Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011042.1 Kokia drynarioides strain JFW-HI SEQ_126013, 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: 19685
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:7312 original size:21 final size:23

Alignment explanation


    Indices: 7287--7328  Score: 61
    Period size: 21  Copynumber: 1.9  Consensus size: 23

       7277 GAAACACCAA

                                   
       7287 AAAGAAA-AGAAAAAT-CTCACT
          1 AAAGAAATAGAAAAATACTCACT

                        *        
       7308 AAAGAAATAGAAGAATACTCA
          1 AAAGAAATAGAAAAATACTCA

       7329 TAGGCTAGCT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21    7  0.39
  22    7  0.39
  23    4  0.22

ACGTcount: A:0.62, C:0.12, G:0.12, T:0.14


Consensus pattern (23 bp):   
AAAGAAATAGAAAAATACTCACT

Found at i:19610 original size:30 final size:28

Alignment explanation


    Indices: 19572--19683  Score: 82
    Period size: 30  Copynumber: 3.8  Consensus size: 28

      19562 TCTTGTAGGT

                                          
      19572 CCCTAAACTATC-CAAAAATTACATTTTGA
          1 CCCTAAACT-TCACAAAAATTACATTTT-A

                        * *       *        
      19601 CCCTCAAACTTCTCCAAAATTATATTTTTAA
          1 CCCT-AAACTTCACAAAAATTACA-TTTT-A

                         *                
      19632 CCCTAAACTTTCAAAAAAATTACATTATTA
          1 CCCTAAAC-TTCACAAAAATTACATT-TTA

                *       * *       
      19662 CCCCCAAACTTCTCCAAAATTA
          1 -CCCTAAACTTCACAAAAATTA

      19684 TA


Statistics
Matches: 66,  Mismatches: 11, Indels: 11
        0.75            0.12        0.12

Matches are distributed among these distances:
  29    6  0.09
  30   31  0.47
  31   29  0.44

ACGTcount: A:0.40, C:0.27, G:0.01, T:0.32


Consensus pattern (28 bp):   
CCCTAAACTTCACAAAAATTACATTTTA

Found at i:19617 original size:31 final size:30

Alignment explanation


    Indices: 19582--19680  Score: 105
    Period size: 31  Copynumber: 3.2  Consensus size: 30

      19572 CCCTAAACTA

                                           
      19582 TCCAAAAATTACATTTTGACCCTCAAACTTC
          1 TCCAAAAATTACATTTT-ACCCTCAAACTTC

                       *                    
      19613 TCC-AAAATTATATTTTTAACCCT-AAACTT-
          1 TCCAAAAATTACA-TTTT-ACCCTCAAACTTC

               *                   *        
      19642 TCAAAAAAATTACATTATTACCCCCAAACTTC
          1 TC-CAAAAATTACATT-TTACCCTCAAACTTC

                   
      19674 TCCAAAA
          1 TCCAAAA

      19681 TTATA


Statistics
Matches: 56,  Mismatches: 6, Indels: 12
        0.76            0.08        0.16

Matches are distributed among these distances:
  29    2  0.04
  30   20  0.36
  31   32  0.57
  32    2  0.04

ACGTcount: A:0.40, C:0.26, G:0.01, T:0.32


Consensus pattern (30 bp):   
TCCAAAAATTACATTTTACCCTCAAACTTC

Found at i:19670 original size:61 final size:60

Alignment explanation


    Indices: 19572--19685  Score: 176
    Period size: 61  Copynumber: 1.9  Consensus size: 60

      19562 TCTTGTAGGT

                        *                   *                           
      19572 CCCTAAACTATCCAAAAATTACATTTTGACCCTCAAACTTCTCCAAAATTATATTTTTAA
          1 CCCTAAACTATCAAAAAATTACATTTTGACCCCCAAACTTCTCCAAAATTATATTTTTAA

                     *                                             
      19632 CCCTAAACTTTCAAAAAAATTACATTATT-ACCCCCAAACTTCTCCAAAATTATA
          1 CCCTAAACTATC-AAAAAATTACATT-TTGACCCCCAAACTTCTCCAAAATTATA


Statistics
Matches: 49,  Mismatches: 3, Indels: 3
        0.89            0.05        0.05

Matches are distributed among these distances:
  60   11  0.22
  61   36  0.73
  62    2  0.04

ACGTcount: A:0.40, C:0.26, G:0.01, T:0.32


Consensus pattern (60 bp):   
CCCTAAACTATCAAAAAATTACATTTTGACCCCCAAACTTCTCCAAAATTATATTTTTAA
Done.