Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_958 ID=scaffold_958-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: 3960
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.17

Warning! 1972 characters in sequence are not A, C, G, or T


Found at i:191 original size:17 final size:18

Alignment explanation


    Indices: 160--193  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

        150 ATAGCAAAAG

                      *       
        160 TTTAATAATGGAAAAGAA
          1 TTTAATAATGAAAAAGAA

                             
        178 TTTAA-AATGAAAAAGA
          1 TTTAATAATGAAAAAGA

        194 CTGTTTTATG


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17   10  0.67
  18    5  0.33

ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26


Consensus pattern (18 bp):   
TTTAATAATGAAAAAGAA

Found at i:3116 original size:18 final size:18

Alignment explanation


    Indices: 3093--3135  Score: 77
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       3083 TTGATTAGTC

                              
       3093 TCGGTTTACGTCTTCTTT
          1 TCGGTTTACGTCTTCTTT

                              
       3111 TCGGTTTACGTCTTCTTT
          1 TCGGTTTACGTCTTCTTT

              *    
       3129 TCAGTTT
          1 TCGGTTT

       3136 CGGTTTACCT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  18   24  1.00

ACGTcount: A:0.07, C:0.21, G:0.16, T:0.56


Consensus pattern (18 bp):   
TCGGTTTACGTCTTCTTT
Done.