Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013361.1 Kokia drynarioides strain JFW-HI SEQ_128384, 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: 3945
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29


Found at i:984 original size:59 final size:59

Alignment explanation


    Indices: 889--1151  Score: 327
    Period size: 59  Copynumber: 4.5  Consensus size: 59

        879 GTCCCTGAAC

                *           *                                *     *   
        889 CTTCAAAAAATTACC-GTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCGAAG
          1 CTTCCAAAAATTACCATTTTACCCCCGAATTCCCAAAAATCCCATTTTTAACCCCAAAG

                         * *        *                *                 
        947 CTTCCAAAAATTATCGTTTTACCCTCGAATTCCCAAAAATCTCATTTTTAACCCCAAAG
          1 CTTCCAAAAATTACCATTTTACCCCCGAATTCCCAAAAATCCCATTTTTAACCCCAAAG

                         *           *                        *   * *   
       1006 CTTCC-AAAATTATCATTTTACCCCTGAATTCCCAAAAATCCCATTTTTTGACCTCGAAG
          1 CTTCCAAAAATTACCATTTTACCCCCGAATTCCCAAAAATCCCA-TTTTTAACCCCAAAG

                             *        *                                *
       1065 CTTCC-AAAATTACCATCTTACCCCCAAACTT-CCAAAAATCCCATTTTTAACCCCAAAT
          1 CTTCCAAAAATTACCATTTTACCCCCGAA-TTCCCAAAAATCCCATTTTTAACCCCAAAG

                                 *       
       1123 CTTCCAAAAATTACCATTTTATCCCCGAA
          1 CTTCCAAAAATTACCATTTTACCCCCGAA

       1152 CTTTCAAAAT


Statistics
Matches: 176,  Mismatches: 25, Indels: 7
        0.85            0.12        0.03

Matches are distributed among these distances:
  58   63  0.36
  59  111  0.63
  60    2  0.01

ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30


Consensus pattern (59 bp):   
CTTCCAAAAATTACCATTTTACCCCCGAATTCCCAAAAATCCCATTTTTAACCCCAAAG

Found at i:1098 original size:28 final size:28

Alignment explanation


    Indices: 992--1170  Score: 137
    Period size: 28  Copynumber: 6.1  Consensus size: 28

        982 AAAATCTCAT

                                      *  
        992 TTTTAACCCCAAAGCTTCCAAAATTATCA
          1 TTTTAACCCCAAA-CTTCCAAAATTACCA

                       *            * *   
       1021 TTTT-ACCCCTGAA-TTCCCAAAAATCCCA
          1 TTTTAACCCC-AAACTT-CCAAAATTACCA

                  *     *  *               
       1049 TTTTTTGACCTCGAAGCTTCCAAAATTACCA
          1 --TTTTAACC-CCAAACTTCCAAAATTACCA

             *   *                * *   
       1080 TCTTACCCCCAAACTTCCAAAAATCCCA
          1 TTTTAACCCCAAACTTCCAAAATTACCA

                                           
       1108 TTTTTAACCCCAAATCTTCCAAAAATTACCA
          1 -TTTTAACCCCAAA-CTTCC-AAAATTACCA

                 *    *     *           
       1139 TTTTATCCCCGAACTTTCAAAATTACCA
          1 TTTTAACCCCAAACTTCCAAAATTACCA

                
       1167 TTTT
          1 TTTT

       1171 GCCCTTGAGT


Statistics
Matches: 117,  Mismatches: 23, Indels: 21
        0.73            0.14        0.13

Matches are distributed among these distances:
  27    2  0.02
  28   44  0.38
  29   26  0.22
  30   20  0.17
  31   22  0.19
  32    3  0.03

ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32


Consensus pattern (28 bp):   
TTTTAACCCCAAACTTCCAAAATTACCA

Found at i:1100 original size:117 final size:118

Alignment explanation


    Indices: 889--1151  Score: 363
    Period size: 117  Copynumber: 2.2  Consensus size: 118

        879 GTCCCTGAAC

                *           *                                                
        889 CTTCAAAAAATTACC-GTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCGAAGCTTCCA
          1 CTTCCAAAAATTACCATTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCGAAGCTTCCA

                   * * *      * *              *                 
        953 AAAATTATCGTTTTACCCTCGAATTCCCAAAAATCTCATTTTTAACCCCAAAG
         66 AAAATTACCATCTTACCCCCAAATTCCCAAAAATCCCATTTTTAACCCCAAAG

                         *           *                            *          
       1006 CTTCC-AAAATTATCATTTTACCCCTGAATTCCCAAAAATCCCATTTTTTGACCTCGAAGCTTCC
          1 CTTCCAAAAATTACCATTTTACCCCCGAATTCCCAAAAATCCCA-TTTTTGACCCCGAAGCTTCC

                                                                  *
       1070 -AAAATTACCATCTTACCCCCAAACTT-CCAAAAATCCCATTTTTAACCCCAAAT
         65 AAAAATTACCATCTTACCCCCAAA-TTCCCAAAAATCCCATTTTTAACCCCAAAG

                                 *       
       1123 CTTCCAAAAATTACCATTTTATCCCCGAA
          1 CTTCCAAAAATTACCATTTTACCCCCGAA

       1152 CTTTCAAAAT


Statistics
Matches: 127,  Mismatches: 15, Indels: 7
        0.85            0.10        0.05

Matches are distributed among these distances:
 116    8  0.06
 117   78  0.61
 118   41  0.32

ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30


Consensus pattern (118 bp):   
CTTCCAAAAATTACCATTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCGAAGCTTCCA
AAAATTACCATCTTACCCCCAAATTCCCAAAAATCCCATTTTTAACCCCAAAG

Done.