Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00702.N2

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: 7936
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42


Found at i:2131 original size:27 final size:27

Alignment explanation


    Indices: 2078--2137  Score: 77
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       2068 TTATCCTTTA

                          *             
       2078 TTTGAAATTTGCTGGTTTTATCATTTGT
          1 TTTG-AATTTGCTGCTTTTATCATTTGT

                                  *     
       2106 TTTGAATTTGCTGCTGTTT-TCCTTTGT
          1 TTTGAATTTGCTGCT-TTTATCATTTGT

                 
       2133 TTTGA
          1 TTTGA

       2138 TTTTTTTTTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  27   22  0.76
  28    7  0.24

ACGTcount: A:0.13, C:0.10, G:0.18, T:0.58


Consensus pattern (27 bp):   
TTTGAATTTGCTGCTTTTATCATTTGT

Found at i:2900 original size:27 final size:26

Alignment explanation


    Indices: 2858--2939  Score: 85
    Period size: 27  Copynumber: 3.0  Consensus size: 26

       2848 TTTTAACTTT

                                       
       2858 CTGGTGTTATTCTTTATTTGAATTTTG
          1 CTGGTGTTA-TCTTTATTTGAATTTTG

                                        
       2885 CTGGTGTTATCATTTATTTTGAA-TTTG
          1 CTGGTGTTATC-TTTA-TTTGAATTTTG

               *    *       *           
       2912 CTGCTGTTTTCCTTTGTTTTGAATTTTG
          1 CTGGTGTTAT-CTTT-ATTTGAATTTTG

       2940 TTGTTTGTTT


Statistics
Matches: 47,  Mismatches: 3, Indels: 9
        0.80            0.05        0.15

Matches are distributed among these distances:
  26    2  0.04
  27   34  0.72
  28   11  0.23

ACGTcount: A:0.13, C:0.10, G:0.18, T:0.59


Consensus pattern (26 bp):   
CTGGTGTTATCTTTATTTGAATTTTG

Found at i:3821 original size:16 final size:15

Alignment explanation


    Indices: 3795--3828  Score: 50
    Period size: 16  Copynumber: 2.2  Consensus size: 15

       3785 ATCATCTCTC

                        *  
       3795 TCTTTTTTTCCCTTT
          1 TCTTTTTTTCCCATT

                            
       3810 TCTTTATTTTCCCATT
          1 TCTTT-TTTTCCCATT

               
       3826 TCT
          1 TCT

       3829 GTTTCCTATG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    5  0.29
  16   12  0.71

ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68


Consensus pattern (15 bp):   
TCTTTTTTTCCCATT

Found at i:3863 original size:10 final size:11

Alignment explanation


    Indices: 3847--3880  Score: 52
    Period size: 10  Copynumber: 3.1  Consensus size: 11

       3837 TGAAGAACAG

                       
       3847 CTCTCTTTCTT
          1 CTCTCTTTCTT

                        
       3858 -TCTCTTTCATT
          1 CTCTCTTTC-TT

                       
       3869 CTCTCTTTCTT
          1 CTCTCTTTCTT

             
       3880 C
          1 C

       3881 ATATCAACAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  10    8  0.38
  11    5  0.24
  12    8  0.38

ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62


Consensus pattern (11 bp):   
CTCTCTTTCTT

Found at i:6145 original size:26 final size:26

Alignment explanation


    Indices: 6109--6161  Score: 106
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       6099 AAGGAAAAAC

                                      
       6109 TAAGTTTATTGAATTGAGAGGTTTGT
          1 TAAGTTTATTGAATTGAGAGGTTTGT

                                      
       6135 TAAGTTTATTGAATTGAGAGGTTTGT
          1 TAAGTTTATTGAATTGAGAGGTTTGT

             
       6161 T
          1 T

       6162 TTTGCTATAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47


Consensus pattern (26 bp):   
TAAGTTTATTGAATTGAGAGGTTTGT

Found at i:7652 original size:32 final size:32

Alignment explanation


    Indices: 7587--7652  Score: 78
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       7577 AGCCTTATCC

                      *  *           ** *   
       7587 CGCTAGTTTCGTGCCTTGCAAGCTTTGCGTCT
          1 CGCTAGTTTCATGACTTGCAAGCTTCACCTCT

                               *            
       7619 CGCTAGTTTCATGACTTGCTAGCTTCACCTCT
          1 CGCTAGTTTCATGACTTGCAAGCTTCACCTCT

              
       7651 CG
          1 CG

       7653 TTACTTTTGC


Statistics
Matches: 28,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  32   28  1.00

ACGTcount: A:0.12, C:0.30, G:0.21, T:0.36


Consensus pattern (32 bp):   
CGCTAGTTTCATGACTTGCAAGCTTCACCTCT

Found at i:7907 original size:17 final size:18

Alignment explanation


    Indices: 7887--7920  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       7877 CATATCATTA

                *             
       7887 AATATATAT-TTTATGTG
          1 AATAAATATGTTTATGTG

                             
       7904 AATAAATATGTTTATGT
          1 AATAAATATGTTTATGT

       7921 TACATATATG


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    8  0.53
  18    7  0.47

ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50


Consensus pattern (18 bp):   
AATAAATATGTTTATGTG

Done.