Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002412.1 Kokia drynarioides strain JFW-HI SEQ_114509, 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: 10927
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36

Warning! 27 characters in sequence are not A, C, G, or T


Found at i:984 original size:59 final size:59

Alignment explanation


    Indices: 595--1044  Score: 628
    Period size: 58  Copynumber: 7.7  Consensus size: 59

        585 TAAACTCACC

                                       *                               
        595 AAAAATTACCATTTTACCCCCAAACTTTCAAAAATCCCATTTTTGACCCCGAACTTTC-
          1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCT

            *                  **   *                        **        
        653 CAAAATTACCATTTTACCCTTAAATTTCCAAAAATCCCATTTTTGACCCTAAACTTTCT
          1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCT

                *     *         *       *                         *    
        712 AAAACTTACCGTTTTA-CCCTAAACTTCTAAAAATCCCATTTTTGACCCCGAACCTTCT
          1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCT

                                                              *        
        770 AAAAATTACCA-TTTACCCCCAAACTTCCAAAAATCCCA-TTTTGACCCCAAACTTTCT
          1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCT

                                *                       *             *
        827 AAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCGAACTTTCC
          1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCT

                                                              *   * *  
        886 AAAAATTACCA-TTTA-CCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTACT
          1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCT

                                              *                         
        943 AAAAATTACCATTTTACCCCCAAACTTCCAAAAACCCCATTTTTGACCCCGAACCTTTC-
          1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAA-CTTTCT

            *                  * *                      
       1002 GAAAATTACCATTTTACCCTCGAACTTCCAAAAAT-CCATTTTT
          1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT

       1045 TTTCGAACCT


Statistics
Matches: 345,  Mismatches: 40, Indels: 14
        0.86            0.10        0.04

Matches are distributed among these distances:
  57   79  0.23
  58  158  0.46
  59  105  0.30
  60    3  0.01

ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31


Consensus pattern (59 bp):   
AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCT

Found at i:3445 original size:17 final size:18

Alignment explanation


    Indices: 3411--3446  Score: 56
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       3401 TATAAATAAA

                              
       3411 TAAATATTCTTATTTTAT
          1 TAAATATTCTTATTTTAT

                       *      
       3429 TAAATATT-TTTTTTTAT
          1 TAAATATTCTTATTTTAT

             
       3446 T
          1 T

       3447 TTTTTTTATA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    9  0.53
  18    8  0.47

ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67


Consensus pattern (18 bp):   
TAAATATTCTTATTTTAT

Found at i:7925 original size:21 final size:21

Alignment explanation


    Indices: 7882--7925  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       7872 TCTAGTTCGA

                         **      
       7882 TTAAATAAATTATTTAAAAAT
          1 TTAAATAAATTATAAAAAAAT

                                  
       7903 TTAAATAAA-TATAAAAAATAT
          1 TTAAATAAATTATAAAAAA-AT

              
       7924 TT
          1 TT

       7926 TTTAAAGAAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20    7  0.35
  21   13  0.65

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (21 bp):   
TTAAATAAATTATAAAAAAAT

Found at i:10138 original size:20 final size:18

Alignment explanation


    Indices: 10102--10148  Score: 76
    Period size: 20  Copynumber: 2.5  Consensus size: 18

      10092 GTTTAAATTG

                              
      10102 ATTTAAATTTATTTTTAA
          1 ATTTAAATTTATTTTTAA

                                
      10120 ATTTAAATTTATCTTTTTAA
          1 ATTTAAATTTA--TTTTTAA

                     
      10140 ATTTAAATT
          1 ATTTAAATT

      10149 GGCTTAAGAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  18   11  0.41
  20   16  0.59

ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60


Consensus pattern (18 bp):   
ATTTAAATTTATTTTTAA

Found at i:10892 original size:3 final size:3

Alignment explanation


    Indices: 10878--10927  Score: 93
    Period size: 3  Copynumber: 17.0  Consensus size: 3

      10868 AATAAGGCTT

                                                                           
      10878 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

               
      10925 TAA
          1 TAA


Statistics
Matches: 46,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   2    2  0.04
   3   44  0.96

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
TAA

Done.