Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007694.1 Kokia drynarioides strain JFW-HI SEQ_122325, 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: 20621
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33


Found at i:3659 original size:24 final size:24

Alignment explanation


    Indices: 3632--3688  Score: 69
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       3622 GCAATCTTAG

                     *              
       3632 ATACAGAATTGAATACAATTTCAA
          1 ATACAGAATAGAATACAATTTCAA

                 *     *           *
       3656 ATACAAAATAGGATACAATTTCAG
          1 ATACAGAATAGAATACAATTTCAA

            *        
       3680 GTACAGAAT
          1 ATACAGAAT

       3689 CATATCTTAC


Statistics
Matches: 27,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  24   27  1.00

ACGTcount: A:0.49, C:0.12, G:0.12, T:0.26


Consensus pattern (24 bp):   
ATACAGAATAGAATACAATTTCAA

Found at i:5780 original size:30 final size:29

Alignment explanation


    Indices: 5713--5782  Score: 86
    Period size: 30  Copynumber: 2.3  Consensus size: 29

       5703 TTTAATTGTC

                                     *   
       5713 TATATTTTTATAATTTTTAAAAAATTAAA
          1 TATATTTTTATAATTTTTAAAAAATAAAA

               *        *      *           
       5742 TCAAATTTTTATTATTTTTTAAAAATCAAAA
          1 T-ATATTTTTATAATTTTTAAAAAAT-AAAA

                      
       5773 TATATTTTTA
          1 TATATTTTTA

       5783 CTTTTATTAA


Statistics
Matches: 34,  Mismatches: 5, Indels: 3
        0.81            0.12        0.07

Matches are distributed among these distances:
  29    1  0.03
  30   29  0.85
  31    4  0.12

ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53


Consensus pattern (29 bp):   
TATATTTTTATAATTTTTAAAAAATAAAA

Found at i:10235 original size:12 final size:12

Alignment explanation


    Indices: 10220--10256  Score: 74
    Period size: 12  Copynumber: 3.1  Consensus size: 12

      10210 AATATCTTTT

                        
      10220 ATAATATTAAAA
          1 ATAATATTAAAA

                        
      10232 ATAATATTAAAA
          1 ATAATATTAAAA

                        
      10244 ATAATATTAAAA
          1 ATAATATTAAAA

             
      10256 A
          1 A

      10257 ATTATTCTTG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   25  1.00

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


Consensus pattern (12 bp):   
ATAATATTAAAA

Found at i:10901 original size:55 final size:56

Alignment explanation


    Indices: 10838--10956  Score: 179
    Period size: 56  Copynumber: 2.1  Consensus size: 56

      10828 TTATAAGTAC

                                                                     
      10838 TATTTCTTTTGAATCAATTGTT-TATATGTTTAAATCGATTGTTAT-GTTGGAATAT
          1 TATTTCTTTTGAATCAATTGTTATATATGTTTAAATCGATTGTTATAG-TGGAATAT

             *            **                      *                 
      10893 TGTTTCTTTTGAATTGATTGTTATATATGTTTAAATCGTTTGTTATAGTGGAATAT
          1 TATTTCTTTTGAATCAATTGTTATATATGTTTAAATCGATTGTTATAGTGGAATAT

                    
      10949 TATTTCTT
          1 TATTTCTT

      10957 CTTCTTTTGA


Statistics
Matches: 57,  Mismatches: 5, Indels: 3
        0.88            0.08        0.05

Matches are distributed among these distances:
  55   19  0.33
  56   37  0.65
  57    1  0.02

ACGTcount: A:0.25, C:0.05, G:0.15, T:0.55


Consensus pattern (56 bp):   
TATTTCTTTTGAATCAATTGTTATATATGTTTAAATCGATTGTTATAGTGGAATAT

Found at i:14876 original size:24 final size:24

Alignment explanation


    Indices: 14849--14898  Score: 64
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      14839 GCATTAGCAC

                  *  *    *         
      14849 TAACACTTGTTATAGCAACATCAG
          1 TAACACCTGCTATAACAACATCAG

                       *            
      14873 TAACACCTGCTGTAACAACATCAG
          1 TAACACCTGCTATAACAACATCAG

              
      14897 TA
          1 TA

      14899 GCTCTAATAC


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26


Consensus pattern (24 bp):   
TAACACCTGCTATAACAACATCAG

Found at i:17483 original size:17 final size:15

Alignment explanation


    Indices: 17461--17504  Score: 52
    Period size: 15  Copynumber: 2.8  Consensus size: 15

      17451 AGAGTAACTG

                             
      17461 CTGTTAACCAACCATAA
          1 CTGTTAA-CAA-CATAA

                       *   
      17478 CTGTTAACAACTTAA
          1 CTGTTAACAACATAA

                   *    
      17493 CTGTTAATAACA
          1 CTGTTAACAACA

      17505 ACTATCAACT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  15   14  0.58
  16    3  0.12
  17    7  0.29

ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30


Consensus pattern (15 bp):   
CTGTTAACAACATAA

Found at i:17495 original size:15 final size:17

Alignment explanation


    Indices: 17461--17499  Score: 55
    Period size: 15  Copynumber: 2.4  Consensus size: 17

      17451 AGAGTAACTG

                             
      17461 CTGTTAACCAACCATAA
          1 CTGTTAACCAACCATAA

                         *   
      17478 CTGTTAA-CAA-CTTAA
          1 CTGTTAACCAACCATAA

                   
      17493 CTGTTAA
          1 CTGTTAA

      17500 TAACAACTAT


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

Matches are distributed among these distances:
  15   11  0.52
  16    3  0.14
  17    7  0.33

ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31


Consensus pattern (17 bp):   
CTGTTAACCAACCATAA
Done.