Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold863

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: 5042
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37


Found at i:2607 original size:18 final size:18

Alignment explanation


    Indices: 2584--2618  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2574 AGATTTTTAA

                              
       2584 AAAATATTAATTTAATAT
          1 AAAATATTAATTTAATAT

                             
       2602 AAAATATTAATTTAATA
          1 AAAATATTAATTTAATA

       2619 CTATAATTAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (18 bp):   
AAAATATTAATTTAATAT

Found at i:2994 original size:37 final size:41

Alignment explanation


    Indices: 2911--2998  Score: 112
    Period size: 37  Copynumber: 2.2  Consensus size: 41

       2901 TAAATTAGTA

                                               *   * *
       2911 TATTACTAATACATAATATTATAATATATTATAATGTATTAG
          1 TATTACTAATACATAATA-TATAATATATTATAATATATAAC

                                                     
       2953 TATTACTAATACATAA-A-ATAAT-TA-TATAATATATAAC
          1 TATTACTAATACATAATATATAATATATTATAATATATAAC

                     
       2990 TATTACTAA
          1 TATTACTAA

       2999 AAATATTAAT


Statistics
Matches: 43,  Mismatches: 3, Indels: 5
        0.84            0.06        0.10

Matches are distributed among these distances:
  37   19  0.44
  38    2  0.05
  39    5  0.12
  41    1  0.02
  42   16  0.37

ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42


Consensus pattern (41 bp):   
TATTACTAATACATAATATATAATATATTATAATATATAAC

Found at i:3000 original size:30 final size:31

Alignment explanation


    Indices: 2957--3024  Score: 79
    Period size: 30  Copynumber: 2.2  Consensus size: 31

       2947 TATTAGTATT

                *                            
       2957 ACTAATACAT-AAAATAATTATATA-ATATATA
          1 ACTATTACATAAAAAT-ATTA-ATACATATATA

                                      *    
       2988 ACTATTAC-TAAAAATATTAATACATGTATA
          1 ACTATTACATAAAAATATTAATACATATATA

                   
       3018 ACTATTA
          1 ACTATTA

       3025 TTATAATATA


Statistics
Matches: 33,  Mismatches: 2, Indels: 5
        0.82            0.05        0.12

Matches are distributed among these distances:
  29    3  0.09
  30   18  0.55
  31   12  0.36

ACGTcount: A:0.53, C:0.09, G:0.01, T:0.37


Consensus pattern (31 bp):   
ACTATTACATAAAAATATTAATACATATATA

Found at i:3267 original size:20 final size:21

Alignment explanation


    Indices: 3237--3275  Score: 71
    Period size: 20  Copynumber: 1.9  Consensus size: 21

       3227 CTTTAAATAA

                                 
       3237 TTTTAACTCAAGTGAAAGATT
          1 TTTTAACTCAAGTGAAAGATT

                               
       3258 TTTTAA-TCAAGTGAAAGA
          1 TTTTAACTCAAGTGAAAGA

       3276 CTACTCCCTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20   12  0.67
  21    6  0.33

ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36


Consensus pattern (21 bp):   
TTTTAACTCAAGTGAAAGATT

Found at i:4979 original size:13 final size:13

Alignment explanation


    Indices: 4963--5007  Score: 56
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       4953 ATTATTTATA

                         
       4963 AATTAATTTAATT
          1 AATTAATTTAATT

                  *    * 
       4976 AATTAAATTAACT
          1 AATTAATTTAATT

                          
       4989 AAGTTAATTT-ATT
          1 AA-TTAATTTAATT

                  
       5002 AATTAA
          1 AATTAA

       5008 ATAATTTTCT


Statistics
Matches: 27,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  12    4  0.15
  13   17  0.63
  14    6  0.22

ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47


Consensus pattern (13 bp):   
AATTAATTTAATT
Done.