Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002500.1 Kokia drynarioides strain JFW-HI SEQ_114657, 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, 756

Length: 1261
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23


Found at i:683 original size:43 final size:41

Alignment explanation


    Indices: 635--779  Score: 107
    Period size: 43  Copynumber: 3.4  Consensus size: 41

        625 GTGCCTTCGA

                                        *             
        635 TGTGCGGGAGCATCGGACACCATCGGCAGCTTAGGCCGATGG
          1 TGTGCGGGA-CATCGGACACCATCGGCAACTTAGGCCGATGG

                                * *  *    *   *             
        677 TAGTGCGGGACAATCGGGA-TCTATGGGCACCTTGGTGCCTCAGAT-G
          1 T-GTGCGGGAC-ATC-GGACACCATCGGCAACTTAG-G-C-C-GATGG

                 * *                                 
        723 TGTG-AGAACATCGGACACCATCGGCAACTTAGGCCGATGG
          1 TGTGCGGGACATCGGACACCATCGGCAACTTAGGCCGATGG

                             
        763 TGGTGCGGGACCATCGG
          1 T-GTGCGGGA-CATCGG

        780 GAAACATCGG


Statistics
Matches: 77,  Mismatches: 14, Indels: 23
        0.68            0.12        0.20

Matches are distributed among these distances:
  39    3  0.04
  40    3  0.04
  41    4  0.05
  42    8  0.10
  43   42  0.55
  44    7  0.09
  45    4  0.05
  46    3  0.04
  47    3  0.04

ACGTcount: A:0.21, C:0.24, G:0.36, T:0.19


Consensus pattern (41 bp):   
TGTGCGGGACATCGGACACCATCGGCAACTTAGGCCGATGG

Found at i:958 original size:36 final size:35

Alignment explanation


    Indices: 907--993  Score: 95
    Period size: 35  Copynumber: 2.5  Consensus size: 35

        897 GCCGATGGTG

                 *             *      *         
        907 GTGCGAGACCATCGGGAAGTATCAGGTACCTTGTAT
          1 GTGCGGGACCATCGGGAAGCAT-AGGCACCTTGTAT

                      *           *   *        
        943 GTGCGGGACCGTCGGGAAGCATTGGCCCCTTGTAT
          1 GTGCGGGACCATCGGGAAGCATAGGCACCTTGTAT

                    *        
        978 GTGCGGGAGCAT-GGGA
          1 GTGCGGGACCATCGGGA

        994 CACCATCGGC


Statistics
Matches: 43,  Mismatches: 8, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  34    4  0.09
  35   20  0.47
  36   19  0.44

ACGTcount: A:0.20, C:0.21, G:0.38, T:0.22


Consensus pattern (35 bp):   
GTGCGGGACCATCGGGAAGCATAGGCACCTTGTAT

Found at i:1005 original size:35 final size:35

Alignment explanation


    Indices: 907--1005  Score: 92
    Period size: 35  Copynumber: 2.8  Consensus size: 35

        897 GCCGATGGTG

                 *            **      **        
        907 GTGCGAGACCATCGGGAAGTATCAGGTACCTTGTAT
          1 GTGCGGGACCATCGGGAACCATC-GGCCCCTTGTAT

                      *       *   *            
        943 GTGCGGGACCGTCGGGAAGCATTGGCCCCTTGTAT
          1 GTGCGGGACCATCGGGAACCATCGGCCCCTTGTAT

                    *                    
        978 GTGCGGGAGCAT-GGGACACCATCGGCCC
          1 GTGCGGGACCATCGGGA-ACCATCGGCCC

       1006 AAAAAAAGTG


Statistics
Matches: 52,  Mismatches: 10, Indels: 3
        0.80            0.15        0.05

Matches are distributed among these distances:
  34    4  0.08
  35   29  0.56
  36   19  0.37

ACGTcount: A:0.19, C:0.25, G:0.35, T:0.20


Consensus pattern (35 bp):   
GTGCGGGACCATCGGGAACCATCGGCCCCTTGTAT
Done.