Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g01610.P2

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: 16279
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39


Found at i:2886 original size:16 final size:16

Alignment explanation


    Indices: 2865--2896  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       2855 GCGTGGAAGA

                            
       2865 AAGAGAATAGTTTCAG
          1 AAGAGAATAGTTTCAG

                            
       2881 AAGAGAATAGTTTCAG
          1 AAGAGAATAGTTTCAG

       2897 TTGAATATTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25


Consensus pattern (16 bp):   
AAGAGAATAGTTTCAG

Found at i:4279 original size:39 final size:39

Alignment explanation


    Indices: 4225--4307  Score: 130
    Period size: 39  Copynumber: 2.1  Consensus size: 39

       4215 CCACTGGCCA

                    *                              
       4225 CCACCATCGTCGTTCACCAGTCAGGCAGTCACCACCGGT
          1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT

                                     *        **   
       4264 CCACCATCATCGTTCACCAGTCAGGTAGTCACCATTGGT
          1 CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT

                 
       4303 CCACC
          1 CCACC

       4308 CGTCACCACC


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  39   40  1.00

ACGTcount: A:0.22, C:0.40, G:0.18, T:0.20


Consensus pattern (39 bp):   
CCACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGT

Found at i:6628 original size:31 final size:31

Alignment explanation


    Indices: 6592--6654  Score: 126
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       6582 TTCCTTATTT

                                           
       6592 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
          1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

                                           
       6623 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC
          1 CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

             
       6654 C
          1 C

       6655 TTCTCGTACT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.06, C:0.33, G:0.03, T:0.57


Consensus pattern (31 bp):   
CCTTTTTGTTTTCATTATTCTCTCTTCCTCC

Found at i:11669 original size:42 final size:42

Alignment explanation


    Indices: 11603--11717  Score: 115
    Period size: 42  Copynumber: 2.7  Consensus size: 42

      11593 CATTCTCTTT

                       * *  *  *               *      
      11603 TCTATTCCAGGTAAATACCGCTCATATCCCACCTTGGAATAA
          1 TCTATTCCAGGGATATCCCTCTCATATCCCACCTTAGAATAA

                                     *      *          
      11645 TCTATTCCAGGGATATCCCTCTCATTTGCCC-TCTTAGAATAA
          1 TCTATTCCAGGGATATCCCTCTCATAT-CCCACCTTAGAATAA

              *     *      *      *        
      11687 TCAATTCCGGGGATACCCCTCTGATATCCCA
          1 TCTATTCCAGGGATATCCCTCTCATATCCCA

      11718 TCCCGGTCCG


Statistics
Matches: 59,  Mismatches: 12, Indels: 4
        0.79            0.16        0.05

Matches are distributed among these distances:
  41    3  0.05
  42   53  0.90
  43    3  0.05

ACGTcount: A:0.26, C:0.30, G:0.13, T:0.30


Consensus pattern (42 bp):   
TCTATTCCAGGGATATCCCTCTCATATCCCACCTTAGAATAA

Found at i:11857 original size:16 final size:16

Alignment explanation


    Indices: 11838--11891  Score: 74
    Period size: 16  Copynumber: 3.4  Consensus size: 16

      11828 CATTCCGAGG

                            
      11838 ATATCCCGGCTTAGGT
          1 ATATCCCGGCTTAGGT

                    *       
      11854 ATATCCCGACTTAGG-
          1 ATATCCCGGCTTAGGT

               *       *    
      11869 ATAGCCCGGCTGAGGT
          1 ATATCCCGGCTTAGGT

                   
      11885 ATATCCC
          1 ATATCCC

      11892 ACCTGCGGAT


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  15   12  0.38
  16   20  0.62

ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26


Consensus pattern (16 bp):   
ATATCCCGGCTTAGGT

Found at i:15592 original size:39 final size:39

Alignment explanation


    Indices: 15542--15622  Score: 126
    Period size: 39  Copynumber: 2.1  Consensus size: 39

      15532 ACCGGCCACA

                  *                                
      15542 ACCATCGTCGTTCACCAGTCAGGCAGTCACCACCGGTAC
          1 ACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTAC

                                   *        *    * 
      15581 ACCATCATCGTTCACCAGTCAGGTAGTCACCATCGGTCC
          1 ACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTAC

               
      15620 ACC
          1 ACC

      15623 CGTCACCACC


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  39   38  1.00

ACGTcount: A:0.23, C:0.38, G:0.19, T:0.20


Consensus pattern (39 bp):   
ACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTAC
Done.