Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008130.1 Kokia drynarioides strain JFW-HI SEQ_122788, 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: 19382
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:5434 original size:22 final size:22

Alignment explanation


    Indices: 5409--5475  Score: 125
    Period size: 22  Copynumber: 3.0  Consensus size: 22

       5399 AGATATACCG

                       *          
       5409 TATCGATAGCTAAGAATAACGT
          1 TATCGATAGCTGAGAATAACGT

                                  
       5431 TATCGATAGCTGAGAATAACGT
          1 TATCGATAGCTGAGAATAACGT

                                  
       5453 TATCGATAGCTGAGAATAACGT
          1 TATCGATAGCTGAGAATAACGT

             
       5475 T
          1 T

       5476 GTATACTGGT


Statistics
Matches: 44,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  22   44  1.00

ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28


Consensus pattern (22 bp):   
TATCGATAGCTGAGAATAACGT

Found at i:13899 original size:9 final size:9

Alignment explanation


    Indices: 13885--13915  Score: 62
    Period size: 9  Copynumber: 3.4  Consensus size: 9

      13875 AACATTAATT

                     
      13885 AAATTTTTA
          1 AAATTTTTA

                     
      13894 AAATTTTTA
          1 AAATTTTTA

                     
      13903 AAATTTTTA
          1 AAATTTTTA

                
      13912 AAAT
          1 AAAT

      13916 ATATAAAACT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   22  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (9 bp):   
AAATTTTTA

Found at i:13922 original size:18 final size:18

Alignment explanation


    Indices: 13885--13923  Score: 60
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      13875 AACATTAATT

                         * *  
      13885 AAATTTTTAAAATTTTTA
          1 AAATTTTTAAAATATATA

                              
      13903 AAATTTTTAAAATATATA
          1 AAATTTTTAAAATATATA

               
      13921 AAA
          1 AAA

      13924 CTATTTTTTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (18 bp):   
AAATTTTTAAAATATATA

Found at i:13944 original size:29 final size:30

Alignment explanation


    Indices: 13897--13957  Score: 72
    Period size: 29  Copynumber: 2.0  Consensus size: 30

      13887 ATTTTTAAAA

                         *                  
      13897 TTTTTAAAATTTTTAAAAT-ATATAAAACTAT
          1 TTTTTAAAA-TTTAAAAATCAT-TAAAACTAT

                                      *   
      13928 TTTTTAAAA-TTAAAAATCATTAAAATTAT
          1 TTTTTAAAATTTAAAAATCATTAAAACTAT

             
      13957 T
          1 T

      13958 AAAAACTATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  29   16  0.59
  30    2  0.07
  31    9  0.33

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48


Consensus pattern (30 bp):   
TTTTTAAAATTTAAAAATCATTAAAACTAT

Found at i:13958 original size:9 final size:9

Alignment explanation


    Indices: 13885--13961  Score: 50
    Period size: 9  Copynumber: 8.3  Consensus size: 9

      13875 AACATTAATT

                 *   
      13885 AAATTTTTA
          1 AAATTATTA

                 *   
      13894 AAATTTTTA
          1 AAATTATTA

                 *   
      13903 AAATTTTTA
          1 AAATTATTA

                    * 
      13912 AAATATATAA
          1 AAAT-TATTA

                    *   
      13922 AACTATTTTTTA
          1 AA--A-TTATTA

                     
      13934 AAATTA--A
          1 AAATTATTA

                *    
      13941 AAATCATTA
          1 AAATTATTA

                     
      13950 AAATTATTA
          1 AAATTATTA

               
      13959 AAA
          1 AAA

      13962 ACTATTTTTT


Statistics
Matches: 55,  Mismatches: 7, Indels: 12
        0.74            0.09        0.16

Matches are distributed among these distances:
   7    6  0.11
   9   36  0.65
  10    6  0.11
  12    6  0.11
  13    1  0.02

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


Consensus pattern (9 bp):   
AAATTATTA
Done.