Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g02115.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: 4982
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28


Found at i:76 original size:12 final size:12

Alignment explanation


    Indices: 59--93  Score: 52
    Period size: 12  Copynumber: 2.8  Consensus size: 12

         49 TTTAACTGTC

                        
         59 TCTTCTTTTTCT
          1 TCTTCTTTTTCT

                        
         71 TCTTCTTTTTCT
          1 TCTTCTTTTTCT

             *         
         83 TTTTGCTTTTT
          1 TCTT-CTTTTT

         94 TTCCTCCTTA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  12   15  0.71
  13    6  0.29

ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77


Consensus pattern (12 bp):   
TCTTCTTTTTCT

Found at i:4964 original size:14 final size:14

Alignment explanation


    Indices: 4915--4955  Score: 59
    Period size: 14  Copynumber: 3.0  Consensus size: 14

       4905 GAATTATCCC

                          
       4915 CAAAAAAAA-AAAA
          1 CAAAAAAAACAAAA

                           
       4928 -AAAACAAAACAAAA
          1 CAAAA-AAAACAAAA

                          
       4942 CAAAAAAAACAAAA
          1 CAAAAAAAACAAAA

       4956 GAAGGAAAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  12    4  0.16
  13    4  0.16
  14   13  0.52
  15    4  0.16

ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00


Consensus pattern (14 bp):   
CAAAAAAAACAAAA

Found at i:4965 original size:19 final size:18

Alignment explanation


    Indices: 4915--4955  Score: 66
    Period size: 19  Copynumber: 2.3  Consensus size: 18

       4905 GAATTATCCC

                              
       4915 CAAAA-AAAAAAAAAAAA
          1 CAAAACAAAAAAAAAAAA

                               
       4932 CAAAACAAAACAAAAAAAA
          1 CAAAACAAAA-AAAAAAAA

                 
       4951 CAAAA
          1 CAAAA

       4956 GAAGGAAAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  17    5  0.23
  18    4  0.18
  19   13  0.59

ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00


Consensus pattern (18 bp):   
CAAAACAAAAAAAAAAAA
Done.