Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g02051.M2

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: 4248
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31


Found at i:4145 original size:27 final size:25

Alignment explanation


    Indices: 4115--4169  Score: 65
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       4105 AAAAAAAGAT

                                       
       4115 AATTTAAATGAAATAAGAAAAAATTTA
          1 AATTTAAATGAAAT-A-AAAAAATTTA

                  *   *       *      
       4142 AATTTACATGGAATAAAATAATTTA
          1 AATTTAAATGAAATAAAAAAATTTA

               
       4167 AAT
          1 AAT

       4170 GAAATGACAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  25   12  0.48
  26    1  0.04
  27   12  0.48

ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33


Consensus pattern (25 bp):   
AATTTAAATGAAATAAAAAAATTTA

Found at i:4163 original size:46 final size:45

Alignment explanation


    Indices: 4098--4240  Score: 153
    Period size: 47  Copynumber: 3.1  Consensus size: 45

       4088 TATAAAAAAA

                   *                                       
       4098 TTACATGAAAAAAAGATAATTTAAATGAAATAAGAAAAAATTTAAAT
          1 TTACATGGAAAAAA-ATAATTTAAATGAAATAA-AAAAAATTTAAAT

                      *                     *             
       4145 TTACATGGAATAAAATAATTTAAATGAAATGACAAAAAA-TTAAAT
          1 TTACATGGAAAAAAATAATTTAAATGAAAT-AAAAAAAATTTAAAT

             * *         * *                      *         
       4190 TAAAATAGGAAGATAGATAATTTAAATGAAATGAAAAAGAATTTAAAT
          1 TTACAT-GGAA-AAAAATAATTTAAATGAAAT-AAAAAAAATTTAAAT

               
       4238 TTA
          1 TTA

       4241 AATGAAAT


Statistics
Matches: 81,  Mismatches: 11, Indels: 7
        0.82            0.11        0.07

Matches are distributed among these distances:
  45   10  0.12
  46   26  0.32
  47   37  0.46
  48    8  0.10

ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29


Consensus pattern (45 bp):   
TTACATGGAAAAAAATAATTTAAATGAAATAAAAAAAATTTAAAT

Found at i:4232 original size:21 final size:22

Alignment explanation


    Indices: 4108--4247  Score: 85
    Period size: 21  Copynumber: 6.1  Consensus size: 22

       4098 TTACATGAAA

                                   
       4108 AAAAGATAATTTAAA-TGAAAT-
          1 AAAA-ATAATTTAAATTGAAATG

                  *          * *    
       4129 AAGAAAAAATTTAAATTTACATGG
          1 AA-AAATAATTTAAATTGAAAT-G

                                    
       4153 AATAAAATAATTTAAA-TGAAATG
          1 -A-AAAATAATTTAAATTGAAATG

                             *       
       4176 ACAAAA-AA-TTAAATTAAAATAGG
          1 A-AAAATAATTTAAATTGAAAT--G

                                     
       4199 AAGATAGATAATTTAAA-TGAAATG
          1 AA-A-A-ATAATTTAAATTGAAATG

                 *          *     
       4223 AAAAAGAATTTAAATTTAAATG
          1 AAAAATAATTTAAATTGAAATG

               
       4245 AAA
          1 AAA

       4248 T


Statistics
Matches: 93,  Mismatches: 11, Indels: 29
        0.70            0.08        0.22

Matches are distributed among these distances:
  20    5  0.05
  21   27  0.29
  22   22  0.24
  23    5  0.05
  24    8  0.09
  25   13  0.14
  26    8  0.09
  27    5  0.05

ACGTcount: A:0.60, C:0.01, G:0.11, T:0.28


Consensus pattern (22 bp):   
AAAAATAATTTAAATTGAAATG
Done.