Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2759

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: 23890
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31


Found at i:11439 original size:1 final size:1

Alignment explanation


    Indices: 11433--11458  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

      11423 TTTGCTTCCT

                                      
      11433 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

      11459 GGACTTTGGA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:12904 original size:44 final size:43

Alignment explanation


    Indices: 12625--12992  Score: 200
    Period size: 44  Copynumber: 8.5  Consensus size: 43

      12615 ATTATACAGG

                                      *    **    *    *   
      12625 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAA-AATTTCAGA
          1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCA---GAGA

                                  *     *   *      *     
      12670 TCTTATCTCCCTGAGATTACAGCGGAGCGGATCAAAG-ATAGTAA
          1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAG--A

              *       *          *      *              
      12714 TCCTATCTCCTTGAGATTACAATGGAGCGGATT-AA--AG-GA
          1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAGA

                     *              *   *    * * *      
      12753 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACATCAG-G-
          1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAGCAGAGA

                                      *    **    *    *   
      12794 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
          1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCA---GAGA

                           *                 *          
      12840 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
          1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG-CAGAGA

                                  *         *        ** 
      12884 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACA-CTA
          1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG-CAGAGA

              *                         **       ** *    
      12927 TCCTATCTCCCTGA-AGTTACAGTGGAGTGGATTAAAATAAAGGA
          1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAGCAGA-GA

                     *     *      
      12971 TCTTATCTCTCTGAGGTTACAG
          1 TCTTATCTCCCTGAGATTACAG

      12993 CAGAGTAGGT


Statistics
Matches: 250,  Mismatches: 55, Indels: 37
        0.73            0.16        0.11

Matches are distributed among these distances:
  38    1  0.00
  39   24  0.10
  40    1  0.00
  41   30  0.12
  42    9  0.04
  43   32  0.13
  44   86  0.34
  45   34  0.14
  46   32  0.13
  47    1  0.00

ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27


Consensus pattern (43 bp):   
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCAGAGA

Found at i:12973 original size:87 final size:88

Alignment explanation


    Indices: 12794--12993  Score: 217
    Period size: 87  Copynumber: 2.3  Consensus size: 88

      12784 TCACATCAGG

                                  *                         *           *    
      12794 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTA
          1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAA--TCAGATCCTATCTCCCTGAAGTTA

                          *   **     
      12859 CAGTGGAGCAGATTGAAGCCAGAGA
         64 CAGTGGAGCAGATTAAAGAAAGAGA

                                      *    *           *                     
      12884 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-A-CACTATCCTATCTCCCTGAAGTTAC
          1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCA-GATCCTATCTCCCTGAAGTTAC

                   **        *       
      12947 AGTGGAGTGGATTAAAATAAAG-GA
         65 AGTGGAGCAGATT-AAAGAAAGAGA

                     *     *       
      12971 TCTTATCTCTCTGAGGTTACAGC
          1 TCTTATCTCCCTGAGATTACAGC

      12994 AGAGTAGGTC


Statistics
Matches: 94,  Mismatches: 14, Indels: 7
        0.82            0.12        0.06

Matches are distributed among these distances:
  86    2  0.02
  87   53  0.56
  88    4  0.04
  89    1  0.01
  90   34  0.36

ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27


Consensus pattern (88 bp):   
TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCAGATCCTATCTCCCTGAAGTTACA
GTGGAGCAGATTAAAGAAAGAGA
Done.