Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012120.1 Kokia drynarioides strain JFW-HI SEQ_127119, 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: 5965
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:721 original size:29 final size:32

Alignment explanation


    Indices: 670--739  Score: 85
    Period size: 29  Copynumber: 2.3  Consensus size: 32

        660 TGTTTGAAGG

                                            
        670 TGGTACCTGAAGTTTCAAAATG-T-C-CAATA
          1 TGGTACCTGAAGTTTCAAAATGTTACACAATA

                               *            *
        699 TGGTACCTGAAGTTT-AATTATGTTACACAATC
          1 TGGTACCTGAAGTTTCAA-AATGTTACACAATA

                     
        731 TGGTACCTG
          1 TGGTACCTG

        740 TTGGTAAAGT


Statistics
Matches: 35,  Mismatches: 2, Indels: 5
        0.83            0.05        0.12

Matches are distributed among these distances:
  28    2  0.06
  29   18  0.51
  30    1  0.03
  31    1  0.03
  32   13  0.37

ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Consensus pattern (32 bp):   
TGGTACCTGAAGTTTCAAAATGTTACACAATA

Found at i:913 original size:15 final size:15

Alignment explanation


    Indices: 893--942  Score: 64
    Period size: 15  Copynumber: 3.2  Consensus size: 15

        883 AAAAAGTCGG

                      * *  
        893 TTCTTTCTTTTCTTC
          1 TTCTTTCTTTCCATC

                           
        908 TTCTTTCTTTCCATC
          1 TTCTTTCTTTCCATC

                             
        923 TTCTTCTTCTTTCCATC
          1 TTC-T-TTCTTTCCATC

               
        940 TTC
          1 TTC

        943 AAAAAGCCGG


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  15   16  0.52
  16    1  0.03
  17   14  0.45

ACGTcount: A:0.04, C:0.32, G:0.00, T:0.64


Consensus pattern (15 bp):   
TTCTTTCTTTCCATC

Found at i:934 original size:17 final size:18

Alignment explanation


    Indices: 903--942  Score: 73
    Period size: 17  Copynumber: 2.3  Consensus size: 18

        893 TTCTTTCTTT

                              
        903 TCTTCTTCTTTCTTTCCA
          1 TCTTCTTCTTTCTTTCCA

                              
        921 TCTTCTTC-TTCTTTCCA
          1 TCTTCTTCTTTCTTTCCA

                 
        938 TCTTC
          1 TCTTC

        943 AAAAAGCCGG


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  17   14  0.64
  18    8  0.36

ACGTcount: A:0.05, C:0.35, G:0.00, T:0.60


Consensus pattern (18 bp):   
TCTTCTTCTTTCTTTCCA

Found at i:2009 original size:3 final size:3

Alignment explanation


    Indices: 2003--2034  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       1993 ATTTTAGTTG

                                                      
       2003 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

       2035 AGCGCATTAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (3 bp):   
AAT

Done.