Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008490.1 Kokia drynarioides strain JFW-HI SEQ_123165, 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: 12941
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33


Found at i:1132 original size:36 final size:38

Alignment explanation


    Indices: 1068--1139  Score: 96
    Period size: 36  Copynumber: 1.9  Consensus size: 38

       1058 TTTTTTTGTT

                                   *               
       1068 TATATTTAACTTTAATTTGTAATTATTATTT-TTTAATA
          1 TATATTTAACTTT-ATTTGTAATAATTATTTCTTTAATA

                                                
       1106 TATATTTAA-TTT-TTTGATAATAATTATTTCTTTA
          1 TATATTTAACTTTATTTG-TAATAATTATTTCTTTA

       1140 CATTTTTACA


Statistics
Matches: 31,  Mismatches: 1, Indels: 5
        0.84            0.03        0.14

Matches are distributed among these distances:
  35    4  0.13
  36   11  0.35
  37    7  0.23
  38    9  0.29

ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61


Consensus pattern (38 bp):   
TATATTTAACTTTATTTGTAATAATTATTTCTTTAATA

Found at i:2993 original size:2 final size:2

Alignment explanation


    Indices: 2986--3010  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       2976 ATTCGTCATT

                                                 
       2986 TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC T

       3011 TTATTTTTAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Found at i:6950 original size:18 final size:20

Alignment explanation


    Indices: 6909--6958  Score: 61
    Period size: 19  Copynumber: 2.6  Consensus size: 20

       6899 TTTCTTAATA

                                
       6909 AAAATTACAAAATAATTTTC
          1 AAAATTACAAAATAATTTTC

                                 
       6929 AAAATT-CAAAAT-ATTTAT-
          1 AAAATTACAAAATAATTT-TC

                   *    
       6947 AAAATTATAAAA
          1 AAAATTACAAAA

       6959 ATTTCAAAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  18   10  0.37
  19   11  0.41
  20    6  0.22

ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34


Consensus pattern (20 bp):   
AAAATTACAAAATAATTTTC

Found at i:6958 original size:19 final size:19

Alignment explanation


    Indices: 6909--6967  Score: 63
    Period size: 18  Copynumber: 3.2  Consensus size: 19

       6899 TTTCTTAATA

                                
       6909 AAAATTACAAAATAATTTTC
          1 AAAATTACAAAAT-ATTTTC

                                
       6929 AAAATT-CAAAATATTTAT-
          1 AAAATTACAAAATATTT-TC

                   *           
       6947 AAAATTATAAAA-A-TTTC
          1 AAAATTACAAAATATTTTC

                
       6964 AAAA
          1 AAAA

       6968 AATAATAATC


Statistics
Matches: 35,  Mismatches: 1, Indels: 9
        0.78            0.02        0.20

Matches are distributed among these distances:
  16    1  0.03
  17    6  0.17
  18   11  0.31
  19   11  0.31
  20    6  0.17

ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34


Consensus pattern (19 bp):   
AAAATTACAAAATATTTTC
Done.