Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_163 ID=scaffold_163-JGI_221_v2.0

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: 11070
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.32

Warning! 700 characters in sequence are not A, C, G, or T


Found at i:235 original size:20 final size:21

Alignment explanation


    Indices: 191--233  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        181 AACAACTCAC

                                 
        191 TTAGTTGAATGAATAAAAAGT
          1 TTAGTTGAATGAATAAAAAGT

                  *   *          
        212 TTAGTTTAATTAATAAAAAGT
          1 TTAGTTGAATGAATAAAAAGT

             
        233 T
          1 T

        234 AGAATCCCAC


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.47, C:0.00, G:0.14, T:0.40


Consensus pattern (21 bp):   
TTAGTTGAATGAATAAAAAGT

Found at i:2587 original size:12 final size:10

Alignment explanation


    Indices: 2561--2586  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       2551 TATTATGGAA

                      
       2561 TGTGTGCACG
          1 TGTGTGCACG

                      
       2571 TGTGTGCACG
          1 TGTGTGCACG

                  
       2581 TGTGTG
          1 TGTGTG

       2587 TTTGTGTTTT


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

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.08, C:0.15, G:0.42, T:0.35


Consensus pattern (10 bp):   
TGTGTGCACG

Found at i:8530 original size:22 final size:21

Alignment explanation


    Indices: 8500--8699  Score: 130
    Period size: 23  Copynumber: 8.7  Consensus size: 21

       8490 TATAACCCCC

                                  
       8500 CCAAACACAACCAATTTACTCT
          1 CCAAACACAACCAATTTAC-CT

             *       *            
       8522 CGAAACACAGCCAATTTACCCT
          1 CCAAACACAACCAATTTA-CCT

                                     
       8544 CCAAACACAACCATATATATAACCT
          1 CCAAACACAACCA-AT-T-T-ACCT

              *             *      
       8569 CCGAACACAACCAAGTATACCTT
          1 CCAAACACAACCAA-TTTACC-T

                                  
       8592 CCAAACACAACCAATTTATCCT
          1 CCAAACACAACCAATTTA-CCT

             **    *        *   * 
       8614 CTGAACATAACCAAATGTACTT
          1 CCAAACACAACC-AATTTACCT

              *      *                
       8636 GCAAAACACCACCATATATATAACCT
          1 -CCAAACACAACCA-AT-T-T-ACCT

              *             *      
       8662 CCGAACACAACCAACTATACCCT
          1 CCAAACACAACCAA-TTTA-CCT

                           
       8685 CCAAACACAACCAAT
          1 CCAAACACAACCAAT

       8700 ATACTCTTTA


Statistics
Matches: 138,  Mismatches: 24, Indels: 32
        0.71            0.12        0.16

Matches are distributed among these distances:
  22   50  0.36
  23   52  0.38
  24    3  0.02
  25   29  0.21
  26    4  0.03

ACGTcount: A:0.42, C:0.34, G:0.04, T:0.19


Consensus pattern (21 bp):   
CCAAACACAACCAATTTACCT

Done.