Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1739

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: 12341
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37


Found at i:736 original size:20 final size:20

Alignment explanation


    Indices: 693--855  Score: 150
    Period size: 20  Copynumber: 7.7  Consensus size: 20

        683 TTTTACCCAG

                                
        693 ATGTATCGATACA-GTTTCA
          1 ATGTATCGATACATGTTTCA

                            * * 
        712 ATGTATCGATACATGTATGA
          1 ATGTATCGATACATGTTTCA

                                 
        732 ATGTATCGATACAT-TCTTCA
          1 ATGTATCGATACATGT-TTCA

                                *        
        752 ATGTATCGATACATTCTATTTTTTACCCA
          1 ATGTATCGAT--A--C-A-TGTTT---CA

                           *     
        781 GATGTATCGATACATTTTTCA
          1 -ATGTATCGATACATGTTTCA

                            * * 
        802 ATGTATCGATACATGTATGA
          1 ATGTATCGATACATGTTTCA

                          *     
        822 ATGTATCGATACATTTTTCA
          1 ATGTATCGATACATGTTTCA

                          
        842 ATGTATCGATACAT
          1 ATGTATCGATACAT

        856 CTAGTTAAAA


Statistics
Matches: 121,  Mismatches: 10, Indels: 25
        0.78            0.06        0.16

Matches are distributed among these distances:
  19   14  0.12
  20   78  0.64
  21    2  0.02
  22    1  0.01
  24    6  0.05
  25    2  0.02
  26    4  0.03
  27    1  0.01
  28    1  0.01
  29    2  0.02
  30   10  0.08

ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40


Consensus pattern (20 bp):   
ATGTATCGATACATGTTTCA

Found at i:760 original size:40 final size:40

Alignment explanation


    Indices: 693--855  Score: 193
    Period size: 40  Copynumber: 3.9  Consensus size: 40

        683 TTTTACCCAG

                          *                         
        693 ATGTATCGATACA-GTTTCAATGTATCGATACATGTATGA
          1 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA

                           *                   *           * 
        732 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATTTTTTACCCA
          1 ATGTATCGATACATTTTTCAATGTATCGATACA-TGTA-----T---GA

                                                     
        781 GATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
          1 -ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA

                                              
        822 ATGTATCGATACATTTTTCAATGTATCGATACAT
          1 ATGTATCGATACATTTTTCAATGTATCGATACAT

        856 CTAGTTAAAA


Statistics
Matches: 106,  Mismatches: 7, Indels: 21
        0.79            0.05        0.16

Matches are distributed among these distances:
  39   13  0.12
  40   51  0.48
  41    4  0.04
  44    1  0.01
  46    1  0.01
  49    4  0.04
  50   32  0.30

ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40


Consensus pattern (40 bp):   
ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA

Found at i:834 original size:90 final size:89

Alignment explanation


    Indices: 682--855  Score: 321
    Period size: 90  Copynumber: 1.9  Consensus size: 89

        672 AAAAGTCACA

                                                                             
        682 TTTTTACCCAGATGTATCGATACAGTTTCAATGTATCGATACATGTATGAATGTATCGATACATT
          1 TTTTTACCCAGATGTATCGATACAGTTTCAATGTATCGATACATGTATGAATGTATCGATACATT

                                    
        747 CTTCAATGTATCGATACATTCTAT
         66 CTTCAATGTATCGATACATTCTAT

                                     *                                       
        771 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
          1 TTTTTACCCAGATGTATCGATACA-GTTTCAATGTATCGATACATGTATGAATGTATCGATACAT

             *                  
        836 TTTTCAATGTATCGATACAT
         65 TCTTCAATGTATCGATACAT

        856 CTAGTTAAAA


Statistics
Matches: 82,  Mismatches: 2, Indels: 1
        0.96            0.02        0.01

Matches are distributed among these distances:
  89   24  0.29
  90   58  0.71

ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40


Consensus pattern (89 bp):   
TTTTTACCCAGATGTATCGATACAGTTTCAATGTATCGATACATGTATGAATGTATCGATACATT
CTTCAATGTATCGATACATTCTAT

Found at i:4170 original size:22 final size:21

Alignment explanation


    Indices: 4145--4199  Score: 56
    Period size: 22  Copynumber: 2.5  Consensus size: 21

       4135 TTATAATAAC

                                  
       4145 TTAAACTGATTTAATCCGAATA
          1 TTAAACTGATTTAAT-CGAATA

                   * *     *    *
       4167 TTAAACTCAATTAATTGAATG
          1 TTAAACTGATTTAATCGAATA

                        
       4188 TTAAACTCGATT
          1 TTAAACT-GATT

       4200 GCTCTGTTAC


Statistics
Matches: 26,  Mismatches: 6, Indels: 2
        0.76            0.18        0.06

Matches are distributed among these distances:
  21   11  0.42
  22   15  0.58

ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38


Consensus pattern (21 bp):   
TTAAACTGATTTAATCGAATA

Found at i:9393 original size:15 final size:15

Alignment explanation


    Indices: 9373--9403  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       9363 TTTTGTCAAA

                           
       9373 TCAAGTAAGATTGTG
          1 TCAAGTAAGATTGTG

                           
       9388 TCAAGTAAGATTGTG
          1 TCAAGTAAGATTGTG

             
       9403 T
          1 T

       9404 ACGAATTATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35


Consensus pattern (15 bp):   
TCAAGTAAGATTGTG
Done.