Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005455.1 Kokia drynarioides strain JFW-HI SEQ_119497, 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: 2652
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32


Found at i:475 original size:3 final size:3

Alignment explanation


    Indices: 469--501  Score: 57
    Period size: 3  Copynumber: 10.7  Consensus size: 3

        459 AATATTTTCT

                                                       
        469 TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA TA
          1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA

        502 TGATTAATAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   3   26  0.90
   4    3  0.10

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (3 bp):   
TAA

Found at i:507 original size:12 final size:12

Alignment explanation


    Indices: 468--511  Score: 54
    Period size: 12  Copynumber: 3.6  Consensus size: 12

        458 AAATATTTTC

                        
        468 TTAATAATAATA
          1 TTAATAATAATA

            *            
        480 ATAATAATAATAA
          1 TTAATAATAAT-A

                         
        493 TTAATAAT-ATGA
          1 TTAATAATAAT-A

                   
        505 TTAATAA
          1 TTAATAA

        512 AAGAAAAAGG


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

Matches are distributed among these distances:
  12   20  0.71
  13    8  0.29

ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39


Consensus pattern (12 bp):   
TTAATAATAATA

Found at i:921 original size:25 final size:25

Alignment explanation


    Indices: 888--946  Score: 109
    Period size: 25  Copynumber: 2.4  Consensus size: 25

        878 ACGGTCGGAC

                *                    
        888 CGACGCGCGTGATCGGGCGCGGCGA
          1 CGACACGCGTGATCGGGCGCGGCGA

                                     
        913 CGACACGCGTGATCGGGCGCGGCGA
          1 CGACACGCGTGATCGGGCGCGGCGA

                     
        938 CGACACGCG
          1 CGACACGCG

        947 ACAACGCGCG


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  25   33  1.00

ACGTcount: A:0.15, C:0.34, G:0.44, T:0.07


Consensus pattern (25 bp):   
CGACACGCGTGATCGGGCGCGGCGA

Found at i:1711 original size:59 final size:59

Alignment explanation


    Indices: 1620--1751  Score: 174
    Period size: 59  Copynumber: 2.2  Consensus size: 59

       1610 AAGCTGTCCA

                                                 *                     
       1620 AAAATTCCATTTTTAGCCCCGAACTTCAAAAAATCCCGTTTTTAACCCTGAAACTTCCC
          1 AAAATTCCATTTTTAGCCCCGAACTTCAAAAAATCCCATTTTTAACCCTGAAACTTCCC

                             ***       *      *        *  *           *
       1679 AAAATTCCATTTTTAGCTTTGAACTTCCAAAAATTCCATTTTTGACTCTGAAACTTCCT
          1 AAAATTCCATTTTTAGCCCCGAACTTCAAAAAATCCCATTTTTAACCCTGAAACTTCCC

                          
       1738 AAAATTACCATTTT
          1 AAAATT-CCATTTT

       1752 ACCCCCGGAT


Statistics
Matches: 63,  Mismatches: 9, Indels: 1
        0.86            0.12        0.01

Matches are distributed among these distances:
  59   56  0.89
  60    7  0.11

ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36


Consensus pattern (59 bp):   
AAAATTCCATTTTTAGCCCCGAACTTCAAAAAATCCCATTTTTAACCCTGAAACTTCCC

Found at i:1730 original size:29 final size:30

Alignment explanation


    Indices: 1616--1751  Score: 143
    Period size: 29  Copynumber: 4.6  Consensus size: 30

       1606 CCCTAAGCTG

                                   *      
       1616 TCCAAAAATTCCATTTTTAGCCCCG-AACT
          1 TCCAAAAATTCCATTTTTAGCCCTGAAACT

              *      *  *      *          
       1645 TCAAAAAATCCCGTTTTTAACCCTGAAACT
          1 TCCAAAAATTCCATTTTTAGCCCTGAAACT

               *                 **       
       1675 TCCCAAAATTCCATTTTTAGCTTTG-AACT
          1 TCCAAAAATTCCATTTTTAGCCCTGAAACT

                                  *        
       1704 TCCAAAAATTCCATTTTT-GACTCTGAAACT
          1 TCCAAAAATTCCATTTTTAG-CCCTGAAACT

               *              
       1734 TCCTAAAATTACCATTTT
          1 TCCAAAAATT-CCATTTT

       1752 ACCCCCGGAT


Statistics
Matches: 88,  Mismatches: 15, Indels: 6
        0.81            0.14        0.06

Matches are distributed among these distances:
  28    1  0.01
  29   45  0.51
  30   35  0.40
  31    7  0.08

ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36


Consensus pattern (30 bp):   
TCCAAAAATTCCATTTTTAGCCCTGAAACT

Found at i:1752 original size:59 final size:60

Alignment explanation


    Indices: 1704--1878  Score: 250
    Period size: 59  Copynumber: 3.0  Consensus size: 60

       1694 GCTTTGAACT

                             *                                      *   
       1704 TCCAAAAATTCCATTTTTGACTCT-GAAACTTCCTAAAATTACCATTTTACCCCCGGATG
          1 TCCAAAAATTCCATTTTCGACTCTCGAAACTTCCTAAAATTACCATTTTACCCCCGAATG

                                             *                       *   
       1763 TCCAAAAACTT-CATTTTCGACT-TCGAAACTTTCTAAAATTACCATTTTACCCCCGGATG
          1 TCCAAAAA-TTCCATTTTCGACTCTCGAAACTTCCTAAAATTACCATTTTACCCCCGAATG

                    *                 *                               
       1822 TCCAAAAACTCCATTTTCGAC-CTCGTAACTTCCTAAAATTACCATTTTTACCCCCGA
          1 TCCAAAAATTCCATTTTCGACTCTCGAAACTTCCTAAAATTACCA-TTTTACCCCCGA

       1879 GACTCCGAAA


Statistics
Matches: 105,  Mismatches: 6, Indels: 9
        0.88            0.05        0.08

Matches are distributed among these distances:
  58    2  0.02
  59   90  0.86
  60   13  0.12

ACGTcount: A:0.30, C:0.29, G:0.07, T:0.33


Consensus pattern (60 bp):   
TCCAAAAATTCCATTTTCGACTCTCGAAACTTCCTAAAATTACCATTTTACCCCCGAATG
Done.