Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00885.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: 4695
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37


Found at i:355 original size:19 final size:21

Alignment explanation


    Indices: 327--374  Score: 64
    Period size: 20  Copynumber: 2.4  Consensus size: 21

        317 TTATTATTTA

                                 
        327 TTTTAGTTTTGATTCTAA-AT
          1 TTTTAGTTTTGATTCTAATAT

                      *   *      
        347 TTTTA-TTTTTATTTTAATAT
          1 TTTTAGTTTTGATTCTAATAT

                    
        367 TTTTAGTT
          1 TTTTAGTT

        375 AAAATTTTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  19   10  0.42
  20   12  0.50
  21    2  0.08

ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69


Consensus pattern (21 bp):   
TTTTAGTTTTGATTCTAATAT

Found at i:618 original size:43 final size:43

Alignment explanation


    Indices: 522--626  Score: 158
    Period size: 43  Copynumber: 2.4  Consensus size: 43

        512 TTTAAATTTA

                                                       
        522 ATGACTTTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAAGGAC
          1 ATGACTTTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAAGGAC

                  *                         *         * 
        565 -TGGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC
          1 AT-GACTTTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAAGGAC

                          *    
        608 ATGACTTTTAGCGGTGTTT
          1 ATGACTTTTAGCGGCGTTT

        627 TTTTAAATAA


Statistics
Matches: 55,  Mismatches: 5, Indels: 4
        0.86            0.08        0.06

Matches are distributed among these distances:
  42    1  0.02
  43   53  0.96
  44    1  0.02

ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28


Consensus pattern (43 bp):   
ATGACTTTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAAGGAC

Found at i:3799 original size:27 final size:27

Alignment explanation


    Indices: 3761--3881  Score: 154
    Period size: 27  Copynumber: 4.5  Consensus size: 27

       3751 CGTTATTTGA

                               *       
       3761 AGGGTAAAATGACCGTAATGCCCTTGT
          1 AGGGTAAAATGACCGTAATACCCTTGT

                                       *
       3788 AGGGTAAAATGACCGTAATACCAC-TGA
          1 AGGGTAAAATGACCGTAATACC-CTTGT

                          *    *   *   
       3815 AGGGTAAAATGACCATAATTCCCCTGT
          1 AGGGTAAAATGACCGTAATACCCTTGT

                        **             
       3842 AGGGTAAAATGAATGTAATACCCTTGT
          1 AGGGTAAAATGACCGTAATACCCTTGT

             *           
       3869 ATGGTAAAATGAC
          1 AGGGTAAAATGAC

       3882 AATTATGACC


Statistics
Matches: 80,  Mismatches: 12, Indels: 4
        0.83            0.12        0.04

Matches are distributed among these distances:
  26    1  0.01
  27   78  0.98
  28    1  0.01

ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25


Consensus pattern (27 bp):   
AGGGTAAAATGACCGTAATACCCTTGT

Found at i:3821 original size:54 final size:54

Alignment explanation


    Indices: 3757--3881  Score: 171
    Period size: 54  Copynumber: 2.3  Consensus size: 54

       3747 AGGTCGTTAT

                              *        *               *           
       3757 TTGAAGGGTAAAATGACCGTAATGCCCTTGTAGGGTAAAATGACCGTAATACCAC
          1 TTGAAGGGTAAAATGACCATAATGCCCCTGTAGGGTAAAATGAACGTAATACC-C

                                   *                    *         
       3812 -TGAAGGGTAAAATGACCATAATTCCCCTGTAGGGTAAAATGAATGTAATACCC
          1 TTGAAGGGTAAAATGACCATAATGCCCCTGTAGGGTAAAATGAACGTAATACCC

               * *           
       3865 TTGTATGGTAAAATGAC
          1 TTGAAGGGTAAAATGAC

       3882 AATTATGACC


Statistics
Matches: 62,  Mismatches: 7, Indels: 3
        0.86            0.10        0.04

Matches are distributed among these distances:
  53    1  0.02
  54   61  0.98

ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26


Consensus pattern (54 bp):   
TTGAAGGGTAAAATGACCATAATGCCCCTGTAGGGTAAAATGAACGTAATACCC

Found at i:4074 original size:27 final size:27

Alignment explanation


    Indices: 4044--4103  Score: 77
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       4034 TGTCACATTC

                                        
       4044 ACTGTTACAGGTGG-TTATGCTACAATT
          1 ACTGTTACAGGTGGCTT-TGCTACAATT

                *   *               *  
       4071 ACTGATACTGGTGGCTTTGCTACATTT
          1 ACTGTTACAGGTGGCTTTGCTACAATT

                  
       4098 ACTGTT
          1 ACTGTT

       4104 TTTGGCAGCT


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  27   26  0.93
  28    2  0.07

ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40


Consensus pattern (27 bp):   
ACTGTTACAGGTGGCTTTGCTACAATT
Done.