Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1694

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: 9100
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32


Found at i:88 original size:15 final size:17

Alignment explanation


    Indices: 68--99  Score: 50
    Period size: 15  Copynumber: 2.0  Consensus size: 17

         58 TGTTTATATT

                             
         68 AAATT-AATTT-TTATA
          1 AAATTAAATTTATTATA

                             
         83 AAATTAAATTTATTATA
          1 AAATTAAATTTATTATA

        100 CTTCTTGATC


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  15    5  0.33
  16    5  0.33
  17    5  0.33

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


Consensus pattern (17 bp):   
AAATTAAATTTATTATA

Found at i:8106 original size:21 final size:20

Alignment explanation


    Indices: 8082--8150  Score: 59
    Period size: 19  Copynumber: 3.5  Consensus size: 20

       8072 AATAATTAAA

                                 
       8082 ATATAATATAAATTAATATAT
          1 ATATAATATAAATTAATA-AT

                 **   *         
       8103 ATATAGGATACATTAA-AAT
          1 ATATAATATAAATTAATAAT

            *     *        *    
       8122 TTATAACATAAATTATTAAT
          1 ATATAATATAAATTAATAAT

                *    
       8142 ATATTATAT
          1 ATATAATAT

       8151 TTTATATAAA


Statistics
Matches: 36,  Mismatches: 11, Indels: 3
        0.72            0.22        0.06

Matches are distributed among these distances:
  19   13  0.36
  20   10  0.28
  21   13  0.36

ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42


Consensus pattern (20 bp):   
ATATAATATAAATTAATAAT

Found at i:8203 original size:22 final size:22

Alignment explanation


    Indices: 8162--8203  Score: 59
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       8152 TTATATAAAA

                           *      
       8162 ATATAATATTTTAAATATATTT
          1 ATATAATATTTTAAAAATATTT

                                 
       8184 ATATAA-ATTTTAATAAATAT
          1 ATATAATATTTTAA-AAATAT

       8204 ATTTATTCAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21    7  0.39
  22   11  0.61

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


Consensus pattern (22 bp):   
ATATAATATTTTAAAAATATTT

Found at i:8558 original size:17 final size:18

Alignment explanation


    Indices: 8536--8593  Score: 57
    Period size: 17  Copynumber: 3.2  Consensus size: 18

       8526 ATTTATTAAA

                      *       
       8536 TTTATTTATATTAT-TTT
          1 TTTATTTATAATATATTT

                   *          
       8553 TTTATTTTTAATATATTT
          1 TTTATTTATAATATATTT

                                 
       8571 TTTAATAATTA-AATATATTT
          1 TTT-AT--TTATAATATATTT

               
       8591 TTT
          1 TTT

       8594 GTTAATATTG


Statistics
Matches: 34,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  17   12  0.35
  18    6  0.18
  19    2  0.06
  20   12  0.35
  21    2  0.06

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


Consensus pattern (18 bp):   
TTTATTTATAATATATTT
Done.