Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_79 ID=scaffold_79-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: 16876
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.31

Warning! 752 characters in sequence are not A, C, G, or T


Found at i:3969 original size:3 final size:3

Alignment explanation


    Indices: 3961--4013  Score: 79
    Period size: 3  Copynumber: 17.7  Consensus size: 3

       3951 ACCTCATATG

                                    *                *            *        
       3961 AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AGT AAT AAT AAC AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                  
       4009 AAT AA
          1 AAT AA

       4014 ACTAATTAAA


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   3   44  1.00

ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30


Consensus pattern (3 bp):   
AAT

Found at i:10860 original size:50 final size:50

Alignment explanation


    Indices: 10780--10972  Score: 262
    Period size: 50  Copynumber: 3.8  Consensus size: 50

      10770 ATTTGGGTAA

                                   *                          
      10780 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
          1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG

                     *   *           *                        
      10830 AGAGGTCCCTTGTGAGACCATGTTTAGGACATGGCGTTGGCACCGAGATG
          1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG

                       *                        * *        *   
      10880 AGAGGTTCCC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
          1 AGAGG-TCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG

                **                              *      
      10930 AGAACATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
          1 AG-AGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCA

      10973 TGTTATTATC


Statistics
Matches: 125,  Mismatches: 15, Indels: 5
        0.86            0.10        0.03

Matches are distributed among these distances:
  50   91  0.73
  51   34  0.27

ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23


Consensus pattern (50 bp):   
AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
Done.