Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005133.1 Kokia drynarioides strain JFW-HI SEQ_118969, 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: 1913
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34


Found at i:54 original size:33 final size:32

Alignment explanation


    Indices: 12--201  Score: 204
    Period size: 33  Copynumber: 5.8  Consensus size: 32

          2 CCCCCAACAG

                             *  * *          
         12 CTTCTACCCCTTCAACAACAGCTTCACCATCAA
          1 CTTCTACCCCTTCAACATCACCCTC-CCATCAA

                                         *   
         45 CTTCTACCCCTTCAACATCACCCTCCCCAACAA
          1 CTTCTACCCCTTCAACATCACCCT-CCCATCAA

                     *                      *
         78 CTTCTACCCTTTCAACATCACCCTCCTCATCAG
          1 CTTCTACCCCTTCAACATCACCCTCC-CATCAA

                                   *   **     
        111 CTTCTACCCCTTCAACATCACCTTTCTTAAT-AA
          1 CTTCTACCCCTTCAACATCACC-CTC-CCATCAA

               *     *                *    *
        144 CTTTTACCCTTTCAACATCACCC-CCTATCAG
          1 CTTCTACCCCTTCAACATCACCCTCCCATCAA

                                       
        175 CTTCTACCCCTTCAACATCACCCTCCC
          1 CTTCTACCCCTTCAACATCACCCTCCC

        202 CAATAGTCAA


Statistics
Matches: 130,  Mismatches: 21, Indels: 13
        0.79            0.13        0.08

Matches are distributed among these distances:
  30    2  0.02
  31   23  0.18
  32    4  0.03
  33   96  0.74
  34    5  0.04

ACGTcount: A:0.25, C:0.45, G:0.02, T:0.28


Consensus pattern (32 bp):   
CTTCTACCCCTTCAACATCACCCTCCCATCAA

Found at i:109 original size:66 final size:66

Alignment explanation


    Indices: 3--204  Score: 266
    Period size: 66  Copynumber: 3.1  Consensus size: 66

          1 CC

                    *         *       *  * *          *                      
          3 CCCCAACAGCTTCTACCCCTTCAACAACAGCTTCAC-CATCAACTTCTACCCCTTCAACATCACC
          1 CCCCAACAACTTCTACCCTTTCAACATCACCCTC-CTCATCAGCTTCTACCCCTTCAACATCACC

              
         67 CT
         65 CT

                                                                            *
         69 CCCCAACAACTTCTACCCTTTCAACATCACCCTCCTCATCAGCTTCTACCCCTTCAACATCACCT
          1 CCCCAACAACTTCTACCCTTTCAACATCACCCTCCTCATCAGCTTCTACCCCTTCAACATCACCC

             
        134 T
         66 T

            * **  *     *                                                    
        135 TCTTAATAACTTTTACCCTTTCAACATCACCC-CCT-ATCAGCTTCTACCCCTTCAACATCACCC
          1 CCCCAACAACTTCTACCCTTTCAACATCACCCTCCTCATCAGCTTCTACCCCTTCAACATCACCC

             
        198 T
         66 T

                  
        199 CCCCAA
          1 CCCCAA

        205 TAGTCAATAG


Statistics
Matches: 119,  Mismatches: 16, Indels: 4
        0.86            0.12        0.03

Matches are distributed among these distances:
  64   31  0.26
  65    4  0.03
  66   84  0.71

ACGTcount: A:0.26, C:0.46, G:0.02, T:0.27


Consensus pattern (66 bp):   
CCCCAACAACTTCTACCCTTTCAACATCACCCTCCTCATCAGCTTCTACCCCTTCAACATCACCC
T

Found at i:1174 original size:16 final size:16

Alignment explanation


    Indices: 1128--1162  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       1118 GAAGATTTTA

                     **     
       1128 GGGATTTCATGAATTG
          1 GGGATTTCAAAAATTG

                            
       1144 GGGATTTCAAAAATTG
          1 GGGATTTCAAAAATTG

               
       1160 GGG
          1 GGG

       1163 TTTTAAGAAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.29, C:0.06, G:0.34, T:0.31


Consensus pattern (16 bp):   
GGGATTTCAAAAATTG
Done.