Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007784.1 Kokia drynarioides strain JFW-HI SEQ_122418, 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, 940

Length: 1567
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37


Found at i:736 original size:59 final size:59

Alignment explanation


    Indices: 614--828  Score: 224
    Period size: 59  Copynumber: 3.6  Consensus size: 59

        604 TAAACTATCA

                    *                                    *             * 
        614 AAAAATTATATTTTGACCCCCAAACTTCTCTAAAATTATATTTTTAACC-CTGAACTTTCT
          1 AAAAATTACATTTTGACCCCCAAACTT-TCTAAAATTATATTTTTGACCTC-GAACTTTTT

                          *      *                     *               
        674 AAAAATTACATTTTTACCCCCGAACTTTCTAAAATTATATTTTGGACCTCGAACTTTTT
          1 AAAAATTACATTTTGACCCCCAAACTTTCTAAAATTATATTTTTGACCTCGAACTTTTT

                          *    **                **                     
        733 AAAAATTACATTTTTACCCTTAAACTTT-TCAAAATTCCATTTTTGACCTC-AA-TTTTT
          1 AAAAATTACATTTTGACCCCCAAACTTTCT-AAAATTATATTTTTGACCTCGAACTTTTT

                                   *     * *        
        790 CCAAAAATTACATTTTGA-CCCCGAACTTCCAAAAATTAT
          1 --AAAAATTACATTTTGACCCCCAAACTTTCTAAAATTAT

        829 GCTTTTACCC


Statistics
Matches: 130,  Mismatches: 20, Indels: 12
        0.80            0.12        0.07

Matches are distributed among these distances:
  57    5  0.04
  58   16  0.12
  59   84  0.65
  60   25  0.19

ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40


Consensus pattern (59 bp):   
AAAAATTACATTTTGACCCCCAAACTTTCTAAAATTATATTTTTGACCTCGAACTTTTT

Found at i:759 original size:30 final size:29

Alignment explanation


    Indices: 614--897  Score: 170
    Period size: 30  Copynumber: 9.7  Consensus size: 29

        604 TAAACTATCA

                    *     *      *         
        614 AAAAATTATATTTTGACCCCCAAACTTCTCT
          1 AAAAATTACATTTTTA-CCCCGAACTT-TCT

                    *           *         
        645 -AAAATTATATTTTTAACCCTGAACTTTCT
          1 AAAAATTACATTTTT-ACCCCGAACTTTCT

                                          
        674 AAAAATTACATTTTTACCCCCGAACTTTCT
          1 AAAAATTACATTTTTA-CCCCGAACTTTCT

                    *      *   *        * 
        704 -AAAATTATATTTTGGACCTCGAACTTTTT
          1 AAAAATTACATTTT-TACCCCGAACTTTCT

                                **        
        733 AAAAATTACATTTTTACCCTTAAACTTT-T
          1 AAAAATTACATTTTTACCC-CGAACTTTCT

            *      *           *     *    *
        762 CAAAATTCCATTTTTGACCTC-AATTTTTCC
          1 AAAAATTACATTTTT-ACCCCGAA-CTTTCT

                          *             *
        792 AAAAATTACATTTTGACCCCGAAC-TTCC
          1 AAAAATTACATTTTTACCCCGAACTTTCT

                    ***               **  
        820 AAAAATTATGCTTTTACCCTCGAA-TACCT
          1 AAAAATTACATTTTTACCC-CGAACTTTCT

                   *            *         
        849 -AAAATTCCATTTTTAACCCTGAACTTTCT
          1 AAAAATTACATTTTT-ACCCCGAACTTTCT

            **                   
        878 TGAAATTACCA-TTTTACCCC
          1 AAAAATTA-CATTTTTACCCC

        898 CAATATCCAA


Statistics
Matches: 195,  Mismatches: 42, Indels: 34
        0.72            0.15        0.13

Matches are distributed among these distances:
  28   34  0.17
  29   67  0.34
  30   91  0.47
  31    3  0.02

ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39


Consensus pattern (29 bp):   
AAAAATTACATTTTTACCCCGAACTTTCT

Done.