Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.009G203600.1-JGI_221_v2.1

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: 2633
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31


Found at i:2046 original size:21 final size:21

Alignment explanation


    Indices: 2022--2066  Score: 81
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2012 GATCCAAGCT

                 *               
       2022 CCAGATCTGCTTCCATTGATC
          1 CCAGACCTGCTTCCATTGATC

                                 
       2043 CCAGACCTGCTTCCATTGATC
          1 CCAGACCTGCTTCCATTGATC

               
       2064 CCA
          1 CCA

       2067 ACTATAGAGC


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.20, C:0.38, G:0.13, T:0.29


Consensus pattern (21 bp):   
CCAGACCTGCTTCCATTGATC

Found at i:2098 original size:66 final size:66

Alignment explanation


    Indices: 1979--2111  Score: 185
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       1969 TCCAAGCTCT

                                *  *                        *     *          
       1979 AGACCTGCTTCCATCGATCCTAATTATAGAGCAGATCCAAGCTCCAGATCTGCTTCCATTGATCC
          1 AGACCTGCTTCCATCGATCCCAACTATAGAGCAGATCCAAGCTCCAGAGCTGCTCCCATTGATCC

             
       2044 C
         66 C

                          *                 *     **    *                    
       2045 AGACCTGCTTCCATTGATCCCAACTATAGAGCGGATCCGGGCTCTAGAGCTGCTCCCATTGATCC
          1 AGACCTGCTTCCATCGATCCCAACTATAGAGCAGATCCAAGCTCCAGAGCTGCTCCCATTGATCC

             
       2110 C
         66 C

             
       2111 A
          1 A

       2112 ATTATAGAGT


Statistics
Matches: 58,  Mismatches: 9, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  66   58  1.00

ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26


Consensus pattern (66 bp):   
AGACCTGCTTCCATCGATCCCAACTATAGAGCAGATCCAAGCTCCAGAGCTGCTCCCATTGATCC
C

Found at i:2104 original size:45 final size:45

Alignment explanation


    Indices: 2049--2211  Score: 220
    Period size: 45  Copynumber: 3.6  Consensus size: 45

       2039 GATCCCAGAC

                 *             *               *         
       2049 CTGCTTCCATTGATCCCAACTATAGAGCGGATCCGGGCTCTAGAG
          1 CTGCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG

                                       *                 
       2094 CTGCTCCCATTGATCCCAATTATAGAGTGGATCCGAGCTCTAGAG
          1 CTGCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG

                  *       *                    *   *     *
       2139 -TCGCTTCCATTGACCCCAATTATAGAGCGGATCCAAGCGCTAGAA
          1 CT-GCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG

                   *                    
       2184 CTGCTCCGATTGATCCCAATTATAGAGC
          1 CTGCTCCCATTGATCCCAATTATAGAGC

       2212 TGCTCCAGAG


Statistics
Matches: 103,  Mismatches: 13, Indels: 4
        0.86            0.11        0.03

Matches are distributed among these distances:
  44    1  0.01
  45  101  0.98
  46    1  0.01

ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25


Consensus pattern (45 bp):   
CTGCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG
Done.