Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001321.1 Kokia drynarioides strain JFW-HI SEQ_112751, 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: 34255
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:52 original size:25 final size:24

Alignment explanation


    Indices: 24--74  Score: 59
    Period size: 24  Copynumber: 2.1  Consensus size: 24

         14 TAATATAATT

                         *            
         24 ATTATTAAAATATGA-ATTAGTAAAA
          1 ATTA-TAAAATATAATATTAG-AAAA

                   *                
         49 ATTATAATATATAATATTAGAAAA
          1 ATTATAAAATATAATATTAGAAAA

              
         73 AT
          1 AT

         75 AATACATAAC


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  24   14  0.61
  25    9  0.39

ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37


Consensus pattern (24 bp):   
ATTATAAAATATAATATTAGAAAA

Found at i:3621 original size:21 final size:21

Alignment explanation


    Indices: 3568--3621  Score: 51
    Period size: 20  Copynumber: 2.6  Consensus size: 21

       3558 TTCAAAATCT

                                  
       3568 TAAACTTTAAT-TTCTTTTATA
          1 TAAA-TTTAATATTCTTTTATA

                    *              
       3589 T-AATTTGTATATT-TTTTATGA
          1 TAAATTT-AATATTCTTTTAT-A

                        
       3610 TAAATTTAATAT
          1 TAAATTTAATAT

       3622 AGTTTAATTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 8
        0.73            0.05        0.22

Matches are distributed among these distances:
  19    3  0.11
  20   10  0.37
  21    9  0.33
  22    5  0.19

ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57


Consensus pattern (21 bp):   
TAAATTTAATATTCTTTTATA

Found at i:19904 original size:53 final size:53

Alignment explanation


    Indices: 19844--19949  Score: 194
    Period size: 53  Copynumber: 2.0  Consensus size: 53

      19834 TCAATGCTGC

                             *                                   
      19844 AATTTCATTTACTCTATGTATATCTATCTGCCCTTTTGCAAACCATCTCCATT
          1 AATTTCATTTACTCTATATATATCTATCTGCCCTTTTGCAAACCATCTCCATT

                         *                                       
      19897 AATTTCATTTACTTTATATATATCTATCTGCCCTTTTGCAAACCATCTCCATT
          1 AATTTCATTTACTCTATATATATCTATCTGCCCTTTTGCAAACCATCTCCATT

      19950 GCCATTAATA


Statistics
Matches: 51,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  53   51  1.00

ACGTcount: A:0.25, C:0.25, G:0.05, T:0.44


Consensus pattern (53 bp):   
AATTTCATTTACTCTATATATATCTATCTGCCCTTTTGCAAACCATCTCCATT

Found at i:22875 original size:37 final size:37

Alignment explanation


    Indices: 22825--22900  Score: 152
    Period size: 37  Copynumber: 2.1  Consensus size: 37

      22815 AATTGAAAAG

                                                 
      22825 TTAATTTAATTTTAGGCAACTGGTTTGTACTAATTTA
          1 TTAATTTAATTTTAGGCAACTGGTTTGTACTAATTTA

                                                 
      22862 TTAATTTAATTTTAGGCAACTGGTTTGTACTAATTTA
          1 TTAATTTAATTTTAGGCAACTGGTTTGTACTAATTTA

              
      22899 TT
          1 TT

      22901 TACGTATAAA


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  37   39  1.00

ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50


Consensus pattern (37 bp):   
TTAATTTAATTTTAGGCAACTGGTTTGTACTAATTTA

Found at i:22968 original size:32 final size:32

Alignment explanation


    Indices: 22932--22992  Score: 77
    Period size: 32  Copynumber: 1.9  Consensus size: 32

      22922 TTAATTCTTA

                          *        *        
      22932 TTAATACATTACATTTAAATTATTGAACTATG
          1 TTAATACATTACATATAAATTATAGAACTATG

                 **   *                  
      22964 TTAATGTATTGCATATAAATTATAGAACT
          1 TTAATACATTACATATAAATTATAGAACT

      22993 GTTAATTTTT


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  32   24  1.00

ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43


Consensus pattern (32 bp):   
TTAATACATTACATATAAATTATAGAACTATG

Found at i:23427 original size:23 final size:23

Alignment explanation


    Indices: 23395--23445  Score: 68
    Period size: 26  Copynumber: 2.1  Consensus size: 23

      23385 TTTATATCTT

                                   
      23395 ATTATTAAAT-ATTAAGAAGTTA
          1 ATTATTAAATAATTAAGAAGTTA

                                      
      23417 ATTATGTAAATAAAATTAAGAAGTTA
          1 ATTAT-TAAAT--AATTAAGAAGTTA

               
      23443 ATT
          1 ATT

      23446 CAAATAACTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  22    5  0.20
  23    5  0.20
  26   15  0.60

ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39


Consensus pattern (23 bp):   
ATTATTAAATAATTAAGAAGTTA

Found at i:27651 original size:14 final size:14

Alignment explanation


    Indices: 27632--27658  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      27622 TTTAAAATTA

                          
      27632 AATTAAATTAAAAG
          1 AATTAAATTAAAAG

                         
      27646 AATTAAATTAAAA
          1 AATTAAATTAAAA

      27659 ATTTTCAAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30


Consensus pattern (14 bp):   
AATTAAATTAAAAG
Done.