Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000238.1 Kokia drynarioides strain JFW-HI SEQ_110962, 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: 8791
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36

Warning! 76 characters in sequence are not A, C, G, or T


Found at i:1920 original size:30 final size:29

Alignment explanation


    Indices: 1860--1920  Score: 79
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       1850 TTAAATTAGT

                                  *      
       1860 AAAGATAAAATTACACTTTATCCCTTAAA
          1 AAAGATAAAATTACACTTTATCACTTAAA

                                     *     
       1889 AAAGATAAAATTACGA-TTTAATCATTTAAA
          1 AAAGATAAAATTAC-ACTTT-ATCACTTAAA

              
       1919 AA
          1 AA

       1921 TTACATTTTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  29   17  0.61
  30   11  0.39

ACGTcount: A:0.52, C:0.11, G:0.05, T:0.31


Consensus pattern (29 bp):   
AAAGATAAAATTACACTTTATCACTTAAA

Found at i:1953 original size:22 final size:21

Alignment explanation


    Indices: 1894--1955  Score: 54
    Period size: 22  Copynumber: 2.8  Consensus size: 21

       1884 TTAAAAAAGA

                     *     *     
       1894 TAAAATTACGATTTAATCATT
          1 TAAAATTACAATTTACTCATT

                        *          
       1915 TAAAAATTACATTTTTACT-ATT
          1 T-AAAATTACA-ATTTACTCATT

                               
       1937 GTAAAACTTACAATTTACT
          1 -TAAAA-TTACAATTTACT

       1956 TTCGACCTCC


Statistics
Matches: 33,  Mismatches: 4, Indels: 7
        0.75            0.09        0.16

Matches are distributed among these distances:
  21    1  0.03
  22   21  0.64
  23   11  0.33

ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44


Consensus pattern (21 bp):   
TAAAATTACAATTTACTCATT

Found at i:8531 original size:40 final size:40

Alignment explanation


    Indices: 8486--8583  Score: 130
    Period size: 40  Copynumber: 2.4  Consensus size: 40

       8476 AAAAATAAAA

                                                       
       8486 TTATAAAAATTATAATAAAATTA-AA-AAAATTAG-AAATTTT
          1 TTATAAAAATTATAA-AAAATTATAATAAAATT-GTAAA-TTT

                      *                             
       8526 TTATAAAAATCATAAAAAATTATAATAAAATTGTAAATTT
          1 TTATAAAAATTATAAAAAATTATAATAAAATTGTAAATTT

                              
       8566 TTATAAAATATTATAAAA
          1 TTATAAAA-ATTATAAAA

       8584 TGCATAAAAA


Statistics
Matches: 52,  Mismatches: 2, Indels: 7
        0.85            0.03        0.11

Matches are distributed among these distances:
  39    7  0.13
  40   28  0.54
  41   17  0.33

ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38


Consensus pattern (40 bp):   
TTATAAAAATTATAAAAAATTATAATAAAATTGTAAATTT

Found at i:8555 original size:11 final size:10

Alignment explanation


    Indices: 8482--8583  Score: 66
    Period size: 10  Copynumber: 10.2  Consensus size: 10

       8472 CAATAAAAAT

                      
       8482 AAAATTAT-A
          1 AAAATTATAA

                      
       8491 AAAATTATAA
          1 AAAATTATAA

                       
       8501 TAAAATTA-AA
          1 -AAAATTATAA

                    * 
       8511 AAAATTA-GA
          1 AAAATTATAA

              **  *    
       8520 AATTTTTTATA
          1 AAAATTATA-A

                 *    
       8531 AAAATCATAA
          1 AAAATTATAA

                      
       8541 AAAATTATAA
          1 AAAATTATAA

                   *   
       8551 TAAAATTGTAA
          1 -AAAATTATAA

             ***      
       8562 ATTTTTATAA
          1 AAAATTATAA

              *       
       8572 AATATTATAA
          1 AAAATTATAA

              
       8582 AA
          1 AA

       8584 TGCATAAAAA


Statistics
Matches: 71,  Mismatches: 17, Indels: 9
        0.73            0.18        0.09

Matches are distributed among these distances:
   9   20  0.28
  10   29  0.41
  11   22  0.31

ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36


Consensus pattern (10 bp):   
AAAATTATAA

Done.