Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: COLO4_32364

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, 622

Length: 1038
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27


Found at i:686 original size:42 final size:42

Alignment explanation


    Indices: 639--733  Score: 111
    Period size: 42  Copynumber: 2.3  Consensus size: 42

        629 ATGTGGCTAT

                             *                         
        639 AGAGAAGGACACTCCCATAGTTGACACTGA-TGCTGCGGTTAG
          1 AGAGAAGGACACTCCCACAGTTGACA-TGATTGCTGCGGTTAG

            *          *    *       *  *    *         
        681 GGAGAAGGACATTCCCGCAGTTGAGATTATTGTTGCGGTTAG
          1 AGAGAAGGACACTCCCACAGTTGACATGATTGCTGCGGTTAG

                       
        723 AGAGAAGGACA
          1 AGAGAAGGACA

        734 TCGACATTGA


Statistics
Matches: 44,  Mismatches: 8, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  41    2  0.05
  42   42  0.95

ACGTcount: A:0.29, C:0.17, G:0.32, T:0.22


Consensus pattern (42 bp):   
AGAGAAGGACACTCCCACAGTTGACATGATTGCTGCGGTTAG

Found at i:853 original size:27 final size:27

Alignment explanation


    Indices: 816--927  Score: 129
    Period size: 27  Copynumber: 4.1  Consensus size: 27

        806 AGAAAGATGT

                 *      *             *
        816 TCCCGTAGTTGGCACTCATGCTGAAAT
          1 TCCCGCAGTTGGGACTCATGCTGAAAC

                              *   *   * 
        843 TCCCGCAGTTGGGACTCACGC-CATAGC
          1 TCCCGCAGTTGGGACTCATGCTGA-AAC

                                      * 
        870 -CTCCGCAGTTGGGACTCATGCTGAAGC
          1 TC-CCGCAGTTGGGACTCATGCTGAAAC

                                       
        897 TCCCGCAGTTGGGACTCATGCTGAAAC
          1 TCCCGCAGTTGGGACTCATGCTGAAAC

                
        924 TCCC
          1 TCCC

        928 ACGGAGATGG


Statistics
Matches: 72,  Mismatches: 9, Indels: 8
        0.81            0.10        0.09

Matches are distributed among these distances:
  26    2  0.03
  27   68  0.94
  28    2  0.03

ACGTcount: A:0.20, C:0.32, G:0.25, T:0.23


Consensus pattern (27 bp):   
TCCCGCAGTTGGGACTCATGCTGAAAC
Done.