Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g02456.P3

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: 4226
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36


Found at i:1733 original size:14 final size:14

Alignment explanation


    Indices: 1708--1755  Score: 55
    Period size: 14  Copynumber: 3.4  Consensus size: 14

       1698 TTTGTGCTCA

                          
       1708 TTTTTTCT--TTTT
          1 TTTTTTCTGATTTT

                          
       1720 TTTTTTCTGATTTT
          1 TTTTTTCTGATTTT

            *              
       1734 CTTTTTCTGAATTTT
          1 TTTTTTCTG-ATTTT

                   
       1749 TATTTTT
          1 T-TTTTT

       1756 TTTAAAATTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  12    8  0.27
  14   12  0.40
  15    5  0.17
  16    5  0.17

ACGTcount: A:0.08, C:0.08, G:0.04, T:0.79


Consensus pattern (14 bp):   
TTTTTTCTGATTTT

Found at i:3754 original size:42 final size:42

Alignment explanation


    Indices: 3704--3830  Score: 161
    Period size: 42  Copynumber: 3.0  Consensus size: 42

       3694 CTTCATTTTC

                        **  *                *         
       3704 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
          1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A

                                           *      *   
       3747 T-GATGCCATAGCCCAGCTATGGTCTTACACCTATTCATATA
          1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA

                                                       
       3788 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
          1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA

              
       3829 TC
          1 TC

       3831 TCACTGATGC


Statistics
Matches: 74,  Mismatches: 8, Indels: 6
        0.84            0.09        0.07

Matches are distributed among these distances:
  41   10  0.14
  42   63  0.85
  43    1  0.01

ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30


Consensus pattern (42 bp):   
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA

Found at i:3892 original size:47 final size:47

Alignment explanation


    Indices: 3789--3915  Score: 166
    Period size: 47  Copynumber: 2.7  Consensus size: 47

       3779 ATTCATATAT

                      *     *          *      *        *   
       3789 CGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCACATATCTCAC
          1 CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATATCACAC

            *                               *    *         
       3835 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
          1 CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATATCACAC

                                   *          
       3882 CGATGCCATATCCCAGATATGGTTTTATACAGAA
          1 CGATGCCATATCCCAGATATGGTCTTATACAGAA

       3916 ATCACTTGTC


Statistics
Matches: 69,  Mismatches: 11, Indels: 1
        0.85            0.14        0.01

Matches are distributed among these distances:
  46   26  0.38
  47   43  0.62

ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28


Consensus pattern (47 bp):   
CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATATCACAC

Found at i:3972 original size:31 final size:31

Alignment explanation


    Indices: 3937--4085  Score: 253
    Period size: 31  Copynumber: 4.8  Consensus size: 31

       3927 CTTGTCACTT

                              *            
       3937 GTAGCCGAAGCTACCACTATTCACTGATCAG
          1 GTAGCCGAAGCTACCACTTTTCACTGATCAG

                   *        *              
       3968 GTAGCCGGAGCTACCATTTTTCACTGATCAG
          1 GTAGCCGAAGCTACCACTTTTCACTGATCAG

                                           
       3999 GTAGCCGAAGCTACCACTTTTCACTGATCAG
          1 GTAGCCGAAGCTACCACTTTTCACTGATCAG

                 *                      *  
       4030 GTAGCAGAAGCTACCACTTTTCACTGATTAG
          1 GTAGCCGAAGCTACCACTTTTCACTGATCAG

                                     
       4061 GTAGCCGAAGCTACCACTTTTCACT
          1 GTAGCCGAAGCTACCACTTTTCACT

       4086 TGTCATTGAT


Statistics
Matches: 110,  Mismatches: 8, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31  110  1.00

ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27


Consensus pattern (31 bp):   
GTAGCCGAAGCTACCACTTTTCACTGATCAG

Done.