Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold12228.1

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: 2335
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37


Found at i:561 original size:105 final size:104

Alignment explanation


    Indices: 413--605  Score: 300
    Period size: 105  Copynumber: 1.8  Consensus size: 104

        403 TCCTCATTGA

                                                            *                
        413 AATACCATACCTACATTTTATACTCGGTATGGAAAATACCATACCTACGTTTCACAACTCGGTAT
          1 AATACCATACCTACATTTTATACTCGGTATGGAAAATACCATACCTACATTTCACAACTCGGTAT

                    *                               
        478 GGGA-AATGCCATACCTACATTTCTTAACCCAGTATAGAT
         66 -GGATAATACCATACCTACATTTCTTAACCCAGTATAGAT

                         *                     **                            
        517 AATACCATACCTATATTTCTCA-ACTCGGTATGGATGATACCATACCTACATTTCACAACTCGGT
          1 AATACCATACCTACATTT-T-ATACTCGGTATGGAAAATACCATACCTACATTTCACAACTCGGT

                                     
        581 ATGGATAATACCATACCTACATTTC
         64 ATGGATAATACCATACCTACATTTC

        606 GCACTTTGCC


Statistics
Matches: 81,  Mismatches: 5, Indels: 5
        0.89            0.05        0.05

Matches are distributed among these distances:
 104   20  0.25
 105   60  0.74
 106    1  0.01

ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31


Consensus pattern (104 bp):   
AATACCATACCTACATTTTATACTCGGTATGGAAAATACCATACCTACATTTCACAACTCGGTAT
GGATAATACCATACCTACATTTCTTAACCCAGTATAGAT

Found at i:621 original size:35 final size:35

Alignment explanation


    Indices: 413--605  Score: 246
    Period size: 35  Copynumber: 5.5  Consensus size: 35

        403 TCCTCATTGA

                              *  *            *
        413 AATACCATACCTACATTTTA-TACTCGGTATGGAA
          1 AATACCATACCTACATTTCACAACTCGGTATGGAT

                          *                     
        447 AATACCATACCTACGTTTCACAACTCGGTATGGGA-
          1 AATACCATACCTACATTTCACAACTCGGTAT-GGAT

               *               **   * *    *   
        482 AATGCCATACCTACATTTCTTAACCCAGTATAGAT
          1 AATACCATACCTACATTTCACAACTCGGTATGGAT

                         *     *               
        517 AATACCATACCTATATTTCTCAACTCGGTATGGAT
          1 AATACCATACCTACATTTCACAACTCGGTATGGAT

            *                                  
        552 GATACCATACCTACATTTCACAACTCGGTATGGAT
          1 AATACCATACCTACATTTCACAACTCGGTATGGAT

                               
        587 AATACCATACCTACATTTC
          1 AATACCATACCTACATTTC

        606 GCACTTTGCC


Statistics
Matches: 136,  Mismatches: 20, Indels: 5
        0.84            0.12        0.03

Matches are distributed among these distances:
  34   20  0.15
  35  113  0.83
  36    3  0.02

ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31


Consensus pattern (35 bp):   
AATACCATACCTACATTTCACAACTCGGTATGGAT

Done.