Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002305.1 Kokia drynarioides strain JFW-HI SEQ_114343, 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: 8592
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:7046 original size:41 final size:43

Alignment explanation


    Indices: 6964--7051  Score: 126
    Period size: 41  Copynumber: 2.1  Consensus size: 43

       6954 AAAGAGTGTT

                                          *     *      
       6964 TATTGTATTTTCAATTTGTTTGTTGTTTTACGAATTGTTTTAA
          1 TATTGTATTTTCAATTTGTTTGTTGTTTTAAGAATTATTTTAA

                                           * *         
       7007 TATTGT-TTTT-AATTTGTTTGTTGTTTTAATATTTATTTTAA
          1 TATTGTATTTTCAATTTGTTTGTTGTTTTAAGAATTATTTTAA

                
       7048 TATT
          1 TATT

       7052 TTTAAATGTA


Statistics
Matches: 41,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  41   31  0.76
  42    4  0.10
  43    6  0.15

ACGTcount: A:0.22, C:0.02, G:0.11, T:0.65


Consensus pattern (43 bp):   
TATTGTATTTTCAATTTGTTTGTTGTTTTAAGAATTATTTTAA

Found at i:7063 original size:24 final size:24

Alignment explanation


    Indices: 7036--7094  Score: 66
    Period size: 26  Copynumber: 2.4  Consensus size: 24

       7026 GTTGTTTTAA

                     *         *    
       7036 TATTTAT-TTTAATATTTTTAAAT
          1 TATTTATATATAATATTTTAAAAT

                         *            
       7059 GTATTTGATATATCATATTTTAAAAT
          1 -TATTT-ATATATAATATTTTAAAAT

                      
       7085 TATTTATATA
          1 TATTTATATA

       7095 ATAAAATAAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  24   10  0.33
  25    7  0.23
  26   13  0.43

ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58


Consensus pattern (24 bp):   
TATTTATATATAATATTTTAAAAT

Found at i:7071 original size:21 final size:21

Alignment explanation


    Indices: 7030--7071  Score: 50
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       7020 TTGTTTGTTG

                     *     *     
       7030 TTTTAATATTTATTTTAATAT
          1 TTTTAATATGTATTTGAATAT

                                  
       7051 TTTTAA-ATGTATTTGATATAT
          1 TTTTAATATGTATTTGA-ATAT

       7072 CATATTTTAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  20    8  0.44
  21   10  0.56

ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62


Consensus pattern (21 bp):   
TTTTAATATGTATTTGAATAT

Found at i:7077 original size:26 final size:24

Alignment explanation


    Indices: 7047--7094  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       7037 ATTTATTTTA

                   *                  
       7047 ATATTTTTAAATGTATTTGATATATC
          1 ATATTTTAAAAT-TATTT-ATATATC

                                  
       7073 ATATTTTAAAATTATTTATATA
          1 ATATTTTAAAATTATTTATATA

       7095 ATAAAATAAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24    5  0.24
  25    5  0.24
  26   11  0.52

ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54


Consensus pattern (24 bp):   
ATATTTTAAAATTATTTATATATC
Done.