Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009682.1 Kokia drynarioides strain JFW-HI SEQ_124400, 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: 5158
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34


Found at i:1008 original size:25 final size:25

Alignment explanation


    Indices: 975--1073  Score: 137
    Period size: 25  Copynumber: 3.9  Consensus size: 25

        965 CGCTTCTGTT

                                     
        975 CAGCACTGTGTGTGCTTCTGTTACC
          1 CAGCACTGTGTGTGCTTCTGTTACC

                               *     
       1000 CAGCACTGTGTGTGCTTCTATTACC
          1 CAGCACTGTGTGTGCTTCTGTTACC

              *                   *  
       1025 CAACACTGTGTGTGCTTCTGTTTCC
          1 CAGCACTGTGTGTGCTTCTGTTACC

             *                       
       1050 TTAGCACT-TGTGTGCTTACTGTTA
          1 -CAGCACTGTGTGTGCTT-CTGTTA

       1074 AGTACTTTGG


Statistics
Matches: 65,  Mismatches: 7, Indels: 3
        0.87            0.09        0.04

Matches are distributed among these distances:
  25   55  0.85
  26   10  0.15

ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39


Consensus pattern (25 bp):   
CAGCACTGTGTGTGCTTCTGTTACC

Found at i:2229 original size:31 final size:31

Alignment explanation


    Indices: 2169--2229  Score: 77
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       2159 TCAATGCATG

                         *        *        
       2169 AATTTTGATTGTGGTTCAAATGTACATATTA
          1 AATTTTGATTGTGATTCAAATGCACATATTA

                      *        *    *     
       2200 AATTTTGATTTTGATTCAATTGCATATATT
          1 AATTTTGATTGTGATTCAAATGCACATATT

       2230 TAAAAAATAA


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  31   25  1.00

ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49


Consensus pattern (31 bp):   
AATTTTGATTGTGATTCAAATGCACATATTA

Found at i:4749 original size:22 final size:23

Alignment explanation


    Indices: 4721--4813  Score: 91
    Period size: 22  Copynumber: 4.0  Consensus size: 23

       4711 TAAACGGAAC

                                   
       4721 AAACAGAGAGTAC-CGAAGTACT
          1 AAACAGAGAGTACACGAAGTACT

                           *    *  
       4743 AAACAGAGAGTACA-TAAGTGCT
          1 AAACAGAGAGTACACGAAGTACT

                       * *    *    *  
       4765 AGGCAACAGAGCGCACACAAAGTGCT
          1 A---AACAGAGAGTACACGAAGTACT

                                   
       4791 AAACAGAGAGTACACGAAGTACT
          1 AAACAGAGAGTACACGAAGTACT

       4814 GAGCACACAA


Statistics
Matches: 57,  Mismatches: 9, Indels: 9
        0.76            0.12        0.12

Matches are distributed among these distances:
  22   20  0.35
  23   18  0.32
  25   11  0.19
  26    8  0.14

ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13


Consensus pattern (23 bp):   
AAACAGAGAGTACACGAAGTACT

Found at i:4795 original size:23 final size:23

Alignment explanation


    Indices: 4721--4886  Score: 116
    Period size: 23  Copynumber: 7.5  Consensus size: 23

       4711 TAAACGGAAC

                      *    *    *  
       4721 AAACAGAGAGTAC-CGAAGTACT
          1 AAACAGAGAGCACACAAAGTGCT

                      *    *       
       4743 AAACAGAGAGTACA-TAAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

                       *              
       4765 AGGCAACAGAGCGCACACAAAGTGCT
          1 A---AACAGAGAGCACACAAAGTGCT

                      *    *       
       4791 AAACAGAGAGTACACGAA--G-T
          1 AAACAGAGAGCACACAAAGTGCT

                  *                
       4811 --AC--TGAGCACACAAAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

              *                    
       4830 AATCAGAGAGCACACAAAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

              **            *      
       4853 AATTAGAGAGCACACACAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

              *        
       4876 AATCAGAGAGC
          1 AAACAGAGAGC

       4887 GCGCTAGTGT


Statistics
Matches: 116,  Mismatches: 16, Indels: 23
        0.75            0.10        0.15

Matches are distributed among these distances:
  16    9  0.08
  18    3  0.03
  19    1  0.01
  20    1  0.01
  21    2  0.02
  22   20  0.17
  23   61  0.53
  25   11  0.09
  26    8  0.07

ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13


Consensus pattern (23 bp):   
AAACAGAGAGCACACAAAGTGCT

Found at i:4987 original size:24 final size:26

Alignment explanation


    Indices: 4949--4996  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

       4939 TCTACATGGG

                                       
       4949 CATAATCTCTCATAT-TCATCATTTCT
          1 CATAATCTCTCATATATCA-CATTTCT

                                    
       4975 CATAAT-T-TCATATATCACATTT
          1 CATAATCTCTCATATATCACATTT

       4997 ACATTTCTCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24   11  0.52
  25    4  0.19
  26    6  0.29

ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46


Consensus pattern (26 bp):   
CATAATCTCTCATATATCACATTTCT
Done.