Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g02513.F3

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: 5166
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29


Found at i:2255 original size:27 final size:27

Alignment explanation


    Indices: 2225--2361  Score: 159
    Period size: 27  Copynumber: 4.8  Consensus size: 27

       2215 TCCTCCTCCA

                                     * 
       2225 CCCCCTCCACCAAAAGCTCCTCCAGTG
          1 CCCCCTCCACCAAAAGCTCCTCCAGCG

                                                
       2252 -CCCCTCCACCCCCTCCACCAAAAGCTCCTCCAGCG
          1 CCCCCTCCA------CCA--AA-AGCTCCTCCAGCG

                                       
       2287 CCCCCTCCACCAAAAGCTCCTCCAGCG
          1 CCCCCTCCACCAAAAGCTCCTCCAGCG

                                      *
       2314 CCCCCTCCACCAAAAGCTCCTCCAGCA
          1 CCCCCTCCACCAAAAGCTCCTCCAGCG

                       *         
       2341 CCCCCTCCACCGAAAGCTCCT
          1 CCCCCTCCACCAAAAGCTCCT

       2362 GCTGCACCCC


Statistics
Matches: 97,  Mismatches: 3, Indels: 20
        0.81            0.03        0.17

Matches are distributed among these distances:
  26    8  0.08
  27   59  0.61
  28    2  0.02
  30    3  0.03
  32    3  0.03
  34    2  0.02
  35   12  0.12
  36    8  0.08

ACGTcount: A:0.22, C:0.56, G:0.09, T:0.12


Consensus pattern (27 bp):   
CCCCCTCCACCAAAAGCTCCTCCAGCG

Found at i:2368 original size:27 final size:27

Alignment explanation


    Indices: 2258--2371  Score: 183
    Period size: 27  Copynumber: 4.2  Consensus size: 27

       2248 AGTGCCCCTC

                                       
       2258 CACCCCCTCCACCAAAAGCTCCTCCAG
          1 CACCCCCTCCACCAAAAGCTCCTCCAG

             *                         
       2285 CGCCCCCTCCACCAAAAGCTCCTCCAG
          1 CACCCCCTCCACCAAAAGCTCCTCCAG

             *                         
       2312 CGCCCCCTCCACCAAAAGCTCCTCCAG
          1 CACCCCCTCCACCAAAAGCTCCTCCAG

                         *         * * 
       2339 CACCCCCTCCACCGAAAGCTCCTGCTG
          1 CACCCCCTCCACCAAAAGCTCCTCCAG

                  
       2366 CACCCC
          1 CACCCC

       2372 TCCTCCTCCA


Statistics
Matches: 82,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  27   82  1.00

ACGTcount: A:0.22, C:0.56, G:0.11, T:0.11


Consensus pattern (27 bp):   
CACCCCCTCCACCAAAAGCTCCTCCAG

Found at i:2461 original size:36 final size:35

Alignment explanation


    Indices: 2342--2520  Score: 180
    Period size: 36  Copynumber: 5.0  Consensus size: 35

       2332 CCTCCAGCAC

                      *    *         **         *
       2342 CCCCTCCACCGAAAGCTCCTGCTGCACCCCTCCTCCT
          1 CCCCTCCACCAAAAGGTCCTGCTG-TGCCC-CCTCCA

                       *          * *            
       2379 CCACCTCCACCGAAAGGTTCC-ACGGTGCCCCCTCCA
          1 CC-CCTCCACCAAAAGG-TCCTGCTGTGCCCCCTCCA

                                *              
       2415 CCCCTCCACCAAAAGGTCCTTCTGTGCCCCCTCCA
          1 CCCCTCCACCAAAAGGTCCTGCTGTGCCCCCTCCA

                                         *      
       2450 CCTCCTCCACCAAAAGGTCCTGCTGTGCCTCCTCCA
          1 CC-CCTCCACCAAAAGGTCCTGCTGTGCCCCCTCCA

                  *         *            *     
       2486 CCCCCTGCACCAAAAGCTCCTGCTGTGCCTCCTCC
          1 -CCCCTCCACCAAAAGGTCCTGCTGTGCCCCCTCC

       2521 CCCACCAGGT


Statistics
Matches: 124,  Mismatches: 13, Indels: 11
        0.84            0.09        0.07

Matches are distributed among these distances:
  34    3  0.02
  35   28  0.23
  36   68  0.55
  37    7  0.06
  38   15  0.12
  39    3  0.02

ACGTcount: A:0.16, C:0.51, G:0.13, T:0.19


Consensus pattern (35 bp):   
CCCCTCCACCAAAAGGTCCTGCTGTGCCCCCTCCA

Found at i:2466 original size:71 final size:72

Alignment explanation


    Indices: 2339--2526  Score: 209
    Period size: 72  Copynumber: 2.6  Consensus size: 72

       2329 GCTCCTCCAG

                         *              **         *           *             
       2339 CACCCCCTCCACCGAAAGCTCCTGCTGCACCCCTCCTCCTCCACCTCCACCGAAAGGTTCC-ACG
          1 CACCCCCTCCACCAAAAGCTCCTGCTG-TGCCC-CCTCCACCACCTCCACCAAAAGG-TCCTACG

                      
       2403 GTGCCCCCTC
         63 GTGCCCCCTC

                              *    *                *                  * *   
       2413 CA-CCCCTCCACCAAAAGGTCCTTCTGTGCCCCCTCCACCTCCTCCACCAAAAGGTCCTGCTGTG
          1 CACCCCCTCCACCAAAAGCTCCTGCTGTGCCCCCTCCACCACCTCCACCAAAAGGTCCTACGGTG

              *    
       2477 CCTCCTC
         66 CCCCCTC

                    *                      *     *     
       2484 CACCCCCTGCACCAAAAGCTCCTGCTGTGCCTCCTCCCCCACC
          1 CACCCCCTCCACCAAAAGCTCCTGCTGTGCCCCCTCCACCACC

       2527 AGGTGCACGG


Statistics
Matches: 95,  Mismatches: 17, Indels: 6
        0.81            0.14        0.05

Matches are distributed among these distances:
  70    3  0.03
  71   32  0.34
  72   37  0.39
  73   21  0.22
  74    2  0.02

ACGTcount: A:0.16, C:0.53, G:0.13, T:0.18


Consensus pattern (72 bp):   
CACCCCCTCCACCAAAAGCTCCTGCTGTGCCCCCTCCACCACCTCCACCAAAAGGTCCTACGGTG
CCCCCTC
Done.