Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_5378

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: 11248
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:2717 original size:27 final size:25

Alignment explanation


    Indices: 2643--2736  Score: 91
    Period size: 27  Copynumber: 3.6  Consensus size: 25

       2633 TGACCATGCG

                                   *   
       2643 GCACTAAAGTGTGCGAGTTTGATATTA
          1 GCACT-AAGTGTGCGAG-TTGATTTTA

                           *           
       2670 GCACTAAGT-TGCGATTTGATTTCGTA
          1 GCACTAAGTGTGCGAGTTGATTT--TA

                                       
       2696 GCACTAAGTGTGCGAGTTGATTATATA
          1 GCACTAAGTGTGCGAGTTGATT-T-TA

            *    *        
       2723 TCACTGAGTGTGCG
          1 GCACTAAGTGTGCG

       2737 GACTCAATAT


Statistics
Matches: 57,  Mismatches: 6, Indels: 8
        0.80            0.08        0.11

Matches are distributed among these distances:
  24    6  0.11
  25    5  0.09
  26   15  0.26
  27   30  0.53
  28    1  0.02

ACGTcount: A:0.26, C:0.14, G:0.27, T:0.34


Consensus pattern (25 bp):   
GCACTAAGTGTGCGAGTTGATTTTA

Found at i:6906 original size:10 final size:10

Alignment explanation


    Indices: 6891--6931  Score: 55
    Period size: 10  Copynumber: 3.9  Consensus size: 10

       6881 ATATACTTCG

                      
       6891 ATTTTTTTTA
          1 ATTTTTTTTA

                        
       6901 ATTTTTTTTCGA
          1 ATTTTTTTT--A

            *         
       6913 TTTTTTTTTA
          1 ATTTTTTTTA

                     
       6923 ATTTTTTTT
          1 ATTTTTTTT

       6932 CGAATTTCCT


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  10   18  0.67
  12    9  0.33

ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80


Consensus pattern (10 bp):   
ATTTTTTTTA

Found at i:6908 original size:11 final size:11

Alignment explanation


    Indices: 6892--6931  Score: 62
    Period size: 11  Copynumber: 3.6  Consensus size: 11

       6882 TATACTTCGA

                       
       6892 TTTTTTTTAAT
          1 TTTTTTTTAAT

                   **  
       6903 TTTTTTTCGAT
          1 TTTTTTTTAAT

                       
       6914 TTTTTTTTAAT
          1 TTTTTTTTAAT

                   
       6925 TTTTTTT
          1 TTTTTTT

       6932 CGAATTTCCT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  11   25  1.00

ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82


Consensus pattern (11 bp):   
TTTTTTTTAAT

Found at i:6913 original size:21 final size:22

Alignment explanation


    Indices: 6887--6934  Score: 89
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       6877 TTTTATATAC

                                  
       6887 TTCGA-TTTTTTTTAATTTTTT
          1 TTCGATTTTTTTTTAATTTTTT

                                  
       6908 TTCGATTTTTTTTTAATTTTTT
          1 TTCGATTTTTTTTTAATTTTTT

                 
       6930 TTCGA
          1 TTCGA

       6935 ATTTCCTCTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  21    5  0.19
  22   21  0.81

ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73


Consensus pattern (22 bp):   
TTCGATTTTTTTTTAATTTTTT

Found at i:6962 original size:11 final size:11

Alignment explanation


    Indices: 6892--6963  Score: 56
    Period size: 11  Copynumber: 6.5  Consensus size: 11

       6882 TATACTTCGA

                    *  
       6892 TTTTTTTTAAT
          1 TTTTTTTTGAT

                   *   
       6903 TTTTTTTCGAT
          1 TTTTTTTTGAT

                    *  
       6914 TTTTTTTTAAT
          1 TTTTTTTTGAT

                   *    
       6925 TTTTTTTCGAAT
          1 TTTTTTTTG-AT

              ** *   * 
       6937 TTCCTCTT-CT
          1 TTTTTTTTGAT

                       
       6947 TTTTTTTTGAT
          1 TTTTTTTTGAT

                  
       6958 TTTTTT
          1 TTTTTT

       6964 CAATTACAAT


Statistics
Matches: 44,  Mismatches: 15, Indels: 4
        0.70            0.24        0.06

Matches are distributed among these distances:
  10    6  0.14
  11   32  0.73
  12    6  0.14

ACGTcount: A:0.11, C:0.08, G:0.04, T:0.76


Consensus pattern (11 bp):   
TTTTTTTTGAT

Found at i:11021 original size:13 final size:13

Alignment explanation


    Indices: 11005--11053  Score: 53
    Period size: 13  Copynumber: 3.5  Consensus size: 13

      10995 AAAAAAAATC

                         
      11005 AAAAAAAATTTGA
          1 AAAAAAAATTTGA

                         
      11018 AAAAAAAATTTGA
          1 AAAAAAAATTTGA

                       *  * 
      11031 TTGAAAAAAAAATTCA
          1 ---AAAAAAAATTTGA

                   
      11047 AAAAAAA
          1 AAAAAAA

      11054 GTGAAAAAAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
  13   20  0.65
  16   11  0.35

ACGTcount: A:0.71, C:0.02, G:0.06, T:0.20


Consensus pattern (13 bp):   
AAAAAAAATTTGA
Done.