Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007235.1 Kokia drynarioides strain JFW-HI SEQ_121850, 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: 5163
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37


Found at i:608 original size:32 final size:32

Alignment explanation


    Indices: 567--747  Score: 256
    Period size: 32  Copynumber: 5.7  Consensus size: 32

        557 GTGTAGGTTG

                                            
        567 GATAGCTCTTACGAGCATACTATTTACTGATT
          1 GATAGCTCTTACGAGCATACTATTTACTGATT

                                 *    *     
        599 GATAGCTCTTACGAGCATACTGTTTATTGATT
          1 GATAGCTCTTACGAGCATACTATTTACTGATT

                              *      *      
        631 GATAGCTCTTACGAGCATGCTATTTGCTGATT
          1 GATAGCTCTTACGAGCATACTATTTACTGATT

                *       *                   
        663 GATAACTCTTACAAGCATACT-TTTACTGATT
          1 GATAGCTCTTACGAGCATACTATTTACTGATT

                               *   **       
        694 GATAGCTCTTACGAGCATATTATGCACTGATT
          1 GATAGCTCTTACGAGCATACTATTTACTGATT

                        *         
        726 GATTAGCTCTTATGAGCATACT
          1 GA-TAGCTCTTACGAGCATACT

        748 GCGAATTTAC


Statistics
Matches: 130,  Mismatches: 17, Indels: 3
        0.87            0.11        0.02

Matches are distributed among these distances:
  31   27  0.21
  32   86  0.66
  33   17  0.13

ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38


Consensus pattern (32 bp):   
GATAGCTCTTACGAGCATACTATTTACTGATT

Found at i:698 original size:95 final size:97

Alignment explanation


    Indices: 567--744  Score: 270
    Period size: 95  Copynumber: 1.9  Consensus size: 97

        557 GTGTAGGTTG

                *       *                                        * ** *      
        567 GATAGCTCTTACGAGCATACTATTTACTGATTGATAGCTCTTACGAGCATACTGTTTATTGATTG
          1 GATAACTCTTACAAGCATACTATTTACTGATTGATAGCTCTTACGAGCATACTATGCACTGATTG

                                            
        632 A-TAGCTCTTACGAGCATGCTATTTGCTGATT
         66 ATTAGCTCTTACGAGCATGCTATTTGCTGATT

                                                               *             
        663 GATAACTCTTACAAGCATACT-TTTACTGATTGATAGCTCTTACGAGCATATTATGCACTGATTG
          1 GATAACTCTTACAAGCATACTATTTACTGATTGATAGCTCTTACGAGCATACTATGCACTGATTG

                       *      
        727 ATTAGCTCTTATGAGCAT
         66 ATTAGCTCTTACGAGCAT

        745 ACTGCGAATT


Statistics
Matches: 73,  Mismatches: 8, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  95   39  0.53
  96   34  0.47

ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38


Consensus pattern (97 bp):   
GATAACTCTTACAAGCATACTATTTACTGATTGATAGCTCTTACGAGCATACTATGCACTGATTG
ATTAGCTCTTACGAGCATGCTATTTGCTGATT

Found at i:1723 original size:21 final size:21

Alignment explanation


    Indices: 1699--1745  Score: 58
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       1689 CATGGTTGAG

                *             *  
       1699 CACATGGGCATGTGGAAGGGC
          1 CACACGGGCATGTGGAAGAGC

                     *     *     
       1720 CACACGGGCGTGTGGGAGAGC
          1 CACACGGGCATGTGGAAGAGC

                 
       1741 CACAC
          1 CACAC

       1746 AGCCGTGTGA


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.23, C:0.26, G:0.40, T:0.11


Consensus pattern (21 bp):   
CACACGGGCATGTGGAAGAGC

Found at i:1752 original size:21 final size:21

Alignment explanation


    Indices: 1709--1754  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       1699 CACATGGGCA

                    *       * *  
       1709 TGTGGAAGGGCCACACGGGCG
          1 TGTGGAAGAGCCACACAGCCG

                 *               
       1730 TGTGGGAGAGCCACACAGCCG
          1 TGTGGAAGAGCCACACAGCCG

                
       1751 TGTG
          1 TGTG

       1755 ATCCCTGTAG


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.20, C:0.24, G:0.43, T:0.13


Consensus pattern (21 bp):   
TGTGGAAGAGCCACACAGCCG

Found at i:2942 original size:20 final size:20

Alignment explanation


    Indices: 2917--2957  Score: 66
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       2907 TTATACAATT

                                 
       2917 TGTAAATA-TGAAGCACTAAA
          1 TGTAAATATTG-AGCACTAAA

                                
       2937 TGTAAATATTGAGCACTAAA
          1 TGTAAATATTGAGCACTAAA

             
       2957 T
          1 T

       2958 TTTTAAAATA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  20   18  0.90
  21    2  0.10

ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29


Consensus pattern (20 bp):   
TGTAAATATTGAGCACTAAA
Done.