Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold613

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: 18542
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.28

Warning! 2268 characters in sequence are not A, C, G, or T


Found at i:9726 original size:21 final size:21

Alignment explanation


    Indices: 9702--9756  Score: 94
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       9692 CACGGTTGGG

                                 
       9702 TACATGGGCGTGTAGAATGGC
          1 TACATGGGCGTGTAGAATGGC

                                 
       9723 TACATGGGCGTGTAGAATGGC
          1 TACATGGGCGTGTAGAATGGC

                          
       9744 TACACT-GGCGTGT
          1 TACA-TGGGCGTGT

       9757 GGGAGAGACA


Statistics
Matches: 33,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  21   32  0.97
  22    1  0.03

ACGTcount: A:0.22, C:0.16, G:0.36, T:0.25


Consensus pattern (21 bp):   
TACATGGGCGTGTAGAATGGC

Found at i:13598 original size:29 final size:28

Alignment explanation


    Indices: 13566--13649  Score: 73
    Period size: 28  Copynumber: 2.9  Consensus size: 28

      13556 AAAGGATATC

                                         
      13566 CTTTGTGGAAAAACTCTGGAAAGGTAAAA
          1 CTTTGTGG-AAAACTCTGGAAAGGTAAAA

                    **        *          *
      13595 CTTTGTGGCGAAC-CTGTAAAAGG-ACAAC
          1 CTTTGTGGAAAACTCTG-GAAAGGTA-AAA

                             *         
      13623 CTTTGTGGCAAAACTCTAGAAAGGTAA
          1 CTTTGTGG-AAAACTCTGGAAAGGTAA

      13650 GTTTTTATGG


Statistics
Matches: 42,  Mismatches: 8, Indels: 10
        0.70            0.13        0.17

Matches are distributed among these distances:
  27    4  0.10
  28   18  0.43
  29   17  0.40
  30    3  0.07

ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24


Consensus pattern (28 bp):   
CTTTGTGGAAAACTCTGGAAAGGTAAAA

Found at i:13674 original size:57 final size:57

Alignment explanation


    Indices: 13554--13675  Score: 145
    Period size: 57  Copynumber: 2.1  Consensus size: 57

      13544 AAAACGTCAG

                    * *                  *               *          *
      13554 TAAAAGGATATCCTTTGTGGAAAAACTCTGGAAAGGTAAAACTTTGTGGCGAACCTG
          1 TAAAAGGACAACCTTTGTGGAAAAACTCTAGAAAGGTAAAACTTTATGGCGAACCTA

                                *                  ***       *       
      13611 TAAAAGGACAACCTTTGTGGCAAAACTCTAGAAAGGTAAGTTTTTATGGTGAACCTA
          1 TAAAAGGACAACCTTTGTGGAAAAACTCTAGAAAGGTAAAACTTTATGGCGAACCTA

             *      
      13668 TTAAAGGA
          1 TAAAAGGA

      13676 TGCCTTTGTG


Statistics
Matches: 54,  Mismatches: 11, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  57   54  1.00

ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27


Consensus pattern (57 bp):   
TAAAAGGACAACCTTTGTGGAAAAACTCTAGAAAGGTAAAACTTTATGGCGAACCTA

Found at i:13688 original size:27 final size:29

Alignment explanation


    Indices: 13657--13716  Score: 79
    Period size: 30  Copynumber: 2.1  Consensus size: 29

      13647 TAAGTTTTTA

                          *              
      13657 TGGTGA-ACCT-ATTAAAGGATGCCTTTG
          1 TGGTGAGACCTAATAAAAGGATGCCTTTG

                      *                   
      13684 TGGTGAGTACTTAATAAAAGGATGCCTTTG
          1 TGGTGAG-ACCTAATAAAAGGATGCCTTTG

               
      13714 TGG
          1 TGG

      13717 GAATCTCTGG


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  27    6  0.21
  29    3  0.11
  30   19  0.68

ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33


Consensus pattern (29 bp):   
TGGTGAGACCTAATAAAAGGATGCCTTTG

Found at i:14639 original size:31 final size:31

Alignment explanation


    Indices: 14601--14663  Score: 108
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      14591 CTCCACCTCC

                                           
      14601 CACCTACTTCCTCTATCGCCAGCGACTATTA
          1 CACCTACTTCCTCTATCGCCAGCGACTATTA

                                * *        
      14632 CACCTACTTCCTCTATCGCCGGTGACTATTA
          1 CACCTACTTCCTCTATCGCCAGCGACTATTA

             
      14663 C
          1 C

      14664 TCGGGTAAGA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.21, C:0.38, G:0.11, T:0.30


Consensus pattern (31 bp):   
CACCTACTTCCTCTATCGCCAGCGACTATTA
Done.