Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010740.1 Kokia drynarioides strain JFW-HI SEQ_125693, 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: 4378
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31


Found at i:560 original size:45 final size:45

Alignment explanation


    Indices: 496--632  Score: 177
    Period size: 45  Copynumber: 3.0  Consensus size: 45

        486 GCATAGCTCA

                     *           *                       
        496 TCAAGCCAATGATATCAGCCTTAGTTTGACGAGCCATCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTAAGTTTGACGAGCCATCGCAATAC

                                                 *  *     
        541 TCAAGCCAAGGATATCAGCCTCAA-TTTGACGAGCCACCGTAATAC
          1 TCAAGCCAAGGATATCAGCCT-AAGTTTGACGAGCCATCGCAATAC

                 **           *             *       *    
        586 TCAAGGGAAGGATATCAGACTAAGTTTGACGATCCATCGCGATAC
          1 TCAAGCCAAGGATATCAGCCTAAGTTTGACGAGCCATCGCAATAC

              
        631 TC
          1 TC

        633 TATTCCTCCC


Statistics
Matches: 79,  Mismatches: 11, Indels: 4
        0.84            0.12        0.04

Matches are distributed among these distances:
  44    2  0.03
  45   76  0.96
  46    1  0.01

ACGTcount: A:0.32, C:0.26, G:0.20, T:0.23


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTAAGTTTGACGAGCCATCGCAATAC

Found at i:3986 original size:4 final size:4

Alignment explanation


    Indices: 3964--4029  Score: 62
    Period size: 4  Copynumber: 16.2  Consensus size: 4

       3954 AACGCATTAC

                   *   *                     *   *      *               
       3964 CTTT CTCT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT

                                  
       4012 CTTT CCTTT CTTT CTTT C
          1 CTTT -CTTT CTTT CTTT C

       4030 CCGTTTATTT


Statistics
Matches: 50,  Mismatches: 9, Indels: 6
        0.77            0.14        0.09

Matches are distributed among these distances:
   3    3  0.06
   4   40  0.80
   5    7  0.14

ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64


Consensus pattern (4 bp):   
CTTT

Found at i:3998 original size:17 final size:15

Alignment explanation


    Indices: 3964--4030  Score: 63
    Period size: 13  Copynumber: 4.7  Consensus size: 15

       3954 AACGCATTAC

                  *        
       3964 CTTTCTCTCCTTCTT
          1 CTTTCTTTCCTTCTT

                           
       3979 CTTTCTTTCC-TC-T
          1 CTTTCTTTCCTTCTT

             *               
       3992 CCTTC-TTCCTTTCTTT
          1 CTTTCTTTCC-TTC-TT

                           
       4008 CTTTCTTTCC-T-TT
          1 CTTTCTTTCCTTCTT

                      
       4021 CTTTCTTTCC
          1 CTTTCTTTCC

       4031 CGTTTATTTG


Statistics
Matches: 44,  Mismatches: 3, Indels: 12
        0.75            0.05        0.20

Matches are distributed among these distances:
  12    4  0.09
  13   17  0.39
  14    4  0.09
  15   10  0.23
  16    5  0.11
  17    4  0.09

ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63


Consensus pattern (15 bp):   
CTTTCTTTCCTTCTT
Done.