Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g02298.F1

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, 673

Length: 1122
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22


Found at i:259 original size:32 final size:32

Alignment explanation


    Indices: 223--321  Score: 189
    Period size: 32  Copynumber: 3.1  Consensus size: 32

        213 ACTCCAGCAC

                                            
        223 CCCCAACCAAGGCCCCCACTCCACCATATAAA
          1 CCCCAACCAAGGCCCCCACTCCACCATATAAA

                                            
        255 CCCCAACCAAGGCCCCCACTCCACCATATAAA
          1 CCCCAACCAAGGCCCCCACTCCACCATATAAA

                                             
        287 CCACCAACCAAGGCCCCCACTCCACCATATAAA
          1 CC-CCAACCAAGGCCCCCACTCCACCATATAAA

              
        320 CC
          1 CC

        322 ACCAGCTCCT


Statistics
Matches: 66,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  32   34  0.52
  33   32  0.48

ACGTcount: A:0.34, C:0.51, G:0.06, T:0.09


Consensus pattern (32 bp):   
CCCCAACCAAGGCCCCCACTCCACCATATAAA

Found at i:299 original size:33 final size:33

Alignment explanation


    Indices: 225--325  Score: 195
    Period size: 33  Copynumber: 3.1  Consensus size: 33

        215 TCCAGCACCC

                                             
        225 CCAACCAAGGCCCCCACTCCACCATATAAACC-
          1 CCAACCAAGGCCCCCACTCCACCATATAAACCA

                                             
        257 CCAACCAAGGCCCCCACTCCACCATATAAACCA
          1 CCAACCAAGGCCCCCACTCCACCATATAAACCA

                                             
        290 CCAACCAAGGCCCCCACTCCACCATATAAACCA
          1 CCAACCAAGGCCCCCACTCCACCATATAAACCA

               
        323 CCA
          1 CCA

        326 GCTCCTGCGC


Statistics
Matches: 68,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  32   32  0.47
  33   36  0.53

ACGTcount: A:0.36, C:0.50, G:0.06, T:0.09


Consensus pattern (33 bp):   
CCAACCAAGGCCCCCACTCCACCATATAAACCA

Found at i:380 original size:54 final size:53

Alignment explanation


    Indices: 321--529  Score: 180
    Period size: 54  Copynumber: 4.0  Consensus size: 53

        311 CCATATAAAC

                         *                       *                
        321 CACCAGCTCCTGCGCCACCAACCAAGGCTCCTACTCCACCATATAAGCCCCCAG
          1 CACCAGCTCC-GCACCACCAACCAAGGCTCCTACTCCCCCATATAAGCCCCCAG

                                                         *        
        375 CACCA-----GCACCACCAACCAAGGCTCCTACTCCCCCATATAAACCCCCTA-
          1 CACCAGCTCCGCACCACCAACCAAGGCTCCTACTCCCCCATATAAGCCCCC-AG

             *  *  *        *   **      *     *                  *
        423 CTCCCGCACCGGCACCTCCAGTCAAGGCCCCTACACCCCCATATAAGCCCCCAA
          1 CACCAGCTCC-GCACCACCAACCAAGGCTCCTACTCCCCCATATAAGCCCCCAG

                *                 *  *  *  *                      
        477 CACCTGCTCCAGCACC-CCAACTAAAGCACCAACTCCCCCATATAAGCCCCCAG
          1 CACCAGCTCC-GCACCACCAACCAAGGCTCCTACTCCCCCATATAAGCCCCCAG

        530 TTCCTACACC


Statistics
Matches: 124,  Mismatches: 23, Indels: 17
        0.76            0.14        0.10

Matches are distributed among these distances:
  48   41  0.33
  49    1  0.01
  53   30  0.24
  54   52  0.42

ACGTcount: A:0.28, C:0.50, G:0.11, T:0.12


Consensus pattern (53 bp):   
CACCAGCTCCGCACCACCAACCAAGGCTCCTACTCCCCCATATAAGCCCCCAG

Found at i:432 original size:48 final size:48

Alignment explanation


    Indices: 286--420  Score: 198
    Period size: 48  Copynumber: 2.8  Consensus size: 48

        276 CACCATATAA

                           *  *                 *        *  
        286 ACCACCAACCAAGGCCCCCACTCCACCATATAAACCACCAGCTCCTGC
          1 ACCACCAACCAAGGCTCCTACTCCACCATATAAACCCCCAGCTCCAGC

            *                                *        *     
        334 GCCACCAACCAAGGCTCCTACTCCACCATATAAGCCCCCAGCACCAGC
          1 ACCACCAACCAAGGCTCCTACTCCACCATATAAACCCCCAGCTCCAGC

                                    *              
        382 ACCACCAACCAAGGCTCCTACTCCCCCATATAAACCCCC
          1 ACCACCAACCAAGGCTCCTACTCCACCATATAAACCCCC

        421 TACTCCCGCA


Statistics
Matches: 77,  Mismatches: 10, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  48   77  1.00

ACGTcount: A:0.30, C:0.50, G:0.09, T:0.11


Consensus pattern (48 bp):   
ACCACCAACCAAGGCTCCTACTCCACCATATAAACCCCCAGCTCCAGC
Done.