Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_84 ID=scaffold_84-JGI_221_v2.0

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: 43412
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.12

Warning! 28149 characters in sequence are not A, C, G, or T


Found at i:79 original size:50 final size:50

Alignment explanation


    Indices: 3--219  Score: 238
    Period size: 50  Copynumber: 4.2  Consensus size: 50

          1 TA

                       **                * *                   
          3 CTTACATGGGAGTTCTCATAC-CGGTGCCCATGCCATGTCCCAGACATGGT
          1 CTTACATGGGACCTCTCAT-CTCGGTGCCAACGCCATGTCCCAGACATGGT

                 **              *                  *         
         53 CTTACGGGGGACCTCTCATCTTGGTGCCAACGCCATGTCCTAGACATGGT
          1 CTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGT

                    *                              *          
        103 CTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCACAGACATGGT
          1 CTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGT

                                         *      **                  
        153 CTTACATGGGACCTCTCATAATCTCAATGATGCCAATTCCATGTCCCAGACATGGT
          1 CTTACATGGGACCTCTC---ATCTC---GGTGCCAACGCCATGTCCCAGACATGGT

             *         
        209 CATACATGGGA
          1 CTTACATGGGA

        220 TCTCATTCCC


Statistics
Matches: 140,  Mismatches: 20, Indels: 8
        0.83            0.12        0.05

Matches are distributed among these distances:
  49    1  0.01
  50  100  0.71
  53    5  0.04
  56   34  0.24

ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26


Consensus pattern (50 bp):   
CTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGT

Found at i:37705 original size:84 final size:84

Alignment explanation


    Indices: 37602--38215  Score: 984
    Period size: 84  Copynumber: 7.4  Consensus size: 84

      37592 CAAAGGATCC

                                *                               **           
      37602 CGGTGGAATCAGCACTTAGCTACCACCTTATAATCAATGATACGGGGAATCAAAACATAGCAACC
          1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC

                          *    
      37667 CCTTTCACAATCAATGATA
         66 CCTTTCACAATCAAGGATA

                                                                *   *        
      37686 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAACACGTAGCAACC
          1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC

                               
      37751 CCTTTCACAATCAAGGATA
         66 CCTTTCACAATCAAGGATA

                       *                                                     
      37770 CGGTGGAATCAACACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
          1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC

                               
      37835 CCTTTCACAATCAAGGATA
         66 CCTTTCACAATCAAGGATA

              *                                                              
      37854 CGATGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
          1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC

                        *      
      37919 CCTTTCACAATCTAGGATA
         66 CCTTTCACAATCAAGGATA

             *                                *                         *  * 
      37938 CAGTGGAATCAGCACTTAGCAACCACCTTATAATTAATGATACGGGGAATCAGCACATAGTAATC
          1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC

                               
      38003 CCTTTCACAATCAAGGATA
         66 CCTTTCACAATCAAGGATA

            ***      *                            *                          
      38022 ATTTGGAATTAGCACTTAGCAACCACCTTATAATCAATTATACGGGGAATCAGCACATAGCAACC
          1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC

                               
      38087 CCTTTCACAATCAAGGATA
         66 CCTTTCACAATCAAGGATA

              *                                                              
      38106 CGATGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
          1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC

                   **     *   *
      38171 CCTTT--TTATCAATGATT
         66 CCTTTCACAATCAAGGATA

                      *                   
      38188 CGG-GGAATCTGCACTTAGCAACC-CCTTA
          1 CGGTGGAATCAGCACTTAGCAACCACCTTA

      38216 CATTCAAAGA


Statistics
Matches: 495,  Mismatches: 35, Indels: 4
        0.93            0.07        0.01

Matches are distributed among these distances:
  80    5  0.01
  81   19  0.04
  82   10  0.02
  84  461  0.93

ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23


Consensus pattern (84 bp):   
CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
CCTTTCACAATCAAGGATA

Found at i:40921 original size:42 final size:42

Alignment explanation


    Indices: 40841--40922  Score: 96
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      40831 CATTTTCTCT

                                            **        
      40841 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
          1 ATGCCATAGTCCAACTATGGTCTTACACATATGCACATATTG

                          *    *                      
      40883 ATGCCATAG-CCTAGCTATTGTCTTACACAGTA-GCACATAT
          1 ATGCCATAGTCC-AACTATGGTCTTACACA-TATGCACATAT

      40923 CACACCGTTG


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
  41    2  0.06
  42   30  0.88
  43    2  0.06

ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33


Consensus pattern (42 bp):   
ATGCCATAGTCCAACTATGGTCTTACACATATGCACATATTG
Done.