Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1232

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: 7678
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36


Found at i:1563 original size:29 final size:30

Alignment explanation


    Indices: 1495--1566  Score: 85
    Period size: 29  Copynumber: 2.4  Consensus size: 30

       1485 TTTTTATTTG

                  *  *                *   
       1495 ATATAAGAATTTATTTAGATATAAATCAAA
          1 ATATAAAAACTTATTTAGATATAAATAAAA

             *                             
       1525 ACATAAAAACTTATTT-GA-ATATAATAAAA
          1 ATATAAAAACTTATTTAGATATA-AATAAAA

                         
       1554 ATATAAAAACTTA
          1 ATATAAAAACTTA

       1567 CTTATGTAAA


Statistics
Matches: 36,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  28    3  0.08
  29   20  0.56
  30   13  0.36

ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33


Consensus pattern (30 bp):   
ATATAAAAACTTATTTAGATATAAATAAAA

Found at i:3054 original size:30 final size:31

Alignment explanation


    Indices: 3020--3077  Score: 75
    Period size: 29  Copynumber: 1.9  Consensus size: 31

       3010 AAACCTCATG

                                            
       3020 AGATAAATAAAATTATTT-TTAA-ATTTAAAA
          1 AGAT-AATAAAATTATTTCTTAATATTTAAAA

                     *   *              
       3050 AGATAATAATATTTTTTCTTAATATTTA
          1 AGATAATAAAATTATTTCTTAATATTTA

       3078 GTAACAAAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  29   11  0.46
  30    8  0.33
  31    5  0.21

ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47


Consensus pattern (31 bp):   
AGATAATAAAATTATTTCTTAATATTTAAAA

Found at i:3443 original size:11 final size:11

Alignment explanation


    Indices: 3411--3456  Score: 56
    Period size: 11  Copynumber: 4.1  Consensus size: 11

       3401 TCAGTTTTTT

                       
       3411 TATTTTAAATA
          1 TATTTTAAATA

             *         *
       3422 TTTTATTAAATG
          1 TATT-TTAAATA

                       
       3434 TATTTTAAATA
          1 TATTTTAAATA

                 *     
       3445 TATTTAAAATA
          1 TATTTTAAATA

             
       3456 T
          1 T

       3457 TAATTCGATT


Statistics
Matches: 29,  Mismatches: 5, Indels: 2
        0.81            0.14        0.06

Matches are distributed among these distances:
  11   20  0.69
  12    9  0.31

ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54


Consensus pattern (11 bp):   
TATTTTAAATA

Found at i:3807 original size:19 final size:19

Alignment explanation


    Indices: 3769--3808  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       3759 TAAATTTAAA

                      **   *   
       3769 TATTTTTTAATTTAATATT
          1 TATTTTTTAAAATAAAATT

                               
       3788 TATTTTTTAAAATAAAATT
          1 TATTTTTTAAAATAAAATT

              
       3807 TA
          1 TA

       3809 AATTGAAATG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (19 bp):   
TATTTTTTAAAATAAAATT

Found at i:4620 original size:2 final size:2

Alignment explanation


    Indices: 4613--4650  Score: 69
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       4603 ATCATTACAG

                                                                      
       4613 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       4651 TGACAGGAAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   34  0.97

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


Consensus pattern (2 bp):   
TA

Done.