Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_725 ID=scaffold_725-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: 4447
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.30

Warning! 209 characters in sequence are not A, C, G, or T


Found at i:2511 original size:23 final size:21

Alignment explanation


    Indices: 2481--2532  Score: 59
    Period size: 22  Copynumber: 2.4  Consensus size: 21

       2471 ATGAATCAAT

                         *    *   
       2481 AAAGAAAATAATGTTTGTTTAA
          1 AAAGAAAA-AATGCTTGTATAA

                     *            
       2503 AGAAGAAAAGATGCTTGTATAA
          1 A-AAGAAAAAATGCTTGTATAA

                    
       2525 AAAGAAAA
          1 AAAGAAAA

       2533 GTCACTTACA


Statistics
Matches: 26,  Mismatches: 3, Indels: 3
        0.81            0.09        0.09

Matches are distributed among these distances:
  21    7  0.27
  22   12  0.46
  23    7  0.27

ACGTcount: A:0.56, C:0.02, G:0.17, T:0.25


Consensus pattern (21 bp):   
AAAGAAAAAATGCTTGTATAA

Found at i:2525 original size:22 final size:22

Alignment explanation


    Indices: 2479--2533  Score: 62
    Period size: 21  Copynumber: 2.6  Consensus size: 22

       2469 TTATGAATCA

                       *     *    
       2479 ATAAAGAA-AATA-ATGTTTGT
          1 ATAAAGAAGAAAAGATGCTTGT

            *                     
       2499 TTAAAGAAGAAAAGATGCTTGT
          1 ATAAAGAAGAAAAGATGCTTGT

                          
       2521 ATAAA-AAGAAAAG
          1 ATAAAGAAGAAAAG

       2534 TCACTTACAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  20    7  0.24
  21   11  0.38
  22   11  0.38

ACGTcount: A:0.55, C:0.02, G:0.18, T:0.25


Consensus pattern (22 bp):   
ATAAAGAAGAAAAGATGCTTGT

Found at i:3676 original size:2 final size:2

Alignment explanation


    Indices: 3669--3702  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       3659 TCTATATCAT

                                                              
       3669 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

       3703 CCCCTCGCTT


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

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Done.