Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g01684.M1

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: 4993
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35


Found at i:4140 original size:27 final size:27

Alignment explanation


    Indices: 4110--4194  Score: 97
    Period size: 27  Copynumber: 3.3  Consensus size: 27

       4100 CCTGATTATT

                                      *
       4110 TGAATTATGTTAGAATCCATGATTGAG
          1 TGAATTATGTTAGAATCCATGATTGAA

                          *   *         
       4137 TGAATTA--TTAG-GTCCTTGATT-ATA
          1 TGAATTATGTTAGAATCCATGATTGA-A

                                      *
       4161 TGAATTATGTTAGAATCCATGATTGAC
          1 TGAATTATGTTAGAATCCATGATTGAA

                   
       4188 TGAATTA
          1 TGAATTA

       4195 ATTCGGTAAT


Statistics
Matches: 47,  Mismatches: 6, Indels: 10
        0.75            0.10        0.16

Matches are distributed among these distances:
  23    1  0.02
  24   15  0.32
  25    4  0.09
  26    4  0.09
  27   22  0.47
  28    1  0.02

ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40


Consensus pattern (27 bp):   
TGAATTATGTTAGAATCCATGATTGAA

Found at i:4148 original size:51 final size:51

Alignment explanation


    Indices: 4092--4194  Score: 179
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       4082 AAATTATACA

                             *                          *      
       4092 ATTAGGTCCCTGATTATTTGAATTATGTTAGAATCCATGATTGAGTGAATT
          1 ATTAGGTCCCTGATTATATGAATTATGTTAGAATCCATGATTGACTGAATT

                     *                                         
       4143 ATTAGGTCCTTGATTATATGAATTATGTTAGAATCCATGATTGACTGAATT
          1 ATTAGGTCCCTGATTATATGAATTATGTTAGAATCCATGATTGACTGAATT

             
       4194 A
          1 A

       4195 ATTCGGTAAT


Statistics
Matches: 49,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  51   49  1.00

ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41


Consensus pattern (51 bp):   
ATTAGGTCCCTGATTATATGAATTATGTTAGAATCCATGATTGACTGAATT

Found at i:4164 original size:24 final size:24

Alignment explanation


    Indices: 4092--4168  Score: 66
    Period size: 24  Copynumber: 3.1  Consensus size: 24

       4082 AAATTATACA

                     *       *      
       4092 ATTAGGTCCCTGATTATTTGAATT
          1 ATTAGGTCCATGATTATATGAATT

                    *            *      
       4116 ATGTTAGAATCCATGATTGA-GTGAATT
          1 A--TTAG-GTCCATGATT-ATATGAATT

                     *              
       4143 ATTAGGTCCTTGATTATATGAATT
          1 ATTAGGTCCATGATTATATGAATT

              
       4167 AT
          1 AT

       4169 GTTAGAATCC


Statistics
Matches: 42,  Mismatches: 6, Indels: 10
        0.72            0.10        0.17

Matches are distributed among these distances:
  23    1  0.02
  24   17  0.40
  25    4  0.10
  26    4  0.10
  27   15  0.36
  28    1  0.02

ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43


Consensus pattern (24 bp):   
ATTAGGTCCATGATTATATGAATT
Done.