Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001339.1 Kokia drynarioides strain JFW-HI SEQ_112785, 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: 3753
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31


Found at i:1968 original size:43 final size:43

Alignment explanation


    Indices: 1904--2194  Score: 320
    Period size: 43  Copynumber: 6.8  Consensus size: 43

       1894 AATGTTAGTG

                     *      *                          
       1904 GCGTTTGTGGGAAAAGTGCCGCTAAAGACCATGGTCTTTAGCA
          1 GCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGGTCTTTAGCA

             *       *     *          *      *         
       1947 GTGTTTGTGGGAAAATCGCCGCTAAAAACCATGTTCTTTAGCA
          1 GCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGGTCTTTAGCA

                        *      *                       
       1990 GCGTTTGTGAGATAAGCGCTGCTAAAGACCATGGTCTTTAGCA
          1 GCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGGTCTTTAGCA

            *          *                               *
       2033 ACGTTTGTGCAAAAAAGCGCCGCTAAAGACCATGGTCTTTAGCG
          1 GCGTTTGTG-AGAAAAGCGCCGCTAAAGACCATGGTCTTTAGCA

             *          *     *   *      *    *         
       2077 GGGCTTT-TG-GGAAAGCACCGTTAAAGATCATGTTCTTTAGC-
          1 GCG-TTTGTGAGAAAAGCGCCGCTAAAGACCATGGTCTTTAGCA

                         *                      *     **
       2118 GACGTTTGTGAGATAAGCGCCGCTAAAGACCATGGTTTTTAGGG
          1 G-CGTTTGTGAGAAAAGCGCCGCTAAAGACCATGGTCTTTAGCA

                                              
       2162 GCGTTTGTGCA-AAAAGCGCCGCTAAAGACCATG
          1 GCGTTTGTG-AGAAAAGCGCCGCTAAAGACCATG

       2195 TTCTATAACG


Statistics
Matches: 206,  Mismatches: 35, Indels: 14
        0.81            0.14        0.05

Matches are distributed among these distances:
  41    4  0.02
  42   29  0.14
  43  135  0.66
  44   35  0.17
  45    3  0.01

ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26


Consensus pattern (43 bp):   
GCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGGTCTTTAGCA

Found at i:2135 original size:129 final size:129

Alignment explanation


    Indices: 1905--2194  Score: 397
    Period size: 129  Copynumber: 2.2  Consensus size: 129

       1895 ATGTTAGTGG

                    **     *                           *             * *     
       1905 CGTTTGTGGGAAAAGTGCCGCTAAAGACCATGGTCTTTAGCAGTGTTTGTGGGAAAATCGCCGCT
          1 CGTTTGTGCAAAAAGCGCCGCTAAAGACCATGGTCTTTAGCAGGGTTTGTGGGAAAAGCACCGCT

                                                   *                        
       1970 AAAAACCATGTTCTTTAGCAGCGTTTGTGAGATAAGCGCTGCTAAAGACCATGGTCTTTAGCAA
         66 AAAAACCATGTTCTTTAGCAGCGTTTGTGAGATAAGCGCCGCTAAAGACCATGGTCTTTAGCAA

                                                      *                      
       2034 CGTTTGTGCAAAAAAGCGCCGCTAAAGACCATGGTCTTTAGCGGGGCTTT-TGGG-AAAGCACCG
          1 CGTTTGTGC-AAAAAGCGCCGCTAAAGACCATGGTCTTTAGCAGGG-TTTGTGGGAAAAGCACCG

            *    * *                                                  *     *
       2097 TTAAAGATCATGTTCTTTAGC-GACGTTTGTGAGATAAGCGCCGCTAAAGACCATGGTTTTTAGG
         64 CTAAAAACCATGTTCTTTAGCAG-CGTTTGTGAGATAAGCGCCGCTAAAGACCATGGTCTTTAGC

            **
       2161 GG
        128 AA

                                            
       2163 CGTTTGTGCAAAAAGCGCCGCTAAAGACCATG
          1 CGTTTGTGCAAAAAGCGCCGCTAAAGACCATG

       2195 TTCTATAACG


Statistics
Matches: 143,  Mismatches: 15, Indels: 7
        0.87            0.09        0.04

Matches are distributed among these distances:
 128   24  0.17
 129   80  0.56
 130   36  0.25
 131    3  0.02

ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27


Consensus pattern (129 bp):   
CGTTTGTGCAAAAAGCGCCGCTAAAGACCATGGTCTTTAGCAGGGTTTGTGGGAAAAGCACCGCT
AAAAACCATGTTCTTTAGCAGCGTTTGTGAGATAAGCGCCGCTAAAGACCATGGTCTTTAGCAA

Done.