Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009543.1 Kokia drynarioides strain JFW-HI SEQ_124255, 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, 648

Length: 1080
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32

Warning! 3 characters in sequence are not A, C, G, or T


Found at i:1060 original size:58 final size:59

Alignment explanation


    Indices: 962--1080  Score: 213
    Period size: 58  Copynumber: 2.0  Consensus size: 59

        952 ATTTTGTACC

                                              *                        
        962 ATTTTGGTAAATAATATGATAGGGATATTATTTTTATAATTAATTATTTTTTATATTAT
          1 ATTTTGGTAAATAATATGATAGGGATATTATTTTGATAATTAATTATTTTTTATATTAT

                    *                                                  
       1021 ATTTTGGTCAATAATATGAT-GGGATATTATTTTGATAATTAATTATTTTTTATATTAT
          1 ATTTTGGTAAATAATATGATAGGGATATTATTTTGATAATTAATTATTTTTTATATTAT

              
       1079 AT
          1 AT


Statistics
Matches: 58,  Mismatches: 2, Indels: 1
        0.95            0.03        0.02

Matches are distributed among these distances:
  58   39  0.67
  59   19  0.33

ACGTcount: A:0.34, C:0.01, G:0.11, T:0.54


Consensus pattern (59 bp):   
ATTTTGGTAAATAATATGATAGGGATATTATTTTGATAATTAATTATTTTTTATATTAT

Found at i:1063 original size:28 final size:28

Alignment explanation


    Indices: 962--1063  Score: 73
    Period size: 29  Copynumber: 3.5  Consensus size: 28

        952 ATTTTGTACC

                  *   *                  
        962 ATTTTGGTAAATAATATGATAGGGATATT
          1 ATTTTGATAATTAATATGAT-GGGATATT

                 *             * ***       
        991 ATTTTTATAATTAATTAT-TTTTTATATTAT
          1 ATTTTGATAATTAA-TATGATGGGATA-T-T

                  *                      
       1021 ATTTTGGTCAA-TAATATGATGGGATATT
          1 ATTTTGAT-AATTAATATGATGGGATATT

                           
       1049 ATTTTGATAATTAAT
          1 ATTTTGATAATTAAT

       1064 TATTTTTTAT


Statistics
Matches: 53,  Mismatches: 14, Indels: 13
        0.66            0.17        0.16

Matches are distributed among these distances:
  27    2  0.04
  28   15  0.28
  29   17  0.32
  30   17  0.32
  31    2  0.04

ACGTcount: A:0.35, C:0.01, G:0.13, T:0.51


Consensus pattern (28 bp):   
ATTTTGATAATTAATATGATGGGATATT

Found at i:1075 original size:28 final size:28

Alignment explanation


    Indices: 986--1078  Score: 82
    Period size: 28  Copynumber: 3.2  Consensus size: 28

        976 TATGATAGGG

                      *                 
        986 ATATTATTTTTATAATTAATTATTTTTT
          1 ATATTATTTTGATAATTAATTATTTTTT

                         *             * ***
       1014 ATATTATATTTTGGTCAA-TAA-TATGATGGG
          1 ATA-T-TATTTTGAT-AATTAATTAT-TTTTT

                                        
       1044 ATATTATTTTGATAATTAATTATTTTTT
          1 ATATTATTTTGATAATTAATTATTTTTT

                   
       1072 ATATTAT
          1 ATATTAT

       1079 AT


Statistics
Matches: 48,  Mismatches: 11, Indels: 12
        0.68            0.15        0.17

Matches are distributed among these distances:
  27    2  0.04
  28   22  0.46
  29    8  0.17
  30   14  0.29
  31    2  0.04

ACGTcount: A:0.33, C:0.01, G:0.08, T:0.58


Consensus pattern (28 bp):   
ATATTATTTTGATAATTAATTATTTTTT
Done.