCCTCGGGAC
          1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGAAC

                                                 *  
       2908 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGAC
          1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGAAC

                        *                   *       
       2948 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
          1 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGAAC

                *         *              *    *    *  
       2988 TTAGTCCGGATATGGTCACTTAGCAC-AAAGC-CTTCGGGAC
          1 TTAGCCCGGATAT-ATCAC-TAGCACGAATGCTCCTCGGAAC

                      
       3028 TTAGCCCGGA
          1 TTAGCCCGGA

       3038 CATCATTCAA


Statistics
Matches: 153,  Mismatches: 15, Indels: 4
        0.89            0.09        0.02

Matches are distributed among these distances:
  40  139  0.91
  41    8  0.05
  42    6  0.04

ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23


Consensus pattern (40 bp):   
TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGAAC

Found at i:2920 original size:80 final size:80

Alignment explanation


    Indices: 2828--3037  Score: 307
    Period size: 80  Copynumber: 2.6  Consensus size: 80

       2818 TCTTCGAGGT

                 *         *                     *                           
       2828 TTAGCACGGATATATTACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACG
          1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACG

                        *  
       2893 AATGCTCCTCGGGAC
         66 AATGCTCCTCGGAAC

                                            *                                
       2908 TTAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATACATCACTAGCACG
          1 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACG

                   *       
       2973 AATGCTCTTCGGAAC
         66 AATGCTCCTCGGAAC

                *         *              *                      
       2988 TTAGTCCGGATATGGTCACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGGA
          1 TTAGCCCGGATAT-ATCAC-TAGCACGAATGCTCTTCGGGACTTAGCCCGGA

       3038 CATCATTCAA


Statistics
Matches: 118,  Mismatches: 10, Indels: 4
        0.89            0.08        0.03

Matches are distributed among these distances:
  80  104  0.88
  81    8  0.07
  82    6  0.05

ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23


Consensus pattern (80 bp):   
TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACG
AATGCTCCTCGGAAC

Found at i:3384 original size:29 final size:29

Alignment explanation


    Indices: 3345--3421  Score: 102
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       3335 CTTAATAATC

                                   *       
       3345 AACCACGCACACTTAGTGCCATGTACTTT-A
          1 AACC-CGCACACTTAGTGCCATGCA-TTTCA

               *                         
       3375 AACTCGCACACTTAGTGCCATGCATTTCA
          1 AACCCGCACACTTAGTGCCATGCATTTCA

             *                
       3404 AGCCCGCACACTTAGTGC
          1 AACCCGCACACTTAGTGC

       3422 TGAAAACCAA


Statistics
Matches: 42,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  28    3  0.07
  29   36  0.86
  30    3  0.07

ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25


Consensus pattern (29 bp):   
AACCCGCACACTTAGTGCCATGCATTTCA
Done.