Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002143.1 Kokia drynarioides strain JFW-HI SEQ_114087, 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: 2206
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:728 original size:14 final size:15

Alignment explanation


    Indices: 709--737  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

        699 AAAATTGAAA

                           
        709 AATAATTAA-AAAAT
          1 AATAATTAATAAAAT

                           
        723 AATAATTAATAAAAT
          1 AATAATTAATAAAAT

        738 TTAAAAAATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    9  0.64
  15    5  0.36

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


Consensus pattern (15 bp):   
AATAATTAATAAAAT

Found at i:1899 original size:69 final size:69

Alignment explanation


    Indices: 1817--1957  Score: 246
    Period size: 69  Copynumber: 2.0  Consensus size: 69

       1807 AATTTTTATT

                            *                                                
       1817 TAAATATTTAAAATTATTAAATAATGTATTATCAAATCAACACATTATTTGATAAAAATTATAAA
          1 TAAATATTTAAAATTAATAAATAATGTATTATCAAATCAACACATTATTTGATAAAAATTATAAA

                
       1882 ATAA
         66 ATAA

                                          *                             *   *
       1886 TAAATATTTAAAATTAATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAAT
          1 TAAATATTTAAAATTAATAAATAATGTATTATCAAATCAACACATTATTTGATAAAAATTATAAA

                
       1951 ATAA
         66 ATAA

               
       1955 TAA
          1 TAA

       1958 TAATTTTTAT


Statistics
Matches: 68,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  69   68  1.00

ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38


Consensus pattern (69 bp):   
TAAATATTTAAAATTAATAAATAATGTATTATCAAATCAACACATTATTTGATAAAAATTATAAA
ATAA

Found at i:1903 original size:17 final size:17

Alignment explanation


    Indices: 1868--1908  Score: 57
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       1858 ACATTATTTG

                 *           
       1868 ATAAAAATTATAAAATA
          1 ATAAATATTATAAAATA

                              
       1885 ATAAATATT-TAAAATTA
          1 ATAAATATTATAAAA-TA

                   
       1902 ATAAATA
          1 ATAAATA

       1909 ATGTATTGTC


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  16    5  0.23
  17   17  0.77

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (17 bp):   
ATAAATATTATAAAATA

Found at i:2026 original size:84 final size:83

Alignment explanation


    Indices: 1886--2167  Score: 325
    Period size: 93  Copynumber: 3.2  Consensus size: 83

       1876 TATAAAATAA

                                                                             
       1886 TAAATATTTAAAATTAATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAAT
          1 TAAATATTTAAAATTAATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAAT

                              
       1951 ATAATAATAATTTTTATT
         66 ATAATAATAATTTTTATT

                                   *                                         
       1969 TAAATATTTAAAATTAATAAATATTAGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAA
          1 TAAATATTTAAAATTAATAAATAAT-GTATTGTCAAATCAACACATTATTTGATAAAAATTG---

                                         
       2034 TATAATAATAATAATAATAATTTGTACTT
         62 --TAAT-ATAATAATAAT--TTT-TA-TT

                    *       *                     *      *     *   *    *    
       2063 TAAATA-TGAAAATTTGATAAATAATGTATTGTCAAATTAACACAATATTTAATATAAATAGTAA
          1 TAAATATTTAAAA-TTAATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAA

                                  
       2127 TATAATAATAATCTTTTTTATT
         65 TATAATAATAA---TTTTTATT

                                
       2149 TAAATAATGTT-AAATTAAT
          1 TAAAT-AT-TTAAAATTAAT

       2168 TTTAAATGTA


Statistics
Matches: 170,  Mismatches: 11, Indels: 32
        0.80            0.05        0.15

Matches are distributed among these distances:
  83   24  0.14
  84   36  0.21
  86    7  0.04
  87   17  0.10
  88   10  0.06
  89    5  0.03
  90   12  0.07
  92    3  0.02
  93   38  0.22
  94   18  0.11

ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41


Consensus pattern (83 bp):   
TAAATATTTAAAATTAATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAAT
ATAATAATAATTTTTATT

Done.