Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006621.1 Kokia drynarioides strain JFW-HI SEQ_121211, 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: 14814
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34


Found at i:2838 original size:49 final size:48

Alignment explanation


    Indices: 2721--3060  Score: 149
    Period size: 49  Copynumber: 7.0  Consensus size: 48

       2711 CGATCTGCAT

                   *          *  *      *   *         *       
       2721 GGTACTAAATTCGCCGTTACGGCTTAAATTTTTCCTTT-TATGTCTCTGA
          1 GGTACTAGATTCGCCGTTGCGACTTAAACTTTCCCTTTGTATCT-TCT-A

                 *  *  *   *      *                          
       2770 GGTACGAGGTTTG-CATTGCGAATTAAACATTTCCCTTTGTATCTTCTA
          1 GGTACTAGATTCGCCGTTGCGACTTAAAC-TTTCCCTTTGTATCTTCTA

               *                 *       *          *          
       2818 GGTGCTAGATTCGCCGTTGCGGCTTAAATTTTTCCC-TT-CAT-TGTCTAA
          1 GGTACTAGATTCGCCGTTGCGACTTAAA-CTTTCCCTTTGTATCT-TCT-A

                 *  *            **            *     *        
       2866 GGTACAAGGTTCGCCGTTGCGGTTTAAACCTTTCCTTTTGTGTCTTCGT-
          1 GGTACTAGATTCGCCGTTGCGACTTAAA-CTTTCCCTTTGTATCTTC-TA

                  *           *                     *          
       2915 GGTACTGGATTCGCCGTTACGACTTAAATCTTTCCC-TT-CATGCTTCTGA
          1 GGTACTAGATTCGCCGTTGCGACTTAAA-CTTTCCCTTTGTAT-CTTCT-A

                     *     **  *                             **
       2964 GGTA-TAAGGTTCGCTATTACGACTTAAAACTTTTCCCTTTGTATCTTCGC
          1 GGTACT-AGATTCGCCGTTGCGACTT-AAAC-TTTCCCTTTGTATCTTCTA

                  *    * *    **                  **       
       3014 GGTACTGGATTTGTCGTTATGACTTAAATCTTTCCCTTCATATCTTC
          1 GGTACTAGATTCGCCGTTGCGACTTAAA-CTTTCCCTTTGTATCTTC

       3061 ATGGTAATGA


Statistics
Matches: 216,  Mismatches: 55, Indels: 40
        0.69            0.18        0.13

Matches are distributed among these distances:
  46    1  0.00
  47    7  0.03
  48   59  0.27
  49  105  0.49
  50   33  0.15
  51    9  0.04
  52    2  0.01

ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41


Consensus pattern (48 bp):   
GGTACTAGATTCGCCGTTGCGACTTAAACTTTCCCTTTGTATCTTCTA

Found at i:2900 original size:97 final size:97

Alignment explanation


    Indices: 2720--3054  Score: 334
    Period size: 97  Copynumber: 3.4  Consensus size: 97

       2710 TCGATCTGCA

                    *                           *  *    *          *     *   
       2720 TGGTACTAAATTCGCCGTTACGGCTTAAATTTTTCCTTTTATGTCTCTGAGGTACGAGGTTTG-C
          1 TGGTACTAGATTCGCCGTTACGGCTTAAATTTTTCCCTTCAT-TGTCTGAGGTACAAGGTTCGCC

                   *                         
       2784 ATTGCGAATTAAACATTTCCCTTTGTATCTTC-
         65 ATTGCGATTTAAACATTTCCCTTTGTATCTTCG

                 *              *                           *                
       2816 TAGGTGCTAGATTCGCCGTTGCGGCTTAAATTTTTCCCTTCATTGTCTAAGGTACAAGGTTCGCC
          1 T-GGTACTAGATTCGCCGTTACGGCTTAAATTTTTCCCTTCATTGTCTGAGGTACAAGGTTCGCC

            *     *       *     *     *      
       2881 GTTGCGGTTTAAACCTTTCCTTTTGTGTCTTCG
         65 ATTGCGATTTAAACATTTCCCTTTGTATCTTCG

                   *              *       *                        *         
       2914 TGGTACTGGATTCGCCGTTACGACTTAAATCTTTCCCTTCA-TGCTTCTGAGGTATAAGGTTCGC
          1 TGGTACTAGATTCGCCGTTACGGCTTAAATTTTTCCCTTCATTG--TCTGAGGTACAAGGTTCGC

            *   *      *    *                  
       2978 TATTACGACTTAAAACTTTTCCCTTTGTATCTTCG
         64 CATTGCGA-TTTAAACATTTCCCTTTGTATCTTCG

            *      *    * *     * *       *           
       3013 CGGTACTGGATTTGTCGTTATGACTTAAATCTTTCCCTTCAT
          1 TGGTACTAGATTCGCCGTTACGGCTTAAATTTTTCCCTTCAT

       3055 ATCTTCATGG


Statistics
Matches: 198,  Mismatches: 34, Indels: 10
        0.82            0.14        0.04

Matches are distributed among these distances:
  96   19  0.10
  97   98  0.49
  98   22  0.11
  99   59  0.30

ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41


Consensus pattern (97 bp):   
TGGTACTAGATTCGCCGTTACGGCTTAAATTTTTCCCTTCATTGTCTGAGGTACAAGGTTCGCCA
TTGCGATTTAAACATTTCCCTTTGTATCTTCG
Done.