Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1782

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: 18103
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32


Found at i:2304 original size:3 final size:3

Alignment explanation


    Indices: 2296--2334  Score: 78
    Period size: 3  Copynumber: 13.0  Consensus size: 3

       2286 CCCACTCCAA

                                                               
       2296 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

       2335 TATTATTATT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   36  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:4879 original size:5 final size:5

Alignment explanation


    Indices: 4864--4892  Score: 51
    Period size: 5  Copynumber: 6.0  Consensus size: 5

       4854 ACCAAAGGGG

                                               
       4864 GAAAA -AAAA GAAAA GAAAA GAAAA GAAAA
          1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA

       4893 ACATCGAATC


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   4    4  0.17
   5   19  0.83

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (5 bp):   
GAAAA

Found at i:13811 original size:34 final size:34

Alignment explanation


    Indices: 13746--13928  Score: 253
    Period size: 34  Copynumber: 5.4  Consensus size: 34

      13736 ACGGTTCAAT

                            *          *      
      13746 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

                   *         *                
      13779 TTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

                                              
      13813 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

              *             *        * *      
      13847 TTATTGATT-AATGGGTGATTTGGTGGTTTACCA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

                   *                   *  *   
      13880 TTGTTGACTAAATGGGAGATTTGGTAGGTTGCCA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

                           
      13914 TTGTTGATTAAATGG
          1 TTGTTGATTAAATGG

      13929 TGGTTTTTAC


Statistics
Matches: 131,  Mismatches: 17, Indels: 3
        0.87            0.11        0.02

Matches are distributed among these distances:
  33   40  0.31
  34   91  0.69

ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40


Consensus pattern (34 bp):   
TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA

Found at i:13860 original size:67 final size:67

Alignment explanation


    Indices: 13746--13924  Score: 243
    Period size: 67  Copynumber: 2.7  Consensus size: 67

      13736 ACGGTTCAAT

                            *          *               *                     
      13746 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTGTTGA-TTAATGGGAAATTTGGTAGCTTA

               
      13810 CCA
         65 CCA

                                                *            **       * *    
      13813 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTATTGATTAATGGGTGATTTGGTGGTTTAC
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAATGGGAAATTTGGTAGCTTAC

              
      13878 CA
         66 CA

                   *                   *  *              
      13880 TTGTTGACTAAATGGGAGATTTGGTAGGTTGCCATTGTTGATTAA
          1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAA

      13925 ATGGTGGTTT


Statistics
Matches: 99,  Mismatches: 12, Indels: 2
        0.88            0.11        0.02

Matches are distributed among these distances:
  67   75  0.76
  68   24  0.24

ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41


Consensus pattern (67 bp):   
TTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAATGGGAAATTTGGTAGCTTAC
CA

Found at i:14286 original size:19 final size:19

Alignment explanation


    Indices: 14230--14292  Score: 90
    Period size: 19  Copynumber: 3.3  Consensus size: 19

      14220 TGGTTGTCGA

                             **
      14230 GGTACTATTCACGTATATA
          1 GGTACTATTCACGTATACG

                               
      14249 GGTACTATTCACGTATACG
          1 GGTACTATTCACGTATACG

                       *       
      14268 GGTACTATTCAAGTATACG
          1 GGTACTATTCACGTATACG

             *    
      14287 GTTACT
          1 GGTACT

      14293 GTACACGTGA


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  19   40  1.00

ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35


Consensus pattern (19 bp):   
GGTACTATTCACGTATACG
Done.