Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003050.1 Kokia drynarioides strain JFW-HI SEQ_115577, 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: 24822
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31

Warning! 51 characters in sequence are not A, C, G, or T


Found at i:1298 original size:2 final size:2

Alignment explanation


    Indices: 1291--1321  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       1281 ATCTCCCTCC

                                                          
       1291 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C

       1322 AAACACACAG


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

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48


Consensus pattern (2 bp):   
CT

Found at i:2728 original size:70 final size:69

Alignment explanation


    Indices: 2633--2822  Score: 197
    Period size: 61  Copynumber: 2.8  Consensus size: 69

       2623 TCGATAAACA

                                           * *                *              
       2633 ATTATCATTTTAACTTAATTATTTTTATTTTTATTTTAAAAAAAAATAAATATTTATCAAAACAA
          1 ATTATCATTTTAACTTAATTATTTTTATTTTAACTTT--AAAAAAATAAACATTTATCAAAACAA

                  
       2698 CGTAGT
         64 CGTAGT

                            *                                                
       2704 ATTATC-TTTTAACTTTA-TAGTTTTTATTTTAACTTTAAAAAAATAAACATTTATC--AA-AAC
          1 ATTATCATTTTAACTTAATTA-TTTTTATTTTAACTTTAAAAAAATAAACATTTATCAAAACAAC

                 
       2764 --A--
         65 GTAGT

                                                              *          
       2765 ATTA-C-TTTTAAACTTAA-TAGTTTTTATTTTAACTTTAAAAAAGATAAGCATTTATCAA
          1 ATTATCATTTT-AACTTAATTA-TTTTTATTTTAACTTTAAAAAA-ATAAACATTTATCAA

       2823 GACATTTATT


Statistics
Matches: 108,  Mismatches: 6, Indels: 17
        0.82            0.05        0.13

Matches are distributed among these distances:
  60    5  0.05
  61   35  0.32
  62   12  0.11
  63    1  0.01
  65    3  0.03
  66    2  0.02
  68   18  0.17
  69    2  0.02
  70   24  0.22
  71    6  0.06

ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46


Consensus pattern (69 bp):   
ATTATCATTTTAACTTAATTATTTTTATTTTAACTTTAAAAAAATAAACATTTATCAAAACAACG
TAGT

Found at i:2792 original size:61 final size:62

Alignment explanation


    Indices: 2704--2836  Score: 200
    Period size: 61  Copynumber: 2.2  Consensus size: 62

       2694 ACAACGTAGT

                            *                                              
       2704 ATTATCTTTT-AACTTTATAGTTTTTATTTTAACTTTAAAAAA-ATAAACATTTATCAAAACA
          1 ATTA-CTTTTAAACTTAATAGTTTTTATTTTAACTTTAAAAAAGATAAACATTTATCAAAACA

                                                           *          *   
       2765 ATTACTTTTAAACTTAATAGTTTTTATTTTAACTTTAAAAAAGATAAGCATTTATCAAGACA
          1 ATTACTTTTAAACTTAATAGTTTTTATTTTAACTTTAAAAAAGATAAACATTTATCAAAACA

            *          
       2827 TTTA-TTTTAA
          1 ATTACTTTTAA

       2837 CGTTGTCAAT


Statistics
Matches: 66,  Mismatches: 4, Indels: 4
        0.89            0.05        0.05

Matches are distributed among these distances:
  60    5  0.08
  61   41  0.62
  62   20  0.30

ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46


Consensus pattern (62 bp):   
ATTACTTTTAAACTTAATAGTTTTTATTTTAACTTTAAAAAAGATAAACATTTATCAAAACA

Found at i:6994 original size:18 final size:19

Alignment explanation


    Indices: 6960--6995  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       6950 ACATATCCTA

                               
       6960 TTTAATAATTCAATTTTTG
          1 TTTAATAATTCAATTTTTG

                  *           
       6979 TTTAATTATT-AATTTTT
          1 TTTAATAATTCAATTTTT

       6996 ATACGGTATT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64


Consensus pattern (19 bp):   
TTTAATAATTCAATTTTTG

Found at i:16033 original size:27 final size:27

Alignment explanation


    Indices: 16003--16056  Score: 108
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      15993 GCTTAATGAG

                                       
      16003 AACGGAAGCTCACAAAAGTCAAACAAT
          1 AACGGAAGCTCACAAAAGTCAAACAAT

                                       
      16030 AACGGAAGCTCACAAAAGTCAAACAAT
          1 AACGGAAGCTCACAAAAGTCAAACAAT

      16057 CACCAGATGG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   27  1.00

ACGTcount: A:0.52, C:0.22, G:0.15, T:0.11


Consensus pattern (27 bp):   
AACGGAAGCTCACAAAAGTCAAACAAT
Done.