Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g01870.F1

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, 896

Length: 1494
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26


Found at i:618 original size:21 final size:20

Alignment explanation


    Indices: 592--631  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 20

        582 ATGAAAAAGC

                                 
        592 CCAATGCTGCTATTCGAGATG
          1 CCAATGCTGCT-TTCGAGATG

                         *     
        613 CCAATGCTGCTTTGGAGAT
          1 CCAATGCTGCTTTCGAGAT

        632 AAACCCAGAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    7  0.39
  21   11  0.61

ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30


Consensus pattern (20 bp):   
CCAATGCTGCTTTCGAGATG

Found at i:976 original size:24 final size:24

Alignment explanation


    Indices: 942--1048  Score: 90
    Period size: 24  Copynumber: 4.5  Consensus size: 24

        932 TAGAAAACCT

                 *                   
        942 GGAGGCATGCCTGGTGGG-TTTCCA
          1 GGAGGAATGCCTGG-GGGTTTTCCA

              *                    *
        966 GGTGGAATGCCTGGGGGTTTTCCT
          1 GGAGGAATGCCTGGGGGTTTTCCA

                 *        *   * *  *
        990 GGAGGTATGCCTGGAGGTATGCCC
          1 GGAGGAATGCCTGGGGGTTTTCCA

                 *        *        *
       1014 GGAGGTATGCCTGGAGGTTTTCCT
          1 GGAGGAATGCCTGGGGGTTTTCCA

                 *     
       1038 GGAGGCATGCC
          1 GGAGGAATGCC

       1049 AGGTGGCATG


Statistics
Matches: 69,  Mismatches: 13, Indels: 2
        0.82            0.15        0.02

Matches are distributed among these distances:
  23    3  0.04
  24   66  0.96

ACGTcount: A:0.13, C:0.20, G:0.41, T:0.26


Consensus pattern (24 bp):   
GGAGGAATGCCTGGGGGTTTTCCA

Found at i:1002 original size:12 final size:12

Alignment explanation


    Indices: 972--1064  Score: 96
    Period size: 12  Copynumber: 7.8  Consensus size: 12

        962 TCCAGGTGGA

                    *   
        972 ATGCCTGGGGGT
          1 ATGCCTGGAGGT

            * *         
        984 TTTCCTGGAGGT
          1 ATGCCTGGAGGT

                        
        996 ATGCCTGGAGGT
          1 ATGCCTGGAGGT

                 *      
       1008 ATGCCCGGAGGT
          1 ATGCCTGGAGGT

                        
       1020 ATGCCTGGAGGT
          1 ATGCCTGGAGGT

            * *        *
       1032 TTTCCTGGAGGC
          1 ATGCCTGGAGGT

                 *  *  *
       1044 ATGCCAGGTGGC
          1 ATGCCTGGAGGT

                     
       1056 ATGCCTGGA
          1 ATGCCTGGA

       1065 AATGTTGATT


Statistics
Matches: 65,  Mismatches: 16, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  12   65  1.00

ACGTcount: A:0.14, C:0.20, G:0.40, T:0.26


Consensus pattern (12 bp):   
ATGCCTGGAGGT

Found at i:1060 original size:48 final size:48

Alignment explanation


    Indices: 939--1060  Score: 145
    Period size: 48  Copynumber: 2.5  Consensus size: 48

        929 CAGTAGAAAA

                                ** *     *           *      
        939 CCTGGAGGCATGCCTGGTGGGTTTCCAGGTGGAATGCCTGGGGGTTTT
          1 CCTGGAGGCATGCCTGGTGGCATGCCAGGAGGAATGCCTGGAGGTTTT

                    *        *  *     *     *               
        987 CCTGGAGGTATGCCTGGAGGTATGCCCGGAGGTATGCCTGGAGGTTTT
          1 CCTGGAGGCATGCCTGGTGGCATGCCAGGAGGAATGCCTGGAGGTTTT

                          *           
       1035 CCTGGAGGCATGCCAGGTGGCATGCC
          1 CCTGGAGGCATGCCTGGTGGCATGCC

       1061 TGGAAATGTT


Statistics
Matches: 61,  Mismatches: 13, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  48   61  1.00

ACGTcount: A:0.13, C:0.21, G:0.40, T:0.25


Consensus pattern (48 bp):   
CCTGGAGGCATGCCTGGTGGCATGCCAGGAGGAATGCCTGGAGGTTTT
Done.