Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000795.1 Kokia drynarioides strain JFW-HI SEQ_111865, 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: 2202
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35


Found at i:930 original size:24 final size:26

Alignment explanation


    Indices: 903--950  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

        893 ATAGAAATAT

                                       
        903 AAATG-TGATATATGA-A-ATTATGAG
          1 AAATGATGA-ATATGAGAGATTATGAG

                                    
        927 AAATGATGAATATGAGAGATTATG
          1 AAATGATGAATATGAGAGATTATG

        951 CCCATGTAGA


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

Matches are distributed among these distances:
  24   11  0.52
  25    4  0.19
  26    6  0.29

ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31


Consensus pattern (26 bp):   
AAATGATGAATATGAGAGATTATGAG

Found at i:1060 original size:23 final size:23

Alignment explanation


    Indices: 1034--1106  Score: 103
    Period size: 23  Copynumber: 3.2  Consensus size: 23

       1024 AGCACGTTTC

                                   
       1034 GTGCCCTCTGTTCAGCACTATGT
          1 GTGCCCTCTGTTCAGCACTATGT

                           *       
       1057 GTGCCCTCTGTTCAGTACTATGT
          1 GTGCCCTCTGTTCAGCACTATGT

                 *      *      *   
       1080 GTG-CTTCTGTTTAGCACTTTGT
          1 GTGCCCTCTGTTCAGCACTATGT

                 
       1102 GTGCC
          1 GTGCC

       1107 TACTGTTTCC


Statistics
Matches: 44,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  22   18  0.41
  23   26  0.59

ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40


Consensus pattern (23 bp):   
GTGCCCTCTGTTCAGCACTATGT

Found at i:2064 original size:28 final size:28

Alignment explanation


    Indices: 2032--2087  Score: 67
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       2022 ATTTTTATCT

                 *                       
       2032 AAAAAAAATCAAAATAATTTTCAAAATTG
          1 AAAAATAATCAAAA-AATTTTCAAAATTG

                   * * *               
       2061 AAAAATACTTATAAAATTTTCAAAATT
          1 AAAAATAATCAAAAAATTTTCAAAATT

       2088 TATATTTTAA


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  28   13  0.57
  29   10  0.43

ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32


Consensus pattern (28 bp):   
AAAAATAATCAAAAAATTTTCAAAATTG

Found at i:2123 original size:22 final size:19

Alignment explanation


    Indices: 2093--2151  Score: 68
    Period size: 22  Copynumber: 3.0  Consensus size: 19

       2083 AAATTTATAT

                                
       2093 TTTAAAAAAAATCTAAAATA
          1 TTTAAAAAAAAT-TAAAATA

                                  
       2113 TATATAAAAAAAAGTTAAAAT-
          1 T-T-TAAAAAAAA-TTAAAATA

                               
       2134 TTT-AAAAAAATTAAAATA
          1 TTTAAAAAAAATTAAAATA

       2152 ATAATTTTGG


Statistics
Matches: 35,  Mismatches: 0, Indels: 10
        0.78            0.00        0.22

Matches are distributed among these distances:
  17    7  0.20
  18    7  0.20
  19    1  0.03
  20    2  0.06
  21    2  0.06
  22   15  0.43
  23    1  0.03

ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31


Consensus pattern (19 bp):   
TTTAAAAAAAATTAAAATA
Done.