Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g02357.F2

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: 3649
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32


Found at i:3401 original size:47 final size:46

Alignment explanation


    Indices: 3248--3428  Score: 265
    Period size: 46  Copynumber: 3.9  Consensus size: 46

       3238 ATGAAATGTG

                                           *   *           
       3248 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATG-AAATGAA
          1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAA

                                           *     *       *
       3294 TAAGACCATGGTTGAAAGATACCATGGCAACTTGACATAAAATGAG
          1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA

                                                 *         
       3340 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAAATGAA
          1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAC-AGAAAATGAA

            *     *                                   
       3387 CAAGACAATGGTTGAAAGATACCATGGCAACATGACAGAAAA
          1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAA

       3429 CAAGTAAAAT


Statistics
Matches: 122,  Mismatches: 11, Indels: 4
        0.89            0.08        0.03

Matches are distributed among these distances:
  46   81  0.66
  47   41  0.34

ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19


Consensus pattern (46 bp):   
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA

Found at i:3423 original size:93 final size:92

Alignment explanation


    Indices: 3241--3428  Score: 286
    Period size: 93  Copynumber: 2.0  Consensus size: 92

       3231 CTCTGATATG

                 *                                *   * *        *     *     
       3241 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
          1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAACAAGACAATGGT

                               *     * 
       3306 TGAAAGATACCATGGCAACTTGACATA
         66 TGAAAGATACCATGGCAACATGACAGA

                                                       *                     
       3333 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAAATGAACAAGACAATGG
          1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGG-AAATGAACAAGACAATGG

                                        
       3398 TTGAAAGATACCATGGCAACATGACAGA
         65 TTGAAAGATACCATGGCAACATGACAGA

               
       3426 AAA
          1 AAA

       3429 CAAGTAAAAT


Statistics
Matches: 86,  Mismatches: 9, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  92   41  0.48
  93   45  0.52

ACGTcount: A:0.43, C:0.14, G:0.23, T:0.19


Consensus pattern (92 bp):   
AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAACAAGACAATGGT
TGAAAGATACCATGGCAACATGACAGA

Found at i:3435 original size:93 final size:92

Alignment explanation


    Indices: 3247--3454  Score: 281
    Period size: 93  Copynumber: 2.2  Consensus size: 92

       3237 TATGAAATGT

                                            *   * *        *     *           
       3247 GTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGTTGAAAG
          1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAACAAGACAATGGTTGAAAG

                         *     *    ** 
       3312 ATACCATGGCAACTTGACATAAAATGA
         66 ATACCATGGCAACATGACAGAAAACAA

                                                 *                           
       3339 GTAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAAATGAACAAGACAATGGTTGAAA
          1 GTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGG-AAATGAACAAGACAATGGTTGAAA

                                        
       3404 GATACCATGGCAACATGACAGAAAACAA
         65 GATACCATGGCAACATGACAGAAAACAA

                * **  *            
       3432 GTAAAATTATAGTTGAAAGATAC
          1 GTAAGACCATGGTTGAAAGATAC

       3455 TATGACATCA


Statistics
Matches: 101,  Mismatches: 14, Indels: 1
        0.87            0.12        0.01

Matches are distributed among these distances:
  92   36  0.36
  93   65  0.64

ACGTcount: A:0.44, C:0.14, G:0.23, T:0.20


Consensus pattern (92 bp):   
GTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAACAAGACAATGGTTGAAAG
ATACCATGGCAACATGACAGAAAACAA

Done.