Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009145.1 Kokia drynarioides strain JFW-HI SEQ_123849, 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: 17830
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:1973 original size:15 final size:16

Alignment explanation


    Indices: 1953--1991  Score: 62
    Period size: 15  Copynumber: 2.5  Consensus size: 16

       1943 AATTTTTTAA

                            
       1953 AAATTATAAAAAT-AT
          1 AAATTATAAAAATGAT

                   *        
       1968 AAATTATTAAAATGAT
          1 AAATTATAAAAATGAT

                    
       1984 AAATTATA
          1 AAATTATA

       1992 TTTTTATTAT


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

Matches are distributed among these distances:
  15   12  0.57
  16    9  0.43

ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36


Consensus pattern (16 bp):   
AAATTATAAAAATGAT

Found at i:2025 original size:29 final size:30

Alignment explanation


    Indices: 1970--2026  Score: 71
    Period size: 29  Copynumber: 1.9  Consensus size: 30

       1960 AAAAATATAA

                 *                *       
       1970 ATTATTAAAATGATAAATTATATTTTTATT
          1 ATTATAAAAATGATAAATTATAATTTTATT

                           *   *        
       2000 ATTATAAAAAT-ATACATTTTAATTTTA
          1 ATTATAAAAATGATAAATTATAATTTTA

       2027 ATTCTCTTTA


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  29   13  0.57
  30   10  0.43

ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51


Consensus pattern (30 bp):   
ATTATAAAAATGATAAATTATAATTTTATT

Found at i:3105 original size:22 final size:21

Alignment explanation


    Indices: 3075--3115  Score: 55
    Period size: 22  Copynumber: 1.9  Consensus size: 21

       3065 ACGTTTGTTT

                *    *            
       3075 GTTTTTTTTTTTTTCCTTTTAC
          1 GTTTGTTTTCTTTT-CTTTTAC

                               
       3097 GTTTGTTTTCTTTTCTTTT
          1 GTTTGTTTTCTTTTCTTTT

       3116 CTCTTTCCTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    5  0.29
  22   12  0.71

ACGTcount: A:0.02, C:0.12, G:0.07, T:0.78


Consensus pattern (21 bp):   
GTTTGTTTTCTTTTCTTTTAC

Found at i:8726 original size:98 final size:99

Alignment explanation


    Indices: 8615--8902  Score: 443
    Period size: 99  Copynumber: 2.9  Consensus size: 99

       8605 ACTCATGTCC

                  *       *              *                        *      *   
       8615 CATGCCTGTGTGTCTCTAATACATAAACAATGAGTTACACGGCTTGGACACACGACTGTGTGACC
          1 CATGCCCGTGTGTCCCTAATACATAAACAGTGAGTTACACGGCTTGGACACACGCCTGTGTAACC

                             *                
       8680 CTTGCACCTT-TTTTTCTCACACACGGTCTAACA
         66 CTTGCACCTTATTTTTCCCACACACGGTCTAACA

                                       *          *    *             *       
       8713 CATGCCCGTGTGTCCCTAATACATAAATAGTGAGTTACTCGGCCTGGACACACGCCTATGTAACC
          1 CATGCCCGTGTGTCCCTAATACATAAACAGTGAGTTACACGGCTTGGACACACGCCTGTGTAACC

                                              
       8778 CTTGCACCTTATTTTTCCCACACACGGTCTAACA
         66 CTTGCACCTTATTTTTCCCACACACGGTCTAACA

              *                                               * *            
       8812 CAAGCCCGTGTGTCCCTAATACATAAACAGTGAGTTACACGGCTTGGACATAAGCCTGTGTAACC
          1 CATGCCCGTGTGTCCCTAATACATAAACAGTGAGTTACACGGCTTGGACACACGCCTGTGTAACC

             *                        
       8877 CCTGCACCTTATTTTTCCCACACACG
         66 CTTGCACCTTATTTTTCCCACACACG

       8903 CTTGTGTCTC


Statistics
Matches: 171,  Mismatches: 18, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  98   66  0.39
  99  105  0.61

ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27


Consensus pattern (99 bp):   
CATGCCCGTGTGTCCCTAATACATAAACAGTGAGTTACACGGCTTGGACACACGCCTGTGTAACC
CTTGCACCTTATTTTTCCCACACACGGTCTAACA

Done.