Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01822.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, 594

Length: 990
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31


Found at i:484 original size:23 final size:23

Alignment explanation


    Indices: 439--484  Score: 58
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        429 TGCAGTTTAA

                *             *    
        439 TTTGTATTTTGGGCCTTGTTATT
          1 TTTGGATTTTGGGCCTTGGTATT

                                    
        462 TTTGGATTTTGGG-CTTAGGTATT
          1 TTTGGATTTTGGGCCTT-GGTATT

        485 ATTATGGACA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  22    3  0.15
  23   17  0.85

ACGTcount: A:0.11, C:0.07, G:0.26, T:0.57


Consensus pattern (23 bp):   
TTTGGATTTTGGGCCTTGGTATT

Found at i:524 original size:14 final size:14

Alignment explanation


    Indices: 505--552  Score: 51
    Period size: 14  Copynumber: 3.1  Consensus size: 14

        495 TTGGACTTTA

                          
        505 ATTTTGGTTTTTGT
          1 ATTTTGGTTTTTGT

                              
        519 ATTTTGGTTTATTTTGTT
          1 ATTTTGG--T-TTTTG-T

            *             
        537 TTTTTGGTTTTTGT
          1 ATTTTGGTTTTTGT

              
        551 AT
          1 AT

        553 GGGCCCGGGT


Statistics
Matches: 28,  Mismatches: 2, Indels: 8
        0.74            0.05        0.21

Matches are distributed among these distances:
  14    9  0.32
  15    5  0.18
  16    2  0.07
  17    5  0.18
  18    7  0.25

ACGTcount: A:0.08, C:0.00, G:0.19, T:0.73


Consensus pattern (14 bp):   
ATTTTGGTTTTTGT

Found at i:535 original size:17 final size:18

Alignment explanation


    Indices: 513--546  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        503 TAATTTTGGT

                              
        513 TTTTG-TATTTTGGTTTA
          1 TTTTGTTATTTTGGTTTA

                   *         
        530 TTTTGTTTTTTTGGTTT
          1 TTTTGTTATTTTGGTTT

        547 TTGTATGGGC


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    5  0.33
  18   10  0.67

ACGTcount: A:0.06, C:0.00, G:0.18, T:0.76


Consensus pattern (18 bp):   
TTTTGTTATTTTGGTTTA

Found at i:878 original size:29 final size:29

Alignment explanation


    Indices: 846--910  Score: 96
    Period size: 29  Copynumber: 2.2  Consensus size: 29

        836 CATCTGTGTA

                   *              *       
        846 TGTGTTTGCTTATTACTATCGTCTG-CGTG
          1 TGTGTTTCCTTATTACTATCGTATGTC-TG

                                         
        875 TGTGTTTCCTTATTACTATCGTATGTCTG
          1 TGTGTTTCCTTATTACTATCGTATGTCTG

                   
        904 TGTGTTT
          1 TGTGTTT

        911 TAAGGCCTTC


Statistics
Matches: 33,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  29   32  0.97
  30    1  0.03

ACGTcount: A:0.11, C:0.15, G:0.22, T:0.52


Consensus pattern (29 bp):   
TGTGTTTCCTTATTACTATCGTATGTCTG
Done.