Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001508.1 Kokia drynarioides strain JFW-HI SEQ_113055, 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: 1777
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30


Found at i:274 original size:17 final size:17

Alignment explanation


    Indices: 249--281  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        239 GTAATAGATA

                *            
        249 AAGTTACAAATACAGTC
          1 AAGTCACAAATACAGTC

                            
        266 AAGTCACAAATACAGT
          1 AAGTCACAAATACAGT

        282 TACAGATGCA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21


Consensus pattern (17 bp):   
AAGTCACAAATACAGTC

Found at i:986 original size:53 final size:52

Alignment explanation


    Indices: 899--1048  Score: 174
    Period size: 53  Copynumber: 2.8  Consensus size: 52

        889 TTATTACAGA

                   *             *  *    *                       
        899 CCATGTGTCTTAAAACAATATGCATACACTCTGACATACGCCCATGTATCAGC
          1 CCATGTGCCTTAAAAC-ATATACACACACCCTGACATACGCCCATGTATCAGC

                                                *          *     
        952 CCATGTGCCTTAAAACAGTATACACACACCCTGACACACGCCCATGTGTCAGC
          1 CCATGTGCCTTAAAACA-TATACACACACCCTGACATACGCCCATGTATCAGC

              *       **                                
       1005 CCGTGTGCCTCCAAACTATATACACACACACCCTGACATACGCC
          1 CCATGTGCCTTAAAAC-ATAT--ACACACACCCTGACATACGCC

       1049 TGTGTGCCAA


Statistics
Matches: 83,  Mismatches: 10, Indels: 6
        0.84            0.10        0.06

Matches are distributed among these distances:
  52    1  0.01
  53   61  0.73
  54    1  0.01
  55   20  0.24

ACGTcount: A:0.31, C:0.35, G:0.13, T:0.21


Consensus pattern (52 bp):   
CCATGTGCCTTAAAACATATACACACACCCTGACATACGCCCATGTATCAGC

Found at i:1053 original size:53 final size:53

Alignment explanation


    Indices: 910--1067  Score: 165
    Period size: 53  Copynumber: 2.9  Consensus size: 53

        900 CATGTGTCTT

                  *   *  *    *                 *       *       *
        910 AAAACAATATGCATACACTCTGACATACGCCCATGTATCAGCCCATGTGCCTT
          1 AAAACAGTATACACACACCCTGACATACGCCCATGTGTCAGCCCGTGTGCCTC

                                     *                           
        963 AAAACAGTATACACACACCCTGACACACGCCCATGTGTCAGCCCGTGTGCCTC
          1 AAAACAGTATACACACACCCTGACATACGCCCATGTGTCAGCCCGTGTGCCTC

            *                                 **    *  *         
       1016 CAAACTA-TATACACACACACCCTGACATACGCCTGTGTGCCAACCCGTGTGC
          1 AAAAC-AGTAT--ACACACACCCTGACATACGCCCATGTGTCAGCCCGTGTGC

       1068 TTCATCTTAT


Statistics
Matches: 88,  Mismatches: 14, Indels: 4
        0.83            0.13        0.04

Matches are distributed among these distances:
  53   52  0.59
  54    1  0.01
  55   35  0.40

ACGTcount: A:0.30, C:0.35, G:0.15, T:0.20


Consensus pattern (53 bp):   
AAAACAGTATACACACACCCTGACATACGCCCATGTGTCAGCCCGTGTGCCTC
Done.