Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012983.1 Kokia drynarioides strain JFW-HI SEQ_128001, 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: 5888
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:330 original size:12 final size:11

Alignment explanation


    Indices: 314--347  Score: 50
    Period size: 11  Copynumber: 3.0  Consensus size: 11

        304 GTTTTGTTTA

                       
        314 ATTTAATTTTT
          1 ATTTAATTTTT

                *       
        325 ATTTTATTTGTT
          1 ATTTAATTT-TT

                       
        337 ATTTAATTTTT
          1 ATTTAATTTTT

        348 TTATTTAGTA


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

Matches are distributed among these distances:
  11   10  0.50
  12   10  0.50

ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74


Consensus pattern (11 bp):   
ATTTAATTTTT

Found at i:968 original size:21 final size:20

Alignment explanation


    Indices: 942--984  Score: 68
    Period size: 21  Copynumber: 2.1  Consensus size: 20

        932 CAAAATAGTA

                                 
        942 AAAAAAAACAGCAACCAAAAC
          1 AAAAAAAACAGC-ACCAAAAC

                    *           
        963 AAAAAAAATAGCACCAAAAC
          1 AAAAAAAACAGCACCAAAAC

              
        983 AA
          1 AA

        985 CAATATAATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  20   10  0.48
  21   11  0.52

ACGTcount: A:0.72, C:0.21, G:0.05, T:0.02


Consensus pattern (20 bp):   
AAAAAAAACAGCACCAAAAC

Found at i:2913 original size:43 final size:43

Alignment explanation


    Indices: 2852--2955  Score: 158
    Period size: 43  Copynumber: 2.4  Consensus size: 43

       2842 TGTTATTCAT

                                                        
       2852 TGACATGTTATTAAATTATATTACTTAACCCGTT-TTAATATCG
          1 TGACATGTTATTAAATTATATTACTTAACCC-TTATTAATATCG

                                      *  *             
       2895 TGACATGTTATTAAATTATATTACTTGACTCTTATTAATATCG
          1 TGACATGTTATTAAATTATATTACTTAACCCTTATTAATATCG

            *                  
       2938 CGACATGTTATT-AATTAT
          1 TGACATGTTATTAAATTAT

       2956 GTAGTTCATC


Statistics
Matches: 57,  Mismatches: 3, Indels: 3
        0.90            0.05        0.05

Matches are distributed among these distances:
  42    8  0.14
  43   49  0.86

ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45


Consensus pattern (43 bp):   
TGACATGTTATTAAATTATATTACTTAACCCTTATTAATATCG

Found at i:3682 original size:43 final size:43

Alignment explanation


    Indices: 3635--3738  Score: 118
    Period size: 43  Copynumber: 2.4  Consensus size: 43

       3625 GAACTGCACA

                 *                        **           
       3635 AATAATATGTTACGATATTAACAAGAGTCATTTAATATAATTT
          1 AATAACATGTTACGATATTAACAAGAGTCAAGTAATATAATTT

                     **           ** *  *              
       3678 AATAACATGCCACGATATTAACTCGGGTTAAGTAATATAATTT
          1 AATAACATGTTACGATATTAACAAGAGTCAAGTAATATAATTT

                              
       3721 AATAACATGTTAACGATA
          1 AATAACATGTT-ACGATA

       3739 ACATACTTCT


Statistics
Matches: 49,  Mismatches: 11, Indels: 1
        0.80            0.18        0.02

Matches are distributed among these distances:
  43   43  0.88
  44    6  0.12

ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35


Consensus pattern (43 bp):   
AATAACATGTTACGATATTAACAAGAGTCAAGTAATATAATTT
Done.