Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004862.1 Kokia drynarioides strain JFW-HI SEQ_118529, 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: 7950
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36


Found at i:1789 original size:19 final size:19

Alignment explanation


    Indices: 1767--1818  Score: 52
    Period size: 20  Copynumber: 2.7  Consensus size: 19

       1757 AATTATGAAC

                             * *
       1767 TTTTTATAAATTTTGATTTT
          1 TTTTTAT-AATTTTGATGTA

                     *          
       1787 TTTTTATTATTTTTGA-GTA
          1 TTTTTA-TAATTTTGATGTA

                         
       1806 TTTTTATAATTTT
          1 TTTTTATAATTTT

       1819 TTAAATTATT


Statistics
Matches: 27,  Mismatches: 4, Indels: 4
        0.77            0.11        0.11

Matches are distributed among these distances:
  18    6  0.22
  19    7  0.26
  20   13  0.48
  21    1  0.04

ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71


Consensus pattern (19 bp):   
TTTTTATAATTTTGATGTA

Found at i:1819 original size:19 final size:20

Alignment explanation


    Indices: 1767--1819  Score: 63
    Period size: 19  Copynumber: 2.7  Consensus size: 20

       1757 AATTATGAAC

                     *       * *
       1767 TTTTTATAAATTTTGATTTT
          1 TTTTTATAATTTTTGATGTA

                   *            
       1787 TTTTTATTATTTTTGA-GTA
          1 TTTTTATAATTTTTGATGTA

                          
       1806 TTTTTATAATTTTT
          1 TTTTTATAATTTTT

       1820 TAAATTATTT


Statistics
Matches: 28,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  19   14  0.50
  20   14  0.50

ACGTcount: A:0.23, C:0.00, G:0.06, T:0.72


Consensus pattern (20 bp):   
TTTTTATAATTTTTGATGTA

Found at i:4035 original size:22 final size:21

Alignment explanation


    Indices: 3996--4040  Score: 56
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       3986 TTTTCATTAT

                              *  
       3996 TATTAAAAAAAATAGAAAGTA
          1 TATTAAAAAAAATAGAAACTA

                                   
       4017 TATT-AAAAAAATAGGGAAACTA
          1 TATTAAAAAAAATA--GAAACTA

              
       4039 TA
          1 TA

       4041 ACATATATCA


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  20    9  0.43
  21    4  0.19
  22    8  0.38

ACGTcount: A:0.62, C:0.02, G:0.11, T:0.24


Consensus pattern (21 bp):   
TATTAAAAAAAATAGAAACTA

Found at i:5925 original size:14 final size:13

Alignment explanation


    Indices: 5891--5956  Score: 60
    Period size: 14  Copynumber: 4.9  Consensus size: 13

       5881 ACATGTAGTA

                    *    
       5891 ATATGCGAACCCT
          1 ATATGCGAGCCCT

               *          
       5904 ATAGGCGAGCCCGT
          1 ATATGCGAGCCC-T

                          
       5918 ATATGCGAGCCTCT
          1 ATATGCGAGCC-CT

                 *  *   *
       5932 ATATGTGAACCCC
          1 ATATGCGAGCCCT

               *        
       5945 ATAGGCGAGCCC
          1 ATATGCGAGCCC

       5957 CTGTATGCAA


Statistics
Matches: 42,  Mismatches: 9, Indels: 4
        0.76            0.16        0.07

Matches are distributed among these distances:
  13   20  0.48
  14   21  0.50
  15    1  0.02

ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20


Consensus pattern (13 bp):   
ATATGCGAGCCCT

Found at i:5975 original size:41 final size:41

Alignment explanation


    Indices: 5891--5984  Score: 109
    Period size: 41  Copynumber: 2.3  Consensus size: 41

       5881 ACATGTAGTA

                 *      *            *       * *     
       5891 ATATGCGAACCCTATAGGCGAGCCCGTATATGCGAGCCTCT
          1 ATATGTGAACCCCATAGGCGAGCCCCTATATGCAAACCTCT

                                       *              
       5932 ATATGTGAACCCCATAGGCGAGCCCCTGTATGCAAA-CTCCT
          1 ATATGTGAACCCCATAGGCGAGCCCCTATATGCAAACCT-CT

               *        
       5973 ATAAGTGAACCC
          1 ATATGTGAACCC

       5985 AAATGTGCGA


Statistics
Matches: 45,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  40    2  0.04
  41   43  0.96

ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21


Consensus pattern (41 bp):   
ATATGTGAACCCCATAGGCGAGCCCCTATATGCAAACCTCT
Done.