Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01270.F4

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: 3543
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35


Found at i:48 original size:7 final size:7

Alignment explanation


    Indices: 36--65  Score: 60
    Period size: 7  Copynumber: 4.3  Consensus size: 7

         26 GAATCAAACC

                   
         36 CAGCAGG
          1 CAGCAGG

                   
         43 CAGCAGG
          1 CAGCAGG

                   
         50 CAGCAGG
          1 CAGCAGG

                   
         57 CAGCAGG
          1 CAGCAGG

              
         64 CA
          1 CA

         66 AAGAGAGAGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   23  1.00

ACGTcount: A:0.30, C:0.30, G:0.40, T:0.00


Consensus pattern (7 bp):   
CAGCAGG

Found at i:970 original size:39 final size:39

Alignment explanation


    Indices: 924--1001  Score: 156
    Period size: 39  Copynumber: 2.0  Consensus size: 39

        914 TTTCTTTTTC

                                                   
        924 CTATCCACTTTTAAAGTTTCCTCTTTCCATCCTTTTACT
          1 CTATCCACTTTTAAAGTTTCCTCTTTCCATCCTTTTACT

                                                   
        963 CTATCCACTTTTAAAGTTTCCTCTTTCCATCCTTTTACT
          1 CTATCCACTTTTAAAGTTTCCTCTTTCCATCCTTTTACT

       1002 TTTTCGTTCA


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  39   39  1.00

ACGTcount: A:0.18, C:0.31, G:0.03, T:0.49


Consensus pattern (39 bp):   
CTATCCACTTTTAAAGTTTCCTCTTTCCATCCTTTTACT

Found at i:986 original size:22 final size:22

Alignment explanation


    Indices: 924--991  Score: 56
    Period size: 22  Copynumber: 3.3  Consensus size: 22

        914 TTTCTTTTTC

                                  
        924 CTATCCACTTTTAAAGTTTCCT
          1 CTATCCACTTTTAAAGTTTCCT

              *      **        *  
        946 CTTTCCA-TCCT----TTTACT
          1 CTATCCACTTTTAAAGTTTCCT

                                  
        963 CTATCCACTTTTAAAGTTTCCT
          1 CTATCCACTTTTAAAGTTTCCT

              *    
        985 CTTTCCA
          1 CTATCCA

        992 TCCTTTTACT


Statistics
Matches: 32,  Mismatches: 9, Indels: 10
        0.63            0.18        0.20

Matches are distributed among these distances:
  17   11  0.34
  18    2  0.06
  21    2  0.06
  22   17  0.53

ACGTcount: A:0.19, C:0.31, G:0.03, T:0.47


Consensus pattern (22 bp):   
CTATCCACTTTTAAAGTTTCCT

Found at i:3459 original size:49 final size:49

Alignment explanation


    Indices: 3382--3478  Score: 149
    Period size: 49  Copynumber: 2.0  Consensus size: 49

       3372 TCCTCTAAAT

                *        *        *                *         
       3382 ATATTTGAAAAAATTTAGAGATGATTAAGCATACTTGTAGTGGACACAG
          1 ATATGTGAAAAAACTTAGAGATAATTAAGCATACTTGTAATGGACACAG

                            *                               
       3431 ATATGTGAAAAAACTTGGAGATAATTAAGCATACTTGTAATGGACACA
          1 ATATGTGAAAAAACTTAGAGATAATTAAGCATACTTGTAATGGACACA

       3479 TACCCAGTAT


Statistics
Matches: 43,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  49   43  1.00

ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29


Consensus pattern (49 bp):   
ATATGTGAAAAAACTTAGAGATAATTAAGCATACTTGTAATGGACACAG
Done.