Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_557 ID=scaffold_557-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: 8057
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.24

Warning! 2301 characters in sequence are not A, C, G, or T


Found at i:2552 original size:13 final size:13

Alignment explanation


    Indices: 2531--2565  Score: 52
    Period size: 13  Copynumber: 2.7  Consensus size: 13

       2521 ATAAGTTGCT

                *      * 
       2531 GTTAGTTAAATTA
          1 GTTAATTAAATAA

                         
       2544 GTTAATTAAATAA
          1 GTTAATTAAATAA

                     
       2557 GTTAATTAA
          1 GTTAATTAA

       2566 TTTGTTTAAA


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

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43


Consensus pattern (13 bp):   
GTTAATTAAATAA

Found at i:3553 original size:14 final size:14

Alignment explanation


    Indices: 3534--3575  Score: 57
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       3524 TAGTTTAATG

                          
       3534 ATTTTTATTTTTTT
          1 ATTTTTATTTTTTT

                      *   
       3548 ATTTTTATTTATTT
          1 ATTTTTATTTTTTT

                          
       3562 ATTTCTTAGTTTTT
          1 ATTT-TTA-TTTTT

       3576 AAGTTAGATA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  14   17  0.71
  15    3  0.12
  16    4  0.17

ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79


Consensus pattern (14 bp):   
ATTTTTATTTTTTT

Found at i:7778 original size:18 final size:18

Alignment explanation


    Indices: 7757--7811  Score: 67
    Period size: 18  Copynumber: 3.1  Consensus size: 18

       7747 AAAAGTTCGA

                    *         
       7757 AAAAAATTTGAAAAAAAT
          1 AAAAAATTCGAAAAAAAT

                  *            
       7775 AAAAAAATCGAAAAGAAA-
          1 AAAAAATTCGAAAA-AAAT

                    *         
       7793 AAAAAATTGGAAAAAAAT
          1 AAAAAATTCGAAAAAAAT

             
       7811 A
          1 A

       7812 TTGCATACGG


Statistics
Matches: 31,  Mismatches: 4, Indels: 4
        0.79            0.10        0.10

Matches are distributed among these distances:
  17    3  0.10
  18   25  0.81
  19    3  0.10

ACGTcount: A:0.75, C:0.02, G:0.09, T:0.15


Consensus pattern (18 bp):   
AAAAAATTCGAAAAAAAT

Found at i:7880 original size:64 final size:65

Alignment explanation


    Indices: 7804--7928  Score: 234
    Period size: 64  Copynumber: 1.9  Consensus size: 65

       7794 AAAAATTGGA

                                     *                                       
       7804 AAAAAATATTGCATACGGTCTAGGTGCGGACGAAAAGAACGTGAAAGATCCGTAAAAAAAAGCAG
          1 AAAAAATATTGCATACGGTCTAGGTACGGACGAAAAGAACGTGAAAGATCCGTAAAAAAAAGCAG

                                                                         
       7869 AAAAAA-ATTGCATACGGTCTAGGTACGGACGAAAAGAACGTGAAAGATCCGTAAAAAAAA
          1 AAAAAATATTGCATACGGTCTAGGTACGGACGAAAAGAACGTGAAAGATCCGTAAAAAAAA

       7929 AAGAGTCTGG


Statistics
Matches: 59,  Mismatches: 1, Indels: 1
        0.97            0.02        0.02

Matches are distributed among these distances:
  64   53  0.90
  65    6  0.10

ACGTcount: A:0.48, C:0.14, G:0.23, T:0.15


Consensus pattern (65 bp):   
AAAAAATATTGCATACGGTCTAGGTACGGACGAAAAGAACGTGAAAGATCCGTAAAAAAAAGCAG
Done.