Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g01190.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: 3960
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33


Found at i:3519 original size:20 final size:20

Alignment explanation


    Indices: 3489--3533  Score: 65
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       3479 CTGTTTTATT

                                
       3489 ATGGG-CCAACTGTATTAAA
          1 ATGGGCCCAACTGTATTAAA

                          *    *
       3508 ATGGGCCCAACTGTGTTAAT
          1 ATGGGCCCAACTGTATTAAA

                  
       3528 ATGGGC
          1 ATGGGC

       3534 AAGACCCAAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  19    5  0.22
  20   18  0.78

ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27


Consensus pattern (20 bp):   
ATGGGCCCAACTGTATTAAA

Found at i:3656 original size:28 final size:27

Alignment explanation


    Indices: 3562--3668  Score: 74
    Period size: 28  Copynumber: 3.7  Consensus size: 27

       3552 ACTTGTAATA

                           * *   *      
       3562 GGGCTACGGCCCAGACTGATACTGATAT
          1 GGGCTA-GGCCCAGATTAATATTGATAT

                                 *           
       3590 GGGCTAGGCCCAGTATGCTCTGATATTG-TAAT
          1 GGGCTAGGCCCAG-A---T-TAATATTGAT-AT

                                         
       3622 AGGGCTATGGCCCAGATTAATATTGATAT
          1 -GGGCTA-GGCCCAGATTAATATTGATAT

                               
       3651 GGGCTAAGGCCCAG-TTAA
          1 GGGCT-AGGCCCAGATTAA

       3669 CACTGATTTC


Statistics
Matches: 66,  Mismatches: 3, Indels: 21
        0.73            0.03        0.23

Matches are distributed among these distances:
  27   11  0.17
  28   19  0.29
  29   10  0.15
  30    2  0.03
  31    1  0.02
  32    9  0.14
  33    7  0.11
  34    7  0.11

ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26


Consensus pattern (27 bp):   
GGGCTAGGCCCAGATTAATATTGATAT

Found at i:3689 original size:62 final size:61

Alignment explanation


    Indices: 3554--3698  Score: 170
    Period size: 61  Copynumber: 2.4  Consensus size: 61

       3544 ATATCTCGAC

                          *          *                          * *      
       3554 TTGTAATAGGGCTACGGCCCAGACTGATACTGATATGGGCTAGGCCCAGTATGCTCTGATA
          1 TTGTAATAGGGCTATGGCCCAGACTAATACTGATATGGGCTAGGCCCAGTATACACTGATA

                                   *     *                                 
       3615 TTGTAATAGGGCTATGGCCCAGATTAATATTGATATGGGCTAAGGCCCAGT-TAACACTGAT-
          1 TTGTAATAGGGCTATGGCCCAGACTAATACTGATATGGGCT-AGGCCCAGTAT-ACACTGATA

              *                     
       3676 TTCTGAATAGGGCT-TAGGCCCAG
          1 TTGT-AATAGGGCTAT-GGCCCAG

       3699 TAAGGCTTGA


Statistics
Matches: 73,  Mismatches: 7, Indels: 7
        0.84            0.08        0.08

Matches are distributed among these distances:
  61   42  0.58
  62   31  0.42

ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28


Consensus pattern (61 bp):   
TTGTAATAGGGCTATGGCCCAGACTAATACTGATATGGGCTAGGCCCAGTATACACTGATA
Done.