Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g02348.N4

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: 9731
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:178 original size:6 final size:6

Alignment explanation


    Indices: 167--192  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

        157 ACCATCCTCT

                                          
        167 TCTTCA TCTTCA TCTTCA TCTTCA TC
          1 TCTTCA TCTTCA TCTTCA TCTTCA TC

        193 GCTGTTATCG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50


Consensus pattern (6 bp):   
TCTTCA

Found at i:2718 original size:19 final size:20

Alignment explanation


    Indices: 2696--2736  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       2686 TTTATTTTAA

                                
       2696 AATT-AAAAAAACTATTAGT
          1 AATTAAAAAAAACTATTAGT

                        *       
       2715 AATTAAAAAAAATTATTAGT
          1 AATTAAAAAAAACTATTAGT

              
       2735 AA
          1 AA

       2737 AGAGGCTATA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  19    4  0.20
  20   16  0.80

ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32


Consensus pattern (20 bp):   
AATTAAAAAAAACTATTAGT

Found at i:6895 original size:20 final size:20

Alignment explanation


    Indices: 6862--6904  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       6852 ATCAGTATTC

                                
       6862 TTATCATGAATTTTAGGATT
          1 TTATCATGAATTTTAGGATT

                 *   *      *   
       6882 TTATCCTGAGTTTTAGTATT
          1 TTATCATGAATTTTAGGATT

               
       6902 TTA
          1 TTA

       6905 ATTTGGATTT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.26, C:0.07, G:0.14, T:0.53


Consensus pattern (20 bp):   
TTATCATGAATTTTAGGATT

Found at i:9285 original size:18 final size:19

Alignment explanation


    Indices: 9253--9291  Score: 71
    Period size: 18  Copynumber: 2.1  Consensus size: 19

       9243 TACACCTTCT

                               
       9253 TTACTAATAATTTTTTTAA
          1 TTACTAATAATTTTTTTAA

                               
       9272 TTACTAAT-ATTTTTTTAA
          1 TTACTAATAATTTTTTTAA

              
       9290 TT
          1 TT

       9292 TTAAAATAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18   12  0.60
  19    8  0.40

ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62


Consensus pattern (19 bp):   
TTACTAATAATTTTTTTAA

Found at i:9696 original size:22 final size:21

Alignment explanation


    Indices: 9662--9702  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       9652 AAAATAAAAA

                         *       
       9662 TAAAAATAATTTTCAAATTTT
          1 TAAAAATAATTTTAAAATTTT

                                
       9683 TAAAAATAATTTTTAAAATT
          1 TAAAAATAA-TTTTAAAATT

       9703 CAAAATATTT


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

Matches are distributed among these distances:
  21    9  0.50
  22    9  0.50

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46


Consensus pattern (21 bp):   
TAAAAATAATTTTAAAATTTT
Done.