Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006542.1 Kokia drynarioides strain JFW-HI SEQ_121127, 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, 826

Length: 1377
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.40


Found at i:1022 original size:13 final size:13

Alignment explanation


    Indices: 1004--1085  Score: 71
    Period size: 13  Copynumber: 6.5  Consensus size: 13

        994 TAAGTTACCC

                    *    
       1004 TTTTTAATATTAT
          1 TTTTTAATGTTAT

                        * 
       1017 TTTTT-ATGTTGTT
          1 TTTTTAATGTT-AT

                    *    
       1030 TTTTTAATATTAT
          1 TTTTTAATGTTAT

               *       * 
       1043 TTTGT-ATGTTGT
          1 TTTTTAATGTTAT

                         
       1055 TTTTTAATGTTAT
          1 TTTTTAATGTTAT

               *       * 
       1068 TTTGT-ATGTTGT
          1 TTTTTAATGTTAT

                  
       1080 TTTTTA
          1 TTTTTA

       1086 TTATGTCTGA


Statistics
Matches: 53,  Mismatches: 12, Indels: 8
        0.73            0.16        0.11

Matches are distributed among these distances:
  12   23  0.43
  13   26  0.49
  14    4  0.08

ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71


Consensus pattern (13 bp):   
TTTTTAATGTTAT

Found at i:1031 original size:12 final size:12

Alignment explanation


    Indices: 1016--1086  Score: 70
    Period size: 12  Copynumber: 5.7  Consensus size: 12

       1006 TTTAATATTA

                        
       1016 TTTTTTATGTTG
          1 TTTTTTATGTTG

                      *  *
       1028 TTTTTTTAATATTA
          1 -TTTTTT-ATGTTG

                *       
       1042 TTTTGTATGTTG
          1 TTTTTTATGTTG

                        *
       1054 TTTTTTAATGTTA
          1 TTTTTT-ATGTTG

                *       
       1067 TTTTGTATGTTG
          1 TTTTTTATGTTG

                    
       1079 TTTTTTAT
          1 TTTTTTAT

       1087 TATGTCTGAC


Statistics
Matches: 46,  Mismatches: 10, Indels: 5
        0.75            0.16        0.08

Matches are distributed among these distances:
  12   21  0.46
  13   21  0.46
  14    4  0.09

ACGTcount: A:0.15, C:0.00, G:0.13, T:0.72


Consensus pattern (12 bp):   
TTTTTTATGTTG

Found at i:1033 original size:25 final size:25

Alignment explanation


    Indices: 1004--1085  Score: 137
    Period size: 25  Copynumber: 3.2  Consensus size: 25

        994 TAAGTTACCC

                            *         
       1004 TTTTTAATATTATTTTTTATGTTGTT
          1 TTTTTAATATTATTTTGTATGTTG-T

                                     
       1030 TTTTTAATATTATTTTGTATGTTGT
          1 TTTTTAATATTATTTTGTATGTTGT

                    *                
       1055 TTTTTAATGTTATTTTGTATGTTGT
          1 TTTTTAATATTATTTTGTATGTTGT

                  
       1080 TTTTTA
          1 TTTTTA

       1086 TTATGTCTGA


Statistics
Matches: 54,  Mismatches: 2, Indels: 1
        0.95            0.04        0.02

Matches are distributed among these distances:
  25   31  0.57
  26   23  0.43

ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71


Consensus pattern (25 bp):   
TTTTTAATATTATTTTGTATGTTGT

Found at i:1033 original size:26 final size:26

Alignment explanation


    Indices: 1004--1084  Score: 137
    Period size: 26  Copynumber: 3.2  Consensus size: 26

        994 TAAGTTACCC

                            *         
       1004 TTTTTAATATTATTTTTTATGTTGTT
          1 TTTTTAATATTATTTTGTATGTTGTT

                                      
       1030 TTTTTAATATTATTTTGTATGTTG-T
          1 TTTTTAATATTATTTTGTATGTTGTT

                    *                 
       1055 TTTTTAATGTTATTTTGTATGTTGTT
          1 TTTTTAATATTATTTTGTATGTTGTT

                
       1081 TTTT
          1 TTTT

       1085 ATTATGTCTG


Statistics
Matches: 52,  Mismatches: 2, Indels: 2
        0.93            0.04        0.04

Matches are distributed among these distances:
  25   24  0.46
  26   28  0.54

ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72


Consensus pattern (26 bp):   
TTTTTAATATTATTTTGTATGTTGTT
Done.