Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005904.1 Kokia drynarioides strain JFW-HI SEQ_120255, whole genome shotgun sequence

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, 630

Length: 1051
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31


Found at i:829 original size:29 final size:31

Alignment explanation


    Indices: 784--908  Score: 154
    Period size: 29  Copynumber: 4.2  Consensus size: 31

        774 GTGTCACCTG

                                       *   
        784 TTTTTGACCCCGAAACTTCCAAAAA-TCCCA
          1 TTTTTGACCCCGAAACTTCCAAAAATTACCA

                       *                   
        814 TTTTTGA-CCCTAAACTTCCAAAAATTACCA
          1 TTTTTGACCCCGAAACTTCCAAAAATTACCA

                                        *   
        844 -TTTT-ACCCCCG-AACTTCCAAAAA-TCCCA
          1 TTTTTGA-CCCCGAAACTTCCAAAAATTACCA

                           *   *           
        872 TTTTTGACCCCGAAAATTCTAAAAATTACCA
          1 TTTTTGACCCCGAAACTTCCAAAAATTACCA

                  
        903 TTTTTG
          1 TTTTTG

        909 CTCCCGGATG


Statistics
Matches: 81,  Mismatches: 7, Indels: 13
        0.80            0.07        0.13

Matches are distributed among these distances:
  28    5  0.06
  29   41  0.51
  30   25  0.31
  31   10  0.12

ACGTcount: A:0.34, C:0.29, G:0.06, T:0.32


Consensus pattern (31 bp):   
TTTTTGACCCCGAAACTTCCAAAAATTACCA

Found at i:880 original size:58 final size:60

Alignment explanation


    Indices: 791--906  Score: 191
    Period size: 59  Copynumber: 2.0  Consensus size: 60

        781 CTGTTTTTGA

                                              *   *                     
        791 CCCCGAAACTTCCAAAAATCCCATTTTTGA-CCCTAAACTTCCAAAAATTACCATTTTAC
          1 CCCCGAAACTTCCAAAAATCCCATTTTTGACCCCGAAAATTCCAAAAATTACCATTTTAC

                                                      *               
        850 CCCCG-AACTTCCAAAAATCCCATTTTTGACCCCGAAAATTCTAAAAATTACCATTTT
          1 CCCCGAAACTTCCAAAAATCCCATTTTTGACCCCGAAAATTCCAAAAATTACCATTTT

        907 TGCTCCCGGA


Statistics
Matches: 53,  Mismatches: 3, Indels: 2
        0.91            0.05        0.03

Matches are distributed among these distances:
  58   24  0.45
  59   29  0.55

ACGTcount: A:0.35, C:0.31, G:0.04, T:0.29


Consensus pattern (60 bp):   
CCCCGAAACTTCCAAAAATCCCATTTTTGACCCCGAAAATTCCAAAAATTACCATTTTAC

Done.