Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009803.1 Kokia drynarioides strain JFW-HI SEQ_124524, 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: 7355
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:3659 original size:10 final size:9

Alignment explanation


    Indices: 3641--3708  Score: 50
    Period size: 9  Copynumber: 7.6  Consensus size: 9

       3631 GATTTTATGG

                     
       3641 TTTTTAAAT
          1 TTTTTAAAT

                      
       3650 TTTTTAAAAT
          1 TTTTT-AAAT

               *  *  
       3660 TTTATATAT
          1 TTTTTAAAT

                  *  
       3669 TTTTTATA-
          1 TTTTTAAAT

               *      
       3677 TTTGTATAA-
          1 TTTTTA-AAT

             *   *   
       3686 TCTTTGAAT
          1 TTTTTAAAT

                     
       3695 TTTTTAAAT
          1 TTTTTAAAT

                 
       3704 TTTTT
          1 TTTTT

       3709 TATAAAAATT


Statistics
Matches: 46,  Mismatches: 10, Indels: 6
        0.74            0.16        0.10

Matches are distributed among these distances:
   8    7  0.15
   9   31  0.67
  10    8  0.17

ACGTcount: A:0.29, C:0.01, G:0.03, T:0.66


Consensus pattern (9 bp):   
TTTTTAAAT

Found at i:4665 original size:56 final size:59

Alignment explanation


    Indices: 4570--4679  Score: 163
    Period size: 56  Copynumber: 1.9  Consensus size: 59

       4560 CACTTTAATG

                                         ** *              *           
       4570 TTAAATTAATATAATACTTATCAAGATAAGTATTAAATTAAATTTAATATTAAATATTA
          1 TTAAATTAATATAATACTTATCAAGATAAACACTAAATTAAATTTAACATTAAATATTA

                                                                  
       4629 TTAAATTAATATAAT-C-TA-CAAGATAAACACTAAATTAAATTTAACATTAAA
          1 TTAAATTAATATAATACTTATCAAGATAAACACTAAATTAAATTTAACATTAAA

       4680 ATAATTACTT


Statistics
Matches: 47,  Mismatches: 4, Indels: 3
        0.87            0.07        0.06

Matches are distributed among these distances:
  56   29  0.62
  57    2  0.04
  58    1  0.02
  59   15  0.32

ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38


Consensus pattern (59 bp):   
TTAAATTAATATAATACTTATCAAGATAAACACTAAATTAAATTTAACATTAAATATTA

Found at i:5725 original size:20 final size:21

Alignment explanation


    Indices: 5695--5736  Score: 61
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       5685 ACATTCGTCT

                                  
       5695 TAAATTAACATTATT-TAGATA
          1 TAAATTAACA-TATTATAGATA

                                 
       5716 TAAA-TAACATATTATAGATA
          1 TAAATTAACATATTATAGATA

             
       5736 T
          1 T

       5737 TTAGGTAGAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  19    4  0.20
  20   12  0.60
  21    4  0.20

ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40


Consensus pattern (21 bp):   
TAAATTAACATATTATAGATA

Found at i:6168 original size:43 final size:43

Alignment explanation


    Indices: 6109--6314  Score: 213
    Period size: 43  Copynumber: 4.8  Consensus size: 43

       6099 TTATGTGGAA

                 *     *                    *          
       6109 AAACGTCGCTATAGAACATGGTCTTTAGCGGCACTTCTTCCAC
          1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTTCCAC

                    *                                   
       6152 AAACGCCGTTAAAGAACATGGTCTTTAGCGGCGCTTAC--CCAC
          1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTT-CTTCCAC

              **           *    *          *    *       
       6194 AATTGCCGCTAAAGACCATGTTCTTTAGCGGTG-TTTTTCCCAC
          1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTT-CCAC

                   *        *          *  *        *    
       6237 AAACGCCCCTAAAGAATATGGTCTTTACCGACGCTT-TCCCCAC
          1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCT-TCCAC

                                       *       
       6280 AAACGCCGCTAAAGAACATGGTCTTTAACGGCGCT
          1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCT

       6315 NTTTAGTGGC


Statistics
Matches: 132,  Mismatches: 25, Indels: 12
        0.78            0.15        0.07

Matches are distributed among these distances:
  41    2  0.02
  42   31  0.23
  43   96  0.73
  44    3  0.02

ACGTcount: A:0.27, C:0.29, G:0.19, T:0.26


Consensus pattern (43 bp):   
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTCTTCCAC

Found at i:6258 original size:85 final size:86

Alignment explanation


    Indices: 6109--6306  Score: 238
    Period size: 85  Copynumber: 2.3  Consensus size: 86

       6099 TTATGTGGAA

                 *     *                    **  *              **            
       6109 AAACGTCGCTATAGAACATGGTCTTTAGCGGCACTTCTT-CCACAAACGCCGTTAAAGAACATGG
          1 AAACGCCGCTAAAGAACATGGTCTTTAGCGG-TGTTTTTCCCACAAACGCCCCTAAAGAACATGG

                  *  *            
       6173 TCTTTAGCGGCGC-TTACCCAC
         65 TCTTTACCGACGCTTTACCCAC

              **           *    *                                      *     
       6194 AATTGCCGCTAAAGACCATGTTCTTTAGCGGTGTTTTTCCCACAAACGCCCCTAAAGAATATGGT
          1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGTTTTTCCCACAAACGCCCCTAAAGAACATGGT

                           *     
       6259 CTTTACCGACGCTTTCCCCAC
         66 CTTTACCGACGCTTTACCCAC

                                       
       6280 AAACGCCGCTAAAGAACATGGTCTTTA
          1 AAACGCCGCTAAAGAACATGGTCTTTA

       6307 ACGGCGCTNT


Statistics
Matches: 92,  Mismatches: 19, Indels: 3
        0.81            0.17        0.03

Matches are distributed among these distances:
  84    4  0.04
  85   58  0.63
  86   30  0.33

ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26


Consensus pattern (86 bp):   
AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGTTTTTCCCACAAACGCCCCTAAAGAACATGGT
CTTTACCGACGCTTTACCCAC
Done.