Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011995.1 Kokia drynarioides strain JFW-HI SEQ_126993, 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, 1000

Length: 6735
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:3057 original size:24 final size:26

Alignment explanation


    Indices: 3029--3088  Score: 88
    Period size: 24  Copynumber: 2.3  Consensus size: 26

       3019 AAACTAATCA

                           *          
       3029 TTTTAAAAATAAATTTGAAT-A-TTT
          1 TTTTAAAAATAAATTAGAATAATTTT

                                      
       3053 TTTTAAAAATAAATTAGAATAATTTT
          1 TTTTAAAAATAAATTAGAATAATTTT

                      
       3079 TGTTTAAAAA
          1 T-TTTAAAAA

       3089 ATATACACGA


Statistics
Matches: 32,  Mismatches: 1, Indels: 3
        0.89            0.03        0.08

Matches are distributed among these distances:
  24   19  0.59
  25    1  0.03
  26    4  0.12
  27    8  0.25

ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47


Consensus pattern (26 bp):   
TTTTAAAAATAAATTAGAATAATTTT

Found at i:4866 original size:29 final size:30

Alignment explanation


    Indices: 4825--4896  Score: 101
    Period size: 29  Copynumber: 2.4  Consensus size: 30

       4815 CCCACTTGCG

                         *        *       
       4825 GTGTGTCTCTGTCTGTGCTACATG-TTGTT
          1 GTGTGTCTCTGTCCGTGCTACAAGCTTGTT

                                          
       4854 GTGTGTCTCTGTCCGTGCTACAAGCTTGTT
          1 GTGTGTCTCTGTCCGTGCTACAAGCTTGTT

            **           
       4884 ACGTGTCTCTGTC
          1 GTGTGTCTCTGTC

       4897 AATGCTATAT


Statistics
Matches: 38,  Mismatches: 4, Indels: 1
        0.88            0.09        0.02

Matches are distributed among these distances:
  29   22  0.58
  30   16  0.42

ACGTcount: A:0.08, C:0.22, G:0.26, T:0.43


Consensus pattern (30 bp):   
GTGTGTCTCTGTCCGTGCTACAAGCTTGTT

Found at i:4903 original size:30 final size:29

Alignment explanation


    Indices: 4827--4903  Score: 91
    Period size: 30  Copynumber: 2.6  Consensus size: 29

       4817 CACTTGCGGT

                       *        *      **
       4827 GTGTCTCTGTCTGTGCTACATGTTGTTGT
          1 GTGTCTCTGTCAGTGCTACAAGTTGTTAC

                       *                  
       4856 GTGTCTCTGTCCGTGCTACAAGCTTGTTAC
          1 GTGTCTCTGTCAGTGCTACAAG-TTGTTAC

                        *     
       4886 GTGTCTCTGTCAATGCTA
          1 GTGTCTCTGTCAGTGCTA

       4904 TATATTTGTT


Statistics
Matches: 41,  Mismatches: 6, Indels: 1
        0.85            0.12        0.02

Matches are distributed among these distances:
  29   20  0.49
  30   21  0.51

ACGTcount: A:0.12, C:0.22, G:0.25, T:0.42


Consensus pattern (29 bp):   
GTGTCTCTGTCAGTGCTACAAGTTGTTAC

Found at i:4962 original size:13 final size:14

Alignment explanation


    Indices: 4935--4963  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       4925 CTCGATGATG

                          
       4935 TGTTATTTGTGTAA
          1 TGTTATTTGTGTAA

                          
       4949 TGTTATTT-TGTAA
          1 TGTTATTTGTGTAA

              
       4962 TG
          1 TG

       4964 AGATATCTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    7  0.47
  14    8  0.53

ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59


Consensus pattern (14 bp):   
TGTTATTTGTGTAA
Done.