Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2665

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: 22957
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33


Found at i:4851 original size:20 final size:21

Alignment explanation


    Indices: 4813--4861  Score: 59
    Period size: 19  Copynumber: 2.4  Consensus size: 21

       4803 TTTTAAAAAT

                                 
       4813 ATTTTTATATTTACTTTTAAA
          1 ATTTTTATATTTACTTTTAAA

                                  
       4834 ATTTTTA-ATTTA-TATTT-AA
          1 ATTTTTATATTTACT-TTTAAA

            *        
       4853 CTTTTTATA
          1 ATTTTTATA

       4862 ATCCATATTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  19    9  0.36
  20    9  0.36
  21    7  0.28

ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63


Consensus pattern (21 bp):   
ATTTTTATATTTACTTTTAAA

Found at i:5930 original size:14 final size:15

Alignment explanation


    Indices: 5911--5942  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       5901 CATGTTTCTC

                           
       5911 TTTA-TTTTTAAATA
          1 TTTATTTTTTAAATA

                           
       5925 TTTATTTTTTAAATA
          1 TTTATTTTTTAAATA

               
       5940 TTT
          1 TTT

       5943 TACTATACTC


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    4  0.24
  15   13  0.76

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (15 bp):   
TTTATTTTTTAAATA

Found at i:6625 original size:21 final size:21

Alignment explanation


    Indices: 6584--6628  Score: 74
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       6574 AATTTTAAAA

                                 
       6584 TTTTTAATTTATATTTAACTT
          1 TTTTTAATTTATATTTAACTT

                                  
       6605 TTTTATAATTTATATTT-ACTT
          1 TTTT-TAATTTATATTTAACTT

               
       6626 TTT
          1 TTT

       6629 CTCATCAATC


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  21   11  0.48
  22   12  0.52

ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69


Consensus pattern (21 bp):   
TTTTTAATTTATATTTAACTT

Found at i:14167 original size:21 final size:21

Alignment explanation


    Indices: 14141--14181  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      14131 AGACGAGCAA

                   * *           
      14141 TACTCCACAGCAGGTGGAGTG
          1 TACTCCAAAACAGGTGGAGTG

                                
      14162 TACTCCAAAACAGGTGGAGT
          1 TACTCCAAAACAGGTGGAGT

      14182 TTGAGCAGAT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20


Consensus pattern (21 bp):   
TACTCCAAAACAGGTGGAGTG

Found at i:20492 original size:36 final size:35

Alignment explanation


    Indices: 20415--20493  Score: 86
    Period size: 36  Copynumber: 2.2  Consensus size: 35

      20405 GACAACTTGC

                         *                   * 
      20415 ACTTAGTCAATCCTCCAGGCTTAAACAATACACCG
          1 ACTTAGTCAATCCACCAGGCTTAAACAATACACAG

                        *   *       *        *   
      20450 AGCTTAGTCAATGCACTAGGCTTAGACAATACGTCAG
          1 A-CTTAGTCAATCCACCAGGCTTAAACAATAC-ACAG

                   
      20487 ACTTAGT
          1 ACTTAGT

      20494 AAATACAATA


Statistics
Matches: 36,  Mismatches: 6, Indels: 3
        0.80            0.13        0.07

Matches are distributed among these distances:
  35    1  0.03
  36   32  0.89
  37    3  0.08

ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25


Consensus pattern (35 bp):   
ACTTAGTCAATCCACCAGGCTTAAACAATACACAG
Done.