Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014795.1 Kokia drynarioides strain JFW-HI SEQ_129837, 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: 35749
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36


Found at i:10124 original size:25 final size:26

Alignment explanation


    Indices: 10087--10135  Score: 64
    Period size: 25  Copynumber: 1.9  Consensus size: 26

      10077 TTTTAATTCA

                             *        
      10087 TACTTAAACTTTTTT-TTTAATTTGG
          1 TACTTAAACTTTTTTATCTAATTTGG

                   **               
      10112 TACTTAATTTTTTTTATCTAATTT
          1 TACTTAAACTTTTTTATCTAATTT

      10136 CATATTTAAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  25   13  0.65
  26    7  0.35

ACGTcount: A:0.24, C:0.08, G:0.04, T:0.63


Consensus pattern (26 bp):   
TACTTAAACTTTTTTATCTAATTTGG

Found at i:20767 original size:15 final size:15

Alignment explanation


    Indices: 20718--20772  Score: 51
    Period size: 15  Copynumber: 3.8  Consensus size: 15

      20708 CTATCATCAC

                       *   
      20718 TTAATTAATTAACTA
          1 TTAATTAATTATCTA

            *           *  
      20733 GTAA-TAA-TATATA
          1 TTAATTAATTATCTA

              *    *       
      20746 TTTATTATTTATCTA
          1 TTAATTAATTATCTA

                        
      20761 TTAATTAATTAT
          1 TTAATTAATTAT

      20773 AATGAATACG


Statistics
Matches: 29,  Mismatches: 9, Indels: 4
        0.69            0.21        0.10

Matches are distributed among these distances:
  13    6  0.21
  14    5  0.17
  15   18  0.62

ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53


Consensus pattern (15 bp):   
TTAATTAATTATCTA

Found at i:21381 original size:5 final size:5

Alignment explanation


    Indices: 21373--21404  Score: 64
    Period size: 5  Copynumber: 6.4  Consensus size: 5

      21363 TATAATATAT

                                                  
      21373 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC AT
          1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC AT

      21405 GTTATAAACA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   27  1.00

ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22


Consensus pattern (5 bp):   
ATAAC

Found at i:26458 original size:16 final size:15

Alignment explanation


    Indices: 26437--26467  Score: 53
    Period size: 16  Copynumber: 2.0  Consensus size: 15

      26427 TTTAATATAC

                            
      26437 TGTAATTTAGTCTTTT
          1 TGTAATTTAGT-TTTT

                           
      26453 TGTAATTTAGTTTTT
          1 TGTAATTTAGTTTTT

      26468 ATTTTTTTGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    4  0.27
  16   11  0.73

ACGTcount: A:0.19, C:0.03, G:0.13, T:0.65


Consensus pattern (15 bp):   
TGTAATTTAGTTTTT

Found at i:27287 original size:21 final size:21

Alignment explanation


    Indices: 27248--27289  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      27238 CGTCATGCGG

                          *      
      27248 TTGATCAACAATCAGTCAACA
          1 TTGATCAACAATCAATCAACA

                      * *        
      27269 TTGATCAACAGTTAATCAACA
          1 TTGATCAACAATCAATCAACA

      27290 ATCAAGTAAA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26


Consensus pattern (21 bp):   
TTGATCAACAATCAATCAACA

Found at i:32765 original size:13 final size:13

Alignment explanation


    Indices: 32747--32771  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      32737 AAGATTAAGG

                         
      32747 TTAATAATATAAT
          1 TTAATAATATAAT

                        
      32760 TTAATAATATAA
          1 TTAATAATATAA

      32772 AATATTTAAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (13 bp):   
TTAATAATATAAT
Done.