Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006333.1 Kokia drynarioides strain JFW-HI SEQ_120908, 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: 5919
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33


Found at i:5154 original size:39 final size:40

Alignment explanation


    Indices: 5061--5161  Score: 123
    Period size: 40  Copynumber: 2.5  Consensus size: 40

       5051 AGCAGCTTTT

                       * *   *                       
       5061 TAGCGGCGTTTGTACAAAAAATGCCATAAAAAGTAAAGCAA
          1 TAGCGGCGTTTTTTC-ATAAATGCCATAAAAAGTAAAGCAA

                  *                 *                
       5102 TAGCGGTGTTTTTTCATAAATGCCGT-AAAAGCTAAAGCAA
          1 TAGCGGCGTTTTTTCATAAATGCCATAAAAAG-TAAAGCAA

               *                
       5142 TAGTGGCGTTTTTTCATAAA
          1 TAGCGGCGTTTTTTCATAAA

       5162 CGTCGCAAAA


Statistics
Matches: 52,  Mismatches: 7, Indels: 3
        0.84            0.11        0.05

Matches are distributed among these distances:
  39    5  0.10
  40   35  0.67
  41   12  0.23

ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29


Consensus pattern (40 bp):   
TAGCGGCGTTTTTTCATAAATGCCATAAAAAGTAAAGCAA

Found at i:5182 original size:39 final size:40

Alignment explanation


    Indices: 5088--5187  Score: 121
    Period size: 40  Copynumber: 2.5  Consensus size: 40

       5078 AAAATGCCAT

                *               *             *    *
       5088 AAAAAGTAAAGCAATAGCGGTGTTTTTTCATAAATGCCGT
          1 AAAAGGTAAAGCAATAGCGGCGTTTTTTCATAAACGCCGC

                 *           *                  *   
       5128 AAAAGCTAAAGCAATAGTGGCGTTTTTTCATAAACGTCGC
          1 AAAAGGTAAAGCAATAGCGGCGTTTTTTCATAAACGCCGC

                            *    
       5168 AAAAGGTAAA-CAATAACGGC
          1 AAAAGGTAAAGCAATAGCGGC

       5188 ATTTATGTGA


Statistics
Matches: 50,  Mismatches: 10, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  39    8  0.16
  40   42  0.84

ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25


Consensus pattern (40 bp):   
AAAAGGTAAAGCAATAGCGGCGTTTTTTCATAAACGCCGC

Found at i:5310 original size:41 final size:41

Alignment explanation


    Indices: 5253--5446  Score: 219
    Period size: 41  Copynumber: 4.7  Consensus size: 41

       5243 GCCGCAAGGG

                              *  *     *             
       5253 AAAAGGTATGAGCATTAGTGGTGTTTACGAGAAAACACCGT
          1 AAAAGGTATGAGCATTAGCGGCGTTTATGAGAAAACACCGT

                     *                * *       *  **
       5294 AAAAGGTATAAGCATTAGCGGCGTTTTTTAGAAAACGCCAC
          1 AAAAGGTATGAGCATTAGCGGCGTTTATGAGAAAACACCGT

                 *      *                          * 
       5335 AAAAGTTATGAGGATTAGCGGCGTTTATGAGAAAACACCCT
          1 AAAAGGTATGAGCATTAGCGGCGTTTATGAGAAAACACCGT

                      *           *              *    
       5376 AAAAAGGTATTAGCATTAGCGGTGTTTATGAGAAAACGCCGT
          1 -AAAAGGTATGAGCATTAGCGGCGTTTATGAGAAAACACCGT

                 *                        
       5418 AAAAGATGA-GAGCATTAGCGGCGTTTATG
          1 AAAAGGT-ATGAGCATTAGCGGCGTTTATG

       5447 GGTAAAACTC


Statistics
Matches: 125,  Mismatches: 26, Indels: 4
        0.81            0.17        0.03

Matches are distributed among these distances:
  41   89  0.71
  42   36  0.29

ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25


Consensus pattern (41 bp):   
AAAAGGTATGAGCATTAGCGGCGTTTATGAGAAAACACCGT

Found at i:5467 original size:83 final size:81

Alignment explanation


    Indices: 5217--5446  Score: 237
    Period size: 83  Copynumber: 2.7  Consensus size: 81

       5207 AAAAGATAAG

                      *       *                *            *     *  *     * 
       5217 AGCATTAGCGACGTTTATAAGAAAACGCCGCAAGGGAAAAGGTATGAGCATTAGTGGTGTTTACG
          1 AGCATTAGCGGCGTTTATGAGAAAACG-C-C-A--CAAAA-GTATGAGGATTAGCGGCGTTTATG

                      *           
       5282 AGAAAACACCGTAAAAGGTATA
         60 AGAAAACACCCTAAAAGGTATA

                            * *                                              
       5304 AGCATTAGCGGCGTTTTTTAGAAAACGCCACAAAAGTTATGAGGATTAGCGGCGTTTATGAGAAA
          1 AGCATTAGCGGCGTTTATGAGAAAACGCCACAAAAG-TATGAGGATTAGCGGCGTTTATGAGAAA

                             *
       5369 ACACCCTAAAAAGGTATT
         65 ACACCCT-AAAAGGTATA

                       *                 **                              
       5387 AGCATTAGCGGTGTTTATGAGAAAACGCCGTAAAAG-ATGAGAGCATTAGCGGCGTTTATG
          1 AGCATTAGCGGCGTTTATGAGAAAACGCCACAAAAGTATGAG-G-ATTAGCGGCGTTTATG

       5447 GGTAAAACTC


Statistics
Matches: 124,  Mismatches: 15, Indels: 12
        0.82            0.10        0.08

Matches are distributed among these distances:
  81    6  0.05
  82   35  0.28
  83   56  0.45
  84    1  0.01
  85    1  0.01
  86    1  0.01
  87   24  0.19

ACGTcount: A:0.36, C:0.14, G:0.26, T:0.23


Consensus pattern (81 bp):   
AGCATTAGCGGCGTTTATGAGAAAACGCCACAAAAGTATGAGGATTAGCGGCGTTTATGAGAAAA
CACCCTAAAAGGTATA
Done.