Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1788

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: 12565
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37


Found at i:1649 original size:38 final size:37

Alignment explanation


    Indices: 1593--1691  Score: 128
    Period size: 36  Copynumber: 2.7  Consensus size: 37

       1583 CGACAAGTAA

                 *      **                        
       1593 TATTTAGGTGGCTTTGCCAATTCCACTATGATTGTCAG
          1 TATTTGGGTGGCAGTGCCAA-TCCACTATGATTGTCAG

                                              *  
       1631 TATTTGGGTGGCAGTGCCAAT-CACTATGATTGTTAG
          1 TATTTGGGTGGCAGTGCCAATCCACTATGATTGTCAG

            *             *          
       1667 AATTTGGGTGGCAGCGCCAATCCAC
          1 TATTTGGGTGGCAGTGCCAATCCAC

       1692 GGAAAAATAA


Statistics
Matches: 54,  Mismatches: 6, Indels: 3
        0.86            0.10        0.05

Matches are distributed among these distances:
  36   33  0.61
  37    4  0.07
  38   17  0.31

ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33


Consensus pattern (37 bp):   
TATTTGGGTGGCAGTGCCAATCCACTATGATTGTCAG

Found at i:6367 original size:37 final size:37

Alignment explanation


    Indices: 6326--6410  Score: 116
    Period size: 37  Copynumber: 2.3  Consensus size: 37

       6316 CGGTGGCTTG

                                  *          *  *
       6326 GCCAATCCACTATGATTGTCAGTATTTGGGTGGTAGT
          1 GCCAATCCACTATGATTGTCAGAATTTGGGTGGCAGC

                             * *       *         
       6363 GCCAATCCACTATGATTTTTAGAATTTTGGTGGCAGC
          1 GCCAATCCACTATGATTGTCAGAATTTGGGTGGCAGC

                       
       6400 GCCAATCCACT
          1 GCCAATCCACT

       6411 GAAAAATAAA


Statistics
Matches: 42,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  37   42  1.00

ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33


Consensus pattern (37 bp):   
GCCAATCCACTATGATTGTCAGAATTTGGGTGGCAGC

Found at i:10570 original size:19 final size:21

Alignment explanation


    Indices: 10532--10571  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      10522 ATGTTATTTT

                                 
      10532 TATTTAAAATAAATTAATTAA
          1 TATTTAAAATAAATTAATTAA

                 *               
      10553 TATTTTAAA-AAA-TAATTAA
          1 TATTTAAAATAAATTAATTAA

      10572 ATGAAGTGTT


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

Matches are distributed among these distances:
  19    7  0.39
  20    3  0.17
  21    8  0.44

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42


Consensus pattern (21 bp):   
TATTTAAAATAAATTAATTAA
Done.