Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01316.N1

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, 935

Length: 1559
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33


Found at i:702 original size:16 final size:15

Alignment explanation


    Indices: 676--707  Score: 55
    Period size: 16  Copynumber: 2.1  Consensus size: 15

        666 ACTAGATTGG

                           
        676 CAAAAGCCGAAAAGT
          1 CAAAAGCCGAAAAGT

                            
        691 CAAAATGCCGAAAAGT
          1 CAAAA-GCCGAAAAGT

             
        707 C
          1 C

        708 GGTATTTTGG


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    5  0.31
  16   11  0.69

ACGTcount: A:0.50, C:0.22, G:0.19, T:0.09


Consensus pattern (15 bp):   
CAAAAGCCGAAAAGT

Found at i:1159 original size:27 final size:27

Alignment explanation


    Indices: 1116--1251  Score: 148
    Period size: 27  Copynumber: 5.0  Consensus size: 27

       1106 AAGCGTTTTA

                  *     *              
       1116 GTGGCTATGCCATAAATATCTGATCTG
          1 GTGGCTCTGCCACAAATATCTGATCTG

                  *   *                
       1143 GTGGCTTTGCTACAAATATCTGATCTG
          1 GTGGCTCTGCCACAAATATCTGATCTG

                          *       *    
       1170 GTGGCTCTGCCACATATATCTGTTCTG
          1 GTGGCTCTGCCACAAATATCTGATCTG

                         * *            
       1197 GTGGCTCTGCCACGATTATCTGTATCTG
          1 GTGGCTCTGCCACAAATATCTG-ATCTG

               *     *     *      *    
       1225 GTGACTCTGTCAC-ATTATCTGTTCTG
          1 GTGGCTCTGCCACAAATATCTGATCTG

             
       1251 G
          1 G

       1252 CAGCCATGGT


Statistics
Matches: 94,  Mismatches: 14, Indels: 3
        0.85            0.13        0.03

Matches are distributed among these distances:
  26    5  0.05
  27   74  0.79
  28   15  0.16

ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37


Consensus pattern (27 bp):   
GTGGCTCTGCCACAAATATCTGATCTG

Found at i:1198 original size:54 final size:55

Alignment explanation


    Indices: 1116--1251  Score: 168
    Period size: 54  Copynumber: 2.5  Consensus size: 55

       1106 AAGCGTTTTA

                  *     * *       *          *   *                 
       1116 GTGGCTATGCCATAAATATCTGATCTGGTGGCTTTGCTACAAATATCTG-ATCTG
          1 GTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTATCTG

                                                    * *            
       1170 GTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTATCTG
          1 GTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTATCTG

               *     *                  
       1225 GTGACTCTGTCACAT-TATCTGTTCTGG
          1 GTGGCTCTGCCACATATATCTGTTCTGG

       1252 CAGCCATGGT


Statistics
Matches: 71,  Mismatches: 10, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  54   53  0.75
  55   18  0.25

ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37


Consensus pattern (55 bp):   
GTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTATCTG
Done.