Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_712 ID=scaffold_712-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: 4927
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.31

Warning! 535 characters in sequence are not A, C, G, or T


Found at i:563 original size:20 final size:20

Alignment explanation


    Indices: 538--575  Score: 76
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        528 TAAACCATAC

                                
        538 TTTTTTATTTTTAAAATATA
          1 TTTTTTATTTTTAAAATATA

                              
        558 TTTTTTATTTTTAAAATA
          1 TTTTTTATTTTTAAAATA

        576 CACTACATTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (20 bp):   
TTTTTTATTTTTAAAATATA

Found at i:805 original size:15 final size:15

Alignment explanation


    Indices: 782--817  Score: 63
    Period size: 15  Copynumber: 2.4  Consensus size: 15

        772 CTTTTATTTG

                *          
        782 TTTCCTTACACTGTA
          1 TTTCTTTACACTGTA

                           
        797 TTTCTTTACACTGTA
          1 TTTCTTTACACTGTA

                  
        812 TTTCTT
          1 TTTCTT

        818 CCTCCTTACA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.17, C:0.22, G:0.06, T:0.56


Consensus pattern (15 bp):   
TTTCTTTACACTGTA

Found at i:2346 original size:21 final size:20

Alignment explanation


    Indices: 2322--2363  Score: 77
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       2312 AATATAAACC

                                
       2322 ATAT-TTTTTTATTTTTAAA
          1 ATATATTTTTTATTTTTAAA

                                
       2341 ATATATTTTTTATTTTTAAA
          1 ATATATTTTTTATTTTTAAA

               
       2361 ATA
          1 ATA

       2364 CACCACATTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  19    4  0.18
  20   18  0.82

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (20 bp):   
ATATATTTTTTATTTTTAAA

Done.