Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01023.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, 1000

Length: 3232
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30


Found at i:999 original size:6 final size:6

Alignment explanation


    Indices: 983--1012  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

        973 GTGGGTGTTT

                   *                          
        983 CTGGTG TTGGTG CTGGTG CTGGTG CTGGTG
          1 CTGGTG CTGGTG CTGGTG CTGGTG CTGGTG

       1013 TTGGCCCTGG


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.00, C:0.13, G:0.50, T:0.37


Consensus pattern (6 bp):   
CTGGTG

Found at i:1000 original size:12 final size:12

Alignment explanation


    Indices: 983--1031  Score: 62
    Period size: 12  Copynumber: 4.1  Consensus size: 12

        973 GTGGGTGTTT

                        
        983 CTGGTGTTGGTG
          1 CTGGTGTTGGTG

                  *     
        995 CTGGTGCTGGTG
          1 CTGGTGTTGGTG

                      **
       1007 CTGGTGTTGGCC
          1 CTGGTGTTGGTG

                *       
       1019 CTGGAGTTGGTG
          1 CTGGTGTTGGTG

             
       1031 C
          1 C

       1032 AAGTGGTGGT


Statistics
Matches: 30,  Mismatches: 7, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  12   30  1.00

ACGTcount: A:0.02, C:0.16, G:0.47, T:0.35


Consensus pattern (12 bp):   
CTGGTGTTGGTG

Found at i:1006 original size:18 final size:18

Alignment explanation


    Indices: 983--1031  Score: 53
    Period size: 18  Copynumber: 2.7  Consensus size: 18

        973 GTGGGTGTTT

                            **
        983 CTGGTGTTGGTGCTGGTG
          1 CTGGTGTTGGTGCTGGCC

                  *     *     
       1001 CTGGTGCTGGTGTTGGCC
          1 CTGGTGTTGGTGCTGGCC

                *        
       1019 CTGGAGTTGGTGC
          1 CTGGTGTTGGTGC

       1032 AAGTGGTGGT


Statistics
Matches: 24,  Mismatches: 7, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  18   24  1.00

ACGTcount: A:0.02, C:0.16, G:0.47, T:0.35


Consensus pattern (18 bp):   
CTGGTGTTGGTGCTGGCC

Found at i:2239 original size:24 final size:24

Alignment explanation


    Indices: 2212--2258  Score: 58
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2202 CTCTAGAGAT

                    *   * *         
       2212 CGTGACCGTGATCGTGATAGGGAG
          1 CGTGACCGAGATAGGGATAGGGAG

                 *                 
       2236 CGTGATCGAGATAGGGATAGGGA
          1 CGTGACCGAGATAGGGATAGGGA

       2259 TCGATATAGG


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.26, C:0.13, G:0.43, T:0.19


Consensus pattern (24 bp):   
CGTGACCGAGATAGGGATAGGGAG

Found at i:2241 original size:18 final size:18

Alignment explanation


    Indices: 2218--2252  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2208 AGATCGTGAC

                    *         
       2218 CGTGATCGTGATAGGGAG
          1 CGTGATCGAGATAGGGAG

                             
       2236 CGTGATCGAGATAGGGA
          1 CGTGATCGAGATAGGGA

       2253 TAGGGATCGA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.26, C:0.11, G:0.43, T:0.20


Consensus pattern (18 bp):   
CGTGATCGAGATAGGGAG

Found at i:2866 original size:3 final size:3

Alignment explanation


    Indices: 2858--2890  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

       2848 ATTAACACTT

                                                       
       2858 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
          1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA

       2891 CTTTAGAAAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33


Consensus pattern (3 bp):   
TGA

Found at i:3013 original size:18 final size:18

Alignment explanation


    Indices: 2990--3043  Score: 56
    Period size: 19  Copynumber: 2.9  Consensus size: 18

       2980 CTGTTGGCTG

                              
       2990 TTTTGTTGTATTATTTAT
          1 TTTTGTTGTATTATTTAT

                     *          
       3008 TTTTGTCCTTTATT-TTTAT
          1 TTTTGT--TGTATTATTTAT

                *            
       3027 TTTTATTGTTATTATTT
          1 TTTTGTTG-TATTATTT

       3044 TTGGCTTGTT


Statistics
Matches: 29,  Mismatches: 3, Indels: 7
        0.74            0.08        0.18

Matches are distributed among these distances:
  17    1  0.03
  18   10  0.34
  19   13  0.45
  20    5  0.17

ACGTcount: A:0.15, C:0.04, G:0.07, T:0.74


Consensus pattern (18 bp):   
TTTTGTTGTATTATTTAT
Done.