Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold329

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: 46733
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:4842 original size:93 final size:93

Alignment explanation


    Indices: 4711--4882  Score: 281
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       4701 GCCCATAAGT

                  *                     * *                                  
       4711 GAACTCGGAATCAAATCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCAGAATCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                                        
       4776 CGAGCTCGGATGCCTAGTTACATCTCTC
         66 CGAGCTCGGATGCCTAGTTACATCTCTC

                     *    *        *                                         
       4804 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCAGAATCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                *         
       4869 CGAGTTCGGATGCC
         66 CGAGCTCGGATGCC

       4883 CAAATATCCT


Statistics
Matches: 72,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  93   72  1.00

ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21


Consensus pattern (93 bp):   
GAACTCAGAATCAAATCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC

Found at i:4878 original size:46 final size:46

Alignment explanation


    Indices: 4703--4878  Score: 187
    Period size: 46  Copynumber: 3.8  Consensus size: 46

       4693 TGTAACCCGC

                             *    *             * *       
       4703 CCATAAGTGAACTCGGAATCAAATCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT

                                                    *        
       4749 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T

            *   ***        *                *              
       4795 ACATCTCTCGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
          1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT

                                           *     
       4842 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA

       4879 TGCCCAAATA


Statistics
Matches: 107,  Mismatches: 16, Indels: 14
        0.78            0.12        0.10

Matches are distributed among these distances:
  43    1  0.01
  44    3  0.03
  46   67  0.63
  47   31  0.29
  49    4  0.04
  50    1  0.01

ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21


Consensus pattern (46 bp):   
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT

Found at i:12691 original size:42 final size:42

Alignment explanation


    Indices: 12617--12715  Score: 128
    Period size: 42  Copynumber: 2.4  Consensus size: 42

      12607 CTTCGTTTAG

                                                    *  
      12617 CCGATGATGCACTTATGTGCCAGCATAATTGCTTC-AGTATAT
          1 CCGATGATGCACTTATGTGCCAGCATAATTGCTTCGA-TACAT

                     *             *  **              
      12659 CCGATGATGGACTTATGTGCCAGTATCTTTGCTTCGATACAT
          1 CCGATGATGCACTTATGTGCCAGCATAATTGCTTCGATACAT

             *             
      12701 CTGATGATGCACTTA
          1 CCGATGATGCACTTA

      12716 CGAGCCACTA


Statistics
Matches: 49,  Mismatches: 7, Indels: 2
        0.84            0.12        0.03

Matches are distributed among these distances:
  42   48  0.98
  43    1  0.02

ACGTcount: A:0.24, C:0.21, G:0.20, T:0.34


Consensus pattern (42 bp):   
CCGATGATGCACTTATGTGCCAGCATAATTGCTTCGATACAT

Found at i:12733 original size:42 final size:42

Alignment explanation


    Indices: 12617--12736  Score: 127
    Period size: 42  Copynumber: 2.9  Consensus size: 42

      12607 CTTCGTTTAG

                                                    *  
      12617 CCGATGATGCACTTATGTGCCAGC-ATAATTGCTTCAGTATAT
          1 CCGATGATGCACTTATGTGCCA-CTATAATTGCTTCAGTACAT

                     *            *   **               
      12659 CCGATGATGGACTTATGTGCCAGTATCTTTGCTTC-GATACAT
          1 CCGATGATGCACTTATGTGCCACTATAATTGCTTCAG-TACAT

             *             * *        *         
      12701 CTGATGATGCACTTACGAGCCACTATGATTGCTTCA
          1 CCGATGATGCACTTATGTGCCACTATAATTGCTTCA

      12737 ACTTATTGAT


Statistics
Matches: 63,  Mismatches: 12, Indels: 5
        0.79            0.15        0.06

Matches are distributed among these distances:
  41    1  0.02
  42   62  0.98

ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33


Consensus pattern (42 bp):   
CCGATGATGCACTTATGTGCCACTATAATTGCTTCAGTACAT

Found at i:16695 original size:17 final size:17

Alignment explanation


    Indices: 16669--16705  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      16659 TTTGAAAAGG

                             
      16669 AAAATAAATGAATCCTA
          1 AAAATAAATGAATCCTA

                 *        *  
      16686 AAAATGAATGAATCTTA
          1 AAAATAAATGAATCCTA

               
      16703 AAA
          1 AAA

      16706 CTTAATAAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24


Consensus pattern (17 bp):   
AAAATAAATGAATCCTA
Done.