Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001634.1 Kokia drynarioides strain JFW-HI SEQ_113272, 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: 45399
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 55 characters in sequence are not A, C, G, or T


Found at i:32190 original size:30 final size:30

Alignment explanation


    Indices: 32118--32190  Score: 85
    Period size: 31  Copynumber: 2.4  Consensus size: 30

      32108 GATTAAATCA

                                  *       
      32118 AAATTAAAGTTTCAAGTATATATTTGAACC
          1 AAATTAAAGTTTCAAGTATATAATTGAACC

                   *       *               *
      32148 ATAATTAGAGTTTCACGTATATAATT-ACACT
          1 A-AATTAAAGTTTCAAGTATATAATTGA-ACC

                        
      32179 AAATTAAAGTTT
          1 AAATTAAAGTTT

      32191 ATATATATAT


Statistics
Matches: 36,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  30   12  0.33
  31   24  0.67

ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38


Consensus pattern (30 bp):   
AAATTAAAGTTTCAAGTATATAATTGAACC

Found at i:32217 original size:35 final size:33

Alignment explanation


    Indices: 32165--32232  Score: 82
    Period size: 35  Copynumber: 2.0  Consensus size: 33

      32155 GAGTTTCACG

                              *   *          
      32165 TATATAATTACACTAAATTAAAGTTTATATATA
          1 TATATAATTACACTAAATCAAAATTTATATATA

                  *                       *    
      32198 TATATATTTACACATTAAATCAAAATTTATGTATA
          1 TATATAATTACAC--TAAATCAAAATTTATATATA

      32233 ATTTTAAAAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  33   12  0.41
  35   17  0.59

ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43


Consensus pattern (33 bp):   
TATATAATTACACTAAATCAAAATTTATATATA

Found at i:42845 original size:35 final size:34

Alignment explanation


    Indices: 42782--42855  Score: 89
    Period size: 35  Copynumber: 2.1  Consensus size: 34

      42772 TAAAAATGTT

                                              *
      42782 TATTTGAAATTTTTTAATATTTAATATTTTAAATG
          1 TATTTGAAATTTTTTAATATTT-ATATTTTAAATA

                                                 
      42817 TATTTGATAATTATTTTAACT-TTT-TATTTTAAATA
          1 TATTTGA-AATT-TTTTAA-TATTTATATTTTAAATA

                
      42852 TATT
          1 TATT

      42856 AATTTAATAT


Statistics
Matches: 35,  Mismatches: 1, Indels: 6
        0.83            0.02        0.14

Matches are distributed among these distances:
  35   21  0.60
  36    4  0.11
  37    9  0.26
  38    1  0.03

ACGTcount: A:0.35, C:0.01, G:0.04, T:0.59


Consensus pattern (34 bp):   
TATTTGAAATTTTTTAATATTTATATTTTAAATA

Found at i:42974 original size:26 final size:27

Alignment explanation


    Indices: 42910--42976  Score: 66
    Period size: 26  Copynumber: 2.4  Consensus size: 27

      42900 TACTTACCAC

                                *   *     
      42910 TTCATGTAAAAACTATTAAATTAATTTCAT
          1 TTCATGT-AAAA--ATTAAAGTAAATTCAT

              *                        
      42940 TTTAT-TAAAAATTAAAGTAAATT-AT
          1 TTCATGTAAAAATTAAAGTAAATTCAT

                        
      42965 TTCATGTAAAAA
          1 TTCATGTAAAAA

      42977 ATTTAAGATA


Statistics
Matches: 32,  Mismatches: 4, Indels: 6
        0.76            0.10        0.14

Matches are distributed among these distances:
  25    6  0.19
  26   17  0.53
  28    4  0.12
  29    1  0.03
  30    4  0.12

ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42


Consensus pattern (27 bp):   
TTCATGTAAAAATTAAAGTAAATTCAT

Found at i:44769 original size:18 final size:18

Alignment explanation


    Indices: 44746--44782  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      44736 ACAATTCATA

                              
      44746 TCACTTTCAATTCCAATT
          1 TCACTTTCAATTCCAATT

                     *  *     
      44764 TCACTTTCACTTTCAATT
          1 TCACTTTCAATTCCAATT

             
      44782 T
          1 T

      44783 TGATCACAAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49


Consensus pattern (18 bp):   
TCACTTTCAATTCCAATT
Done.