Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010863.1 Kokia drynarioides strain JFW-HI SEQ_125831, 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: 4362
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:615 original size:24 final size:23

Alignment explanation


    Indices: 578--627  Score: 64
    Period size: 24  Copynumber: 2.1  Consensus size: 23

        568 TTTTAAGTAT

                     *      *      
        578 TAAATGTCTGTTAATATTAATAA
          1 TAAATGTCTATTAATAATAATAA

                               *    
        601 TAAATGTGCTATTAATAATGATAA
          1 TAAATGT-CTATTAATAATAATAA

               
        625 TAA
          1 TAA

        628 TAATAATAAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  23    7  0.30
  24   16  0.70

ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40


Consensus pattern (23 bp):   
TAAATGTCTATTAATAATAATAA

Found at i:1759 original size:30 final size:29

Alignment explanation


    Indices: 1697--2093  Score: 362
    Period size: 29  Copynumber: 13.5  Consensus size: 29

       1687 GAACTGTTCA

                               *          
       1697 AAAAATT-CATTTTTATCCTCG-AACTTCC
          1 AAAAATTCCATTTTTA-CCCCGAAACTTCC

                  *                      *
       1725 AAAAATCCCATTTTTGACCCCGAAACTTCA
          1 AAAAATTCCATTTTT-ACCCCGAAACTTCC

                 *              *     *  
       1755 AAAAAATCCATTTTTACCCCAAAACTACC
          1 AAAAATTCCATTTTTACCCCGAAACTTCC

                                 *        
       1784 AAAAATTCCATTTTTGACCCCAAAACTTCC
          1 AAAAATTCCATTTTT-ACCCCGAAACTTCC

                                          
       1814 AAAAATTCCATTTTTACCCTCG-AACTTCC
          1 AAAAATTCCATTTTTACCC-CGAAACTTCC

                  *            *        * 
       1843 AAAAATCCCATTTTTAACCTCGAAACTTTC
          1 AAAAATTCCATTTTT-ACCCCGAAACTTCC

                               *          
       1873 AAAAATTCCATTTTTACACTCG-AACTTCC
          1 AAAAATTCCATTTTTAC-CCCGAAACTTCC

                 **             **        
       1902 AAAAACCCCATTTTTGACCCTAAAACTT-C
          1 AAAAATTCCATTTTT-ACCCCGAAACTTCC

            *                             
       1931 TAAAATTCCATTTTTACCCTCG-AACTTCC
          1 AAAAATTCCATTTTTACCC-CGAAACTTCC

                  *            * *        
       1960 AAAAATCCCATTTTTGACCTCAAAACTTCC
          1 AAAAATTCCATTTTT-ACCCCGAAACTTCC

                     *            *        
       1990 AAAAAATTCTATTTTTGACCCCAAAACTTCC
          1 -AAAAATTCCATTTTT-ACCCCGAAACTTCC

                    *                 *   
       2021 AAAAATTCTATTTTTACCCTCG-AACCTCC
          1 AAAAATTCCATTTTTACCC-CGAAACTTCC

                                *         *
       2050 -AAAATCTCCATTTTTGACCTCGAAAC-TCT
          1 AAAAAT-TCCATTTTT-ACCCCGAAACTTCC

            *              
       2079 TAAAATTACCATTTT
          1 AAAAATT-CCATTTT

       2094 GTGCCCGAGT


Statistics
Matches: 310,  Mismatches: 38, Indels: 40
        0.80            0.10        0.10

Matches are distributed among these distances:
  28   20  0.06
  29  136  0.44
  30  127  0.41
  31   27  0.09

ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33


Consensus pattern (29 bp):   
AAAAATTCCATTTTTACCCCGAAACTTCC

Found at i:1786 original size:59 final size:58

Alignment explanation


    Indices: 1693--2039  Score: 414
    Period size: 59  Copynumber: 5.9  Consensus size: 58

       1683 CCTTGAACTG

                                   *                              *    
       1693 TTCAAAAAATT-CATTTTTATCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAAC
          1 TTCAAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAAC

                     *               *    *        *                   
       1751 TTCAAAAAAATCCATTTTTACCCCAAAACTACCAAAAATTCCATTTTTGACCCCAAAAC
          1 TTCAAAAAATTCCATTTTTACCCC-GAACTTCCAAAAATCCCATTTTTGACCCCAAAAC

               *                                            *   * *    
       1810 TTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCGAAAC
          1 TTCAAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCCCAAAAC

                                    *              *              *     
       1869 TTTC-AAAAATTCCATTTTTACACTCGAACTTCCAAAAACCCCATTTTTGACCCTAAAAC
          1 -TTCAAAAAATTCCATTTTTAC-CCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAAC

                *                                               *      
       1928 TTC-TAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCAAAAC
          1 TTCAAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCCCAAAAC

                         *             *             * *           
       1986 TTCCAAAAAATTCTATTTTTGACCCCAAAACTTCCAAAAATTCTATTTTT-ACCC
          1 TT-CAAAAAATTCCATTTTT-ACCCC-GAACTTCCAAAAATCCCATTTTTGACCC

       2040 TCGAACCTCC


Statistics
Matches: 248,  Mismatches: 31, Indels: 18
        0.84            0.10        0.06

Matches are distributed among these distances:
  57    1  0.00
  58   66  0.27
  59  135  0.54
  60   22  0.09
  61   24  0.10

ACGTcount: A:0.36, C:0.29, G:0.03, T:0.33


Consensus pattern (58 bp):   
TTCAAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAAC
Done.