Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007964.1 Kokia drynarioides strain JFW-HI SEQ_122612, 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: 5841
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:1880 original size:16 final size:16

Alignment explanation


    Indices: 1854--1892  Score: 53
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       1844 AATTTGATTA

                             
       1854 AAAATATTAAAAAT-TC
          1 AAAA-ATTAAAAATCTC

                             
       1870 AACAAATTAAAAATCTC
          1 AA-AAATTAAAAATCTC

                  
       1887 AAAAAT
          1 AAAAAT

       1893 CTCGGTTCAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  16   15  0.71
  17    6  0.29

ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26


Consensus pattern (16 bp):   
AAAAATTAAAAATCTC

Found at i:3254 original size:29 final size:29

Alignment explanation


    Indices: 3211--3276  Score: 91
    Period size: 30  Copynumber: 2.3  Consensus size: 29

       3201 TTAGATTTTT

                                     **  
       3211 TTAAAA-TTGGAAAAAAAATTT-AAGTCC
          1 TTAAAAGTTGGAAAAAAAATTTAAAACCC

                                          
       3238 TTAAAAGTTGGTAAAAAAAATTTAAAACCC
          1 TTAAAAGTTGG-AAAAAAAATTTAAAACCC

                     
       3268 TTAAAAGTT
          1 TTAAAAGTT

       3277 AAATTTTTTG


Statistics
Matches: 34,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  27    6  0.18
  28    4  0.12
  29   11  0.32
  30   13  0.38

ACGTcount: A:0.52, C:0.08, G:0.11, T:0.30


Consensus pattern (29 bp):   
TTAAAAGTTGGAAAAAAAATTTAAAACCC

Found at i:3878 original size:20 final size:22

Alignment explanation


    Indices: 3831--3881  Score: 67
    Period size: 20  Copynumber: 2.5  Consensus size: 22

       3821 AATCGATACC

                                  
       3831 AAAATTTT-TAA--TATTATAT
          1 AAAATTTTCTAATGTATTATAT

                                  
       3850 AAAATTTTCTAATGTATTAT-T
          1 AAAATTTTCTAATGTATTATAT

                        
       3871 AAAA-TTTCTAA
          1 AAAATTTTCTAA

       3882 ATAATATCAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
  19    8  0.28
  20   10  0.34
  21    5  0.17
  22    6  0.21

ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49


Consensus pattern (22 bp):   
AAAATTTTCTAATGTATTATAT

Found at i:3972 original size:77 final size:78

Alignment explanation


    Indices: 3830--3973  Score: 177
    Period size: 77  Copynumber: 1.9  Consensus size: 78

       3820 TAATCGATAC

                 *        *                  *  *   *                 *      
       3830 CAAAATTTTTAATATTATATAAAATTTTCTAATGTATTATTAAAATTTCTAAATAATATCAATAT
          1 CAAAAATTTTAATAGTATATAAAATTTTCTAATATAATATCAAAATTTCTAAATAATACCAATAT

                         
       3895 TTGTATGTGATGT
         66 TTGTATGTGATGT

                                   *                                      *  
       3908 CAAAAATTTTAA-AGTATACTAATATTTT-TAATATAATATCAAAATTTCTAACA-AATACCGAT
          1 CAAAAATTTTAATAGTATA-TAAAATTTTCTAATATAATATCAAAATTTCTAA-ATAATACCAAT

                
       3970 ATTT
         64 ATTT

       3974 TTTACATGAT


Statistics
Matches: 56,  Mismatches: 8, Indels: 5
        0.81            0.12        0.07

Matches are distributed among these distances:
  77   36  0.64
  78   20  0.36

ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44


Consensus pattern (78 bp):   
CAAAAATTTTAATAGTATATAAAATTTTCTAATATAATATCAAAATTTCTAAATAATACCAATAT
TTGTATGTGATGT

Found at i:4013 original size:77 final size:75

Alignment explanation


    Indices: 3812--4014  Score: 169
    Period size: 77  Copynumber: 2.6  Consensus size: 75

       3802 AAATTTTACT

                *            *                             *    *  *   *     
       3812 AATACTTTTAATCGATACCAAAATTTTTAATATTATATA-AAATTTTCTAATGTATTATTAAAAT
          1 AATATTTTTAAT-GATATCAAAATTTTT-A-ATTA-ATACAAATTTTTTAATATAATATCAAAAT

                        * 
       3876 TTCTAAATAATATC
         62 TTCTAAATAATACC

                   *   *    *           *  *      *                          
       3890 AATATTTGTATGTGATGTCAAAAATTTTAAAGT-ATACTAATATTTTTAATATAATATCAAAATT
          1 AATATTTTTA-ATGATATC-AAAATTTTTAATTAATACAAAT-TTTTTAATATAATATCAAAATT

                          
       3954 TCTAACA-AATACC
         63 TCTAA-ATAATACC

            *                                               
       3967 GATATTTTTTACATGATATCAAAATTTTTAATTAATACAAATTTTTTA
          1 AATA-TTTTTA-ATGATATCAAAATTTTTAATTAATACAAATTTTTTA

       4015 TTCGAATACT


Statistics
Matches: 97,  Mismatches: 21, Indels: 15
        0.73            0.16        0.11

Matches are distributed among these distances:
  75    3  0.03
  76    3  0.03
  77   50  0.52
  78   32  0.33
  79    9  0.09

ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44


Consensus pattern (75 bp):   
AATATTTTTAATGATATCAAAATTTTTAATTAATACAAATTTTTTAATATAATATCAAAATTTCT
AAATAATACC
Done.