Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014012.1 Kokia drynarioides strain JFW-HI SEQ_129043, 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: 55924
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33

Warning! 159 characters in sequence are not A, C, G, or T


Found at i:1227 original size:23 final size:23

Alignment explanation


    Indices: 1189--1240  Score: 79
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       1179 GCTATGTGCA

                        *          
       1189 CCTACT-GATTGTACTGTGTGTG
          1 CCTACTGGATTGCACTGTGTGTG

                                   
       1211 CCTACTGGATTGCACTGTGTGTG
          1 CCTACTGGATTGCACTGTGTGTG

             *     
       1234 CTTACTG
          1 CCTACTG

       1241 TTTCCCCAAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  22    6  0.22
  23   21  0.78

ACGTcount: A:0.13, C:0.21, G:0.27, T:0.38


Consensus pattern (23 bp):   
CCTACTGGATTGCACTGTGTGTG

Found at i:2252 original size:32 final size:32

Alignment explanation


    Indices: 2184--2242  Score: 88
    Period size: 31  Copynumber: 1.9  Consensus size: 32

       2174 TCAAAAAGTT

                                            
       2184 AAAGGACTAAAAATGAAAATAATCAAAATTGA
          1 AAAGGACTAAAAATGAAAATAATCAAAATTGA

                     *                    
       2216 AAAGGA-TATAAATGAAAAT-AT-AAAATT
          1 AAAGGACTAAAAATGAAAATAATCAAAATT

       2243 TGACCAAAGG


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  29    6  0.23
  30    2  0.08
  31   12  0.46
  32    6  0.23

ACGTcount: A:0.63, C:0.03, G:0.12, T:0.22


Consensus pattern (32 bp):   
AAAGGACTAAAAATGAAAATAATCAAAATTGA

Found at i:3210 original size:13 final size:11

Alignment explanation


    Indices: 3183--3225  Score: 52
    Period size: 11  Copynumber: 3.8  Consensus size: 11

       3173 AGTTAAATAT

                       
       3183 TATTTTATTAA
          1 TATTTTATTAA

                        
       3194 TATTTTACTTAA
          1 TATTTTA-TTAA

                       *
       3206 -ATATTTATTAT
          1 TAT-TTTATTAA

                     
       3217 TATTTTATT
          1 TATTTTATT

       3226 TAGAAAATGG


Statistics
Matches: 28,  Mismatches: 1, Indels: 6
        0.80            0.03        0.17

Matches are distributed among these distances:
  11   18  0.64
  12   10  0.36

ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65


Consensus pattern (11 bp):   
TATTTTATTAA

Found at i:31928 original size:2 final size:2

Alignment explanation


    Indices: 31921--31948  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      31911 AATATGTTCC

                                                     
      31921 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      31949 GTATGTATGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:37772 original size:82 final size:82

Alignment explanation


    Indices: 37619--37780  Score: 209
    Period size: 82  Copynumber: 2.0  Consensus size: 82

      37609 TTACCCGCCT

                                                      *                      
      37619 CAAATAAAATACAAATTATTAAGTTTAATACTTTCAATAATATTTAATATCAATAAAAAATAATT
          1 CAAATAAAATACAAATTATTAAGTTTAATACTTTCAATAATACTTAATATCAATAAAAAATAATT

                   *         
      37684 TATTATTTACAAAATAC
         66 TATTATTAACAAAATAC

                         *                 *       *           * *     **  * 
      37701 CAAATAAAATACAGATTATT-AGTTTTAATATTTTCAATTATACTTAATATTATTAAAATTTACT
          1 CAAATAAAATACAAATTATTAAG-TTTAATACTTTCAATAATACTTAATATCAATAAAAAATAAT

              *             
      37765 TTTTTATTAACAAAAT
         65 TTATTATTAACAAAAT

      37781 GTGTCACTTA


Statistics
Matches: 68,  Mismatches: 11, Indels: 2
        0.84            0.14        0.02

Matches are distributed among these distances:
  81    2  0.03
  82   66  0.97

ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42


Consensus pattern (82 bp):   
CAAATAAAATACAAATTATTAAGTTTAATACTTTCAATAATACTTAATATCAATAAAAAATAATT
TATTATTAACAAAATAC
Done.